Joel Piperberg Millersville University InstructorвЂ™s Manual ____________________________________________________ to accompany BioInquiry Making Connections in Biology Nancy L. Pruitt Colgate University Larry S. Underwood Northern Virginia Community College William Surver Clemson University John Wiley & Sons, Inc. New York / Chichester / Brisbane / Toronto / Singapore / Weinheim Copyright 2000 By John Wiley and Sons This material may be reproduced for instructional purposes by people using the text. Introduction Overview - Using BioInquiry in Large Classes The idea behind the BioInquiry learning system is obviously to integrate material from the text, the CDROM and the Website for the purpose of enhancing the learning experience. Depending on available facilities and time constraints, this may be easier said than done. At my university, we have just, as I write this, obtained facilities capable of allowing students to connect to the Web in a lecture hall during the lecture; we have had such facilities in the teaching laboratories for about two years. Furthermore, while we have had the ability to connect to the Web and project it on a screen for classroom/lecture hall demonstration purposes, the set-up until now would have been troublesome even if we did not also have to compete for the equipment with other faculty members. Under such circumstances, I would, therefore, find it inconvenient to move back and forth during a lecture period between lecture, the Web and the CD-ROM. My guess is that the facilities at most schools would present faculty with similar problems. Time constraints present a similar problem. Our course is a one-semester, 3-credit course with 2 hours of lecture and 2 hours of lab per week. It is, therefore, difficult to take time from lecture for journeys to the Web or the CD-ROM. Courses with 3 hours of lecture per week and/or 2 semesters to cover the material would obviously have more time to use the Web and CD-ROM components of the Learning System during lecture periods, as long as appropriate facilities are available. However, even that amount of extra time might be insufficient to cover the planned amount of course material, if the system is used during lecture periods. Some topics covered in the past might need to be sacrificed due to the resultant loss of lecture time. Another potential problem would be the small number of students who own laptops and can bring them into a lecture hall that possesses the requisite number of hook-ups. That's the bad news. The good news is that the system need not be used in the lecture hall. It is much more workable, in my opinion, to urge the students to make use of the Website and the CD-ROM outside of class time, either in their own rooms, which now are usually connected to the Web, or in a computer lab that is similarly connected. You could also use both components during a laboratory session, since the number of students would be more manageable in that setting. In addition, at this point, it is much more likely that a teaching laboratory would be connected to the Web and/or have computer facilities than would a lecture hall. If you wish and if you have the requisite equipment, you could use some of the components of the CD-ROM or Website as you would have used overhead transparencies or slides in more traditional presentations. With the CD-ROM/Website, you would have the advantage of animation in some cases. On the other hand, students could have their own computers handy and you could tell them where to look on the CD-ROM or the Web. This would obviously require students with computers and enough electric outlets and web hook-ups so that everyone could get to the same site or place on the CD-ROM. Overall, it would be most efficient for the instructor to project the relevant animations or illustrations. Students could then review the material while studying at home. Some of the animations and/or exercises on the CD-ROM or at the Website can be adapted for assignments. In specific chapters, I will mention those instances where that approach might be practical. You can send the students home with questions on the CD-ROM exercises asking them to turn them into you for a grade. Make up your own questions or feel free to use the CD-ROM sample test questions found in each chapter of this manual. One of the most effective strategies that I have used to enhance the learning experience of my students is one undoubtedly used by many, if not all, professors. It is relatively "low tech" and some teachers are philosophically opposed to it, but I have found that this method solves a number of problems that can arise in a classroom. I am alluding to the distribution or sale at cost of lecture outlines to the students. One of the biggest problems I had early in my career was constant interruption by students during lectures. I don't mind (in fact, I encourage) questions about the material. The interruptions of which I speak are requests to repeat a list of items, a description, a definition, the spelling of a word, etc. This slowed down the class without adding something positive to it, which an insightful question on the material would do. I took to making abbreviated versions of my lecture notes available to the students. This served many functions. Since I stick relatively close to these notes under most circumstances, the organization of the lecture is laid out for the students. The outlines include the lists, definitions and spellings that students often ask me to repeat. I do leave a lot of the detail out of these outlines so that students must attend class to get all of the information, and they must also take notes. However, there is enough in the outlines to prevent most students from being solely stenographers. The pressure is off of them enough to allow them to listen to what I am saying. I also put important figures in the notes that match the transparencies that I use. This allows the students to take notes on these drawings without needing to frantically copy the drawing before concentrating on the substance of the material. Presently, the student notes are sold in the University Bookstore, and students can buy them if they wish. They are not required, since some students prefer not to use them. In the future, I intend to put them on a website so that students can simply download them. Please make use of the outlines available with this manual. Rearrange them if you like. By removing the more detailed parts of the outlines, you would have ready-made student outlines. To avoid confusion, I should also point out that the underlined portions of the outlines in the Instructors Manual represent material covered on the CD-ROM. Some of this material is covered only on the CDROM and some is also covered in the text. I did not devise a method to make that particular distinction. You also may suggest that your students purchase the "Take Note!" supplement to the text, which is a notebook containing key figures from the text, enlarged like transparencies, but in black-and-white. The students can concentrate on taking notes on these figures in class without having to sketch images. Overview - Supporting the Lab The CD-ROM and Website can be effective supplements to a laboratory exercise. I feel that you should usually draw the line at basing an entire lab on Web- or CD-ROM-based activities. This is especially true of a course intended exclusively or predominantly for non-majors. These students need lab experience in their educational program. In many cases, this course may be the only lab experience they will get. Most, if not all, of this experience should in my opinion be "wet" lab experience in which students carry out simple experiments, collect data and analyze it. Many of the CD-ROM and Website elements will be useful as part of the lab or as a prelude to it. If the lab is equipped for computers, you could run your students through some background material relating to the lab exercise prior to carrying out the actual exercise. You could also request that your students look this material over before coming to lab. If you want to make sure that your students look at the material, you can provide incentive in the form of a quiz on Web or CD-ROM content. There will be specific suggestions relating to this in each chapter of the manual. Questions from This Instructor's Manual Available to Students in the "Test Your Knowledge" Section of the BioInquiry Web Site Below please find a list of questions from the sample test questions and CD-ROM Questions sections of this InstructorвЂ™s Manual that are also part of the вЂњTest Your KnowledgeвЂќ section of the BioInquiry Web Site. Please note that вЂњTest Your KnowledgeвЂќ is a self-test and that students have access to the answers to these questions. CHAPTER 1 QUESTION (Test Your Knowledge Questions) 1. When is it thought that the world's population will level off? 2. Which of the following are characteristics of livingвЂ¦? 3. Which brand of science is the youngest? 4. What is considered to be the beginning of modern biology? 5. What is the mechanism of the change in species? 6. What plants did Mendel use to discover his laws ofвЂ¦? 7. The unique network of chemical reactions in the cell isвЂ¦ 8. The tendency of living organisms to maintain constantвЂ¦ 9. The concept of ecosystems recognizes thatвЂ¦ 10. Which of the following words is most closely associatedвЂ¦ IM Question # Self-Test Question # 1 2 3 4 7 8 11 12 13 14 1 2 3 4 5 6 7 8 9 10 IM Question # Self-Test Question # 1 2 5 6 12 15 17 20 1 2 3 4 5 6 7 8 18 9 19 10 CHAPTER 2 QUESTION (Test Your Knowledge Questions) 1. The idea of evolutionвЂ¦Darwin. 2. Whose theory that geologic changesвЂ¦? 3. Whose letter to Darwin in 1858 describingвЂ¦? 4. In order for a population to remain relatively constantвЂ¦? 5. Which of the following is indirect evidence in support ofвЂ¦? 6. Two populations of the same species of squirrelsвЂ¦? 7. Dolphins, sharks and the extinct icthyosaursвЂ¦? 8. If a comet struck the surface of the Earth killing mostвЂ¦? (CD-ROM question) 9. You are studying three organisms that occupy the sameвЂ¦ (CD-ROM question) 10. Which of the following is an example of divergentвЂ¦ CHAPTER 3 QUESTION (Test Your Knowledge Questions) 1. The specialized reproductive cells of an organism mayвЂ¦ 2. Which word below describes an organism that has twoвЂ¦? 3. What is the largest number of alleles for a particular geneвЂ¦? 4. Wild type fruit flies have broad, straight wings andвЂ¦? 5. What proportion of the offspring in the cross mentionedвЂ¦? 6. What is the probability that a cross betweenвЂ¦? 7. What is another name for the sudden appearance of a newвЂ¦? 8. The phenomenon whereby a single gene affects two orвЂ¦ 9. Albino tigers are relatively rare in the wild. Equally rare isвЂ¦ (CD-ROM question) 10. The (blank) are the (blank) reproductive part of the flower. IM Question # Self-Test Question # 3 7 8 19 20 23 25 30 31 1 2 3 4 5 6 7 8 9 4 10 IM Question # Self-Test Question # 3 5 12 14 24 30 1 2 3 4 5 6 4 7 6 8 15 9 21 10 CHAPTER 4 QUESTION (Test Your Knowledge Questions) 1. Which of the following were tenets of the Cell Theory? 2. What is responsible for the ability of carbon to serve asвЂ¦? 3. You are studying a single-stranded nucleic acid moleculeвЂ¦? 4. What group of membrane molecules plays a role in cellвЂ¦? 5. What kind of cell is found in multicellular organisms? 6. Which structures below are totally or partially composedвЂ¦? (CD-ROM question) 7. In what kind of reaction is water used to separate two ofвЂ¦? (CD-ROM question) 8. Which part of an amino acid is responsible for theвЂ¦? (CD-ROM question) 9. A substance X moves across the cell membrane with theвЂ¦? (CD-ROM question) 10. In which cellular location would you expect to find highвЂ¦? CHAPTER 5 QUESTION (Test Your Knowledge Questions) 1. Chromatin is composed of what substances? 2. Which of the following is involved in cell division? 3. The members of an homologous pair of chromosomes areвЂ¦ 4. An organism contains 18 chromosomes in its gamete. 5. Cells that have stopped dividing are said to be in whatвЂ¦? 6. An organism has 42 chromosomes. How many linkageвЂ¦? 7. Some genes are capable of moving from one chromosomalвЂ¦ (CD-ROM question) 8. Of what are the spindle fibers composed? (CD-ROM question) 9. During which stage of mitosis do chromosomes beginвЂ¦? (CD-ROM question) 10. In what process and stage do homologous chromosomesвЂ¦? (CD-ROM question) 11. What kind of reaction is responsible for breaking apartвЂ¦? IM Question # Self-Test Question # 1 2 8 12 22 24 26 1 2 3 4 5 6 7 11 8 12 9 17 10 31 11 IM Question # Self-Test Question # 1 3 17 19 22 27 30 36 1 2 3 4 5 6 7 8 5 9 18 10 CHAPTER 6 QUESTION (Test Your Knowledge Questions) 1. Which of the following would not be a role of the geneticвЂ¦? 2. What DNA sequence would be complementary to theвЂ¦? 3. Which type of RNA possesses an anticodon? 4. To what part of an mRNA is the anticodon of a tRNAвЂ¦? 5. What is the name for a cluster of genes in a bacteriumвЂ¦? 6. A change in chromosome number involving only a singleвЂ¦? 7. What is another name for DNA sequences that moveвЂ¦? 8. A vehicle for carrying foreign DNA into a host bacteriumвЂ¦? (CD-ROM question) 9. What kind of bonds hold the paired bases in a DNAвЂ¦? (CD-ROM question) 10. Each time a ribosome translocates (moves) down anвЂ¦? CHAPTER 7 QUESTION (Test Your Knowledge Questions) IM Question # Self-Test Question # 4 8 12 23 31 32 38 41 42 48 1 2 3 4 5 6 7 8 9 10 QUESTION (Test Your Knowledge Questions) IM Question # Self-Test Question # 1. What is the approximate number of species presentlyвЂ¦? 2. The science of describing, classifying and organizingвЂ¦ 3. Who is responsible for the binomial nomenclature that isвЂ¦? 4. Kingdoms are divided intoвЂ¦ 5. The first cells on the planet almost certainly lived off ofвЂ¦ 6. (blank) evolved the ability to harness the energyвЂ¦ocean. (CD-ROM question) 7. Which kingdom is thought to contain cells that closelyвЂ¦? (CD-ROM question) 8. Organisms from the phylum Zoomastigina cause whichвЂ¦? (CD-ROM question) 9. Members of which of the following phyla have cell wallsвЂ¦? (CD-ROM question) 10. When I was in college, the freshman quad was populatedвЂ¦? 1 6 10 19 24 29 1 2 3 4 5 6 6 7 20 8 24 9 35 10 1. Which group of scientists ascribed evolution to suddenвЂ¦? 2. Continuous variation in a trait isвЂ¦ 3. A gene L is known to have to alleles, a dominant one (L)вЂ¦? 4. You place a MM moth and a Mm moth on a sootвЂ¦? 5. The cheetah is reputed to be the fastest land mammal. 6. The frequency distribution of birth weights in humanвЂ¦? 7. The alteration in allelic frequencies that results fromвЂ¦ 8. Which of the following results in neutral selection? 9. Genetic drift invariably results in a loss ofвЂ¦ 10. Which case below would be an example of gene flow? CHAPTER 8 CHAPTER 9 QUESTION (Test Your Knowledge Questions) 1. Which statement below is consistent with the First LawвЂ¦? 2. According to the Second Law of Thermodynamics, вЂ¦ 3. Which of the following is an example of potential energy? 4. Metabolic specificity is reflected in the ability of enzymesвЂ¦ 5. Which pathway is known as the anaerobic pathway ofвЂ¦? 6. In what form do carbon atoms leave the Krebs cycle? 7. What is the product of anaerobic respiration in animals? 8. Where in chloroplasts are the photosynthetic pigmentsвЂ¦? 9. In hot, dry climates, plants are often forced to close their, вЂ¦ (CD-ROM question) 10. A substrate X is converted to a product Y by an enzyme. IM Question # Self-Test Question # 3 5 16 25 29 30 34 52 57 1 2 3 4 5 6 7 8 9 15 10 IM Question # Self-Test Question # 3 7 12 27 34 43 64 70 77 82 1 2 3 4 5 6 7 8 9 10 CHAPTER 10 QUESTION (Test Your Knowledge Questions) 1. What feature of kit foxes helps them regulate their bodyвЂ¦? 2. Which of the arrangements below is the correct hierarchyвЂ¦? 3. The maintenance of nearly constant internal conditions isвЂ¦ 4. What type of feeding is typical of sponges? 5. What is the major mechanism by which single-celled andвЂ¦? 6. What is the major advantage realized from internalizedвЂ¦? 7. Which of the following proteins plays an important role in...? 8. What evidence suggests that the hormones found inвЂ¦? 9. What is the most common form of reproduction? 10. GametophytesвЂ¦ CHAPTER 11 QUESTION (Test Your Knowledge Questions) 1. Where are changes in the extracellular environmentвЂ¦? 2. What is the sequence of the unidirectional flow ofвЂ¦? 3. What stimulus causes the potassium ion channelsвЂ¦? 4. A cell that responds to a particular hormone is calledвЂ¦? 5. What moves chyme from the stomach into the smallвЂ¦? 6. How are the pacemaker cells of the heart like neurons? 7. What is the name of the process by which the fluid of theвЂ¦? 8. Which hormone is found in both males and females? 9. What ovarian structure makes and secretes progesterone? 10. What kind of cell makes antibodies? IM Question # Self-Test Question # 4 13 18 36 53 73 88 114 126 140 1 2 3 4 5 6 7 8 9 10 IM Question # Self-Test Question # 8 17 24 28 36 45 50 61 95 1 2 3 4 5 6 7 8 9 3 10 CHAPTER 12 QUESTION (Test Your Knowledge Questions) 1. What is responsible for producing a significant amount ofвЂ¦? 2. You go on a hike and see a plant that has a conspicuousвЂ¦? 3. The gametes of angiosperms are made in what structures? 4. What color(s) of light is (are) reflected to a high degreeвЂ¦? 5. Corn and crabgrass are able to survive in drier climatesвЂ¦? 6. The fleshy root tissues of some plants: 7. What inorganic forms of nitrogen can a plant absorb andвЂ¦? 8. What is the force responsible for moving water upвЂ¦? 9. What is the first cell of the female gametophyteвЂ¦? (CD-ROM question) 10. What is the dominant form in the life cycles of mostвЂ¦? CHAPTER 13 QUESTION (Test Your Knowledge Questions) 1. Which group of early behavioral biologists subscribed toвЂ¦? 2. With what study did sociobiology link the study ofвЂ¦? 3. A hungry rat is placed in a cage. The cage has no foodвЂ¦ 4. A decrease in learning time as a result of learningвЂ¦ 5. Why do Paramecia referred to as pawns lack the abilityвЂ¦? 6. What was responsible for the buildup in banana slugвЂ¦? 7. Which of the following is not a cost of territoriality? 8. A hiker picks up a log under which is an insect. As soonвЂ¦? 9. What is the immediate response of many animals withвЂ¦? (CD-ROM question) 10. Why do workers in a bee colony never lay eggs? IM Question # Self-Test Question # 4 12 14 16 21 27 29 33 48 1 2 3 4 5 6 7 8 9 18 10 IM Question # Self-Test Question # 5 9 16 19 23 24 27 42 56 60 1 2 3 4 5 6 7 8 9 10 CHAPTER 14 QUESTION (Test Your Knowledge Questions) 1. The study of how living in a particular habitat affectsвЂ¦ 2. Restoration ecology is perhaps the best known subвЂ¦? 3. What word describes a population in which the birth andвЂ¦? 4. What is the name for the number of deaths per year in aвЂ¦? 5. A graph of exponential population growth can best beвЂ¦ 6. The collection of factors that limit growth are oftenвЂ¦ 7. A population growth curve increases gradually at first, вЂ¦ 8. Species with adaptations that allow them to increase theirвЂ¦ 9. For what kinds of things do organisms compete? 10. What is (are) the possible results of intense competitionвЂ¦? CHAPTER 15 QUESTION (Test Your Knowledge Questions) 1. The biotic components of the environment areвЂ¦ 2. Which of the following is an important characteristic ofвЂ¦? 3. Swamp plants will not grow in (blank) soils. 4. What molecule supplies carbon to plants? 5. Which of the following explains the effect of latitudeвЂ¦? 6. The total weight of organisms in a particular trophic levelвЂ¦ 7. The amount of energy trapped by all plants and algae in aвЂ¦ 8. Which of the following strategies would be to someвЂ¦? 9. With what molecule in the atmosphere do CFCs interact? 10. In what form is energy that has been absorbed from theвЂ¦? IM Question # Self-Test Question # 4 6 9 13 23 36 38 80 82 84 1 2 3 4 5 6 7 8 9 10 Acknowledgments I would like to thank a number of people for their help in writing the Instructors' Manual. Nancy Pruitt, Larry Underwood, and William Surver wrote a fine text and executed a unique concept for a non-majors Biology course. I thank Joe Hefta and David Harris for getting me involved and for their faith in me. Jennifer Cerciello was always there when problems cropped up during the seeming eternity of the project. She was always just an e-mail or phone call away to answer questions and exhibited extreme patience when the deadline became a thing of the past. I would also like to thank my colleagues at Millersville and Simmons College with whom I have frequently discussed the art of teaching: Sandra Williams, Karen Talentino, Louis Irwin, the late Richard Nickerson, Carol Hepfer, Syd Radinovsky, David Dobbins, David Ostrovsky, Guy Steucek, Susan DiBartolomeis, Jay MonГ©, LaVern Whisenton-Davidson, David Zegers, Larry Reinking, Lauri Norbeck and Bill Yurkiewicz. A number of their ideas and suggestions appear in this manual. I am indebted to them for their contributions to this manual and for their help and support during my tenure at both institutions. Most of all, I thank my wife Cheryl and my children Jamie and Jason, who, during the course of this project, got much less attention from me than they deserve. I apologize for my singlemindedness and fixation on the project; I will try to make it up to them. Joel Piperberg Lancaster PA April 2000 xi CHAPTER 1 BIOLOGY: WHAT IS LIFE? Lecture/CD-ROM Outline Why Study Biology? I. Biology is relevant вЂ“ biology & biotechnology will be used to solve some global problems & improve our lives; in fact, this has already happened A. Great advances have been made in the treatment of once-dreaded diseases 1. 19 th & 20th centuries вЂ“ diseases caused by pathogens (viruses, bacteria, parasites) controlled (antibiotics, immunization, etc.); the war is, however, not over вЂ“ diseases are re-emerging 2. Today, emphasis turning to those related to physiological malfunction or failure вЂ“ kidney dialysis, transplants; cancer surgery & chemotherapy 3. Diseases, considered to be fatal in the past, can now be treated successfully or cured 4. The situation should improve further in the future B. Bioengineering 1. The new Green Revolution вЂ“ huge multinational effort to develop new crop plant varieties; some will be genetically enhanced to resist pests, be cold-tolerant & drought-resistant 2. Could help alleviate world hunger 3. Biological background will help citizens understand promises, limitations, costs & benefits C. Population has grown steadily for a millennium; should level off in 21st century 1. Awareness of need to do so is growing; leveling will not be easy or quick 2. Tough decisions will need to be made at every level of society вЂ“ individuals, couples, nations, beyond 3. Where should we put new cities, new farm land, natural parks & sanctuaries? 4. Monitor & manage existing wild areas; add, restore or maintain other areas (applied ecology) D. Emerging technologies (especially computers) will bridge gap between biology & technology 1. New career opportunities will arise вЂ“ biotechnology (laboratory-oriented) & applied technology (field-oriented) вЂ“ some will straddle lab and field II. Biology can be controversial A. Some controversial questions that have been raised: 1. If I practice family planning, what birth control methods shall I use? 2. How much should we spend to save endangered species? 3. Is it ethical to use human fetal tissue in biomedical research? 4. Is it right to save the spotted owl at the cost of jobs for loggers, builders & factory workers? 5. At what age does a human fetus become a human being? 6. Are irradiated foods safe to eat? 7. Are there dangers in cloning animals? Should humans be cloned? 8. By introducing genes from one organism into another, are we creating new species? 9. Are we playing God? B. Some controversies remain within biology; others involve economic, moral, ethical & religious considerations вЂ”> science cannot answer the latter group by itself 1. Biology can help understanding: identify options, describe impacts 2. Who should answer the above questions? вЂ“ the "authorities," an informed populace? What Is Biology? I. Biology is the study of life, a way of understanding nature, a human endeavor; strives to understand, explain, integrate, and describe the natural world of living things II. What is life? вЂ“ difficult to define; biologists focus on how life works; for them, life is that set of characteristics that distinguish living organisms from inanimate objects (including dead organisms) A. Living organisms: 1. Are highly organized, complex entities 2. Are composed of one or more cells that contain a blueprint of their characteristics, a genetic program 3. Acquire and use energy 4. Carry out and control numerous chemical reactions 5. Grow in size and change in appearance and abilities 6. Maintain a fairly constant internal environment 7. Produce offspring similar to themselves 8. Respond to changes in their environments 9. May evolve into new types of organisms B. Living organisms possess all of these characteristics simultaneously; inanimate systems may possess some of them III. Biology is a branch of science? A. Science is a way of knowing the natural world вЂ“ the word "science" is used in two contexts 1. Science is an activity; it is what scientists do 2. Science is also the body of knowledge that is derived from that activity B. Biology, while similar to other branches of science, also differs 1. It is younger вЂ“ natural science studied for 1000s of years; physics since 1500s; modern biology began with Darwin in mid-1800s 2. Biology's subject matter (life) is different from that of other sciences; with other sciences, it is easier to make predictions вЂ“ biology deals with options, much less absolute IV. Biology is integrated with other sciences A. Organisms that biologists study are subject to the laws of physics & chemistry B. To understand the history of life, you must understand geology, the study of rocks that contain fossils C. Mathematics is used to analyze & interpret biological data that have been collected What Are the Major Theories of Biology? I. Evolution by natural selection вЂ“ Darwin proposed a testable explanation for life's diversity A. Theory has two parts 1. Species (specific kinds of organisms) change or evolve over the generations 2. Natural selection is the mechanism of this change in species B. Accepted by nearly all scientists as biology's most important theory 1. Most think that contemporary biology began with publication of The Origin of Species in 1859 2. More than any other idea, evolution ties together & interrelates with all the other ideas & theories of biology II. Inheritance вЂ“ how are traits inherited by offspring from parents? вЂ“ Gregor Mendel & his pea plants A. The principles of inheritance he proposed apply to all organisms 1. Traits are passed from one generation to the next via hereditary factors that we now call genes 2. Mendel published results in 1865 but was ignored for 35 years; rediscovered early in 20th century & gave rise to genetics and molecular biology B. Inheritance is intimately connected with evolution III. Cells вЂ“ Matthias Schleiden & Theodor Schwann proposed the Cell Theory A. Elements of the Cell Theory 1. All organisms are composed of cells 2. All cells come from pre-existing cells 3. The cell is the smallest unit capable of exhibiting all of the characteristics of life B. Technology drove this discovery вЂ“ microscope had to be developed around the beginning of the 17th century and then refined; before this, cells were invisible IV. Biological classification вЂ“ started much earlier than most biological ideas A. Carolus Linneaus, late 18th century вЂ” classified living organisms according to their similarities & differences B. Once the theory of evolution appeared, classification schemes were based less on similarities & differences and more on evolutionary relatedness among species 1. Species that diverged from the same ancestors were grouped into the same categories 2. This kind of classification persists today V. Bioenergetics вЂ“ the energy that powers life; operates according to rules that govern energy in inanimate Universe A. Antoine Laurent Lavoisier, late 18th century вЂ“ placed chemistry of life into context of larger understanding of physics & bioenergetics B. Culminated in understanding of unique network of chemical reactions in cells (metabolism) VI. Homeostasis вЂ“ Claude Bernard, mid 19th century, realized that organisms function best when internal conditions are maintained within rather narrow limits A. Organisms tolerate widely varying external conditions by maintaining stable internal conditions B. The way in which this stability (homeostasis) is maintained constitutes the study of physiology VII. Ecosystems вЂ“ organisms interact with each other & their environments A. Changes in any part of biological community or physical environment can alter other parts 1. Concept of ecosystems recognizes that organisms do not exist alone 2. They are part of populations of similar organisms, communities of many different living things & environments with important nonliving features B. Youngest of biology's major ideas вЂ“ a product largely of the 20th century 1. Has no readily identifiable parent 2. Forged more slowly by widely separated & diverse group of specialists 3. Perhaps the most complex of these concepts since it fuses together major ideas of biology & other sciences as well 4. It is the backbone of ecology How Is Biology Studied? - Background on the Scientific Method I. Five key words describe the activities of biologists in their efforts to define the full scope of the living world (from molecules to ecosystems) вЂ“ observation, questioning, hypothesis, testing, explanation II. They summarize how biologists learn about life, how they study nature; they define the scientific method (the set of procedures that form the rational approach to studying the natural world) The Scientific Method - How Does It Work? I. Observation вЂ“ can be something entirely new, a new way of looking at things or a realization that natural world is at odds with currently accepted ideas; leads to questions (ex.: frog deformities, below) II. Questioning вЂ“ some questions science doesn't & can't address (supreme being?, right & wrong, etc.) A. Scientists ask questions that can be answered by experimentation or direct observation of material universe B. Biologists use observation & experience to ask how something happens or why something appears or acts as it does III. Hypothesis вЂ“ a tentative explanation, possible answer A. When they formulate a new hypothesis, scientists adhere to a set of assumptions; theyвЂ¦вЂ¦.. 1. Accept world as a real place that can be studied objectively 2. Believe that world is neither chaotic nor dependent upon supernatural or metaphysical realm вЂ“ hypotheses based on untestable factors outside the material world are not considered scientific 3. Believe that the events & phenomena of the material world have causes вЂ“ understanding causes means understanding why the world is the way it is & not some other way 4. Believe that simplest explanation that adequately accounts for all observations is preferred over other more complex explanations вЂ“ Occam's (medieval scholar, philosopher) razor B. Hypotheses are always tentative & remain so until rigorously tested & found to be consistent with original observations & often many new ones C. A scientist should be ready to abandon any hypothesis when a better one, more consistent with observations, is proposed вЂ“ a distinction between religion & science IV. Testing вЂ“ systematic observations, controlled experiments, detailed studies used to test hypotheses A. Occupies most of a working scientist's time B. Begins when scientist makes logical predictions based on hypothesis вЂ”> then performs controlled tests to determine their accuracy 1. If outcome is different from prediction, hypothesis is not supported & may be inaccurate 2. If outcome matches prediction, then hypothesis is supported & validity is one step closer to being accepted; usually require many successful tests before acceptance as valid V. Explanation вЂ“ a mature hypothesis, one that has been tested; all explanations subject to review & reconsideration when new evidence is presented or better explanations are proposed A. New information usually received skeptically B. Theory вЂ“ with consistent confirmation, lack of exceptions & time, scientific explanation may be elevated to status of theory 1. Nonscientists believe a theory is pure speculation without practice or evidence 2. Scientists consider a theory a demonstrable or well established principle; a proposition for which there is overwhelming supporting evidence 3. Many explanations in biology, e.g. evolution by natural selection, have passed so many rigorous tests that most consider them to be true The Scientific Method - Deformities in the Pacific Tree Frog As An Example I. Observation - schoolchildren on field trip in Minnesota made startling discovery (1995) A. Found young frogs suffering from deformities (misshapen limbs, extra & missing limbs) 1. Reported findings to local authorities who verified & extended discovery 2. Many Minnesota ponds had frogs with similar deformities 3. Widely reported in scientific journals & popular media B. Others elsewhere found same thing вЂ“ within a few years, deformed frogs, toads, & salamanders seen in 42 of United States & numerous Canadian sites C. Million dollar plus series of studies initiated including that of Pieter Johnson (undergraduate) along with Paul Ehrlich of Stanford вЂ“ found four affected California ponds out of 35 II. Questioning A. Frog deformities centered on three possibilities: 1. Was cause of frog deformities a chemical pollutant buildup in reproductive environment? вЂ“ chemicals cause deformities; most defects occurred during tadpole вЂ”> adult transition 2. Could deformities be related to ozone layer degradation? вЂ“ ozone protects life from UV radiation & is being degraded by human activities; UV causes cancer & birth defects 3. Could frog deformities be caused by parasites? вЂ“ parasites (worms, bacteria, fungi) can cause deformities in other organisms; frogs host many parasites B. Johnson determined that cause of Pacific tree frog deformities was not chemical pollutants вЂ“ ponds were free of pesticides, heavy metals, etc. C. Johnson observed that ponds also were home to particular type of snail that happened to be the intermediate host of parasitic flatworm (a trematode) that can infest frogs & other vertebrates III. Hypothesis - Johnson hypothesized that tree frog deformities were caused by the trematodes IV. Testing - How did Johnson test his hypothesis about tree frogs? A. Dissected hundreds of affected frogs & found trematodes clustered around malformed limbs вЂ“ good indirect evidence of cause & effect B. Collected 200 Pacific tree frog eggs from site north of study region from which no deformed frogs reported вЂ”> hatched & raised in lab in individual containers C. Collected parasites from study ponds (emerge from snail hosts mainly at night) 1. Exposed tadpoles to varying parasite concentrations & see what happens 2. Exposed frogs often had deformities; unexposed frogs had none; higher incidence of defects with higher parasite concentration D. Conclusion: trematodes cause the deformities seen in Pacific tree frogs V. Explanation вЂ“ frog experiments will be repeated by others A. If results are borne out, how universal are they? 1. Will they explain other deformities in other animals in other locations? вЂ“ affected Wisconsin frogs have no trematodes until after limb buds develop; maybe California frogs are different 2. Maybe pollutants or UV light increase susceptibility to parasites B. Most scientists believe it unlikely that one cause acting alone can explain deformities C. Studies will continue world-wide Analogies, Anecdotes and Illustrations Biology: Why Study It? Teaching is a wonderful profession. There's nothing like giving a good lecture and knowing that you clearly presented complex material to your students or helping a student one-on-one to understand a concept s/he thought was inaccessible. Unfortunately, the profession can be discouraging as well. I have been teaching Introductory or General Biology for almost 18 years as a faculty member and another 5 years as a postdoctoral fellow. I have taught majors and non-majors alike. The majors usually understand why they should study biology. The same can often not be said of the non-majors. I cannot say how many times I have been approached by a student who says something like "I'm a business (or some other non-science) major. Why does this school make me take a lab science course?". Usually, I answer that question the same way BioInquiry does. I tell the student that science in general and biology specifically are intimately related to his/her life. I suggest that as a responsible citizen, s/he will probably be asked to vote on issues related to science and biology and support political candidates who espouse certain biology-related positions. I point out that they or someone they love may someday have a health problem that requires them to make a decision about treatment and that a rudimentary knowledge of the workings of living organisms may come in handy at such a time. I even fall back on the argument that an educated person should have a liberal education and be expected to know something about disciplines other than his/her own. In the end, your best bet is to convince your students that biology is relevant to their lives by pointing out that relevance as often as possible. It helps if you can get them to understand the basic concepts as much as possible; the best way to win that battle is to make them think they can comprehend it. Once you have demonstrated that they can understand biology, even the most hated parts of it like chemistry and biochemistry, you have crossed a major hurdle. The best and most effective tool, in my opinion, for achieving that goal is the use of analogy. Analogy: How Can It Help? Analogy allows you to teach complicated concepts by using things familiar to the students to illustrate the concepts. Some students may find this method unproductive. I had one student who could tell when I was ready to launch another one and would say, "There he goes again!". I could never decide if she found them useless or if she was simply going for a laugh. Most students, however, have not had a problem with my use of analogies and most seem to find them helpful. I have never been able to plan the use of analogies the first time. The best analogies seem to come to me spontaneously during lectures. I suppose that while talking about the material I am able to make connections that help me to explain concepts through the use of similar examples from daily life. I have established some rules for myself that deal with the use of such analogies. First, if one comes to me, I use it directly in most cases. This is difficult for me since such spontaneity is not normally in my nature, but I have come to realize that if I do not use it right away, I may forget it. Be willing to try anything (within reason) once. Second, if an analogy works, keep using it and if you think of additions to it at another time, do not be afraid to incorporate changes and/or additions. Third, if an analogy does not work, do not hesitate to drop it. Tinker with it a bit if you wish first. Fourth, use humor wherever you can. Students, no matter who they are, respond well to it, and it helps them remember what you are trying to teach them. One more thing вЂ” the weirder, the better. If your analogies are unusual, they usually work even better. Fifth, be willing to use anything that comes to mind as a source for material: movies, TV shows, books, politics, dams, traffic patterns, everyday life, household appliances (telephones, television, computers, refrigerators, etc.). Controversy If the structure of your course allows it, run discussions (or let students run them) of controversial issues in biology like Evolution vs. Creationism, genetic testing, genetic engineering, food irradiation, cigarette smoking bans, cloning of humans and other animals (Dolly), the genetic basis of homosexuality, genetic differences between males and females, tissue transplantation and donation, the use of fetal tissues in research, human impact on the environment, the use of animals in research, etc. We do this as part of a course other than our General Biology course, a Freshman Honors Seminar that is most often taken by non-majors. This seminar course usually accomplishes the goal of helping students recognize the relevance of biology to their lives. Comments on the course solicited in surveys each time it is taught confirm this fact. Students frequently respond that they never thought that biology touched on so many issues that were or would be important to them. The Scientific Method When you tell your class about how the scientific method works, select a simple observation that everyone in the class should be able to understand: a light that will not go on when you enter the room and flip the switch, a car that will not start when the key is turned, or some other similar everyday experience. Propose that a room light will not turn on when the switch is engaged; this is an example of an observation. Then devise a question related to your observation like "Is the light bulb burned out?". Next, formulate an hypothesis based on your observations and question. For instance, you might explain the dark condition of the room to be the result of a burned-out light bulb, and you predict that replacement of the bulb will fix the lamp. You then test your hypothesis by replacing the bulb after checking that the test bulb works in a fixture that is known to be functioning (the control). If the new light bulb turns on when you flip the switch, your hypothesis was correct. If the light does not go on, you must discard your hypothesis and formulate another. Next you may hypothesize that a fuse has blown and test that hypothesis. You continue this approach until you arrive at a satisfactory answer. At each step, ask your class to supply you with the hypotheses and the test results. If you prefer, you may use the example of the deformed Pacific tree frogs presented in BioInquiry. The Scientific Method and The Gambler I often tell my students that the scientific method reminds me of Kenny Rogers' song The Gambler. As Kenny said "You've gotta know when to hold 'em/know when to fold 'em/know when to walk away/and know when to run." If your prediction was not borne out, it is possible that the procedure for your test was not the correct. Before you discard your hypothesis, you should review your procedure first. In other words, you should "know when to hold 'em." If you check your procedure and find that it was not faulty, you should then discard your hypothesis and come up with an alternate one. It is important not to discard a hypothesis too soon, but you should know when to "fold 'em." If your failed hypothesis can be replaced by a slightly different hypothesis, you should "walk away" from the first and test the second one. However, if your hypothesis was way off the mark, you should know when it is necessary to make a drastic change in your hypothesis and your approach and be willing to do so. In other words, you should "know when to run." Sample Test Questions Multiple Choice, Conceptual, and Open-Ended Questions From the Text 1. When is it thought that the world's population will level off? a. in the 21st century c. never e. in the year 2525 b. in the 22nd century d. in the 23rd century 2. Which of the following are characteristics of living organisms? a. they acquire and use energy c. they respond to environmental changes e. all of the above b. they contain a genetic program d. they are composed of one or more cells 3. Which branch of science is the youngest? a. physics b. chemistry c. biology d. astronomy e. Earth science 4. What is considered to be the beginning of modern biology? a. the discovery of cells d. Linnean classification b. the Cell Theory e. Darwin's The Origin of Species c. Mendel's discovery of the laws of inheritance 5. Aside from being a younger science, how does biology differ from other sciences? Biology's subject matter is different from that of other sciences. With other sciences, it is easier to make predictions. Biology deals with options and is much less absolute. 6. How is biology related to and integrated with other sciences? The organisms that biologists study are subject to the laws of chemistry and physics and to understand the history of life on the planet, one must study geology and study the rocks that contain fossils. Mathematics is essential for the analysis and interpretation of biological data collected by researchers. . 7. What is the mechanism of the change in species? a. natural selection b. artificial selection c. reproduction d. acquisition of traits e. a and d 8. What plants did Mendel use to discover his laws of inheritance? a. hawkweed b. string beans c. peas d. snap dragons e. roses 9. What technological advancement was responsible for driving the development of the Cell Theory? The invention and refinement of the microscope drove the development of the Cell Theory for obvious reasons. You could not learn much about the cell if you could not see it. The microscope was introduced in the 17th century and the necessary refinements were not fully developed until the early 19th century. 10. Early classification systems were based on the similarities and differences of living organisms. On what were they based after Darwin's theory? After Darwin published The Origin of Species, classification schemes were based on evolutionary relatedness among species. 11. The unique network of chemical reactions in the cell is referred to as __________. a. chemistry b. metabolism c. allosterism d. determinism e. homeostasis 12. The tendency of living organisms to maintain constant internal conditions within rather narrow limits is called _________. a. metabolism b. allosterism c. bioenergetics d. ecology e. homeostasis 13. The concept of ecosystems recognizes that a. organisms interact with each other and their environments b. changes in any part of a biological community or physical environment can alter other parts c. is one of the youngest of biology's major ideas d. is the backbone of the study of ecology e. all of the other answers 14. Which of the following words is most closely associated with the word "hypothesis"? a. true b. false c. testable d. axiom e. proof 15. How is science different from religion? A scientist will abandon an hypothesis when a better one, more consistent with observations, is proposed. Religion is based on faith and the statements in religious books like the Bible are not testable. 16. What is the difference between the way nonscientists and scientists view a theory? Nonscientists view a theory as pure speculation without evidence. Scientists consider a theory to be a demonstrable or well-established principle, a proposition for which there is overwhelming supporting evidence. Before an idea becomes a theory it has passed a large number of rigorous tests. 17. What were three possible causes of the deformities recently discovered in young frogs? Which of the three is presently considered to be the most likely explanation? First, it was thought that the deformities could be the result of a build-up of chemical pollutants in the reproductive environment of the affected frogs. Some thought the deformities might be due to the ozone layer degradation which would result in elevated exposure of frogs to the mutating influence of UV light. Third, some felt that parasites might cause the deformities. The third possibilityвЂ”parasitesвЂ”is presently considered to be the most likely explanation for the anomalies. 18. You isolate trematodes from a pond in which frogs are exhibiting limb deformities. You expose developing frogs from a pond not exhibiting such deformities to varying concentrations of the trematode parasites. If the results are similar to previously reported experiments, what will happen? Exposed frogs will often have deformities while unexposed frogs will have none. You will also see a higher incidence of defects in frogs exposed to higher parasite concentrations. Using BioInquiry in Large Classes Integrating Components into the Lecture The idea behind the BioInquiry learning system is to integrate material from the text, the CD-ROM and the Website for the purpose of enhancing the learning experience. Depending on available facilities and time constraints, this may be easier said than done. At my university, we have just, as I write this, obtained facilities capable of allowing students to connect to the Web in a lecture hall during the lecture; we have had such facilities in the teaching laboratory for about two years. Furthermore, while we have had the ability to connect to the Web and project it on a screen for classroom/lecture hall demonstration purposes, the set-up until now would have been troublesome even if you did not also have to fight over the equipment with some other faculty member. Under those circumstances, I would, therefore, find it inconvenient to move back and forth during a lecture period between lecture, the Web and the CD-ROM. My guess is that the facilities at most schools would present faculty with similar problems. Time constraints present a similar problem. Our course is a one-semester, three-credit course with two hours of lecture and two hours of lab per week. It is, therefore, difficult to take time from lecture for journeys to the Web or the CD-ROM. Courses with three hours of lecture per week and/or two semesters to cover the material would obviously have more time to use the Web and CD-ROM components of the Learning System during lecture periods, as long as appropriate facilities are available. However, even that amount of extra time might not be sufficient to cover the planned amount of course material without sacrificing topics that have been covered in the past, if the system is used during lecture periods. Another potential problem would be the small number of students who own laptops and can bring them into a lecture hall with the requisite number of hook-ups. That's the bad news. The good news is that the system need not be used in the lecture hall. It is much more workable, in my opinion, to urge the students to make use of the Website and the CD-ROM outside of class time, either in their own rooms, which now are usually connected to the Web, or in a computer lab that is similarly connected. You could also use both components during a laboratory session, since the number of students would be more manageable in that setting. In addition, at this point, it is much more likely that a teaching laboratory would be connected to the Web and/or have computer facilities than would a lecture hall. If you wish and if you have the requisite equipment, you could use some of the components of the CD-ROM or Website as you would have used overhead transparencies or slides in more traditional presentations with the CD-ROM/Website you would have the advantage of animation in some cases. On the other hand, students could have their own computers handy and you could tell them where to look on the CD-ROM or the Web. This would obviously require students with computers and enough electric outlets and web hook-ups so that everyone could get to the same site or place on the CD-ROM. In most cases, it would be most efficient for the instructor to project the relevant animations or illustrations. Students could then review the material while studying at home. Some of the animations and/or exercises on the CD-ROM or at the Website can be adapted for assignments. In specific chapters, I will mention those instances where that approach might be practical. You can send the students home with questions on the CD-ROM exercises asking them to turn them into you for a grade. Make up your own questions or feel free to use the CD-ROM sample test questions found in each chapter of this manual. One of the most effective strategies that I have used to enhance the learning experience of my students is one undoubtedly used by many, if not most, professors. It is relatively "low tech" and some teachers are philosophically opposed to it, but I have found that this method solves a number of problems that can arise in a classroom. I am alluding to the distribution or sale at cost of lecture outlines to the students; alternatively, one could place such notes on a personal homepage and allow students to download them or any other course material (old exams, assignments, data for laboratory reports, etc.). One of the biggest problems I had early in my career was constant interruptions by students during lectures. I don't mind (in fact, I encourage) questions about the material. The questions I speak of are requests to repeat a list of items, a description, a definition, the spelling of a word, etc. This slowed down the class without adding something positive to it, which an insightful question on the material would do. I took to making abbreviated versions of my lecture notes available to the students. This served many functions. Since I stick relatively close to these notes under most circumstances, the organization of the lecture is laid out for the students. The outlines include the lists, definitions and spellings that students often ask me to repeat. I do leave a lot of the detail out of these outlines so that students must attend class to get all of the information and they must take notes. However, there is enough in the outlines to prevent most students from being solely stenographers. The pressure is off of them enough to allow them to listen to what I am saying. I also put important figures in the notes that match the transparencies that I use. This allows the students to take notes on these drawings without needing to frantically copy the drawing before concentrating on its substance. Presently, the student notes are sold in the University Bookstore and students can buy them if they wish. They are not required, since some students prefer not to use them. In the future, I intend to make them available from a homepage so that students can simply download them. Please make use of the outlines available with this manual. Rearrange them if you like. By removing the more detailed parts of the outlines, you would have ready-made student outlines. Read More About It The History of Biology and the Workings of Science Two books by Ernst Mayr (Toward a New Philosophy of Biology and The Growth of Biological Thought) are excellent discussions dealing with the history and philosophy of biology. They are difficult and challenging, but superb. Recommend them to interested students whether they be majors or nonmajors. While it is not strictly about biology, Carl Sagan's The Demon-Haunted World: Science as a Candle in the Dark is a superb volume dealing with the difference between science and pseudoscience. It is a longer discussion of the scientific method and how scientific information is accumulated and also deals with the need for skepticism in the face of some sensational observations (UFOs, crop circles, ghosts, etc.). I have used it to spur discussion in the seminar course mentioned previously, and it was a successful vehicle for those discussions. Supporting the Lab The BioInquiry CD-ROM and Website can be effective supplements to a laboratory exercise. I suggest that most of the time you draw the line at basing an entire lab on Web- or CD-ROM-based activities. This is especially true of a course intended exclusively or predominantly for non-majors. These students need lab experience in their educational program. In many cases, this course may be the only lab experience they will ever get. Most, if not all, of this experience should in my opinion be "wet" lab experience in which students carry out simple experiments, collect, and analyze data. Such experiences will give the students at least a rudimentary exposure to the process of science. This knowledge will be important for students who, in the future, will be asked to make decisions in their personal lives that are based on some degree of knowledge of science. They will also be asked to cast votes on science-related public policy issues. Many of the CD-ROM and Website elements will be useful as part of the lab or as a prelude to it. If the lab is equipped, you could run your students through some background material relating to the lab exercise prior to carrying out the actual exercise. You could also request that your students look this material over before coming to lab. If you want to make sure that they look at the material, you can provide incentive in the form of a quiz on Web or CD-ROM content. For example, in our General Biology course, each lab exercise is preceded by a brief quiz covering predominantly the previous exercise. However, about 30% of each quiz dealt with material to be demonstrated in that week's lab. The purpose is to encourage students to read the lab exercise prior to class. Each chapter of the manual will contain specific suggestions for integrating elements of the BioInquiry Learning System into the laboratory. CHAPTER 2 EVOLUTION: WHY ARE THERE SO MANY LIVING THINGS? Lecture/CD-ROM Outline Evolution: An Overview I. Evolution has become a unifying principle in biology A. It is a concept of such central importance that nearly all other facets of the field are directly related to it & influenced by it B. "....nothing in biology makes sense except in the light of evolution." вЂ” Theodosius Dobzhansky, American geneticist (1973) II. For >150 years, evolution has stimulated controversy; most disagreements come from nonscientists who have examined it in the light of their own fields A. Some have found it useful to adopt parts of the concept out of context 1. Some politicians & economists have fixated on "survival of the fittest" вЂ”> justify big countries or companies gobbling up small ones 2. This phrase is not synonomous with ruthlessness; least conspicuous individuals can be the ones most likely to survive B. Some find the theory disturbing to their belief in higher order; theologians & philosophers split some see no conflict & can accept evolution easily; others find it difficult to do so C. But evolution is a biological theory & is not intended to be useful outside of science III. When theory was first proposed, it also sparked controversy within science & biology A. Science is a human endeavor & scientists are human 1. As process of discovery progresses, their perceptions change; old ideas replaced by new ones 2. But they are also skeptical of new ideas 3. Some data can be interpreted differently by different scientists 4. The more revolutionary a new idea is, the greater the demand for confirming data B. Even today the theory of evolution is both widely accepted & hotly debated 1. Nearly all biologists today accept the theory's central proposition - all living things are descended from common ancestors & they can change & give rise to new species 2. Controversy comes when explaining how this might happen 3. New data are collected constantly вЂ”> understanding shifts, changes & grinds forward 4. New refinements are regularly proposed вЂ”> some accepted, some rejected, all questioned Where Did the Idea of Evolution Come From?: Early History I. The idea of evolution preceded Darwin - the question of why there are so many different forms of life dates to ancient times II. Ancient philosophers explained nature in terms of what they imagined to be true, not based on observation; often used elaborate mental constructs A. If conflict appeared between observation & imagination вЂ”> philosophers went with latter B. Through human history, answers to perplexing questions passed orally through generations in the form of myths, stories, and dances, many of which were lost C. By Middle Ages, organisms thought to be arranged in "Ladder of Life" - God at top rung, then angels, men, women, children, other organisms (simplest & least complex on lowest rung) 1. System thought to be perfect & complete; no need for species to change 2. No room for evolution III. Beginning in the 1500s, European philosophers began to exhibit discontent A. Could no longer ignore conflict between observation & accepted explanations of natural world B. Some philosophers recognized importance of observation 1. Copernicus proposed that the earth was not the center of the Universe & that it circled the sun 2. Then chemists discovered that matter was made of more elements than fire, water, earth & air C. 1790s - Newton described gravity as force that connects all matter in the Universe; ancients were familiar with gravity's effects but had no name for it & could not imagine its extent IV. Discontent began to appear relative to views on the diversity of life A. Early 1800s - Georges Cuvier, French scientist, raised the study of fossils to the level of science 1. Struck by differences between fossils from one rock layer & those right above & below 2. Cuvier hypothesized that natural catastrophes wiped out existing species which were then replaced with new ones B. 1830 - Charles Lyell, English geologist - proposed theory of Uniformitarianism; held that geologic changes take place slowly 1. Also said what we see happening today could explain happenings in the past 2. Understanding the present is the key to understanding the past 3. Because of erosion & other forces, transitions between rock layers may be destroyed or may have taken longer to occur than now thought (breaks may not be instant but millions of years) 4. Organisms living during transition periods are lost to erosion & have vanished without a trace C. Perceptions of biologists began to change in 1700s 1. Georges Louis Leclerc Comte de Buffon & Erasmus Darwin (Charles' grandfather) separately proposed that species could be modified & changed with time 2. Each proposed concept of evolution but their ideas were not widely noticed D. 1809 - Jean Baptiste Lamarck, French biologist, published theory of the inheritance of acquired characteristics; since replaced by Darwin's theory & Mendel's theory 1. Suggested organisms could acquire new characteristics during their lifetimes (giraffes could lengthen their necks by stretching for uppermost leaves) 2. Believed that once acquired, the traits could be passed to offspring; species could then change Where Did the Idea of Evolution Come From?: A Brief Biography of Darwin I. Charles Darwin - even as a child, Darwin was interested in biology A. Darwin's father was prominent physician; his mother was daughter of Josiah Wedgwood (porcelain) вЂ”> Darwin born February 12, 1809 into life of relative ease 1. Erasmus Darwin (grandfather) - poet, philosopher, naturalist died when he was nine 2. Young Charles was interested in nature & biology especially beetles B. His father expected him to become a physician; witnessed operations without anesthesia вЂ”> decided that medicine was not for him 1. Then, he began to study for the ministry, but was not inclined toward this occupation either 2. Family friend secured him position as naturalist on British survey ship, the Beagle, commanded by Captain Robert FitzRoy 3. His father at first refused & then agreed to let him go hoping he would find himself II. His voyage on the Beagle shaped many of his ideas about biology; it began December 27, 1831 A. Purpose of voyage was to sail around the world & survey little known coastal areas especially east & west coasts of South America 1. Darwin was to collect specimens & information on organisms seen along the way 2. For him, voyage was difficult (chronic sea sickness); went ashore as often as possible, made observations & collected thousands of specimens 3. Darwin took many books with him, including the Bible which he read extensively & Lyell's Geology which he began to better understand during his journey B. As time passed, a new idea about biology took shape 1. He saw confirming evidence that species can change; found fossils including extinct relatives of peccaries & armadillos; found many species of beetles different from those in England 2. He asked himself where the diversity he was seeing came from & came up with evolution 3. Spoke of some of his thoughts to FitzRoy who believed species were created by God, placed on Earth by Him & were not able to change; FitzRoy challenged Darwin on every point 4. 1836 - he & the Beagle return to England; he began his life's work 5. 1839 - he marries & moves out of London to the village of Down C. Worked to demonstrate two major ideas 1. Would show that closely related species evolve from & share common ancestors and 2. Would propose mechanism to explain how the process of evolution works - natural selection D. Did not publish his theory right away; sought more data & more confirming evidence III. Many of Darwin's contemporaries came to the same conclusions A. 1858 - long letter from Alfred Russel Wallace who had been in Brazil & East Indies 1. Collected specimens & sent them back to England; thought about evolution 2. During a malarial attack, his ideas about evolution crystallized 3. Wrote them down & sent them to Darwin asking that they be circulated among their peers B. Letter was a near disaster for Darwin - Wallace had reached same conclusions about the mechanism of evolution as had Darwin; Darwin was being scooped 1. Asked friends Charles Lyell & Joseph Hooker for advice 2. Had written an unpublished summary of his work in 1842; clearly predated Wallace's letter 3. Lyell & Hooker arranged for letter & summary to be presented at meeting of Linnaean Society of London on July 1, 1858 4. A year later, Darwin published complete theory in The Origin of Species, after sitting on it for >20 years C. Contributions of Darwin & Wallace were significant - others had come up with elements earlier 1. They were first to coherently formulate a theory for which evidence had been growing 2. That they could both come up with it at same time though a half a world apart said that it was an idea whose time had come 3. Starting in 1700s, goals of scientists were to explain, understand, & describe nature based on observation; Wallace & Darwin pioneered this method 4. Drawing conclusions based on observations led them to theory of evolution IV. How did Darwin account for species? A. In his book, Darwin dealt with two separate, closely related concepts 1. Presented evidence that evolution had occurred, that species can & do change; closely related species share common ancestors; others had suggested this, but his evidence set him apart 2. Also explained how process of change occurred - natural selection (differential survival & reproduction of individuals with certain, advantageous characteristics) B. 150 years later after its introduction into science, there is much supporting evidence & it is well established Where Did the Idea of Evolution Come From?: Darwin's Observations I. First observation - populations have inherent potential to increase exponentially (unlimited growth) A. Darwin was extending the ideas of Thomas Robert Malthus (18th century economist-clergyman) 1. Malthus was concerned with rate of human population increase & its effects; felt world was getting overcrowded with humans & that growth was outstripping food production 2. He believed that there was a constant struggle for survival & that war, famine & disease were inevitable outcomes that would control human population B. Darwin realized this was potentially true for all populations (examples: sunfish, fruit flies, baleen whales) - in all cases, observed capacity to increase always > replacement requirement II. Second observation - populations are fairly constant in size over long periods of times A. Have capacity to increase exponentially, but usually do not B. Factors regulating population numbers are complex & most not well studied until after Darwin C. For species to persist, its population must remain relatively constant - births should match deaths 1. If each reproducing pair produces two surviving young вЂ”> populations are stable 2. Populations with fewer than two offspring per reproducing pair -> dwindle & become extinct 3. If pairs consistently produce, on average, >2 young вЂ”> population generally overpopulates III. Third observation - natural resources are limited; competition important in limiting survival A. Malthus proposed food was limited resource for humans; Darwin extended it for other species & resources - space, food/nutrients, shelter, fresh water, habitat B. As populations increase, more & more individuals depend on & need to exploit fewer & fewer resources; the essence of competition IV. Fourth observation - there is variation within individuals of a population & variations are inherited A. Differences exist within all populations & species - subtle differences in size, coloration, shape 1. Blackbirds have large variation in wing length 2. Marine animals go to sea to get food for young - when return, find young in crowd through subtle differences in coloration, vocalization, smell & behavior B. Darwin did not know how variations were passed on to next generation; we now know that gene mutation is responsible (natural selection's raw material) C. Individual differences affect survival; those Darwin observed led him to two conclusions (below) Where Did the Idea of Evolution Come From?: Darwin's Deductions I. Deduction 1 - only some organisms survive; there is struggle for existence among individuals in population - from Observations 1, 2 & 3 A. Darwin felt individual differences might affect an organism's ability to survive 1. Rabbits with longer legs & bigger muscles are more likely to outrun foxes & survive 2. Young marine animals that can find their mothers when separated are more likely to survive 3. Aggressive bucks with large antlers are more likely to collect & defend harems B. Animals possess traits that enhance survival of individuals 1. These traits will lead to changes in populations & ultimately species 2. Such traits that enhance survival are adaptations; they define the success of any species II. Deduction 2 - individuals with favorable variations are more likely to survive & reproduce A. Individuals with the best adaptations probably survive & are more likely to reproduce & pass their successful adaptations on to offspring 1. Fast rabbits & fast foxes 2. Plants with foul-tasting leaves are avoided; they survive & pass on the ability to make foultasting leaves B. Called "[t]his preservation of favorable variations & the rejection of injurious variations" natural selection 1. Best adapted organism may still not survive; worst adapted could survive to reproduce 2. Natural selection looks beyond such exceptions 3. Most highly adapted вЂ”> most likely to survive; less well adapted вЂ”> most likely to be selected against III. Deduction 3 - accumulation of variation over many generations is evolution; when great enough вЂ”> new species; a gradual process A. As rabbits are hunted, faster rabbits survive pursuit by foxes -> rabbit population becomes faster; hunting becomes harder for foxes because rabbit population as a whole is changed to be faster B. Darwin never found irrefutable example of formation of new species; his evidence was indirect; we now have concrete examples C. Phylogenetic trees may be used to show relationships among various related species What Exactly Are Species? I. Species are distinct if they do not interbreed in nature A. Horses & jackasses interbreed, yielding mules, but mules are sterile - not same species, because "interbreed in nature" implies resulting offspring able to reproduce B. Dogs & wolves distinguished by shape of muzzles & where they are found вЂ” interbreed if given opportunity & offspring are fertile but still considered separate species II. All species have differences within them & traits in population change; eventually new species arise A. Speciation does not happen suddenly & does not happen at the same rate in all cases 1. Blue geese & snow geese are examples of differences that exist within single species, they may have only started to differentiate 2. Wolves & dogs are a bit farther along in process 3. Horses & jackasses have proceeded to the point where reproduction is affected 4. Mule deer & white-tailed deer have fully differentiated into distinct species - can't reproduce B. While it is happening, Darwinian evolution is slow, tedious, and barely detectable How Does the Process of Evolution Work?: Indirect Evidence Supporting the Theory of Evolution I. Animal & plant husbandry - farmers improve domesticated animals & plants by breeding those individuals that had the traits the farmer wanted A. Some selected cattle for size вЂ”> ended up with Herefords & Angus breeds noted for steaks B. Others selected for cows who produced the most milk -> ended up with dairy breeds C. It was concluded that the same process could happen just as well in natural species D. Nature doesn't always favor the "fastest, strongest, biggest, smartest;" may favor the calmest (waste less energy); direction of evolution difficult to predict & not under control of species II. Fossils - example is evolution of modern horse A. Earliest fossil horses looked nothing like modern horses B. ~60 million years ago - Hyracotherium (fox-sized forest dwelling creature with teeth adapted for browsing; four toes on forefeet, each with tiny hoof) C. Fossils demonstrate gradual increase in overall size, transition to grazing-adapted teeth, reduction in number of toes, enlargement & lengthening of one remaining toe into modern hoof D. Newer fossils show horse evolution more complex; same lineage gave rise to mules & zebras III. Homologous structures - structures often dissimilar in form & function that have underlying structural similarities (example: vertebrate forelimbs show great variations in form & function) A. Each type of forelimb has its own specific use & has obvious & significant differences 1. Dig deeper & see similarities - bone structures all similar (one end of single long upper bone connected to shoulder, other end connected to two additional side-by-side long bones) 2. Smaller bones follow forming wrists, palm bones, paws B. Explanation - all mammals evolved from common ancestor (reptile with generalized forelimb) 1. Natural selection worked on generic forelimb, evolved variety now seen (flippers, wings, etc.) IV. Analogous structures - structures that have similar form & function, but are structurally quite different (example: wings of birds, bats & insects); how different? - insects have no bones A. Terrestrial flight requires smooth surface in shape of airfoil able to produce lift & some means of locomotion - requirement met in vertebrates & insects 1. Evolved separately from different structures to serve same purpose - variety of insect wings came from exoskeleton extensions; vertebrate wings came from forelimb modifications 2. Natural selection shaped features they already had into superficially similar structures to overcome environmental challenge (need to fly) B. Convergent evolution - unrelated organisms evolving similar adaptive characteristics (ex.: body shape in dolphins, sharks & icthyosaurs) V. Life's chemistry - chemicals of life are complex A. Proteins - complex; long chains of amino acids (there may be hundreds) seen in every organism, but unique to each one; similar within a species, more distantly related species differ more B. The more closely related two organisms are, the more closely their proteins resemble each other 1. Differences Darwin noted started as minute differences in proteins which might cause minute changes in the organism 2. If changes become sufficiently great вЂ”> new species How Does the Process of Evolution Work?: Allopatric Speciation I. Speciation (species giving rise to new species) may occur when populations become isolated A. Ex.: Hawaiian Islands - volcanic islands at first devoid of life; air & ocean currents helped to colonize them 1. Success rate may be as low as one new introduction every 70,000 years; would have brought ~275 species of flowering plants to islands; from these >1000 new species evolved 2. Most of the new species are seen nowhere else on Earth, like silversword species, which is closely related to tarweeds of North American southwest B. All species occupy a finite range вЂ“ some small (pupfish in one hot spring), some large, none everywhere; oceanic islands are often the exclusive homes of specific species 1. A matter of adaptations & tolerances вЂ“ they have adaptations to tolerate conditions in home range; lack adaptations to tolerate conditions outside that range 2. Organisms cannot expand their territories due to a combination of limiting factors: range of tolerance, strength of their adaptations & nature of their environment C. How do new species evolve? 1. Within optimal territories, the environment is easily tolerable; natural selection favors most highly adapted species & hones the successful ones вЂ”> populations grow 2. Eventually, a limit is reached beyond which they cannot easily grow; all territories occupied, competition intensifies, predators & disease increase, food sources are stretched -> crowding 3. Individual differences persist in crowded population; if some tolerate new conditions, this is an advantage -> if they move (even a few miles or feet), overcrowding stress could decrease 4. Movement does not always occur; maybe none can tolerate new conditions or a barrier exists that is too intense (no native conifers in Hawaiian Islands even though plentiful in Americas) II. To reach & be successful in new territory, three opportunities must be realized; if not, it won't occur A. Geographic opportunity for newcomers вЂ“ original physical barrier must be surmountable (birds fly over; luck вЂ“ drought may dry river; some carried вЂ“ fish eggs, seeds; float; wind) B. Physiological opportunity to enter new territory вЂ“ new one must at least be tolerable; can occur if conditions change making bad environment tolerable; limits (salt H2 O to estuary, not fresh) C. Ecological opportunity вЂ“ newcomers will not be able to tolerate intense competition for critical resources with other, better adapted organisms III. Once move is made, conditions not the same as in old environment вЂ“ first few seasons critical A. Numbers are few & adjustments to the new environment are imperfect; natural selection again B. Most tolerant organisms are favored, survive, have offspring, & pass on successful adaptations; least tolerant selected against вЂ”> over time, characteristics within new population change C. Speciation has not occurred as long as the populations can interbreed; if they are completely isolated, speciation is more likely D. Eventually, populations become so different that they cannot interbreed вЂ”> speciation IV. Speciation as result of geographic isolation is allopatric (allo- different; -patric - native land) speciation A. This is speciation occuring between isolated populations (those originating in different territories) B. Geographic isolation was thought to be the most common scenario within which speciation occurs How Does the Process of Evolution Work?: Sympatric Speciation I. Can speciation occur between populations whose ranges overlap? - geographic isolation unnecessary; ex.: goldenrod gall fly (northeastern & north central US) depends on goldenrod for reproduction A. Adults emerge in Spring, live about ten days during which time they mate B. Females lay one egg each in the unopened terminal leaf bud of plant 1. Eggs hatch & larvae burrow several millimeters into stem where they reside 2. Their presence stimulates plant to grow galls (swollen areas of plant tissue where larvae feed, grow, & eventually overwinter) C. Two distinct species seen in north & central US using two different goldenrod species (late & tall) 1. Live in same field close to one another & attract different predators (late - chickadees, downy woodpeckers; tall - burrowing wasps) - reproductively isolated, different selection pressures 2. Tall males prefer to mate with tall females (lay eggs on tall goldenrod); late males prefer to mate with late females (like to lay eggs on late goldenrod) - maintain reproductive isolation 3. Hybrids of the two species have lower survival rates than pure bred individuals of either one 4. Hybrids that survive can mate & prefer neither species nor egg-laying site; late females if no choice lay eggs on tall goldenrod & vice versa вЂ”> not yet separate species but could get there II. Called sympatric speciation - occurs within one territory (sym- - same; patric- - native land) A. Species isolated by occupying different habitats (specific area occupied by a species) in given range (larger geographic area occupied by a species) B. Controversial to a degree - questions about details, not basic premise of evolution or selection 1. How isolated in overlapping populations? - may occupy different territories (treetops vs. ground), courtship displays (bonding, physiological arousal to make eggs) 2. Can be instantaneous (in single generation) - mechanism will be discussed later after genetics III. Allopatric & sympatric speciation may occur together вЂ”> allopatric first, then sympatric if get back together after partial isolation by habits, displays, breeding season, preferred foods, etc. A. If not isolated by differences вЂ”> merge back into single species with more individual differences B. May be the cause of color phases in species - Arctic foxes are white & blue (really gray) C. Blue foxes common on islands; when it is warm, they are isolated; when it is cold, islands are connected and foxes interbreed, so there is one species with two color phases How Does the Process of Evolution Work?: Darwin's Finches вЂ” A Case Study I. Darwin's finches - 13 species of finches native to the Galapagos; drab colored, sparrow-like birds A. Galapagos formed from underground volcanoes; lifeless at first, then plants, followed by insects B. Galapagos finch ancestors came from South American mainland where they are now extinct 1. A few found the islands (geographic opportunity) 2. The islands are remarkably desert-like; there is little rain, like western South American mainland, so the birds are able to survive here (physiological opportunity) 3. When finches arrived, there was no competition, lots of food & space - original finch was ground-dwelling, seed- eater 4. For a time, they thrived & some of them adapted to fit their environment 5. As numbers increased, competition among them increased; some wandered off the island & were lost, others found new islands (19 others in group) & were isolated from other islands C. Different islands had different environments e.g. available foods (seeds on ground, insects off the ground in shrubs, etc.) 1. Finches might have been selected for way of life & bill according to things like food source (ground-dwelling, large crushing bills vs. non-ground dwelling, finer, longer pointed beaks) 2. In at least partial isolation, sympatric speciation would lead to populations drifting apart 3. If some wandered back to original island,the differences might be sufficient to isolate them reproductively & speciation could continue sympatrically II. Today, each island has its own assemblage of species A. Each species is rather specialized, occupying narrow range of habitats, eating narrow range of foods, restricted to one or a few islands B. Larger islands tend to have more species than smaller ones, but all have at least one Are There Patterns in Evolution? I. Unrelated organisms living in similar environments sometimes evolve similar characteristics A. The mara of South America - rodents that are not rabbits yet share several of their traits - long hind legs, long ears, flattened faces 1. Maras & rabbits live in similar environments & face similar challenges 2. Solutions for one group are equally useful for others B. Natural selection is a mindless, random, chaotic process that has no purpose other than to adapt populations to existing environmental conditions 1. Guides in no direction other than survival; common patterns repeat if they enhance survival II. Organisms raised in similar environments can evolve similarly - convergent evolution A. Unrelated organisms evolve similar adaptive characteristics - what they share in common is that they occupy the same environment & evolve similar adaptations to that environment B. Example: desert plants can look like same species although they are different species 1. Thus, they all have fleshy stems for water storage 2. They also have spines for protection and reduced leaves III. Closely related species living in different territories sometimes tend to drift apart A. Over time, their characteristics become increasingly different until new species result divergent evolution B. Example: small Hyracotherium evolved through several intermediate species and into today's horses, zebras, & onagers - today's horses have diverged from Hyracotherium & each other C. Example: The wombat, koala and kangaroo have common ancestor, most likely an opposumlike marsupial that lived about 100 million years ago IV. Adaptive radiation is an extreme example of divergent evolution A. One species can move into new territory & evolve into several closely related yet different species 1. Called adaptive radiation; a number of species evolve from a single ancestral species 2. Silverswords, their relatives, & another Hawaiian bird group (honey creepers) are examples B. An extreme example of adaptive radiation occurred among mammals 65 million years ago 1. Mammals had evolved millions of years earlier, but remained a relatively minor group because of intense competition from highly successful dinosaurs 2. Dinosaurs were already specialized to many environments 3. Extinction of dinosaurs created huge evolutionary opportunities for mammals; exploded into new forms 4. Mammals never got as big as dinosaurs, but occupied nearly all of their ecological niches V. The evolution of one species may influence the evolution of another A. Usually, species don't evolve in vacuum 1. Evolutionary changes in one species create environmental pressures on adjacent species 2. Parallel evolutionary changes occurring simultaneously between interacting species is called co-evolution B. Example: cheetahs & their prey (Thompson's gazelles) in Africa 1. Cheetah is the world's fastest mammal (can run 80 mph); exceptional acceleration - dead stop to 60 mph in three bounds 2. Thompson's gazelle is only slightly slower; as speed of one improved so did that of the other 3. Gazelles also don't run in straight line; even near top speed, they can change direction rapidly 4. At these speeds, cheetah can lose visual contact with gazelle easily 5. Cheetahs evolved two black lines down from just below each eye toward tip of nose to serve as a sighting mechanism; must keep gazelle between lines to feed Variations from Darwin's Original Model I. Darwin described evolution as a slow & gradual process - gradualism; favored by many early evolutionists including geologist Lyell, Darwin's friend A. Said species evolve through gradual, steady, linear accumulation of small changes 1. Fit neatly into Lyell's Uniformitarianism theory; stated that geological events happen slowly B. Sometimes, patterns of change become complex & branches occur in several directions 1. But even in these complex groups, a single species exhibits gradual, slow, linear change 2. Became accepted, assumed pattern for evolution II. Evolution may occur much more rapidly than thought earlier - Niles Eldredge & Steven Jay Gould A. They described pattern in which stasis (lack of change) is the norm for most species most of time 1. For millions of years, characteristics of species stay relatively constant 2. If evolution does occur, within a few tens of thousands of years, species change & may evolve into new species - punctuated equilibrium 3. Evolution is series of fits & starts rather than smooth & linear B. Example: fossils of now extinct trilobites (hard-bodied animals not unlike modern crabs, insects) 1. Eldredge & Gould saw distinct absence of fossilized trilobites representing intermediate forms 2. Still being debated vigorously III. Evolution does not always occur - natural selection can only work on variations that already occur within population; variations can not be created on demand A. Many northern animals are white, at least in winter, for camouflage 1. White hairs are often hollow, filled with dead air, excellent insulation 2. Natural selection favored organisms that were lightest in color when they moved into Arctic 3. Not all Arctic animals are white (ravens - black) - no lightest color individuals to favor so they stayed black B. Natural selection has been important to ravens by working on other sources of variation 1. Unusually large for birds in crow family since heat is created by body bulk (other Arctic animals are white & the largest of their kind) 2. Ravens - especially adept at finding food; some poke eyes out of caribou, wait for them to die C. Evolution works best in species with large populations & wide ranges in individual variations 1. Mid-1940s - New York City had huge house fly problem 2. 1947 - DDT available, widely & indiscriminately used вЂ”> fly population plummeted 3. Early 1950s - flies returned; sprayed DDT, but had no effect since new flies were immune to it; a few flies in original population were immune -> they survived & thrived-> species recovered 4. Insects with less variation disappeared from New York City since they lacked tolerant forms D. Many species lack range of variation in house flies & most populations are relatively small 1. Natural selection takes time even with punctuated equilibrium (tens of thousands of years) 2. If environment changes too rapidly, evolution will not keep pace E. Some non-evolving species continue to survive - coelacanths identical to fossil forms survive in restricted, isolated, deep waters offshore from Madagascar; once roamed whole ocean 1. Became extinct in habitats that changed; survived in those that have not 2. Recently, new population found near Indonesia F. Most species become extinct - sooner or later, pace of environmental change & intensity of environmental pressure overwhelm species' ability to adjust & evolve 1. With possible exception of microbes, no species lives forever How Well Was the Theory of Evolution Accepted? I. After it was published, Darwin's theory was hotly debated - had little trouble convincing others that evolution happened; relatively easy to accept for his contemporaries A. Changeable species was not a new idea - Darwin's own grandfather & others had proposed it before he was born B. His mechanism of natural selection as a driver of evolution was harder for many to accept & if his mechanism was incorrect so was his theory C. Critics were saying evolution happened but not the way he thought II. Criticisms centered around three important points A. Darwin completely lacked direct evidence for natural selection & his indirect evidence was far from convincing; such circumstantial evidence was not sufficient for many Victorian thinkers 1. They tended to demand absolute proof & this was lacking 2. Darwin used two indirect examples of natural selection: its leading to swifter, leaner wolves & the relationship between reproduction of flowering plants & bees harvesting sweet nectar B. Darwin could not adequately deal with the question of heredity & variations within populations 1. Natural selection suggested that organisms should become more & more alike as they became adapted to their environment; once perfectly adapted they should be exactly alike 2. Darwin could not present one example of this 3. It may not have been obvious in Darwin's time that environments frequently change & that the direction of natural selection would thus change 4. Neither he nor his contemporaries knew the source of individual differences in populations C. Darwin got caught up in an argument that is still not resolved - is evolution slow & continuous or jerky & discontinuous? 1. Sometimes describes it as slow & intermittent, but generally settled for slow & steady 2. Sided with Lyell's theory of uniformitarianism, tying the two together; they had common foes 3. Even his staunchest defenders (Francis Galton & Thomas Henry Huxley) had doubts accepted natural selection but feeling that it operated infrequently 4. Others felt that if he was wrong about slow & steady, the whole theory would be in question III. Darwin was able to face other arguments more successfully A. Explained evolution of gaudy coloration & flamboyant structures among male birds - proposed theory of sexual selection 1. Female birds choose mates & are attracted to males with extreme features & mate with them 2. Their colorful or extreme features are passed on to their male offspring B. Altruistic behavior - has little value to individuals, but benefits the group 1. Worker bees are essential to hive, but never reproduce & pass their traits on to offspring 2. Why didn't natural selection work against such behavior? How could it evolve? 3. Darwin saw that natural selection could work on entire lineages rather than just on individuals 4. By caring for closely related individuals, family members care for those who share their traits 5. If successful, they ensure that their traits are passed on to succeeding generations 6. In the 1960s, details of kin selection (individuals helping relatives raise young) interpreted within context of natural selection IV. After Darwin's death, debates continued A. Natural selection lost ground, alternative explanations proposed & rejected B. Evidence accumulated over time; some, like Mendel's Laws, were already described, but ignored Where Are We Now? I. Evolution is generally accepted by the vast majority of contemporary biologists A. What is being argued is details of how it happens - the theory will be refined but not discarded 1. Evolution has been challenged for 150 years & it is still accepted as is natural selection B. New techniques are now being used to decipher relationships between organisms 1. Resemblance of organisms is no longer the only way to assess the closeness of relationship 2. Biochemical analyses allow comparison of organisms' chemical composition (proteins, DNA) II. Why is the theory of evolution still accepted? A. It is useful - it explains & ties together whole sets of observations 1. It explains why there are so many different kinds of organisms on Earth 2. It explains why organisms resemble each other & share many characteristics - even those most distantly related (all cells digest glucose & share other biochemical capabilities) 3. Also explains why species are different - natural selection makes isolated species more & more different B. It also fits within the framework of other theories - it is compatible with biology's other major theories & is the central theory that holds them together Analogies, Anecdotes and Illustrations Charles Darwin and Abraham Lincoln Charles Darwin was born on February 12, 1809, the same day as Abraham Lincoln. All things considered that date was not a bad day for the planet. How Darwin Got the Opportunity to Sail on the Beagle According to The People's Almanac #2 and other sources, Darwin's father wanted Charles to train for the ministry. When Darwin was offered the opportunity to go on the voyage of the Beagle, his father told him that he could not go unless he could find "any man of common sense" who would advise him to go. Darwin's uncle, Josiah Wedgwood, a member of the Wedgwood family of china manufacturers, stated that the study of natural science, that is God's creation, was an appropriate pursuit for a minister. Darwin's father relented and Charles joined Captain Robert FitzRoy on the Beagle. FitzRoy wanted a naturalist aboard to gather proof of the literal truth of the book of "Genesis." As a final ironic twist, when the five-year voyage was over, so was Darwin's career as a clergyman and eventually the literal interpretation of "Genesis" was eroded. Survival of the Fittest The phrase most often associated with the theory of evolution is "survival of the fittest," but it was not initially used by Darwin. According to the biography Darwin by Desmond and Moore, the phrase was coined by Herbert Spencer and first used in his book Principles of Biology as a replacement for "natural selection." Alfred Russel Wallace urged Darwin to use the phrase, pointing out that its use dodged the anthropomorphism of words like "selecting," "preferred," and "favouring," words that Darwin used repeatedly. These words suggested that an intelligence was directing which traits would persist from generation to generation, a concept foreign to Darwin's idea of the engine of evolution. While Darwin felt that the use of "survival of the fittest" was inadequate - it played down the analogy between nature's selection and that practiced by animal breeders, he began to use it, hoping that it would get him off the "anthropomorphic hook" described by Desmond and Moore. Darwin Did Not Originate the Idea of Evolution A common misconception of many students is that Darwin was the first to introduce the idea of evolution. This is untrue. In the 1700s, the Comte de Buffon and Darwin's grandfather Erasmus proposed independently that species could be modified and changed with time. In the early 1800s, Lamarck put forward the theory of the inheritance of acquired characteristics to explain the changes in species. Darwin's theory proposing natural selection as the driving force of evolution replaced Lamarck's and Mendel's theory of inheritance eventually replaced his model for the inheritance of traits. Darwin and Wallace - Two Class Acts Darwin did not publish his theory until he was forced to when he received a letter from Alfred Russel Wallace. The letter contained a description of the natural selection that was the cornerstone of his theory and asked Darwin to circulate his ideas among their peers. Ironically, the letter was, in part, a result of Darwin's encouragement. Darwin asked his friends Lyell and Hooker for advice. They arranged for Wallace's letter and a summary that Darwin had written in 1842 that clearly predated Wallace's letter, along with excerpts from other essays and letters. The communications from both authors were presented together at a meeting of the Linnean Society of London on July 1, 1858. The most striking aspect of this part of Darwin's story is the class shown by both principals. Darwin never considered suppressing the letter that he felt had scooped him and prior to the arrangements to present simultaneously the work of both men, he said, "I would far rather burn my whole book than that Wallace or any other man should think that I behaved in a paltry spirit." When Wallace heard what had happened, he was not only gracious, but he also was happy that his letter had persuaded Darwin to publish his ideas after 20 years. Wallace later said, "The one great result which I claim for my paper of 1858 is that it compelled Darwin to write and publish his Origin of Species without further delay." When one considers what might happen nowadays, the behavior of Darwin and Wallace is even more remarkable. One need only remember the legal wrangles that occurred over the discovery of HIV (the AIDS virus) to be amazed that Darwin and Wallace acted so honorably. Later, it became clear that the mechanisms of Darwin and Wallace had some differences. Wallace's view of selection was that the environment eliminated the unfit; Darwin envisioned ruthless competition between individuals. Wallace also dealt with the question of the purpose of natural selection. Darwin believed that there was no purpose and entirely dismissed the question. Three Interesting (At Least to Me) Connections to Darwin Before Darwin set sail on the Beagle, he sought advice from a number of people including the botanist and brilliant microscopist Robert Brown, who discovered the nucleus and Brownian motion. According to the biography by Desmond and Moore, Brown gave advice to Darwin about which microscope to buy for the trip. Darwin promised to collect some Patagonian orchids for Brown. Another connection of significance to Brown arose in 1858. Brown's death caused a postponement of the last scheduled meeting of the Linnean Society of London before the normal summer break. Another meeting was squeezed in before the break on July 1, 1858. It was at this meeting that Wallace's and Darwin's papers describing natural selection were presented. Captain Francis Beaufort was the British Admiralty hydrographer (coastal map-maker) nominally in charge of the voyage of the Beagle. A major task of the Beagle's crew was to map islands and coastlines and to sound harbors and channels. This task was begun during the preceding voyage, but the charts from that voyage needed to be checked and extended. In addition, they were supposed to log tides and weather conditions. Captain FitzRoy and his colleagues would be the first to plot wind forces around the globe using Beaufort's scale. The scale is the same one referred to in the Billy Joel song Storm Warning. Darwin, on occasion, would attend parties at the home of Charles Babbage along with other members of the intellectual elite of Britain during that period of time. Babbage was the designer of what was called an analytical engine or a mechanical calculator. Some consider him to be the father of the computer. Political Ironies - Past and Present One of the major influences on Darwin's development of the concept of natural selection was the work of Malthus, an economist for the East India Company. At the center of his theory was the idea that as population increases faster than the food supply, struggle and starvation become inevitable. Malthus believed that public charities (relief for the poor) only made the problem worse. Such charitable handouts, Malthus felt, made the poor comfortable and eventually served to encourage them to breed, leading to a vicious circle. This would lead to greater numbers of mouths to feed and consequently poor mouths to feed. In turn, this would place more demands on welfare. The Poor Law Amendment Bill was becoming law while Darwin and his shipmates were traveling around the world. Its effect was to end aid for all but the poorest, sickest and/or oldest in society. The goal was to make the poor more self-reliant. In Darwin's day, the people who wished to continue helping the poor, as had been done in the past, and who did not subscribe to Malthus' view of aid to the poor were also usually the same people who were most vocal about opposing Darwin's theory of evolution. On the other hand, those who supported Darwin's theory were often also the people who wished to decrease welfare. At the risk being somewhat simplistic, nowadays things have switched a bit. The people who are most likely to support the deepest cuts in welfare today and, thus, those who make essentially the same arguments about welfare that Malthus did are the people most likely to have doubts about the theory of evolution, an idea that grew, to a large extent, out of Malthus' ideas. I find it ironic that Malthus' argument is used to support the position of those who would severely cut welfare (often our ultraconservatives), but that those same arguments are ignored by those people in this group who reject the theory of evolution. Furthermore, many of the people at the other extreme (the very liberal) who accept as true evolution and, by extension, the ideas of Malthus that are intimately connected to it, differ with Malthus on the worth of welfare. How I love irony! Darwin's Illness Very few people realize that Darwin was ill for much of his life. He suffered from fairly severe seasickness during his five year voyage on the Beagle. Consequently, he spent a significant amount of time in his hammock. In South America, he was bitten multiple times by insects and suffered through the rough conditions characteristic of world travel at that time. After his return to England, he was ill for most of his remaining years and became a chronic invalid. Many of his bouts of illness seemed to be related to his anxiety about what the publication of his theory would do to his social position, and they seemed to center around stomach and intestinal problems, the symptoms of which included nausea and vomiting. Before the voyage on the Beagle, he had considered training to become a clergyman so that he could do what many clergymen of the time did when not directly involved in religious affairs вЂ” become an amateur naturalist. Many of the members of the scientific societies throughout the country were such country parsons and many were accomplished naturalists. Many were Darwin's friends and most did not accept evolution as an explanation for life's diversity. Early in Darwin's life, academe was dominated by these same people. Darwin believed вЂ” and probably rightly so вЂ” that his belief in evolution would make him a social outcast once it was revealed. Darwin's response was to delay publication of his theory until he had so much evidence to support it that it would have to be accepted. He enlisted the aid of many of his colleagues, including Wallace, some of whom traveled the world sending specimens back to England as he had done. But, this time, he was on the receiving end. He would also cautiously hint about his evolutionary leanings to sound out his colleagues. He would listen to their criticisms of his ideas and then try to figure out ways to combat those criticisms. During the twenty years that it took to publish his theory, the composition of the scientific community changed, shifting from domination by the clergy to that of younger professional scientists like his friends and supporters Thomas Henry Huxley and Joseph Hooker. The strain of this period frequently got to him, forcing him to curtail his work for weeks or even months at a time. He sought a number of unconventional cures, including special diets and a water cure, since no one could specifically diagnose the cause of his malady; some of these cures seemed to work for a time, but his sickness always returned. He eventually died in 1882 at the age of 73, a few months after a massive heart attack. The Huxley-Wilberforce Confrontation Darwin's theory was not well received by the clergy, since it ran counter to the first chapter of "Genesis" and implied that Man had an ancestor in common with the ape. Some took this to mean that Man was descended from monkeys. The Bishop of Oxford Samuel Wilberforce referred to Darwin's Origin of Species as an "utterly rotten fabric of guess and speculation." In a famous incident, a meeting was held at which Wilberforce spoke eloquently against the theory of evolution using information supplied by Richard Owens, the Superintendent of Natural History at the British Museum and an opponent of the theory as well. Also attending the meeting was Thomas Henry Huxley, one of Darwin's staunchest defenders who liked to call himself "Darwin's bulldog." After his remarks, Wilberforce turned to Huxley, asking "Is it on your grandfather's or your grandmother's side that the ape ancestry came in?" Following the laughter engendered by this witty comment, Huxley answered. "I asserted, and I repeat, that a man has no reason to be ashamed of having an ape for an ancestor. If there were an ancestor whom I should feel shame in recalling, it would be a man of restless and versatile intellect, who, not content with success in his own sphere of activity, plunges into scientific questions with which he has no real acquaintance, only to obscure them by aimless rhetoric and distract the attention of his hearers from the point at issue by digressions and appeal to religious prejudice." A number of fist fights followed his comments and a lady fainted. Even today, the theory of evolution can lead to similarly vociferous confrontations. Sample Test Questions Multiple Choice, Conceptual, and Open-Ended Questions From the Text 1. The idea of evolution ________ Darwin. a. was originated by c. was never really considered by e. eluded b. preceded d. destroyed the reputation of 2. Whose theory that geologic changes take place extremely slowly influenced Darwin's development of the theory of evolution by natural selection? a. Charles Lyell b. Thomas Henry Huxley c. Erasmus Darwin d. Lamarck e. Mendel 3. An early proposed evolutionary scheme suggested that physical traits acquired by an animal during its lifetime could be passed on to its offspring. Who was responsible for this theory? a. Buffon b. Charles Darwin c. Mendel d. Erasmus Darwin e. Lamarck 4. What did Darwin consider to be the mechanism that drives the process of evolution? a. artificial selection b. natural selection c. mutation d. constancy e. a and b 5. Whose letter to Darwin in 1858 describing a similar mechanism of evolution prompted Darwin to publish at long last his theory of evolution? a. Huxley b. Erasmus Darwin c. Alfred Russel Wallace d. Mendel e. Joseph Hooker 6. In order for a population to remain relatively constant and thus stable, what must happen? a. the population must reproduce exponentially d. births should match deaths b. the death rate must increase e. the death rate must stay constant c. the birth rate must remain constant 7. What happens to a population that generally produces two offspring for every reproducing pair? It dwindles and will eventually become extinct. What happens to a population in which reproducing pairs average 2.3 offspring per pair? The population will become overpopulated. 8. Which of the following is a natural resource that would be likely to engender the kind of competition that would tend to limit population size? a. space b. food c. shelter d. fresh water e. all of the above 9. Who proposed that competition among humans for food served to limit the population and led to things like famine, war and disease, an idea that Darwin extended to other animals in his theory of evolution? Thomas Robert Malthus, an 18 th century economist-clergyman. 10. A few individuals in a population possess large and more powerful leg muscles than the general population. About ten generations later, this trait has become more plentiful in the population. What has has led to this increase in the number of these rabbits in the population and what is a word that accurately describes the process? The individuals with the larger and more powerful leg muscles have a better chance of surviving to reproduce perhaps because they can run faster to escape predators or to capture prey. As a result, more of them survive to reproduce and send the genes responsible for the larger and more powerful leg muscles into the next generation. Their numbers increase from generation to generation. The process is called adaptation and the population is becoming better adapted to its environment. 11. What distinguishes species in nature? Species are considered distinct if they do not interbreed in nature. If horses and jackasses mate, they have offspring called mules. Why are they considered to be separate species? They are considered to be separate species because, mules while they do live and are useful, are also sterile. In order for two organisms to fulfill the definition of interbreeding, the offspring must be fertile. Since mules are sterile, their parents, the horse and the jackass are not members of the same species. 12. Which of the following is indirect evidence in support of the theory of evolution? a. improvement of domesticated animals and plants by breeding individuals with desired traits b. the fossil record that shows a clear relationship between living and extinct animals c. homologous structures in different organisms that are dissimilar in form and function but that have underlying structural similarities d. analogous structures that have similar form and function but that differ structurally e. all of the above 13. In order for organism to reach and be successful in a new territory, three opportunities must present themselves and be realized. What are they? There must be a geographic opportunity that removes a barrier to the new territory. A bird could fly over an obstacle or a drought dry a river. Once an organism makes it to a new territory, the organism must at least be able to tolerate it. If not, the organism would die. This is called a physiological opportunity to enter the new territory. This opportunity may also be realized if a previously intolerable territory becomes tolerable. Lastly, there must be an ecological opportunity. If the newcomer finds itself in intense competition for critical resources with other, better adapted organisms, it will be unlikely to survive. If there is little or no competition, it may be able to exploit the new territory. 14. Which of the following would be most closely associated with allopatric speciation? a. lake b. savannah c. mountain range d. roadbed e. snow 15. Two populations of the same species of squirrels occupy the same range that includes a forest. One of the groups spends all of its time in oak trees; the other spends its time in pine trees. Over a long period of time, the two populations evolve into two different species. This is an example of _______ speciation? a. sympatric b. allopatric c. parapatric d. symphonic e. conspecific 16. Why did the bills of the different species of finches on the Galapagos Islands have different shapes? The shapes of their bills varied according to the finchesвЂ™ food sources. Their bills became adapted to the food source of choice for each species. 17. Dolphins, sharks and the extinct icthyosaurs all exhibit streamlined shapes that help them move smoothly through the water. Such similar forms in distantly related organisms that live is similar environments is an example of _________ evolution. a. divergent b. convergent c. cod. punctuated e. adaptive 18. The thirteen species of DarwinвЂ™s finches evolved from a common ancestor. The resultant species of finches were closely related but clearly distinct. This is an example of _________. a. co-evolution b. adaptive confusion c. convergent evolution d. adaptive radiation e. c and d 19. The separation of two populations of a species into different environments or territories can result in differences between the two populations. Eventually, they may change enough to become two different species with the original species being a common ancestor. This describes what happened when Hyracotherium evovled into todayвЂ™s horses, zebras and onagers. It is an example of _______ evolution. a. divergent b. convergent c. cod. punctuated e. adaptive 20. If a comet struck the surface of the Earth killing most of the mammals, it is possible that reptiles might fill the opened environmental niches by evolving into a number of closely related organisms with different traits related to their new niches. This is an example of __________. a. co-evolution b. adaptive confusion c. convergent evolution d. adaptive radiation e. c and d 21. There are a number of examples in nature of flowers having established relationships with one particular insect so that that one insect is the only one that pollinate that particular flower. The connection between the two is so intimate that if one of them became extinct so would the other. Of what kind of evolution is this an example? Co-evolution. 22. Darwin described evolution as a slow, gradual process, gradualism; since then Eldredge and Gould have made an alternate proposal called punctuated equilibrium. Describe how punctuated equilibrium differs from gradualism. Eldredge and Gould suggested that most species change very little over long periods of time, a pattern called stasis. They also suggested that if evolution occurred, it did so over a very brief period of time evolutionarily, say tens of thousands of years. This process may result in the appearance of new species. Thus, according to this proposal, evolution proceeds in a series of fits and starts rather than in a slow, smooth and linear fashion. 23. What is wrong with the following statement? Changes in an organismвЂ™s territory cause the appearance of new mutations which are then acted upon by natural selection so that those that provide an advantage in the altered territory are passed on more often to the next generation. The changes in the territory do not cause new mutations to appear. If the population is large enough, it is likely that advantageous mutations existed in the population prior to the changes in the territory. It is these mutations that are acted upon by natural selection. 24. What is the ultimate fate of all species? Extinction. 25. What are some of the major criticisms of DarwinвЂ™s theory? First, Darwin lacked direct evidence for natural selection and his indirect evidence was not as convincing as it might have been. Second, Darwin could not adequately deal with the question of heredity and variations within populations. Third, Darwin got caught up in the argument about the speed of evolution and could not decide whether evolution was slow and continuous or jerky and discontinousness. 26. The peacockвЂ™s gaudy tail is thought to be the result of females (peahens) being attracted to males with extreme features and mating with them. This would tend to send the genes for the gaudiest tails on males to the next generation. What is the name of this type of selection? It is called sexual selection. 27. How can altruistic behavior вЂ” behavior that has little value to the individuals performing it but benefits the group as a whole вЂ” evolve? If an organism cares for a closely related individual, one which shares its traits, it can ensure that its traits are sent into succeeding generations. This is even true if the organism performing the altruistic behavior dies as a result as long as its sacrifice helps to ensure the survival of one or more closely related organisms that reproduce subsequently. Multiple Choice, Conceptual, and Open-Ended Questions From the CD-ROM 1. What was Darwin's role on the Beagle? He was the naturalist on the Beagle. His job was to go ashore at each stop to study plants and animals, the people and the terrain. 2. What were the main purposes of the Beagle's voyage? Its job was to chart the South American coast and get longitudinal fixings all around the world. 3. What books had the most influence on Darwin during the voyage? The Bible and Lyell's Geology. What caused Darwin to spend considerable amounts of time in his hammock? Sea-sickness. 4. What impressed Darwin about the tropical rainforest of Brazil? The diversity of life and the struggle of plants and animals to survive. 5. What did the fossils and skeletal remains Darwin found in Argentina and elsewhere suggest to him? The fossils and skeletal remains suggested an association between living species and their extinct ancestors. 6. What did Darwin's discovery of marine fossils high in the Andes suggest to him? It suggested that Lyell's theory that land features like mountains arose gradually from the Earth's crust was supported. The discovery of marine fossils in the Andes meant that these mountains had once been the ocean floor. 7. Which spot that Darwin visited yielded the most data and may have played the biggest role in the development of his theory? The Galapagos Islands. 8. How did Darwin explain the differences in the tortoises on the various islands of the Galapagos group? Darwin proposed that they had one common ancestor, but changed over many generations because of their isolation on the separate islands. 9. If a pair of flies could produce ten flies per generation, how many flies would there be at the end of five generations? 2,592. After ten generations? 282 million. After 30 generations? 2.75 x 1025 . Of what kind of growth is this an example? Exponential growth. 10. Bacteria have a generation time of 20 minutes. How many would there be after 36 hours if you began with a single bacterium? A huge number whose mass would surpass that of the planet Earth. 11. In the CD-ROM simulation of the limitation of population size in nature, what prevented exponential growth of the fly population and resulted in a relatively constant population size through the generations? Flies were continually dying off because the amount of water in the habitat was limited, leading to competition. Flies were thus continually dying off to be replaced by newly hatched flies. 12. What is now known to provide the raw material for natural selection? a. competition b. hydrolysis c. genetic mutation d. death e. renaturation 13. In the CD-ROM simulation of predation on green and blue varieties of flies, which variety is most likely to survive and why? The green flies are more likely to survive, because they are camouflaged against the green backdrop of the habitat and are, thus, harder for predators to see. More green flies survive to reproduce and send their genes into the next generation. Over time the number of green flies in the population grows while the number of blue flies falls. 14. The CD-ROM contains a hypothetical phylogenetic tree. What kinds of differences set apart the different species of flies shown on that tree? Among the traits that differ throughout the tree are the size and angle of placement of the wings, the number of wings, the presence or absence of wings and the color of the body. 15. Which finch's beak is best suited for collecting nectar in the Hall of Darwin CD-ROM exercise (Section 2.3). The bottom finch has a long beak that can reach deep a flower to retrieve nectar. Which beak is best suited for eating seeds? The short, broad beak on the second bird from the top is the best for crushing and eating seeds. 16. Behind the door in the Hall of Darwin (Section 2.3) that hides the display on homologous structures, which of the skeletons have a humerus? All of them. Which of them have a radius and an ulna? All of them but one. The horse has a bone called the radioulna which results from the fusion of the radius and ulna. 17. What part of the skeleton forms the wing of the bat as seen in the Homologous Structures Room of the Hall of Darwin? The greatly lengthened phalanges (fingers) of the bat have skin stretched between them to form the wing. 18. You are studying three organisms that occupy the same habitat. They look very much alike but are clearly members of different species. This is an example of ___________. a. convergent evolution c. adaptive radiation e. de-evolution b. divergent evolution d. co-evolution 19. Which of the following is an example of divergent evolution? a. Darwin's finches c. a and b b. adaptive radiation d. icthyosaurs, sharks and dolphins e. a, b and c Using BioInquiry in Large Classes Integrating Components into the Lecture There are a number of exercises on Chapter 2 of the CD-ROM that should prove useful in illustrating the central concepts of evolution and the details of the voyage of the Beagle. You should recommend that your students take a look at them. In Section 2.1 of the CD-ROM, the major stops along the Beagle's route are shown as are the items that Darwin took with him. What Darwin did at each location is also shown with pictures and narration by an animated Darwin. In Section 2.2 of the CD-ROM, the students should look at the demonstrations of Darwin's observations and the deductions to which those observations led him. The first observation is represented by an animated illustration of uninterrupted, exponential growth of a population of fruit flies and shows effectively how quickly a population can grow. The second observation that populations remain constant over time is also well demonstrated by an animation. There is no animation showing the limitation of natural resources (Darwin's third observation), but the point is made. Darwin's deduction flowing from these three observations (that there is a struggle for existence among individuals in a population) is demonstrated with another fruit fly animation. The fourth observation that the individuals in a species display variation is simply but ably demonstrated. The next animation which shows Darwin's second deduction (that natural selection is the engine of evolution, i.e. that individuals with favorable variations are more likely to survive and reproduce) is the best of the lot. It is set up like a video game where there are two colors (blue and green) of fruit flies in the population that lives in a green environment. You are a predator and it is your job to click on and thus kill fruit flies to obtain energy for survival. As you may have guessed, the blue fruit flies stand out against the green background and are more easily killed. In a little while, the number of blue fruit flies in the population drops precipitously while the number of green fruit flies increases. This is an extremely effective example of how natural selection works. Urge your students to try it. They can even adjust the speed of their prey. The third deduction that the accumulation of variation over many generations results in evolution is made clear by a simple drawing of a phylogenetic tree. This entire section is an excellent and effective summary of the thought processes that led Darwin to the theory of evolution by natural selection. Use it in class if you like and if you have the equipment to project it. If not, encourage the students to explore it on their own. Section 2.3 contains illustrations of homologous structures and also the evolution of many species of finches from a single ancestral species that arrived at the Galapagos. These exercises are found in the Hall of Darwin, a cyberspace museum. Both demonstrations accomplish what they set out to do and should help your students. While not terribly elaborate, Section 2.4 of the CD-ROM effectively illustrates the concepts of convergent and divergent evolution. The CD-ROM has photos of species exhibiting both kinds of evolution. Read More About It There are a number of books that would be excellent to enhance the students' knowledge of Darwin and his theory. Two Darwin biographies, Darwin by Adrian Desmond and James Moore and Charles Darwin: A New Life by John Bowlby, provide fascinating insights into Darwin the man and how he arrived at one of the most important (if not the most important) ideas in science in general and biology specifically. They seem to differ on the explanation for Darwin's illness through most of his adult life. Desmond and Moore believe that his illnesses were caused by his worry about what effect the revelation of his ideas would have on those he considered his friends and how that might affect his place in society as well as that of his wife and children. Bowlby suggests that his lifelong infirmity was due to repressed emotions produced by his mother's death when he was eight. Both arguments are well supported. It is likely that there are elements of truth in both views. Both emphasize that Darwin was afraid that he had passed on to all of his children his own weak constitution and the distress that this fear caused him. If a student wishes to explore the more philosophical issues connected with evolution, s/he might want to pick up Darwin's Dangerous Idea: Evolution and the Meanings of Life by Daniel C. Dennett. This book was a finalist for the 1995 National Book Award. It is accessible, thought provoking, and ranges over a number of issues related to evolution. The Blind Watchmaker by Richard Dawkins discusses the evidence that evolution proceeds without design. The title of the book makes reference to the 18th century theologian William Paley who felt that the intricacy of the living world indicated a purpose and a guiding hand supposedly leading to that pinnacle of evolution, humanity. He likened the complexity of nature to that of a watch and suggested that neither a watch nor the infinitely more complex living world could have appeared by accident or chance; a designer or watchmaker was required. Paley thus considered the greater complexity and seeming purposefulness of nature and the living world as overpowering evidence for the existence of God. Dawkins makes a case for the role of chance and accident in evolution. He identifies natural selection as the watchmaker of the living world, but calls it the blind watchmaker, because it has no purpose and no foresight. He assembles arguments to support those elements of evolutionary theory that people find hardest to believe. The book is considered controversial by some but that makes it even more worth the effort to read it. Students may also read any of Stephen Jay Gould's collections of essays on evolution, among The Panda's Thumb, Bully for Brontosaurus, Ever Since Darwin, The Flamingo's Smile, and Hen's Teeth and Horse's Toes. Wonderful Life is his book about the Burgess Shale, which contains fossils of extinct organisms that are best described strange and wonderful. All of them are easily read by a non-scientist and explain some of the intricacies of evolutionary theory. For a description of the Scopes "Monkey" Trial and the politics and carnival atmosphere surrounding it recommend Summer of the Gods by Edward J. Larson which won the 1998 Pulitzer Prize. In addition to chronicling the trial, it deals with the lasting impact that the trial has had on religion, culture, education, and politics. Supporting the Lab Any of the CD-ROM exercises mentioned above could be used to demonstrate Darwin's observations and the deductions to which those observations led. They would work well in a laboratory setting either with students (individually or in groups) doing the exercises themselves or with the instructor projecting them on the screen and treating them as a demonstration. They probably would be best as a prelude to a laboratory exercise dealing with evolution or population genetics. One effective exercise that we have done is to run down a list of human traits while recording the proportion of students that carries each of the traits being discussed: tongue rolling, hitchhiker's thumb, right- or left-handedness, PTC tasting, etc. Such an activity is usually enjoyed by the class and makes a number of important points. For instance, students learn that the dominant trait is not always the most plentiful. They learn that the frequencies of particular alleles are highly variant from trait to trait. They also learn that the "best" trait is not always dominant and the "worst" is not always recessive. If you choose to do an exercise or simulation dealing with the Hardy-Weinberg equation, the animations on the CD-ROM would serve as a good introduction to the idea of exponential growth (Section 2.2). In that same section, the animations that demonstrate the tendency of populations to remain constant in the presence of limited resources or the one that demonstrates how natural selection works are also valuable, useful, and accessible. The visit to the Hall of Darwin (Section 2.3) and its presentation on homologous structures and Darwin's finches would also be a suitable introduction to labs covering evolution, either during the lab itself or as an assignment for students to do on their own prior to a laboratory session. Answers to Review Questions 1. The central proposition of the theory of evolution is that all living things are descended from common ancestors and that they can change and give rise to new species. 2. Fossils have allowed scientists to observe relationships between organisms over time. Once Cuvier elevated the study of fossils to the level of a science, he and other investigators were struck by the differences between fossils from one rock layer and those right above and below it. What he saw led Cuvier to hypothesize that natural catastrophes wiped out existing species, which were then replaced with new ones. Subsequent discoveries have filled in the fossil record even more. These findings have more completely defined the evolutionary relationships between organisms down through time. The fossil record serves as a record of evolution in progress. 3. Other investigators had already recognized that evolution occurs. Darwin and Wallace were the first to formulate coherently a theory for which evidence had been growing for some time and that explained the mechanism that drove the evolution that others had already recognized. Their conclusions were based on their observations. They proposed that natural selection explained how the process of change seen in evolution occurred. They defined natural selection as differential survival and reproduction of individuals with certain, advantageous characteristics. Darwin and Wallace came up with a mechanism that could drive evolution and provided evidence (especially Darwin) to support their proposal. 4. The theory of evolution is essentially the idea that species can and do change and that closely related species share common ancestors. Natural selection is not evolution, but it is been described as the driving force or engine of evolution. 5. The statement "populations have the ability to increase exponentially" means that populations have the potential for unlimited growth. Populations experiencing exponential growth increase in number at a set rate every generation. This generally results in rapid increases in such a population. 6. Populations usually do not increase exponentially, but instead remain constant in size because there are a number of factors that regulate population size by elevating the death rate and/or lowering the birth rate. If a population's death rate equals its birth rate, the population will remain constant. Natural resources are generally limited; this sets up a competition that becomes important in limiting survival. Such competition occurs for resources such as food, space, shelter, fresh water, habitat, and others. The competition for limited resources can lead to elevated death rates that offset any elevated birth rates. Alternatively, some of these factors (insufficient food or space) can also decrease the birth rate. 7. As populations increase, more and more individuals depend on and need to exploit fewer and fewer of the limited existing resources. This results in competition for those limited resources. Those individuals who are better equipped by their traits to compete better for those limited resources will be more likely to survive and reproduce and send the genes coding for their traits into the next generation. This is natural selection, the essence of evolution. 8. Darwin meant that individuals in a population are competing for the available, limited resources to the point that failure to obtain a sufficient amount of them will result in death and/or limited reproduction for the less well-adapted individual. That, in effect, is a struggle for existence for that individual and his/her descendants. 9. Natural selection is a "preservation of favorable variations and the rejection of injurious variations." In general, it means that the most highly adapted organisms for an environment are most likely to survive and reproduce, while the less well adapted organisms are less likely to survive and reproduce. 10. For sexually reproducing organisms, a species consists of one or more populations composed of individuals that are interbreeding and producing fertile offspring; they are reproductively isolated from other such groups. 11. Homologous structures are structures that are often dissimilar in form and function while having underlying structural similarities. Examples are the different forelimbs that one sees in vertebrates: wings in birds, arms and hands in humans, etc. Each type of forelimb has its own specific use and has obvious and significant differences. If one digs deeper, similarities can be seen. Bone structures are all similar; one end of a single long bone is attached to the shoulder, while the other end is connected to two additional side-by-side long bones. The explanation for these underlying similarities is that all vertebrates have evolved from common ancestors. Natural selection has worked on the generic forelimb of the common ancestor, thus evolving the variety now seen. 12. Such structures as insect wings and bird wings evolved to serve the same purpose. Terrestrial flight requires certain features (smooth surface, the shape of an airfoil that can produce lift, some means of locomotion). These structures evolved separately to have these same required features and fulfill the same purpose, but they evolved from different structures; wings in insects evolved from extensions of the exoskeleton, while in vertebrates, they evolved from forelimb modifications. Natural selection shaped features these organisms already had into superficially similar structures to overcome the environmental challenge of the need to fly. This similarity is an example of analogous structures arising from convergent evolution. They are different since they arose from such different structures. 13. The proteins of dogs and wolves should be much more similar than the proteins of dogs and trees, because dogs and wolves are much more closely related than dogs and trees. 14. To colonize a new territory successfully, three opportunities must be realized. First, the original physical barrier to entry into the new territory must be surmountable by the colonizing organism. Second, the new territory must be tolerable for the colonizing organism. Third, there must not be intense competition for critical resources between the newcomers to the territory and other better adapted organisms that already live there. 15. Allopatric speciation is the result of geographic isolation in which isolated populations of the same species go in separate evolutionary directions because of differences in their respective environments. Sympatric speciation occurs between populations whose ranges overlap. An example of allopatric speciation would be Darwin's finches. They colonized the Galapagos Islands, which had a number of different habitats. They adapted to these different habitats and eventually evolved into different species. An example of sympatric speciation is the goldenrod gall fly for which there are two species that live in the north and central United States. They can live in the same field, attract different predators and have different selection pressures. One species lays its eggs on tall goldenrod, while the other lays its eggs on late goldenrod. They are reproductively isolated since hybrids have a lower survival rate. Technically, they are not yet separate species, but they could get there. 16. In convergent evolution, organisms raised in similar environments can evolve similarly. Common patterns repeat if they enhance survival. On the other hand, closely related species living in different territories sometimes tend to drift apart. Over time, their characteristics become increasingly different until new species result. Examples of convergent evolution are the mara of South America, rodents that are not rabbits but share several of their traits (long hind legs, long ears, flattened faces) and the dolphins, sharks and icthyosaurs that share body shapes so they can cut quickly through ocean water while being distinct species. Another example of convergent evolution is desert plants that possess fleshy stems for water storage, spines for protection and reduced leaves. Examples of divergent evolution are Hyracotherium that evolved through several intermediate species into today's horses, zebras and onagers; the wombat, koala, and kangaroo that evolved from a common ancestor; and Darwin's finches. 17. The extinction of dinosaurs followed by the proliferation of mammals is an example of an extreme form of divergent evolution called adaptive radiation. 18. The evolution of cheetahs and their prey, Thompson's gazelles, in the direction of increasing speed for each is an example of co-evolution. Cheetahs have also evolved a sighting mechanism to help in keeping the gazelles in their sight lines. In addition, a number of flowers have evolved to be pollinated by one specific species of insect. The relationships between the different species of goldenrod and the goldenrod gall fly and the microorganisms that populate the gut of termites may also be examples. 19. Gradualism suggests that evolution occurs through a gradual, steady, linear accumulation of small changes. On the other hand, punctuated equilibrium suggests that evolution may occur much more rapidly than originally thought. In this pattern, species characteristics stay relatively constant for millions of years. At times, however, evolution can speed up so that within a few tens of thousands of years, species can change and evolve into new species. Thus, gradualism can be characterized as smooth and linear while punctuated equilibrium can be characterized as evolution in a series of fits and starts. They are similar in that natural selection is the mechanism that drives both types of evolution and in that evolution in both cases occurs in response to changes in the environment the organism occupies or its movement to a new and different environment. 20. Species do not always evolve into new species. Species may not evolve and manage to survive anyhow. Such species are able to survive in environments that do not change. Most species become extinct sooner or later when the pace of environmental change and intensity of environmental pressure overwhelm a species' ability to adjust and evolve. CHAPTER 3 MENDELIAN GENETICS: HOW ARE TRAITS INHERITED? Lecture/CD-ROM Outline Background I. Darwin's critics pointed out that there was no satisfactory explanation for how traits passed from parent to offspring & no explanation for source of variation in natural populations A. Some ideas proposed as mechanism of heredity were very improbable & not satisfactory 1. Many, including Darwin, believed that traits from parents blended in offspring 2. Parents' traits sometimes appear as blended intermediates in children, but more often do not 3. Some are passed on apparently unaltered; others hide for generations & reappear unpredictably B. If blending inheritance were true, all organisms in a population should appear quite similar 1. If blending occurs, calculations predict that population variation would be gone within about ten generations 2. All individuals would be identical & evolution would cease II. Unknown to Darwin & his critics, these problems addressed by the experiments of a Moravian monk A. Presented two lectures at Natural History Society of BrГјnn B. Gregor Mendel published his work in 1866, but it was ignored for about 35 years C. Darwin died in 1882 unaware of Mendel's work & its importance to the theory of evolution by natural selection How Are Traits Passed from Generation to Generation?: Mendel and His Peas I. Mendel - first to recognize that traits in individuals are controlled by hereditary units he called factors A. First to describe passage of these factors through the generations 1. Father of modern genetics 2. First developed the rules we now use to predict inheritance B. At least three reasons for his success 1. He focused on just a few traits (seven) instead of many traits as others did 2. He thoroughly documented & quantified all of his experimental results 3. He chose to study these traits in the garden pea, Pisum sativum II. A brief history of Mendel & his new approach to the problem of heredity A. Gregor Mendel (born Johann) - son of peasant farmers; time on farm taught him the value of plant breeding in developing productive crop varieties 1. At 21, he entered priesthood & took clerical name of Gregor by which he is remembered 2. In a remote monastery of what is now Czech Republic, had time to do plant breeding 3. Mendel read widely & was aware of Darwin; knew of unanswered questions about heredity arising from Darwin's theory B. Fortuitously chose to study the pea which is easily manipulated in breeding experiments & comes in distinct varieties or strains 1. Studied traits that occur in two distinct forms, e.g. purple or white flowers; puffy, inflated or narrow, constricted pea pods 2. Began by developing true-breeding varieties for each of seven traits (14 in all); when bred among themselves, all offspring of a given variety were identical to the parent for that trait 3. When he was certain that the varieties bred true, he engineered matings between plants showing different forms of each trait C. Mendel's seven pea plant traits & their varieties 1. Plant height - tall plant or short plant 2. Flower color - purple or white 3. Flower position - terminal flowers or axial flowers 4. Pod color - green or yellow 5. Pod shape - smooth pod or constricted pod 6. Seed color - green pea or yellow pea interiors 7. Seed shape - smooth seed or wrinkled seed D. Analyzed his data mathematically 1. Counted the number of plants showing each parental form of trait 2. Calculated ratios of offspring showing each form of trait How Are Traits Passed from Generation to Generation?: Mendel's First Discovery I. Sexually reproducing organisms produce specialized reproductive cells (gametes: male [sperm] & female [eggs]); when egg & sperm fuse (fertilization) вЂ”> new individual produced A. In flowering plants like the pea, sperm contained in pollen, eggs contained in ovules B. When fertilized, ovules mature into seeds; ovules found within structures in flower (carpel) 1. Peas are often (but not always) self-fertilizing; pollen lands on carpel of same plant 2. If cover flower so insects cannot bring outside pollen, sperm & eggs from same plant combine in bud to give rise to peas (seeds for next generation) II. Mendel's procedure - opened flower buds & cut off pollen-bearing structures (anthers) from some flowers; could then fertilize eggs with sperm of his choosing A. Started with two varieties of plants 1. One with smooth, round pea ancestry in text (purple flower on CD-ROM) 2. Other with wrinkled pea ancestry in text (white flower on CD-ROM) B. Cross-fertilized them (sperm of one, egg of other), creating hybrids 1. Cut stigma off some flowers making them solely a male parent; if cut off anthers, plants would be solely a female parent 2. Brushed female part of one type of plant (stigma) with pollen from other type 3. Pollen grain germinates on stigma & pollen tube travels down style to ovules 4. Once tube reaches ovule, male gamete unites with female gamete & fertilization is complete 5. Fertilized ovule swells into a seed; petals drop off as ovary swells into a pod 6. Seeds must be planted so they can germinate & grow into mature plant to determine results of hybridization III. Results: if blending inheritance true вЂ”> offspring should be intermediate: partially wrinkled (light purple on CD-ROM, blending of purple & white) butвЂ¦.. A. Hybrid peas of first generation (first filial or F1 generation) вЂ”> all round (purple on CD-ROM) B. If self-fertilize F1 after mature (second filial or F2 generation) вЂ”> some round (5474), some wrinkled (1850); ratio of about 3 round:1 wrinkled (ratio of 3 purple : 1 white on CD-ROM) IV. What occurs if second generation is allowed to grow & self-fertilize? What happens in test crosses? A. Self-fertilization of F2 plants 1. Wrinkled peas bred true вЂ”> produced only wrinkled (white) offspring 2. About one-third of F2 round peas bred true вЂ”> only round offspring 3. About two-thirds of F2 round peas gave rise to round & wrinkled offspring in third generation B. Test crosses of F2 generation - F2 plants crossed with the double recessive parent (see CD-ROM) 1. Test cross of double recessive white F2 plants вЂ”> all double recessive (white-flowered) 2. Test cross of ~one-third of purple F2 plants вЂ”> all purple-flowered offspring 3. Test cross of ~two-thirds of purple F2 plants вЂ”> ~half of offspring have purple flowers & ~half have white flowers C. Mendel concluded two types of purple-flowered (dominant phenotype) plants - homozygotes that yield only dominant offspring & heterozygotes that yield about half white & half purple 1. Realized that test cross could be used to determine genotype of dominant phenotype organism V. Results similar for all seven paired characters including flower color (purple or white; see CD-ROM) A. For all crosses between parents exhibiting alternate forms of single trait вЂ”> offspring exhibited only one form of trait (the dominant allele) B. When F1 self-fertilized, ~75% showed one form of trait, ~25% exhibited alternate form C. Examine Exploration: Monohybrid Cross section on CD-ROM (Section 3.1) for flower color How Are Traits Passed from Generation to Generation?: Mendel's Interpretations I. Assumed that each form of trait was controlled by a hereditary factor A. Realized that his results could be explained if factors occurred in pairs within individual plants 1. Peas with long wrinkled ancestry have two factors for wrinkled seeds (white flowers on CD-ROM) 2. Peas with long round ancestry has two factors for round seeds (purple flowers on CD-ROM) B. Concluded that when organisms breed, factors passed on whole & usually unaltered to offspring; realized each parent passes only one factor for each trait to offspring C. For each trait, each individual has one maternally- & one paternally-derived factor 1. If the two factors are identical for trait (as in true-breeding) -> homozygous (homo- the same) 2. If the two factors are different for trait (as in hybrids) вЂ”> heterozygous (hetero- different) D. His interpretations are still relevant, but the vocabulary has changed 1. A gene is the hereditary information that determines a single trait, e.g. seed texture, flower color in peas (CD-ROM) 2. The different forms a gene might take (Mendel's factors) are called alleles вЂ“ wrinkled or round peas, white or purple flowers (CD-ROM) II. Dominant traits mask the presence of recessive alleles A. Call allele for round seeds R & allele for wrinkled seeds r 1. If both parents carry two identical alleles for wrinkled seeds (rr) вЂ”> each offspring will get r allele from father and r allele from mother; they will be rr and wrinkled just like parents 2. If one parent is RR & the other is rr вЂ”> offspring will get R from one parent & r from other вЂ”> thus F1 generation is Rr (heterozygous) but all are round, no wrinkled B. Mendel called trait that appeared in F1 generation the dominant trait; the trait hidden in F1 generation he called the recessive trait (it was completely masked by the dominant trait) 1. Recessive trait is only seen when both alleles carried by organism are recessive so you know its genetic make-up 2. Can't tell genetic make-up of organism showing dominant allele by just looking at it вЂ”> could be heterozygous or homozygous for dominant trait; either appears same C. Terms are used to distinguish between forms of traits expressed & those that the organism carries 1. The term phenotype describes the traits that are expressed in an individual; those apparent by looking at individual 2. The term genotype used to describe the genetic complement, all the alleles within individual D. Can learn about the genotypes underlying different phenotypes by performing controlled crosses between individuals & then calculating offspring ratio 1. In human populations, cannot do controlled crosses so we rely on family trees (pedigrees) to follow the pathway of alleles through generations III. Mendel's observations are widely applicable - the understanding of inheritance was important but there are also applications in the area of human health & well-being e.g. sickle cell anemia A. Sickle cell anemia is a hereditary disease in which the blood of affected individual has reduced capacity for delivering oxygen to tissues 1. Affected gene encodes information for making part of hemoglobin molecule (carries O2; gives red blood cells [RBCs] their color) 2. In normal people, RBCs are biconcave disks; travel easily through arteries, veins, capillaries, & carry O2 to tissues B. RBCs of affected people appear normal if O2 plentiful 1. If O2 declines as it does if exiting tissues through capillaries & veins, hemoglobin in RBCs forms insoluble fibrous strands that distort RBC shape into long, thin sickles 2. Even lower O2 levels can cause sickling in other locations 3. Distorted cells cannot easily pass through narrow capillaries which become clogged; tissues are starved for O2 4. Cells may rupture, causing severe anemia, great pain, serious tissue damage; without medical attention, sufferers may die C. Two hemoglobin alleles: HbA - normal hemoglobin protein; HbS - allele for sickle cell anemia 1. Homozygous individuals for normal hemoglobin (HbA/HbA) have no disease 2. Homozygotes for sickle cell allele (HbS/HbS) are afflicted with disease 3. Heterozygotes (HbA/HbS) are sickle-cell carriers - ~1% of RBCs exhibit sickling trait D. Under normal circumstances, show no disease symptoms 1. Carriers' seem normal as long as they avoid strenuous exercise, high altitudes, other situations in which O2 levels in blood might get very low 2. Mate homozygous normal woman to sickle-cell male вЂ”> all offspring are carriers IV. Punnett squares predict possible genotypes - developed in early 20th century by British geneticist Reginald C. Punnett A. Alleles of parents are arranged on top & sides of matrix as shown below 1. Each block of square represents possible genotype that could result from cross of purebreeding sickle-cell male & pure-breeding normal female 2. All offspring of this cross are carriers of sickle-cell HbS HbS HbA HbA/HBS HbA/HBS HbA HbA/HBS HbA/HBS Pure-Breeding Normal Female x Pure-Breeding Sickle-Cell Male B. Other crosses HbA HbS HbA HbS HbA HbA/HBA HbA/HBS HbA HbA/HBA HbA/HBS HbA HbA/HBA HbA/HBS HbS HbS/HBS Pure-Breeding Normal Female x Sickle-Cell Carrier Male 1 Normal: 1 Sickle-Cell Carrier All Offspring Normal HbA/HBS Sickle-Cell Carrier Female x Sickle-Cell Carrier Male 1 Normal : 2 Sickle-Cell Carrier : 1 Affected 3 Normal : 1 Affected How Are Traits Passed from Generation to Generation?: Mendel's First Law I. Mendel's Law of Segregation - alleles are randomly donated from parents to offspring II. Results of cross between two heterozygotes (3:1 phenotypic ratio & 1:2:1 genotypic ratio) led Mendel to this conclusion A. He recognized that ratios implied that heterozygous parents are equally likely to donate either of their two different alleles to offspring B. Donation of alleles to offspring is random III. The key points of the theory are the following: A. All traits are determined by two factors (alleles) B. Factors (alleles) segregate (separate) during the formation of gametes, the result is each gamete contains only one factor (allele) for each trait C. Two factors (alleles) are joined together again in the offspring IV. Formal statement: a parent contributes only one of its two alleles for a trait to its offspring; each embryo has exactly same chance of receiving a particular allele from each parent How Are Traits Passed from Generation to Generation?: Mendel's Second Law I. Mendel's Law of Independent Assortment - Mendel's factors can sometimes act independently A. Mendel performed crosses where he followed two traits at a time вЂ”> all of his original conclusions applied to both traits 1. The two traits appeared to operate utterly independently of one another 2. The alleles of one gene are passed to offspring independently of the alleles of other genes B. There are exceptions, but they do not invalidate Mendel's general conclusions 1. Genes are carried on chromosomes, each of which can carry many, many genes 2. When genes for two different traits are found on the same chromosome, they have a tendency to travel together 3. Genes that occur on different chromosomes do segregate independently; even those on the same chromosome may exhibit some degree of independence 4. Peas were not the only organisms used for studies; Drosophila melanogaster (fruit flies) were also used (tiny, easy to keep, short life cycle, lots of eggs/offspring so ratios easy to calculate) II. The dihybrid cross - example using two traits of fruit flies: body color & wing size A. In wild, flies have broad, straight wings & pale-colored bodies with dark transverse stripes; trait usually found in organisms in their natural or wild state is called wild type 1. Above traits dominant to alternatives: vestigial (shriveled) wings & ebony body color; recessive forms of traits usually referred to as mutants (but mutants can be dominant) 2. Fruit fly genes usually named for mutant form; upper case letters designate dominant alleles & lower case letters designate recessive alleles B. Sample parental cross with two traits - cross broad-winged (VV), striped (EE) parent (wild type for both traits) & Vestigial-winged (vv), ebony (ee) parent (mutant for both traits) 1. P1 VVEE x vvee вЂ”> F1 VvEe 2. The F1 from the above cross will exhibit the dominant forms of both traits: broad wings & pale, striped bodies; will also be heterozygous for both traits C. Cross members of the F1 generation (dihybrid cross) - VvEe x VvEe 1. Each new fly will get one allele for wing shape & one allele for body color from each parent 2. According to Law of Segregation, the allele the offspring gets for each trait is random; just as likely that parent will donate a V as a v, same goes for E and e 3. Law of Independent Assortment also applies; alleles can end up in the offspring in any combination as long as each new fly ends up with two alleles for each trait 4. Possible gametes: VE, Ve, vE, ve from VvEe organism; result of cross (see Punnett square below) is nine different genotypes & four different phenotypes in very specific 9:3:3:1 ratio VE Ve vE ve Genotypic Ratio VvEe x VvEe Broad winged, Striped body x Broad winged, Striped body 9 V_E_ : 3 V_ee : 3 vvE_ : 1 vvee VE VVEE VVEe VvEE VvEe Ve VVEe VVee VvEe vE VvEE VvEe vvEE vvEe ve VvEe Vvee Phenotypic Ratio Vvee vvEe vvee 1 VVEE 2 VVEe 1 VVee 2 VvEE 4 VvEe 2 Vvee 1 vvEE 2 vvEe 1 vvee D. Results of dihybrid cross - 9 wild type for both traits : 3 wild type wing size, mutant body color : 3 mutant wing size, wild type body color : 1 mutant for both traits 1. The 9:3:3:1 ratio is characteristic of offspring of a dihybrid cross in which both traits follow Mendel's laws of segregation and independent assortment 2. Mendel did many dihybrid crosses with different pairs of the seven traits he studied вЂ”> ratio was always 9:3:3:1 How Are Traits Passed from Generation to Generation?: Chance Determines Which Alleles An Individual Inherits I. Cystic fibrosis (CF) - caused by recessive allele of CF gene, carried by about one in 25 North American Caucasians (most common genetic disorder in this group) A. Affects about one in 2500 babies in this population 1. Characterized by production of thick, sticky mucus in lungs; hard to move it from airways 2. Victims suffer from chronic infections that progressively destroy lungs B. Parents may be carrier without showing symptoms of disease since allele is recessive; genetic testing can determine if an individual is a carrier 1. Cross female heterozygous for CF gene to male lacking the disease-causing allele 2. Chances of having a carrier are equal to chances of having a child who is not 3. Would have to check child to know for sure its genotype II. Donating alleles during reproduction is like tossing a coin; both are random events A. Best prediction of the outcome of random event is the probability that each of the possible outcomes will occur B. Probability (likelihood) of an event вЂ“ in random events, probability that any single outcome will occur equals the number of times it can or does occur divided by the total number of possibilities 1. Probability of heads if flip coin is 1/2 (0.5); probability of four on roll of a die is 1/6 (0.17) 2. An event that always occurs has probability of 1/1 (1.0); impossible event - probability of 0 III. Probability & allele distribution at conception вЂ“ example: parent heterozygous for gene G (Gg) A. Each gamete produced by that parent (egg or sperm) has one of two alleles вЂ” G or g вЂ” not both 1. If neither allele is favored when gametes are produced, the probability P that any one gamete contains G allele & is passed on is 1/2 or 0.5 2. Likewise, the probability that the g allele is passed on is P(g) = 1/2 or 0.5 B. The Sum Rule - the probability that either G or g is passed on is sum of the two probabilities, 0.5 + 0.5 = 1.0 1. Since either G or g is passed on, but not both, this is called a mutually exclusive event; like a coin flip, can never get both heads & tails from same toss of coin 2. The Sum Rule вЂ“ applies to mutually exclusive events; combined probability of two or more mutually exclusive events occurring is equal to the sum of their individual probabilities IV. What happens if two events are not mutually exclusive, but are instead independent of one another & happen simultaneously? - the Product Rule A. This is the situation when gametes of two heterozygotic (Gg) parents join at fertilization, each donating one allele to single offspring 1. What is the probability that this couple's one child will be gg? вЂ“ P(gg) in offspring = P(g from mother) x P(g from father) = 0.5 x 0.5 = 0.25; called the product rule 2. The joint probability that both of two independent events will occur is the product of the individual probabilities of each B. The more times an event occurs, the more likely it becomes that the ratio of different outcomes matches (or more correctly approaches) probabilities 1. Because Mendel performed so many crosses with his pea plants, the ratios of different phenotypes were very close to the theoretical values 2. They were very close but never right on Why Aren't Members of the Same Species Identical? I. Almost every organism, every phenotype, is the result of thousands or tens of thousands of genes working together A. When you deal with two traits in the fruit fly, two heterozygotes could produce offspring with up to four different phenotypes 1. There is a mathematical rule that expresses the number of different phenotypes that can result from a cross between heterozygotes for any number of traits 2. Number of possible phenotypes = 2n where n = the number of traits or genes considered; the two represents the two different forms of each trait (the two possible alleles) 3. The number of possible different phenotypes for 100 traits = 2100 = 1.26765 x1030; for 1000 traits this number is 21000 = 11 x 10300 4. This huge number of new combinations of alleles that can occur with each offspring is an important source of variety in populations like that needed for evolution by natural selection 5. An example of genetic recombination вЂ” production of new combinations of genes not found in either parent B. It is estimated that on average ~30% of human genes are heterozygous in a way that influences phenotypes & thus they serve as a source of variety 1. Of an estimated 100,000 human genes then, 30,000 are heterozygous 2. The possible number of human phenotypes would then be 230,000 3. Thus, even when 70% of human genes are homozygous & not a source of variability, there is an infinite number of different phenotypes 4. Outside of identical twins it is not surprising that no two people present the same phenotype II. Unlike examples thus far, there may be many different alleles for a trait in a population A. Three different alleles determine human blood type (A,B,O) B. Any individual can carry only two of three possible alleles III. It is combinations of traits that give an organism a competitive advantage A. Desert plant with allele creating waxy coating would prevent water loss 1. Might also be a barrier to CO2 uptake B. If plant had alleles that let it take up CO2 only at unwaxed entry points, this would be an advantage 1. Combination of waxy cuticle & unwaxed entry points would be a big advantage; bigger than either one on its own (waxy cuticle or specific gas exchange sites) C. Natural selection operates not on single traits but on whole organisms who are combinations of many traits IV. Mutations are another source of genetic variety - in domestic plants & animals, occasionally see new characteristic never before seen in that group or any of its ancestors A. Darwin called these occurrences "sports of nature", we call them mutants 1. Darwin could not explain them but he recognized that they provide variety upon which natural selection can act 2. Mendel's laws do not explain the origin of mutations but once present in population, a new trait obeys all of Mendel's laws as if it had always been present B. A mutation is the sudden appearance of a new allele 1. Can occur at any time, but become heritable when genes are copied & partitioned into gametes during sexual reproduction 2. When making gametes, copies of genes are made for the purpose by process of replication 3. Replication is pretty accurate, but not perfect; a mistake can slip in & new allele results 4. Such errors can often be fatal вЂ” why? C. An organism is a well coordinated machine; if add new part, it probably will not work well with other parts that were designed to work with the part the mutation replaced 1. Alternatively, the mutant part may have no effect on function or 2. It may work even better than the original D. History of life on Earth is history of random mutations; they are ultimate source of new alleles 1. Most are lost forever due to their deleterious effects 2. Many are simply carried along from generation to generation, because they have no effect on the survival or reproduction of their recipients 3. If copying error produces organism better suited to survive, these mutations produce many offspring & leave many copies of the new allele in the next generation 4. If errors never occurred during replication, all life on Earth would resemble first living thing 5. Despite their mostly deleterious effects, evolution would be impossible without them Do Mendel's Laws Always Apply? I. Mendel reported results in 1865 in a series of lectures & published in German in 1866 A. Journal was widely distributed, but few of his contemporaries recognized significance of his results B. His quantitative approach was ahead of its time but was virtually unknown & unappreciated by his contemporaries C. In early 20th century, three botanists (Karl Correns in Germany, Gustav Tschermak in Austria, Hugo de Vries in the Netherlands) all rediscovered his original paper, realized its significance D. Mendel died in 1884, too soon to see his work appreciated II. Mendel's laws are extended by experimental evidence A. Karl Correns, 1899 - performed controlled crosses using flowering plant called the four-o'clock 1. Flowers have three colors: red, white, pink 2. If cross pure-breeding red with pure-breeding white вЂ”> hybrid offspring had pink flowers (shade intermediate between those of parents); he might have believed in blending but.... 3. Correns crossed F1 pink flowered plants вЂ”> all three traits, red, white & pink, exhibited B. Dominance relations 1. Ratio of phenotypes in Correns' experiment was 1 red : 2 pink : 1 white 2. This is exactly the genotypic ratio seen in a monohybrid cross (between two heterozygotes for a single trait) 3. Red flowers were homozygous for red allele; white flowers homozygous for white allele 4. If red allele & white allele were in same plant, neither masked the presence of the other so flowers were pink; phenotype of heterozygote is intermediate - incomplete dominance 5. Does not invalidate Mendel; each allele is a discrete entity, remaining intact, not blending R1 R2 R1 R1R1 (red) R1R2 (pink) R2 R1R2 (pink) R2R2 (white) Pink Four-O'clocks Male x Pink Four-O'clocks Female Genotypic Ratio 1R1R1 : 2 R1R2 : 1 R2R2 Phenotypic Ratio 1 red : 2 pink : 1 white III. Lethality - if particular combination of alleles is deadly to new embryo, embryo dies & phenotype not represented in next generation at all A. First documented soon after Mendel's work rediscovered 1. Dominant lethal allele kills its recipient 2. Recessive lethal allele is only deadly if paired with another recessive lethal allele (homozygote) B. Lucien Cuernot, French geneticist (1904) - worked on inheritance of coat color in mice 1. Found yellow coat color was dominant to wild type brownish color (agouti) 2. Cross heterozygous yellow mice carrying agouti allele -> phenotypic ratio: 2 yellow : 1 agouti instead of 3 : 1 ratio predictedby Mendel's laws 3. Test crosses between yellow mice and homozygous agouti mice proved all yellow mice were heterozygous; found no mice homozygous for dominant allele 4. Homozygous dominant embryos die early in development accounting for 2:1 ratio 5. This trait is dominant for yellow coat color but recessive for lethality C. Recessive lethals not weeded out by natural selection since carriers can survive & reproduce normally; only removed when random chance pairs them with similar alleles causing death D. How do dominant lethals survive in a population? - person having this allele should die 1. Huntington's disease - uncontrolled movements & mental deterioration followed by death 2. Need only one copy of Huntington's allele to exhibit lethal phenotype but onset occurs late in life (between 30 & 60); afflicted person may have passed it on before s/he knows it's there 3. About half of afflicted person's offspring will inherit it IV. One gene can influence two or more traits A. Texture of seed coat gene in peas (smooth vs. wrinkled) also affects the tiny starch grains that provide food for the developing pea plant (they differ in shape & size) 1. The phenomenon whereby a single gene affects two or more traits - pleiotropy B. Can sometimes explain pleiotropy by examining a gene's effect at early stage of life - the W trait in cats; cats heterozygous or homozygous for the W allele have pure white fur 1. These same cats are deaf in one or both ears - what is connection? 2. Melanocytes are connection - produce pigmentation of fur & also play role in the inner ear of the animal where they contain the hair cells that sense sounds 3. If cats have W allele, melanocytes fail to develop properly affecting both traits V. Two or more genes can influence a single trait - some traits do not fall into discrete categories, but instead individuals can be arranged in a continuum like height or weight A. Part of the variation attributed to factors like nutritional status, childhood diseases, etc. 1. Much of what determines height has underlying genetic cause but no single gene for human height has been identified 2. Exception is achondroplasia or dwarfism where one gene (a single dominant allele) prevents carrier from growing to normal adult height 3. Human height is a trait that is controlled by many genes; it is a polygenic trait B. Traits that are controlled by a single gene (monogenic traits) with two alleles will occur as two or three distinct phenotypes C. If as few as three different genes, each represented by only two alleles, work together to determine a single trait, the distribution of phenotypes within a population becomes continuous D. Other examples: weight, coat color in many mammals, even some traits that do form discrete phenotypes (the number of whiskers on the face of a mouse) VI. Mendel's work generated new fields of inquiry A. It was not initially clear how Mendel's laws & Darwin's theory complemented one another 1. Many believed that genetic traits must occur as discrete, all-or-none phenotypes; the ability of polygenic traits to create a continuum of phenotypes was unknown 2. Darwin's champions insisted that gradual differences between individuals could not be explained by Mendelian genetics but were necessary for natural selection 3. Many believed that the two theories were incompatible B. 1930s - controversy put to rest when a new field of biology emerged, population genetics 1. It employed mathematics and statistics to prove that the variety required for natural selection could arise from Mendelian genetics 2. Population geneticists used mathematical models to study the movements of many genes through entire populations over time rather than focusing on one or a few genes in individuals Where Are We Now? I. Over the past few decades, we have made many advances related to genetics A. We have identified the genes that cause many human genetic disorders B. We have developed tests for detecting these disorders prenatally & in prospective parents C. We have engineered therapies to minimize or eliminate many genetic diseases II. A class of genes has been discovered that "remember" their parental origins вЂ” imprinted genes A. Alleles of maternal origin act differently from those of paternal origin B. Eric Keverne & Azim Surani (Cambridge University) - discovered that in mice, certain alleles from the mother contribute more to the development of the brain's reasoning portion, the cortex 1. The same alleles from the father have greater impact on the development of the brain region responsible for the more primitive functions such as feeding, fighting, & reproduction 2. Paternal alleles build the placenta & make the hormones responsible for growth of the fetus 3. The alleles of certain genes that contribute to cortex development are silenced if they come from sperm (chemically modified so that they are unable to function) 4. Likewise, maternal alleles that contribute to growth hormones & placenta development are similarly silenced III. Neither Keverne nor Surani speculate on how human intelligence & behavior might be affected by imprinted genes; some human genetic disorders hint we are not entirely dissimilar from mouse A. Example: children suffering from Prader-Willi syndrome 1. Have brain disorder that causes overeating, obesity, a placid personality, mild retardation, & reduced sexual drive 2. These behaviors are under the control of the brain's primitive regions (areas whose development can be traced to paternal alleles) 3. Maternal alleles for these brain areas are normally silenced 4. Prader-Willi sufferers lack the paternal allele due to a deleterious mutation 5. Maternal alleles for these brain areas cannot make up for absence of the paternal alleles B. Example: Angelman syndrome, another human genetic disorder 1. Occurs when a baby is born lacking a certain maternal allele that resides on chromosome 15 2. These children have defects in activities controlled by higher brain centers: mental retardation, speech deficiencies, jerky movements 3. Symptoms occur even though the paternal chromosome 15 is present and intact 4. Implies that the paternal alleles on on chromosome 15 cannot substitute for the absence of those of maternal origin 5. Too soon to say whether intelligence is maternal in origin Analogies, Anecdotes and Illustrations Who Is Johann Mendel? Johann Mendel was born in 1822 in Austrian Silesia. He was the son of poor peasants. We, of course, do not know him as Johann Mendel. After his training to become a priest was completed, he was given the name Gregor, the name by which we know him today. Irony It is one of the biggest ironies in the history of science. For a period of about 35 years, some of the greatest minds in science wrestled with the problem of heredity when the answer had already been found and reported by Mendel in 1865 in his two lectures to the Natural History Society of BrГјnn. In 1866, the content of these lectures was published in the proceedings of that society. That report is considered by many to be one of the classics of scientific literature. In many ways, it is a model scientific paper. Its author clearly states his objectives. The data he had collected were presented economically. The conclusions he drew were unique and carefully presented. Clearly, Mendel's discovery was ahead of its time. As is often the case, the environment was not ripe for the acceptance of his proposal. Other scientists, most of them more prominent than Mendel, were not prepared to recognize the significance of his findings. Between 1865 and 1900, when his research was rediscovered, the groundwork was laid for its eventual acceptance. There was a transition during this time from the idea of blending inheritance that had held sway for some time to the idea of the particulate nature of the hereditary material, whatever that material turned out to be. According to Ernst Mayr in his book The Growth of Biological Thought: Diversity, Evolution, and Inheritance, it was during this period "that the right questions were first asked, that an interest in the corpuscular and chemical nature of the transmitted genetic material developed, and that the cytological foundation was laid without which no causal theory of inheritance could have been elaborated." When 1900 arrived, scientists were finally prepared to recognize the importance of Mendel's findings when they were rediscovered. In the final irony, Mendel did not live to see his work accepted and become the basis of a new scientific discipline. He had died of nephritis in 1884 at the age of 62, 16 years before the rediscovery of his research. Mendel: Not Simply an Obscure Monk According to Mayr in The Growth of Biological Thought, the impression is often given that Mendel was an obscure monk, almost making it seem that he was lucky to have made such an important discovery. While he was intellectually isolated to a great extent at the time he was performing his experiments on pea plants, he was extremely well prepared for the research he was carrying out. Mendel was educated at two excellent high schools followed by two years at the University of Vienna in order to be qualified to teach physics and other sciences at the high school level. He was, therefore, an extremely welltrained young man who could count among his teachers some of the most accomplished physicists and biologists of his day. One of his professors was the botanist Franz Unger, who had adopted a theory of evolution in 1852. Unger was convinced that variants arose in populations and that over time these changes could build up to the point where a new species could be produced. Mendel was thus exposed to and stimulated by the idea that the study of varieties of organisms would be a key factor in understanding the origin of species. Apparently, his purpose in undertaking the research that culminated in his 1866 paper was to test Unger's theory; in order to do this, he would have to study varieties. Mendel's evolutionary approach led him to analyze a population of organisms rather than single individuals. His work extended over eight planting seasons and involved the study of at least tens of thousands and probably hundreds of thousands seeds and plants. He maintained exacting records of weather, sun spots, and other phenomena; furthermore, he had a fascination for numerical relationships. He was consequently well prepared for a populational approach to the study of inheritance. If Mendel was a well-trained biologist (he apparently had an excellent grasp of the botanical literature), he might have even been better trained as a physicist.. His favorite high school teacher was a physicist and while he was a teacher, he taught more physics than any other subject. While in Vienna, he took courses with Doppler of Doppler effect fame and other physicists. He also served as demonstrator at the University of Vienna Physics Institute. This experience probably taught him to keep careful experimental records and to use a numerical and perhaps a basic statistical approach to his studies. Thus, his concepts were primarily biological while his methods came from physics. Why Was Mendel's Work Initially Ignored? When Darwin finally published The Origin of Species in 1859, a major chunk of missing information was an understanding of inheritance. Darwin and others, like August Weissman, would subsequently propose various theories of inheritance, none of which were correct; some of them, however, contained elements of Mendel's theory. Given the quality of Mendel's work, the clarity of his writing, the simplicity of his theory, and the need for a theory of heredity at the time Mendel published, it is at first surprising that he was so completely ignored. According to Mayr, one reason is that Mendel had relatively few publications to his credit. In the fifteen years during which he conducted his crosses, Mendel published only his lecture to the BrГјnn Natural History Society and another short paper on hawkweed genetics. Letters he wrote to NГ¤geli, a wellknown botanist, indicated that he had confirmed his results in peas in a number of other plants. Mendel never informed the world of the confirmation of his earlier results. The journal of the BrГјnn Society containing Mendel's paper was distributed to the libraries of about 115 institutions. Mendel had 40 reprints made of his article and sent them to a number of prominent scientists, among them the aforementioned NГ¤geli. This led to active correspondence between Mendel and NГ¤geli that included the letters about Mendel's confirmation experiments in 1869. Only Mendel's letters survived, perhaps, because Mendel's papers, including his notes and manuscripts, were burned either late in his life or after his death. NГ¤geli was, to put it mildly, unsupportive (see below). Mendel, who has been characterized as exceedingly modest, apparently made no effort to contact other botanists or to lecture at other scientific meetings after being discouraged by NГ¤geli. In fact, again according to Mayr, he called his seven years of work with more than 30,000 plants "one isolated experiment." Mendel apparently tended toward understatement. Another factor leading Mendel to be less than pushy might have stemmed from his training as a physicist. It is almost sure that Mendel encountered complicating phenomena such as linkage, crossing over, and polyploidy in his work with peas. It appears that he may have ignored traits exhibiting these phenomena, since they caused deviations from his hypothesis. Later, he was stumped completely by the parthenogenesis he found in the hawkweeds that he worked with at the recommendation of NГ¤geli. Consequently, he might have thought that his results were not true for all species of plants and, in fact, at least one quote attributed to him confirms this. Physicists, in his time, always looked for general laws. His work with hawkweeds and irregularities he may have seen in the peas may have convinced him that his laws with peas did not apply to other plants or have any general application. Consequently, he may have not put forward the effort to disseminate his findings more widely. Mendel also attempted to confirm his results by hybridizing species rather than varieties within a species as he had done in the pea experiments. The lack of confirmation may have discouraged him further even though he knew that hybridizing species and varieties were not the same. Also causing difficulty for the appreciation of his results was the fact that evolutionists were more interested in gradual continuous variation than in the discrete changes with which Mendel dealt. They could not see the connection between Mendel's discrete traits and the continuous ones. We now know, of course, that continuous traits are often polygenic in nature and that each of the genes involved in the trait can be inherited in a classical Mendelian fashion. Mendel discontinued his work with peas in 1864 as a result of a heavy infestation of pea weevils and exciting work in other plant genera. Finally, he suffered the fate of many excellent scientists when, in 1871, he stopped all of his work with crosses upon being elected abbot of his monastery. He became absorbed with administrative tasks that took up most of his time. Finally, Mendel's contemporaries were not very interested in pure transmission genetics. Their interest in transmission genetics was only in its connection to other phenomena that interested them more. Mayr believes that even if Darwin had known of Mendel's results he would have missed the point since he would not have seen the connection between Mendelian inheritance and gradual variation. Mendel Gets Some Bad Advice Given his communications with Mendel, NГ¤geli, the prominent botanist and student of hybrids, would, one would think, have appreciated the importance of Mendel's findings. Instead, it seems, considering his actions, either that he did not understand Mendel's theory and findings or that he opposed them. The latter seems more likely. He did not encourage Mendel and, in fact, it appears that he did the opposite. He also did not invite Mendel to publish his results in one of the more prestigious botanical journals of the day where more investigators would have seen the paper. Instead, he suggested that Mendel try his theory out on hawkweeds, a group of organisms in which it is now known that parthenogenesis is common. This process would give results that are incompatible with Mendel's theory. One historian of science has characterized their correspondence as "totally disastrous." When NГ¤geli published a generally well regarded book on evolution and inheritance in 1884, he did not include one mention of Mendel or his research in his long chapter dealing with hybridization experiments. Mayr blames scientific intolerance for NГ¤geli's professional snub of Mendel. He points out that NГ¤geli was one of the few biologists who believed that pure blending inheritance was the hereditary mechanism. To acknowledge and accept Mendel's ideas would have required NГ¤geli to reject his own, an act of which he appears to have been incapable. It appears that NГ¤geli simply dismissed Mendel's work out of hand, assuming he was wrong. Why Were So Many of the Early Mendelians Botanists? This is not an easy question to answer and there is no single reason, but a couple of things may have contributed. Mayr speculates that there might have been a richer tradition of breeding varieties of plants than there was for animals. The reason for this could have been that plants are under most circumstances easier to grow and breed than are animals. It has also been proposed that plants might have more discontinuous characters in leaves and flowers than are found in domestic animals like sheep, cattle, and pigs. Most traits studied by animal breeders were highly polygenic and, therefore, not well suited for revealing Mendel's basic principles. Not long after Mendel's rediscovery, animal researchers began to carry out genetic studies on domestic fowl, rodents, and the fruit fly Drosophila. It did not take long for the work in animal genetics to catch up to and surpass that in plant genetics. A Coincidence Carl Correns, one of the three rediscoverers of Mendel, was a student of NГ¤geli and, in fact, married NГ¤geli's niece. Thus, one of the men who is credited with rediscovering Mendel's results was related by marriage to and a student of the man who is partially responsible for Mendel's findings being ignored for 35 years. August Weissman Set the Stage for Mendel's Rediscovery August Weissman is widely considered to be one of the greatest biologists of all time. His interests were wide-ranging; he worked on cytology, development, and inheritance. He was unusual in that unlike others who worked in those areas, he was an ardent selectionist and, after initially accepting the concept of the inheritance of acquired characteristics, he eventually rejected it entirely. He realized early on that the truth of Darwinism could never be settled without a far-reaching theory of inheritance. He was also unique for his period in his approach to scientific inquiry. He was known for his careful, rational analysis of every scientific problem he investigated. When he studied a particular process or phenomenon, he reasoned out all of the possible explanations. In the vast majority of cases, the alternatives he considered included the explanation we now accept as the correct one. Unfortunately, due to the insufficient data available to him during his career, he sometimes rejected the correct alternative. This should not, however, take away from the degree of his accomplishment. He was careful and collected as much information as possible before choosing his solution. He formulated the first comprehensive theory of genetics and his work paved the way for research that followed for a generation. Correns said that the rediscovery of Mendelian rules in 1900 was not a great intellectual achievement after Weissman had prepared the way. Genotype vs. Phenotype It is important to define the terms genotype and phenotype clearly. We can once again look at the meanings of the roots. The root geno- is from the Greek meaning race, offspring, sex. Thus, genotype suggests the actual type of the offspring or the actual genetic make-up of the organism. The root pheno- , on the other hand, also from Greek means show, seem, appear. Thus, phenotype refers to the type that the offsprng appears to be, the actual appearance of the organism. Thus, if a genotypic ratio is desired as the answer to a problem about a cross, the correct answer will include all of the possible genetic compositions of the offspring and their relative amounts. On the other hand, if the phenotypic ratio is desired as an answer, the correct answer will include all of the different manifestations of the trait seen in the offspring and their relative amounts. It should be emphasized for the students that different genotypes can often give rise to the same phenotype. Dominant vs. Recessive Of all the terms to which general biology students are exposed, it seems to me that dominant and recessive are the two that are most often understood. Point out to students that the phenotype of an organism is quite easy to determine simply by looking at the genotype, as long as one is aware of which form of the gene or trait is dominant and which is recessive. If the student has written this information down before attacking the problem, there should be no difficulty. Teaching Monohybrid Crosses There seem to be two types of students that I encounter when teaching Mendelian genetics to students. At the risk of being too simplistic, they either get it or they don't. If they don't get it, it often seems to be due to a mental block. If a student tells him/herself that they can't understand it, this belief becomes a self-fulfilling prophecy. The approach I use is to give students a group of genetics problems as an assignment. Before I describe the approaches to be used, I make sure that they understand the definition and significance of some essential terms: heterozygous, homozygous, dominant, recessive, phenotype, and genotype. Once the definitions have been presented, I usually do some representative problems in class, often letting the students choose the problems I do. Not surprisingly, they choose the problems worth the largest number of points. I use this approach to drill them on a number of standard steps that I feel it advisable for them to follow. I tell them to start by reading each problem a sentence at a time and writing down the information that they encounter. I suggest that they write down abbreviations for the dominant and recessive alleles introduced in the problem by using the standard notation (capital letters for dominat alleles, the same letter in lower case for the recessive allele). Once they have defined the trait in this way, it is next important for them to note the genotype and/or phenotype of the parents. I point out the words and phrases they should look for to accomplish this task: homozygous dominant, homozygous recessive, heterozygous, an individual expressing the dominant form of the trait when one of his parents exhibited the recessive form, etc. I try to make sure that they know how to interpret these clues and stress that writing this information down is essential. Trying to remember these abbreviations and parental genotypes instead of writing them down can be disastrous, especially for beginners. Next, I point out that they must determine the type of gametes that can be made by each parent. In monohybrid crosses, this is not terribly difficult, but it requires an understanding of the difference between the genetic make-up of an organism and its gametes. I emphasize that organisms normally carry two copies of each gene, while gametes contain only one. This is, of course, the embodiment of Mendel's Law of Segregation and there are three possibilities. If an organism is homozygous dominant (AA, for example), it can make only one kind of gamete, one that carries a single copy of the dominant form of the gene (A, in this example). Similarly, an organism that is homozygous recessive (for example, aa) can only make one type of gamete, one that carries a single copy of the recessive form of the gene (in this case, a). In contrast to the first two cases, heterozygotes (for example, Aa) can make two kinds of gamete (either A or a, in this example) in equal amounts. Once the type(s) of gamete that each parent can make has been established, the students can then be shown how to set up a Punnett square for the cross. The gametes produced by one parent are listed along the horizontal border of the square, while the gametes of the other parent are listed along the vertical border of the square. Next, show them how to fill in the square, compile the data, and determine the genotypic and phenotypic ratios exhibited by the offspring. I am not usually a fan of memorization, but in the case of monohybrid crosses, it can be useful. There are, after all, only six possible crosses and the results of most of them are trivial. Thus, I ask my students to list the possibilities for me, and I write them on the blackboard along with the genotypic and phenotypic ratios. Before doing this, I define the alleles of the trait as described above: A - normal pigmentation; a - albino. To get the students more involved, ask them to define an imaginary trait with recessive and dominant alleles and have them suggest the abbreviations to be used for each allele. The chart I put on the board would then look something like the chart below: Cross 1. AA x AA 2. AA x aa 3. Aa x AA 4. aa x aa 5. Aa x aa 6. Aa x Aa Genotypic Ratio All AA All Aa 1 AA : 1 Aa All aa 1Aa : 1 aa 1 AA : 2 Aa : 1 aa Phenotypic Ratio All normal coloration All normal coloration All normal coloration All albino 1 normal : 1 albino 3 normal : 1 albino Once a student understands this relatively simple chart, any genetics problem involving a monohybrid cross should be relatively simple. I point out to the students that of the six possible crosses four of them give trivial phenotypic ratios (crosses 1 - 4 above). The genotypic ratios of these four crosses are relatively simple as well. I point out that half of the answers to the question "What is the phenotypic ratio resulting from this cross?" are "all dominant." I then ask them what they would guess if they had no idea about the results of the cross. Finally, I emphasize that only two of the six crosses give results that are at all tricky (crosses 5 and 6) and show them that even these results are fairly obvious. How Many Gametes Can This Organism Make? One of the most difficult concepts for students to grasp is the number of times a particular gene is represented in an organism's gametes as opposed to the number of copies of that gene that are present in the somatic cells of that organism. Sometimes they are not even sure what a gamete is when they are first asked. This is one of those vocabulary words they hate so much. Point out to them that each somatic cell (a cell that is not a gamete or germ cell) has two copies of each gene; these copies may be the same (a homozygote) or different (a heterozygote). Ask them to tell you the maximum number of different forms of a particular gene that one somatic cell may carry. They should, of course, answer two. See if they have been paying attention. Ask them the minimum number as well. Then point out that the gametes that unite to form a zygote (more vocabulary) and eventually an adult organism each carry one form of each gene so that when they unite, the zygote, the somatic cells, and the organism derived therefrom will have two copies of each gene. Once this concept is established for a single gene, you can ask them how many different kinds of gametes an organism can make with respect to a single gene if the organism is a homozygote with respect to the gene in question. It should be obvious to your students that by definition a homozygote for a particular gene carries only one form (allele) of that gene and can, therefore, make only one kind of gamete. If you wish, carry them through this little exercise by asking leading questions. Then repeat the exercise for a heterozygote; one would hope that they would understand that these organisms can make two types of gametes with respect to the gene in question and that these two types would be represented equally in the organism's total complement of gametes. I usually find it necessary to stress repeatedly that gametes only carry one copy of each gene while organisms and thus somatic cells carry two copies. Then really test them. Give them an organism that is heterozygotic with respect to a number of genes, e.g. AaBbCcDdEeFf. At first, they may treat you like you are a carrier of the plague. Reassure them that the problem is easier than it looks. Tell them to break it down on a gene-by-gene basis. Ask how many gametes can be made with respect to the A gene (two), then the B gene (two), etc. I usually tell them to write the number above each gene in the genotype. Then, I tell them to multiply the numbers together. Thus, in the above example the total number of possible gametes is 64 (26). Ask them what happens, if the organism is homozygous for one of the genes, e. g. the C gene. They should realize that they would then write a 1 above the C gene so that when the numbers are multiplied, the total number of possible gametes would be 32 (see below). 2 2 2 2 2 2 2 2 1 2 2 2 AaBbCcDdEeFf 2 x 2 x 2 x 2x2x2 AaBbCcDdEeFf AaBbCCDdEeFf = 64 2 x 2 x 1 x 2x2x2 AaBbCCDdEeFf = 32 It should be clear to your students that they easily can figure out the number of gametes for any organism you give them. If you wish, reassure them that you will not ask them to list all of the gametes (unless the total is four or eight or some other small number). What Is the Probability of Getting This Offspring From That Cross? If your students learn the six monohybrid crosses listed above, they can figure out the probability of getting a particular type of organism in a complex cross fairly easily. For example, let's look at a trihybrid cross between two organisms heterozygous (AaBbCc) for all three genes with which we are concerned. We could figure out the number of gametes each organism can make (eight), construct a slightly nasty Punnett square with 64 squares, count up all the different possible offspring and figure out the probability of getting a particular genotype (AABbcc, for example) or phenotype (for example, organisms exhibiting the dominant phenotype for genes A and C and the recessive phenotype for gene B; A_bbC_) in our offspring. It is much easier, however, to deal with each gene independently and apply what we have learned about phenotypic and genotypic ratios for our six possible monohybrid crosses. The probability of getting a homozygous dominant offspring (AA) from a cross of two heterozygotes for the A trait would, of course, be 1/4 (0.25). Similarly, the probabilities of getting Bb and cc are 1/2 (0.5) and 1/4 (0.25), respectively. To find the probability of getting an AABbcc offspring from the above cross, one would simply have to multiply the probabilities of the outcome for each gene separately (1/4 x 1/2 x 1/4 = 1/32; 0.25 x 0.5 x 0.25 = 0.03125). The probabilities of the selected phenotype can be determined in a similar fashion. The probability of offspring exhibiting the dominant trait in a cross of two heterozygotes would be 3/4 or 0.75, while the probability of exhibiting the recessive trait would be 1/4 or 0.25. Thus, the probability of an A_bbC_ offspring would be 3/4 x 1/4 x 3/4 = 9/64 or 0.75 x 0.25 x 0.75 = 0.140625. Using this simple procedure, your students should be able to figure out similar problems dealing with five or more genes. Next, have them try a slightly more difficult problem. Ask them to figure out the probability of getting an AaBbCc offspring from the following two parents: AaBBCc x aaBbCc. Once again, the students should approach this problem by dealing with each gene independently. The probability of getting Aa, Bb and Cc offspring from these parents would be 1/2, 1/2, and 1/2, respectively. Thus, the probability of getting an AaBbCc offspring would be the product of the three probabilities above (1/8 or 0.0625). Next, have them figure out the probability of an AABbcc organism from a cross of the two parents above. See if they can figure out on their own that the probability of such an offspring from those parents is 0. The reason, of course, is that the probability of obtaining an AA offspring from a cross between an Aa and an aa parent is 0. Multiplying the probabilities of a Bb and cc offspring from these parents (1/2 and 1/4, respectively) by the probability of an AA offspring (0) would yield 0 x 1/2 x 1/4 or 0, an impossible result. Stress that the method described above illustrates Mendel's Law of Independent Assortment. Mendel's Laws Don't Always Apply Sometimes the results of crosses do not turn out as Mendel's Laws predict. Ratios other than the classic phenotypic ratios (all dominant, all recessive, 3 dominant :1 recessive, 1 dominant : 1 recessive) are obtained under these circumstances. For example, as in the classic case of the snapdragon, the result of a parental cross between pure-breeding red-flowered and pure-breeding white-flowered plants yields an F1 generation of solely pink-flowered plants. When two F1 plants are crossed, the offspring appear in a 1:2:1 ratio (red : pink : white). In order for a snapdragon to have red flowers, it must carry two red alleles for the flower color gene; a white-flowered plant carries two white alleles for the same gene. If a plant carried one red and one white allele for the flower color gene and normal Mendelian inheritance were operating, we would expect heterozygous plants such as this to have red flowers, assuming that the red allele is dominant. Instead, the heterozygotes have pink flowers; the red allele is not fully dominant. The red and white flower colors can reappear if the heterozygotes are crossed; one-fourth of the offspring will be red, one-fourth white, and half pink. Since the heterozygotes and the homozygous dominant organisms exhibit different phenotypes, the normal 3 : 1 phenotypic ratio is broken up into a 1 :2 : 1 phenotypic ratio that corresponds to the normal 1 : 2: 1 genotypic ratio. The phenomenon that causes the change from the 3 : 1 to the 1 : 2 : 1 ratio is called incomplete dominance. This, of course, can be confused with codominance and students, at times, have trouble distinguishing between them. It can be explained, however. Red snapdragons are red, since each red allele carried by the plant facilitates the production of a certain amount of plant pigment; two red alleles thus allow the production of enough red pigment to make the flowers red. If the plant is heterozygous, it carries only one red allele and can only make enough red pigment to make the flower pink. If the plant carries no red alleles but only white alleles, it can make no red pigment (in fact, no pigment at all). The white color of the flower is the color of the materials of which the flower is made. The plant does not make a white pigment; one might say that white is the default color of the flower. Therefore, red and pink flower color is the result of the presence of differing amounts of red pigment; white flower color results from its absence. Codominance, on the other hand, involves the expression of both traits in a heterozygote. Neither dominates over the other, and they are both expressed to an essentially equal extent. The best-known example of codominance is the human ABO blood groups. Explain to your students that there are three alleles, usually represented IA, IB and IO. Both the IA and IB alleles are dominant with respect to the IO allele which behaves like a normal recessive allele, but neither IA nor IB can dominate over the other. Therefore, an IAIB individual is blood type AB. IOIO individuals are blood type O. A person with an A blood type can have either of the following genotypes: IAIA or IAIO; a type B person is either IBIB or IBIO.. Another alteration of normal ratios results when a particular combination of alleles is deadly to a developing embryo. BioInquiry uses as an example of this type of non-Mendelian inheritance coat color in mice. It was determined that yellow coat color was dominant to the wild type brown (agouti) coat color. When heterozygous yellow mice carrying the agouti trait are crossed, a phenotypic ratio of 3 yellow : 1 agouti is expected, but a ratio of 2 yellow : 1 agouti is obtained. Test crosses have been used to show that all yellow mice are heterozygous. It has been determined that homozygous dominant embryos die early in development, accounting for the 2 : 1 phenotypic ratio. The allele responsible for yellow coat color can, therefore, be termed dominant for yellow coat color but recessive for lethality. In your discussion of lethal mutations, you might want to bring up the case of Huntington's disease which is the result of a dominant allele. Students often pose the question raised in the book: how does a dominant lethal allele persist in the population? The answer is, of course, that the lethality does not usually appear until after the afflicted person has reproduced and passed the lethal Huntington's allele to half of his/her offspring. You can include a story about Woody Guthrie, the folk singer and composer of "This Land Is Your Land," who died in 1967 of Huntington's disease. The students may know about his son Arlo, who had a 50% chance of inheriting the disease, but so far appears to be safe. A misconception held by many General Biology students is that each gene deals with one - and only one - trait. Any number of examples exist of genes that affect more than one trait. The coat color trait in mice listed above is one example; it controls coat color, but can also adversely affect viability. The book also mentions the seed coat texture gene (round vs. wrinkled) in Mendel's peas. It has been shown that this gene also affects the size and shape of the tiny starch grains that provide food for the developing pea plant. The book also mentions the W gene the dominant form of which leads to white fur in cats; the same allele causes deafness in one or both ears. The mutant allele affects melanocytes, which play an essential role in both traits. Yet another example is the trait that gives rise to albino tigers. These tigers are rare in the wild, but they have become quite common in zoos since the zoos breed them as attractions. They do not do well in the wild, since the same mutant trait that affects their coat color making it white also causes them to be cross-eyed, a condition that puts an animal that must hunt to survive at a decided disadvantage. Being cross-eyed in a zoo is, however, not as much of a problem, since your food, if you are a tiger, is tossed into your cage already dead. You don't have to hunt down a steak. The phenomenon whereby a single gene affects two or more traits is called pleiotropy. The reverse situation is also true. Not only can one gene affect two or more traits but two or more genes can also affect the same trait. Most students are surprised by this as well, especially if they are only exposed to Mendelian inheritance. Traits like height, coat color in many animals, number of whiskers in the face of a mouse, weight, and intelligence are thought to be controlled by many genes; they are polygenic (many genes) traits. Some of these traits may also be greatly affected by the environment. Sample Test Questions Multiple Choice, Conceptual, and Open-Ended Questions From the Text 1. What early proposal for the mechanism of inheritance, if true, would result in all organisms in a population appearing quite similar or even being identical? a. Mendelian inheritance c. blending inheritance e. heterozygous inheritance b. Aristotlean inheritance d. parental inheritance 2. Which of the following is a reason for Mendel's success in determining inheritance patterns? a. He focused on just a few traits. d. He focused on many traits. b. He chose the garden pea as his experimental organism. e. a, b, and c c. He thoroughly documented and quantified all of his results. 3. The specialized reproductive cells of an organism may be called a. sperm b. eggs c. zygotes d. gametes e. a, b, and d 4. In flowering plants, what contains the sperm? Pollen.. In flowering plants, what structure contains the eggs? Eggs are contained within ovules which are found in flower structures called carpels. 5. Purple flowers in peas are dominant to white. A pure-breeding purple-flowered plant is crossed to a pure-breeding white flowered plant. What is the genotype of the offspring? The offspring are all heterozygotes or Pp where P stands for the purple allele and p stands for the white allele. What is the phenotype of the offspring? All of the offspring have purple flowers. If two of the offspring from the previous cross are crossed, what should the phenotypic ratio of the offspring be? 3 purple-flowered plants : 1 white-flowered plant. 6. A purple-flowered pea plant is test-crossed. About 50% of the offspring are purple-flowered and about 50% have white flowers. What is the genotype of the purple-flowered plant? It is a heterozygote, Pp. If the purple-flowered parent were homozygous dominant, all of the offspring would have had purple flowers when test-crossed to a white-flowered plant. 7. Which word below describes an organism that has two genetic factors identical for a particular trait? a. homozygous b. heterozygous c. heterogametic d. homogametic e. a and d 8. What is the largest number of alleles for a particular gene that is normally carried by an organism? a. 0 b. 1 c. 2 d. 3 e. 10 9. What is the number of alleles for a particular gene carried by an organism homozygous for that gene? a. 0 b. 1 c. 2 d. 3 e. 10 10. What is the number of alleles for a certain gene carried by an organism heterozygous for that gene? a. 0 b. 1 c. 2 d. 3 e. 10 11. Define allele. Alleles are the different forms a gene might take. 12. Distinguish between genotype and phenotype. The genotype of an organism is its genetic composition or makeup with respect to a particular gene or genes. Phenotype refers to the expression of the traits in an organism, those apparent by looking at the organism. 13. Why is it more difficult to do genetic analysis of humans so that the genotypes underlying different phenotypes can be better understood? The normal approach to learning about the genotypes underlying different phenotypes is to perform controlled crosses between individuals and then calculating the ratios seen in the offspring. This approach of controlled crosses do not work in humans for moral and ethical reasons. Consequently, studies on human genetics rely on family trees or pedigrees to follow the pathways of different alleles through populations. 14. A sickle-cell carrier marries a sickle-cell sufferer. What proportion of their children will be carriers? One half of their children will be sickle-cell carriers. What proportion will be normal? None will be fully normal. 15. Two carriers of sickle-cell marry and have a child. What is the probability that their first child will suffer from sickle-cell anemia? One fourth or 25%. 16. How many different kinds of gametes with respect to the A gene can an organism homozygous dominant for that gene make make and what are the relative percentages of any different gametes? Only one kind, A. Thus, 100% of the gametes are A. How many different kinds of gametes can an organism heterozygous for the A gene make and what are the relative percentages of any different gametes? The organism can make two kinds of gametes present in equal amounts. Thus, 50% of the gametes are A and 50% are a. 17. How many different gametes can an organism with the following genotype make with respect to the genes mentioned: AaBBCcDdEeffGg? 32 different types of gametes. 18. Why is Drosophila melanogaster a good organism to use for genetic studies? The fruit fly Drosophila is small, easy to keep, and has a short life cycle. When they reproduce, they produce lots of eggs and offspring. This makes ratios fairly easy to calculate. 19. Wild type fruit flies have broad, straight wings and pale-colored bodies with dark transverse stripes. Some fruit flies mutant for the wing size trait have vestigial wings, an allele that is recessive to the wild type allele. Ebony body color is recessive to the normal pale, striped body color. Two flies heterozygous for both traits mentioned above are mated. What proportion of their offspring will exhibit the dominant phenotype for both traits? a. 50% b. 9/16 c. 3/16 d. 1/16 e. 1/4 20. What proportion of the offspring in the cross mentioned in Question 19 are vestigial winged and have ebony body color and what proportion have pale, striped bodies and vestigial wings? a. 50%, 50% b. 9/16, 3/16 c. 3/16, 1/16 d. 1/16, 3/16 e. 1/4, 3/4 21. What is the phenotypic ratio obtained when a vestigial winged, ebony colored fruit fly is crossed with a fruit fly heterozygous for both traits? a. 1 : 1 b. 9 : 3 : 3 : 1 c. 3 : 1 d. 9 : 7 e. 1 : 1 : 1 : 1 22. What is the probability that a cross between two AaBbCcDdEeFfGgHh organisms will yield an organism that has the following genotype: AABbccDdEeFFGgHh? 1/2048 or 0.000488. 23. What is the probability that a cross between AABbccDdEeFFGgHh will yield an organism that has the following genotype: AABbccddEeFfGgHH? a. 1/256 b. 0 c. 1/128 d. 1/512 e. 1/2048 24. What is the number of possible different phenotypes that can be obtained from 200 different genes each of which has two different alleles? 2200 different phenotypes. 25. What is another name for the sudden appearance of a new allele? Darwin called it a sport of nature? a. cross b. mutation c. variation d. reproduction e. none of the above 26. What are the three kinds of results that random mutations cause with respect to evolutionary fitness of an organism? Many or even most mutations may be deleterious causing the death of the organism possessing them or at the very least the organism will have some deficit in function. These mutations are consequently lost forever or not passed on to the next generation in great quantities. Many mutations are simply carried along from generation to generation, because they have no effect on the survival or reproduction of their recipients. Such mutations do not significantly change the function of their gene product . In some cases, a mutation arises that causes its gene product to work even better than the original form. The organism thus produced is better suited to survive and/or reproduce. Organisms possessing these mutations produce many offspring and leave many copies of the new allele in the next generation. Despite their mostly deleterious effects, evolution would be impossible without mutations. 27. Yellow coat color (Y) is dominant to the wild type brownish color (agouti; y) in mice. Marvin Kratzmeyer, a struggling young geneticist, crosses some yellow mice to wild type agouti mice. About half of the offspring are yellow and half agouti. What are the genotypes of the two parents in this cross? The yellow parent is heterozygous for the coat color trait (Yy), the agouti parent is homozygous for the agouti allele. If the yellow parent is crossed to another yellow parent, what results in terms of genotypic and phenotypic rations would you expect? Normally, a cross of two heterozygotes should give a 3 : 1 phenotypic ratio. In this case, that would mean that 75% of the offspring should be yellow and 25% agouti. However, in this case, two-thirds of the organisms are yellow and one-third have agouti coats, a 2 yellow : 1 agouti ratio. This represents an apparent distortion of the expected 1 YY : 2 Yy : 1 yy genotypic ratio. The yellow offspring are the Yy offspring and the agouti offspring, of course, have the yy genotype. The homozygous yellow (YY) organisms died in utero since this allele when homozygous is lethal. It is dominant for coat color but recessive for lethality. 28. Rabbits heterozygous for the Pelger trait and exhibiting that phenotype are crossed. The offspring appear in a 2 :1 ratio (Pelger : normal). Please explain this strange ratio. The Pelger anomaly results from the presence of one Pelger allele combined with the normal allele for the trait, the heterozygote. The normal offspring are homozygous for the normal allele. Organisms homozygous for the Pelger allele die and do not appear among the offspring. This allele when homozygous must be lethal. 29. Why does the dominant lethal allele for Huntington's disease manage to survive in the population? People who inherit the Huntington's allele usually reproduce and pass the allele along to half of their offspring before the trait is expressed. It normally is expressed between the ages of 30 and 60. 30. The phenomenon whereby a single gene affects two or more traits is _________. a. homozygosity b. heterozygosity c. pleiotropy d. incomplete dominance e. codominance 31. Albino tigers are relatively rare in the wild. Equally rare is crossed eyes. In fact, genetic research has demonstrated that all albino tigers are also cross eyed. These two traits are inherited together and have been shown to be caused by the same gene. This is an example of ___________. a. homozygosity b. heterozygosity c. codominance d. incomplete dominance e. pleiotropy 32. A population of animals is examined for the distribution of body weight throughout the population. When the results are graphed, the weights of the animals exhibit a normal distribution. The data are a contiuum rather than falling into discrete categories. What kind of inheritance is most likely to be responsible for this pattern? It is most likely that body weight in these animals is controlled by a number of different genes. It is probably a polygenic trait. 33. What new field of biology employed mathematics and statistics to prove that the variety required for natural selection could arise from Mendelian genetics? Population genetics. 34. A team of researchers discovers that a certain allele from the male parent adversely affects a specific aspect of brain development. The same allele contributed by the female has no adverse effect on the brain development of the offspring. In both cases, the offspring is heterozygous for this trait. Despite an identical genetic complement with respect to this allele, the parent from which the allele is obtained has an effect on its expression. This is an example of what phenomenon? Imprinted genes. Multiple Choice, Conceptual, and Open-Ended Questions From the CD-ROM 1. Who is the Father of Modern Genetics? a. Karl Correns b. Charles Darwin c. Gregor Mendel d. Alfred Russel Wallace e. Galileo 2. What are the alleles that Mendel dealt with for the following traits: Flower position? Terminal and axial position. Pod color? Yellow and green. Pod shape? Inflated and constricted. Seed color? Yellow and green. 3. Why did Mendel choose the pea plant for his research? He chose pea plants, because he could identify traits with discrete variations. He was able to produce plants which were pure-breeding with relative ease. Furthermore, he could cross pea plants easily through controlled pollination (cross pollination). 4. The ______ are the ______ reproductive part of the flower. a. stigma, male b. anthers, female c. anthers, stigma d. anthers, male e. stigma, anthers 5. What procedure did Mendel follow to get a pea plant that acted exclusively like a male parent? He cut off the stigma leaving only the male flower parts, the anthers intact. 6. What process does the removal of either the male or female reproductive part of the flower prevent? It prevents self-pollination. 7. What structure must the pollen grain form to bring the male pea plant gamete into contact with the ovule so that fertilization may occur? The pollen tube. 8. In the Monohybrid Cross exercise of Section 3.1 of the CD-ROM, a female, pure-breeding purple parent is mated to a pure-breeding, white male pea plant. What would the results be if a purebreeding, white female plant were mated to a pure-breeding, purple male? All of the offspring, males and females, would be purple. What is the name of the generation of which the products of this parental cross are a part? The first filial or F1 generation. 9. Which allele in the monohybrid cross described in #8 above is the dominant allele for flower color? The purple allele. 10. How do the results of the F1 cross to form the F2 generation on the phenotypic cross panel of the CD-ROM prove that blending inheritance does not happen? One-fourth of the offspring in the F2 generation are white. If blending inhertiance were operating, all offspring in the F2 generation would be the same color as their parents in the F1 generation. White offspring could not appear in the F2 generation if blending inheritance was operating. 11. What are the genotypes of the parents in the parental cross of the pure-breeding purple and purebreeding white parents in the genotypic cross panel of Section 3.1 of the CD-ROM? The purple parent's genotype is PP; the white parent's genotype is pp. What would the gametes of these parents be with respect to the flower color gene? The PP purple parent makes gametes containing a single P allele; the pp white parent makes gametes containing a single p allele. What are the genotypes of the offspring of this parental generation cross? The offspring are all purple heterozygotes (Pp). 12. What proportion of the purple offspring in the F2 generation of the genotypic cross in Section 3.1 of the CD-ROM is heterozygotic? Two-thirds are heterozygotic. What proportion of the F2 offspring are homozygous recessive? One-fourth. 13. According to the Exploration: Test Cross part of Section 3.1 of the CD-ROM, what is a test cross? A test cross is a cross in which an organism is crossed with the double recessive parent for the trait being studied. 14. What is the advantage of doing a test cross? A test cross allows you to distinguish between homozygous dominant and heterozygous organisms that are phenotypically identical. When a double recessive parent for a particular trait is crossed to a homozygous dominant organism, all of the offspring will exhibit the dominant phenotype. If heterozygotes are mated to the double recessive parent for a trait, about half of the offspring will exhibit the dominant phenotype and about half will exhibit the recessive phenotype. These results are so distinguishable and unambiguous that a test cross can be used to distinguish between organisms that are homozygous dominant and heterozygous for a particular trait. 15. A curly-haired man marries a woman with straight hair. They have ten children, all of whom have wavy hair. One of their wavy-haired daughters marries a man with wavy hair, and they have twelve children. Four of their children have straight hair, eight of their children have wavy hair and four have curly hair. What kind of inheritance pattern does this exemplify? This trait appears to exhibit incomplete dominance. 16. Who discovered incomplete dominance? a. Karl Correns b. Gregor Mendel c. Charles Darwin d. Thomas Huxley e. a and b 17. For what kind of inheritance pattern could incomplete dominance be mistaken? Incomplete dominance could be mistaken for blending inheritance. If Correns had not done the F1 cross, he might have become a supporter of blending inheritance. However, the F2 generation included not only pink four-o'clock flowers but also the original red and white parents. This could not have happened if blending inheritance were operating. 18. What was the phenotypic ratio of the F2 generation of the four-o'clock plants? 1 red flower : 2 pink flowers : 1 white flower. What ratio does the phenotypic ratio resemble? It not only resembles but matches the genotypic ratio for the F2 generation. Using BioInquiry in Large Classes Integrating Components into the Lecture Again, if the lecture hall is adequately equipped and time permits, Section 3.1 of the CD-ROM provides an excellent description of Mendel's methodology with the pea plants. It also visually demonstrates the traits that Mendel used in his work. This can be presented by the instructor alone in class or the students can follow along with him on their own computers. If the facilities are not available or if the instructor does not wish to take the time, the students should be encouraged to run through this section of the CD-ROM in its entirety. In addition to Mendel's procedures, it emphasizes the F1 and F2 crosses along with the data collected and the resulting phenotypes obtained. In a unique little feature, the CD-ROM allows the student to serve as Mendel's hypothetical lab assistant and to pick the flowers that are involved in each cross and then displays the results on screen. Part of the screen also includes a simulated data book in which the results are stated and discussions of their significance appear. Finally, the main points of Mendel's principle of segregation are summarized on screen. The CD-ROM also handles the genotypic outcomes of the F1 and F2 crosses separately. The student is required to correctly identify the genotypes of the parents and the offspring from each cross. In each case, the student must also specify the gametes that each parent can make. The demonstration will not allow the student to identify the genotypes of offspring or the gametes incorrectly. The significance and utility of the test cross is also demonstrated effectively. Students carry out a cross of purple and white pea plant flowers. Based upon the results, the student must correctly specify the genotype of the purple flowers used in the test cross. This and the other demonstrations and exercises described above support the lecture and complement what can be presented in a traditional lecture environment. They work quite well and aid the learning process. Section 3.3 of the CD-ROM includes an essentially identical series of exercises that illustrate incomplete dominance in Correns' four o'clock plants. It is just as effective in demonstrating this type of inheritance as was Section 3.1 in demonstrating classical Mendelian inheritance patterns. Read More About It A number of books deal with Mendel and his discoveries. The Growth of Biological Thought: Diversity, Evolution, and Inheritance by Ernst Mayr contains a fascinating section dealing with Mendel and his rediscoverers. Mayr also thoroughly discusses the reasons Mendel's results were ignored for so long and why they were rediscovered when they were. Some of this material is summarized above in the Analogies, Anecdotes and Illustrations section. Mayr also describes in some detail the views of inheritance that preceded Mendel and the people responsible for developing these views. He describes how the earlier views of inheritance prepare the environment that would finally be a fertile one for Mendel's principle to take root. Mayr also discusses the subsequent flowering of genetics and its growth into the genetics we know today. It is an enthralling and comprehensive account. Supporting the Lab We usually schedule a laboratory exercise on genetics. In it, we have the students carry out a brief demonstration of blending inheritance involving samples of red and white liquid, usually diluted milk with and without red food coloring. If time is an issue, you may handle this demonstration as a thought experiment and ask your class to tell you what they think would happen if you mixed the red and white samples to make offspring of the two "parents." Then ask them what will happen when two of these offspring combine their essences to make the next generation. The result, of course, would be that the pink color generated when the essences of the red and white parents are combined would not change color further when the essences of the offspring are combined. This demonstration could be complemented by one involving colored pop beads that illustrates Mendel's particulate notion of inheritance. It shows that the recessive parental alleles can reappear in the phenotypes of the F2 generation. The series of CD-ROM exercises mentioned above could also be used effectively in the laboratory to illustrate Mendel's experiments and the principles derived from them. This could then be supplemented by a series of genetics problems that the students could be given as an assignment. Some of these problems could be done in class as part of the lab or they can be addressed in subsequent labs, review sessions, or office hours on a one-to-one basis. Answers to Review Questions 1. Most of Mendel's contemporaries did not use the experimental approach that he used or document and quantify all of their experimental results thoroughly in the way he did. Furthermore, he focused on a few traits (only seven), instead of the much larger number of traits with which others dealt. He also apparently had an hypothesis about how inheritance worked and figured out the right way to test that hypothesis. Lastly, the garden pea was the ideal choice for such studies. The pea plant was easily manipulated in breeding experiments and, furthermore, came in distinct varieties or strains. Mendel studied traits that occur in two distinct forms (purple or white flowers, round or wrinkled seeds, puffy, inflated, or narrow, constricted pea pods, etc.). He began by developing true-breeding varieties for each trait. When these varieties were bred among themselves, all of the offspring of a given variety were identical in phenotype for that trait to the parents. When he was certain that his varieties were breeding true, he engineered matings between plants displaying different forms of each trait and observed and quantified the results. He analyzed his data mathematically by counting the number of offspring showing each parental form of a trait and calculated ratios of offspring showing each form of the trait. 2. The phenotype of the F1 generation is round seeds. The genotype of the F1 generation is Rr where R stands for the round allele and r stands for the wrinkled allele. These organisms are heterozygous for the seed shape gene. 3. A gamete is a specialized reproductive cell produced by sexually reproducing organisms. The male gamete is the sperm and the female gamete is the egg. Gametes generally carry one copy of each gene while other cells (somatic cells) in a mature pea plant carry two copies of each gene. At most, a gamete can only carry one allele for a particular gene, while a somatic cell can carry, at most, two alleles for a particular gene. 4. The results for these crosses appear below where P represents the dominant purple allele and p represents the recessive white allele. F1 Cross F2 Cross P Purple-Flowered Male x White-Flowered Female Genotypic Ratio All Pp Phenotypic Ratio All Purple P p Pp (purple) Pp (purple) p Pp (purple) Pp (purple) P Purple-Flowered (Pp) Male x Purple-Flowered (Pp) Female Genotypic Ratio 1 PP : 2Pp : 1 pp Phenotypic Ratio 3 Purple : 1 White p P PP (purple) Pp (purple) p Pp (purple) pp (white) 5. A person who has freckles is either heterozygous or homozygous for this dominant allele. If you crossed this individual to an individual homozygous for the recessive form of the gene, results would tell you the genotype of the freckled individual. If all of the offspring were freckled, the freckled parent must have been homozygous for the freckled allele; if about half of the offspring were freckled and the other half lacked freckles, the parent was heterozygous for that trait. It would, of course, require a significant number of offspring to be sure. 6. The man is a carrier of the sickle cell trait since his father must have been homozygous for the trait and, therefore, must have passed the allele on to his son. Since the family of the woman has no history of sickle cell disease, it is unlikely that she will be a carrier of the sickle cell allele. Thus, none of their children would be likely to have sickle cell anemia. About half of their children would be carriers of the disease, since the man would pass his sickle cell allele to approximately half of his children. 7. An allele is one form of a gene. There may be and, in fact, usually there exists more than one form or allele for a particular gene. A gene is an expanse of DNA or part of a chromosome coding for a particular trait. An allele is one form or version of that trait or expanse of DNA. There may be more than one form of a particular gene. A gene may also be described as a trait and an allele as a specific manifestation of that trait. Flower color in pea plants is an example of a gene. Two alleles for that gene are white and purple flower color. 8. There are nine possible genotypes in a dihybrid cross between individuals heterozygous for both traits and four possible phenotypes. 9. An individual with the genotype AABB can form one type of gamete (AB). An individual with the genotype AaBb can form four types of gametes (equal numbers of AB, Ab, aB and ab gametes). 10. The dihybrid cross demonstrates Mendel's Law of Independent Assortment. It states that the two traits dealt with in a dihybrid cross operate utterly independently of one another. The alleles of one gene are passed to offspring independently of the alleles of the other gene dealt with in the dihybrid cross. 11. A cross between individuals heterozygous for five different genes can result in as many as 32 (25) different phenotypes. The large number of new allelic combinations (especially if one considers more than just five genes) is an important source of variation in populations like that needed for evolution by natural selection. 12. If one assumes that the mutation arose in just one gamete (while all of the others carried the Q allele) and that that gamete dies before fertilization, the q allele will not appear in the next generation since all of the other gametes carry the Q allele. On the other hand, if the mutation occurred early in the development of the organism in question, the q allele could appear in the next generation. This would require that the mutation's appearance in the cells of this organism that give rise to the gametes. If this happened a significant proportion of the organism's gametes would carry the q allele and the death of one would not preclude the appearance of the q allele in the next generation. As long as one of the gametes carrying the mutant q allele fused with another gamete to form a zygote the q allele would appear in the next generation. Gametes - all carry Q allele except one that carries q allele and that one gamete dies Gametes - carry mostly the Q allele and numerous q alleles, one of which dies Q Q q Q Q QQ QQ Q QQ Qq Q QQ QQ Q QQ Qq 13. It is not always the case that one allele for a gene is totally dominant to all other alleles for that gene. One example would be the flowering plant called the four o'clock. If a pure-breeding red plant is crossed to a pure-breeding white plant, the hybrid (heterozygous) offspring are intermediate in color, i.e. pink. This is called incomplete dominance, since neither allele dominates over the other. 14. In genetic terms, true breeding means that the organism is homozygous for either the dominant or recessive allele. Mice with yellow fur could not be true breeding, since yellow mice are actually heterozygous carrying the dominant yellow allele and the wild type allele resulting in brownish coat color (agouti). In addition to being dominant for yellow coat color, this allele is recessive for lethality. An organism carrying two copies of the yellow allele (homozygous yellow) would die early in development. Thus, there can be no true breeding yellow mice. 15. Had Mendel studied human height, he would not have been dealing with a few distinct phenotypes. The resultant offspring would have fallen into a continuous distribution of heights, since human height is controlled by many genes; it is a polygenic trait. The methods Mendel used on his pea plants would most likely not have worked on human height. Consequently, he probably would not have derived his principles of inheritance. He was able to derive these principles largely because he was studying traits with a limited number of distinct phenotypes. Human height, because it is polygenic and exhibits continuous distribution, would obscure the very relationships Mendel was seeking. CHAPTER 4 CELLS: WHAT ARE THE BUILDING BLOCKS OF LIFE? Lecture/CD-ROM Outline What Is the Cellular Nature of Life? I. The cell is the fundamental unit of life, the smallest entity able to exhibit the characteristics of life A. Cells acquire and use energy B. Cells acquire and organize materials - they grow and reproduce II. Microscopes made possible the discovery of cells - understanding of cell structure & function parallels development of the microscope A. 17th century, before microscopes - organs and tissues described in detail B. Robert Hooke, Englishman, Curator of Experiments at new Royal Society of London (1662) prepared demonstrations/experiments each week for society 1. Built primitive microscope (first with two lenses; also contained lamp & condenser for illumination); examined many things including thin pieces of cork 2. Described cork as "a great many little Boxes;" reminded him of monks' rooms (cellulae/cells) 3. Thought it explained cork properties (it floats, easily crushed, doesn't soak up water) 4. Published observations in Micrographia in 1665 C. 1674 - Royal Society learns of work of Anton van Leeuwenhoek (Dutchman; Delft Holland); built microscopes 1. Scopes were of excellent quality; lenses nearly perfect (took lens-making secrets to his grave) 2. Obtained magnification of 200X; could see bacteria 3. Over 53 year period, he communicated with Royal Society about his observations D. 1675 - Leeuwenhoek looked at cloudy green water from lake near his home вЂ”> saw & described many tiny creatures; called them animalcula (animalcules) 1. Soon he saw these creatures wherever he looked (mud, teeth scrapings, drinking water, etc.) 2. Hooke was sent to verify his results and did 3. He was thus the first to see living single-celled microorganisms (bacteria, algae, protists) E. 1800 - light scope allowed better view; also new histological procedures greatly improve quality of material; up to 1000X magnification (chloroplasts visible) F. Electron scope вЂ“ study cell ultrastructure; see complex membrane arrangement in chloroplasts; some of these are thylakoids that function during photosynthesis III. The Cell Theory was proposed in the early 1800s - about a hundred years after Leeuwenhoek, discoveries began to accumulate showing that cells are characteristic of living matter A. R. J. H. Dutrochet (French, 1824) - "all organic tissues are cellular tissues variously modified" B. Matthias Schleiden & Theodor Schwann who would later formulate the Cell Theory; met at a dinner party in 1837 C. Schleiden, interested in plant cell origins, proposed & tested three hypotheses: 1. Cells appear at the surfaces of previously formed tissues 2. Cells arise from preexisting cells 3. Cells appear spontaneously within the spaces between other cells D. Schleiden felt #2 was correct since small cells arose throughout tissue mass in no particular pattern 1. Tried to explain how it might happen; soon others found error after he published in 1838 2. Had said nucleus forms spontaneously in existing cell & cell arises as bubble on nuclear surface E. Schwann - interested in animal tissues; found frog larvae spinal cords had cellular structure 1. Cells previously defined on basis of square or ovoid shape; nerve cells are long & thin with obscure membranes 2. Discussions with Schleiden made him wonder if animal growth results from cell accumulation 3. Demonstrated this in developing embryos; also observed that noncellular substances (teeth, feathers, hair, fingernails) arose from cells 4. 1839 - published book that reprinted Schleiden's paper; ended with chapter on Cell Theory F. Their Cell Theory brought together 200 years of observations into concise, testable statement 1. Cells are the fundamental units of life. 2. All organisms are composed of one or more cells. 3. All cells arise from preexisting cells. - added later What Is the Chemical Nature of Cells? I. Since Schleiden & Schwann, much has been learned about cell structure and function; made possible by two developments outside biology A. Microscopes are greatly improved but detail in images not improved at magnifications >~1000X 1. 1931 - invention of electron microscope overcame this limit going to several hundreds of thousands 2. By 1980s, could see parts of cell approaching size of individual molecules B. Chemists came to appreciate dynamic complexity of cellular chemistry & creatively studied it 1. Reactions control, transfer, store, & use energy 2. Raw materials pass into cells where they are stored, exported, traded, or taken apart -> as a result, cells grow & divide II. The building blocks of cells are complex molecules that are based on the chemistry of carbon; such molecules called organic (first meant having to do with carbon; now means having to do with life) A. Carbon (C) has unique ability to form four covalent bonds (strong attraction between two atoms that share electrons) 1. C can share electrons with four other atoms, some or all of which can be carbons 2. Can make huge variety of linear or cyclic C backbone chains from which branches can form B. Large organic compounds in cells classified into four broad classes of biological macromolecules: carbohydrates, lipids, proteins, nucleic acids 1. Important for energy storage and transfer, metabolic processes, structural components, & storage of genetic information 2. All four are built from smaller organic building blocks - carbohydrates (simple sugars), lipids (fatty acids & others), proteins (amino acids), nucleic acids (nucleotides) III. Usually macromolecules are formed & broken down by similar chemical reactions A. Condensation reactions вЂ“ results in assemblage of smaller molecules into larger molecules 1. Two smaller molecules come together with formation of new covalent bond 2. One H2 O is formed for each new bond by loss of OH (hydroxyl) from one molecule & H from other 3. Process continues until entire macromolecule is synthesized B. Hydrolysis reactions вЂ“ result in cleavage of macromolecules into smaller molecules 1. Large molecules are broken down; covalent bonds formed during condensation are cleaved 2. One water molecule needed for each bond broken 3. OH from water added to one product & H to the other Biological Macromolecules: Carbohydrates I. Carbohydrates (CHOs) - simple sugars (monosaccharides) & compounds made of sugar building blocks; contain hydrogen, oxygen & carbon A. Serve variety of functions in living organisms including energy storage & structural support B. Exhibit three levels of organization 1. Monosaccharide вЂ“ simplest carbohydrates, a single sugar molecule 2. Disaccharide вЂ“ two monosaccharides join together to form them (glucose + fructose вЂ”> sucrose) 3. Polysaccharide - more than two monosaccharides join via condensation to form polysaccharides II. Monosaccharides - may have as few as three or as many as seven Cs bound into a linear array to form molecule backbone A. Most abundant are 5 & 6 C monosaccharides (pentoses & hexoses, respectively) B. Monosaccharides are quite water-soluble; in water, their ends curl around & form rings C. In this form, they link together to form polysaccharides D. Examples of monosaccharides are hexoses (glucose, fructose, galactose) & the pentoses (ribose & deoxyribose) CH2 OH H C C H OH O C C HO O HOH2 C H C H C H CH 2OH C OH H H HO C C H H OH OH GLUCOSE FRUCTOSE III. Disaccharides - composed of two monosaccharides joined together by a covalent bond A. Sucrose (table sugar) - composed of two different monosaccharides, glucose & fructose B. Maltose (malt sugar) - composed of two glucose units C. Lactose (milk sugar) - one galactose unit and one glucose unit Condensation of Glucose Monosaccharides CH 2OH CH 2OH C H C O H OH H C C HO H C C + OH O H OH H C C HO OH H C H H C OH OH H H 2O CH 2OH C H C HO CH2 OH O H OH H C C H H C C O C O H OH H C C H C OH H H OH OH IV. Polysaccharides - long monosaccharide chains (100s or 1,000s); 3D nature of carbohydrates arises from varied glucose polymer arrangements & various linkages between individual glucose units A. Starch - polysaccharide made in plants from thousands of repeating glucose units; stored for energy & hydrolyzed (broken down) into glucose which is used for energy; helical structure B. Glycogen - polysaccharide made in animals from many glucose units; highly branched; stored in liver & muscles as quick, ready source of chemical energy C. Cellulose - polysaccharide made of repeating glucose units; unbranched; found in plants (cotton, paper, important in structure of many woody plants); most abundant organic material on Earth 1. Glucose units are linked in such a way that they are unavailable as energy source 2. We lack enzymes that can break it down so it passes through digestive tract unchanged 3. Thus, it is excellent source of dietary fiber 4. Microorganisms that live in guts of termites & ruminants can digest it; this is how cows, sheep, & deer survive by eating cellulose-containing plant material Biological Macromolecules: Lipids I. Lipids (fats) are heterogeneous, diverse class of molecules sharing a single property - not soluble in water (hydrophobic; water-fearing); soluble in nonpolar, organic solvents (ether, chloroform) A. Some serve as energy reserves, others are structural in cell membranes, others as hormones & other types of cellular messengers; includes fats, cholesterol, steroids, phospholipids, oils, waxes B. Not strictly polymers of repeating building block subunits C. Two major categories - complex lipids (fatty acids part of structure) & simple lipids (no fatty acids) II. Fatty acids of complex lipids are long chains of C atoms with a single, nongreasy acidic group; (carboxyl; -COOH) on one end; about 100 naturally occurring fatty acids A. Differ in number of Cs in chain & presence or absence of double bonds between Cs in chain 1. Chains have many carbons usually connected by nonpolar covalent bonds (gives chain its hydrophobic chemistry) 2. Double bonded Cs do not bind as many hydrogen atoms as those connected by single bonds 3. Two general types of fatty acids - saturated & unsaturated B. Saturated fatty acids have no double bonds; abundant in tropical oils & many animal fats; their Cs are fully saturated with hydrogens 1. Good to keep saturated fats lower in diet - high saturated fat levels in diet correlate with high serum cholesterol 2. Saturated fats have a high melting point relative to mono- & polyunsaturated fats; stay solid (like shortening) at temperatures at which unsaturated fats are liquid (like vegetable oils) 3. Omega-3 fatty acids (polyunsaturated; found in fish oils) - very beneficial; if high in diet, lowers incidence of heart disease, hypertension, inflammation C. Unsaturated fatty acids have varying numbers of double bonds, not fully saturated with hydrogens; more common in plants 1. Monounsaturates (common in some vegetable oils like olive oil) - one double bond 2. Polyunsaturates (other vegetable oils, fish oils) - two or more double bonds III. Fatty acids usually bound to glycerol to form glycerides; two kinds вЂ“ storage (triglycerides) & structural glycerides (phospholipids); synthesized by condensation reactions A. Triglycerides - involves molecule of glycerol (3-carbon alcohol) & three fatty acids 1. Each fatty acid hooked to one of three glycerol Cs via condensation reaction 2. Very hydrophobic; oilseed plants (soy, sunflower), most animals store chemical energy in them 3 H2 O O H O H H C O H + HO C O (CH2 ) n CH 3 H C O C O (CH2 ) n CH 3 H C O H + HO C O (CH2 ) n CH 3 H C O C O (CH2 ) n CH 3 H C O H + HO C (CH2 ) n CH 3 H C O C (CH2 ) n CH 3 H Glycerol H 3 Fatty Acids Ester Linkage B. Phospholipids - glycerol bound to two fatty acids & hydrophilic head group (phosphorus atom & other water-soluble atoms); serve as structural lipids 1. Combination of hydrophobic & hydrophilic portions gives them unique chemical properties in watery environments 2. Oily portions clump together; hydrophilic portions seek water; leads to lipid bilayer with hydrophobic portions in core & hydrophilic heads interacting with water on either side 3. Such a stable bilayer is basis for cellular membranes; also contains proteins & CHOs O H Phosphate Ester Linkage O R group can be added to phosphate HO P O Polar H C O C O (CH2 )n CH 3 H C O C (CH2 )n CH 3 C H O Ester Linkage H Nonpolar IV. Simple lipids - have no fatty acids as part of structure A. Steroids - like cholesterol that contributes to atherosclerosis (thickening of arteries) if overabundant in blood B. Cholesterol is important component of membranes in animal cells; helps maintain right consistency (pliability, resilience) for optimum membrane performance C. Steroid hormones - sex steroids (testosterone, estrogen, progesterone); made from cholesterol & structurally similar Biological Macromolecules: Proteins I. Proteins - the most complex, varied macromolecules; the most ubiquitous in cells; play multiple roles A. Direct products of genes that determine specific amino acid sequence for each one B. Function determined by features of both its primary & higher order structures C. Functions вЂ“ variety of functions including structural molecules, enzymes, & cellular messengers 1. Some function as organic catalysts (enzymes) - speed rates of specific chemical reactions 2. Others responsible for cell movement & movement of substances within cells 3. Structural materials forming parts of scaffolding inside cells (cytoskeleton) 4. Structural materials that contribute to cartilage, fingernails, hair, other noncellular materials 5. Many play important roles as cellular regulators & messengers II. Protein building blocks are amino acids (small, water-soluble compounds built around central C) A. Central C atom binds to four groups or atoms 1. Nitrogenous amino group (вЂ”NH3 ) 2. Carboxyl group (вЂ”COOH) 3. Single hydrogen atom (вЂ”H) 4. Side group or residue (R) group - differs in each amino acid (20 naturally occurring aminos); may be single H atom or group of atoms, distinguishes one amino acid from another B. Proteins formed when amino acids are strung together by means of strong peptide bonds 1. Form via condensation reaction between the carboxyl group of one amino acid & the amino group of another; water is product of reaction 2. Forms independent of the variable R group so any sequence is possible (infinite number) 3. During protein formation, each amino acid is added in order by subsequent reaction 4. Cells make only about a couple hundred thousand different kinds (~50,000 identified) 5. Cell proteins have precise & unique amino acid sequences (up to 10,000 or small peptides) A Dipeptide Formed By Condensation-Dehydration + H H R N C H H O + C H H R N C H H O O C O H 2O + H H R O N C C H H Peptide Bond O R N C H H C O III. Levels of structure вЂ“ the 3D nature of proteins A. Primary structure - number & sequence of amino acids in a protein; initially forms linear chain; ultimately determines higher order structure 1. Proteins with similar function often have similar structure 2. Compare primary structures of similar proteins in different species to determine relatedness 98% of chimpanzee hemoglobin sequence is same as that of human hemoglobin B. Secondary structure вЂ“ results from H bonds forming between adjacent or nearly adjacent amino acids; forms helices, pleated sheets, & random coils C. Tertiary structure вЂ“ further folding due to chemical bonding between R groups on same chain D. Quaternary structure вЂ“ some have this; contain в‰Ґ2 chains of amino acids (hemoglobin) IV. Higher order structures (secondary, tertiary, quaternary) - proteins curl, bend, & fold back on themselves to form three-dimensional shapes A. 3D shapes account for the special shapes & varied functions of proteins 1. Muscle contractile proteins are long & fibrous 2. Enzymes are often globular with pockets for binding to their specific substrates B. Maintenance of these higher level structures depends on such factors as temperature & chemical make-up of the cell 1. Changes in these factors may result in permanent damage (denaturation) to protein 2. Denaturation changes shape of protein & thus affects its particular function; protein can sometimes renature & regain function Biological Macromolecules: Nucleic Acids I. Nucleic acids are polymers of nucleotides A. Nucleotides are a combination of three types of molecules 1. A ring-shaped 5-carbon sugar (ribose or deoxyribose) 5' CH 5' CH 2OH O OH 4' 1' H H 3' O OH 4' H H 2OH 2' 1' H H 3' OH H Deoxyribose H H 2' OH OH Ribose 2. A phosphate group 3. Nitrogen-containing base - adenine (A), guanine (G), cytosine (C), thymine (T), uracil (U) Generalized Stucture of Purines and Pyrimidines N 7 4 6 N1 5 Pyrimidine 8 4 N9 O Sugar N3 5 2 N3 Purine 2 6 N1 O Sugar B. Both nitrogenous base & phosphate group are attached to sugar 1. Nucleotides with a ribose sugar do not contain thymine 2. Nucleotides with a deoxyribose sugar do not contain uracil C. Two types of nitrogenous bases - pyrimidines & purines 1. Pyrimidines (C, T, U) - composed of one ring 2. Purines (A, G) - composed of two fused rings II. Two different kinds of polymer - ribonucleic & deoxyribonucleic acid A. Ribonucleic acid (RNA) - nucleotides contain ribose B. Deoxyribonucleic acid (DNA) - nucleotides contain deoxyribose III. Bonds between nucleotides link the phosphate group of one nucleotide & the sugar of the next A. Polymer backbone is alternating phosphate-sugar-phosphate-sugar-phosphate-sugar etc. B. Nitrogenous bases are oriented perpendicular to this chain O OH O- OH O Base 1 P O- O 4' 1' H H H 3' H H 2' OH O Base O 3'-5' phosphodiester linkage 1' H H H H 2' H 3' H H 2' OH phosphate ester linkage 5'C 4' 1' P O O 5' C O H 3' Base 2 P O- 4' O O O H 2O 2 O 5' C H H 2' H OH } } phosphate ester linkage O H 3' Condensation-Dehydration 3'C 1' H P O- O 5' C 4' 1 O O 5' C Base P OH H H C. Consequences of the structure of nucleic acids 1. Formation of a nucleic acid is independent of the sequence of nitrogenous bases; any sequence is possible 2. The nitrogenous bases are not occupied with the business of holding nucleotides together O P P O Cytosine Thymidine Guanine O P Guanine Adenine Cytosine Thymidine Adenine O O O O P P P P P O IV. Nucleotides & nucleic acids are central to life A. Adenosine triphosphate (ATP) - ubiquitous small molecule made of a ribonucleotide bound to two phosphates (three altogether); bonds carry small energy packet used in many cell activities B. Nucleotide coenzymes (NAD+, FAD) - play important role in cellular energetics & metabolism C. Nucleotide polymers (RNA, DNA) - contain & convey hereditary information Membranes Surround All Cells: Introduction to Structure I. Function of membrane surrounding cell is to separate the contents of the cell from surroundings A. Also found within cells; forms compartments that isolate & concentrate cell functions & processes B. Also provides pathway for exchange; materials & signals pass back & forth through them C. Because of structure, membrane prevents water-soluble molecules from entering & leaving cell indiscriminately, but proteins can regulate movement of such molecules D. Proteins are responsible for the many specific functions of different membranes 1. Some function in cell identification 2. Others are enzymes, controlling chemical reactions occurring in or on either side of membrane 3. Act as couplers, connecting one cell to another 4. Others are intimately tied to passage of materials into & out of cell II. Membrane structure A. By 1935, it was known that membranes were composed of lipids & proteins but did not know how they were arranged; view has changed often since then B. S. Jonathan Singer & Garth Nicolson (1972) вЂ“ proposed fluid-mosaic model; lipids provide dynamic, fluid nature of membranes; proteins arranged in mosaic pattern throughout membrane 1. Membranes are made up mostly of a lipid (mostly phospholipids, some sterols) bilayer, proteins & carbohydrates; cholesterol is most commonly occurring sterol in membranes 2. Bilayer is dynamic, fluid construction; lipids can move in place & laterally in bilayer plane 3. Location of membrane proteins - some rest on surface of bilayer; others are deeply embedded in bilayer or penetrate it completely 4. Proteins move within plane of membrane forming active mosaic of particles within bilayer 5. Term fluid mosaic describes dynamic nature of lipids & proteins in membrane C. Sterols are oriented with hydrophilic region toward membrane surface & hydrophobic tail embedded in phospholipid bilayer 1. Animal cells contain higher percentage of cholesterol than any other cell; it is absent from most plant & bacterial cells 2. Disturb close association of membrane phospholipids; membranes with large amounts of sterols are more flexible 3. Cholesterol can be both good and bad вЂ“ see Text Section 4.2.1 III. Membrane proteins: general information вЂ“ found scattered throughout bilayer; give membrane its mosaic appearance A. Organelles may contain as many as 50 different membrane proteins B. Each surface of membrane contains different proteins вЂ”> different properties for extracellular & cytoplasmic surface C. Many membrane proteins, if not all, are glycoproteins 1. They aid membrane stability 2. They serve as recognition sites for bacteria & viruses 3. They have marker properties (ABO blood groups, immune system) Membranes Surround All Cells: Types of Membrane Proteins and Carbohydrates I. Integral proteins вЂ“ proteins that penetrate bilayer; most pass all the way through & are exposed on both sides (transmembrane proteins); function in variety of ways A. Energy transfer during cellular respiration & photosynthesis B. Receptors for hormones, antigens, & growth factors C. Channels and carrier proteins for passage of materials across membranes D. Enzymes or signal transmitters II. Peripheral proteins вЂ“ do not penetrate bilayer; formed by covalent bonds (mistake) to membrane lipids or integral proteins A. Best known are on inner (cytoplasmic) surface of red blood cell plasma membranes; those of outer (extracellular) surface are less well understood & less plentiful B. Form network of fibers that provides support for membrane C. Important when cell undergoes rapid changes in cell shape III. Lipid-anchored proteins вЂ“ specialized type of regulator proteins; found on either membrane surface; important when normal cells transform into malignant cells (not well understood) A. Connected by carbohydrates to phospholipid bilayer; only beginning to be understood B. Malfunctions in lipid-anchored proteins have been implicated in transformation of normal to malignant cells; two of them (Src & Ras) are located on the cytoplasmic surface of membrane C. Some serve as receptors that respond to external signals (recognition sites for certain hormones, growth factors, neurotransmitters) D. Some involved in immune response E. Viruses recognize specific membrane proteins that allow them to attach to specific cells IV. Carbohydrates in membranes are typically attached to either proteins (glycoproteins) or lipids (glycolipids) A. Carbohydrates are hydrophilic & extend outward from membrane surface nearly always into space outside cell (extracellular space) not into interior B. Functions of membrane carbohydrates 1. Some membrane glycoproteins act as glue to hold similar cells together to form tissue 2. Play a role in cellular identity & individuality like blood group antigens 3. Involved in some infectious diseases - flu virus gets into cell by binding to certain glycolipids V. Extracellular matrix (ECM) - primarily for support but also involved in cell division, wound healing, cell-to-cell communication A. ECM altered in cancer cells B. Some ECM fibers are joined to membrane Materials Enter and Leave Cells Through Their Membranes: Diffusion & Osmosis I. Diffusion - at temperatures characteristic of life, all molecules move (faster at higher temperatures) A. Depending on state, move to differing extents 1. Solids - molecules move, but restricted by molecular bonds 2. Fluids (liquids & gases) - less constrained; bump into each other & rebound randomly; get pushed into areas where collisions are less & less frequent вЂ”> become evenly distributed B. Diffusion is net movement of molecules from areas of high concentration to areas of low concentration by means of random collisions C. Imagine a cell surrounded by potential nutrients dissolved in water 1. If nutrient is at high concentration outside cell & low inside вЂ”> cell will obtain nutrients if they can pass through membrane D. Smaller solutes (particle dissolved in a solvent) & hydrophobic substances diffuse more readily through cell membranes; larger, more hydrophilic solutes pass more slowly or not at all II. Osmosis - special type of diffusion involving movement of water across a membrane A. Water moves from area of high water concentration to areas of low water concentration 1. As general rule, solution with lower solute concentration has higher water concentration 2. In pure water, water diffuses into the cell вЂ”> cell swells вЂ”> may burst; an environment around a cell with solute concentration lower than that inside cell is called hypotonic 3. Normal cell placed in heavily salted water loses water to surroundings & shrinks; surroundings with higher solute concentration than the cell interior is called hypertonic 4. If solute concentration outside cell is same as that inside cell, it is isotonic; there is no net water movement across membrane, a cell neither swells nor shrinks, gross movement occurs B. Tonicity comparisons depend not on the types of particles in solution but the numbers in solution C. U-tube experiment (movie) - bend tube into вЂњUвЂќ shape & separate two sides with artificial membrane (works like cell membrane) 1. Solutions on each side have different solute concentrations 2. Which way will water move? вЂ“ toward compartment with the higher solute concentration D. Animal cells (movie) вЂ“ what happens when living animal cells are placed in hypertonic, hypotonic, or isotonic solutions? E. Plant cells (movie) - what happens when living plant cells are placed in hypertonic, hypotonic, or isotonic solutions?; what is role of cell wall? III. Diffusion & osmosis are some of most common & powerful means of exchange between cell & environment A. Diffusion is used to obtain oxygen for cells & rid cells of excess water and metabolic wastes (CO2) B. Osmosis & diffusion cost the cell no energy; molecules move spontaneously IV. Simple diffusion across membrane occurs when nonpolar (hydrophobic) molecules move through spaces in bilayer; most water-soluble molecules/ions can not pass A. Move from area of higher concentration to area of low concentration B. Continues as long as concentration gradient maintained C. Some solutes cannot cross membrane by diffusion; it serves as a selective barrier вЂ“ important function; something more than simple diffusion is required to move things across Materials Enter and Leave Cells Through Their Membranes: Passive Transport, Membrane Channels, Membrane Carriers and Facilitated Diffusion I. Transport proteins вЂ“ integral proteins that regulate the movement of substances across the membrane (channel proteins, carrier proteins) A. Some act as channels through which materials may pass (channel proteins) B. Sometimes вЂњdoorвЂќ or gate on protein must be opened for transport to occur (gated channels) C. Others must change shape (conformation) for transport to occur (carrier proteins) II. Channel proteins - some large or hydrophilic substances cross membrane through these proteins A. Form holes through which molecules can diffuse - some are permanently open; others open or close depending on signals originating from the cell or its surroundings B. Most are highly selective - serve as pores for certain molecules & exclude others C. Called facilitated diffusion; it is transport of molecules that cannot pass directly through bilayer but are still transported; diffusion since molecules go down their concentration gradients 1. Some molecules diffuse directly through channel proteins 2. Others pass through gated channels which first must be opened III. Other molecules are transported across membrane by special carrier proteins A. First, they bind to molecule & then by changing shape they are able to move substances across the membrane B. Also facilitated diffusion IV. Molecules transported in this way move down concentration gradient; costs little or no energy (passive transport) Materials Enter and Leave Cells Through Their Membranes: Active Transport by Carrier Proteins, Exocytosis, & Endocytosis I. Active transport - molecules are moved in direction opposite to concentration gradient (from area of low concentration to an area of high concentration); see movie on CD-ROM A. Active transport requires the cell to expend energy B. Active transport is accomplished by a different class of membrane proteins (carrier proteins) 1. Binds substance to be transported, carries it to the other side of membrane where it is released 2. At same time, carrier binds to second (energy-providing) molecule & extracts energy required to move cargo up gradient 3. Once transport is completed, carrier protein returns to original shape C. Factors like size & charge of molecules may influence ability to be transported II. Sometimes molecules & even whole cells can move across the membrane in bulk A. Items contact cell membrane, are engulfed by it, & end up in membrane-enclosed vesicles inside the cell - endocytosis B. The export of cellular products in bulk (reverse of endocytosis) - exocytosis What Are the Types of Cells? I. Cells come in many shapes & sizes вЂ“ fundamental unit of life; humans - >200 different cell types A. Cells vary greatly in shape - spherical, elongated, box-shaped, flat 1. Sometimes shapes are very unusual, defy description; others change shape frequently B. Cells vary in kinds & complexity of parts found outside their membranes; some bare, some have extensive cell walls, slimy coats, elongated structures that push/pull them through surroundings 1. Internally, some are rather simple, others extensively compartmentalized with organelles 2. Organelles - specialized structures in cell that participate in various cellular activities 3. Some cells have specialized organelles that are used for specific functions (e.g., sarcoplasmic reticulum in muscle) 4. Those organelles mentioned below are found in most eukaryotic cells II. Cells lumped into two broad types - prokaryotes & eukaryotes Prokaryotic Cells Have Few Internal Parts I. Prokaryotes - include true bacteria (Eubacteria) & more primitive Archaebacteria; seem simpler, have many fewer internal parts than eukaryotes; smaller, ~10% the size of typical eukaryotic cells A. Prokaryotes have been on Earth as much as 3.8 million years (fossils found) thus they have had more time to evolve & adjust to more of Earth's environments than other organisms B. Found nearly everywhere 1. Spores in each breath; bacteria on nearly every surface & nearly every drop of water 2. In intestines, some are welcome, helpful (in exchange for space, nutrients вЂ”> give us vitamins, help absorb water) 3. Found naturally in soil, air, hot springs, acid pools, salad dressings, highly salty water, sauces, festering sores 4. Some are enemies - cause diseases (tuberculosis, syphilis, food poisoning) 5. Some are our allies - decompose carcasses, recycle nutrients, tidy up ecosystems, put oxygen in ponds & nitrates in soils II. Structurally relatively simple A. Some structures help them withstand hostile environments & attach to surfaces 1. Cell membrane around cell 2. Thick cell wall around membrane - made of complex polypeptides and/or polysaccharides 3. Capsule or slime layer found beyond some cell walls B. Long fingerlike projections extend beyond cell surface (pili) 1. Provide for attachment of some bacteria to their hosts & sometimes to other prokaryotes 2. Through sex pili, they exchange genetic information (primitive sexual reproduction) C. One or more long whiplike structures (flagella) - extend beyond cell wall, spin & propel cell D. Why do they appear simple? вЂ”> virtually no internal parts or organization; no nucleus 1. One long chromosome - continuous loop of coiled DNA 2. Numerous ribosomes in cytoplasm - construct new proteins III. Organelles of prokaryotic cells A. Nucleoid - region in prokaryotes that contains genetic material (DNA) 1. Unlike in eukaryotes, there is no membrane surrounding this region 2. DNA still functions as blueprint for synthesis of proteins B. Mesosomes - found in prokaryotes; cytoplasmic structures that result from infoldings of plasma membrane; provide surface area for various metabolic reactions C. Cell wall - additional covering outside cell membrane; provides support & protection for cells containing it D. Capsule - protective layer on outside of some prokaryotes 1. Gives certain characteristics to prokaryotes - infectious properties of certain bacteria 2. Type of capsule identified by variety of biological stains E. Plasma membrane - found in all cells; serves as barrier between contents of cell & its external environment; selective so far as what it will allow to pass Eukaryotic Cells Have Numerous Internal Structures: Background Information I. Eukaryotic cells come in a bewildering array of types & forms - plants, animals, fungi, protists A. Protists - single-celled organisms; most are microscopic but larger than prokaryotes; some (amoebas) can just be seen without microscope (they are the size of a period at end of sentence) B. Multicellular organisms - several different types of cells joined to form a single organism; humans have trillions of cells of >200 different types II. Eukaryotes are considerably more complex internally than prokaryotes A. Possess intracellular compartments enclosed in membranes that isolate & concentrate essential functions and processes B. Surrounding membranes similar to cell membranes (fluid mosaic phospholipid bilayers with proteins) - proteins may differ from those in the cell membrane Eukaryotic Cells Have Numerous Internal Structures: The Organelles I. Nucleus - usually the most obvious organelle, central to cell activities; control center of cell A. Surrounded by porous double membrane B. Contains cell's hereditary material (DNA), its chromosomes (blueprint of genetic instructions for making cellular proteins) C. Chromosomes are not circular but shorter, linear structures; number varies depending on species (2 вЂ”>1000); complexes of DNA & protein D. Nucleolus вЂ“ found in nucleus; small, irregularly shaped structure of DNA & RNA where: 1. Ribosomal RNA (rRNA), one of two major components of ribosomes, is synthesized from genes (rDNA) located here 2. Ribosomes assembled from rRNA and proteins synthesized in cytoplasm; may be free or bound to RER II. Cell wall - additional covering outside cell membrane; provides support & protection for cells containing it; composed mostly of polysaccharide cellulose III. Plasma membrane - fluid-mosaic membrane; phospholipid bilayer with proteins scattered throughout; serves as selective barrier between cell contents and its surroundings IV. Centrioles - found outside of and adjacent to nucleus in animal cells & some plant cells; play an important role in organizing parts of cytoskeleton A. Composed of microtubules & found in animal cells B. Serve as attachment points for spindle fibers during cell division V. Endoplasmic reticulum (ER) - in cytoplasm; a convoluted sheet of membrane enclosing a space within the cell that is separate from the cytoplasm; forms network of membranes throughout cell A. Its twists & turns form many folds & pockets through cell interior; two types - rough & smooth B. Rough endoplasmic reticulum (RER) - relatively close to nucleus; covered with tiny bumps (ribosomes); proteins synthesized here then primarily processed & sorted in Golgi C. Smooth endoplasmic reticulum (SER) - further from nucleus; no ribosomes; encloses separate compartment; SER membrane proteins make other products (lipids, carbohydrates) D. SER is involved in various activities 1. Synthesis of steroid hormones 2. Mobilization of glucose 3. Breakdown of fats 4. Reactions that break down toxic substances 5. Processing of calcium ions VI. Golgi complex - stacks of larger membrane-enclosed sacs; serves as a packaging center for the cell A. In it, cellular products (proteins, lipids, carbohydrates) are modified, packaged, prepared, & stored for final destination and/or secretion B. These products released from Golgi in tiny sacs that pinch off from its membrane C. Many of these products are exported from the cell by exocytosis; others are targeted to intracellular sites, specific organelles VII. Endomembranal system - ER connects nuclear membrane, Golgi complex, & cell membrane into supraorganelle A. Cell's factory production line - instructions for building proteins pass from nucleus to RER where ribosomes make proteins B. Proteins move into RER compartment where they control the manufacture of other products or where they are prepared for other destinations C. Some travel from ER compartment to Golgi complex where they are packaged into vesicles & sent to other cellular locales VIII. Several types of vesicles depending on what they contain & what occurs inside them; tiny membrane-bound bubbles A. Food vesicles - formed by endocytosis, take in material from extracellular space B. Food vesicles fuse with lysosomes (membrane-bound organelles arising from Golgi); contain digestive enzymes that break down carbohydrates, proteins, lipids 1. Lysosomes process cellular debris & worn out organelles or those no longer needed as in red blood cells 2. When they rupture, lysosomes release these enzymes which then destroy the cell 3. They function normally to destroy dead cells C. Peroxisomes (microbodies) - small membrane-bound organelles similar to lysosomes 1. Contain many different enzymes like catalase that breaks down hydrogen peroxide (toxic product of several cellular activities) & others that form hydrogen peroxide 2. Found in abundance in the liver of vertebrates & also in leaves & other plant tissues D. Some leave SER & join Golgi complex & then form from Golgi as well; store various substances that will eventually be secreted to cell exterior E. Other vesicles store starch, carbohydrates, fats, atmospheric gases, organic acids, water, etc. IX. Two organelles deal specifically with energy required for cell activities; both have circular DNA, are elongated & surrounded by 2 membranes & contain ribosomes (size similar to those of prokaryotes) A. Mitochondria - found in almost all cells; inner membrane highly folded, increasing surface area on which energy-transducing activity takes place 1. Cell's energy organelles (most energy reactions occur here) 2. Contain own DNA; suggests to some that they were once free-living, bacteria-like organisms B. Chloroplasts - membranous organelle found only in photosynthetic cells (plants, algae) 1. Have a third system of membranes, an internal membranous complex on which photosynthesis reactions occur 2. Light energy is converted into chemical energy in chloroplasts 3. Light-dependent and -independent reactions of photosynthesis occur here X. Surface structures A. Plant & algal cells surrounded by thick cell walls made of cellulose (complex carbohydrates); protects cell & gives it great strength - mentioned earlier B. Organelles that are used for mobility - found in protists & some multicellular organisms 1. Flagellae - superficially similar to those in prokaryotes; have very different internal structure 2. Ciliates - covered with hairlike structures (cilia); beat back/forth in unison вЂ”> produce motion; structurally identical to flagellae but shorter and more numerous 3. Multicellular organisms - sperm flagellae; cilia in several tissues (trachea, oviduct, nasal passages) 4. Cilia & flagellae, where found, are made up of complexes of microtubules as are centrioles & basal bodies (organelles that control organization and motion of cilia & flagellae) XI. Cytoskeleton - internal infrastructure; network of protein-containing fibers in cytoplasm with various functions; three types - microfilaments, intermediate filaments, & microtubules A. Microtubules - thin, hollow tubes constructed from repeating protein units 1 Components of cilia, flagellae, spindle apparatus, & cytoskeleton 2 Perform a variety of functions including cell movement, cytoplasmic movement of organelles, & cell division B. Microfilaments - actin-containing protein fibers that maintain cell shape, muscle contraction, cytoplasmic streaming & rigidity, anchor & connect organelles, move parts & products 1. Movement inside cells through cytoplasm (cytoplasmic streaming) 2. Information transfer 3. Anchoring of mRNAs 4 Cell movement and support 5. Reinforce and support cell membrane C. Intermediate filaments - mostly keratin; form scaffold within cytoplasm XII. Cytoplasm/cytosol - liquid portion of cells; consists mostly of H2O; contains cellular organelles A. Cellular activities occur here including energy reactions, cell movement, & conduction of outside signals B. Vacuoles - membrane sacs which take up most of interior of mature plant cells 1. May store water which gives plant support 2. May also store pigments & other substances 3. In some plants, vacuoles contain digestive enzymes which gives them properties similar to lysosomes XIII. Eukaryotic features characteristic of certain cell types A. Animal & protozoan cells - no thick cell walls & no chloroplasts; generally mobile B. Plant & algal cells - have thick cellulose cell walls, chloroplasts; make own food (autotrophic) C. Photosynthetic plant cells - usually have large, conspicuous, fluid-filled vacuole absent in algae D. Fungi cells - no chloroplasts (heterotrophic); have thick cell walls Prokaryotes and Eukaryotes: The Similarities and the Differences I. Both prokaryotes & eukaryotes are surrounded by a plasma membrane, but very different in structure II. Prokaryotes - belong to the Kingdom Eubacteria which includes bacteria & cyanobacteria and the Kingdom Archaebacteria A. Lack a nuclear membrane & thus do not have a defined nucleus B. Lack membranous organelles like mitochondria, Golgi apparatus, & ER III.. Eukaryotic cells - Kingdoms Plantae, Animalia, Protista, Fungi; have a nuclear envelope which separates nucleus from cytoplasm; also possess membranous organelles Plant Cells and Animal Cells: The Similarities and the Differences I. Both plants and animals are constructed from eukaryotic cells A. Contain similar organelles (both contain nucleus & other membranous organelles like mitochondria & Golgi apparatus B. Both are surrounded by a cell membrane which covers & protects the cell contents II. Some fundamental differences A. Plants have additional covering, the cell wall, primarily composed of cellulose; provides strength & rigidity to plant cells B. Plants are photosynthetic due to the presence of chloroplasts; light energy is converted into chemical energy in chloroplasts C. Plant cells also have large vacuoles used for the storage of water & other substances D. Animal cells lack cell walls and are thus more flexible & less defined than plant cells E. Animal cells contain other organelles not found in plants like lysosomes formed from Golgi F. Animal cells contain centrioles whereas most plant cells do not; important in cell division Where Do Cells Come From? I. Today, we know that cells come from other cells, but slightly >100 years ago, this was not the case II. The Cell Theory ran contrary to the theory of Spontaneous Generation A. Spontaneous generation is the belief that under the right circumstances life could generate spontaneously from non-living matter; had been held since antiquity by many prominent scientists B. In 19th century, this theory was challenged by carefully designed experiments which suggested that life did not arise spontaneously but from preexisting life (Pasteur) 1. After the Cell Theory was first proposed, Rudolf Virchow proposed that cells arise from preexisting cells; contributed to debate on spontaneous generation 2. If cells arise from pre-existing cells, they couldn't spontaneously generate B. Not strict proof; more evidence, stronger evidence needed III. Louis Pasteur & the Theory of Spontaneous Generation A. 1854 - worked on fermentation; found that healthy vats of fermenting sugar beets contained yeast (produced alcohol) while sick vats contained rod shaped microorganisms (produced lactic acid) B. Felix Archemede Pouchet, French scientist - his paper claimed to prove spontaneous generation 1. Hermetically sealed flask of boiling water 2. After cooling, introduced hay, oxygen also previously exposed to high temperature, resealed flask, waited вЂ”> organisms appear in a few days; thought spontaneous generation proved C. Pasteur again - realized that while heated flasks cooled, they could draw air into flasks along with microorganisms 1. Spontaneous generation believers criticized early experiments, because vessels were closed; Pasteur designed vessels that were open to the air 2. Built apparatus in which air drawn into flask on cooling first passed over red-hot metal (killed organisms) вЂ”> nothing grew 3. Pasteur made nutrient broth, poured it into straight-necked flask & immediately bent the neck 4. Bent portion open to air, but also served as a trap for microbes getting in; as the flasks cooled, water condensed in bend low point; microbes drawn in trapped вЂ”> no growth 5. Pasteur heated each flask to temperature that would kill existing bacteria or bacterial spores in flasks & then allowed them to cool 6. Broth in every flask remained sterile; some remain today from the original experiment & after 130 years, nothing is growing in them yet 7. To demonstrate that microorganisms were trapped in bent necks, he tipped several flasks & collected contents of neck in broth вЂ”> bacteria grew in a few days 8. Convincing demonstration against spontaneous generation вЂ”> argument continued for years; detractors claimed heating air killed elements requisite for life вЂ”> argument not settled D. Commission appointed by the French Academy to decide the issue - Pasteur produced sealed flasks of broth that for four years had not grown organisms 1. Darkened hall & used spotlight to expose dust particles floating in air; claimed dust included spores of organisms 2. Broth protected from spores so no organisms grew A Brief Look at Viruses I. Pasteur and others asserted that infectious diseases of plants & animals were caused by bacteria A. One by one, infectious agents of diseases were isolated & identified as bacteria B. But, in some cases, no infectious bacteria could be isolated from infected organisms - some diseases of tobacco plants & cattle 1. Sap of plants infected with tobacco mosaic virus & plasma of cattle with hoof-and-mouth disease stayed infectious after passage through filters whose pores exclude smallest bacteria 2. Concluded these diseases were caused by non-bacterial agents too small to be seen by microscopes 3. These agents were given the name viruses long before they were actually observed II. Wendell Stanley, Rockefeller Institute (1935) - crystallized tobacco mosaic virus suggesting simple, regularly repeating structure (far too simple to be cellular in nature) A. Wrongly concluded they were made solely of protein B. Later shown to consist of nucleic acid cores (RNA or DNA) surrounded by protective protein coat C. Some viruses (AIDS-causing HIV[human immunodeficiency virus]) are also enclosed by a lipid membrane III. Are viruses living? - they are biological entities made of biological molecules; they reproduce & evolve but most biologists do not consider them to be alive for the following reasons A. Viruses are acellular - organisms often classified by how many cells they have; viruses have none B. Viruses are totally dependent on other organisms 1. Virus must enter a host cell to reproduce 2. It is utterly dependent on the host for energy, raw materials, & machinery to make proteins C. When dried, some viruses form crystals - a trait shared by many nonliving substances (protein, salt, sugar) - no living cells form crystals when dried IV. What is a virus & how do they work? A. Bacteriophages - consist of a protein coat (capsid), which encloses a small segment of genetic material (DNA or RNA) 1. Require bacteria as hosts; thought to be at least one bacteriophage for each bacterium 2. Can only reproduce by injecting their genetic material into a host 3. Understanding this contributed to the understanding of chemical composition of genes - see Hershey & Chase experiment in Section 5.3 of CD-ROM B. HIV - causative agent of AIDS; contains RNA as genetic material & thus it is called a retrovirus 1. RNA of virus is surrounded by a protein capsid which, in turn, is surrounded by a lipidcontaining envelope 2. HIV virus attacks cell associated with the immune system in humans 3. HIV-infected individuals have higher risk of contracting diseases that would normally be eliminated by their immune systems (see CD-ROM Chapter 11) V. Virus evolution - probably arose as bits of DNA or RNA that escaped from organism chromosomes A. Fragments contained genes that encoded proteins for protective viral coat & genes that enabled them to infect cell & appropriate its cellular machinery B. Two lines of evidence 1. There are bits of nucleic acid that are not viruses but that leave chromosomes & take up residence at different places in chromosomes or in different cells (transposons) 2. Genes of many viruses closely resemble a few of the genes of living organisms (usually those the virus infects); virus genes came from the similar cellular genes VI. Importance of viruses to living things - cause serious diseases in most organisms A. Have complex, fascinating life histories like herpes simplex type I (causes cold sores; see below) or HIV (AIDS; retrovirus with RNA as its genetic material with a protein coat inside a lipid bilayer) B. Virus invades the cells of host organism (humans in this case); attaches by means of its protein coat 1. Its DNA/RNA core is inserted into the cell where it seeks the cells' ribosomes to use in synthesizing proteins which are incorporated into new viruses 2. Eventually, cell is filled with new viruses & bursts, releasing viruses to seek new hosts & start over; soon enough cells are damaged to produce noticeable symptoms, e.g. cold sore C. Host fights back - subtle changes occur in susceptible cell membranes & interfere with viruses' ability to enter cells вЂ”> sore stops growing вЂ”> then it heals D. Some viruses enter some host nerve cells & go into dormant stage 1. May remain this state for several years until something triggers it into activity 2. Trigger may be elevated body temperature or dry, cracked lips A New Type of Cells вЂ“ The Archaea I. Carl Woese, Univ. of Illinois, 1977 вЂ“ proposed a new cell type; compared bacterial rRNA sequences A. Found more variation within Kingdom Monera than between Monera & cells of other kingdoms B. Methanogens вЂ“ primitive bacteria that make methane had ribosomes so different that Woese considered them new cell type 1. Called them Archaebacteria; since renamed Archaea 2. Largely ignored II. Otto Kandler et al., Germany вЂ“ discovered methanogen cell walls were vastly different chemically from those of other bacteria; studied methanogens & related bacteria вЂ”> verified their uniqueness III. Institute for Genomic Research, Rockville MD, 1996 вЂ“ published complete genome of methanogen Methanococcus janaschii A. Identified 1,738 protein-coding genes; vast majority (62%) utterly unique B. Of remaining genes, most more closely related to those of eukaryotic cells than to those of bacteria C. Woese's contentions vindicated, but acceptance far from universal Analogies, Anecdotes and Illustrations Leeuwenhoek and Sperm Among the cells discovered by Anton van Leeuwenhoek (along with his co-discoverer Stephen Hamm) were sperm. According to The People's Almanac #2, upon the discovery in 1677, Leeuwenhoek described the cells he saw as moving "forward with a snakelike motion of the tail." Given the era in which the observation was made, he felt moved to include a disclaimer in his report stating that he had not obtained the sample by "any sinful contrivance," but that his "observations were made upon the excess with which Nature provided [him] in [his] conjugal relations." Despite this, few scientists at the time made the connection between the cells he had observed and conception. Some felt they were parasites. Later, when the connection had been made, some investigators thought that miniature organisms resided in the sperm head and that they expanded slowly upon entering the female. One investigator claimed to see microscopic roosters and horses in the heads of sperm from roosters and horses, respectively. It was even reported later that a tiny human could be seen in the fetal position in the head of human sperm. The tiny figure was called an homunculus. Polymerization Analogy can be employed effectively to describe the process of polymerization. I usually liken a polymer to a model train. It could consist of the same kind of car hooked together end-to-end. (Let's assume for the moment that a train doesn't necessarily need an engine.) On the other hand, many different kinds of cars can be hooked together in a variety of sequences. Whether the train contains only one type of car or many, the ends of each car are identical like the couplers on a model train (or a real one for that matter). The same is true of the monomers that join to form a polymer. Whether these units are identical or different, their ends are identical and can thus engage in the repeated formation of the same bond just like the model or real trains. Condensation and Hydrolysis Reactions Polymers are formed by repeated reactions (condensation reactions) that are used to assemble the monomer units of which they are composed. The same type of reaction is used to assemble the building blocks of triglycerides and phospholipids (glycerol, fatty acids, phosphate groups). In all of these cases, a water molecule (in the form of a hydroxyl ion and a hydrogen ion) is removed from the area across which the bond will form. Since water is a product of the reaction, it is called condensation, like the process that generates water droplets on a cold mirror or piece of glass that is brought into a warmer, humid room. Sometimes this type of reaction is referred to as dehydration, since the resulting composite molecule consists of exactly the same atoms as the monomer units of which it is composed less one water molecule for each bond. Once polymers have formed, they can be disassembled monomer by monomer via an hydrolysis reaction. In such a reaction, water is introduced into the bond previously formed by condensation resulting in the separation of the two monomer units that had been participating in the bond. The word hydrolysis is composed of two roots: hydro- meaning water and вЂ“lysis meaning a loosening. Thus, it means a loosening of the connection between two monomers through the involvement of water. A Few Words About the Names of Bonds in Macromolecules As any instructor of a non-majors introductory biology course probably knows, one of the things that students object to most is the vocabulary that one encounters in a science course. I donвЂ™t think that the vocabulary in science is any more onerous than in other disciplines (like Economics or Psychology, for example), but that seems to be the perception of this group of students. While the vocabulary can be substantial and even, at times, difficult, it is not impossible to learn. This is especially true if you emphasize for the students the meanings of the roots that are often used to assemble scientific terms. Most of these are roots already known to the students. As examples of this approach, the names of the bonds that hold together macromolecules are useful. Bonds that join the monomer units of carbohydrates are called glycosidic linkages. The root glyco- means sweet (from Greek). It makes sense that the name of the bond in a carbohydrate polymer should make reference to the most well known (and appreciated) property of sugars. The name of the peptide bonds that hold proteins or polypeptides together is derived from the root pept- that means digested or cooked (again from the Greek). Meat is familiar to most students and is, of course, predominantly protein. It is usually served after having been cooked and is digested following ingestion. Either of these connections might be employed effectively to help students remember which bonds are found in which macromolecules. Sometimes the roots of the name for the bond are unavailable or not particularly useful for our purposes. In those cases, we can always fall back on memorization. In general, I am not fond of memorization as a tool for learning, but sometimes it is the best method available. This is true of the ester linkages of triglycerides and phospholipids. The name for this bond was coined by the German chemist L. Gmelin to refer to a compound formed by a reaction between an alcohol and an acid (in this case, glycerol is the alcohol and the fatty acid is the acid) with the elimination of a molecule of water. The bond (simplistically) has the following arrangement of atoms: CвЂ”OвЂ”C. A variation of this bond is found in phospholipids where a phosphate group is joined to one of the carbons in glycerol. The orientation of atoms in this bond (PвЂ”OвЂ”C) resembles the ester linkage; a phosphorus atom replaces one of the carbons of the ester linkage. As a result, this bond is referred to as a phosphate ester, an ester linkage containing a phosphorus atom and involving a phosphate group which is, by the way, acidic. A similar bond is seen in polynucleotides where the phosphate (acid) of one nucleotide is joined to an hydroxyl group of the other nucleotideвЂ™s sugar (an alcohol since it contains a hydroxyl group). The resultant bond looks like two phosphate ester linkages hooked up in series (CвЂ”OвЂ”PвЂ”OвЂ”C) and is referred to as a phosphodiester (two phosphate esters) linkage. Polysaccharides A number of points can be made about the different kinds of polysaccharides. They help the students to connect the chemistry of these molecules to their function. As you outline the structure of glycogen, emphasize the branching. For non-majors, a detailed discourse on the bond structures is not necessary. For majors, distinguishing between 1,4-glycosidic and 1,6-glycosidic linkages and О±- and ОІ-glycosidic linkages would be more important. Point out the functional significance of branching. If a polysaccharide were linear, only two monosaccharides, at most, could be added to or subtracted from its length at one time. With branching, however, many more than two monosaccharides can be added or subtracted at once. This allows for quicker assembly and disassembly of glycogen. It also allows more efficient packing of the glucose in the cell. Ask leading questions of the students to get them to an understanding of this principle. Emphasize the relationship of structure and function, which will undoubtedly come up again. You can continue this approach by talking about the two different types of starch: amylose, which is unbranched, and amylopectin, which is branched (fewer but longer branches than glycogen). Ask the students to speculate about the reasons for the differences between the two branched polysaccharides, e.g., branches in plant cells can be longer because plant cells are longer. Mention the difference in the bonds that hold together cellulose and glycogen (ОІ-glycosidic linkages vs. О±-glycosidic linkages). Inform the class that mammals lack the enzyme needed to digest cellulose by breaking the ОІ-glycosidic linkage; then ask which polysaccharide is the most prominent in grass (cellulose, of course). Next, ask them how certain mammals can obtain their nutrients by eating grass, which is composed largely of a carbohydrate they are unable to digest. The answer, of course, is that the mammals that use grass and other plant material as their primary food source (herbivores) get a little help from their friends. Their guts are populated by microorganisms that can digest cellulose by breaking the linkages between glucose monomers that mammals cannot break. Ask the students whay these microorganisms must have that the mammals do not (an enzyme that breaks the bonds in cellulose, of course). Thus, a mutualistic relationship has developed between these organisms. The herbivores collect the food material that they are unable to digest. The microorganisms in their guts break down the cellulose in the ingested grass releasing the component glucose. The microorganisms take the glucose they require for their survival and leave the rest for the mammals that collected the cellulose. Both types of organisms benefit from this symbiotic relationship, a type of symbiosis called mutualism. I advise you to ask leading questions to get the students to tell you this story rather than giving it to them outright. This method consumes a bit more time, but is, in the end, I believe, more effective. Also, ask about the significance of dietary fiber in the human diet and how the inability of humans to break the ОІ-glycosidic linkage helps to keep waste material moving through the digestive system. Being a hydrophilic molecule, the cellulose of plant material attracts water to it and helps to lubricate its passage through the intestinal tract. I usually get a laugh when I say that the cellulose fiber in our diets greases the skids. Ask the students how this might account for the evidence that high dietary fiber tends to lower the chances of cancer in the digestive tract. Perhaps any carcinogens in the feces spend less time in the tract and thus have decreased opportunities to cause a cancerous transformation. Hydrophobic and Hydrophilic: Chemistry and Vocabulary While non-majors often take Biology courses to fulfill science requirements by ducking Chemistry and Mathematics courses, the bad news is that non-majors can not and (I believe) should not be able to do so. Given that they will be exposed to at least some rudimentary chemistry, a somewhat difficult concept for them to grasp is often the difference between hydrophobic and hydrophilic molecules. Again, knowledge of the roots of these words is helpful. It has already been mentioned previously that the root hydromeans water (Greek). The roots phobic and philic (both from Greek) mean fear or dread and love or loving, respectively. Consequently, a compound that is referred to as hydrophobic is one that вЂќfears waterвЂќ and does not вЂњlikeвЂќ to associate with it chemically. Hydrophilic compounds, on the other hand, do вЂњlikeвЂќ to associate with water chemically and do so preferentially. Hydrophobic molecules associate with each other whenever possible and avoid water. I require my students, whether majors or not, to be able to identify molecules as having either hydrophobic or hydrophilic qualities. While this intimidates them at first, I try to convince them that it is not that difficult a task. I tell them that a molecule has at least some hydrophobic character if it has long carbon chains (roughly 3 or more carbons) or carbon-containing rings, which are really only carbon chains whose ends have been connected. I also point out that, on occasion, such rings can contain nitrogen. By this time, I have already explained non-polar covalent bonds to my students. They understand that molecules containing such bonds exhibit equal charge distribution across their bonds and, therefore, do not interact well with water. I point out that the bonds in carbon rings and chains are nonpolar covalent bonds and the connection is usually made. Identification of hydrophilic molecules can also be handled relatively simply. I tell my students that if they see a chemical structure with certain chemical groups (вЂ”OH, вЂ”NH2 or вЂ”NH3+, вЂ”COOH or вЂ”COO-, вЂ”SH) projecting from it, the structure in question shows at least some hydrophilic character. Thus, a molecule (or portion thereof) containing a carbon chain or ring and none of the functional groups identified as hydrophilic would be considered to be totally hydrophobic. On the other hand, a molecule (or portion thereof) without a carbon chain or ring but containing the specified hydrophilic groups could be considered to be totally hydrophilic. Those molecules containing both carbon chains/rings and a hydrophilic group would have both hydrophilic and hydrophobic character. Such molecules are called amphipathic (amph- around, on both sides, double; path- suffering), since they вЂњsuffer doublyвЂќ by being both hydrophilic and hydrophobic. Your students may identify with this, since they are suffering doubly from chemistry they thought they were avoiding (just kidding!). Examples of such molecules are, of course, phospholipds and nucleotides. Hydrophobic and Hydrophilic: A Demonstration I find it useful to demonstrate these two concepts as well. Fortunately, this is easy to do and relatively inexpensive as well. Most students have been to a beach at some time in their lives and, on those occasions, they have undoubtedly gone into souvenir shops. Such shops invariably have numerous souvenirs (key chains, paperweights, etc.) that I lump together under the category of solubility toys. Most of them contain two liquids: one colorless (usually water) and one blue (usually mineral oil with a hydrophobic dye in it). Since, as we all know, oil and water do not mix, these two liquids, each of which occupies roughly half of the container, do not mix. If the container is shaken vigorously, it initially appears that the blue dye is uniformly spread throughout the container. As soon as shaking has stopped, however, the two liquids (mineral oil and water) immediately begin to separate into distinct layers that form an interface, at which usually floats a tiny surfer or sail boat, somewhere in the center of the container. The blue dye remains with the hydrophobic mineral oil layer and does not leach out into the water, since it is hydrophobic and does not вЂњlikeвЂќ to associate with an aqueous environment. Assure your students that no matter how hard they shake the solubility toy, the blue dye will remain with the mineral oil. There are also more elaborate and expensive solubility toys available that employ two or more colors of dye and multiple fluid chambers. They might be considered a bit of overkill for educational purposes, but they are fun. Just in case your students are not convinced of the relevance of this bit of chemistry to their lives, tell them about drugs and vitamins that are hydrophobic. Some of these chemicals, if present in the body at higher concentrations, can be dangerous. They tend to be localized in fatty tissues, since they are hydrophobic and can build up to dangerously high levels. Hydrophilic compounds, since they are hydrophilic, on the other hand, are more easily cleared from the body via the urine if taken in too high an amount. Vitamin A, when taken in excess, can build up in fatty tissues in just the way described. It can interfere with human fetal development and lead to problems with limb development specifically. Hydrophobic insecticides can build up in organisms farther up the food chain, because they collect in the fatty tissues of organisms that have been exposed to them. When these organisms are eaten, the pesticides in their fatty tissues are added to those in the fatty tissues of their predators. Such predators may, in turn, be eaten by other predators further concentrating the pesticides in their tissues. Chicken Soup, Micelles and the Behavior of Phospholipids in Water Since they are amphipathic, phospholipids exhibit interesting behavior when they are in contact with water. This behavior plays an important role in determining the structure of both internal and external cellular membranes. If spread over the surface of water in a tank, the hydrophilic heads of phospholipids interact with the water. The fatty acid tails of the phospholipids orient toward the air and interact with each other laterally. When you are looking down on a bowl of GrandmaвЂ™s chicken soup with its little puddles of fat floating on top of the soup, you are looking directly down on the phospholipid tails. Notice also that if you move one fat puddle toward another with your spoon, the two puddles of fat will fuse when they contact each other. This is a well-known property of lipids. Emphasize this fact for your students. If you now stir up the soup, some of the phospholipids will be driven beneath the surface of the soup. This presents them with a completely different environment, and they вЂњrespondвЂќ accordingly. The polar heads of these phospholipids orient toward the surrounding water molecules, while the hydrophobic fatty acid tails congregate together, interacting with each other. The resultant structure, a micelle, is a sphere of phospholipids with hydrophilic heads on the outer surface interacting with water and the hydrophilic tails interacting in the center of the sphere. Micelles are particularly useful in bathing and as a further clarification of how chemistry can be useful. I start by questioning students how they would characterize dirt chemically. If they seem to be having trouble coming up with an answer, I remind them that television commercials often refer to it as greasy dirt. I then ask them to imagine that they havenвЂ™t bathed for a while, that they are, thus, covered with вЂњgreasy dirt,вЂќ and that they step into the shower to remedy the situation. They step under the spray and soap up. As they do, they are creating micelles with the soap. I ask the students where the вЂњgreasy dirtвЂќ goes, and they usually answer (sometimes with some prodding), вЂњInto the center of the micelle where they interact with the phospholipid tails.вЂќ By then, they figure out that the act of rinsing off simply involves stepping under a stream of water, which interacts with the phospholipid heads on the outside of each micelle and carries the micelles and their contents of greasy dirt off their bodies and down the drain. Saturated and Unsaturated Fats: A Study in Form and Function Saturated and unsaturated fatty acids are another good example of the relationship between structure and function. Saturated fatty acids are fatty acids whose carbons are connected only by single bonds. They are called saturated fatty acids, since this bonding arrangement allows the carbon atoms in the chain to bind the maximum number of hydrogen atoms; the chains are, thus, saturated with hydrogens. As a result of the single bonds, saturated fatty acid chains are straight. These straight chains can pack together tightly and the contact between adjacent saturated fatty acids is maximized. Fats containing lots of saturated fatty acids, like those in animals, tend to be solid at room temperature for this reason. Fatty acid chains that are unsaturated have at least one double bond along their length. They are called unsaturated fatty acids, since the double bonds between adjacent carbon atoms in the chain lead to a decrease in the number of hydrogens bound to the chain as compared to a saturated chain with the same number of carbons. If there is more than one double bond in the chain, the fatty acid is said to be polyunsaturated. At each double bond in an unsaturated fatty acid, the chain has a bend or kink in it. Chains containing such kinks cannot pack as closely together as the straight chains of saturated fatty acids. Fats containing lots of unsaturated fatty acids, therefore, tend to be liquids at room temperature. They are called oils. While most animal fats are significantly saturated and, thus, solid at room temperature, plants contain fats that are often polyunsaturated and, thus, liquid at room temperature, e.g. vegetable oil and corn oil. Different combinations of saturated and unsaturated fatty acids are put to use in animals that overwinter in places like cold ponds. To maintain life, it is necessary that the cell membrane maintain the same degree of fluidity at all times. If this is not the case, normal membrane function can be compromised. As winter approaches and temperatures decrease, organisms that live in ponds change the composition of their cell membranes. Colder temperatures cause cell membranes to become less fluid, just as storing soft margarine in the refrigerator causes it to be harder. The organisms respond by increasing the percentage of unsaturated fatty acids in their membranes. This introduces more kinks into the fatty acid chains in the membrane and decreases the amount of contact between adjacent fatty acids. As a consequence, the membranes become more fluid, compensating for the decrease in fluidity caused by the drop in temperature. As warmer temperatures return in the Spring, the membrane fluidity increases, going beyond the optimal degree of fluidity. The organisms place more saturated fatty acids in their membranes, the phospholipids pack together more tightly and membrane fluidity returns to optimal levels. Cell Membranes: An Historical Perspective It is especially important for nonmajors to be exposed to the way in which scientific knowledge progresses. They are assailed on a weekly basis, assuming, of course, that they read newspapers and/or pay attention to current events, with breakthroughs in the treatment of cancer and other diseases, cloning, and various and sundry other scientific advances. They get the impression that the scientific achievements they hear about can occur overnight and require little time and effort. Students need to be exposed to a more realistic picture of the development of scientific ideas. The development of the present model of membrane structure is an excellent example. One of the earliest events in the development of a model of membrane structure came out of the observation in the 1890s by Overton that hydrophobic molecules can pass more easily through biological membranes (he used plant root hair cells) than hydrophilic molecules and ions. Since it was known that hydrophobic molecules are more soluble in other hydrophobic molecules, Overton proposed that membranes had the dissolving ability of a fatty oil. In the 1920s, Gorter and Grendel proposed that membranes were composed of a lipid bilayer. They had extracted the membrane lipids of a known number of red blood cells (RBCs) and spread them on the surface of a special tank of water called a Langmuir trough. RBCs are well suited for such a study, since they contain no internal membranes. Thus, the only cellular membranes that can be isolated and extracted from such cells is the plasma membrane itself. The trough allowed them to measure the surface area covered by the membrane lipids. Since RBCs were uniform in size and shape (a biconcave disk), their collective surface area could be calculated. It was determined that the area of the trough covered by extracted lipids was double the collective surface area of the RBCs, leading to the conclusion that a double layer of phospholipids covered the RBC surface. As we now know, the conclusion was correct, but serendipitously so. Gorter and Grendel had actually made two important errors in methodology. First, they assumed that their lipid extraction technique had completely extracted the RBC membranes. This was not the case. Second, they had miscalculated the surface area of the RBCs, since they had used their dry weight to do so. This led to an underestimation of the surface area. They got the correct result, since the two errors had compensated for each other. The lipids had been underextracted to the same extent that the surface area had been underestimated. Investigators checked the properties of artificial membranes against those of natural membranes. In one set of experiments, they constructed a water tank that was divided into two chambers by a metal plate that contained a small hole. Lipids extracted from RBCs were injected into the vicinity of the hole and formed a lipid bilayer that filled the hole. The two chambers were thus separated by a single lipid bilayer. The ability of molecules to pass through the bilayer could then be compared to transport across natural membranes. Other properties of artificial membranes were also found to be comparable to those of natural membranes as well. However, there were some properties of natural membranes that were not possessed by artificial membranes. It seemed that the missing properties could be replaced by working proteins into the model of membrane structure. Davson and Danielli proposed a model in 1934 that included a lipid bilayer coated with globular proteins on both surfaces. While the properties of this model matched those of natural membranes more closely, it did not match perfectly. So Davson and Danielli altered their model to include not only the globular proteins in the previous model, but also some unrolled proteins that were in direct contact with the bilayer while the globular proteins rested on top of them. This model was better but still had some inadequacies. In the early 1950s, they proposed a more elaborate, revised model that corrected the biggest deficiency in the earlier models. The membrane was said to be coated with a monomolecular layer of proteins that occasionally extended through the membrane to form protein-lined pores. The proposed protein-coated pores explained the ability of some hydrophilic molecules and ions to pass through natural membranes. This model with its periodic alterations was widely accepted from the its introduction in the 1930s until it was further altered somewhat in the 1950s by another investigator. One of its proponents was Robertson who collected evidence that the lipid molecules in the membrane were oriented perpendicular to the plane of the membrane and further proposed that all membranes were exactly alike whether they were found at the cell surface or covering a cytoplasmic organelle or surrounding a cyanobacterium, an idea called the Unit Membrane Model of membrane structure. Robertson's Unit Membrane Model was taught and largely accepted for close to another 20 years, but soon his model began to unravel. The model claimed that all membranes, wherever they were found, were alike. Evidence began to accumulate that this was not the case. Differences between membranes were discovered. Membranes were found to vary in thickness, protein content, lipid content, protein:lipid ratio, etc. In 1972, Singer and Nicolson proposed the Fluid-Mosaic Model of membrane structure. It also contained the central feature of a lipid bilayer and associated proteins, but the placement of the proteins was different. Singer and Nicolson envisaged a membrane with proteins scattered throughout as colored tiles are distributed in a mosaic. Some of these proteins were attached at the membrane surface; others were partially embedded in the membrane. Still others passed all the way through the membrane and probably served as transport molecules. The membrane was seen as a fluid structure that allowed lipids and proteins to move laterally through the membrane. The Fluid-Mosaic Model has been the accepted model of membrane structure for almost 30 years. It grew out of the earlier models and demonstrates the way in which scientific ideas develop. Observations are made, hypotheses proposed and tested. Parts of the model that fit past and future observations and experimental results are retained; portions of the model that do not fit are altered and then tested themselves until a model is developed that compares favorably with the data collected. The central element of membrane structure, the lipid bilayer, was arrived at fairly early. The details of protein placement took longer and, to a degree, had to await technological advances. Scientific research and the advance of scientific knowledge take time. While the medical and scientific advances we hear about daily on the news appear to be happening quickly, the vast majority of them is based on years of research conducted in many laboratories worldwide. Diffusion and Osmosis On the surface, it would seem that diffusion and osmosis are relatively easy concepts for students to understand, but there can be difficulties. Diffusion is the spontaneous process by which a substance moves from an area of high concentration to an area of low concentration; eventually, the same concentration is reached in all areas. Molecules can diffuse across membranes into cells. In order to do so, two properties are important: molecular size and the degree of hydrophobicity. If a molecule is more hydrophobic, it will diffuse more easily through the membrane, since hydrophobic substances are soluble in other hydrophobic substances. This is not the whole story, however. Bigger molecules, even if they are hydrophobic, will not diffuse directly through the membrane. This means that molecules that are most likely to diffuse a cell membrane are those that are small and hydrophobic. Conversely, those that are large and hydrophilic are less likely to pass directly through the membrane. This works as a general rule, but nothing is ever that easy. Ask students why, if water is by definition hydrophilic, it passes so easily through the membrane. The answer is, of course, (and someone in the class will usually get it) that water is so small that even its hydrophilic nature cannot prevent its movement across the membrane. Osmosis is the diffusion of water across a semipermeable or selectively permeable membrane from an area of high water concentration to an area of low water concentration. Point out to the class that cells exposed to surrounding fluids of varying solute concentration respond in different ways. Before you take this step, however, a little more vocabulary is a valuable tool. There are three words that make the discussion to come easier and less wordy. They are all based on the same root tonic which refers to solute concentration and the prefixes iso- (equal), hypo- (under, beneath) or hyper- (over, above; excessive). The three words thus formed relate the concentration of the solution being described to some other solution. A solution with a higher solute concentration than the reference solution is said to be hypertonic; a solution with a lower solute concentration than the reference solution is said to be hypotonic; if two solutions have the same concentration they are said to be isotonic relative to each other. While the meanings of these words seem clear, students often have trouble remembering their meanings. I recommend that you try to help your students remember these terms by associating them with words with which they are likely to be familiar. To remember "hypertonic," they can associate it with the word "hyperactive," which refers to someone who is more active than is appropriate for the situation. "Hypotonic" can be easily recalled if it is associated with the words "hypodermic needle." Everyone remembers where that goes (under the skin). Not very many students have trouble remembering what "isotonic" means. When I quiz my students on these words, as I inevitably do, a distressing number of students get them wrong. I have taken to kidding them about getting to learn the words. My tests usually have three questions dealing with these definitions. Most of my students (all but two in fifteen years) get "isotonic" right. Often, students figure the two remaining words will each be the answer of one of the remaining questions. So some will answer both questions with the same word ensuring that they get at least one point. I tell them that a much better way is to learn the definitions and get all of the available points. They usually find this amusing and sometimes it helps. If a cell is placed in an hypotonic solution, water will exhibit net movement into the cell. At first, this seems to be a contradiction; water should move toward the area of lower concentration, but if water is moving into the cell it is moving toward the area of high concentration. How can this be? The answer is, of course, that high solute concentration in the cell denotes low water concentration. Water, then, is moving from an area of high water concentration to an area of low water concentration. If students are confused by this, ask them to imagine two containers with exactly equal volumes of a solution, one of which has a concentration of 0.05 M NaCl, while the other has a concentration of 0.35 M NaCl. They should be able to tell you which of these two solutions should have the most water if you have exactly equal volumes of both. Obviously, the 0.35 M NaCl solution has less water, since the extra NaCl in that solution takes the place of more water than the less plentiful NaCl in the 0.05 M NaCl solution. Thus, a higher concentration of an osmotically active solute like NaCl translates into a lower concentration of water and vice versa. Once this concept is clear, you can move on to the effect osmosis can have on cells. Explain to the class what happens when animal and plant cells are exposed to solutions of varying solute concentration. If a cell is placed in a solution with a concentration lower than its own internal concentration, water will enter the cell. An animal cell, like a red blood cell, will swell as water enters the cell. If the differential between the cell and the surrounding solution is large enough, an amount of water sufficient to burst the cell will enter it. Plant cells in a similar situation will not lyse, but their turgor pressure will increase. When a cell is placed in a solution with a concentration higher than its own internal concentration, the opposite happens, water leaves the cell and moves into the surrounding fluid. Red blood cells shrink and undergo a process called crenation. A plant cell cannot really shrink due to the cell wall, but its cytoplasm pulls away from the cell wall and moves toward the center of the cell, a process called plasmolysis. Louis Pasteur and Spontaneous Generation I'm a sucker for the history of biology and find it particularly relevant for a general biology course. Pasteur's demonstration that spontaneous generation does not occur is a classic elegant experiment. It is a good idea to walk your students through the methodology he used and describe the experiment. Ask leading questions to get them to an understanding of the controls Pasteur used. They should also look at the depiction of the experiment on the BioInquiry CD-ROM. Pasteur built special flasks with S-shaped necks (swanвЂ™s necks) that extended off to one side of the flask. He boiled nutrient rich broth inside the flask killing any microorganisms (a process now called Pasteurization) and allowed the broth to cool. As it cooled, water condensed in the low point of the swanвЂ™s neck; any microorganisms drawn into the flask were trapped in the moisture. Nothing grew in the broth as it should have if spontaneous generation occurs. If Pasteur tipped the flask so that the microbecontaining condensate ended up in the broth or if he broke the neck so that the broth was exposed directly to the air, growth occurred. This was convincing evidence against spontaneous generation. Endosymbiosis Discuss with your students endosymbiosis, the idea that eukaryotic cells arose as combinations of prokaryotic cells with a primitive eukaryotic cell. Concentrate on the two most convincing cases: mitochondria and chloroplasts. These organelles which reside inside eukaryotic cells and which are essential for their survival are like prokaryotic cells in so many ways that an origin for them as prokaryotic cells is extremely believable. Both possess circular DNAs as do prokaryotes. They make some of their own proteins on ribosomes that are closer in size to the ribosomes of prokaryotes than those of eukaryotes like the ones that can be found in the cytoplasm just outside the organelle. They are both semiautonomous and can grow and divide in much the same way as do prokaryotes. It is supposed that at some time in the distant past a large, anaerobic, heterotrophic prokaryote ingested a small, aerobic, heterotrophic prokaryote. Instead of being digested, the smaller aerobic cell resisted digestion in the cytoplasm and took up permanent residence. The aerobic prokaryote remained within the cytoplasm and provided aerobic respiration for its host, while gaining protection and a ready supply of additional nutrients for itself. The relationship between the two cells was a symbiotic one with one cell living inside another and both receiving benefits, an endosymbiotic relationship. The partnership was a success and as the larger cell reproduced so did the endosymbiont. This idea, the endosymbiont theory, has achieved general acceptance largely through the efforts of Lynn Margulis of Boston University. It is thought that a separate and later endosymbiotic event occurred giving rise to green plants and green algae. Supposedly, an early heterotrophic eukaryote ingested a cyanobacterium that was also able to resist digestion, thus, converting the resultant combination into the ancestor of green algae and plants. This event is thought to have occurred later since all eukaryotic cells contain mitochondria while only the algae and green plants possess chloroplasts. Ask a leading question to see if your students can reason this out for themselves. Sample Test Questions Multiple Choice, Conceptual, and Open-Ended Questions From the Text 1. The smallest entity that is able to exhibit the characteristics of life is a(n) a. virus b. cell c. human d. frog e. amoeba 2. The first person to visualize living cells was: a. Leeuwenhoek b. Hooke c. Pasteur d. Darwin e. a and b 3. Which of the following were tenets of the Cell Theory? a. Cells are the fundamental units of life. d. All cells live forever b. All organisms are composed of one or more cells. e. a, b, and c c. All cells arise from preexisting cells. 4. Which of the people below was instrumental in proposing the tenets of the Cell Theory or in arguing for its acceptance? a. Matthias Schleiden b. Theodor Schwann c. Rudolf Virchow d. Charles Darwin e. a, b, and c 5. What is responsible for the ability of carbon to serve as the basis for the molecules that are the building blocks of cells? a. carbon is a big atom b. carbon can be used to make a huge variety of linear chains c. carbon can be used to make a huge variety of cyclic chains d. carbon containing structures can form branches e. b, c,and d 6. Which macromolecule is not formed by polymerization of similar or identical units to form a longer structure? a. proteins b. polynucleotides c. lipids d. polysaccharides e. polypeptides 7. What family of molecules has members that can serve as an energy source in many cell activities, act as a coenzyme, and store genetic information? a. polypeptides b. proteins c. lipids d. nucleic acids e. a and b 8. Which polysaccharide is a helical polymer of glucose used by plants for energy storage? Starch. Which polysaccharide is a branched polymer of glucose used by animals as a quick, ready source of chemical energy? Glycogen. Which polysaccharide is found in plants and made of repeating glucose units in an unbranched chain that plays a structural role in plants? It is also the most abundant organic material on Earth. Cellulose. 9. Cellulose is an important part of the human diet in that it plays the role of dietary fiber and cannot be digested. What is the explanation for our inability to digest cellulose? Humans lack the enzyme that can break cellulose down to its component glucose units so it passes through the digestive tract unchanged. How can mammals like cows and other ruminants survive by eating cellulose-containing plant material? The guts of such animals contain microorganisms that can digest cellulose. The glucose that is thus released by digestion is used to nourish the microorganisms and the ruminants that contain them. 10. You are given a sample of a fat that is liquid at room temperature. Which statement below is true of the sample? a. It contains saturated fatty acids. d. Its fatty acids contain no double bonds. b. It contains unsaturated fatty acids. e. b and c c. Its fatty acids contain some double bonds. 11. How are fatty acids of a phospholipid oriented in a lipid bilayer? Phospholipids have both hydrophilic (the phosphate-containing head group) and hydrophobic (the fatty acid tails) portions. In a lipid bilayer, the fatty acid is oriented toward the center of the bilayer away from the surrounding water. The polar heads of the phospholipids orient toward the outside of the bilayer where it can interact with water. There are two layers, each oriented in this way, so that the fatty acid tails meet in the center of the bilayer. 12. What ultimately accounts for the function of a polypeptide? The function of a polypeptide is determined by its three-dimensional shape. The primary structure (the sequence of amino acids) ultimately determines the shape of the protein, since it carries within its sequence the instructions for building all of the higher levels of structure of a given protein. Changes in the primary structure can thus significantly alter the shape of a protein and consequently its function. 13. You are studying a single-stranded, nucleic acid molecule containing the sugar ribose. Which combination of nitrogenous bases below are you likely to find in the molecule? a. adenine, thymine, cytosine, guanine d. adenine, cytosine, uracil b. adenine, uracil, cytosine, guanine e. adenoid, cytosine, thymine, guanine c. adenine, thiamine, cytosine, guanine 14. What group of membrane molecules plays a role in cell identification, helps to connect cells together, and aids in the movement of molecules across the cell membrane along with other specific membrane functions? a. phospholipids b. polypeptides c. cholesterol d. nucleic acids e. carbohydrates 15. Which molecule below is found in the membrane and contains carbohydrates as part of its structure? a. glycoproteins b. nucleotide sugars c. lipocarbohydrates d. glycolipids e. a and d 16. If you wanted to develop a drug that had a good chance to diffuse through the cell membrane, what two properties would you try to give it? Since the phospholipid bilayer forms a hydrophobic barrier against entry into the cell, hydrophobic molecules which can interact with other nonpolar molecules would be better able to cross the membrane. In addition, smaller molecules move more easily across the membrane. Thus, the drug should be small and hydrophobic. 17. What bacterial cell organelle is composed of complex polypeptides and/or polysaccharides and protects and supports the cell membrane? a. mesosome b. ribosome c. cell wall d. flagella e. pili 18. A red blood cell with an internal concentration equivalent to 0.15 M NaCl is placed in a solution with a concentration of 0.35 M NaCl. What happens to the red blood cell? It loses water to the surroundings and shrinks. What word describes the solution relative to the red blood cell? The solution is hypertonic relative to the red blood cell. What word describes the interior concentration of the red blood cell relative to the surrounding solution? Hypotonic. If the concentration of the solution surrounding the red blood cell were changed to 0.15 M NaCl, what word would describe it relative to the cell? Isotonic. 19. Through which prokaryotic cell structure can one prokaryote exchange genetic information (DNA) with another? a. mesosome b. ribosome c. cell wall d. flagella e. pili 20. Cholesterol is taken into cells via the following mechanism. It is transported in the blood as part of particles referred to as low density lipoprotein (LDL) particles. When a cell requires cholesterol, it places receptors for LDL particles into its membrane. LDL particles bind to the receptors that are localized in regions of the cell membrane called coated pits. The coated pits extend inward from the membrane and eventually pinch off, forming vesicles that fuse with lysosomes. The enzymes of the lysosomes release cholesterol from the LDL particles allowing their usage by the cell. What is the name of the process by which LDL particles enter the cell? Endocytosis. 21. What kind of cell has been present on Earth for the longest period of time (as much as 3.8 billion years)? Prokaryotic cells, including the true bacteria (Eubacteria) & the more primitive Archaebacteria. 22. What structure that extends beyond the cell wall of a bacterium is involved in propelling the bacterial cell forward? a. pili b. capsule c. mesosome d. flagellae e. a and d 23. Which kingdom below contains no prokaryotes? a. Animalia b. Fungi c. Monera d. a, b, and c 24. What kind of cell is found in multicellular organisms? a. prokaryotes b. bacteria c. eukaryotes d. cyanobacteria 25. Which kingdom below contains at least some eukaryotic cells? a. Protista b. Fungi c. Monera d. Animalia e. a and b e. none of the above e. a, b, and d 26. Which trait below describes eukaryotic but not prokaryotic chromosomes? a. contains DNA b. circular c. linear d. branched e. triple helix 27. Mammalian red blood cells contain no membrane-bound organelles. As red blood cells mature, their organelles are destroyed by fusion with another organelle that digests their components. What is the organelle responsible for the digestion? Lysosomes. 28. What traits do mitochondria and chloroplasts have in common? Both are surrounded by a double membrane, contain their own DNA (circular), and possess their own ribosomes which are smaller than those in the cytoplasm just outside the organelle. The ribosomes of chloroplasts and mitochondria closely resemble those of the prokaryotes. 29. Which adaptations below might you expect to see in cells that have large energy (ATP) requirements? a. elevated numbers of mitochondria d. a and c b. mitochondria with triple membranes e. a and b c. more highly folded mitochondrial inner membranes 30. Which structures below are totally or partially composed of microtubules? a. cilia b. flagellae c. basal bodies d. the cytoskeleton e. all of the above 31. What cytoskeletal element consists largely of keratin and forms a scaffold within the cytoplasm? Intermediate filaments. 32. What kind of eukaryotes may have neither thick cell walls nor chloroplasts and are generally mobile? a. animal cells b. protozoans c. plant cells d. bacteria e. a and b 33. Plants and algae are described as autotrophic. What is meant by this? Autotrophic organisms like plants and animals are able to make their own carbon-containing chemicals by using energy sources like sunlight. Heterotrophic organisms must obtain their chemical energy by eating. 34. What kingdom is characterized by eukaryotic cells with no chloroplasts and thick cell walls? Fungi. 35. What kind of eukaryotic cell usually has a large, conspicuous, fluid-filled central vacuole? A plant. 36. Are viruses considered to be living organisms? Please support your answer. Viruses are not considered to be living for a number of reasons. First, they are acellular. According to the Cell Theory, all living organisms consist of one or more cells. Second, viruses are totally dependent on other organisms for reproduction, energy, raw materials, and the machinery to make proteins. Third, when dried, viruses can form crystals, something that no living cell can do. 37. How do viruses take over the metabolic pathways of the cells they infect? They inject their genetic material into the host organism. Once inside the host, if the viral genome survives, it takes over the metabolic pathways of the cell it has invaded. 38. Eukaryotic cells are thought to have arisen by the combination of a primitive anaerobic cell with an aerobic prokaryotic cell. Given recent results, what kind of cell is most likely to have been the one that entered into an endosymbiotic relationship with the aerobic prokaryote? The Archaea are bacteria that contain a number of unique genes; however, the genes other than these are more similar to those of eukaryotes than to those of other bacteria. This suggests that a cell from this group might have been the one that entered into an endosymbiotic relationship with an ancient aerobic bacterium. Multiple Choice, Conceptual, and Open-Ended Questions From the CD-ROM 1. Resolution is perhaps the most important ability of microscopes. It is the ability of a microscope, or any lens system, to distinguish two objects as being separate. A formula (d= 0.61 О»/N. A.), where d is the minimum resolving distance, О» is the wavelength of the illuminating radiation, and N. A., the numerical aperture, describes the light-gathering ability of a lens, determines the ability of a particular lens system to resolve an image. Better resolution is indicated by a smaller value for the variable d. If you wanted to build the best microscope you could with the smallest value possible for d, the minimum resolution distance, what conditions of wavelength and N. A. would you employ? You would use the smallest wavelength of visible light you could (this would be about 400 nm or blue light) in combination with the highest N. A. or light-gathering ability possible. The combination of these two factors would result in a small value for resolution. How do electron microscopes manage to resolve objects better than do even the best light microscopes? Electron microscopes use electrons which have much lower wavelengths than visible light to illuminate the specimen. Thus, the minimum resolving distance becomes extremely small. Numerical apertures for electron microscopes are comparable to those for the light microscope. 2. Glass is used to make lenses for light microscopes. Of what are the lenses for electron microscopes made? Electrons cannot pass easily through glass lenses,which would be required to focus the electrons. However, since electrons are negatively charged, they can be focused by an electromagnet, which can have an effect on charged particles. 3. What is the name of the reaction that connects two sugar units together to form a disaccharide while producing a water molecule as a byproduct? a. hydrolysis b. hydration c. condensation d. oxidation e. cleavage 4. In what kind of reaction is water used to separate two of the building blocks of a macromolecule? a. hydrolysis b. hydration c. condensation d. oxidation e. cleavage 5. What type of reaction is responsible for the attachment of a fatty acid to the glycerol backbone of a phospholipid? a. condensation b. hydrolysis c. hydrophobic d. oxidation e. reduction 6. Which part of an amino acid is responsible for the different properties of each amino acid? a. the central carbon b. the carboxyl group c. the R group d. the amino group e. a and c 7. What is the highest level of structure exhibited by a protein with a single subunit? Tertiary structure. 8. What property of cell membranes is typified by the dynamic nature of membranes that includes the movement of lipids and proteins laterally through the membrane? a. its fluidity b. its mosaic nature c. its hydrophobicity d. its hardness e. its brittleness 9. You are testing the activity of an enzyme under various conditions and find that the activity initially increases as temperature increases. However, at higher temperatures, there is a rapid decrease in enzyme activity after the enzyme registers maximal activity at 42В°C; your tests result in the absence of activity above a temperature of 60В°C. What is the explanation for this phenomenon? Initially, increases in temperature accelerate the speed of molecular motion which will speed up the reaction. The drop in enzyme activity after reaching a peak at 42В°C is due to denaturation of the enzyme at higher temperatures. Since the enzyme's shape is altered drastically by denaturation, it ceases its functioning. 10. You are studying cellular membranes from two different sources. One of them has a significant cholesterol content; the other lacks cholesterol entirely. Which one would be likely to be more flexible? The cholesterol-containing membrane would be more flexible. Cholesterol disturbs the close association of membrane phospholipids leading to increased membrane flexibility. Which of the membranes being studied would be most likely to have come from bacteria? Bacterial membranes generally lack cholesterol. Consequently, the membrane lacking cholesterol would be most likely to have come from bacteria. 11. What common feature of plants and bacteria might explain why cholesterol does not seem to be necessary for maintaining membrane flexibility in these two types of organisms? Both plants and bacteria have cell walls that support and protect the cell membrane perhaps making the flexibility brought to membranes by cholesterol unnecessary. While these cell walls perform the same function with regard to protecting the cell membrane, their compositions are quite different. Furthermore, removal of the cell wall of either organism renders them extremely fragile. 12. What type of membrane protein is most likely to serve as a transport molecule? a. peripheral proteins c. transmembrane proteins e. none of the above b. lipid-anchored proteins d. acidic proteins 13. Lipid-anchored proteins a. have been implicated in the transformation of normal cells into cancer cells b. are attached to the phospholipid bilayer via carbohydrates c. can act as receptors for hormones, neurotransmitters, and growth factors d. are connected to the phospholipid bilayer via fatty acids e. a, b, and c 14. What words below best describe the movement of molecules directly through the membrane from an area of high concentration to an area of low concentration? a. facilitated diffusion b. simple diffusion c. active transport d. passive transport e. b and d 15. A substance X moves across the cell membrane with the help of a protein molecule that provides a hole through which it can pass. What word(s) below accurately describe that protein? a. channel protein b. integral protein c. transmembrane protein d. carrier protein e. a, b, and c 16. A substance Y moves across the cell membrane with the help of a protein molecule that provides a hole through which it can pass. The hole, however, is only open periodically. What word(s) below accurately describe that protein? a. transmembrane protein b. integral protein c. gated channel d. carrier protein e. a, b, and c 17. A substance X moves across the cell membrane with the help of a protein molecule that provides a hole through which it can pass. What word(s) below accurately describe the transport that has occurred? a. active transport b. simple diffusion c. facilitated diffusion d. passive transport e. c and d 18. A substance Z moves across the cell membrane from an area of low concentration to an area of high concentration with the help of a protein molecule that binds to it. A subsequent shape change in the protein helps it to convey Z across the membrane. What word(s) below accurately describe that protein? a. channel protein b. integral protein c. transmembrane protein d. carrier protein e. b, c, and d 19. A substance Z moves across the cell membrane from an area of low concentration to an area of high concentration with the help of a protein molecule that binds to it. A subsequent shape change in the protein helps it to convey Z across the membrane. What word(s) below accurately describe the type of transport that has occurred? a. active transport b. simple diffusion c. facilitated diffusion d. passive transport e. c and d 20. Which bacterial organelle serves as a protective layer on the outside of some prokaryotes and is responsible for the infectious properties of certain bacteria? a. mesosome b. capsule c. cell wall d. flagella e. pili 21. In which cellular location would you expect to find high levels of rRNA synthesis? a. nuclear envelope b. chromosomes c. mesosomes d. nucleolus e. ribosome 22. What microtubule-containing structure organizes the cytoskeleton prior to mitosis in animal cells? a. basal bodies b. centrioles c. chromosomes d. rough ER e. mitochondria 23. If a cell is heavily involved in the synthesis of proteins that are conveyed to the Golgi complex before being secreted from the cell, what organelle would you expect to be prominent in that cell? Rough endoplasmic reticulum. 24. Which of the following is not a function of the smooth endoplasmic reticulum? a. the synthesis of steroid hormones d. reactions that convert non-toxic to toxic substances b. glucose mobilization e. processing of calcium ions c. breakdown of fats 25. Which organelle's job is to modify, package, and prepare cellular products for their final destination and/or secretion? Golgi complex. 26. Which organelle is responsible for creating toxic byproducts (peroxides) of normal cellular reactions and then destroying them before any severe damage can be done? Peroxisomes. 27. You place a nutrient-containing medium attractive to living bacteria open on a benchtop after first boiling the medium to sterilize it. What happens? After a short while, bacteria floating in the air fall into the medium, grow, reproduce and foul the medium. If you place the nutrient-containing medium in a glass vessel, boil it and then allow the vessel to sit on your desk for two weeks, what happens? Boiling the medium kills any microorganisms originally floating around in it. Since the vessel is sealed, any microorganisms in the air cannot get into the medium. Consequently, no microorganisms can get into the medium and grow. It should remain uncontaminated by the growth of these microorganisms. What is the boiling of the medium now called? (Hint: the process is named after the person who conducted similar experiments). Pasteurization. 28. Which organelle is responsible for moving organelles around inside the cell? Microtubules. 29. Which element of the cytoskeleton is involved in the contraction of specialized muscle cells? a. microtubules b. microfilaments c. actin filaments d. tubulin e. b and c 30. What single trait is most important in distinguishing eukaryotic from prokaryotic cells? This trait is suggested by the names prokaryote and eukaryote. a. Eukaryotes have no membrane-bound organelles c. Eukaryotes have no nuclei e. b and d b. Prokaryotes have no membrane-bound organelles d. Prokaryotes have no chloroplasts 31. What are some differences between plant and animal cells? Plants cells have cell walls that provide strength and rigidity to plants; animal cells do not. Plant cells are photosynthetic and contain chloroplasts; animal cells are not photosynthetic and do not possess chloroplasts. Plant cells usually have a large central vacuole used for the storage of water and other substances; animal cells do not. Animal cells lack cell walls and are thus more flexible than plant cells. Animal cells contain organelles that are not as prominent in plant cells like lysosomes and centrioles. Using BioInquiry in Large Classes Integrating Components into the Lecture Quite often when teaching General Biology, instructors take the microscope for granted assuming that all students, even non-majors, have used one вЂ” and they are probably right. However, the principles of microscopy are fairly accessible even though there is some math involved. Ask your students what the most important thing that a microscope does is. They will usually answer magnification, but, of course, the correct answer is resolution. Explain this to your students using the equation for resolving distance (see Question #1 under the CD-ROM questions above). Use Section 4.1 of the CD-ROM to illustrate the improvement in resolution as you move from primitive light microscopes to electron microscopes. See if your students can use the equation to explain why resolution increases with an electron microscope. Section 4.2 of the CD-ROM is divided into two major sections, the first dealing with condensation, hydrolysis, and the synthesis of three of the groups of macromolecules and the second dealing with biological membranes (membrane structure and transport, diffusion and osmosis). The CD-ROM illustrates these principles quite well. I always describe them to the students, but the animations/movies of osmosis, diffusion, simple difffusion, facilitated diffusion, and active transport are excellent and may be used in either the lecture or the laboratory session. You should also recommend that your students go to the CD-ROM on their own if they are having trouble understanding the concepts as presented in class. Section 4.3 emphasizes the differences between plant and animal cells and between prokaryotes and eukaryotes. For clarification, send your students to this part of the CD-ROM. The animation in which a student can enter the cell and look around is unique and effective. Students can click on different organelles after seeing what they look like and information on the organelle's function pops up for the student to look at. On the plants vs. animals and prokaryotes vs. eukaryotes pages, the student can also click on the cells. As they pass the cursor over different cell organelles, the label for each organelle appears pointing to the organelle in each type of cell. If the student clicks on the organelle, information on that organelle pops up. The exercises in this section should help the students study for exams and should be an effective learning tool. Section 4.4 asks the question вЂ” where do cells come from? The first part of this section describes Pasteur's experiment that disproved spontaneous generation. I usually talk about this experiment in lecture for a couple of reasons. First, its methodology is not overly complicated. Second, the results are clear and their implications easy to discern. The animation on the CD-ROM helps to clarify the experiment even further. Refer your students to the animation to supplement your lecture presentation or, if you have the facilities, show it in lecture; it will only takes a few seconds. Section 4.4 also serves as an introduction to viruses featuring bacteriophages and HIV. The pictures included in this section are colorful and excellent and serve as a good supplement to the lecture material. Read More About It The DNA Story The story of the discovery of the structure of DNA is an interesting one that has been the subject of a couple of excellent books. The Double Helix by James Watson is a brief, well written account of the discovery as told by Watson, one of the discoverers. His is an honest and frank account of the events leading to this important discovery. Another book written on a larger scale and covering a broader spectrum of events including the work of Watson and Crick is The Eighth Day of Creation by Horace Freeland Judson. It may be a bit more objective simply because it is not written by one of the principal players. Both are fascinating books accessible to the non-major that give accurate and sometimes unflattering pictures of the inner workings of science. There is also available a video of a movie called The DNA Story in which Jeff Goldblum plays Watson. It also occasionally shows up on cable television. Viruses Viruses often fascinate students, probably for the reason that there is no question that viruses are relevant to their lives. In addition, the way they work is inherently interesting. It is probably best to stay general here though. Save the really detailed stuff for a higher level course. Stress that viruses are not really alive, since they must take over the reproductive machinery of their host. They are not вЂњself-sufficientвЂќ in terms of their ability to reproduce. Also, recommend some books for them to read about the subject. The best book for non-majors is probably The Hot Zone by Richard Preston. It reads like a suspense/horror novel but is true and as scary as anything Stephen King ever wrote. It is also informative and accessible for non-majors. I have only one major problem with the book. I am not happy with the extent to which the author stresses the nonliving aspect of viruses. He could be more forceful about it than he is and could leave some readers without an understanding of this key point. Despite this objection, I recommend the book highly. Another book that is just as scary (maybe even more so) but much more subtle about it is The Coming Plague by Laurie Garrett. This book is much more scholarly and broader handling of the problem of emerging diseases. It deals with a number of different viruses including the Ebola and Warburg viruses, the hantaviruses, HIV, and a number of other viruses. It is filled with statistics and analyses and takes a somewhat sociological view. The chapter on AIDS and HIV is over one hundred pages long. Realistically, students are likely to find it less riveting than The Hot Zone but it is worth their attention. Both are available in paperback. Supporting the Lab The teaching laboratory is again a good place to use these elements of the Learning System in a classroom setting. A number of the features on the CD-ROM will be helpful for students preparing for lab exercises. We do a lab exercise, as do many instructors, in which students build molecular models including water, glucose, amino acids, and fatty acids/lipids. A review of the pertinent section of the CDROM (Section 4.2) before and during the lab should clarify condensation and hydrolysis reactions. The animations of condensation and hydrolysis of carbohydrates, lipids, and proteins are excellent and serve as either a prelude or adjunct to such a laboratory exercise. Students could look at these animations during the lab or before they get there. We give a quiz every week in lab periods; 70% of each quiz covers the previous week's lab exercise, the remaining 30% of the quiz covers the lab scheduled for that week. To encourage students to look at the animations before they arrive in class, you could tell them that quiz questions will be taken from the material they cover. In a laboratory exercise dealing with cell structure, Section 4.3 of the CD-ROM dealing with cell organelles would be helpful. Again, students should look at this material prior to arriving at lab, but it would not hurt to use the animation during the lab exercise as well. These particular animations are extremely effective and informative. Most Introductory or General Biology courses include a lab illustrating membrane function, diffusion, and osmosis. Both are clearly presented on the CD-ROM (Section 4.2) and should be reviewed before such an exercise. Students once again can be encouraged to look at this material prior to a quiz. The effect of isotonic, hypertonic, and hypotonic solutions on red blood cells and plant cells are handled in this section. This is a topic or concept that often gives students difficulty, but it is covered well on the CD-ROM. Answers to Review Questions 1. Mendel's writings were published in a rather obscure journal that was not widely distributed. He was also ahead of his time in his approach to the study of inheritance. It might be argued that the rest of his contemporaries were not ready to accept his ideas even if they were aware of his work. He even sent information about his work to other botanists working on inheritance; he was essentially ignored and one of them advised him to work on hawkweed, a plant with complicated genetics that would have been difficult to use in such studies. 2. Before the cell theory could be developed, cells had to be discovered. Their discovery required the invention of the microscope and, in fact, the understanding of cell structure and function paralleled the development of microscopes. The microscope was first invented in the 17th century and thus cells were not discovered until then. Thus since there were no microscopes in antiquity, there could have been no cell theory or even the beginnings of a cell theory. 3. Leeuwenhoek made excellent lenses and microscopes that could magnify images up to 200 times and was the first person to observe living single-celled microorganisms, among them organisms he called animalcules that he found in the water from a pond near his home. He was also the first to see bacteria and began to see such creatures wherever he looked (in mud, teeth scrapings, drinking water, etc.). 4. Schleiden was primarily interested in plant cells and tissues and their formation, while Schwann was interested in animal cells and tissues and their formation. Both were interested in the origin of new cells and their implications for the organisms (growth, for example). Schleiden tested three hypotheses and came to believe that cells arose from preexisting cells. He thus believed that plant growth was at least partially the result of the production of new cells. After speaking to Schleiden, Schwann began to think in the same way about animals. He was able to demonstrate that this actually happened in the developing embryo and that non-cellular substances (teeth, feathers, hair, fingernails, etc.) arose from cells. In 1839, he published a book that reprinted Schleiden's paper and ended with a chapter on the Cell Theory. Thus, their major difference in interest was in the organisms with which they worked. In all other major ways, they were fully compatible. 5. The major tenets of the Cell Theory are: (1) cells are the fundamental units of life, (2) all organisms are composed of one or more cells, and (3) all cells arise from preexisting cells. The third tenet was added a bit later. 6. All of the four major groups of macromolecules are based upon carbon; thus, they are all organic compounds. Because of carbon's ability to form four covalent bonds, it can form a huge variety of cyclic or linear carbon backbone chains from which branches can form. All of them are built from smaller organic building blocks that are formed by similar chemical reactions (condensation reactions). Once formed, they can also be broken down by similar chemical reactions (hydrolysis reactions). In addition to carbon, they all contain hydrogen and oxygen. Some of them usually contain significant amounts of phosphorus (nucleic acids, lipids; proteins and carbohydrates to a lesser extent) and nitrogen (nucleic acids, proteins, carbohydrates and lipids to a lesser extent). Three of the groups (carbohydrates, proteins, nucleic acids) are polymers in which smaller identical or similar monomers are hooked together end-to-end repeatedly by condensation reactions to form long chains with fairly large molecular weights. Lipids differ in that they are not polymers; instead they are assembled from a few building blocks hooked together by condensation reactions. Lipids also display more structural diversity than the other three groups (forming structures with carbon rings and carbon chains). Among the polymers, only carbohydrates typically form branched structures. Carbohydrates, proteins, and nucleic acids are usually fairly soluble in water, while lipids are defined by their insolubility in water (hydrophobicity). Proteins are the most complex of the macromolecules, the most varied in terms of function and the most ubiquitous in cells. Their function is determined by their primary and higher order structures, and they play multiple roles in living organisms. Both DNA (the double helix) and proteins (multisubunit proteins) can combine more than one chain to form a functional molecule; lipids and carbohydrates generally do not do this. Carbohydrates are the only macromolecules that normally form branches. 7. They are important for energy storage and transfer (carbohydrates, lipids, proteins, when the organism is under nutritional stress, nucleic acids [ATP, NAD, FAD are nucleic acids]), metabolic processes (nucleic acids/enzymes, protein/enzymes), structural components (carbohydrates, lipids, proteins), hormones and other cellular messengers (lipids, nucleic acids [as second messengers], proteins), and the storage of genetic information (nucleic acids). 8. Cell membranes separate the contents of cells from their surroundings and also surround compartments within the cell that isolate and concentrate cell functions and processes. They provide a pathway for exchange of materials and signals, and thus play a role in communication within and between cells. They allow some things to pass through them and restrict and regulate the movement of other substances through them. 9. Materials that are small enough and/or hydrophobic enough can pass through membranes by moving down their concentration gradients in a process called diffusion. Water, which is hydrophilic, but very small, passes freely through membranes moving down its own concentration gradient via osmosis. Neither diffusion nor osmosis requires the expenditure of energy. Large and/or hydrophilic molecules can pass through membranes as well, usually through transport proteins, integral membrane proteins that regulate the movement of substances across membranes. These come in two varieties: channel proteins and carrier proteins. Channel proteins allow materials to pass through them. Some of them possess a gate that must be opened to let them pass through. Carrier proteins must bind to the molecules being transported and change shape for transport to occur. Channel proteins allow molecules to pass through going down their concentration or electrochemical gradients. Some carrier proteins also allow materials to pass down their gradients as well. When channel or carrier proteins assist in moving molecules across a membrane from an area of high concentration to an area of low concentration, the process is called facilitated diffusion. Simple diffusion, osmosis, and facilitated diffusion are collectively called passive transport and require no expenditure of cellular energy. On the other hand, some carrier proteins move substances up their concentration gradients. Such movement is called active transport and does require the expenditure of energy by the cell. Sometimes molecules and even whole cells can move across the membrane in bulk. If such materials move into the cell by an inpocketing of the membrane (pinocytosis) or by extending pseudopodia to engulf a cell (phagocytosis), the process is generally referred to as endocytosis. If vesicles within the cell fuse with the cell membrane, their contents will be released to the space surrounding the cell, a process called exocytosis. Cells that secrete materials do so by this method. Both endocytosis and exocytosis are examples of active transport since they require the expenditure of energy by the cell. 10. Cellular proteins play a number of roles within the cell. As enzymes, they catalyze or speed up chemical reactions within the cell, outside the cell, or in its membrane. Proteins form the cytoskeleton and other important structures both inside and outside of the cells. Membrane proteins act as couplers, connecting one cell to another. Other membrane proteins are involved in the transport of materials across membranes. Some proteins (usually in the membrane) function in cell identification. A number of proteins are involved in the defense of organisms against infection (antibodies, interferon, cytokines). A number of proteins act as hormones or messengers and play regulatory roles, signaling cells to respond to their environments in specific ways. 11. Osmosis should not affect shark cells at all. Since they are isotonic relative to their environment, there should be no net movement of water into or out of shark cells. 12. If solutes are too high or too low in concentration within or outside of a cell, too much water may leave or enter a cell by osmosis. If too much water enters, the cell may ultimately swell and burst, killing it. If too much water leaves the cell, it will shrink and/or the intracellular concentrations of other solutes may exceed normal tolerance levels severely damaging or killing the cell. Furthermore, certain solutes, e.g., hydrogen ions, may create toxic environments if their concentrations drop too low or rise too high. 13. Hydrophilic atoms or molecules are unable to pass directly through the membrane, because membranes are hydrophobic barriers that, by definition, will not allow molecules that are hydrophilic pass through them (with the exception of water because of its extremely small size). Cellular transport proteins and, to some extent, the processes of exocytosis and endocytosis, can overcome this barrier. 14. Both prokaryotes and eukaryotes are surrounded by a plasma membrane, although these membranes are somewhat different. Both eukaryotes and prokaryotes use DNA as their genetic material. Both eukaryotes and prokaryotes carry out essentially the same metabolic processes with some specific differences. The major difference between prokaryotes and eukaryotes is that prokaryotes lack membrane-bound organelles like a nucleus or a mitochondrion. Prokaryotes also have less DNA than eukaryotes and that DNA tends to be complexed with many fewer proteins than eukaryotic DNA; it is referred to as naked or nearly naked DNA. Furthermore, DNA in eukaryotes is linear, while that in prokaryotes is circular. Prokaryotic ribosomes are smaller than those of eukaryotes. The cell walls of prokaryotes perform essentially the same functions as the cell walls of eukaryotes that have them, but are composed of fundamentally different substances. Eukaryotes exhibit much more diverse modes of locomotion than do prokaryotes as well. 15. Prokaryotic cells have relatively simple structures. They are surrounded by a cell membrane with a thick cell wall made of complex polypeptides and/or polysaccharides around the membrane. Some of their cell walls are further surrounded a capsule or slime layer. Their cell membrane serves as a selective barrier between the cell contents and its external environment. The cell wall serves a protective and support function. The capsule, when present, is a protective layer outside the cell wall. It gives certain characteristics to prokaryotes, like the ability of certain bacteria to be infective. Long, fingerlike projections called pili extend beyond the cell surface. They provide for the attachment of some bacteria to their hosts and sometimes to other prokaryotes. Through sex pili, they can exchange genetic material in a form of primitive sexual reproduction called conjugation. They often possess one or more long whiplike structures called flagellae that extend beyond the cell wall, spin, and propel the cell. They look simple because they have virtually no internal parts or organization and no nucleus. They have one long circular DNA and numerous ribosomes within their cytoplasm. The nucleoid is the region within the cytoplasm in which was contained the DNA. Mesosomes are infolded areas of the plasma membrane that provide surface area for various metabolic reactions. 16. Eukaryotic cells are considerably more complex internally than prokaryotic cells. Unlike prokaryotic cells, they possess membrane-bound organelles. The nucleus is the most obvious organelle and its control center. It is covered by a porous double membrane and contains the cell's hereditary material which is stored in a number of linear structures called chromosomes. The nucleolus is a small, irregularly shaped structure of DNA and RNA within the nucleus. It is not membrane-bound and serves as the site of rRNA synthesis. The cell wall is a covering outside the plasma membrane that provides support and protection for cells. The plasma membrane is a phospholipid bilayer with proteins scattered throughout; it serves as a selective barrier between a cell's contents and its surroundings. Centrioles are found outside of the nucleus and adjacent to it in animal cells; they are composed of microtubules, play a role in organizing parts of the cytoskeleton, and serve as an attachment point for spindle fibers during cell division. The endoplasmic reticulum is a convoluted sheet of membrane enclosing a space within the cell. It forms a network of membrane that spreads throughout the cell. It comes in two varieties вЂ” the rough endoplasmic reticulum (RER), and the smooth endoplasmic reticulum (SER). The RER is composed of hollow sheets of membrane (called cisternae) enclosing a space and is often found in stacks within the cell near the nucleus. It is covered with ribosomes and serves as a site of the synthesis of secretory proteins and proteins found embedded in the cell membrane. SER is a collection of membrane tubes and vesicles continuous with the RER. It plays a role in various activities in different cells: it synthesizes steroids, mobilizes glucose, is involved in the breakdown of fats, carries out reactions that break down toxic substances, and sequesters calcium ions. The Golgi complex is a stack of membrane-enclosed sacs that serves as a packaging center for the cell. Within it, cellular products are modified, packaged, prepared, and stored for their final destination and/or secretion. The cell contains a number of vesicles that serve various purposes. Food vesicles contain food material taken in from the extracellular space by endocytosis. Lysosomes contain digestive enzymes and fuse with food vesicles leading to the digestion of the food they contain. They also process cell debris and worn out or unneeded cell organelles. Peroxisomes contain enzymes that break down or produce toxic peroxides. Mitochondria are found in plant and animal cells and possess a double membrane. The inner membrane is thrown into folds (cristae) to increase surface area and contains enzymes that help to synthesize ATP; thus mitochondria are often described as the cell's energy factory. They also contain their own DNA and are semiautonomous. Chloroplasts are surrounded by a double membrane as well; they also contain their own DNA and are considered to be semiautonomous. They are found only in cells that perform photosynthesis and are responsible for that process. They contain an intricate assemblage of internal membranes that contain the photosynthetic pigments; it is here that photosynthesis occurs. Flagellae and cilia that project from the cell surface play a role in cell locomotion. The cytoskeleton is a network of protein fibers in the cytoplasm that performs various functions. It is composed of three types of fibers: microtubules, microfilaments, and intermediate filaments. Microtubules, made of tubulin, are involved in cell movement, the movement of cellular organelles, and the parceling out of chromosomes during cell division. Microfilaments, made of actin, move and anchor organelles and mRNAs through the cytoplasm, are involved in cell movement and reinforce and support the cell membrane. They are responsible for the ability of muscle cells to contract. Intermediate filaments, made primarily of keratin, form a scaffold within the cytoplasm. 17. Instructions for building proteins that are to be secreted by cells or that are destined for particular cellular locations pass from the nucleus to the RER where ribosomes synthesize them. After their synthesis on the RER, the proteins are passed in sequence to the SER and the Golgi complex within which they are altered in various ways to prepare them for ultimate destination. Vesicles bud from the Golgi apparatus and convey the proteins to their destination whether it be secretion at the cell surface or localization to some cell organelle. The passage from one cellular compartment to the next with continuous processing resembles a factory production line. 18. Cilia and flagellae are responsible for cell movement. In cross section, cilia and flagellae are structurally identical. The organization of the microtubules of which they are composed is essentially identical. The major difference in their structure is that cilia are generally shorter and much more numerous. While a cell will have at most only a couple of the longer flagellae, the shorter cilia often cover the whole cell surface or significant portions of the surface. Flagellae achieve cell motion by pushing against the medium in which the cell finds itself thus propeling the cell forward. Cilia beat back and forth in unison and produce motion. They can be seen beating in waves across the cell surface and look much like a breeze blowing across a field of wheat. 19. Both animal and plant cells are eukaryotic cells that possess plasma membranes and many of the same organelles (the nucleus, mitochondria, RER, SER, Golgi apparatus). However, there are some fundamental differences. Plant cells possess cell walls and are photosynthetic since they possess chloroplasts, which are not found in animal cells. Plant cells are also distinguished by their large central vacuoles used for the storage of water and other substances. Animal cells lack cell walls and thus exhibit more mobility because of their more flexible cell surface. Animal cells contain other organelles, like lysosomes and centrioles that are not found often in plants. CHAPTER 5 DNA: WHERE ARE THE GENES? Lecture/CD-ROM Outline Overview I. Instructions for building a whole organism are found in single-celled zygote A. Instructions determine type of organism & all its traits B. The hereditary units are called genes C. With each cycle of cell division, all genes are carefully copied & passed on to each new cell D. Thus, each cell has its own complete set of genes II. By the late 1800s, the nature of genes was not yet known A. Scientists thought genes must be very tiny B. Search for genes began under microscope What Cellular Structure Holds the Genetic Information?: Chromosomes I. Walther Flemming, German anatomist, 1880s - found earliest clues to physical nature of gene A. Had fine scope lenses at his disposal - oil immersion lenses got 1000X magnification with great resolution (the amount of detail that can be seen in magnified image) B. Used a variety of chemical dyes that preferentially cling to certain cellular structures 1. Dyes stained the structures distinctive colors 2. Improved contrast between tiny cellular parts; unfortunately staining cells usually kills them C. Published elaborate drawings of dividing cells from salamander embryos 1. Drew threadlike structures that were essentially invisible when cells were not dividing 2. These structures were thick & sausagelike during division 3. Had an affinity for colored dyes so he called them chromatin (today it describes the decondensed, threadlike chromosomal material of nondividing cell) - DNA, RNA, protein 4. Today, chromosome describes the structures visible during cell division II. Chromosomes are apportioned to daughter cells during mitosis A. Flemming reconstructed sequence of events during cell division which he named mitosis 1. Mitosis is a form of cellular reproduction in which parent cells give rise to cells that are genetically identical to each other and the parent cell 2. Does not involve combining genetic information from two different parents; actually it is a form of asexual cell reproduction B. Occurs in eukaryotic cells & is used for growth, repair, development, & cell replacement C. Involves vast reorganization of cell interior: disappearance of nuclear envelope, chromosome condensation & movement, and cytoskeleton changes 1. Mitosis called equational division since daughter cells at end have the same number of chromosomes as the parent cell forming them 2. Diploid cells give rise to diploid daughter cells 3. Mitosis is continuum with each phase moving dynamically into next What Cellular Structure Holds the Genetic Information?: Mitosis and Cytokinesis I. The steps of mitosis - before mitosis, chromatin is copied fully, a process called replication A. Interphase - each chromosome replicates itself, doubling DNA content B. Prophase - mitosis start; chromatin begins to condense into a full set of rodlike chromosomes 1. Chromosome consists of two identical rods (sister chromatids) connected at a point along length (centromere) four arms emanate from it; spindle fibers attach at centromere 2. At first, the doubled structure of chromosomes cannot be seen 3. As mitosis proceeds, chromosomes get even more compact due to tighter coiling chromosomal DNA; soon becomes clear that each chromosome contains two chromatids 4. Flemming compared fine structure of two rods of chromosome duplex; each point along entire length of rod was exactly duplicated (could tell from chromatid fine detail) 5 The nuclear envelope also disappears in late prophase C. Metaphase - doubled chromosomes move toward the cell center & align in a flat plane at dividing cell equator 1. In animal cells, chromosomes are joined to centrioles by spindle fibers made of microtubules D. Anaphase - centromeres of duplex chromosomes divide; sister chromatids (now chromosomes in own right) move apart, pulled to opposite poles of cells; distance between them increases 1. Process not yet well explained E. Telophase - new chromosomes, no longer double, cluster at opposite poles; compact sausagelike structure unravels; returns to nondividing, threadlike form 1. Two nuclear envelopes assemble surrounding the two new sets of chromosomes 2. Cell nucleus has divided & one full copy of each chromosome distributed to each daughter cell 3. Cytokinesis then follows which splits the parent into two identical daughter cells (see below) 4. Each daughter cell now enters interphase where it may or may not prepare to divide again II. During mitosis, the cytoplasm of the dividing cell is divided into two compartments, each of which will become a new daughter cell with its own nucleus - process is called cytokinesis A. Differs considerably between plant & animal cells, reflecting presence of rigid plant cell wall 1. Plants - membranous vesicles gather at dividing cell equator; contain materials that will form the cell wall & fuse, forming cell plate vesicles, that then fuse with cell membrane вЂ”> two cells 2. Animals - cleavage furrow forms around dividing cell periphery; furrow becomes progressively deeper until it pinches cell & divides its contents into two cells III. During cell division, no cellular structures are as meticulously handled as are chromosomes A. At the beginning of cell division, each chromosome is doubled & consists of two identical chromatids joined at centromere B. Chromosomes are doubled prior to mitosis & meiosis during interphase; needed for both processes 1. Each chromosome is replicated exactly forming two chromatids joined by common centromere 2. Replication must be precise with each allele replicated 3. Chromosome number does not increase after replication, but DNA content doubles C. When chromatids separate, each daughter cell gets one chromatid (now a chromosome) 1. Results in each cell getting a complete & exact copy of parent cell chromosomes 2. Flemming's observations made chromosomes prime candidate for carriers of heredity What Cellular Structure Holds the Genetic Information?: Homologous Chromosomes I. Chromosomes come in matched pairs - can tell because they have some fine structural detail; they have distinct identities with certain individual features (size & shape) A. Chromosomes with the same features appeared in nuclei of different cells within same individual & in cells from different individuals of same species 1. Chromosome number is characteristic of species - humans (46), chimpanzee, our closest evolutionary relative (48), Mendel's peas (14), fruit flies (8), some species of ferns (>1000) 2. Other species may have same number of chromosomes, but members of any one species ordinarily share same number of chromosomes B. Almost all mature plant & animal chromosomes occur in homologous pairs (alike in size, shape) 1. Human cells have diploid number of 46 (23 homologous pairs) 2. After mitosis, there are two daughter cells each with 46 chromosomes with 23 homologous pairs C. In males of some species, one pair of homologous chromosomes is not exactly homologous 1. Humans - one member of the pair is small (Y), the other large (X) 2. Grasshoppers - males have single unpaired chromosome whereas females have corresponding homologous pair 3. These chromosomes help determine the sex of organism (sex chromosomes) II. Occurrence of chromosomes in pairs coincides perfectly with Mendel's description of hereditary factors which also occur in pairs A. Discoveries in cytology & Mendel's genetics were integrated to give rise to a new science of cytogenetics B. The idea that Mendel's Laws are a consequence of chromosomal organization & behavior during cell division was discovered independently by at least four different cytogeneticists in 1902 & 1903 1. Walter Sutton, young American grad student articulated it best (the chromosomal theory of inheritance) - hereditary factors (the genes) are part & parcel of the chromosomes 2. He said, "The two members of each homologous pair of chromosomes carry alleles for the same genes & therefore affect the same traits." 3. The two chromosomes of homologous pair are not often identical, although they carry the code for the same traits (genes) - alleles can differ (heterozygous) or be the same (homozygous) III. Genes reside at specific positions on chromosomes called loci (singular, locus) A. Sickle cell anemia allele - on human chromosome 11 near the tip of chromosome short arm (p arm) 1. Either the same allele or a different one (maybe the normal form) appears at same position on homologous chromosome 2. Position is designated 11p15.5 - 11 for chromosome number, p for short arm, 15.5 for exact position on short arm, know positions of 1000s of genes (more every day), e.g. (see below) B. Gene for early onset breast cancer - 17q21 about midpoint of long arm of chromosome 17 C. Distinction between genes, loci, & alleles - they physically represent same piece of DNA, but differ operationally 1. Gene - segment of DNA that deternines a particular trait 2. Locus - where that gene is located on a particular chromosome 3. Allele - the variation of the gene's trait that is expressed; for most traits, each allele will occur in pairs just like chromosomes (one maternal & one paternal) IV. Chromosomal theory of inheritance presented in 1903 not readily accepted by everyone at the time; there were important problems to resolve before it could be A. Sexual reproduction where male (sperm) & female (egg) gametes fuse to form zygote (fertilization) B. Number of chromosomes donated by male & female is equal; half of zygote's chromosomes from mother, other half from father; in each pair, one chromosome maternal, the other paternal C. E. B. Wilson (1895), prominent cytologist - stated that the equivalence of the chromosomes contributed by the two sexes "indicates that the chromatin is the physical basis of inheritance." 1. If male & female donate equal number of chromosomes, the number of chromosomes in each succeeding generation would double & soon become impossibly large but. . . . 2. We know that chromosome number within species stays constant from generation to generation 3. Thus, there must be a mechanism for preventing chromosome doubling at fertilization Meiosis: The Reduction of Chromosome Number I. Gametes produced in reproductive organs: testes & ovaries in animals, anthers & ovaries in flowering plants; produced by cell division process that is not mitosis, but a different type called meiosis A. Mitosis & meiosis have some similarities, but they differ in important ways that reflect the special role of gametes; meiosis is the prelude to sexual reproduction 1. Multiplies the number of cells by cell division but also reduces the chromosome number in each daughter cell to exactly half the number present before meiosis 2. Daughter cells get one member of each homologous pair & thus one allele for each gene; thus called a reduction division 3. Mitosis produces two daughter cells; meiosis produces four daughter cells B. Cells with both members of each homologous pair are diploid 1. In humans & many other organisms, all body cells except gametes are diploid 2. Cells with only one member of each homologous pair are haploid (only gametes in humans II. By the 1880s, meiosis had already been described in the ovaries of Ascaris A. Ascaris is a parasitic roundworm, perfect organism for this kind of study on meiosis & gametes 1. Ascaris is large worm (almost a yard long) that lives in host digestive tract & lays copious eggs that are passed to outside with host's feces 2. The eggs infect new hosts who eat vegetation grown in contaminated soil 3. Its body is largely occupied by reproductive tissue packed with meiotic cells B. Oskar Hertwig, German zoologist, 1880s - described two unusual cell divisions in Ascaris ovaries 1. Together, the two divisions constitute meiosis 2. Before meiosis, chromosome number of Ascaris is four, after meiosis, each gamete has two C. Only cells destined to become gametes do it; steps resemble mitosis, but daughter cells end up with half of chromosomes in parent cell D. Accomplished with two divisions, one right after the other; chromosomes however, replicate only once, before first cell division 1. Meiosis I results in two haploid cells that undergo another division to make two more daughter cells, each haploid; these cells function as sperm, eggs or spores depending on the species 2. Meiosis II results in splitting of the two chromatids of each chromosome III. The steps of meiosis A. Prophase I - chromatin condenses into compact chromosomes, the nuclear envelope disappears, members of homologous pairs become closely affiliated 1. Chromosomes become visible by coiling of chromosomal DNA; eventually seen to be doubled 2. Nuclear membrane breaks down & chromosomes attach to spindle fibers 3. Chromatids of different members of pairs become perfectly aligned (synapsis) 4. Synapsis results in an exchange of bits & pieces of chromosome between two members of homologous pairs B. Metaphase I - aligned pairs of replicated chromosomes move to equator of dividing cell; members of pair move there together; moving pairs of duplex chromosomes called tetrads 1. The lining up of the pairs is random & is the basis for Mendelian independent assortment C. Anaphase I - begins when members of homologous pairs separate from each other & move toward opposite poles of cells 1. The separation of members of a pair of homologous chromosomes is independent of the separation of any other pair; they undergo independent assortment (Mendel) 2. Mendelian principle of segregation occurs here & is the basis of reduction division 3. Chromatids remain intact & are not broken apart at this time D. Telophase I - chromosomes are clustered at opposite poles of the dividing cell; each cluster contains one member of each homologous pair; chromosomes partially decondense 1. Nuclear envelope may or may not reform around each chromosome set (species dependent) 2. Cytokinesis divides cytoplasm of cells creating two daughter cells; each has half the number of chromosomes as the parent cell E. Interkinesis - short-lived stage between the two meiotic divisions; meiosis not complete until duplexes separate & are distributed to two daughter cells F. Prophase II - partially unraveled chromosomes condense again in both of the cells; some cells skip this phase & go straight to Metaphase II G. Metaphase II - chromosomes move to cell equator; duplex structure apparent; no longer any homologous pairs, so chromosomes line up singly across cell middle attached to spindle fibers H. Anaphase II - centromeres divide & duplex chromosomes separate with newly formed single chromosomes moving to opposite poles I. Telophase II - chromosomes cluster at opposite poles; chromatin decondenses into interphase configuration 1. Nuclear envelopes assemble; cytokinesis вЂ”> four haploid cells 2. These cells will never undergo further division but will function in sexual reproduction The Cell Cycle I. Mitosis, meiosis & cytokinesis are single steps in the cell cycle - a repetitive sequence of events that characterizes the life cycles of all cells A. Cells not in the process of dividing are between mitotic divisions & said to be in interphase 1. Flemming referred to them as resting cells - unfortunate since interphase cells are actively metabolizing & growing 2. Chromosomes are duplicated in preparation for the next round of division during interphase B. Loss of control of the cell cycle is implicated in many cancers; area of intense research II. Cell division is part of a cell cycle with two clearly visible phases - cell's life starts when mother cell divides resulting in two daughter cells & ends with death or when cell divides making two new cells A. M phase - mitosis & all its stages during which chromosomes are separated into two nuclei & cytokinesis during which nuclei are apportioned into two separate cells B. Interphase - not resting period as once thought; newly divided cell has complete chromosome set; if cell is diploid (like most), there are homologous pairs 1. Individual chromosomes exist as single, very long strands 2. Period of active metabolism (G1 phase for first gap); growth, taking in, processing of nutrients & energy; cell makes copies of many of its organelles (not including nucleus) & gets bigger 3. Chromosomes replicated in preparation for division (S phase) III. Features of interphase A. Length of time a cell remains in G1 varies with cell type B. At some point, the cell gets a signal to proceed from G1 to next phase, the S (synthesis) phase 1. Cell growth ceases at this time; most important feature is synthesis of genetic material 2. By S phase end, chromosomes have doubled, copied in entirety; remain attached at centromere as sister chromatides; total number of chromosomes unchanged, but each one is doubled 3. Critical point of cell cycle, since cell is now committed to another round of division; cell proceeds to G2 C. During G2 phase, cell prepares for the upcoming M phase - separates end of S from next division D. G1, S, & G2 typically occupy ~90% of cell cycle; human cells - M lasts about one to two hours 1. In rapidly dividing cells (digestive tract lining, blood cells) - cycle is 16 - 24 hours 2. The cell cycles of more slowly dividing cells (child's liver) may last several months 3. Certain cells stop dividing altogether; such cells are often highly specialized & have lost the ability to divide (nerve cells in central nervous system) 4. Some cells are inhibited from dividing by some external factor - close proximity of other cells in full-grown adult liver prevents liver cells from dividing 5. Cells that have stopped dividing are locked in G0 phase; does not occur in cells that still divide IV. The cell cycle is highly regulated A. Most cancers can be traced to a breakdown in the mechanism that controls the cell cycle in a single wayward cell 1. Breakdown is heritable & is passed on to each daughter cell 2. If such a cell breaks free of its parent organ & takes up residence & uncontrolled growth elsewhere, cancer has metastasized or spread - learn to regulate the cell cycle вЂ”> cancer cure B. Cell cycle control is focused at two places in cycle or checkpoints - first just before genetic material synthesis, second at transition between G2 and M phase 1. Passage through checkpoints is controlled by agents in cytoplasm that trigger synthesis of genetic material & entry into mitosis & meiosis 2. Regulating agents are proteins whose cytoplasmic concentrations rise & fall in a controlled manner at different points in the cycle 3. If agent concentration is high -> cycle progresses, if low -> cycle is suspended, usually in G1 4. Agents activate other proteins, enzymes that start synthesis of duplicated chromosomes at checkpoint 1, stimulate chromatin condensation, etc. as it prepares for division at checkpoint 2 C. Regulating agents can be controlled by stimuli external to the cell (proximity of other cells) 1. If liver is tightly packed with other liver cells (like those from healthy adult organ), their close proximity sends message to cell to cease production of regulating agent 2. If liver is damaged or if a piece is removed surgically, cells surrounding lesion respond with increase in regulating agent & proceed through checkpoints to mitosis вЂ”> more liver cells 3. Replace lost or damaged cells & repair lesion 4. Other external stimuli (presence or absence of hormones) may accomplish the same task in other cell types D Regulating agents are controlled by factors inside the cell itself 1. Cells with UV light or carcinogenic chemical damage can detect their own problems 2. Rather than reproducing & passing injury on to progeny, damaged cells produce proteins that inhibit regulating agents вЂ”> the cell cycle is halted at one of the checkpoints 3. Damaged cell may even commit suicide - p53 is important in detecting damage & preventing injured cell from entering mitosis; p53 has been dubbed the "guardian of the genome" E. Control of the cell cycle is a multilayered operation 1. Internal & external stimuli activate or inhibit regulating agents 2. These, in turn, activate enzymes that make it more or less likely that the cell will divide 3. Internal checkpoints & guardians monitor cell health 4. Error at one or more steps in this operation can be disastrous, giving rise to uncontrolled growth; cancer can be the result of failure of a single step Why Do Some Genetic Traits Tend to Travel Together?: Linkage & Sex Linkage I. Meiosis explained why chromosome number did not double with each succeeding generation & led to acceptance of the chromosomal theory of inheritance II. Another problem for the theory was a lack of correlation between the number of traits & the number of chromosomes in any species; humans have 1000s of traits but only 23 homologous pairs A. All organisms have many more traits than chromosomes so each chromosome carries information for many, many traits 1. Reasonable to assume that genes found on the same chromosome can travel together but..... 2. Homologous chromosomes exchange bits & pieces of genetic material before they are divided up among gametes B. Grouping of many genes on one chromosome explains why the seven traits Mendel studied assorted independently 1. Peas have seven chromosome pairs but many more traits; most of them Mendel did not consider 2. Chromosomes follow independent assortment; individual traits do not assort independently unless they are found on different homologous pairs 3. Some feel Mendel was lucky to have chosen traits that assort independently; had he chosen traits on the same chromosome he would not have come up with independent assortment C. Exceptions to the Law of Independent Assortment found in the early 20th century by T. H. Morgan III. Chromosomes, not genes, follow the Law of Independent Assortment - demonstration A. Thomas Hunt Morgan, Columbia College (now University), embryologist - studied genetics of Drosophila melanogaster when funding was denied to study mammalian embryology 1. Drosophila has been the source of a great deal of our knowledge about fundamental genetics 2. Its genetics is the best known of all multicellular organisms & it is one of the most used animals in elementary genetics laboratories 3. Fruit fly - easily collected, live in half-pint milk bottles, eat simple diet of yeast grown on mashed bananas, has 14 day generation time so one can study many generations in short time 4. Its genome is now being sequenced 5. Has only eight chromosomes - three homologous pairs & one pair of accessory chromosomes: in female, they are XX, in males, they are nonhomologous XY B. Large collection of fruit fly hereditary variation is housed in labs worldwide - much of our knowledge of how genes are inherited & how they function at cell level comes from the fruit fly C. Sex of fruit fly determined by the accessory chromosome found in sperm that fertilizes egg 1. When female makes eggs, they all contain an X chromosome & one member of each of three other homologous pairs 2. Half of sperm get X & other half get Y so sperm determines the sex of fly (same with humans) IV. Calvin Bridges, undergraduate, 1910 - hired to wash Morgan's dishes; noticed white-eyed male fly crawling on bottle about to be washed A. Normal wild type fruit flies have brilliant red eyes so the white eyes were a mutant B. Morgan mated the white-eyed male to wild-type, red-eyed females 1. All of the offspring had red eyes вЂ”> looks like a Mendelian dominant trait 2. When Morgan mated F1 males & females вЂ”> 2459 red-eyed females, 1011 red-eyed males, & 798 white-eyed males; totally unexpected; there should have been white-eyed females 3. Concluded white eyes were incompatible with femaleness; decided to test it C. Crossed white-eyed male with one of its own daughters (should have one red & one white allele) 1. This test cross produced 129 red-eyed females, 132 red-eyed males, 86 white-eyed males & 88 white-eyed females вЂ”> so females could have white eyes 2. Viability of white-eyed flies is slightly lower than red-eyed flies so Morgan concluded he had obtained equal numbers of red- and white-eyed flies 3. Concluded that factors determining sex & eye color are connected, but that either sex can have white eyes if the right cross is carried out D. After about a year (1911), Morgan was convinced of an exact correspondence between white eye gene inheritance patterns & that of the X chromosome and sex determining factors 1. Concluded that eye color gene was on the X chromosome; such traits are said to be sex linked 2. Also concluded Y chromosome did not contain the same gene; conditon called hemizygous 3. 1st experimental evidence for hereditary factors traveling together linked on same chromosome 4. Demonstrated association between genes and chromosomes E. Summary of crosses Parental Cross White-Eyed Male (X wY) x Pure Breeding Red-Eyed Female (XW XW ) Genotypic Ratio 1 X W X w : 1 XW Y Phenotypic Ratio 1 Red-Eyed Female : 1 Red-Eyed Male X XW XW Red-Eyed Male (XW Y) x Red-Eyed Female (XW XW ) Genotypic Ratio 1 XWX W: 1 XW Y Phenotypic Ratio 1 Red-Eyed Female : 1 Red-Eyed Male X W w X Y w (Red-Eyed Female) XW X w (Red-Eyed Female) W X XW XW F1 Cross X W Red-Eyed Male (XW Y) x Red-Eyed Carrier Female (XW Xw ) W Y (Red-Eyed Male) XW Y (Red-Eyed Male) Y Genotypic Ratio 1 X W X W: 1 X WX w : 1 X WY : 1 X wY Phenotypic Ratio 1 Red-Eyed Female : 1 Red-Eyed Carrier Female : 1 Red-Eyed Male : 1 White-Eyed Male XW Y (Red-Eyed Female) (Red-Eyed Male) Genotypic Ratio 1 XW X w: 1 XW Y XW XW XW Y Phenotypic Ratio 1 Red-Eyed Carrier Female : 1 Red-Eyed Male (Red-Eyed Male) XW w X Y W X X (Red-Eyed Female) W X X w (Red-Eyed Carrier Female) White-Eyed Male (Xw Y) x Red-Eyed Female (XW XW ) XW XW (Red-Eyed Female) W X Xw XW XW XW X W X Y (Red-Eyed Male) w X Y (Red-Eyed Male) Y w (Red-Eyed Carrier Female) XW Y (Red-Eyed Male) XW X w XW Y (Red-Eyed Carrier Female) (Red-Eyed Male) White-Eyed Male (X w Y) x Red-Eyed Carrier Female (XW Xw ) Genotypic Ratio 1 XW X w : 1 X w X w : 1 X W Y : 1 X w Y Phenotypic Ratio 1 Red-Eyed Carrier Female : 1 White-Eyed Female : 1 Red-Eyed Male : 1 White-Eyed Male Xw XW Xw Y XW Xw XW Y (Red-Eyed Carrier Female) (Red-Eyed Male) Xw X w Xw Y (White-Eyed Female) (White-Eyed Male) V. Sex linkage is an example of a broader phenomenon in which clusters of traits are often inherited in groups; these are called linkage groups A. Morgan & his colleagues (1915) - found that traits in Drosophila tend to be inherited in four groups corresponding to the four pairs of chromosomes; humans have 23, peas have seven 1. Number of linkage groups corresponds to the haploid chromosome number of a species 2. This would be expected if chromosomes carry hereditary information & if members of homologous pairs each carried alleles for the same group of traits 3. Morgan had been critic of chromosomal theory of inheritance; his results turned him into an ardent supporter - got a Nobel Prize in 1933 for his research confirming it B. Raised question about how traits in linkage group are inherited separately (this does happen) Why Do Some Genetic Traits Tend to Travel Together?: Exchange and Movement of Genetic Material I. Chromosomes can exchange parts during meiosis A. Some results from Morgan's lab seemed to suggest that all traits in a linkage group are not always inherited together; these exceptions to linkage exhibited a clearly repeatable pattern 1. Morgan found a set of three recessive genes (yellow body, white eyes, miniature wings) formed a linkage group associated with X chromosome in fruit flies 2. About 1% of the time, yellow body trait was not inherited together with the white eye trait 3. In nearly 34% of offspring, the yellow body trait did not travel with miniature wing trait 4. Percentage of broken linkage was the same from generation to generation 5. Thus, something regular & predictable happens when gametes form that results in new allele combinations even when they are on the same chromosome B. Turned to cytologists for explanation - F. A. Janssens, Belgian cytologist, 1909 1. Saw that when chromosomes paired with homologues during meiotic prophase I, there were distinctive places where chromatid of one pair member were connected to chromatid of partner 2. Called these points chiasmata (singular - chiasma); crossing over between four chromatids on two members of homologous pair 3. Thought chiasmata are places where chromosomes break & broken ends rejoin, not in original arrangement, but after switching places with the same broken ends on homologous chromatids 4. Electron microscopy & molecular biological data prove he was correct 5. Phenomenon called crossing-over; parts of one member of pair cross over to homologue 6. Important mechanism for creating new gene combinations in gametes & thus offspring; should be added to the list of ways in which alleles recombine by sexual reproduction II. Bits of chromosomes can move - by 1940s, chromosomes were viewed as a stable array of alleles A. Barbara McClintock, established as leading cytogeneticist in 1930s when she determined that crossing-over in corn is an exchange of bits of chromosomes as well as genetic information 1. In 1940s - proposed that certain genes were capable of moving from one chromsomal locus to an entirely different one 2. Found evidence that certain genes jump from place to place in chromosomes B. In 1960s, others found evidence of jumping genes, calling them transposons 1. Certain genes more likely than others to jump & go elsewhere 2. There is evidence for this happening many times over the course of evolution 3. Transposons insert themselves at random into new loci; may disrupt other genes at new address 4. Effects are potentially devastating What Is the Chemical Nature of the Gene?: DNA or Protein I. Properties required for the genetic material - what chemical substance could do this? A. Present in all cells B. Copy themselves in their entirety every time before each cell division C. Determine virtually every trait that living organisms possess D. Fit inside the nucleus of a single cell II. Chromosomes are both protein and nucleic acid A. Friederich Miescher, Swiss medical student who switched studying the chemistry of life, 1860s used dead white blood cells collected from pus on bandages supplied by nearby surgical clinic 1. Was looking for new human proteins 2. Discovered unknown substance that contained C, N, O, & H like proteins but also phosphorus that isn't found in proteins 3. Determined that the substance came from the nucleus & called it nuclein 4. It was a large molecule like proteins but was acidic in character; one of his students later renamed it nucleic acid B. Soon after its discovery, nucleic acid was found to have properties in common with chromatin 1. Both substances were resistant to breakdown in the presence of HCl 2. Both swelled in the presence of salt solutions 3. Other cellular substances reacted differently to these treatments C. By 1881, nucleic acid was localized to chromosomes & found in every organism ever examined D. By 1890s, some thought it was the "idioplasm," the substance responsible for genetic inheritance III. Despite presence of nucleic acids in nucleus, protein seemed at the time to be a better candidate for genetic material A. Protein is the most complex, varied, & ubiquitos substance in living cells B. Plays many roles in cells & is present in the chromosome What Is the Chemical Nature of the Gene?: The Evidence for DNA I. Inheritance of polysaccharide capsule in Pneumococcus A. Pneumococcus (Diplococcus pneumoniae) is a disease-causing bacteria (causes pneumonia); it occurs in two distinct forms; often more than one strain of bacteria (Type I, Type II, etc.) 1. S form - looks smooth & shiny when grown on surface of agar plate (agar is nutrient-rich gelatin used as substrate to grow bacteria in research labs); highly virulent; Type IIIS 2. R form - appears rough & bumpy on agar plates; harmless B. Difference between R & S forms is smooth polysaccharide coat (capsule) enveloping S form 1. S coat makes them indifferent to attack from victim's immune system; one cell of S form injected into a mouse is lethal (it is virulent) 2. R form lacks coat (it is unencapsulated); easily defeated by host's immune system (avirulent) II. Fred Griffith, medical officer working for British Ministry of Health A. Studied the cause & effect of human diseases B. Noticed something strange & interesting about S & R pneumococcus (1928) 1. Mice injected with R form вЂ”> no ill effects 2. Mice injected with S form вЂ”> invariably died 3. Heat killed S bacteria before injecting mice вЂ”> harmless like living R form 4. Mix heat-killed S bacteria + live R bacteria, then inject вЂ”> mice died; isolated bacteria from corpses & grew them вЂ”> formed smooth, shiny colonies on agar plates C. Conclusion - harmless R bacteria transformed into virulent S pneumococci III. Oswald Avery, Colin MacLeod, & Maclyn McCarty, Rockefeller University (now Institute), 1944 A. Heard about Griffith's work & realized that transforming agent had to be genetic substance B. Realized a gene from the dead S bacterium was incorporated into the live R bacterium so they set out to find what the transforming agent was C. Discovered the transformation of R to S bacteria could be accomplished in test tube without mice 1. Broke apart heat-killed S bacteria by repeated cycles of freezing & thawing, releasing the cytoplasm of virulent cells 2. First, placed R bacteria on culture dish вЂ”> they grew; placed S DNA on dish вЂ”> no growth; mixed S DNA & living R bacteria вЂ”> growth of S bacteria along with R bacteria D. Removed or enzymatically destroyed different cell macromolecules, then tested for transformation 1. Removed polysaccharide coats from cell slush with polysaccharide-degrading enzymes вЂ”> transforming agent stayed active 2. Used protein-degrading enzymes (proteases) to degrade cell slush proteins вЂ”> transformation 3. Used RNase to degrade RNA вЂ”> transformation 4.. Extracted broken S cells with alcohol, removing lipids вЂ”> transformation 5. Treated mixture with DNAase (degrades DNA) вЂ”> transforming agent destroyed E. Conclusion: DNA was transforming agent, not polysaccharide, lipid or protein IV. Further evidence for the genetic role of DNA - the Hershey-Chase experiment A. Before Avery, MacLeod, & McCarty, most believed protein was hereditary material; DNA thought to be inert scaffolding that positioned proteins in chromosomes so they could do genetic work 1. After their work, the tide began to shift but some still believed the genes were proteins 2. Doubters disappeared after 1952 paper by A. D. Hershey & Martha Chase, Cold Spring Harbor Laboratory, who studied Escherichia coli & bacteriophage (virus that infects it) B. Viruses are packets of nucleic acid & protein (and sometimes lipid) 1. Dependent on cells they infect for raw materials & machinery to make more viruses 2. Some bacteriophage (bacteria eaters) consist of protein capsule enclosing a DNA strand 3. Attach to bacterial cell membrane & inject genetic material into cell; leave rest of particle behind 4. Viral genetic material mingles with victim's genes & hijacks cell machinery to make new viruses вЂ”> kills bacteria 5. Hershey & Chase decided to mark (tag) DNA & protein differently, follow fate of tagged material & see which one entered bacteria вЂ”> that one was genetic material C. How do you tag such a molecule? - use radioactive isotopes (unstable & emit rays or particles that can be detected) 1. Give radioactive isotopes found in biological molecules to cells 2. Cells use them like nonradioactive counterparts to build radioactive biological macromolecules & incorporate them in cell structures 3. The fate of structures built with radioisotopes can be determined by following the path of radioactivity through the life of the cell D. Hershey & Chase used isotopes specific to proteins (3 5S in cysteine & methionine) & DNA (3 2P) 1. Grew E. coli in 3 2P-rich medium & grew others in 3 5S-rich medium 2. Infect each of these cultures with bacteriophage: first made phage with labeled DNA, second made phage with labeled protein capsule 3. Isolated phage from each culture, infected two fresh bacterial cultures lacking radiolabel for 20 minutes during which time the genetic material was injected into the bacteria 4. Separated cells from viral coats using blender & looked for radiolabel вЂ”> 3 2P of viral DNA found inside E. coli cells, but 3 5S that was in viral coat protein stayed outside E. Firmly established DNA as genetic material 1. Now know that viral DNA enters cells & is incorporated into the cell's own DNA 2. It takes over control of cell вЂ”> becomes virus factory making more viruses that infect other healthy cells What Is the Chemical Nature of the Gene?: DNA Structure I. Nucleic acids - get their name from the fact that they are found primarily in nuclei of eukaryotic cells; two types - deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) II. Each made from building blocks called nucleotides composed of three building blocks A. A phosphate group B. Five-carbon sugar C. Nitrogen-containing base III. Nucleotides are hooked together by condensation-dehydration reactions in which H2 O is released as a byproduct; polynucleotides are broken apart by hydrolysis reactions introducing H2 O into the bond IV. RNA vs. DNA - similarities and differences A. Both DNA and RNA have phosphate groups B. Both have a central pentose sugar but in RNA the sugar is ribose; in DNA, it is deoxyribose C. Both RNA and DNA use the bases cytosine, adenine, and guanine, but RNA has the pyrimidine uracil, while DNA contains the pyrimidine thymine instead Where Are We Now? I. 1985 - about twelve leading European & American molecular biologists gathered in Santa Cruz, CA to discuss Human Genome Project (HGP) A. Previously, many individual investigators had identified human genes with roles in disease, but only a few genes were found; those not implicated in genetic disease were hard to find 1. Huntington's disease gene - found on human chromosome number 4 2. Mutant ОІ-globin gene implicated in sickle cell anemia - on chromosome number 11 3. Duchenne's muscular dystrophy - traced to mutant gene on X chromosome B. By 1990 - research agencies in Europe, U. S., & Japan funded HGP hoping it would identify & locate every one of estimated 50,000 to 100,000 human genes; has several goals 1. To create a map of traits - disease & physical traits, identifying characteristics - by assigning each one to particular chromosome & position on that chromosome - hope to complete by 2003 2. To determine nucleotide sequences of human genome - 3 billion DNA base pairs >1 meter long II. How do you sequence the human genome? A. DNA is cut into smaller pieces from 10,000 - 50,000 base pairs in length; technique used to cut DNA generates series of overlapping fragments B. Each piece (up to several hundred thousand) is separated from the others and amplified (copied over & over) 1. Get several hundred thousand test tubes, each containing millions of copies of one relatively short fragment of human DNA 2. Test tubes with copies of the fragment are assigned to different HGP laboratories where the sequence is determined C. When the sequence of each fragment is known, computers use overlaps to align fragments in the right order D. When each fragment is sequenced & properly aligned вЂ”> goal is realized III. What can we learn from sequences that constitute the human genome? A. Can analyze structure of genes & get information about the proteins they encode 1. Certain characteristic amino acid sequences occur in proteins that recognize & bind DNA 2. Genes encoding these sequences make proteins that interact with DNA; same is true of other proteins & enzymes 3. Goal is to learn structure & function of every protein encoded by human genome B. When chromosomal address & sequence of gene is known вЂ”> routine to develop diagnostic test to determine presence of mutations 1. May give us ability to diagnose genetic disease rapidly & cheaply 2. Examples: cancer, Alzheimer's disease, mental illness, maybe even obesity 3. Treatment could begin early, improving chances for good outcome for many diseases C. Finally, library of human genes can be kept in test tubes around world 1. Researchers will be able to get copies of gene for further study or to use in the manufacture of human proteins for therapeutic purposes IV. How should this new power be used? - critics fear that genetic information will violate our privacy or our rights A. Will people with genetic propensities for certain diseases be denied health insurance B. Will employers demand genetic information from prospective employees? C. Will genetic information begin to define what is "normal" and what is "abnormal," what is acceptable and what is not? D. Could detailed information about our genes be misused? E. Are the benefits of the HGP worth the risks? Analogies, Anecdotes and Illustrations What Role Do a Cell's Chromosomes Play? Mitosis is a difficult topic to describe to all General Biology students, especially non-majors. Before it can be approached, it is best that students understand fully what chromosomes do. I try to do it the following way. I tell the students to think of the chromosomes as the set of instructions needed to build an organism (real creative, so far!). Since the instructions are so important, I tell the students that each page of the instructions is represented twice in the nucleus. This ensures a backup copy of each individual instruction in case one of the copies contains an incorrect instruction (a mutation). If an organism has 20 chromosomes (ten homologous pairs), for example, this means that the full instruction booklet is ten pages long with each homologous pair representing one page. Both members of an homologous pair contain exactly the same subset of instructions. However, while each member of a pair carries the instructions for the same steps in the building of the organism, each specific instruction might differ somewhat. Sometimes, I use the example of a bicycle that a child has received as a gift. It comes in pieces in the box with two sets of instructions for the bike's assembly. These two sets of instructions are not identical. For example, step one on page one of the instructions may describe the painting of the bike. On the first copy of the instructions, it may tell you to paint the bike red; on the second copy, it may instruct you to paint the bike blue. Step four on the first copy of the third page may describe the attachment of the front wheel. Step four on the second copy of the third page will also describe the attachment of the front wheel. This instruction may be exactly the same as the corresponding instruction on the first copy of the third page (if the bike instructions are homozygous with respect to this particular instruction) or it may tell you to attach the wheel with a slightly different nut (if the instructions are heterozygous with respect to this instruction). You could push the analogy a little farther to demonstrate the concepts of dominance and recessivity. If the instruction booklet is heterozygous for a particular step, one of the two versions of the step would always be used to build the bike. This instruction would be the dominant one; the other one would be recessive and would only be used if both instruction booklets contained it. Mitosis Is a Continuum One aspect of mitosis that should be emphasized is the idea that mitosis (and meiosis, too) is a continuum. It does not "click" from one phase to another. It flows from one phase to the next in a smooth transition. Describing the phases is somewhat artificial, but you can give students some things to look for that will tell them what phase of mitosis a particular cell is in. Prophase can be differentiated from interphase quite simply. If the nucleus looks uniformly granular with no individual chromosomes distinguishable, then the cell is in interphase. If chromosomes are visible at all with the nucleus looking like a ball of yarn or with chromosomes that can be seen as separate structures, then the cell is in prophase. As long as the chromosomes can be seen to be contained by the nuclear membrane, the cell remains in prophase. Once the nuclear membrane is gone and the chromomes can be seen to be approaching the cell equator, the cell has entered metaphase. Chromosomes congregated in the center of the cell are indicators of a metaphase cell as long as the chromosomes have not split at the centromeres and started to move toward the opposite poles of the presumptive daughter cells. Once the chromosomes have split and they begin to move to the opposite poles, the cell has moved into anaphase. Telophase has begun when the chromosmes begin to decondense and the nuclear membrane begins to reform. When the nucleus once again looks granular with a fully developed nuclear membrane, the cell is once again in interphase. When Is a Chromatid a Chromosome? Students are also often confused by the distinction between chromatids and chromosomes. This can be clarified in a relatively simple manner. Point out that before mitosis, chromosomes must be replicated. The result of this is a chromosome consisting of two different strands, each of which is called a chromatid. The two chromatids are connected by a structure called the centromere; each chromatid is identical to its mate. At this time, each chromosome consists of two sister chromatids joined at the centromere. Midway through mitosis during anaphase, the centromere of each chromosome splits and the sister chromatids begin moving toward opposite poles. As soon as the centromere splits, each chromatid becomes a chromosome in its own right. Each chromosome consists of one chromatid until it replicates prior to the next mitosis. Thus, chromosomes cycle between consisting of one and two chromatids. Differences Between Cell Division in Plants and Animals The major difference between cell division in animals and plants is the way in which cytokinesis occurs. In animals, actin filaments (microfilaments) form a ring-like structure (the contractile ring) between the two nuclei of the presumptive daughter cells. The contractile ring is attached to the membrane and as its composite actin filaments slide over one another, the ring decreases in diameter. This pulls the attached cell membrane into the center of the cell from all sides. When the membrane reaches the center of the cell, the membranes fuse, effectively pinching the cell into two separate cells with a daughter nucleus in each one. A drawstring bag or purse is an effective analogy for this process. When one pulls on the drawstring, the opening of the bag becomes smaller and smaller. When the membranes meet in the center, they fuse, just like puddles of fat floating on top of chicken soup fuse when pushed together with a spoon. The effect is to form two separate cells. Plant cells cannot do it this way. Ask your students why that is (the cell wall, of course). Plant cells build their cell wall from the inside out. Vesicles carrying material used to build the cell wall fuse in the center of the cell. The membranes of the vesicles carrying this material eventually work their way out to the margins of the cells and fuse there with the cell membrane completing the cell membranes of both daughter cells. The cell wall material deposited between the membrane self-assembles into the cell wall. A second difference between cell division in animals and plants is the presence of centrioles in animal cells and their absence in plant cells. Centrioles serve as a focus for the formation of the mitotic spindle in animal cells; this purpose is fulfilled by the microtubular organizing center (MTOC) in plant cells, a much more amorphous and less noticeable structure. Whose Head Should Henry VIII Have Lopped Off Anyway? A story I like to relate to students when I talk about sex determination is the story of Henry VIII. I try to work biology's relationship to history into my class whenever possible. One thing people remember most about King Henry VIII of England is his understandable (at least considering the times and his situation) obsession with siring a male heir. He lopped off the heads of a couple of his wives at least partially because of their inability to give him a healthy son. Of course, he could not have known how sex was inherited, but if he had, he would have been forced to lop off his own head. After all, it is the male parent who decides the sex of his children. Eggs, under normal circumstances, contain only one X chromosome. The human male, on the other hand, is the heterogametic sex; half of the male's sperm carry the X chromosome and half carry the Y chromosome. Thus, Henry VIII was probably siring primarily daughters because his X-bearing sperm were, more often than not beating his Y-bearing sperm to the egg. The Chromosomal Theory of Inheritance Point out to your students at least some of the evidence that suggested that chromosomes were carrying hereditary information. First and foremost, emphasize the fact that the behavior of chromosomes matches the behavior of genes as described by Mendel. According to Mendel, genes are found in pairs in organisms. Chromosomes occur in pairs. The genes segregate during the formation of gametes, so, it turns out, do chromosomes. The number of chromosomes donated to offspring by the male and female parents is equal. Thus, the chromosome number within the species stays constant, which would be expected if chromosomes carried the genetic material. Finally, sex linkage of traits like colorblindness and eye color in Drosophila is further evidence of chromosomal theory of inheritance. It would be the only thing that would explain the inheritance pattern of such genes. Haploid vs. Diploid As has been mentioned on a number of occasions, vocabulary in any discipline can be a problem for non-majors, but it always seems that the complaints occur more often when a non-major takes a science course. The terms haploid and diploid frequently give students trouble. Once again, the roots might help one remember what each word means. The root hapl- from the Greek means "single or simple," while the root -oid means "like or form." Combining the roots, one comes up with a meaning of "single or simple form." This relates well to the meaning of haploid. Cells described as haploid have half the chromosome complement of normal somatic cells, thus they are a "simpler form" than a normal somatic cell that possesses more chromosomes. One could also approach it from another direction. Haploid cells are a "single form" in which each chromosome is represented only once. In contrast, the chromosomes in diploid cells are found in pairs. The root dipl- means "double or two" and the root -oid still means "like or form;" diploid thus means "double form," which essentially makes it the opposite of haploid. Diploid cells possess two copies of each chromosome. Meiosis вЂ” Producing Gametes Meiosis, in many respects, resembles mitosis. The names of its phases are the same as is their order as well. Perhaps the major difference is the fact that meiosis involves two cycles of division rather than one вЂ” meiosis I and meiosis II. Point out to your students that the first division (meiosis I) is a reduction division that cuts the number of chromosomes in each daughter cell in half. Also point out that it is not just any 50% of the chromosomes that end up in each daughter cell. Each daughter cell gets one member of each homologous pair. Which member of each homologous pair ends up in which daughter cell is a product of random chance. This is the place and time at which the segregation referred to in Mendel's Law of Segregation occurs. It is important to mention this to your students to insure than they make the connection between Mendelian inheritance and meiosis. The second cycle of division in meiosis (meiosis II) is essentially identical to mitosis with one big difference. The number of chromosomes participating is half the number involved in mitosis in the same organism. There are no chromosome pairs present in meiosis II because the members of each pair were separated during meiosis I. The reduction division meiosis I begins after an interphase in which the chromosomes are duplicated, just like what happens during the interphase preceding mitosis. The meiotic stages that follow are a continuum like those in mitosis and, similarly, they can be distinguished by looking for a few key identifying characteristics. Prophase I is marked by the condensation of the chromosomes, the breakdown of the nuclear membrane, and the attachment of spindle fibers to the chromosomes. Point out to the students that one trait allows them to distinguish between prophase of mitosis and prophase I of meiosis. In prophase I, the chromosomes are found in pairs; in prophase of mitosis, the chromosomes are arranged singly. Make clear to the students that the pairing is highly ordered with the chromatids of each chromosome perfectly aligned in a process referred to as synapsis. Ask your students the purpose of this precise alignment. Of course, it is the precise exchange of one piece of a chromosome for the corresponding piece of the other homologous chromosome. Pursue the point by asking them the purpose of such an exchange; of course, it is heightened variability in the offspring. The paired chromosomes begin moving to the cell equator near the end of prophase I. Once the chromosomes have arrived at the center of the cell, one can be sure that metaphase I has commenced. The placement of a member of the homologous pair on one side of the metaphase plate, as it is called, or the other is totally random and this is the point at which Mendelian segregation occurs. Anaphase I begins when the members of each homologous pair begin moving toward opposite poles of the cell. It is at this juncture that the actual reduction in the chromsome number can be said to happen. Anaphase I differs from anaphase of mitosis in that the chromatids of chromosomes do not split during anaphase I as they do during anaphase of mitosis. Cytokineisis will also begin during anaphase I. Cytokinesis continues to completion during telophase I. This is accompanied by the clustering of chromosomes at opposite poles and their partial decondensation. In some cases, the nuclear membrane reforms; in others, it does not. The cells thus produced are haploid and contain half the chromosome complement of the somatic diploid cells. Reduction division has occurred. The second cycle of division in meiosis is in almost every respect exactly like mitosis. The major difference is the number of chromosomes involved. Each cell in meiosis II has only the haploid number of chromosomes. Meiosis II is sometimes preceded by a brief interkinesis stage between the two meiotic divisions. Point out to your students first that this stage is often missing and second that, unlike mitosis which is preceded by an interphase in which the chromosomes are replicated, it includes no chromosomal replication. After interkinesis, if it occurs, comes prophase II in which the partially unraveled chromosomes condense once again in both daughter cells from meiosis I. This stage may, at times, be skipped, in which case the cells skip right to metaphase II. Chromosomes line up singly in the center of the cell. During anaphase II, the centromeres divide, sending one chromatid from each chromosome to the opposite poles, just like what happens in mitotic anaphase. In telophase II, chromosomes cluster at the opposite poles, the chromosomes decondense, and the nuclear membrane reforms. Once cytokinesis is complete, four haploid cells have been produced. Once you have described the stages of meiosis, quiz your students about how they should distinguish between the different stages of mitosis and meiosis. Keep emphasizing the details that allow them to make these distinctions: the number of chromosomes (haploid vs. diploid), the arrangement of chromosomes in pairs or as single chromosomes, the position of the chromosomes in the cell, the degree of chromosomal condensation, the presence or absence of the nuclear membrane, etc. What Is the Difference Between Spermatogenesis and Oogenesis? Once you have described meiosis, fit the picture of sperm and egg development into the framework of meiosis. Sperm development begins with spermatogonia dividing mitotically. Usually, one of the daughter cells becomes a primary spermatocyte that will enter meiosis and another cell that will remain a spermatogonial stem cell. The primary spermatocyte undergoes meiosis I producing two secondary spermatocytes, which subsequently undergo meiosis II. At the end of meiosis II, there are four equally sized cells known as spermatids. These cells then differentiate into mature sperm or spermatozoa. Egg development begins in a similar fashion. Oogonia divide mitotically producing two cells, one of which will remain a stem cell that will divide mitotically to initiate the production of another egg cell and a primary oocyte that will enter meiosis I to produce a very large secondary oocyte and a much smaller polar body through an unequal division. After meiosis II, the secondary oocyte will divide unequally to produce a larger ootid and a smaller polar body. The polar body produced in meiosis I may divide during meiosis to produce two smaller secondary polar bodies. In most cases, any polar bodies produced degenerate or are resorbed. Ask your students why there are differences between oogenesis and spermatogenesis. Why are four viable cells produced during spermatogenesis and only one viable cell produced during oogenesis? They should be able to figure this out with a few hints or leading questions. The answer, of course, is that eggs, which will support the development of the embryo following fertilization, will need as much cytoplasmic material as possible. So, rather than making four smaller, less substantial cells that will have a decreased ability to support successful embryonic development, the process puts "all of its egg in one basket," as it were. The developing embryo will have a better chance at successful development if only one cell with the maximum amount of cytoplasm is produced instead of four cells with significantly lower amounts of cytoplasm that would have a severely diminished chance at survival subsequent to fertilization. Sperm, on the other hand, do not need huge amounts of cytoplasm. Their job is to get to the egg as fast as possible. In fact, extra cytoplasm is extraneous and would hold them back from their appointed task. Thus, a cell is produced that is really nothing more than a nucleus with a tail. The Cell Cycle One of the problems with teaching biology to non-majors is the constant battle of trying to convince these students that what you have to tell them has relevance for their lives. It is not a battle that I (or you) relish fighting, nor, I believe, should we have to, but since the battle must be fought, we must use whatever ammunition is available. The cell cycle is one such piece of ammunition. I am willing to bet that there is not one student in your class whose life has not been touched by cancer. That can be your focus. Describe the parts of the cell cycle, what happens during each and stress those parts that are part of interphase. Make sure that students understand the relationship of mitosis to the cell cycle. Point out that many cells in the body slow their division or stop dividing entirely once they have differentiated, spending much of their time in the so-called G0 phase. Stress that there are intricate, multilayered controls on the progress of a cell through the cell cycle. Ask the students what cancer is. One of them will undoubtedly know that cancer occurs when cells that are supposed to have suspended cell division begin it again and do not stop. Some students think that it means that cells divide faster than normal. This is a misconception; it is not that they divide so rapidly (the speed of division is not significantly different). It is, instead, that they do not stop. The controls of cell division have, in some way, been compromised in cancer or the ability of a damaged cell to exercise programmed cell death has been eliminated in some way. You may also wish to point out the general aim of chemotherapy and radiation as treatments for cancer. These two treatments tend to damage cells that are dividing, as are cancer cells. This explains the classic side-effects of cancer therapies: hair loss, nausea, etc. Hair growth is the result of constant cell division and nausea results from an inability to renew the cells of the intestinal epithelium. Furthermore, cell division is not the only story in cancer. The other important feature of cancer is the regained ability of cancer cells to migrate with impunity to sites where they normally do not belong. This is perhaps the most insidious part of cancer. The process by which cancer cells move to other locations is called metastasis and may be one of the most feared words that a doctor can utter. Your students may have questions about why cells would even possess capabilities to do the kinds of things that lead to cancer if such capabilities were so deadly. The truth of the matter is that cell division and cell movement are two essential properties of embryonic cells that must divide to increase their number and move around to gain the appropriate position for their designated function. In most cases, these abilities are decreased significantly in a mature organism because most cells in such an organism have located themselves appropriately to their function and ceased or markedly decreased the rate of cell division. When these abilities reassert themselves in cells that are not supposed to have them, cancer can result. Did Mendel Fudge His Data? Once it was discovered that chromosomes were the location of the genes, it became clear rapidly that there had to be significantly more than one gene per chromosome. This meant that some genes would be inherited together on the same chromosome. Clearly, this means that some genes would not be inherited according to the Law of Independent Assortment. How then was Mendel able to choose seven genes, all of which could assort independently? Some people contend that he was lucky. Some feel that he picked out only those genes that behaved as his hypothesis suggested. Ask your students whether they believe he cheated or whether they believe he was simply lucky. If he paid attention only to the data that fit his hypothesis, ignoring the rest, is that ethical? Ask your students. You've Got to Know When to Hold 'em, Know When to Fold 'em...... In case your students think that scientists always know what's supposed to happen before they do an experiment, two stories connected with linkage may demonstrate otherwise. Calvin Bridges, a student working in T. H. Morgan's laboratory, discovered the white-eyed Drosophila that Morgan had been looking for on a bottle that was about to be washed. Fortunately, Bridges was paying enough attention while doing a mundane job like washing the dishes to notice something important and act on it. This is similar to the discovery of penicillin by Fleming and no less important. In addition, Morgan was initially a critic of the chromosomal theory of inheritance, but he was open-minded enough that when presented with evidence to the contrary, he altered his position and eventually won a Nobel prize in 1933 for confirming the chromosomal theory of inheritance. Who Says Scientists Are Totally Objective and Impartial? It is important to demonstrate to all students вЂ” majors and non-majorsвЂ”how information is obtained by scientists through experimentation. The search for the identity of the genetic material was an interesting one. It included a number of elegant, insightful experiments, some intriguing personalities, and a little stubborness. This series of experiments is an ideal way to accomplish the abovementioned objective. All of the major experiments in this sequence are simple enough to be understood by nonmajors if they are given enough background information which is also easy for them to follow. Fred Griffith found the first significant piece of the puzzle and he was not even interested in the problem of the genetic material. He was studying the cause and effect of human diseases, specifically a form of pneumonia caused by a Pneumococcus infection. Talk about the different strains of Pneumococcus , the variations in their polysaccharide capsules, and how these differences explain their ability to cause a virulent infection. Then take your students through his experiments step-by-step. Move on to the experiments of Avery, McLeod, and McCarty. These, too, are relatively easy to understand. They left no doubt as to the identity of the genetic material. Emphasize for your students that this work took a number of years. Despite the seeming simplicity of the experiments, they were comprehensive and exacting. Finally, there is the experiment that convinced the bulk of the investigators. This was the HersheyChase experiment in which the investigators radiolabeled the components of viral coats (proteins) and the DNA found inside viruses to determine which entered the host bacteria. This requires that you first describe how infection of bacteria by viruses occurs. It is clear from the viral life cycle that their genetic material must enter the bacterial cells. This, of course, is the basis of the experiment. Point out to your students the use of an ordinary kitchen (Waring) blender in this experiment. It usually impresses the students and helps them remember the experiment. This experiment was responsible for convincing most scientists that DNA was the genetic material. Ironically, this experiment, while classic, is actually not as well designed and does not give results that are as unequivocal as those of Avery, McCarty, and McLeod. Why is the Hershey-Chase experiment felt by many to be more important? The answer lies in the research organism used in the two experiments. By far, the best known scientists involved in the research of this discipline were those who worked on viruses. Bacteria seemed less desirable. Most of the genetic research being done at this time was with viruses which became the "organism" of choice. The mainstream scientists trying to identify the genetic material at this time were virologists and most of them were not prepared to declare the search over until it had been demonstrated in viruses, even if the experiments executed with bacteria were actually better, more conclusive experiments. A more complete description of the political climate surrounding this question can be found in The Eighth Day of Creation by Horace Freeland Judson. Sample Test Questions Multiple Choice, Conceptual, and Open-Ended Questions From the Text 1. Chromatin is composed of what substances? a. RNA b. lipids c. DNA d. protein e. a, c, and d 2. Which of the following is involved in cell division? a. disappearance of nuclear envelope d. changes in the cytoskeleton b. reappearance of nuclear envelope e. all of the above c. chromosome condensation 3. In what phase of the cell cycle is the second chromatid produced? a. prophase b. metaphase c. interphase d. anaphase e. telophase 4. In what part of mitosis do the two sister chromatids separate? a. prophase b. anaphase c. telophase d. metaphase e. prophase II 5. In what part of mitosis do the chromosomes line up at the equator of the dividing cell? a. metaphase b. prophase c. anaphase d. telophase e. interphase 6. What is the name of the process in which the cytoplasm of the mitotic cell is divided equally between the two daughter cells? Cytokinesis. 7. What are the differences between cytokinesis in plants and animals? In an animal, a cleavage furrow forms around the periphery of the dividing cell and becomes progressively deeper until the cell is pinched in two at the center. In dividing plant cells, membranous vesicles gather at the equator of the dividing cell. The vesicles fuse to form cell plate vesicles that then fuse with the cell membrane. 8. The members of an homologous pair of chromosomes are matched in ________. a. size b. shape c. gene content d. a and b e. all of the other answers 9. Must the members of an homologous pair carry the same allele for a particular gene? Please explain your answer. No, the members of an homologous pair of chromosomes may carry the same allele for a particular gene, in which case the organism is homozygous with respect to the gene in question. If the members of an homologous pair carry the same allele for a particular gene, the organism is said to be heterozygous with respect to that gene. 10. A locus is a. an insect pest that devours crops d. a and b b. one of the 10 plagues in the Bible e. a chromatid c. the site on a chromosome at which a particular gene is located 11. An organism contains 26 chromosomes in its non-gamete cells. How many chromosomes will three of its eggs have? a. 13 b. 39 c. 78 d. 26 e. a and d 12. An organism contains 18 chromosomes in its gamete. How many chromosomes would there be in one non-gametic cell? a. 18 b. 9 c. 36 d. 27 e. 54 13. Identify the stage of mitosis or meiosis described below. a. A diploid number of unpaired chromosomes condense and become visible; the nuclear membrane is still intact. Prophase of mitosis. b. A diploid number of paired chromosomes condenses in a nucleus; the nuclear membrane is beginning to disappear and the spindle is beginning to form as centrioles move toward opposite poles of the cell. Prophase of meiosis I. c. A diploid number of unpaired chromosomes align in the center of the cell. Metaphase of mitosis. d. A diploid number of paired chromosomes align in the center of the cell. Metaphase of meiosis II. e. A diploid number of chromosomes located in the center of the cell split at their centromeres. Anaphase of mitosis. f. A diploid number of paired chromosomes at the center of the cell separate so that the members of each pair begin to move toward opposite poles of the cell. Anaphase of meiosis I. g. A haploid number of chromosomes each consisting of two chromatids decondense as cytokinesis produces two cells; the nuclear membranes begin to reform. Telophase of mitosis. h. A haploid number of chromosomes consisting of two chromatids aligns at the center of the cell. Metaphase of meiosis II. I. A haploid number of chromosomes consisting of two chromatids separates at their centromeres and they begin moving to opposite poles of the cell. Anaphase of meiosis II. j. A diploid number of chromosomes consisting of two chromatids continues to condense as the nuclear membrane disappears. Prophase of mitosis or prophase of meiosis I. The description is ambiguous and could describe either of the two stages. k. A haploid number of chromosomes separates at their centromeres and they move toward opposite poles of the cell attached to the spindle. Anaphase of meiosis II. l. A haploid number of chromosomes consisting of one chromatid begin to decondense as they become enclosed in a newly reforming nuclear membrane. Telophase of meiosis II. 14. What is the purpose of synapsis or crossing over? The purpose of synapsis is the precise exchange of bits and pieces of DNA between homologous chromosomes to enhance the variability of an organism's offspring. 15. What is wrong with the following sentence?: Interphase is a resting stage between cell divisions. Interphase is not a resting stage, but it is the time between cell divisions. During interphase, chromosomes are replicated, the cell grows and takes in and processes nutrients and energy, and it makes copies of many of its organelles. Finally, in the latter part of interphase, the cell prepares for M phase. Clearly, interphase is anything but a resting stage. 16. What phase(s) of the cell cycle is (are) part of interphase? Gs, S, and G2. 17. Given that normally differentiated cells routinely stop dividing, in which stage of the cell cycle would they be likely to spend most of their time? G1. 18. There are two checkpoints that are important for the control of the cell cycle. What are they? The first checkpoint is late in G1 just before the switch to S and the accompanying replication of the chromosomes. The second checkpoint is at the transition between the G2 and M phases. 19. You grow liver cells on an agar plate containing nutrients until they uniformly cover the entire Petri dish in a single layer. They then stop dividing. Later, you scrape a circular, dime-sized region of cells from the surface of the agar plate. Explain why the cells stopped dividing at first. Then explain what happens after you scrape the cells from the surface of the plate. The cells stop dividing, because once they are surrounded by other cells, the surrounding cells send a message to the cells they surround telling it to cease division. When you scrape cells from the middle of the plate's surface, the cells on the edge of the wound are no longer surrounded. Thus, they do not receive enough of the signal telling them to stop dividing and they begin to divide again. Once the "wound" or lesion is filled in, cell division ceases as the cells once again receive enough of the signal to suppress mitosis. 20. Another word for uncontrolled cell growth is _________. a. stasis b. homeostasis c. cancer d. diabetes e. rabies 21. In what sense is control of the cell cycle a multilayered operation? Cell cycle in a cell is controlled by both internal and external stimuli which activate or inhibit cell cycle regulatory agents. These regulatory agents, in turn, activate enzymes that make it more or less likely that the cell will divide. Cell health is monitored by internal checkpoints and guardians. Errors at one or more steps in this operation can be disastrous, leading to uncontrolled growth. Cancer can result from a failure in a single state. 22. Cells that have stopped dividing are said to be in what stage of the cell cycle? a. G0 b. G1 c. M d. G2 e. Q 23. If eye color in Drosophila were not sex-linked, what difference would one expect in the results of the cross between a female heterozygous for white eye color and the F1 male of a cross between a purebreeding red-eyed female and a white-eyed male? In both cases, 25% of the offspring will exhibit the white-eyed trait. If it is sex-linked as the eye color trait is, all of the white-eyed flies will be males. If the gene is not sex-linked, half of the white-eyed offspring should be male and the other half female. 24. An organism has 42 chromosomes. How many linkage groups does it have? a. 42 b. 84 c. 40 d. 21 e. none of the above 25. You are studying three mutant traits in a particular organism (striped body, hairy tarsus, short legs). In the vast majority of crosses, these traits are inherited together. However, about 3% of the time the striped body trait is not inherited together with the hairy tarsus trait and about 25% of the time the striped body trait is not inherited along with the short legs trait. This same result was obtained generation after generation. What is the cause of this phenomenon? Crossing over is the cause. In crossing over, members of an homologous pair exchange pieces. This creates new combinations of genes thus enhancing genetic variability. 26. Some genes are capable of moving from one chromosomal locus to another. There is evidence this has happened a number of times over the course of evolution. What are such genes called? a. jumping genes b. gluons c. travelons d. transposons e. a and d 27. What are some properties required of the genetic material? The genetic material must be present in all cells. It must be able to copy itself in its entirety every time before each cell division. The genetic material must be able to determine virtually every trait that living organisms possess. Finally, it must fit inside the nucleus of a single cell. 28. What substances were initially thought to be possibilities for the genetic material and why? DNA and proteins were the two major candidates for the hereditary material. Once the involvement of chromosomes in heredity had been confirmed, DNA and proteins became the major candidates because they were the major components of which chromosomes are made. 29. Why was protein initially considered to be a better candidate for the genetic material than DNA? First, protein is the most complex, varied, and ubiquitous substance in living cells. It plays many roles in cells and is present in chromosomes. 30. How do you tag a molecule with a radioactive isotope? You expose cells or the organism to radiolabeled precursors of the macromolecule you wish to label. These radiolabeled precursors are then incorporated into the larger molecule which is consequently labeled. For example, to label proteins you would use radioactively labeled amino acids; to label polynucleotides you would use radiolabeled nucleotides. 31. What can be learned from DNA sequences in the human genome? Once the sequences in the human genome are known, we can analyze the structure of genes and get information about the proteins they encode. When the chromosomal address and sequence of a gene is known, it may become routine to develop a diagnostic test to determine the presence of mutations. This, may give us the ability to diagnose genetic diseases rapidly and cheaply. Thus treatment could begin early, improving the chances for a good outcome for many diseases. Finally, copies of genes can be used in studies or they can be used to manufacture human proteins for therapeutic purposes. Multiple Choice, Conceptual, and Open-Ended Questions From the CD-ROM 1. Distinguish between a gene, a locus, and an allele. How can they physically represent the same segment of DNA while being different operationally? A gene is a segment of DNA that determines a particular trait. Each gene can be expressed in a vaiety of ways, that is, they can have different forms. Each form of a gene is called an allele. Each organism will carry two copies of each gene. If both copies or alleles are the same, the organism is homozygous. If an organism carries two different alleles, it is heterozygous. The specific location of a gene on a particular chromosome is its locus. The locus for a particular gene is the same in all normal members of a species. 2. During which part of the cell cycle does replication occur? a. prophase I b. anaphase c. prophase II d. interphase e. interkinesis 3. How many chromatids does each chromosome possess just prior to replication? a. none b. one c. two d. four e. three 4. How many chromatids does each chromosome have just after replication? a. none b. one c. two d. four e. three 5. A cell has 14 chromosomes. How many chromosomes will it have after it undergoes mitosis? a. 7 b. 28 c. 14 d. 2 e. none 6. A cell has 26 chromosomes just before cell division. How many chromatids are present? a. 52 b. 26 c. 13 d. 104 e. none 7. Which of the following is not a purpose for which mitosis is used? a. growth b. repair c. development d. cell replacement transformation e. 8. Why is mitosis said to be an equational division? Mitosis is called an equational division, because the daughter cells at the end of mitosis have the same number of chromosomes as the parent cell forming them. 9. What structure holds chromatids together to make a chromosome? A centromere. 10. Why is the apparent division of mitosis into four distinct phases misleading? The phases are actually not distinct. Mitosis is a continuum with each phase moving dynamically into the next. 11. Of what are the spindle fibers composed? a. microtubules b. microfilaments c. flagella d. centrioles e. metaphase 12. During which stage of mitosis do chromosomes begin to move toward opposite sides of the cell? a. prophase b. metaphase c. anaphase d. telophase e. a and c 13. What is the name of a process in which the parent cell is split into two daughter cells? a. mitosis b. meiosis I c. cytokinesis d. meiosis II e. a, b, and c 14. Meiosis is referred to as a reduction division. During which part of meiosis does the actual reduction in chromosome number occur? The chromosome number actually decreases during meiosis I. 15. What kind of cells might be a product of meiosis? a. an egg b. a liver cell c. a spore d. a sperm cell e. a, c, and d 16. How do long and very thin strands of DNA that are essentially invisible during interphase become visible in prophase of mitosis and prophase I of meiosis? The DNA becomes tightly coiled in an organized fashion and becomes thick enough to be resolved in a light microscope. Its doubled structure can also usually be discerned late in prophase of mitosis or prophase I of meiosis. 17. In what process and stage do homologous chromosomes separate? a. anaphase of mitosis c. anaphase II of meiosis b. prophase of mitosis d. meiotic mitosis e. anaphase I of meiosis 18. Which phase of meiosis is often skipped? Prophase II of meiosis. 19. What are some of the reasons that have led Drosophila melanogaster to be one of the most used animals in laboratories studying genetics? It is easily bred in the laboratory in half-pint milk bottles with a simple controlled diet. Hundreds of these fruit flies can complete a generation (from egg to embryo to larva to adult to egg in 14 days. 20. Drosophila have ________ chromosomes. a. 4 b. 8 c. 4 pairs of d. 8 pairs of e. b and c 21. You are studying the chromosomal makeup of a fruit fly. While examining a micrograph of chromosomes prepared from the fruit fly, you note that it has two nonidentical sex chromosomes. What is the sex of the fly? Since the fly has two nonidentical sex chromosomes, one must be an X chromosome and the other a Y chromosome. Thus, the fly must be a male. 22. Which parent in the fruit fly determines the sex of the offspring? Since the female can only donate an X chromosome to her offspring, the male determines the sex of the offspring. If the sperm cell that fertilizes the egg contains a Y chromosome, the offspring will be a male; if the sex chromosome carried by the sperm is an X, the offspring will be female. 23. What is the probability of getting a white-eyed male offspring from a female homozygous for the red allele for eye color and a white-eyed male? a. 0 b. 1/4 c. 1/2 d. 3/4 e. 4/13 24. You mate two fruit flies and find that all of the female offspring have red eyes. About half of the male offspring have red eyes while the other half has white eyes. What are the phenotypes and genotypes of the parent flies? Both parents had red eyes. The female parent, was heterozygous for the eye color gene (XWXw); the male parent was hemizygous and carried the red allele for eye color on his single X chromosome (XWY). 25. There are two crosses of Drosophila that ensure that all offspring вЂ” male or female вЂ” will have red eyes. What are they? XWXW x XWY (a red-eyed female homozygous for the red allele and a redeyed male) & XWXW x XwY (a red-eyed female homozygous for the red allele and a white-eyed male). 26. If all of the female offspring of a female fruit fly homozygous for the red allele for eye color are carriers, what is the genotype of the male fruit fly with which she mated? a. XWY b. XWXW c. XwXw d. XwY e. no male parent could sire all female carriers 27. What must be the genotypes and phenotypes of fruit flies whose offspring include white-eyed females? A white-eyed female can only arise from a mating between a white-eyed male (XwY) and a red-eyed carrier female (XWXw) or between a white-eyed male and a white-eyed female (XwXw). 28. Like fruit flies, human males have an XY genotype that determines their sex; human females are XX. A group of females heterozygous for the gene for colorblindness is studied. The women in the study group have a total of 236 children with men who have normal color vision. There are 114 girls and 122 boys. Fifty-nine of the boys are colorblind and 63 have normal color vision. All of the girls have normal color vision. How is colorblindness inherited in humans? Since only boys are colorblind, one would conclude that inheritance of colorblindness is sex linked with the gene residing on the X chromosome. The Y chromosome does not carry a copy of this gene. The inheritance pattern is exactly like that of eye color in the fruit fly. 29. Which of the following is part of a nucleotide? a. phosphate group b. fatty acid c. nitrogen-containing base d. a, c, and e e. 5-carbon sugar 30. What kind of reaction is responsible for connecting two nucleotides together to form a dinucleotide? a. commercial b. condensation c. elimination d. hydrolysis e. b and d 31. What kind of reaction is responsible for breaking apart the two nucleotides of a dinucleotide? a. commercial b. condensation c. elimination d. hydrolysis e. b and d 32. How many water molecules were formed during the construction of a polynucleotide chain comprised of 2104 nucleotides? a. 2104 b. 4208 c. 2103 d. 4206 e. 1052 33. What are two differences between RNA and DNA? The 5-carbon sugar in RNA is ribose; the sugar in DNA is deoxyribose. Both DNA and RNA contain the bases guanine, cytosine, and adenine. However, RNA's fourth nitrogenous base is uracil while DNA's fourth nitrogenous base is thymine. 34. How many rings are characteristic of a purine nucleotide base? Purine nitrogenous bases have two rings each. How many rings are found in pyrimidine nucleotide bases? Pyrimidines have one ring each. 35. You are growing some Diplococcus pneumoniae on a culture dish. The colonies that grow appear smooth and shiny. What happens if you inject some of these bacteria into a mouse? The mouse develops pneumonia and dies. Bacteria that give rise to smooth colonies are virulent. 36. What kind of macromolecule is most prominent in the capsule of Diplococcus? Polysaccharides. 37. Diplococcus bacteria of the R strain are placed in a test tube along with different macromolecular fractions isolated from Diplococcus bacteria of the S strain (DNA, protein, RNA, polysaccharide coat, lipids). Following exposure to these macromolecular fractions, each set of bacteria was isolated and injected into mice. What happened to the injected mice? The mice injected with bacteria exposed to RNA, protein, lipid, and polysaccharide coat from S strain bacteria survived. The bacteria exposed to S strain DNA died of pneumonia. If bacteria were isolated from any mice that died following injection and cultured on agar plates, what would any colonies that form look like? The colonies would be shiny and smooth-looking due to the presence of the polysaccharide capsule. 38. You discover what appears to be a bacterial life form upon visiting the planet Tralfamadore. Their biochemistry appears very like that on Earth. You find that some of the bacteria kill mice into which they have been injected, while another strain of bacteria does not kill the mice. When grown on an agar plate, the virulent bacteria grow in rough, bumpy colonies; the avirulent bacteria grow in smooth, shiny colonies. You decide to repeat the experiments of Avery, McCarty, and McLeod to determine the nature of their genetic material. You lyse open the virulent bacteria and separate the lysate into five preparations and treat each preparation with an enzyme that degrades a major macromolecule (RNA, DNA, etc.). You then expose different samples of avirulent bacteria to each of these preparations. After injecting the bacteria into mice, you find that all the mice die of pneumonia except the mice treated with protease, an enzyme that degrades proteins. Of what is the genetic material of Tralfamadorean bacteria composed? Since the only mice that died are those that received a preparation in which the proteins had been degraded, proteins would seem to be the genetic material of Tralfamadorean bacteria. 39. Which of the following combinations would result in S strain bacteria that make the capsule required for virulence and which will produce R strain bacteria possessing the avirulent capsule? a. dead R bacteria and live R bacteria - R bacteria b. dead S bacteria and dead R bacteria - No bacteria c. live S bacteria and dead R bacteria - mostly S bacteria and some R bacteria d. live R bacteria and dead S bacteria - mostly R bacteria and some S bacteria e. live R bacteria and DNA from S bacteria - mostly R bacteria and some S bacteria f. live R bacteria and proteins from S bacteria - R bacteria 40. You break open some virulent Pneumococcus bacteria and treat the slush produced with an enzyme. You then use the slush to attempt a transformation of avirulent to virulent bacteria. It does not work. What enzyme did you use? DNase. 41. You radiolabel the DNA of some bacteriophage with 32P and proteins of other bacteriophage with S and infect separate preparations of bacteria with each one of the radiolabeled preparations. Which radioisotope is found inside infected bacteria? Since DNA is the genetic material, it will enter infected bacteria. Thus, only 32P will be found inside bacteria. 35 42. What piece of equipment was used in the Hershey - Chase experiment to shear the viruses off the surface of the bacteria after infection had occurred? A blender. 43. Viruses are not cells and therefore lack the cellular machinery that is used to synthesize the proteins and nucleic acids of which viruses are composed. How then can a virus reproduce to form as many as 200 - 300 copies of itself? When viruses inject their genetic material into the cells they infect, the DNA takes over control of the cell's machinery turning it into a virus factory which can make hundreds of viruses. The cells then burst releasing viruses that are then able to infect healthy cells. Using BioInquiry in Large Classes Integrating Components into the Lecture Once again, it may be impractical to use the CD-ROM or the Web-based part of BioInquiry in a large lecture section. The lecturer is still an essential part of the process and s/he has a limited amount of time in which to work. Furthermore, the requisite technology may not be available in some lecture halls. Having said that, a number of the animations could be useful if worked into the lecture. Of particular value, would be the brief animations illustrating mitosis and meiosis presented in Section 5.1 of the CDROM. (Note: The best still drawings of mitosis and meiosis I have seen are in older editions of Keeton's books. They are black-and-white line drawings with short descriptions of what is happening in each stage printed underneath each drawing.) While the still drawings that one can see in a text book are helpful, these animations illustrate the actual movements of the chromosomes and reinforce the fact that these two processes are both continual in which one stage in the process flows into the next. Part of the mitosis animation includes a movie of mitosis occurring in salamander cells. This is a good complement to the animation. If you cannot show the animations during class, tell your students to look at them at home. Perhaps as useful are those exercises that illustrate the sex linkage experiments (CD-ROM Section 5.2) where the student is asked to gather information as if s/he were a summer intern working in Morgan's lab and the exercises (CD-ROM Section 5.3) where the student is asked to predict the outcomes of the Avery, McCarty & McLeod, and Hershey - Chase experiments. This simulates the experimental method where a scientist comes up with an hypothesis, a prediction, of the results s/he expects. Then the student actually gets to carry out the experiment to a degree. The sex-linkage simulation begins by providing some background information on fruit flies. Once the student begins the sex-linkage exercises, the simulation asks the student to move the flies into the breeding bottle. It also provides the option for the student to try to figure out the results of the cross by trying it with a Punnett square before making the prediction. Once the hypothesis has been made and the experiment "conducted," the student can compare his/her prediction with the actual results and then consult the Conclusions section to see what the experiment should have taught him/her. The nice thing about this exercise is that it makes the student do seemingly trivial control crosses as well as the important experimental ones. The Avery, McCarty, & McLeod and Hershey-Chase experiments are handled in a similar fashion with students getting background information, predicting the results of each experiment one-by-one, and executing the experiment. These are excellent demonstrations probably best left for the students to try at home or in a laboratory session after the principles involved have been presented in lecture. Read More About It There are a number of books that provide extra insight into the topics presented in this chapter. The development of the understanding of linkage is discussed in Mayr's The Growth of Biological Thought. The book also delves into the history of our knowledge of mitosis, meiosis, and our concept of the gene. It tells the story of Morgan's fly room and his initial antipathy to the chromosomal theory of inheritance. The Eighth Day of Creation by Horace Freeland Judson includes a compelling account of the research leading to the discovery that DNA was, in fact, the genetic material. It deals with the initial favoring of protein as the genetic material and talks about the political climate within this branch of biological inquiry which gave greater weight to the experiments involving viruses than those involving bacteria, even though the Avery, McCarty, and McLeod experiments were actually thought by most investigators to be a bit more conclusive. For some insight into where molecular biology is headed and the Human Genome Project, read The Human Blueprint by Robert Shapiro. There are a number of books on the market that deal in one way or another with ethical issues in biology including molecular biology and the Human Genome Project. One of these is Due Consideration by Arthur Caplan, a bioethicist from the University of Pennsylvania. His brief, pithy, and thought-provoking essays are good fodder for classroom discussions. You may want to recommend this book and the others to your students as well. Supporting the Lab A number of the CD-ROM exercises could be done within the framework of a laboratory session. The instructor could bring the students up to speed on mitosis and meiosis, have them look at the animations and other information on the CD-ROM and then have them look at slides of mitosis and/or meiosis to see if they can identify the stages on their own. The exercises on sex-linkage, the Avery experiments, and the Hershy - Chase experiment can be incorporated into a lab exercise in a similar fashion. These simulations can be done after a brief introduction from the instructor and preceding an appropriate laboratory exercise dealing with the principles covered in the simulations. Some of the material at the BioInquiry web site may also be helpful to such a laboratory exercise. Another approach might be to make the prediction - experiment exercises on the CD-ROM the focus of a lab exercise. I am not a fan of doing every lab in this way because of my belief that the "hands-on, wet" lab experience is of paramount importance, especially for a non-major. However, in certain instances (and these could be examples) where the expense or logistics of running some lab exercises might be prohibitive, the use of the CD-ROM can be justified. Answers to Review Questions 1. Studies in cytogenetics suggested that Mendel's "factors," or as we now know them, the genes were located on the chromosomes. The chromosomes occur in pairs as do the genes. The existence of the sex chromosomes also provided some evidence that the genes were located on the chromosomes. Males presumably had to have some genes different from females to explain the physical differences between the sexes. This presumed difference in genes correlated with an observed difference in chromosomes while no other cell feature differed in any obviously observable way. The behavior of chromosomes during mitosis and especially meiosis mirrored the predicted behavior of the genes during those processes. For example, the equal contribution of chromosomes by sperm and egg to the fertilized egg while the amount of cytoplasm differed greatly suggested that the genes resided on the chromosomes. Genetic crosses that displayed linkage phenomena, an exception to Mendel's Law of Independent Assortment, convinced some investigators that different genes could travel together on the same chromosome. Analysis of these crosses allowed the relative positions of genes on chromosomes to be mapped. The linkage groups that were thus defined soon were correlated with particular chromosomes. The strange results (sex linkage) obtained with such traits as eye color in Drosophila and hemophilia in humans could be explained by locating them on the X chromosome. Crossovers of chromosomes during meiosis were eventually correlated with the unexpected inheritance patterns that were being discovered. Exchanges of pieces of chromosomes could be correlated with changes in inheritance. A more recent piece of evidence was the discovery of moving pieces of DNA called transposons whose movement had an effect on the expression of genetic traits. 2. The chromosomes separate at anaphase of mitosis. The chromatin condenses into visible chromosomes during prophase of mitosis. Mitosis must be preceded by chromosome replication so that there are two exact copies of each chromosome. In that way, each of the two daughter cells will get one copy of each chromosome. 3. In animal cells, a cleavage furrow forms around the periphery of the dividing cell. The furrow becomes progressively deeper until it pinches off the cell in the middle and divides its contents into two cells. Plant cells undergo cytokinesis by the gathering of membranous vesicles at the cell equator. These vesicles contain the materials that will form the cell wall. They fuse to form cell plate vesicles which then fuse with the cell membrane dividing the cell into two separate cells. The presence of the rigid cell wall in plants would not allow the type of cytokinesis seen in animal cells. 4. Normally, members of homologous pairs carry the same genes that represent the same traits. This can be seen, since various stains reveal banding patterns in homologous chromosomes that are identical. This identity is seen with a number of different stains. While homologous chromosomes normally carry the same genes, they may carry different alleles for those genes. For example, individuals heterozygous for a particular gene carry a different allele for that gene on each member of the homologous pair that carries that gene. 5. A gene's locus is the specific position that gene occupies on the chromosomes. The gene's locus will not normally change after mitosis or meiosis. If a piece of a chromosome is moved by accident to another chromosome, its locus will change. Such a change in position is called a translocation. Genes may also be deleted if a piece of a chromosome is removed or separated from the rest of the chromosome. 6. It was understood before the turn of the century that egg and sperm made an equal contribution to the genetic makeup of the zygote in terms of the number of chromosomes. If there was no reduction in chromosome number prior to fertilization, the number of chromosomes in each succeeding generation would double. Since the number of chromosomes in each succeeding generation remains the same, such a diminution in chromosome number must occur. 7. A diploid cell is a cell that possesses both members of each homologous pair. A haploid cell possesses only one member of each homologous pair. All human germ cells (sperm and egg) are haploid. All other human cells (somatic cells) are diploid. 8. Most cells will stop dividing at some time in their life; this is a normal occurrence. There are control mechanisms that stop progress through the cell cycle at these times. Under other normal circumstances, cells that have entered this quiescent G0 phase of the cell cycle can begin dividing again for a period of time, after which they cease dividing once again. An example of this would be wound healing. If cells lose those control mechanisms and/or they begin to operate incorrectly, the cell will begin to divide in an uncontrolled manner. This is a potential cause of some types of cancer. 9. There are 22 pairs of autosomal (non-sex) chromosomes in humans plus the X and Y chromosomes. Each pair of autosomal chromosomes would represent a linkage group since each pair carries a different complement of genes. For the same reason, the X and Y chromosomes would each be considered to be a separate linkage group. Thus, there are 24 human linkage groups. 10. The gene for hemophilia resides on the human X chromosome. The hemophilia allele is relatively rare and recessive. Thus, it would be fairly unlikely that a female would have hemophilia since she would have to inherit two copies of this relatively rare allele (also her father would have to be an hemophiliac). A male, however, does not have to inherit two copies of the hemophilia allele, since he has only one X chromosome. If he inherits the allele on his one X chromosome, he will have hemophilia. If a normal female who carries the allele for hemophilia has children with a normal male, half of her daughters will carry the allele, but all of her daughters will be normal. However, half of her sons will have hemophilia. A female can have hemophilia only if her father has hemophilia and her mother is a carrier of hemophilia. Such a situation would be relatively rare. 11. Initially, protein seemed to be the best candidate for the genetic material. It is the most complex, varied, and ubiquitous substance in living cells. It also plays many roles in cells and is present in chromosomes. All of these things seemed to suggest that it might be the genetic material. Griffith's experiments proved that one could alter the genetic constitution of bacteria with some component extracted from other bacteria, a process he called transformation. He called this component the transforming principle. He did not, however, prove what that transforming principle actually does. That was accomplished some years later by Avery, MacLeod, and McCarty. 12. Avery, MacLeod and McCarty treated extracts from bacteria with enzymes that degraded various cellular macromolecules prior to attempting transformation experiments. The only degradative enzyme that disabled the transforming principle was DNase, the enzyme that degrades DNA. Enzymes that degrade proteins, RNA, lipids, and carbohydrates had no effect on the transforming principle. Thus, DNA was shown to be the transforming principle; this meant that it was the genetic material. 13. Hershey and Chase used radioactive isotopes to label DNA and proteins. 32P was used to label DNA since proteins do not normally contain phosphorus; 35S was used to label proteins because DNA does not normally contain sulfur. CHAPTER 6 MOLECULAR BIOLOGY: WHAT IS DNA AND HOW DOES IT WORK? Lecture/CD-ROM Outline Overview I. Old ideas die slowly, even when they are wrong - chemical nature of genes was no exception A. Avery, McCarty, & McLeod and Hershey - Chase experiments had shown DNA to be genetic material, but there were pockets of resistance B. Watson & Crick (W-C), however, embraced DNA, attempted to determine 3D structure of DNA II. Once the structure was known, the way it encodes, expresses, and passes on genetic information could be understood; insights into the mysteries of life followed What Is the Structure of DNA? I. James D. Watson, American, early 1950s - visited the Cavendish Laboratory in Cambridge, England A. Several scientists there were studying 3D structure of proteins & down the road at Kings College in London, others were studying DNA structure - the two groups shared findings B. Watson heard Maurice Wilkins from Kings and became obsessed with DNA C. At Cavendish, Watson shared office with grad student Francis Crick who was using X-ray crystallography to study hemoglobin; Watson was there to study its relative, myoglobin D. Crick got excited about DNA as well II. DNA's structure must be compatible with its four roles A. DNA must be able to make copies of itself - before cell division, chromosomes are duplicated in their entirety & a copy of each is distributed to each daughter cell 1. At the time, it was thought that cell must have mold (template) that could be used to stamp out copies of hereditary information 2. Thought DNA had to act as a template for making more DNA B. DNA must encode information 1. Must be able to encode information that gives rise to discernible traits 2. Different DNAs must have some features in common regardless of source & some differences C. DNA must be able to control cells & must be able to tell them what to do - there had to be a chemical processes that allow genetic information to be expressed D. DNA must be able to change by mutation - structure of DNA must be compatible with mutation; there must be some inherent flexibility that allows change without DNA becoming nonfunctional III. DNA is a double helix A. Nucleotides that make up DNA have three components: phosphate group, 5-C sugar (deoxyribose) & nitrogen-containing organic base 1. Sugar & phosphate alike in all DNA nucleotides, but there are four different bases: adenine (A), guanine (G), thymine (T), & cytosine (C); A & G are purines and C & T are pyrimidines 2. W-C assumed that chemical groups responsible for connecting them together must be those that were most alike in all nucleotides - the phosphate group & sugar 3. Thus, nitrogenous bases could occur in any order without changing basic molecular stucture 4. Consistent with role as repository of information B. Linus Pauling, American biochemist, Caltech - won Nobel Prize for discovery about 3D structure of proteins using X-ray crystallography 1. Tiny bit of crystallized sample (protein, DNA) is bombarded with x-rays which are reflected in characteristic ways & captured on photographic film 2. Spots & areas thus formed reveal atomic arrangement in the sample giving clues to its 3Dstructure 3. Pauling found that some proteins have a regular, repeating structure; made paper models to resemble amino acids & assembled them into a protein model according to X-ray photographs C. D. E. F. 4. Got elegant, twisted helix winding around axis (an elongated spiral); called it alpha (О±) helix, because he was studying alpha keratin (from hairs & fingernails) Helices excited people & W-C thought to look for one in DNA but needed X-ray picture so they turned to Kings College laboratory of Rosalind Franklin 1. Rosalind Franklin - thorough & meticulous; her work was unfinished & she did not want to jump to conclusions about DNA structure until all the data were in 2. Maurice Wilkins at Kings also studied DNA; neither he, Watson, nor Crick treated Franklin as a colleague -> got her x-ray photographs without her knowledge, confirmed DNA was a helix Erwin Chargaff, Columbia University biochemist, 1950 - found that regardless of DNA source, relative amounts of four bases conform to rule 1. Amount of adenine always equals thymine & amount of cytosine always equals guanine 2. Amount of A+T together is independent of C+G; no one understood meaning at the time 3. Known as Chargaff's ratios or rules; eventual structure discovered had to account for them W-C considered that there could be two helices with adenine on one & thymine on the other; if guanine was on one, they proposed guanine on other (pairing relationships) 1. Means that sequence on one chain is complement of sequence on other & both would contain the same, albeit complementary, instructions 2. Used Pauling's model building approach but used metal; made repeating sugar-phosphate backbone (like rails on ladder) & twisted it into helix predicted by pictures 3. Paired bases projecting from the backbone formed rungs of a ladder projecting from rails & satisfied Chargaff's ratios; one strand is complementary to the other 4. Bonds holding nucleotides together in strand are covalent; bonds holding base pairs together are relatively weak hydrogen bonds; many of them acting together are, however, very strong 5. Model was compatible with all four roles of the genetic material Watson, Crick, & Wilkins as head of Kings lab win Nobel in 1962; Franklin did not receive it, because she had died in 1958 at 37; Nobel is not awarded posthumously How Does DNA Make Copies of Itself? I. Living organisms differ from inanimate since they copy information & pass it from generation to generation; replication is the process by which DNA copies itself; must occur before each cell division II. DNA replication precedes cell division A. In their 1953 paper, W-C wrote "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." 1. W-C said replication begins when weak bonds connecting parental strands break & strands separate like the halves of a zipper; specific enzymes involved in this process 2. Exposed bases attract new mates (T pairing with A, C pairing with G, etc.) 3. Each strand acts as a blueprint (template) upon which a new partner is assembled & as each new strand forms, the nucleotides are linked together to form a complete strand 4. Result is two double-stranded daughter helices, each composed of one parental strand & one newly synthesized strand, so the mechanism is called semiconservative replication B. Proposed this solely on the basis of logic, no scientific evidence to support it III. Later experiments provided evidence - Matthew Meselson & Franklin Stahl, Caltech, 1958 A. Used bacteria; they have DNA & short generation time (20 minutes) 1. Came up with way to tell newly made DNA strands from parental ones (used isotopes) 2. Grew bacteria whose parental DNA contained one isotope & new DNA contained another 3. If W-C were right, one strand of each daughter helix should contain one isotope; other strand should contain the other isotope 4. Used heavy isotope of nitrogen (15N) as opposed to normal isotope (14N); anything made with 15N is slightly heavier than it would be with 14N (no other chemical properties differ) B. Procedure of Meselson & Stahl experiment & results 1. Grew bacteria in medium containing only heavy nitrogen; after several generations, all nitrogenous bases contained only heavy nitrogen 2. Then, cultures were washed free from old medium & replaced by new medium with only light N вЂ”> DNA made after wash contained only light N 3. Bacteria were harvested from fresh growth medium at intervals & DNA was separated 4. Applied DNA samples to CsCl gradient in tubes (density increased toward tube bottom) & centrifuged 5. DNA pulled downward until it reached position in the gradient equal to their density 6. DNA with heavy nitrogen sinks lower than light DNA at centrifugation force >100,000 x g 7. Fully heavy parental DNA (both strands heavy) sank to tube bottom; after many generations of growth on light N, the fully light (both strands light) DNA settled near top of tube 8. After one generation on light N, every double helix had one heavy & one light strand & was found in gradient exactly halfway between full heavy & full light DNA IV. Process is fairly accurate, but occasionally makes mistakes; most errors are harmful & there are elaborate repair mechanisms that detect & fix mistakes but some still slip through вЂ”> mutations How Is the Information in DNA Expressed?: Setting the Stage I. Archibald Garrod, English physician, 1902 - treated infant for rare & strange malady; his diapers were stained a dark reddish black; suffered from alkaptonuria A. Urine of such patients contains alkapton bodies (chemicals that turn black on exposure to air) 1. The baby's parents were 1st cousins; Garrod wondered if it could be recessive genetic disorder 2. Proposed that the patient was missing a "certain ferment," an enzyme protein that is used to break down alkapton bodies before they enter urine, thus alkaptons spill over into urine B. Thus, he proposed that the inability to make the enzyme was an inherited trait; connection between genes & proteins II. Proteins: a review - they are amino acid polymers that fold, twist into characteristic 3D structures A. Amino acids differ from each other in side group (R group) composition 1. Differences in R groups give amino acids their characteristic properties just like amino acids give proteins their properties 2. The amino acid sequence in proteins (primary structure) gives them their structure & function B. The genes determine protein primary structure; sequence of nucleotides determines sequence of amino acids C. The process of genes specifying construction of proteins is indirect вЂ” DNA codes for proteins through intermediary, related polymer of ribonucleic acid nucleotides or RNA III. RNA acts as an intermediary A. The large size of DNA makes it impractical to move through the cell so...... 1. DNA that encodes proteins is copied into the complementary sequence of RNA nucleotides 2. Smaller, much more mobile RNA goes to the parts of the cell where sequence is decoded into protein B. Two separate processes involved in decoding DNA - transcription & translation; both rely heavily on RNA 1. Transcription - DNA used as the template to make RNA 2. Translation - RNA serves as the template for the sequence of amino acids in a protein IV. Structure of RNA nucleotides & polynucleotides A. Composed of phosphate group, nitrogenous base (A, G, C ,U [instead of T]), & ribose sugar B. Nucleotides are joined together into single-stranded molecule by covalent bonds V. Differences between DNA & RNA A. They contain different sugars - DNA contains deoxyribose, RNA contains ribose; deoxyribose lacks an oxygen on one of its carbons (the 2' C) B. Nitrogenous bases - DNA contains A, G, T, & C; RNA contains A, G, U, & C - uracil replaces thymine in RNA, thus A pairs with U when DNA is used as a template to make RNA 1. The pyrimidine nucleotides in RNA are cytosine & uracil 2. The purine nucleotides in RNA are adenine and guanine C. DNA is most stable as a double helix; RNA most often exists as single strand of nucleotides, but may occasionally form short-lived associations with complementary sequences on other strands 1. Some RNAs fold back on themselves, forming intrastrand pairings giving the molecule distinctive shape 2. These shapes are important to RNA function D. DNA & RNA differ in size, mobility, & life span 1. DNA molecules tend to be larger; RNAs are smaller 2. DNAs are basically immobile; RNAs are highly mobile, move between nucleus & cytoplasm 3. DNA molecule is fairly long-lived; RNAs are broken down soon after their job is done How Is the Information in DNA Expressed?: Transcription I. All RNAs are transcribed from DNA in nucleus, but not all of them are decoded into proteins; some are part of the machinery that translates other RNAs into proteins - three classes based on function A. Messenger RNA (mRNA) - mRNA carries genetic info from DNA (nucleus) to cytoplasm where it is translated into protein 1. Cell has as many different mRNAs as proteins being made; different proteins made at different times вЂ”> mRNA population of cell changes over time 2. In bacteria, single mRNA may carry enough information to make several different proteins; in eukaryotes, single mRNA usually codes for a single amino acid chain 3. Characteristic shape of mRNA is long, unfolded chain 4. More mRNAs are made than other kinds, but it is the least abundant in the cell since it is the least stable of the three classes; typical mRNA lasts minutes or hours before broken down 5. Rapid turnover is one way in which the cell regulates how much of given protein is produced B. Transfer RNA (tRNA) is interpreter molecule; brings amino acids to site where mRNA translated into protein so it must be able to recognize both the mRNA template & specific amino acids 1. Fold back on themselves to form a distinctive shape that looks like a folded lowercase letter t; held together by tendency for nitrogenous bases within single tRNA to form pairs 2. Three unpaired bases at bottom of t (anticodon region) & loose end that binds to amino acid at top; each tRNA recognizes & binds to only one of 20 different amino acids (specificity crucial) 3. Anticodon region associates with three complementary bases on mRNA during translation so that tRNAs carrying specific aminos will recognize certain parts of mRNA 4. Relatively long-lived, lasting from hours to days before they are broken down & nucleotides are recycled C. Ribosomal RNA (rRNA) - >80% of RNA in most eukaryotes; several different rRNAs & many proteins combine to form ribosomes where translation occurs 1. Ribosomes composed of two subunits: large & small, each made of rRNA & protein; they come together at start of translation & separate when done 2. Fold back on themselves, like tRNAs, in highly ordered complex patterns required for duties 3. rRNA acts like an enzyme accelerating some of the chemical reactions of translation; usually proteins are enzymes but RNAs like these can be catalysts, too II. RNA (all kinds - mRNA, rRNA, tRNA) is synthesized in transcription A. Enzymes involved in and control transcription 1. The enzyme RNA polymerase catalyzes the assembly of RNA & places appropriate complementary RNA nucleotides into new RNA 2. Other enzymes separate the DNA double helix strands to allow transcription B. What raw materials are required for making RNA? 1. The ribonucleotides A, U, G, C that are the building blocks of RNA 2. A template or blueprint of the final product вЂ” DNA 3. Fuel to drive the assembly line linking ribonucleotides - nucleotide triphosphates 4. Equipment to accomplish actual assembly of the final product C. Transcription from DNA must start & end at specific places on DNA 1. Certain sequences within DNA (promoter sequences) signal RNA polymerase to attach to template at that point & begin transcribing some predetermined number of nucleotides 2. Not all promoters are equal; strong ones are better at binding RNA polymerase than weak ones 3. Genes preceded by strong promoters are transcribed often; proteins they encode are required by the cell in large quantities; those not in as much demand have weaker proteins III. Steps in transcription - DNA transcribed in linear sequence & complementary RNA nucleotides are added one-by-one; once mRNA is synthesized, it leaves the nucleus for translation A. Where RNA polymerase sits on DNA, the two DNA strands separate leaving some nitrogenous bases unpaired 1. Exposed bases on DNA attract complementary ribonucleotides: A of DNA to U of RNA, G of DNA to C of RNA, T of DNA to A of RNA, etc. 2. When nucleotides are in position & H-bonded to complementary DNA nucleotides, RNA polymerase chops off two extra phosphates on the second ribonucleotide 3. Energy provided by broken chemical bond is absorbed & used to link two ribonucleotides together B. Without letting go, polymerase moves down one nucleotide, new nucleotide pairs & polymerase connects it C. Process repeated until get fully functional RNA - not clear how polymerase knows when to stop 1. But certain nucleotide sequences can change shape (folding, bending) of new RNA 2. May signal stop in transcription IV. In transcription, information is converted from one nucleic acid to another; language is not identical but quite similar A. Thus, transcription machinery is relatively simple: one kind of enzyme, some energy, raw materials B. Accessory proteins help to fine tune the process How Is the Information in DNA Expressed?: Translation I. Proteins are synthesized in translation - assembly of protein from mRNA template A. More complex & machinery of translation is far more elaborate than that of transcription B. What is needed for translation? 1. Raw materials (amino acids) 2. Energy to drive synthesis 3. Template to determine amino acid sequences 4. Machinery to do synthesis - reliable interpreter (tRNA), stable synthesis platform (ribosome) II. Steps in translation - begins with assembly of players in translation A. Long mRNA strand joins small subunit of ribosome; mRNA ribonucleotides found in sets of three (codon) which pair with anticodon portion of tRNA B. tRNA connected at loose end to particular amino acid joins growing translation apparatus; must be complementary to codon on mRNA & bound in position by weak H bonds C. Large ribosomal subunit enters & hugs smaller subunit & tRNA is bound to mRNA; creates a pocket surrounding next codon on mRNA D. Second tRNA enters carrying appropriate amino acid, fits into pocket, & aligns its anticodon with codon in the pocket (only tRNA with complementary anticodon will fit) E. Amino acid on the first tRNA is released from tRNA & joined to amino acid on the second tRNA (done by rRNA molecule with ability to catalyze chemical reaction, an RNA enzyme) 1. Result is beginning of protein (called peptide since <100 amino acids) F. Peptide grows by addition of new aminos & remains attached to newest tRNA in complex (which is attached to mRNA) until amino acid chain is released at the end of translation G. After tRNA releases its amino to protein, it separates from mRNA & moves back into the cytoplasm to pick a new amino acid on its loose end 1. Ribosome shifts position on mRNA exactly one codon downstream 2. With each ribosome shift, spent tRNA is ejected & position for new charged tRNA opened 3. As position is filled with correct tRNA, a new peptide bond is formed, elongating growing protein by one amino acid H. Eventually, ribosome encounters a codon on mRNA for which there is no tRNA with complementary anticodons (a stop codon) 1. Termination is complete when translation apparatus, with help of accessory proteins (release factors), dissociates into original parts & new protein takes up function How Is the Information in DNA Expressed?: The Genetic Code I. Three RNA nucleotides code for one amino acid - the language of genes is written in sequence of nitrogenous bases, which can be translated three at a time into amino acid words A. Need code to stand for 20 amino acids; alphabet for code has four letters (A, G, C, T or U) 1. Can only make 4 one letter words (41), 16 two-letter words (42) and 64 three-letter words (43) 2. To code unambiguously for 20 amino acids, need at least 20 words so three-letter words would be the minimum B. Marshall Nirenberg & Heinrich Matthaei, early 1960s - developed a technique for cracking code 1. Synthesized artificial genetic message with sequence they specified 2. Start with polyU, mix in test tube with all ingredients needed for translation вЂ”> simple protein made of phenylalanine is result вЂ”> UUU codon codes for phenylalanine 3. Using this technique, they and others cracked the whole code by 1966 II. Features of code A. Code is universal; applies to humans & all other living things - powerful piece of evidence that all organisms on earth share common evolutionary ancestry B. Most amino acids have two & many have four triplet codons that code for them 1. There are similarities in different codons for same amino - many codons for same amino differ only in last nucleotide; has consequences for integrity of the genetic message 2. Mistakes during replication sometimes involve mismatched nucleotides; if a mistake occurs in the last nucleotide of codon, good chance that it will still encode the same amino acid 3. Mistakes in fitting tRNAs into ribosome usually involve mismatches at the last position of pairing so no effect 4. Redundant aspect of code acts as safeguard against errors during replication & translation What Makes Cells Different From Each Other? I. During lifetime, a person may manufacture as many as 100,000 different proteins but only ~5000 are found in any one cell at any given time A. Some made all the time by nearly all the cells of body, e.g. enzymes that supply body with energy B. Others found in only a single cell type - only red blood cell precursors make hemoglobin (95% of protein they make) II. Prokaryotes regulate genetic expression mostly at transcription - FranГ§ois Jacob & Jacques Monod, Pasteur Institute in Paris (late 1940s) studied Escherichia coli & gene regulation (Nobel Prize, 1965) A. E. coli living in flask uses simple sugars provided in medium for energy 1. Main fuel is glucose; if it is in short supply, medium becomes depleted of glucose 2. Lactose may still be plentiful, but, at first, the cell lacks the enzymes needed to use it for food 3. Within about an hour, the cell makes all the enzymes needed to digest lactose, then uses it B. Genes encoding enzymes for digesting lactose are highly regulated in bacteria; made only if lactose is sole food source (lactose induces synthesis of enzymes needed to digest it) 1. Found that E. coli includes not only genes for lactose-digesting enzymes but also other DNA sequences that are critical for regulation of when and if protein-coding genes are expressed 2. Operon - cluster of genes including protein-coding genes & all of regulatory DNA involved in their expression C. Operon in lactose digestion is called lac operon - it is an inducible operon; presence of key substance in environment causes otherwise quiescent genes to be transcribed & translated 1. By using environmental cues to determine which genes are transcribed, a cell can tailor its proteins to prevailing conditions 2. This efficient mechanism saves energy, precious raw materials that are devoted to other tasks 3. Soon found to be widespread in prokaryotes, but eukaryote regulation is far more complex III. Eukaryotes regulate genetic expression at many different levels; transcription is important in eukaryotes as well but there are other levels of regulation A. Transcription factors found in eukaryotes (some also found in prokaryotes) - recognize & bind to specific DNA sequences called regulatory sequences 1. These regulatory sequences lie outside amino acid coding regions; eukaryotic genes have many such sequences 2. Transcription factors act by increasing or decreasing the rate at which specific protein-coding genes are transcribed (how this is accomplished is poorly understood) B. Not all eukaryotic mRNAs translated equally - some are translated many times, others only a few times before they are degraded into ribonucleotides C. Key to mRNA longevity (hence productivity) lies in the sequences at the very end - mRNAs with long adenine chains at end have longer life spans than those with few or none 1. Don't know what controls number of adenines on end How Does DNA Change Over Time? I. Mutations are essential for life A. Without change, there can be no evolution; without evolution, there would be no life B. Mutation can be defined as the sudden appearance of a new allele II. Some mutations involve whole chromosomes A. Polyploidy - arise as a genetic accident but, especially in plants, can be advantageous 1. Sometimes pollen-producing cells undergo meiosis but homologous pairs stay together вЂ”> one gamete gets all of the chromosomes; the other one dies 2. If this gamete fertilizes an egg to which same thing happened, resultant plant has 2 full sets of homologous pairs (4 haploid sets), said to be polyploid (>2 haploid sets of chromosomes) 3. Polyploidy & other changes in chromosome number result in no new alleles so can argue that it is not really a mutation but a form of genetic recombination 4. Polyploid plants are generally bigger, more hardy, & produce more seed than diploid relatives 5. Natural selection favors these traits so much that nearly 50% of flowering plants are polyploids, including many with commercial value (wheat has 6 haploid sets, strawberries 8) 6. A few animal species are polyploid - some amphibians, fishes, some beetles, & earthworms 7. If polyploid gamete successfully fertilizes another yielding viable offspring вЂ”> new species B. Aneuploidy - change in chromosome number involving single chromosome or single homologous pair; pair becomes a threesome or pair loses one chromosome 1. Sometimes during meiosis, members of homologous pair fail to separate from each other nondisjunction вЂ”> one gamete gets two members of one pair, the other gets neither 2. If such gamete joins another -> aneuploid (chromosome # one less or one more than normal) 3. Most human aneuploidies lethal before birth, leading to spontaneous abortion; a few go full term (Down syndrome - usually extra chromosome 21) 4. Down syndrome - about one in every 750 live births; characterized by mental retardation, distinctive facial appearance, positive disposition 5. Other human aneuploidies especially involving X & Y chromosomes are responsible for substantial proportion of congenital abnormailities III. Transposable genetic elements - Barbara McClintock showed that DNA molecules did not always remain intact from generation to generation as had been thought A. McClintock found that certain mutations in corn or maize involve DNA sequences that move from place to place, either on the same chromosome or a different one altogether 1. Called this genetic rearrangement transposition & called moved bits of DNA transposable genetic elements, later transposons 2. The new location into which the transposon is spliced is called target DNA B. While sequences of transposon DNA are not random (only certain sequences can move around), target sites are thought to be random so that transposon can land anywhere C. Can create new combinations of genes & can introduce errors in genetic material D. Transposon analogy - writing an essay with a wordprocessor 1. Choose a few phrases or sentences & cut them from text with cut & paste function 2. If insert these phrases randomly into essay, result might be silly, but meaningless, sentence or could land within key & undermine the meaning of the essay 3. Similarly, if transposon lands in important part of DNA (middle of gene), the result could be harmful 4. Estimated that one in every 500 human mutations results from transposon insertion into gene or into DNA sequences that control gene expression (several hemophilia forms arose this way) IV. Inversions & deletions A. Deletions - parts of chromosome spontaneously deleted B. Inversions - piece of chromosome broken, then reincorporated into chromosome in reversed order V. Some mutations involve single DNA bases or just a few bases - such micromutations are called point mutations (ex.: sickle cell anemia) A. Sickle cell anemia - inherited disease that results when person carries two copies of mutant allele for hemoglobin 1. Hemoglobin is protein composed of four intertwined amino acid chains (two identical alpha [О±] chains & two identical beta [ОІ] chains) 2. О± chains of normals & sickle cell patients are identical 3. ОІ chain sequences of normals & sickle cell patients differ by single amino acids 4. Amino acid glutamate that occurs at sixth position in the normal chain is replaced with valine in sickle cell patient; small difference, big effect B. Hemoglobin ОІ chain encoded in human ОІ-globin gene 1. Glutamate codons (GAA, GAG) are complementary to CTT & CTC in DNA; two of four valine codons are GUA & GUG 2. At some time in human evolution, what happens if error in replication changed middle base of triplet coding for sixth amino in ОІ-globin gene of one person is changed from T to A? 3. You would get sickle cell allele & no immediate consequence since normal allele is still there on the other chromosome; only see effect if individual inherits two sickle cell alleles 4. This is point mutation resulting in exchange of one amino acid for another in final gene product C. Deletions & insertions of single deoxyribonucleotide 1. Genes read like sentences of three-letter words in succession 2. Addition or deletion of single letter in one word would shift reading frame of entire sequence D. Example: normal sequence - JOE ATE HOT DOG 1. Point substitution - JOE TTE HOT DOG; sentence loses some of its meaning, but can still get part of meaning 2. Deletion - JEA THE OTD OG; get frame-shift, none of words following mutation are recognizable; these mutations (frame-shift mutations) are especially deleterious 3. Addition mutations are deleterious in the same way as deletions; they shift reading frame VI. Neutral mutations - most mutations harmful but many have little or no impact on recipients A. Eukaryotic cells have long stretches of DNA that are noncoding & whose functions are not fully understood (estimated that only ~5% of DNA in human cells actually codes for protein) 1. Some noncoding regions are regulatory regions; control which genes are transcribed & translated 2. Other regions transcribed into nontranslated RNAs (tRNA, rRNA) 3. Still others travel through generations as hitchhikers; have no known functions B. Such mutations have no known effect on recipients & are said to be neutral mutations Where Are We Now? I. Advances in manipulating genes/DNA have caused revolution in life sciences - affected basic research aimed at understanding fundamental cell processes, medicine, agriculture, environmental science A. DNA has shown up in courtroom where it is having influence on criminal cases B. Identify genes for specific proteins, cut or copy those genes from source, insert into another organism or species & control expression in new host II. Techniques for manipulating genes - molecular scissors & molecular paste A. Restriction enzymes (restriction endonucleases) - proteins made by bacteria as part of natural defense mechanisms; have been used as molecular scissors to manipulate DNA 1. Evolved as a mechanism for ridding bacteria of unwanted DNA (viruses or other invaders) 2. Cut unwanted DNA into fragments that can be digested & removed by bacterial cell B. Several hundred restriction enzymes have been identified & isolated - each recognizes a specific sequence of DNA nucleotides (recognition site) & cuts both DNA strands at recognition site 1. Each time a particular sequence occurs in DNA, if restriction enzyme present, it will make a cut 2. One of the first was isolated from E. coli; it was called EcoR1 (1st restriction enzyme found in E. coli) & cuts the following sequence: GAATTC CTTAAG 3. EcoR1 cuts recognition sequence in a manner that leaves some unpaired bases on both strands GAATTC CTTAAG G AATTC CTTAA G 4. Unpaired bases of DNA are called "sticky ends;" they have a tendency to find other similar unpaired sequences & form H bonds with them 5. Cut both human DNA & bacterial DNA with EcoR1 in same test tube вЂ”> some human DNA sticky ends would find complementary bacterial DNA sticky ends C. Once such combinations of bacterial & human DNA are formed by H bonding, breaks in the strands can be healed using another bacterial enzyme, DNA ligase (serves as molecular paste) 1. Ligase plays role in DNA replication & heals naturally-occurring breaks in DNA 2. DNA formed from DNAs of different organisms is called recombinant DNA III. Techniques for manipulating genes - made-to-order cells A. Human proteins like insulin (used to treat diabetes) & growth hormone (used to treat growth abnormalities) were expensive or not available at all 1. Sufferers treated with proteins taken from cows or pigs brought to slaughter 2. Inefficient & costly to prepare B. Now have bacteria cultures expressing human genes for these proteins in quantity вЂ” cheaply & accurately; it has revolutionized the pharmaceutical industry C. How can you get bacteria to express human proteins? 1. Bacteria have single circular bacterial chromosome but they can pick additional small pieces of DNA from outside cell 2. Under right conditions, DNA in fluid around bacteria can enter - transformation (Griffith) 3. These conditions are easily mimicked in the lab simply by changing the salt concentration of medium in which bacteria are living 4. Recombinant DNA molecules are made & introduced into medium as plasmids (small circular DNA fragments containing gene of interest [like human insulin gene]) 5. Bacteria that take up plasmid by transformation produce protein encoded by plasmid D. Plasmids in bacterial medium act as vectors (vehicles for carrying foreign DNA into host bacterium) 1. Vectors must contain not only the gene of interest but also sequences that allow their replication inside the host & their passage to daughter cells when the bacterium divides E. Bacteriophage lambda or phage lambda also used as a vector 1. Phage lambda infects bacterial host by injecting its DNA into host cell where it becomes integrated into host chromosome 2. Recombinant DNA molecule containing phage lambda DNA & gene of interest will have all molecular instructions for integrating gene into bacterial chromosome) 3. Once integrated into the host DNA, gene is replicated when the cell divides; also transcribed & translated IV. Gene therapy - treatment of human genetic disorders by introducing healthy genes into human cells A. Recombinant molecule containing healthy gene is synthesized in lab using restriction enzymes & DNA ligase - so far success has been limited B. Problems with gene therapy that limit its success 1. Appropriate vector to carry gene to target cells within human body is hard to find 2. Human viruses have the advantage of delivering DNA effectively, but they must be attenuated or made nonvirulent before their use 3. Attenuation accomplished with DNA technology; viral genes that cause disease symptoms are usually removed from viral DNA before used as vectors for gene therapy 4. Potentially dangerous if virus is not sufficiently attenuated V. DNA in courtroom - there are places in genome in which each person's DNA is unique eventhough humans have many sequences in common A. It is thus a powerful mechanism for identifying individuals involved in crime 1. Usually, there are traces of DNA left at crime scene (a few hairs, drops of blood, semen, & other bodily fluids) 2. When DNA is exposed to restriction enzymes, numbers & lengths of different fragments that result are highly individual for each person (like fingerprint) 3. DNA fragments are separated according to size using gel electrophoresis 4. Pattern of DNA fragments from specimens at crime scene is compared with patterns of DNA fragments from suspects вЂ”> if there's a match, could be proof B. If the amount of DNA at a crime scene is tiny, can amplify it using polymerase chain reaction (PCR) developed in 1983 - has wide application for many aspects of DNA technology 1. With PCR, can make large amounts of DNA from small sample 2. Can amplify one strand to millions in a short time VI. These molecular biology techniques are being used to develop better crops, clean up pollution, & even improve some of our leisure activities Analogies, Anecdotes and Illustrations The О±-Helix vs. the Double Helix One recurring problem with teaching protein and DNA structure is the seemingly unavoidable confusion that arises over the DNA double helix and the protein О±-helix. Once you have told your students about the two kinds of helix, the ship has already sailed. Most students will be able to keep the two straight; inevitably, some will not. I have tried a number of ways to make the distinction simpler. The best method seems to be simply stressing it and pointing out that this confusion crops up. Emphasize that double helix should give them the clue. Most of them remember that DNA is usually double stranded and proteins are single stranded; if they remember that the "double" in double helix should do it. The Nobel Prize: Rosalind Franklin Didn't Get It One of the great tragedies in the history of the Nobel Prize is the story of Rosalind Franklin. For a nonmajors course (majors as well), the story is one that should be told. For good or ill, it humanizes the DNA story and puts science in the same class as other human pursuits. There are a number of accounts (see Read More About It below) about how Watson, Crick, and Wilkins obtained Franklin's X-ray crystallography photographs of DNA. I recommend that you read some of them to get all sides of the story. Relate the story to your students and recommend that they read the books listed below or others that you might know about. (By the way, I would appreciate it if you would let me know if you are aware of some good books that I have not mentioned). Franklin's pictures clearly gave Watson and Crick the boost they needed to build their DNA model and divine the structure. In saying this, I in no way want to take away from Watson and Crick the credit they deserve nor could I. Had Franklin lived until the Nobel was awarded, I believe that she would have shared the Prize with Watson and Crick. However, she had died of cancer in 1958 at the age of 37 and since the Nobel is not awarded posthumously, she did not receive the award and is often forgotten. It was, after all, her data that contributed to the discovery. The irony and tragedy is that the technique (X-ray crystallography) that she used to gather the data probably contributed to her early death. The Nobel Prize: Chargaff Didn't Get It Either Another Nobel sideshow to the Watson and Crick model is the bitterness of Erwin Chargaff. Chargaff made a discovery of paramount importance to the Watson-Crick model. Chargaff analyzed DNA from a number of sources and found that in any sample the amount of adenine was equal to the amount of thymine and the amount of cytosine was equal to the amount of guanine. This discovery came to be known as Chargaff's ratios or Chargaff's rules and played a role in helping Watson and Crick figure out the structure of DNA and how it could carry the genetic code and replicate itself. Quotes from Chargaff in The Eighth Day of Creation about Watson and Crick suggest that he was resentful of the fame and recognition they received. He belittles their knowledge of the literature. One gets the impression that he felt that the recognition should have been at least partly his, if not totally so. He may not be completely unjustified in feeling this way. However, the portrait is one of a man who feels superior to Watson and Crick. Says Chargaff about his first meeting with Watson and Crick: "They impressed me by their extreme ignorance......I never met two men who knew so littleвЂ”and aspired to so much. They were going about it in a roguish, jocular manner, very bright young people who didn't know much. They didn't seem to know of my work, not even of the structure and chemistry of the purines and pyrimidines. But they told me they wanted to construct a helix, a polynucleotide to rival Pauling's alpha helix. They talked so much about 'pitch' that I remember I wrote down afterwards, 'Two pitchmen in search of a helix'" He goes on to describe the atmosphere of the meeting in the following way: "It struck me as a typically British intellectual atmosphere, little work and lots of talk. Crick and Watson are very different from each other. Watson is now an able, effective administrator of science. In that respect he represents the American entrepreneurial type very well. Crick is something else вЂ” brighter than Watson, but he talks a lot, and so he talks a lot of nonsense." He doesn't seem to have liked or respected the British very much either. Perhaps, had he shared the Nobel with Watson and Crick, he would have felt better about them and might have been more charitable in his opinions. Meselson and Stahl: A Good Experiment, Even for Non-Majors The Meselson and Stahl experiment is a classic experiment using techniques that can be explained even to non-majors without too much difficulty. Once the background has been laid out, students can be asked what results they would expect at any generation time if replication were semi-conservative, dispersive (non-conservative), or conservative. In other words, they can hypothesize. You could also give them results (graphically or orally) and ask them to interpret the data for you. I like manufacturing data for them, suggesting that dispersive or conservative replication is operative. This can serve as a valuable demonstration of how the scientific process works. The Meselson - Stahl experiment is a rather sophisticated experiment but it is elegant in its simplicity and the logic involved is accessible to nonmajors as is the technology. In predicting the results, simple math is all that is required. Alkaptonuria and Phenylketonuria Sometimes when you are teaching a course to non-majors, many of whom may be wondering why they have to take a science course, you have to be able to grab their attention. When that is necessary, often the best way to do it is to gross them out. Alkaptonuria is perfect for this. Introduce the topic (be a little subtle at first); tell the class you want to address the issue of what genes do, what they actually code for. Mention Garrod and tell them that he was an English physician who studied some strange diseases in children and that one disease really grabbed his attention. Now you can refer to what grabbed his attention. Tell them that the disease had a very noticeable symptom вЂ” when urine from these individuals hits the air, it turns a dark reddish black (fortunately, there are no really serious symptoms). That usually wakes the students up. Then tell them that Garrod made some well considered educated guesses. First, he concluded that the disease was caused by a variation from normal metabolism. The substance building up in the urine and causing its black color, he decided, was normally broken down before it could appear there. In alkaptonurics, it must be that there is a fault in the metabolism. By Garrod's time, it was fairly well established that enzymes were responsible for controlling metabolism, and he concluded that the enzyme responsible for breaking down the alkapton bodies that caused the black urine was missing. When he noted the parents of the children he was treating were first cousins, he guessed correctly that the origin of the condition was inheritance. Such conditions were soon referred to as inborn errors of metabolism and formed the first clear connection between genes and enzymes/proteins. To reinforce the point, tell your class about some similar diseases. Mention phenylketonuria. Tell them that most, if not all of them, were tested for the presence of this condition soon after birth. It causes a metabolic error similar to the one in alkaptonuria, but this time phenylketones build up in the blood and spill over into the urine. This time, however, the buildup of phenylketones in the blood can cause severe problems leading to mental retardation in chlidren However, if after testing, a baby is determined to be phenylketonuric, s/he is put on a low phenylalanine diet. Since the amino acid phenylalanine is the precursor of the phenylketones, low amounts of phenylalanine in the diet translate into low phenylketone levels in the blood and no mental retardation. Ask your students if they have ever noticed the warning on Nutrasweet-sweetened products like diet sodas and explain if necessary that Nutrasweet consists of two amino acids, one of which is phenylalanine. Hence the warning on the diet soda cans. If that is not enough, you can throw in one of the plagues of the inbred Amish population, Maple Syrup Urine Disease. Almost every time, someone will ask why they call it Maple Syrup Urine Disease. You can then mug knowingly at the audience in response. Why RNA? For some students, the role of RNA is difficult to understand. The following analogy usually works. I liken DNA to the Declaration of Independence or the Constitution. DNA which carries the instructions for building an organism is, of course, kept sequestered in the nucleus where it can be protected from damage within the cell. The original copies of the Declaration and the Constitution, the directions for running our country, usually do not travel around either. They stay under UV-protective glass in the National Archives in Washington, DC, where you can go to see them, if you like (I recommend it). If you want to view a copy of either document, that is easy enough. Facsimiles have been printed in any number of styles: in pamphlets, in books, even on fake parchment. You van view these copies any time you want, and if they are damaged in any way you can just replace them without having done any harm to the originals. The same applies to the story of DNA and RNA. DNA remains in the nucleus where it is safe. RNA copies of DNA are made, and it is these RNA copies of genes that travel to the cytoplasm of a eukaryotic cells where they are used to direct the production of proteins. Were DNA to go out of the nucleus to direct the production of proteins "personally", it might be susceptible to severe damage. If RNA is damaged during the course of protein synthesis, the nucleus simply synthesizes more RNA. Transcription vs. Translation Students often have difficulty keeping the meanings of transcription and translation straight. I try to make it easier by relating the process to other meanings of the particular word. Transcription, for instance, implies making either duplicate copies or copies from one dialect to another of the same language, much like the monks in the Xerox commercials. In biology, it means the production of a complementary RNA copy of a particular segment of DNA. DNA and RNA are both polynucleotides and thus at worst could be considered different dialects of the same language. On the other hand, translation is the conversion of a code carried in the language of a polynucleotide to the language of amino acids, a translation from one language to another. Gamow and the Genetic Code George Gamow , a theoretical physicist who was best known as a proponent of the Big Bang, wrote Watson and Crick in 1953 after seeing one of their papers. He was also familiar with the work of Frederick Sanger who had determined the amino acid sequence of insulin. The two papers had led Gamow to think about the coding problem and using a straightforward line of reasoning, he had come up with a proposal that was largely correct, although it contained some errors in detail. Crick credits Gamow with a provocative idea that forced him and others to start thinking about the coding problem. It also suggested a place to start. In essence, Gamow proposed that one think of the four different nucleotides as the four letters of a particular alphabet. He suggested that one think of the 20 amino acids found in polypeptides as words that can be spelled with that alphabet. Gamow then asked a very simple question. How many one-letter words, he asked, could be made with an alphabet consisting of four letters? The answer of course is 4 or 41. Gamow quickly recognized that this would be inadequate, since he felt that a requirement for the code would be that it needed to be unambiguous. It would not do to have one or more of the code words code for more than one amino acid. This would, it turns out, make the code ambiguous so that an organism would not make the same protein every time. If code words were one letter long, at least 17 of the 20 amino acids would have to be coded ambiguously. So, said Gamow, go to two-letter words. There are 16 or 42 of those. We're doing better! At least five of the 20 amino acids would have to be coded ambiguously. So Gamow suggested that three-letter words should be considered. This results in 64 or 43 code words, more than enough to code for 20 amino acids. There are even words left over for synonyms (in other words, the code becomes redundant) and punctuation (stop signals). So Gamow said the code would consist of three-letter code words. He was, of course, right. So, what was Gamow wrong about? First, Gamow suggested that DNA was the template for protein synthesis instead of RNA. He also suggested that the code was overlapping, suggesting that this would help to save space. It was subsequently realized that an overlapping code as Gamow described it would limit the combinations of amino acids that could appear side-by-side in a protein. Furthermore, it has been shown that combinations forbidden in Gamow's overlapping scheme actually appear in proteins. Thus, the code has been shown to be essentially nonoverlapping. However, it has been shown that the same stretch of DNA can, in some cases, code for more than one protein. I enjoy approaching this problem by asking my class how many one-letter words you can make with DNA's/RNA's four-letter alphabet, then how many two-letter words, etc. This engages them in the problem, gets them thinking about it. Throughout the discussion I ask them questions (leading ones, if necessary). How Does the lac Operon Work? Even though this is not described in the text, I think it is important to expose every student (non-major or major) to the mechanism by which the lac operon works. It's just so neat and it is accessible to non-majors. Start by establishing that in bacteria control of gene expression is basically at the level of transcription. To make things a little simpler, leave out the overriding glucose controls. You can do this simply by stating that if glucose is present, lactose is not used as an energy source and the enzymes necessary to use it are not made. Having said this, now tell the class what happens when lactose does show up in the environment. Of course, to do this you must describe the situation when lactose is absent and to do this you must first describe the lac operon. I gene promoter operator z gene y gene a gene There is the I gene which makes a molecule called the repressor. This repressor will bind to the lac operon at the operator site, a sequence of DNA located just ahead of the three genes that code for the proteins made by the operon. The promoter is the site at which RNA polymerase binds to the DNA before synthesizing the mRNA containing the genetic code for the z, y, and a proteins. When glucose is present in the environment and/or lactose is absent, the repressor molecule binds to the lac operon at its operator site, the DNA sequence of which is recognized by the repressor molecule. When bound at the operator site, the repressor overlaps the promoter somewhat and prevents the binding of RNA polymerase. If RNA polymerase cannot bind, RNA cannot be synthesized from the adjacent z, y, and a genes, the products of which allow metabolism of lactose. Active Repressor I gene promoter operator No mRNAs produced. z gene y gene a gene When lactose (or another ОІ-galactoside) is present to serve as an inducer, it will bind to the repressor, changing its shape and rendering it incapable of binding at the operator. Thus, RNA polymerase gains access to the promoter site and the adjacent structural genes for the enzymes that metabolize lactose and other ОІ-galactosides. The genes are transcribed and the mRNAs produced are translated into the enzymes that metabolize the ОІ-galactosides. Of course, when lactose is metabolized, it can no longer bind the repressor, which then changes back to the form that can bind the operator. The binding of the repressor prevents further production of mRNAs from these genes until the inducing ОІ-galactosides reappear. Inducer Inactive Repressor + mRNAs produced. Active Repressor I gene promoter operator z gene y gene a gene Once you've described the system, ask your students what happens if the gene for the repressor codes for a repressor that cannot bind to the operator (the z, y, and a genes are transcribed constitutively or constantly) or if the repressor can bind to the operator but not to the inducer (the gene is continually shut off). What happens if the operator is altered so that the repressor can no longer bind? Constitutive synthesis is the answer. These questions will tell you whether they understand how the mechanism works and for those that do not, it may help them understand it. Aneuploidy Aneuploidy is a change in chromosome number involving a single chromosome or single homologous pair. Most often, this involves an homologous pair becoming a threesome or a pair losing one chromosome. Such a situation is, of course, most often caused by nondisjunction; this occurs when an homologous pair fails to separate during meiosis. This can result in a gamete that contains two members of a particular homologous pair or one that contains no members of a particular homologous pair. When such a gamete joins a normal one, the result is a zygote and subsequently an organism that has one less or one more chromosome than is normal. Such an organism is called aneuploid. With this information conveyed to the class, fit Down syndrome into the framework. Point out that most trisomies that survive past birth have trisomies of chromosomes with higher numbers, since chromsomal size is inversely related to its number. More simply put, chromosomes with smaller numbers are larger. Ask your students why trisomies of higher-numbered chromosomes seem to survive better. The answer is that if the extra chromosome is smaller, the imbalance created is also smaller. Trisomies of larger chromosomes create larger imbalances and presumably cause even more substantial problems. Students are often fascinated most by sex chromsome aneuploidies. Talk about Turner's syndrome (individuals who have a single X sex chromosome). Point out that individuals who do not receive at least one X chromosome do not survive, while an individual can obviously survive without a Y chromosome. Talk about some of the other well known sex chromosome aneuploidies: XYY and its reputed but not well supported connection to aggressive (criminal) behavior, Klinefelter's syndrome (XXY), etc. Transposons, Inversions, Deletions & Point Mutations: The Book Is the Place to Go The analogy for transposons mentioned in the book is excellent and I will not even attempt to improve upon it. The analogy of writing an essay on a wordprocessor is something with which everyone in the class will have familiarity. It shows what happens at a number of levels. It shows what happens physically when phrases move from place to place within the essay. In addition, it illustrates the effect that transposons can have on the meaning of the genome. If phrases are inserted randomly in an essay, it can make the essay sound funny but not significantly alter its meaning. Alternatively, placement at other locations could severely alter the meaning of the essay. Inversions, deletions and insertions can be effectively illustrated as described in the text. You can make up a brief simple sentence (JOE ATE HOT DOG in the text) and then invert some of the letters, delete a letter, insert a letter or change a letter. This demonstration simply and effectively demonstrates these varied ways of producing a mutation. Types of Mutations There are basically three ways of classifying the effects of mutations. They can be harmful, they can have no effect or they can actually have an advantageous effect. If you consider an organism to be a well-oiled machine, the most likely result of changing a piece of the machinery is to have the operations of the organism's machinery adversely affected. In many cases, however, there may be essentially no effect, that is the mutation is neutral. There are even times when a mutation can improve the operation of the organism. We are the result of "good" mutations. It is essential that you make this point to your students. In reading comments of creation scientists, you will often see them making the case for their position by using the argument that mutations are all bad (everybody knows it!) and how could bad mutations evolve into anything as wonderful as us. This, of course, ignores the point made above that some mutations are good and that if there are some that are good, nature will tend to select for them. Add to that the point that nature will tend to select against the bad mutations as well. This is how "progress" is made in evolution. I sometimes wonder if creationists understand the above points and simply and conveniently ignore them or if they honestly do not know that there are good mutations. Genetic Engineering: Why Is It Important and How Is It Done? You can go into this topic as deeply as you like. It will be important in the future for majors and nonmajors alike to be familiar at least to a rudimentary degree with the techniques of genetic engineering. Some of my Biology major students do not appreciate the amount of biochemistry and molecular biology found in their cell biology course; they feel that they are going to deal with organisms or ecosystems and that they do not need to understand the chemistry and molecular biology of cells. Non-majors often extend this antipathy farther, thinking that genetic engineering is too hard to understand and irrelevant to their lives. Both groups of students are wrong. For majors, these techniques are becoming important in areas not usually considered (until recently) to involve molecular biology (ecology, behavior, etc.). For majors and non-majors, these technologies are becoming increasingly important in the public sector. Public policy in terms of health insurance, DNA fingerprinting related to paternity cases, criminal justice, medicine, etc., the pharmaceutical industry, research funding, and other issues will require our voters to make educated choices. This will be difficult to do without some comprehension of the techniques involved. Through the use of analogies like the classic ones of scissors for restriction endonucleases, and paste or glue for DNA ligases, this technology can be explained effectively. Combining pieces of DNA from different sources to make recombinant DNA by treating them with the same restriction endonuclease, thus producing the same sticky ends, is neat. If presented to students as neat, they will usually agree that it is. In a few minutes, you can go through the insertion of some useful gene, like human insulin or human growth hormone, into a bacterial plasmid, allowing the production of these proteins in large quantities inside bacteria possessing the engineered plasmid. Nonmajors, in my experience, have no trouble understanding this process. Genetic Engineering and Other Topics as Controversial Issues for Discussion in a Seminar It might also be worth discussing public policy issues and controversies that relate to genetic engineering in class, among other things. This can be done as part of your General Biology course or you can do it as part of a separate seminar class. We have taught a Freshman Biology seminar in which issues such as these are discussed. Recently, the course has been taken by Honors students alone but, in the past, it has been required of majors. We have students (singly or in teams) lead discussions on various topics, including genetic engineering. They begin by giving the class brief backgrounds on their chosen topics and then introducing controversial issues/scenarios to prompt classroom discussion. This has been a successful and thought-provoking course. Restiction Endonucleases and DNA Ligase: Their Real Purposes When we talk about the use of restriction endonucleases in genetic engineering, we often neglect to mention the natural function of these enzymes. Bacteria make them as a defense mechanism against foreign pieces of DNA that might end up in a bacterium. For instance, viruses infect bacteria by injecting their DNA into the host bacteria where they take over the metabolic machinery of the bacterium to make new viruses. Ultimately, of course, this takeover will kill the bacteria. They defend themselves by making enzymes that can cut viral DNA into several pieces rendering it nonfunctional before the takeover can occur. Your students may ask why these enzyme do not cut up the DNA of the bacterium. Two of the ways in which their DNA is protected from restriction endonucleases involve the DNA sequences recognized by the enzymes. First, bacteria may lack the sequences in their DNA recognized by the enzymes in viral DNA. Second, sequences recognized by the restiction enzymes when present in the bacteria will often be chemically modified in such a way that the enzyme does not recognize them. When present in viral DNA, these sequences are not chemically modified and therefore susceptible to attack by restiction endonucleases. An interesting way to approach this might be to ask your students how they might protect their DNA from restiction enzymes if they were bacteria while retaining their protective aspects. Sample Test Questions Multiple Choice, Conceptual, and Open-Ended Questions From the Text 1. Which of the following would not be a role or property of the genetic material? a. It must be able to make copies of itself. b. It must encode information c. It must be able to control cells and tell them what to do. d. It must be low in molecular weight. e. It must be able to change by mutation. 2. Which of the following structures is typical of the genetic material, DNA? a. cubicle helix b. triple helix c. double helix d. О±-helix e. c and d 3. What DNA sequence would be complementary to the following DNA sequence: AATGCATCGGA? a. AATGCATCGGA c. UUACGUAGCCT e. none of the other answers b. TTACGTAGCCT d. AAUGCAUCGGA 4. Who discovered the pairing rules of DNA? a. Watson b. Crick c. Franklin d. Chargaff e. Wilkins 5. You are a crew member on the starship Enterprise. Your responsibilities include investigation of biological life forms. You take out your tricorder after landing on the planet Yamihere and find a number of organisms, all of which contain DNA that follows the nitrogenous base pairing rules you are familiar with on Earth. For one of the species, the following relationships hold for the organism's DNA? A+T = 3 G+C millimoles of cytosine = 6 How many millimoles of guanine are present? 6 How many millimoles of thymine are present? 18 How many millimoles of uracil are present? 0, there is no uracil in DNA. You isolate DNA from another organism living on the surface of Yamihere and find that it contains all the bases normally found in DNA but does not obey the pairing rules. Can you explain these strange results? The DNA is single stranded, not double stranded. 6. You grow bacteria on media that contains the heavy isotope of nitrogen (15N) for many generations so that their DNA is saturated with the heavy 15N. The bacteria are moved to a medium containing the lighter isotope of nitrogen (14N) so that any new DNA synthesized would contain the lighter isotope of nitrogen. The DNA from these bacteria is isolated and analyzed on a CsCl gradient after various generation times. At each of the indicated generation times (0, 1, 2, and 3), where would you expect the DNA to be positioned? Also indicate the relative amount of DNA at each position in the gradient. The LL marker on the tubes below indicates double-stranded DNA containing only 14N; the HH marker indicates DNA containing only the 15N isotope. LL LL 100% 100% HH 0 generations 50% LL 75% 50% 25% HH 1 generation LL HH HH 3 generations 2 generations 7. Assume that the semiconservative replication model is not the way in which DNA replicate. Instead, DNA replicates by keeping the parental strands intact and making two new strands that together compose the daughter DNA double helix. This is called conservative replication. What results would you expect at 0, 1, 2, and 3 generations in the experiment described above in question 6. 100% 0 generations LL 50% LL 75% LL 87.5% LL HH 50% HH 25% HH 12.5% HH 1 generation 2 generations 3 generations 8. Who designed the experiment described in question 6 that was instrumental in proving that replication was a semiconservative process? Matthew Meselson and Franklin Stahl. 9. An enzyme is responsible for converting substance D to substance E. What will happen to the concentration levels of substance D and E in an organism that posseses no normal forms of the enzyme responsible for the conversion of D to E? The concentration of D will most likely rise since it is not being broken down by the enzyme. Concentrations of E will most likely decrease since less D is being converted to E, but E is probably being used by the next metabolic step. 10. You are a doctor and have a patient on whom you run a full spectrum of tests. The urine test indicates an abnormally high amount of a substance. Blood tests indicate an abnormally high amount of a substance that is a metabolic precursor of the substance that appears in the urine. What is the most likely explanation for this condition? Probably, the patient has an inborn error of metabolism in which there is an abnormal version of an enzyme involved in metabolism. Because it is faulty, its substrate builds up in the bloodstream and can be converted into another substance by another enzyme before that product spills over into the urine after which it is excreted. 11. Why does a population like the Amish exhibit an abnormally large number of inborn errors of metabolism? There is a relatively large amount of inbreeding in such populations and as a result, usually rare mutations build up to a higher than normal degree. Thus, there are more carriers of such mutations and if two such carriers mate, 25% of their offspring will exhibit these inborn errors of metabolism. 12. What do most of the genes do? Most of the genes code indirectly for the construction of proteins by specifying the order in which amino acids should be connected to assemble it. The order of amino acids specified is called the primary structure of the protein. 13. If DNA stays in the nucleus during the life of a eukaryotic cell, how can DNA code for the construction of proteins which occurs in the cytoplasm? DNA is transcribed into a molecule of messenger RNA (mRNA) which is processed and conveyed to the cytoplasm where the code it carries from the nucleus is used to direct protein synthesis. If it is destroyed and more of the protein is needed, the nucleus simply makes more of the mRNA. 14. What are some differences between RNA and DNA? RNA contains the sugar ribose (has an oxygen atom attached to the 2' carbon of the nucleotide's sugar); DNA lacks an oxygen atom at the same carbon. RNA uses the bases adenine, thymine, guanine, and uracil.: DNA uses the same nitrogenous bases except for thymine which replaces uracil. DNA is most stable as a double helix although it can appear as a single stranded molecule. RNA is generally a single stranded molecule although it can have local areas where it forms a helix with other parts of the same RNA molecule. They also differ in size (DNA is larger), mobility (DNA stays in the nucleus; RNA can move into the cytoplasm after being produced in the nucleus), and life span (DNA is long-lived, RNA transient, being broken down soon after it is made. 15. What is the least stable form of RNA? a. mRNA b. tRNA c. rRNA d. all of them exhibit the same stability e. a and b 16. What is an advantage of the rapid turnover of mRNA? Rapid turnover of mRNA helps the cell to regulate how much of a given protein is synthesized. 17. Which type of RNA possesses an anticodon? a. mRNA b. tRNA c. rRNA d. all of them have anticodons e. a and b 18. Which type of RNA is the most plentiful in a given cell? a. mRNA b. tRNA c. rRNA d. all of them are equally plentiful e. a and b 19. To what part of an mRNA is the anticodon of a tRNA complementary? a. the beginning b. the end c. the codon d. the anticodon e. the stop codon 20. A living organism on another planet has 42 different amino acids in its proteins. As on Earth, DNA codes for the sequence of amino acids in the proteins. Unlike on the Earth, the DNA contains eight different nucleotides. What is the most likely length of the codons in these organisms? It is most likely that the codons are two nucleotides long. The organism needs at least 42 codons to code unambiguously for its 42 amino acids. There are 64 (82) possible two-nucleotide codons in these organisms. This would be more than enough to allow unambiguous coding. 21. The genetic code is universal. What does this mean and what is the significance of this universality? A universal code is one that applies to all of the living organisms on the planet. This is a powerful piece of evidence that all organisms on Earth share a common evolutionary ancestry. 22. What is the name for a cluster of genes in a bacterium including protein coding genes and all of the regulatory DNA involved in controlling their expression? a. operator b. repressor c. operon d. structural gene e. gene cluster 23. What causes the production of the enzymes that are required to digest lactose? The lactosedigesting enzymes of the lac operon are made when lactose is the sole food source. The lactose induces the synthesis of the enzymes needed to digest it. 24. Control of gene expression in eukaryotes as in prokaryotes occurs at the level of transcription through transcription factors that recognize and bind to specific DNA sequences called regulatory sequences. However, they also exhibit control at other levels. What are they? Some mRNAs are translated many times while others are translated only a few times before they are degraded into ribonucleotides. Messenger RNAs with long stretches of adenines at their ends have longer life spans than those with fewer or none. A longer life span means they will be translated more often. 25. A polyploid organism exhibits a. an extra chromosome d. one or more extra chromosome sets b. one less chromosome than normal e. deletions in a single chromosome c. a decrease in chromosome sets 26. What are the general characteristics of polyploid plants? Polyploid plants tend to be bigger, more hardy, and produce more seed than their diploid relatives. 27. A change in chromosome number involving only a single chromosome or single homologous pair is called a. polyploidy b. aneuploidy c. point mutation d. deletion e. insertion 28. What causes aneuploidy? Aneuploidy is caused by the failure of the two members of a homologous pair to separate during meiosis, a process called nondisjunction. As a result, gametes are produced that either lack a representative from one homologous pair or the gametes have an extra member of one homologous pair. 29. What is the fate of most human embryos that have aneuploidies? a. a handicap b. They are normal. c. death d. a minor illness e. a and d 30. What is another name for DNA sequences that move from place to place in the genome, either on the same chromosome or on a different one altogether? a. transposable genetic elements b. bosons c. transposons d. codons e. a and c 31. The addition or deletion of a single nucleotide shifts the reading frame of a gene and thus leads to large and usually severe changes in the sequence of the protein coded for by the gene. What would happen if three nucleotides were added or delelted within a very small region of the gene? The reading frame would be shifted by three nucleotides and would get back in the correct reading frame within a short expanse of the coding sequence. The resultant change in the protein for which the gene codes will be much smaller than with the addition or deletion of a single nucleotide. Of what principle central to the understanding of the genetic code is this fact considered evidence? This is convincing evidence for the triplet codon. Only with a triplet codon would the addition or deletion of three nucleotides reestablish the proper reading frame. 32. Enzymes that are used to cut DNA at specific sites are called a. cutases c. restriction exonucleases e. b and d b. restriction enzymes d. restriction endonucleases 33. What is the natural function of restriction enzymes in bacteria? These enzymes evolved as a mechanism for ridding bacteria of unwanted DNA from viruses and other invaders. They cut the unwanted DNA into fragments that can be digested and removed by the bacterial cell. 34. What is the definition of recombinant DNA? Recombinant DNA is DNA formed from DNAs of different organisms. 35. How can a molecular biologist connect DNAs from two different organisms to make recombinant DNA? If the DNAs from the two different organisms are treated with the same restriction endonuclease, they will be cut at the same recognition site and will possess the same sticky ends. If the two types of DNA are mixed, their sticky ends will pair with each other, hooking together the two foreign pieces of DNA. The association can be made permanent by treating the recombinant DNA with the enzyme DNA ligase which will connect the two foreign pieces of DNA covalently. 36. A vehicle for carrying foreign DNA into a host bacterium is called a(n) a. vector b. ambassador c. victor d. plasmid e. a and d 37. What is the name of the technique that is used to amplify small DNA samples into large amounts of DNA? a. polymerase chain reaction b. PCR c. DCR d. a and b e. replication Multiple Choice, Conceptual, and Open-Ended Questions From the CD-ROM 1. In Section 6.1 of the CD-ROM on the panel titled "DNA Nucleotide Structure," what kind of nitrogenous base is pictured in the drawing of the nucleotide? The nitrogenous base has two rings so it is a purine nitrogenous base. 2. Which of the molecules below is a component of a nucleotide? a. phosphate group b. thymine c. deoxyribose d. thiamine 3. Which of the following is a pyrimidine found in DNA? a. cytosine b. uracil c. a and b d. thymine e. a, b, and c e. a and d 4. What kind of bonds hold together adjacent nucleotides in a DNA strand? a. esters b. covalent bonds c. H bonds d. hydrophobic interactions e. van der Waals forces 5. What kind of bonds hold the paired bases in a DNA double helix together? a. esters b. covalent bonds c. H bonds d. hydrophobic interactions e. van der Waals forces 6. Look at the schematic picture of the DNA double helix in Section 6.1 of the CD-ROM. How many H bonds hold G-C base pairs together? Three H bonds. How many H bonds hold A-T base pairs together? Two H bonds. 7. Look at the schematic drawing of the DNA double helix in Section 6.1 of the CD-ROM. How would you describe the orientation of the two DNA strands relative to each other? They run in opposite directions. Consequently, their alignment is described as antiparallel. 8. Why must the H bonds holding the two strands of the double helix together be broken prior to replication? The bases in the strands of the parental DNA would not be accessible to the enzymes involved in replication if the strands did not separate; thus they would be unable to serve as templates. Replication would not be able to occur. 9. You are studying two pieces of double stranded DNA with exactly the same length. One has a higher G-C content and the other a higher A-T content. Which of the two DNAs will be easier to separate into its component single strands? The double-stranded DNA with higher amouts of A-T base pairs is held together by fewer H bonds than the double helix containing more G-C base pairs. This is because A-T base pairs are held together by only two H bonds while G-C base pairs are held together by three H bonds. Thus, a piece of DNA containing more A-T base pairs would be held together by fewer H bonds and would be easier to separate. 10. What would be the sequence of a DNA strand complementary to the following strand: AGAACCTGA? a. AGAACCTGA c. UCUUGGACU e. none of the other answers b. TCTTGGACT d. AGAACCUGA 11. What is meant by semi-conservative replication? In semi-conservative replication, one of the strands in a newly replicated double helix comes from the parental DNA strand; the other strand is a newly synthesized strand that used the accompanying parental strand as a template. 12. Which of the following is an RNA nucleotide? a. phosphate - deoxyribose - thymine d. phosphate - ribose - uracil b. deoxyribose - thymine e. c and d c. phosphate - ribose - cytosine 13. Which of the following is a DNA nucleotide? a. phosphate - deoxyribose - thymine b. deoxyribose - thymine c. phosphate - ribose - cytosine d. phosphate - ribose - uracil e. c and d 14. What kind of bonds hold together individual adjacent RNA nucleotides in a strand of RNA? a. H bonds b. covalent bonds c. hydrophobic interactions d. ester bonds e. b and d 15. What is the first step in translation just after the mRNA has left the nucleus? Just after leaving the nucleus, the mRNA meets up with the small ribosomal subunit. 16. Once it is released from the ribosome, what happens to a tRNA that has donated its amino acid? It can pick up another amino acid and then go back to the same or another ribosome and participate in translation again. 17. When tRNAs pick up a new amino acid after donating one at the ribosome, can they pick up any amino acid or must it be a specific one? tRNAs can only pick up and donate one specific amino acid. 18. Each time a ribosome translocates (moves) down a mRNA after adding an amino acid to the growing chain and releasing the donating tRNA, how many nucleotides does the ribosome move? a. 1 b. 2 c. 4 d. 3 e. 6 19. What do the following codons code for? AAA lysine, UCC serine, UGA stop codon, GGG glycin, UUC phenylalanine. 20. For what amino acid chain does this mRNA sequence code: AGACUGACAGGGUCGUGA? arg-leu-thr-gly-ser--stop 21. Glutamic acid usually occupies the position of the sixth amino acid in the Beta chain of normal hemoglobin. In the exercise in Section 6.5 of the CD-ROM, what amino acid is substituted for glutamic acid after the mutation shown in the exercise? Valine What kind of mutation is demonstrated in the exercise? A point mutation. What clinical condition does this very mutation cause in humans? Sickle cell anemia. Using BioInquiry in Large Classes Integrating Components into the Lecture There are a number of useful modules on the CD-ROM for this chapter. I recommend that you ask your students to look at them before and/or after the corresponding topics are discussed in class. If you are equipped adequately, you might wish to incorporate parts of these modules, especially the animations, into your lecture. You could show these brief animations before you discuss a particular topic, e.g. replication and/or (maybe even better) after you have described it orally with help from relevant transparencies. Section 6.1 deals with the structure of DNA nucleotides. Students can highlight the components of a nucleotide by pointing to each part with the cursor, lighting up the portion of the structural formula that corresponds to the phosphate group, the sugar, and the nitrogenous base. For students who do not like anything remotely resembling chemistry, the next step is to represent the parts of the nucleotide by icons (especially the nitrogenous base). Eventually, this module ends with an animation that demonstrates how the nucleotides are connected to form a polynucleotide. This demonstration follows a logical sequence that can be easily comprehended by the students. If they have difficulty, they can shift back to an earlier part of the demonstration without much trouble to clarify an issue before proceeding. This allows them to move at their own speed and review if needed. Section 6.2 covers replication with a simple yet effective animation of the process that can be used before attacking the topic and/or after you have described it orally with the help of the relevant transparencies. The animation is accompanied by text that briefly describes the process. Section 6.3 of the CD-ROM contains a module that allows students to explore the structure of RNA and its component nucleotides. It has the same basic features as the Section 6.1 module that illustrates the structure of DNA nucleotides. Have your students note the differences and similarities between DNA and RNA. Once again, the student can highlight the components of each nucleotide and follow the logical step-by-step transition to icons and the assembly of RNA into a polynucleotide. This section also contains effective animations of both transcription and translation. The transcription animation shows the pairing RNA nucleotides with one strand of the DNA that serves as a template for the synthesis of the mRNA that will be translated in the subsequent animation. It even dimly shows the enzyme moving down the template as the RNA is transcribed. The same piece of mRNA which, by the way, carries the eighteen nucleotides that code for the first six amino acids in the hemoglobin ОІ-chain, can then be seen directing translation in the next animation. The translation animation skillfully and accurately illustrates things that are hard to show with still transparencies: the movement of the ribosome down the messenger (translocation), the positioning of the ribosomal A and P sites, the transfer of amino acids from the tRNA in the P site to the tRNA in the A site, the release of the tRNA from which the amino acid has been removed, etc. The use of the first six amino acids from hemoglobin is also a nice touch since it ties Sections 6.3 and 6.5 together. Section 6.3 also contains a transcription-translation exercise in which the student is first asked to transcribe the first eighteen nucleotides of the ОІ-hemoglobin mRNA. Once this has been accomplished, the student then moves on to the translation of this same stretch of mRNA. The students are given three-letter abbreviations for the 20 amino acids and a chart to help them decode the genetic code; they are required to insert the correct amino acid into the appropriate position, thus connecting the first six amino acids into of ОІ-hemoglobin. The exercise effectively tests the students' understanding of both processes. Section 6.5 demonstrates the effect of mutation on the protein coded for by the gene. It starts with the same part of the ОІ-hemoglobin gene employed in the earlier exercises (Section 6.3). It begins by highlighting one of the nucleotides in the sixth codon of the gene and instructing the student to click on the highlighted area. This alters the DNA sequence in the highlighted portion of the gene and highlights the corresponding region of the mRNA transcribed from the gene. Suggest that the students guess at the change that will occur in the mRNA before they click on the highlighted area. Once they do, they can see if they guessed correctly. Assuming they get it, it should reinforce the confidence they have in their level of understanding of the process. If they get it wrong, they can go back and attempt to figure out where they went wrong. When they click on the highlighted area of the mRNA, the change is made and the area that will change in the resultant amino acid chain will be highlighted. They can guess what will happen in general terms before clicking in this area to see the actual results. They may even wish to go back to the genetic code chart in Section 6.3. Of course, they will see a change in the amino acid sequence that can be tracked directly back to the corresponding alteration of the DNA. What makes the demonstration that much more effective is the actual mutation that has just been demonstrated. It is the alteration of glutamic acid to valine in the sixth position of the ОІ-hemoglobin gene, a change that leads to sickle cell anemia in an individual who is homozygous for this mutant form of the gene. To further reinforce the magnitude of the change, Section 6.5 also contains a schematic drawing that compares a normal red blood cell with a sickled red blood cell. The point is well taken and well made. Read More About It A number of books can be read to flesh out the history of the rise of molecular biology. The Double Helix by James Watson is a remarkably candid account of Watson and Crick's discovery of the double helical structure of DNA. It gives a fascinating and not-too-flattering portrait of the attitudes of the principal actors in this story and their principles or lack thereof. The Eighth Day of Creation by Horace Freeland Judson covers the history of the discovery of the double helix and the discoveries that preceded it and followed it. It seems to be a more objective study of the characters involved and gives more comprehensive coverage of the interrelatedness of these studies, the rivalries, and peccadilloes of the investigators and the meaning and significance of the discoveries. It explains in clear language the techniques, principles, and organisms involved in these studies. For coverage of the molecular biology revolution, check out some of the following books. The DNA Story : A Documentary History of Gene Cloning by James Watson and John Tooze talks about the early days of molecular biology research and emphasizes the precautions taken early on to make sure that recombinant organisms would not get out of control. The Genetic Blueprint by Robert Shapiro deals with the potentials and dangers of the molecular biology revolution, as does The Gene Wars: Science, Politics and the Human Genome by Robert Cook-Deegan. For an assessment of where biotechnology will take us in the 21st century, I suggest Visions: How Science Will Revolutionize the 21st Century by Michio Kaku. This book deals with the three scientific areas that the author believes will have the biggest effects on the 21st century and beyond: computers, biotechnology, and quantum mechanics. Kaku also talks about the interrelationships between these three different areas of science. Supporting the Lab Rather than reiterate the nice features of the CD-ROM for this chapter, I will simply suggest that some of these modules might serve as a nice adjunct to laboratory exercise dealing with replication, transcription, and/or translation. For example, we routinely do a simulation of translation in our General Biology class. The CD-ROM animations of transcription and translation can be shown before or after the students attempt the simulation. In our situation, we would prefer to show the animation after the students have attempted the exercise. We have the students role-play the process of translation by giving the students precise instructions describing the role they are to play (A site, P site, the ribosome, aminoacyl-tRNA synthetases, tRNAs, etc.). Each student initially knows only his/her own role. Despite this fact, the students are able to assemble the protein chain without too much trouble. The same thing, of course, occurs in the cell. The tRNAs do not know what the ribosomes and their A and P sites are doing and the aminoacyl-tRNA synthetases do not know what is going on as the peptide bond forms. Answers to the Review Questions 1. Watson and Crick used X-ray (diffraction) crystallography to determine that DNA was a double helix. They did not collect the data they used for this determination themselves, however. The pictures they used were actually taken by Rosalind Franklin. There was a characteristic X-pattern on the pictures that was indicative of helical structure. Proteins can also assume helical shapes as part of their structure (the О±-helices of protein secondary structure). 2. Erwin Chargaff found that regardless of the source of a DNA sample, the relative amounts of the four bases conformed to a rule. The rule was that the amount of adenine in a DNA sample always equals the amount of adenine and that the amount of cytosine always equals the amount of guanine. He also observed that the amount of A+T together is independent of the amount of C+G. He also observed that while the A+T/G+C ratio was the same for all of the tissues in a particular species, it varies from species to species. An understanding of these rules, especially the pairing relationship, helped Watson and Crick to figure out DNA structure and convinced them of its correctness. The model that they built was built to be compatible with the pairing rules and included two polynucleotide chains that were complementary to each other in a way that reflected Chargaff's pairing rules. They realized that this complementarity in the structure could explain DNA's ability to replicate, since the sequence of bases in each chain could specify the bases that appeared opposite them in the other chain. Thus, both chains in a DNA double helix, carry the same, albeit complementary instructions. 3. The four roles that DNA must play in cells are that: (1) DNA must be able to make copies of itself, (2) DNA must encode information, (3) DNA must be able to control cells and tell them what to do, and (4) DNA must be able to change by mutation. The complementarity of the two strands of the double helix explains how DNA can replicate itself, since the sequence of one DNA chain, according to Chargaff's pairing rules, specifies the sequence in the other chain. In addition, the weak H bonds that hold the two strands of the double helix together, while strong collectively, allow the strands to be separated locally in order to facilitate replication and transcription. The sequence of bases in a polynucleotide like that proposed by Watson and Crick is an ideal way to encode information. Furthermore, each nucleotide contains a phosphate group and a sugar that together are responsible for connecting adjacent nucleotides. Thus, the bases can occur in any order without changing the basic molecular structure. It was learned later that RNA copies of one of the DNA strands could be made by separating the strands of the double helix and using one or the other of them as a template for syntheisizing RNA. These RNAs could be used for carrying the instructions to build proteins to the cytoplasm where proteins are made (mRNAs) or they could be used to transfer amino acids to the site of protein synthesis (tRNAs) or they could be used as elements of the structure and enzyme activity of ribosomes that synthesize proteins. This explains how DNA can control cells and tell them what to do. Finally, the conversion of one DNA base to another during replication, for example, would eventually change the corresponding base in the opposite strand. This change would be perpetuated after the next replication. Such changes would then lead to changes in the protein for which the DNA coded. DNA structure eventually was shown to be consistent with each of the four roles. 4. A parental double helix that serves as a template is required for replication as are the enzymes that carry out the reactions involved (e.g., DNA polymerase, etc.), an assortment of nucleotide triphosphates including all four types of DNA nucleotides (A, G, T, C) that provide the energy to drive the reactions, enzymes that help to separate the strands of a double helix, and proteins that help to keep the parental strands separate while replication occurs. The energy needed for DNA replication comes from the nucleotide triphosphates. The two terminal phosphate groups are attached by high energy bonds and those bonds supply the energy used to link them together. The energy is released in two steps. First, the two phosphates are broken off as a unit, forming a pyrophosphate group with a release of the energy in the broken bond. The high energy bond holding the two phosphates together is then broken releasing more energy. 5. Replication takes place in the nucleoid region of prokaryotes which resides within an area of the cytoplasm and takes place within the nuclei of eukaryotes. Transcription in prokaryotes occurs within the nucleoid in the cytoplasm; transcription in eukaryotes occurs within the nucleus. Translation in both prokaryotes and eukaryotes occurs within the cytoplasm. 6. In addition to semiconservative replication, there were two other replication mechanisms considered. Conservative replication results in one daughter helix containing both parental DNA strands (the original parental double helix is conserved) and one daughter composed of newly synthesized DNA. Nonconservative (dispersive) replication would result in two daughter double helices which are composed of both parental and newly synthesized DNA. On average, each daughter double helix would contain about 50% parental and 50% newly synthesized DNA. Results from the Meselson-Stahl experiment can be predicted for each mechanism and then compared to the actual results to determine the mechanism that actually operates. If replication is conservative, after one replication cycle with the Meselson-Stahl protocol, half of the DNA produced should migrate to the position in a CsCl gradient corresponding to fully heavy DNA while the other half migrates to the position corresponding to fully light DNA. The results actually obtained were quite different. All of the DNA migrated in the gradient to a point midway between the fully heavy and fully light positions as would have been predicted for semiconservative replication. Thus, after one replication cycle, conservative replication was eliminated as a possibility. After one replication cycle, nonconservative replication would be expected to result in a broad DNA band centered in the gradient between the fully heavy and fully light positions. This is similar to but not identical to the results obtained. The results after the second replication cycle, however, are unambiguous. With nonconservative replication, the expected results for the end of the second replication cycle would be a broad band of DNA migrating between the midpoint in the gradient and the fully light position. The results obtained were half of the DNA in a sharp, well defined band at the fully light position in the gradient and half of the DNA in a sharp band at the midpoint in the gradient between the fully heavy and fully light positions. This is exactly what would be predicted for the semiconservative mechanism and is not at all close to the predicted results for the nonconservative mechanism. Thus, the nonconservative mechanism was eliminated as a possibility. 7. RNA is used as an intermediary in a two-step process leading from DNA to proteins, because the large size of DNA makes it impractical to move through the cell from the nucleoid to the cytoplasm in prokaryotes or from the nucleus to the cytoplasm in eukaryotes. RNA is smaller and thus much more mobile and can travel to those parts of the cell (the cytoplasm) where protein synthesis occurs. Furthermore, DNA is much safer from damage within the nucleoid or the nucleus than it would be if it were to travel into the cytoplasm to direct protein synthesis. On the other hand, if RNA is damaged in the cytoplasm, more can be synthesized to replace it. 8. DNA and RNA differ in a couple of ways. They contain different sugars. The deoxyribose found in DNA lacks an oxygen attached to the 2'-carbon of the sugar. Ribose, the sugar found in RNA, possesses an oxygen attached at the 2'-position. The nitrogenous bases in DNA and RNA are different. DNA contains adenine, guanine, thymine, and cytosine while RNA also contains four nitrogenous bases with thymine replaced by uracil. DNA is most stable and most often found as a double helix while RNA most often exists as a single-stranded molecule. DNA molecules tend to be much larger than RNA molecules. DNAs are basically immobile while RNAs are highly mobile, moving between the nucleus and the cytoplasm. Finally, DNA is fairly long-lived while RNAs are broken down fairly soon after their job is done. DNA is a double helical molecule which can exhibit higher order folding called supercoiling that allows it to packaged relatively compactly within the nucleus/nucleoid. RNA is usually a single-stranded molecule, but it can form short-lived associations with complementary sequences on other strands or elsewhere within the same strand. When RNAs fold back on themselves in this way, the molecule adopts distinctive shapes that are important for DNA function. DNA is the repository of genetic information; it contains the instructions needed to build the organisms that contain it. The roles of RNA are much more varied. It plays a number of roles in protein synthesis and other cellular processes and can have enzymatic activity. 9. The three main types of RNA are mRNA, tRNA, and rRNA. Messenger RNA (mRNA) carries genetic information from the DNA (nucleus) to the cytoplasm where it is translated into protein. mRNA is typically a long, unfolded chain and exhibits rapid turnover since it is the least stable of the three classes of RNA. Transfer RNA (tRNA) brings amino acids to the sites where mRNA is translated into protein. Thus, it must be able to recognize both the mRNA template and a specific amino acid. tRNAs fold back on themselves to form a distinctive shape that looks like a folded lowercase letter "t." They are held together by the tendency for nitrogenous bases within a single tRNA to form pairs. At the bottom of the "t," there are three unpaired bases (the anticodon region) and at the top, a loose end that binds to the amino acid specific for that tRNA. Each tRNA recognizes and binds to only one of 20 different amino acids, a specificity that is crucial. The anticodon region associates with three complementary bases on the mRNA during translation and thus tRNAs carrying specific amino acids will recognize certain parts of mRNA. tRNAs are relatively long-lived lasting from hours to days. Ribosomal RNA (rRNA) makes up most of the RNA in eukaryotes (>80%). Several different RNAs and many proteins combine to form ribosomes, the site of protein synthesis. rRNAs, like tRNAs, fold back on themselves in highly ordered complex patterns that are required for their duties. rRNAs act like enzymes in that they accelerate some of the chemical reactions of translation. In fact, rRNA has been implicated as the catalyst responsible for forging the peptide bond. 10. The smallest possible number of different tRNAs that must exist in cells is twenty, one for each amino acid. If there were not at least twenty tRNAs, the positioning of amino acids would be ambiguous. 11. If the different tRNAs in cells could bind to just any amino acid, the specificity required of tRNAs and their attached amino acids would be compromised. Very few proteins would possess the correct primary structure and they would thus not function properly. The specificity of tRNAs for particular amino acids assures that the amino acid corresponding to the anticodon (codon) will be placed only in those positions within a growing protein where it belongs. It is this rigid correspondence between the anticodon and the attached amino acid that maintains the integrity of the genetic information. 12. If a ribosome encounters a codon on mRNA that does not correspond to any of the amino acidlinked tRNAs, the growth of the polypeptide chain is terminated. Such a codon is thus called a stop codon. Termination of protein synthesis requires the help of accessory proteins called release factors. 13. Promoters are DNA sequences outside the coding portion of a gene that signal RNA polymerase to attach to the DNA template at that point and begin transcription. Not all promoters are equal; strong ones are better at attracting RNA polymerase than weak ones. Therefore, genes preceded by strong promoters are transcribed often. Such genes encode proteins that are required by the cell in large quantities. Those genes coding for proteins not so much in demand have weaker promoters. There are also regulatory sequences that lie outside the amino acid coding regions. Transcription factors recognize and bind to these specific DNA sequences and act by increasing or decreasing the rate at which specific proteincoding genes are transcribed. Without such sequences, cells would be less able to make appropriate responses to changes in their environment. This could lead to deficits in cellular function at the very least and possibly to illness or death in the organism whose cells lack these DNA sequences. 14. Each cell contains the complete genetic complement of the organism of which it is a part. Yet, each cell only needs a small portion of the organism's full repertoire (coded for by the genes) in order to perform its assigned functions. It would be a waste of time, energy and raw materials to make proteins the cell does not need. Therefore, the cell does not manufacture such unnecessary proteins. Gene expression is regulated at the transcriptional level; environmental changes lead to an increase or decrease in the transcription of particular genes. Alternatively, mRNAs can be translated to varying extents; some are translated many times and others only a few times before they are degraded into ribonucleotides. Messenger RNAs can exhibit varied longevity; mRNAs with longer chains of adenines on their 3'-end have longer life spans than those with few adenines on the 3'-end or none. If a mRNA survives a longer period of time, it will tend to be more productive than a shorter-lived mRNA. 15. The mutation that causes sickle cell anemia is a point mutation. In such a mutation, one base is replaced by another. In other words, a single base (or at most just a few bases) is altered. If only one base is changed, it leads to a change in a single amino acid in the corresponding protein. In sickle cell hemoglobin, only one amino acid out of 146 is changed. The amino acid in the sixth position in the normal hemoglobin ОІ-chain (glutamate) is changed to valine in the sickle cell ОІ-hemoglobin. 16. A frame-shift mutation would be more harmful at the start of the gene. In a frame-shift mutation, the gene (and the protein for which it codes) is normal up to the point at which the addition or deletion occurs. Beyond that point, however, the reading frame is shifted so that the sequence of amino acids in the resultant protein is completely changed from the point of the mutation on. In some cases, a termination codon can appear in a place where it normally would not leading to a truncated protein. If such a mutation occurs near the end of a gene, the protein coded for by the gene will be normal up to the point at which the addition/deletion occured. The protein would be likely to retain at least some of its function. If the mutation occurred near the start of the gene, a more significant portion of its primary structure would be changed or eliminated (if a termination codon appears), and the protein's function would be severely compromised or would disappear entirely. CHAPTER 7 POPULATION GENETICS: HOW DO GENES MOVE THROUGH TIME? Lecture/CD-ROM Outline Overview I. Darwin's description of evolution by natural selection made two important assumptions A. Traits are passed from parents to offspring B. There are important differences between individuals, even of the same species II. The relationship between Darwinian evolution & Mendelian genetics is not immediately obvious A. The relationship had rocky beginnings B. Eventually, Mendelism & Darwinism reconciled in the 1930s & gave rise to a new field of study population genetics 1. Population genetics is the study of how genes of entire populations change over time 2. Thus, it describes how groups of organisms evolve C. This integration of evolution & genetics was a new synthesis of existing ideas - population genetics is the combination of Mendelism & Darwinism III. Variation is central to both theories A. Darwin noticed that individuals in natural populations may show slightly different forms of a given trait or characteristic & recognized it as the raw material of evolution 1. Without variation, there would be nothing upon which natural selection could act B. Mendel used individual variation to derive his laws of inheritance - focused on traits that show only two distinct forms How Do We Characterize Variation? I. Theodosius Dobzhansky, Russian-American geneticist - published book in 1937 (Genetics & The Origin of Species) unified the "experimentalist" & "naturalist" schools of biological thought A. These schools had bickered for years 1. Naturalists felt Darwin's ideas were the most consistent with observations, but rejected Mendel's ideas 2. Experimentalists agreed with Mendelian genetics but rejected natural selection as the driving force of evolution B. Both groups had important & accurate insights into the nature of life, but both were guilty of relying on erroneous assumptions, preventing them from seeing the truth in the other's ideas 1. In the early 20th century, animosities arose between the schools 2. It took new young thinkers (Dobzhansky and others) to bring the factions together & show how evolution by natural selection and laws of heredity are part of the same story II. Variation can be smooth or discontinuous A. To naturalists (field scientists, paleontologists), evolution by natural selection made perfect sense; spent time outdoors observing populations of organisms in their natural settings 1. Had first-hand knowledge of variation among individuals - saw that most traits, when examined in a population of individuals in the same species, exhibited a continuum of forms 2. A few individuals were at either end of spectrum & many others showed intermediate forms B. Mendel, on the other hand, had described individuals with one or another discrete form of a trait (tall vs. short, purple vs. white) & nothing in between III. Naturalists believed survival & reproducibility depended on traits falling within some certain range of spectrum, but this contradicted Mendel's laws A. Realized that organisms' environment might change over time, making a different range of same more advantageous B. In this way, traits within populations change or evolve as environments change & eventually give rise to new species C. Thus, naturalists stubbornly refused to believe that Mendel's factors had a role in evolution IV. Experimentalists chose to focus on sudden changes that occur as a result of mutations A. New forms of traits resulted from mutations of existing alleles, they said B. Evolution was seen as progressing by leaps & bounds driven by sudden, random mutations 1. Thus, they felt that evolution could not possibly be a gradual process 2. New species arose when one or more mutations resulted in an individual unlike any before it C. They worked in a laboratory, focused on individual genes that were Mendel's discrete factors 1. Stubbornly refused to believe that continuous traits that occur in natural populations had any relation to genes or to evolution 2. Believed that natural selection might play a minor role in weeding out deleterious mutations, but that it was not important in evolution & origin of new species V. Herman Nilsson-Ehle, Swedish plant breeder, 1909 - first breakthrough in stalemate A. Worked with wheat kernels; showed that traits appearing in populations as continuous spectrum have genetic basis вЂ”> smooth variation in natural populations now fit into the genetic framework 1. Some kernels were white, others deep red; most are shades in between (pale pink to light red) 2. Trait appeared to exhibit continuous variation, but cross of true-breeding red & purebreeding white kerneled plant produced all light red kernels (F1) that were intermediate 3. Sounds like incomplete dominance -> when cross F1 kernels got F2 with seven color categories (dark red, moderately dark red, red, light red, pink, light pink & white) B. Repeated many times & ratio was always the same (1:6:15:20:15:6 : 1); such predictable results could not be due solely to chance VI. Frequency diagrams illustrate variation A. A simple graph 1. x-axis shows range of different forms that a trait can exhibit within a population (white at one end, red at the other) 2. y-axis shows number of individuals (or some relative number like percent) in population that exhibit each form of trait B. Example: flower color (incomplete dominance) - should be three bars (red, pink, white); pink bar should be about twice as high as the other two C. Example: human height, people come in all different sizes so they blend into one another forming smooth, bell-shaped curve 1. Continuous variation of the type Darwin & naturalists reported: tall, short, many in the middle 2. Highest point on perfect bell curve represents the mean or average form 3. Calculate the average height by summing all heights of all people in population then dividing by the number of people in the population measured; center of traits distribution D. Nilsson-Ehle's wheat kernels in F2 generation were red to white with five intermediate forms 1. Frequency diagram intermediate between perfectly discontinuous & continuous traits 2. If his seedlings are raised in the wild, their environments (sunlight, more water, nutrients) will vary more & so will seed color (each color category will have its own bell curve) 3. Distinct overlap between categories; distinctions blurred so get a continuous color variation spectrum - how can such a continuous spectrum be explained by Mendel's factors? VII. Continuous variation is determined by two or more genes A. Many evolutionarily important traits (height, weight, growth rate) are not traced to a single gene 1. They are due to simultaneous expression of two or more genes all influencing the same trait 2. Such traits are called polygenic or quantitative traits 3. Each single trait has its own specific chromosomal address (locus, loci, plural); fixed position occupied by one of the alleles or forms of that gene 4. Polygenic traits influenced by two or more genes residing at different loci on the same or different chromosomes B. A person can carry at most two alleles for one gene; as many as four, six, & eight alleles for two, three, & four genes, respectively вЂ”> this can give a range of traits; example: wheat kernels 1. Three different genes contribute equally to kernel color 2. When all six alleles code for red pigment, kernel - dark red; if none encode red, kernel - white 3. If only one red allele вЂ”> light pink, etc. 4. Actual kernel color (phenotype) is the sum of the individual effects of each of six alleles 5. In this case, if there are more dominant alleles, color will be darker C. As the number of genes determining a trait increases, variation within the population changes from discrete categories to a smooth continuum 1. Add environmental influence on expression of each allele & frequency diagram goes from a few nonoverlapping bars to a smooth bell curve 2. Explains why a trait influenced by as few as two genes can show a smooth curve; it is what naturalists saw D. No one knows how many traits are polygenic & how many are monogenic 1. Most traits dealing with size, shape, & form are polygenic 2. Mendel's peas have polygenic traits, but he did not study them VIII. Steps in reconciling Darwin & Mendel A. All genes are passed in Mendelian fashion; apply genetics to the study of evolution by natrual selection B. Define evolution not as appearance/disappearance of different species through ages, nor as changes in traits expressed in species, but as changes in population genetic make-up over time How Do Populations Differ? I. Brachydactyly - human trait in which the terminal bones of the fingers & toes do not grow to normal length; sufferers are characterized by stubby digits A. Cause is single dominant gene inherited in strict Mendelian fashion; people with only one allele for brachydactyly exhibit trait, it appears to be dominant 1. If two heterozygotes exhibiting trait mate, 75% of offspring will have at least one allele for trait 2. Yet, fewer than 0.1% of humans are brachydactylous - why? B. To understand, must know what proportion of reproductively active individuals carry the allele for the trait C. Understanding genetics of entire populations, & thus the way they evolve, requires knowledge of all of the alleles in the population, not just those in a single mating pair 1. Task made simpler when, early in 20th century, some mathematical tools were devised 2. Tools allowed calculation of occurrence (frequency) of different alleles in natural populations II. Populations are collections of alleles A. Definitions for a population 1. Traditional - a group of interbreeding organisms of the same species that exist together in both time & space 2. Population genetic - to learn how populations evolve, population is not a group of individuals but a group of alleles (all of the alleles found in a population are called the gene pool) B. Analogy for population genetics (beanbag genetics) - the alleles in a population are visualized as randomly assorting & individually segregating as predicted by Mendel 1. Alleles are like beans in a beanbag; entire beanbag full of beans is population's gene pool 2. Ignores fact that the "beans" can actually influence each other in important ways 3. Consider all the alleles for all the different traits at once or some subset (alleles for single trait) C. Example: hemoglobin ОІ chain - normal allele - HbA; slightly altered allele - HbS; individual with two HbS alleles suffers from sickle-cell anemia III. Alleles occur at certain frequencies - use hemoglobin ОІ chain as example; gene pool contains twice as many alleles as individuals in population (in this "beanbag", two types of beans - HbA, HbS) A. Can calculate the proportion of certain alleles in population especially with only two alleles - they must total 100% 1. Assign letter p as proportion of HbA (dom.) alleles, q as proportion of HbS (rec.) alleles 2. p + q = 1.0; 1.0 represents 100%; p & q - proportions (fractions that must add up to 1) allelic frequencies 3. Can calculate proportion of population carrying two HbS alleles (sickle-cell patients) - count them; not as easy to tell carriers since HbA form is nearly dominant (usually no symptoms) B. But we can use what we know about phenotypes in population to calculate frequencies of p & q IV. The Hardy-Weinberg Principle relates genotypes & allelic frequencies - English mathematician G. H. Hardy & German physician Wilhelm Weinberg, 1908 A. They independently developed the principle for calculating p & q based on phenotypes 1. Assumed populations are very large & that no individuals enter or leave population, that individuals mate at random 2. This means that the frequency of any allele in population will be the same as the frequency of that allele in the haploid gametes 3. Probability that a given egg or sperm carries HbA allele is p & probability of carrying HbS is q 4. Probability that HbA-carrying sperm fertilizes HbA-carrying egg is p x p or p2 & proportion of HbA/HbA individuals in population is p2 5. Likewise, the probability that HbS-carrying sperm fertilizes HbS-carrying egg is q x q or q2 & proportion of HbS/HbS individuals in population is q2 6. Two ways to get a heterozygote, either HbS egg & HbA sperm or vice versa; probability of either case is p x q so the probability of a heterozygote is 2pq [(p x q) + (q x p)] 7. If sum probabilities of all possible genotypes account for whole population thus p2 + 2pq + q2 = 1.0 8. This is an expansion of an algebraic binomial expression: (p + q)2 = 1.0 B. The above principle has come to be known as the Hardy-Weinberg Principle 1. Stated in words, it says that the frequencies of genotypes for a gene with two different alleles are a binomial function of the allelic frequencies 2. Also says that, barring outside influences such as immigration, emigration, or selection, the allelic frequencies of a population will remain the same from one generation to the next 3. Regardless of how the alleles are paired during sexual reproduction, p & q do not change 4. Populations in which p and q don't change are said to be in genetic equilibrium V. Hardy & Weinberg made some assumptions regarding the way in which other factors influence p and q when they derived their equation A. Populations are very large - most natural ones are large enough that this approximates reality; very small populations experience drastic changes in allelic frequencies due only to chance 1. Small populations are not in genetic equilibrium B. Individuals mate at random - many plants & animals in nature do; humans sometimes don't (tightly inbred social groups like religious sects or highly isolated communities) C. Populations do not gain or lose individuals by immigration & emigration - if enter or leave the population, their alleles go with them 1. Extent to which it happens in nature varies considerably 2. When immigration & emigration occur, the population is not in genetic equilibrium D. Natural selection is not occurring - does not always reflect reality; lowers frequency of harmful alleles & raises that of beneficial alleles in nature; not in genetic equilibrium E. Mutation is not occurring at a high enough rate to influence genetic variation - relatively rare; cause only small allelic frequency changes from one generation to the next 1. Generally ignored as a factor influencing genetic variation over just a few generations VI. Hardy-Weinberg allows us to calculate what would happen if natural selection was not occurring then compare that to what does happen in real world A. Sample calculations - assume a population with 2% of people suffering from sickle-cell anemia 1. 0.02 is proportion of population that has two HbS alleles (q2) - typical of rates in sub-Saharan Africa & Near East 2. q2 = 0.02 so q = 0.021/2 (square root of 0.02) = 0.14 3. Since p + q = 1.0 вЂ”> p + 0.14 = 1.0 вЂ”> p = 1.0 - 0.14 = 0.86, thus about 14% of alleles in the population are HbS and about 86% are HbA 4. Can also calculate the proportion of heterozygotes вЂ”> 2pq = 2 (0.14)(0.86) = 0.24 or 24% B. Back to earlier question - why do so few people exhibit the dominant trait of brachydactyly? 1. In a single cross of heterozygotes, the allelic frequencies for p and q are both 0.5 2. In a population, brachydactyly allele is nowhere near 0.5; actually quite low (< 0.001) so very few will inherit it VII. Speciation begins when allelic frequencies of two or more populations start to diverge - natural selection is most important mechanism driving speciation but there are others How Can Allelic Frequencies Change Over Time?: Changing Environments & Heterozygote Advantage I. Sparrow looks for moth (Biston betularia) to eat in Manchester, England, near a textile mill A. 1848 - tree trunks covered with healthy lichens; bark - mottled appearance, patchy brown, white 1. Occasional black moths (carbonaria form) were easy to see on lighter background -> sparrows ate them selectively so their numbers did not build up in population (natural selection) 2. More common speckled moths camouflaged by similarity to tree bark so not eaten as often B. 1900 вЂ“ Manchester mills have belched out black smoke for 50 years; lichens are dead from the pollution 1. Speckled moth cannot hide on tree trunks black with soot but carbonaria form is well hidden 2. Carbonaria form is now very common (almost every moth); speckled form is rare 3. Pressures of natural selection have shifted & moth population has responded II. Natural selection changes allelic frequencies A. Phenomenon described above is called industrial melanism вЂ“ one of the most spectacular & well documented examples of natural selection ever recorded 1. Color is result of a pair of alleles at a single locus; carbonaria form (M) is dominant to speckled form (m) 2. Estimated that before 1848, M allele was ~10% of population's alleles; other 90% -m allele B. What happens if no allele is favored by natural selection or any other mechanism? 1. p = 0.1 (frequency of M allele); q = 0.9 (frequency of m allele); use values in HardyWeinberg equation 2. Frequency of MM = p2 = (0.1)2 = 0.01; frequency of mm = q2 = (0.9)2 = 0.81 3. Frequency of Mm heterozygote = 2pq = 2(0.1)(0.9) = 0.18 4. Thus, 1% of the population is homozygous for carbonaria form, 81% homozygous for speckled form and 18% heterozygous вЂ”> since carbonaria is dominant 19% are carbonaria 5. If every moth regardless of phenotype is equally likely to survive & reproduce вЂ”> neither allelic nor genotypic frequencies change from generation to generation (no natural selection) 6. Allelic proportion in gametes equals the proportion in gene pool & all have an equal chance of combining with all the other gametes in opposite sex вЂ”> genetic equilibrium C. Assume that after air filled with soot, about half of speckled moths were eaten in each generation, but no carbonaria were eaten вЂ“ parental generation was 19 black & 81 speckled for every 100 1. Of the 81 speckled moths, estimate that 40 were eaten вЂ”> only 60 moths reproduce, 41 of which are speckled (speckled went from 81% of population to ~68% [41/60] in 1 generation) 2. Calculate allelic frequencies: 41 mm moths & 18 Mm moths (41 x 2 m alleles from mm moths & 18 m alleles from Mm moths) вЂ”> 100 m alleles out of a total of 120 alleles (60 moths x 2) 3. m allele frequency has dropped from 0.9 to ~0.83 (100/120); M allele up from 0.1 to ~0.17 4. Over several generations of natural selection, relative numbers could change dramatically III. Why hasn't natural selection reduced the frequency of the sickle-cell allele? вЂ“ in certain parts of the world, people who are heterozygous have advantage over either of the homozygotes A. Heterozygote advantage вЂ“ near equatorial belt of central Africa, malaria is endemic 1. Children are exposed year-round with several infections during their early years (up to two million children die of malaria each year) 2. If they survive, they acquire considerable immunity to malaria so they are likely to ward off subsequent infections 3. HbS allele helps them survive вЂ”> tendency of some RBCs in heterozygotes (carriers) to sickle makes them particularly resistant to penetration by malaria parasite 4. Heterozygous children are better able to survive the disease & acquire immunity from later infections 5. HbA/HbA people are more susceptible to malaria; most HbS/HbS people do not survive to have children B. Thus, natural selection can reduce or eliminate detrimental alleles or maintain genetic variation by favoring heterozygotes How Can Allelic Frequencies Change Over Time?: Microevolution & Macroevolution I. Microevolution - moths, sickle-cell anemia are examples (changes in population allelic frequency) A. Can occur in a relatively short time (over just one or a few generations) B. It is also reversible вЂ“ Manchester mills have begun to reduce pollution (last 35 years); lichens are coming back & so is speckled form of moth II. Macroevolution - describes the larger-scale changes that lead to the origin of higher taxa or categories of organisms (orders, families, phyla) A. Most evidence indicates that the higher taxa that characterize macroevolution are formed by the accumulation of many small changes in gene frequencies at the population level B. Microevolution gives rise to macroevolution C. Natural selection is the microevolutionary process in which individuals varying in one or more traits differ in their ability to survive & reproduce D. As a result, frequencies of different alleles shift over one or more generations 1. Selection may favor one extreme form or another, one end of the spectrum of variation 2. Sometimes it is most advantageous to be average 3. Natural selection can favor both ends of the distribution at the expense of the middle How Can Allelic Frequencies Change Over Time?: Favoring Different Parts of a Phenotypic Range I. Directional selection - mean value for trait shifts in particular direction (ex.: long tongues in frogs) A. A long tongue in a frog ensures that it has good chance of securing a ready food supply 1. Frogs with longer tongues are favored; can capture more insects from farther away 2. Such frogs survive more readily & will likely reproduce more вЂ”> their frequency goes up B. However, forces also prevent the tongue from becoming too long, e.g. ability to close mouth C. Forms of traits at one end of variation range get more common with each succeeding generation II. Stabilizing selection вЂ“ sometimes the middle of the variation range is the most advantageous place (ex.: frog movement; must be able to move in two different environments вЂ“ water & land) A. Frog legs are perfect compromise for these two types of locomotion 1. Webbed feet are adapted for swimming 2. Long muscular legs are adapted for jumping B. Frogs with more finlike legs would be less effective on land; those with smaller unwebbed feet would be weaker swimmers вЂ”> selection maintains compromise 1. Frogs with combined features would be more likely to survive and reproduce 2. Their numbers would increase; extreme phenotypes are less well adapted & less numerous C. In unchanging environments, stabilizing selection is the rule D. Large population gene pools usually retain enough variation to produce members at two extremes, even after many generations of stabilizing selection 1. Quantitative traits that exhibit bell-shaped frequency distributions are the result of many alleles functioning at different genetic loci 2. Most successful breeders near the bell curve mean are probably heterozygous at some of these loci 3. By chance, some members of each new generation will have a particular combination of alleles that places their phenotypes at extremes of the curve 4. This is adaptive вЂ“ if the environment changes, the previously unadaptive form may prevail & population will shift (ex.: carbonaria form of moth) 5. Populations that lack variety are likely to become extinct when environmental features change III. Disruptive or diversifying selection вЂ“ sometimes the middle of the range is a problem while either end is advantage (ex.: birds & beak length) A. Assume that bird population has a lot of variation in beak length & that normal food supply for population (some fruit or insect) becomes scarce 1. Some other bird species enters territory & competes for limited food supply 2. Birds with small beak adept at exploiting new & different food source (beetles & worms from small crevices in fallen trees) 3. Large beaks are strong & able to crack seeds of large fruits or crush snail shells 4. Birds with middle-sized beaks are not good at either of the above 5. Selection would favor birds with large or small beaks & work against intermediate form 6. After several generations, two extremes become more common & intermediate forms decrease B. Disruptive selection works against intermediate individuals & favors those at ends of distribution 1. In time, population splits into two subpopulations вЂ”> may lead to formation of two separate species How Can Allelic Frequencies Change Over Time?: Random Changes in Allelic Frequency: Genetic Drift, Founder Effect, and Bottlenecks I. Genetic drift вЂ“ in a small population, chance can be important in determining gene pool composition A. Without influences of selection, flux (immigration, emigration), or mutation, passing alleles from parent to offspring is random process like picking colored beans from a beanbag 1. If draw many beans, numbers of colors you draw will reflect different colors in bag вЂ“ if bag is 50% red & 50% green, then drawn beans should be 50% red & 50% green 2. If draw only a few beans, may draw only red or only green; good chance that drawn sample may not resemble population at large вЂ”> same is true of gene pool 3. Such chance events are called genetic drift; can significantly alter frequency of different alleles in the next generation B. Genetic drift is the alteration in allele frequencies that results from chance variation in survival and/or reproductive success 1. Since it results when small samples of alleles are taken from a larger pool, the complete variety of alleles in parental pool is almost never fully represented in sample 2. Thus, genetic drift invariably results in the loss of genetic variation 3. Since such microevolutionary changes are independent of natural selection, they are called neutral selection 4. Alleles perpetuated or lost due to genetic drift are random, unlike the case of natural selection II. Founder effect - a microevolutionary phenomenon & form of genetic drift; occurs when there is difference in gene pool allelic makeup due to population initiation by small number of individuals A. Tristan da Cunha вЂ“ remote volcanic island ~1500 miles off Africa's west coast in South Atlantic; has a population of ~275, all descended from 15 English settlers who arrived in the 1800s 1. University of Toronto study вЂ“ 57% of islanders suffer from asthma or asthma-like symptoms; in population from which they descend, England, the level is only ~10% 2. Historical records - at least two of original settlers were asthmatic 3. Researchers have concluded that alleles carried by founders of population have made their descendants particularly susceptible to asthma 4. When they arrived from England, they carried alleles that became the basis for a new gene pool, one differing from the parent population in England B. Founder effect is primary factor in abnormally high genetic disease levels in small, closed human populations; ex.: isolated religious groups can have high levels of rare, deadly diseases (Amish) 1. Amish of Lancaster County, Pennsylvania have high incidence of Ellis-van Crevald syndrome; sufferers have short limbs, malformed hearts, & six fingers on each hand 2. ~1% of population normally has Ellis-van Crevald 3. Pennsylvania Amish society started by a few founders who settled in Lancaster from Holland 4. Many trace ancestry to one man, Samuel King in 1800s; either he or his wife carried this allele III. Bottlenecks вЂ“ when population undergoes temporary decline to low numbers from which survivors of all future generations are derived, genetic drift plays role in determining gene pool composition A. 19th century вЂ“ Northern elephant seal heavily hunted; population dropped to <20 individuals 1. Conservation efforts have since resulted in an increase in the population (now >50,000) 2. Created a bottleneck; as with all genetic drift type populations, genetic variation was reduced B. Full range of original population's genetic variation is never fully represented in the few survivors 1. Invariably detrimental and often catastrophic 2. Many populations that lack genetic variability perish after even minor changes in environmental conditions 3. As humans reduce the number of natural habitats & more species become endangered вЂ”> more bottlenecks 4. Even attempts to preserve species cannot bring back the genetic variation of original population C. Conservation genetics is a biology subdiscipline that tries to maintain genetic variation by careful breeding and artificial selection programs How Can Allelic Frequencies Change Over Time?: Random Changes in Allelic Frequency Mutation I. Mutation - in the early 20th century, experimentalists attributed all evolution to sudden, random appearance of new alleles via mutation A. In some ways, the experimentalists were wrong 1. Natural selection & genetic drift are both important factors in establishing frequencies of different alleles 2. New species arise from existing ones when allelic frequencies of different populations diverge enough to prevent them from interbreeding B. But the experimentalists were also right about some things 1. Mutation is a random process that plays a crucial evolutionary role by creating new alleles 2. Without it, there is no genetic variation upon which selection or genetic drift could act II. Hardy & Weinberg assumed that mutation did not occur in their ideal population, but, in real populations, mutations arise with infrequent, but measureable, regularity A. Copenhagen - in a maternity hospital, there are records of nearly 95,000 births; of these ten newborns had achondroplasia (a form of dwarfism; dominant allele) 1. Two had affected parent; thus, eight newborns appeared to be new mutants; from these data, mutation rate can be calculated 2. Mutation rate = 8 mutations/[(2)(95,000) alleles] = 4.2 x 10-5 mutations per allele or about one mutation for every 23,750 alleles B. Rate at which genes mutate differs for different genes & for different species but this order of magnitude (about 10-5 mutations/allele for each generation) is reasonably characteristic III. Mutations introduce new alleles into gene pool вЂ”> get three somewhat arbitrary categories of mutations with respect to three different fates for the recipient based on gene's effects A. Lethal or near-lethal mutations - may hide as recessives in diploid species masked by nonlethal dominant counterparts for generations; selection keeps frequency low or eliminates them B. Most common - selectively or nearly neutral mutations -> may spread through gene pool or be eliminated by random means, like genetic drift 1. Most genetic variation from mutation in natural populations arose originally & was perpetuated in this neutral manner C. Small number of advantageous mutations, selected for within population; if recessive, may hide in gene pool until or unless paired in homozygote where benefits are fully expressed IV. Ability of mutation alone to affect large changes in allelic frequency is negligible, but combined with natural selection & random forces of genetic drift, mutation becomes the stuff of evolution How Can Allelic Frequencies Change Over Time?: Random Changes in Allelic Frequency Gene Flow I. Gene flow - movement between populations; results in introduction of alleles from one population to another via immigration or the loss of alleles from one population to another via emigration A. New species arise when subpopulations become reproductively isolated from each other 1. Sometimes ecological or geographical barriers or differences in behavior prevent two groups from mating вЂ”> effectively creates two gene pools from one 2. As the level of genetic connectedness (ability to inbreed) between two subpopulations declines another Hardy-Weinberg assumption is violated вЂ” random breeding 3. Two separate gene pools are now free to undergo changes in genetic composition by natural selection or genetic drift B. But individuals are often able to move from one population to another, introducing the genetic elements that characterize their parent population through mating & reproduction II. Often effect of gene flow coupled with natural selection is significant (ex.: mosquitoes & DDT) A. After World War II, DDT was used liberally to control populations of various insect pests like malaria-carrying mosquito 1. Kept mosquito numbers down for awhile but resistant strains began to appear 2. A mutant mosquito high in levels of single enzyme (esterase) appeared by random mutation in one population вЂ”> esterase breaks DDT down into harmless metabolites 3. Just after World War II, most mosquitoes had esterase levels too low to detoxify DDT 4. Soon mutant mosquito produced many offspring, some of which produced excess esterase 5. These progeny & their progeny infiltrated mosquito populations of the world, carrying alleles allowing them to produce lots of esterase 6. These alleles flowed from population to population via emigration & immigration & conferred an obvious advantage, so they spread rapidly in new generations B. Most mosquito populations are now DDT-resistant so malaria is on rise in many African & Asian countries вЂ”> thus, pest control programs must take into account principles of population genetics Hardy-Weinberg Revisited I. Stringent restrictions of Hardy-Weinberg are almost never met; genetic (Hardy-Weinberg) equilibrium is rare; most populations are subject to outside influences & all are finite A. Nonetheless, for many populations, the effects of size & outside influences are small enough to be negligible; many natural populations approximate equilibrium, especially in stable environments B. Value of Hardy-Weinberg is not what it says about conforming populations but what it says about & what we can learn about those that do not conform to the principle 1. We can learn exactly how real populations differ from genetic equilibrium 2. We can then determine the factors responsible for the differences II. We have been concerned mostly with processes of microevolution вЂ” the manner in which allelic frequencies change over time & distance within a species A. When conditions are such that changes are vast & irreversible, may get new species entirely B. Gene pool may be sufficiently different from parent population that members of two groups can no longer interbreed C. New species have changed, evolved over time, giving rise to new orders, classes, phyla, & kingdoms Where Are We Now? I. Population genetics principles are useful in understanding problems of human genetic disease, including origins of some disorders & risks to members of families, ethnic groups, populations A. Applied these principles to the study of two genes implicated in breast cancer, BRCA1 & BRCA2 1. Most common alleles for these genes encode normal proteins that play important role in regulating cell division 2. Certain less common alleles (mutant alleles) encode proteins that do not function properly 3. Women who inherit mutant alleles for either gene are at high risk for developing both breast & ovarian cancers B. Mutant BRCA1 & BRCA2 alleles account for ~6-10% of breast cancers in most populations II. Questions about mutant alleles of BRCA genes A. How many different alleles exist that have been implicated in cancer? 1. So far >30 different BRCA1 alleles & >15 BRCA2 alleles have been identified worldwide 2. Many are found in one or a few countries or populations 3. More alleles are expected as studies continue B. Where and when did mutant alleles originate & how have they dispersed from one population to another? 1. Human population structure (patterns of migration, natural selection, marriage traditions) influences the manner in which alleles occur in populations 2. One mutant allele of BRCA1 gene (the 185delAG allele) is found in ~1% of people of Ashkenazi Jewish heritage; also found among Iranian & Iraqi families 3. Mutant allele is missing two nucleotides (A & G), a deletion, at a position in the DNA corresponding to the 185th base pair 4. Original mutation probably occurred before the populations were separated 5. Before 70 BCE, Jewish life centered around the Temple in Jerusalem; in 70 BCE, Romans occupied Jerusalem, destroying the Temple 6. Many Jews fled to Mesopotamia, which now encompasses Iraq 7. Distribution of this allele in the descendants of Jews & Mesopotamians suggests that the mutation probably originated before that time, at least 2000 years ago III. What are risks associated with different mutant alleles & what steps can be taken to minimize them? A. Incidence of 185delAG allele is approximately equal in both Iranian/Iraqi and Ashkenazi Jewish populations, but ..... B. Incidence of ovarian & breast cancers are higher in Ashkenazi women than either Iraqi or Iranian women C. Why do some who inherit alleles develop cancer while others do not? - other factors: environmental, cultural, other genetic differences, can account for discrepancy Analogies, Anecdotes and Illustrations Types of Variation in Genetic Traits As always, examples can help to illustrate both easy and difficult concepts. To illustrate discontinuous variation, give some examples of discontinous traits: purple flowers vs. white flowers, tall pea plants vs. short pea plants, etc. Essentially, all of Mendel's traits qualify as discontinuous traits as do most traits that you find in genetics problems. Continuous (smooth) variation is typified by height in humans, human birthweight, weight, growth rate, skin color, etc. Tell the story outlined in the book about Herman Nilsson-Ehle who showed that traits appearing in populations as continuous have a genetic basis. He studied the inheritance of color in corn kernels; they range from dark red to white in color. Point out that traits exhibiting continuous variation are typically due to the simultaneous expression of two or more genes all influencing the same trait. A Wade in the Gene Pool The textbook uses an excellent analogy for the gene pool and population genetics: beanbag genetics. I have not been able to come up with a better one. Alleles are like the beans in the beanbag and the entire beanbag full of beans is analogous to the population's gene pool. You should teach your students the calculations involved in the Hardy-Weinberg principle. They may grumble and groan about it, especially the non-majors, but it is essential to the understanding of HardyWeinberg. I feel it is best to handle the math part of this in lab (see below in Supporting the Lab). Run your students through some sample Hardy-Weinberg calculations. I would suggest that you give your students some problems to solve, even if it terrifies them. Point out to your students the significance of genetic equilibrium, that a population is in equilibrium when the allelic frequencies in that population remain constant from generation to generation. Point out the assumptions that Hardy and Weinberg made when they derived their equation: large population size, random mating, lack of emigration/immigration, no natural selection and no mutation. Explain how each of these singly or in combination can change allelic frequencies. Explain the value of analysis of population allelic frequencies by the Hardy-Weinberg principle. If allelic frequencies are seen to be changing, it clues in the investigator that one or more of the Hardy-Weinberg assumptions is not true. The population can then be studied to see which of the assumptions is not being met and more can be learned about the forces acting upon it. What Does Natural Selection Do to Allelic Frequencies? Define for your students what natural selection can do in a population genetics sense. Of course, the classic example is industrial melanism in the moths of England before, during, and after the Industrial Revolution. It is a story that is easy to understand, well documented, and about as good an example of natural selection in action as any. It is a classic. I will not bother to reiterate it here; the book does an excellent job and you are undoubtedly familiar with it. You may wish to follow the book's lead and do some hypothetical Hardy-Weinberg calculations using the moths as an example population. The demonstration in the book illustrates in clear terms the effect that shifting fitness of particular alleles can have on a population's allelic frequencies. Another aspect of the effect of natural selection on allelic frequencies is the other classic example of natural selection in action - sickle-cell anemia, an example already used frequently. It is a superb example of the heterozygote advantage, a situation in which the carrier of two alleles for a particular gene has an adaptive advantage over the homozygotes for either of the alleles. As a general rule, children exposed to malaria early in their lives will acquire considerable immunity to malaria if they survive. Such individuals are much more likely to fight off subsequent infections. Homozygotes for the HbA allele have no red blood cell sickling problems, but they are, in an environment where malaria is common, susceptible to its ravages. Homozygotes for the HbS allele, on the other hand, suffer from sickle cell anemia, but the allele provides them with some protection from malaria. Red blood cells sickle in these individuals; it makes them particularly resistant to penetration by the malaria parasite. This makes them much more likely to survive the disease and acquire immunity to later infections. This does not help the HbS homozygotes much, since they are likely to die at a relatively young age of sickle-cell anemia. The heterozygotes for the HBA and HbS alleles are a different story, however. They suffer from relatively minor sickle-cell symptoms when oxygen tension in their blood is low (usually not too serious), but they also acquire immunity to malaria. Thus, they suffer from neither full sickle-cell anemia nor malaria. You can model this using the Hardy-Weinberg equations to show how it would affect allelic frequencies (lab might be a good place to do this). Types of Selection - Directional, Stabilizing, and Disruptive Selection Explain directional selection to the class - a situation where the mean value for a trait shifts in a particular direction. The book uses the example of long tongues in frogs. Ask the class if they can think of other examples (giraffes' necks, etc.). Repeat this activity with respect to stabilizing selection and disruptive selection. Stabilizing selection is the situation where the middle of the variation range is favored and the book uses the example of frog legs which are well adapted for movement in the water and on land. If the legs were too well adapted to one of these environments, they would not be as well suited for the other environment. Again, ask your students to think of others. They might come up with birthweight, human height or weight, the carbonaria form of the moth mentioned earlier, and any number of other such traits. Ask your students why there is an advantage to retaining enough variation to produce members at the extremes of the phenotypic range. The reason, of course, is that it allows a selective advantage if the environment changes. The forms at the extremes may have an advantage in the new environment. Finally, disruptive selection is the situation where the middle of the distribution is nonadaptive while either end confers an advantage. The book uses the example of birds and beak length. Another excellent one is the case of the species of butterflies in which individuals mimic one of two species that taste foul to birds. Birds learn to avoid any butterflies that look sufficiently like these foul-tasting butterflies. A butterfly in the middle of the range of variation will not look enough like either of the foul-tasting butterflies to escape predation. Thus, the extremes of the distribution are favored. Point out that, potentially, disruptive selection may split into two subpopulations which may eventually lead to the formation of two separate species. Genetic Drift Define genetic drift for the class and then give examples of the different kinds: founder effect, genetic bottlenecks, mutation, gene flow. Genetic drift generally takes place in small populations in which chance can be important in determining the composition of the gene pool. It can lead to significant changes in the gene pool from generation to generation. This can be demonstrated effectively in lab exercises (see below). Point out that any of the forms of genetic drift have the effect of decreasing genetic variation in the population. Since genetic drift results from chance variation in survival and/or reproductive success, the changes are independent of natural selection and are called neutral selection. Explain this distinction to your students. Once again, explain each form of genetic drift. The founder effect arises when a small number of individuals from a population carry away from that population a nonrandom collection of alleles and then initiate a new population. Since the complement of alleles in the new population is different from that in the old one, there has been a change. Examples of the founder effect are numerous. The example of the colonizers of Tristan da Cunha is a new one to me and is excellent, but so is the classic example of the Amish. Make the point that many such populations have a significant and abnormal number of metabolic diseases. Ask the students why such diseases are so common in these populations; have them explain it in their own words. See if they can come up with inbreeding. Proceed in the same way with bottlenecks. Bottlenecks occur when populations undergo temporary declines to low numbers from which survivors of all future generations are derived. Under these circumstances, genetic drift plays a role in determining the composition of the gene pool. Point out that it usually results from a disaster affecting the population. Ask your students if they can think of examples. Point out the importance of the constant introduction of new alleles by mutation. It would be a good idea to tell your students about the case mentioned in the book about the appearance of achondroplasia in children whose parents did not exhibit the condition. Take your students through a calculation of the mutation rate for achondoplasia by using the data provided in the text. In your discussion of mutations, emphasize the three different types of mutations: selectively neutral mutatons (the most common), a small number of advantageous ones, and lethal or nearly lethal mutations. Finally, talk about gene flow, the movement of alleles between populations so that alleles from one population move to another via immigration. It can also be viewed as the loss of alleles from one population to another via emigration. The book gives as an example the passage of DDT-resistance among different populations of mosquitoes. Ask your students if they can come up with other examples. Another example is that of the Mongols and their invasion of Europe. How Do We Get Students to Participate in Class? This is not necessarily the right place to talk about this, but here goes. A frequent problem in class is getting students to participate. Sometimes they are extremely reluctant to open their mouths. I routinely give students a participation grade in all of my classes, and this works frequently. On occasion, however, I have had to resort to drastic methods to get them to participate. I have been known to purchase Hershey's Kisses or other similar candies to bring them to class. When a student answers a question correctly, I throw him/her a piece of candy. It may seem silly, but it works. The level of participation picks up every time. It is often sustained for some time after I have run out of rewards. If after a while, I don't bring them back to class, students will boldly ask me when I intend to bring in more candy. I don't recommend it on a regular basis. Frankly, students should be participating. However, something like throwing them candy will often jumpstart them and will have a somewhat extended effect. Sample Test Questions Multiple Choice, Conceptual, and Open-Ended Questions From the Text 1. What two assumptions did Darwin make in his description of evolution by natural selection? First, he assumed that traits are passed from parents to offspring and second, that there are important differences between individuals, even those of the same species. 2. The study of how genes of entire populations change over time is ____________. a. genetics b. evolution c. population genetics d. biology e. naturalism 3. The _________ felt that Darwin's ideas were consistent with observations, but they rejected Mendel's ideas. a. experimentalists b. naturalists c. Mendelians d. orneries e. rejecters 4. Which group of scientists ascribed evolution to sudden changes occurring as a result of mutations? a. experimentalists b. naturalists c. Mendelians d. orneries e. rejecters 5. Why were the experimentalists known by that name? The experimentalists were known as such, because they tended to work in a laboratory and focused on individual genes. 6. Below is a frequency diagram illustrating the distribution of weight in mice. What is the range of weights seen in the population? The mice range in weight from 12 to 40 grams. What is the average weight of the mice in the population? 26 grams. Frequency Diagram of Weight in Mice Number in Population at Each Weight 4000 3000 2000 1000 0 0 5 10 15 20 25 30 35 40 45 Weight (grams) 7. How can a trait demonstrated in a laboratory experiment to be discontinuous appear to be continuous when measured in the wild? In the wild, the environment (differences in water supply, nutrients, exposure to sunlight, etc.) can cause distinct categories to exhibit their own bell curves. This blurs the distinction between each class and leads to a continuous curve in the frequency diagram. 8. Continuous variation in a trait is a. usually traced to a single gene. b. usually determined by two or more genes. c. usually a result of polygenic inheritance. d. all of the other answers e. b and c 9. Two different traits are inherited as polygenic traits. One is shown to be controlled by five genes, the other by thirteen genes. Which one is likely to show the smoothest, most continuous frequency diagram? The trait controlled by thirteen genes would be most likely to show the smoothest, most continuous frequency diagram. If more genes are involved such curves are generally smoother. 10. How can one reconcile the differences between the naturalists and the experimentalists? As the experimentalists claim, all genes are passed in a Mendelian fashion. Natural selection selects for particular alleles or combinations of alleles with the beneficial ones building up in the population. Thus, evolution can be viewed as changes in a population's genetic make-up over time. 11. A population consists of 4000 organisms. How many alleles for a single gene K are found in that population? a. 8000 b. 4000 c. 2000 d. 1000 e. 4850 12. A gene L is known to have two alleles, a dominant one (L) and a recessive (l) one. If the frequency of the dominant L allele is 0.32, what is the frequency of the recessive l allele? a. 0.32 b. 0.64 c. 0.68 d. 0.86 e. 1.68 13. Which of the following is not an assumption made by Hardy and Weinberg when they derived their principle? a. large populations c. no immigration e. b and c b. no emigration d. non-random mating 14. The gene C has two alleles (the dominant allele C and the recessive allele c). They are both present at frequencies of 0.5. What is the frequency of Cc heterozygotes in the population? The formula for the frequency of heterozygotes would be 2pq or 2 (0.5) (0.5) or 0.5. What is the probability of a homozygous dominant individual? The frequency of a homozygous dominant individual would be p2 or (0.5)2 or 0.25. 15. The gene D has two alleles (the dominant allele D and the recessive allele d). The D allele has a frequency of 0.3. What is the frequency of heterozygotes for the D gene in the population? The heterozygote frequency would be calculated with the formula 2pq or 2 (0.3) (0.7) = 0.42. What would be the frequency of the double recessive individuals in the population? The frequency would be q2 or (0.7)2 or 0.49. What would be the frequency of individuals double recessive for the J gene? The data presented in this question are not sufficient to answer this question with any degree of certainty. 16. A population is observed for about ten generations. In that time, the gene F is extensively studied and its allelic frequencies are not seen to change. What word(s) below describe the condition of the population? a. disequilibrium b. hereditary balance c. genetic equilibrium d. chemical equilibrium e. c and d 17. Why is mutation generally ignored as a factor influencing evolution over just a few generations? While mutation does occur constantly, it happens at a relatively low rate and thus causes only a small change in allelic frequency from one generation to the next. 18. A bird population possesses a gene L that controls beak length. The dominant trait L is associated with long beaks. Short beaks are seen in organisms double recessive (ll) for the L gene. In a population of 1000 individuals, 640 have short beaks. What is the frequency of heterozygotes and homozygous dominant organisms in the population? The frequency of the double recessive short-beaked birds was 640/1000 or 0.64. Thus, the frequency of the recessive allele was the square root of the frequency of the double recessive organisms or 0.8. If the frequency of the recessive allele was 0.8, that of the dominant allele was 1 - 0.8 or 0.2. The frequency of heterozygotes would be described by the formula 2pq or 2 (0.2) (0.8) or 0.32. The frequency of the homozygous dominant organisms would be p2 or (0.2)2 or 0.04. 19. A recessive allele for the C gene on Mars leads to a single eye in the middle of an organism's forehead (cyclops). The population of organisms analyzed had 2000 individuals and of these, 720 exhibited the cyclops trait. What were the frequencies of the dominant and recessive alleles and the heterozygotes in the population? The frequency of the recessive phenotype was 720/2000 or 0.36. The frequency of the recessive allele would be the square root of the recessive phenotype frequency or 0.6. The dominant allele would have a frequency of 1 - 0.6 or 0.4. Heterozygotes would be present at a rate equivalent to 2pq or 2 (0.6) (0.4) or 0.48. 20. Double recessive individuals for the trait Q occurred at a frequency of 0.81. What is the frequency of the dominant allele? The frequency of the recessive allele would be the square root of the frequency of the double recessive genotype (0.81) or 0.9. The frequency of the dominant allele would be 1 - 0.9 or 0.1. 21. You are studying the survival of the Biston bestularia moths under controlled experimental conditions in the presence of some hungry sparrows. What is most likely to happen to Mm moths that are placed on lichen-covered tree trunks? a. They are paralyzed c. They are not eaten e. c and d b. They are eaten by the sparrows d. They survive 22. You continue the study in #21 above. You place mm moths on soot-covered tree trunks in the presence of some hungry sparrows. What happens? The moths are speckled and consequently they stand out against the dark tree trunks. The sparrows will be able to see them quite well and will eat them. What happens if you place MM moths on these same tree trunks? MM moths are black. They will blend in well against the dark tree trunks. There is thus a good chance that the moths will not be seen by the sparrows and that they will survive. 23. You place a MM moth and a Mm moth on a soot-covered tree trunk. Which one is most likely to be eaten? a. the MM moth c. Both moths are likely to be eaten e. the mm moth b. the Mm moth d. Neither moth is likely to be eaten 24. You are studying the moth population and find that out of a total of 1000 moths there are 490 speckled (mm) moths. How many heterozygous moths should be in the population? The frequency of speckled moths is 0.49 (490/1000). The frequency of the m allele is 0.7 (the square root of the frequency of mm moths). The frequency of the M allele is therefore 0.3 (1 - 0.7). The frequency of heterozygotes is equal to 2(frequency of m allele)(frequency of M allele) or 0.42 (2 x 0.7 x 0.3). 25. In the first generation under study, the frequency of the M allele is 0.8. At the end of the second generation, the frequency of the speckled moths is 0.16. What color are the tree trunks in the research area most likely to be? Have the lichens begun to grow on the trees again? The frequency of the m allele in the population's first generation is 0.2. In the second generation, the frequency of the recessive (speckled) genotype (mm) is 0.16; thus, the frequency of the m allele is 0.4 (the square root of 0.16). Thus, the frequency of the m allele is increasing. If this is the case, it is most likely that the speckled moths are surviving at higher rates and the tree trunks are most likely white with patches of brown; the lichens are growing on the trees again. 26. Assume there is a study of American blacks whose ancestors were from areas of Africa where malaria has been prevalent for over 400 years. The frequency of the HbS allele in the population of American blacks descended from people who lived in the equatorial belt of central Africa is determined to be lower than in people presently residing in that same area of central Africa. When slaves were brought to America from the equatorial belt of central Africa, it is likely that the frequency of the HbS allele was similar to that of people presently residing there. What are some possible explanations for the decrease in the frequency of the HbS allele in American blacks given that malaria is not very prevalent in the United States? Given that malaria is not widespread in the United States, it is likely that the HbS allele has been selected against since it will have lost its advantage in the United States. Another explanation would be interbreeding with whites and blacks descended from people who lived in nonmalarial areas of the world. 27. A study is undertaken in which changes in allelic frequencies of a few genes are monitored over a few generations. Such a study would be dealing with examples of _________. a. macroevolution b. cell biology c. immunology d. microevolution e. a and d 28. An analysis of larger-scale changes that have resulted in the origin of the higher taxonomic groups of certain related organisms would be classified as a study in ________. a. macroevolution b. cell biology c. immunology d. microevolution e. a and d 29. Why is it said that microevolution gives rise to macroevolution? Microevolution is characterized by small changes in gene frequencies at the population level. It is thought that macroevolution results from the accumulation of such small changes to the point where differences build up to a level sufficient to mark the formation of new species. 30. Natural selection is considered to be a(n) __________ process. a. macroevolutionary b. philosophical c. antithetical d. microevolutionary e. a and d 31. The cheetah is reputed to be the fastest land mammal. The evolutionary process that gave rise to this speed is most likely to be what kind of selection? a. nondirectional selection c. disruptive selection e. directional selection b. stabilizing selection d. diversifying selection 32. The frequency distribution of birthweights in human infants is bell-shaped with most birthweights in the middle of the range of birthweights. What type of selection does this exemplify? a. nondirectional selection c. disruptive selection e. directional selection b. stabilizing selection d. diversifying selection 33. Why would extremes in birthweights be disadvantageous and thus selected against? If babies weigh too little, they will have survival difficulties once they are born. They will be likely to be a bit weak and little able to stand any weight loss. This was especially true before modern medical advances were able to help low-birthweight babies. On the other hand, high birthweight babies are faced with other difficulties especially before the development of the Caesarian section procedure. Such a baby would be too large to be born vaginally and both mother and baby would be in danger of dying. 34. Stabilizing selection is said to be the rule in unchanging environments. Why does it make sense that this would be the case? In an unchanging environment, there will be plenty of time for the optimal form of a particular trait for that environment to evolve. It is most likely that the distribution curve of such traits will be bell-shaped with the optimal trait in the middle of the distribution and extreme forms of the trait ,which are likely to be less well adapted to the environment, present at much lower levels. 35. Why are populations that exhibit stabilizing selection still able to respond adequately to changes in the environment? If the environment changes, the more prevalent forms of the trait may become less well adapted to the newly changed environment. However, if there is sufficient genetic variation, extreme forms of the trait at one end of the distribution or the other may be better adapted to the new environment. If so, although they are not as numerous, they will tend to have a somewhat better chance to survive and reproduce than the much more plentiful form. Consequently, they will send more of their alleles into the next generation and if the change in the environment is maintained, the newly adaptive form of the trait should become more plentiful. 36. What would be likely to happen if the environment of a population with very little variation were to change making the most prevalent form of a particular trait less adaptive? Most likely, the low degree of variation in this population would result in its extinction, as long as the change in the environment is sufficient to decrease severely the fitness of the organisms carrying the most prevalent form of the trait. 37. Which of the following is an example of disruptive selection? a. left and right c. blue and aqua e. b and d b. higher and higher d. fast and faster 38. The alteration in allelic frequencies that results from chance variation in survival and/or reproductive success is called __________. a. genetic variability b. stabilization c. genetic drift d. driftwood e. dispersion 39. One species of butterfly has a wide distribution of wing color patterns and tastes very good to birds that prey on butterflies. At each end of the variation range, the butterflies look quite different, almost like different species. Each of these different-looking members of the same species, however, looks strikingly like one of two different species that taste awful to the predator birds. One taste of butterflies from these two species and a bird will never eat them again. What advantage would the extreme forms of our butterfly have in nature? The extreme forms of these butterflies mimic the appearance of the noxious butterflies. Once a bird has eaten one of the noxious butterflies, it will avoid any butterfly that resembles the foul-tasting ones, including the tasty butterflies that resemble the two noxious species. The tasty butterflies will thus be more likely to survive and reproduce. Tasty butterflies in the middle of the variation range have an appearance intermediate between the two extremes and do not closely resemble either of the noxious butterfly species. What would happen to them in nature? They would not be protected by resemblance to the noxious butterflies and they would fall prey to hungry birds quite often. Thus, they would be less likely to survive and reproduce and the alleles leading to the intermediate appearance would become less plentiful in the population. 40. You study wing coloration in a species of butterfly. There are two quite distinctive colorations at either end of the range of variation. Intermediate forms that possess elements of the coloration of both extreme forms also exist. The extreme forms seem to prosper while the intermediate forms do not survive to reproduce nearly as much. What form of selection is this? a. c and d c. disruptive selection e. directional selection b. stabilizing selection d. diversifying selection 41. Which of the following results in neutral selection? a. disruptive selection b. stabilizing selection c. genetic drift d. founder effect 42. Genetic drift invariably results in a loss of _____________. a. time b. genetic variation c. genetic stability d. randomness e. c and d e. a and b 43. A number of genetic maladies, like maple syrup urine disease and Ellis-van Crevald syndrome, are found in the population of the Amish of Lancaster, Pennsylvania at rates higher than the surrounding general population and the population from which the Amish were originally derived. This is considered an example of what process? a. bottleneck b. founder effect c. heterozygote advantage d. genetic drift e. b and d 44. Jews of Eastern European descent carry a much higher than normal recessive allele for Tay-Sachs disease than the populations that presently surround them or the population from which they were derived. Why might this be? Jews of Eastern Europe were isolated reproductively from the population from which they were derived. Their inbreeding caused this allele to build up to levels higher than the general population. This is an example of the founder affect. 45. Which of the following is a form of genetic drift? a. founder effect b. bottleneck c. heterozygote advantage d. a and b e. a, b, and c 46. A natural disaster occurs killing a large portion of the population of a particular organism. The extent of genetic variation in the surviving organisms is analyzed and compared to the genetic variability that was present before the disaster. What has happened, if anything, to the genetic variation seen in the population after the disaster? The degree of genetic variation has probably decreased. What is the name of the phenomenon demonstrated by this event? It is an example of a population bottleneck. 47. What is responsible for the appearance of new alleles in a population? Mutation. 48. Which case below would be an example of gene flow? a. Two young adults from Chicago get married b. Father O'Riley moves from Dublin, Ireland to New York c. Two members of a beaver population mate d. Juana Montez from Mexico marries Swen Nordstrom from Sweden e. none of the above 49. A maternity hospital keeps copious records over a number of years of births and genetic maladies found in those births. A dominant trait X is found in twelve of 130,000 births. In three of those births, the trait X was present in at least one of the parents. What was the mutation rate for this trait? In three of the births, the trait was already present in one or both of the parents and was thus probably inherited as described by Mendel. In the other nine cases, however, none of the parents exhibited the dominant trait. This means that they did not possess the allele; if they had it, they would have expressed it since it has been shown to be dominant. Consequently, in these nine cases, the allele must have arisen by mutation. The mutation rate can be calculated as follows: 9 mutations/[(2)(130,000)] = 3.5 x 10-5 mutations/allele. Why is the number two used in that calculation? Each individual carries two alleles and so to calculate the number of mutations per allele, this fact must be taken into account. 50. What are the three categories of mutations that arise with respect to the fates of the recipient of the mutation and what will happen with respect to their levels in the population after their introduction? Mutations may be lethal or nearly lethal in which case they can cause severe deficits in the recipient or his/her offspring. These mutations will tend to be selected against; their frequency will thus be kept low or they will be eliminated. They may be selectively neutral or nearly neutral. Such mutations may spread through the gene pool or be eliminated by random means such as genetic drift. A small number of mutations are advantageous. These will be selected for within populations. If they are recessive, they may hide in the gene pool until or unless they are paired in a homozygote where its benefits may be fully expressed. 51. What is the largest number of alleles that any one individual can carry for a particular gene? Two alleles. Multiple Choice, Conceptual, and Open-Ended Questions From the CD-ROM 1. What is the phenotypic ratio of the height categories suggested by the frequency diagram illustration of discontinuous variation in Section 7.1 of the CD-ROM? The phenotypic ratio is 1 short : 2 medium : 1 tall. What type of inheritance pattern does this frequency diagram suggest? It suggests that height is controlled by a single gene locus with two alleles. The 1 : 2 : 1 ratio suggests that the alleles reflect incomplete dominance such that the homozygote of one allele gives rise to a tall individual, while the homozygote of the other allele results in a short individual. Heterozygotes possessing both alleles have an intermediate height. What is the genotypic ratio resulting from this inheritance pattern? As is the case with incomplete dominance, the 1 : 2 : 1 ratio reflects the genotypic ratio. If T is the allele representing tallness and T' the allele representing shortness, the genotypic ratio would be 1 TT : 2 TT' : 1 T'T'. 2. In Section 7.1 of the CD-ROM, how does the frequency diagram for continuous traits differ from that for discontinuous traits? The curve for continuous traits has many more categories for human height than does the frequency diagram for discontinuous traits. As the number of categories increases, what kind of curve does the frequency diagram begin to approximate? A bell-shaped curve. 3. In Section 7.1 of the CD-ROM, how many genes are involved in the hypothetical frequency diagram exercise illustrating continuous variation in human height? There are three genes at different loci, each with two alleles. 4. If the three genes involved in the continuous variation exercise in Section 7.1 of the CD-ROM are designated A, B, and C with capital letters representing the dominant allele of each and the lower case letter representing the recessive allele, what would be the height of a person with the following genotype: AaBBcc? a. 6' 6" b. 4' c. 6' d. 5' 6" e. 3' 6" 5. Two parents with the genotype AABbCc mate. What are the phenotypic ratios of the offspring and what is the height of the parents? The parents are both six feet tall since they each have four dominant alleles, each of which adds six inches to the base height of four feet. The phenotypic ratio is 1 7' child : 4 6' 6" children : 6 6' children : 4 5' 5" children : 1 5' child. 6. In the cross above in problem 5, what is the probability of a child with a height of 5' 5"? a. 1/2 b. 1/8 c. 1/4 d. 0 e. 3/4 7. In the exercise in Section 7.2 that asks you to calculate the number of gametes of each type and allelic frequencies of the gametes, assuming that each female makes ten eggs, how many eggs do the Aa females make that carry the A allele? 210 eggs. What is the allelic frequency of the recessive allele in the entire population? 0.3 or 30%. 8. In the Punnett square in Section 7.2 under the heading of the Next Generation, what is the frequency of the heterozygotes in the offspring? a. 0.49 b. 0.21 c. 0.09 d. 0.42 e. 0.91 9. If the population was followed through ten generations and the assumptions made by Hardy and Weinberg held true, what would the frequency of the heterozygotes be in the tenth generation? If the assumptions made by Hardy and Weinberg held, the population would be in genetic equilibrium and the frequency of the heterozygotes would be the same as in the first generation studied, 0.42 or 42%. 10. Assume you are studying a new population of field mice as described in Section 7.2 of the CDROM. This population has 1620 long-whiskered mice and 380 short-whiskered mice. What is the frequency of the recessive phenotype for this trait? Since long whiskers are the recessive allele, the frequency of the recessive phenotype would be 1620/2000 or 81% (0.81), the number of organisms exhibiting the recessive phenotype divided by the total number of organisms. What is the frequency of the homozygous recessive genotype? Since the recessive phenotype can only occur with a homozygous recessive genotype, both frequencies must be equal. Thus, the frequency of the homozygous recessive genotype is 81% (0.81). What is the frequency of the recessive long-whiskered allele? Since the frequency of the recessive genotype is equal to the frequency of the recessive allele squared, the frequency of the recessive allele can be calculated by taking the square root of the frequency of the recessive genotype. Therefore, in this case, the frequency of the recessive allele would be the square root of 0.81 or 0.9. What is the frequency of the dominant allele? Since the recessive allele's frequency is 0.9, the dominant allele can be calculated by subtracting the recessive allele frequency from 1.0. This can be done since these two alleles are the only alleles present in this population. They are mutually exclusive. Thus, the frequency of the dominant allele is 0.1 (10%). What is the frequency of the homozygous dominant genotype in the population? The frequency of the homozygous dominant genotype (p2) is (0.01)2 or 1%. What percentage of the population exhibits the dominant phenotype? The frequency of the dominant phenotype would be the sum of the frequencies of the homozygous dominant and heterozygote genotypes. The frequency of heterozygotes would be 2 (frequency of dominant allele)(frequency of recessive allele) or 2pq. In this case, the frequency would be (2)(0.1)(0.9) or 0.18 (18%). The frequency of the dominant phenotypes would thus be 0.18 + 0.01 or 0.19 (19%). You could also calculate this frequency by subtracting the frequency of the recessive phenotype from 1.0. 11. In Section 7.3 of the CD-ROM, what happens to the DDT-susceptibility allele over time after DDT has been introduced into the population? After the first exposure to DDT, this allele drops rapidly and gets gradually lower in frequency after that. What happens to the frequency of the DDT-resistance allele over time after DDT-exposure? The DDT-resistance allele increases steadily over time. What happens to the population over time following exposure to DDT? After the first DDT exposure, population drops sharply. If exposure continues, the population eventually reattains its previous levels as the DDTresistance allele replaces the DDT-susceptibility allele. With each exposure to DDT, the population drops, but the drop is smaller with each successive generation. What happens to the genotypes in the population over time? The genotypes were originally mostly homozygous susceptible. As the exposure to DDT continues, the genotypes rapidly progress to being homozygous resistant with just a few heterozygotes since the susceptible alleles have been driven to such a low frequency. 12. What would have happened to the frequencies in the mosquito population if DDT had never been introduced into the population? If DDT had never been introduced into the environment, the popualtion would probably have remained in genetic equilibrium with respect to this gene or allele. Thus, the levels of the DDT susceptibility allele in the population would probably remained high since there were no selection pressures acting on the allele. It would not have changed in frequency. Using BioInquiry in Large Classes Integrating Components into the Lecture Once again, there are animations on the CD-ROM that effectively illustrate important concepts within the subject matter that are important for understanding population genetics. First, in Section 7.1 of the CDROM, a frequency diagram is constructed that demonstrates how height might be distributed in the human population if it were controlled by a single gene locus with two possible alleles. This leads to three height categories (short - 4' 6", medium - 5' 6", and tall - 6' 5") appearing in what looks like a 1 : 2 : 1 phenotypic ratio. Clearly, this is not how height is distributed in the human population. After running the demonstration animation in class or assigning it to your students, ask them to tell you what the ratio of the three categories is and what kind of inheritance pattern they would guess that the frequency diagram represents (of course, it looks like incomplete dominance). Alternatively, you may ask them this and other questions as part of an assignment that they must complete for credit. Next, show your students how having three genes together control human height would change the frequency diagram for human height. Encourage them to point out the differences between the two types of curve. Ask them what would happen if even more genes were involved and if the environment had some influence on the expression of each gene. You also might want them to try some crosses using the parameters described in the exercise to get them to figure out the expected ratios in offspring. The exercise in Section 7.2 of the CD-ROM deals with the calculation of allelic frequencies in a population of male field mice. The trait being dealt with is the dominant allele for short whisker length and the recessive allele for the same gene (long whisker length). This exercise allows the students to practice the procedures for calculating allelic frequencies in a population from the phenotypic frequencies found in that population. They will also learn to predict the frequencies of specific phenotypes in a population if they know the allelic frequencies. Once this is mastered, they should be well on their way to understanding the Hardy-Weinberg principle. You may wish to present this during lecture, have the students do this as an assignment, or work it in as part of a laboratory exercise. Introduce the students to the Hardy-Weinberg equation and encourage them to look at the HardyWeinberg panel in the CD-ROM (Section 7.2) that outlines the Hardy-Weinberg equation and the elements of the equation that can be used to calculate the expected frequencies of homozygous dominant, heterozygous, and homozygous recessive organisms. In Section 7.3 of the CD-ROM, the students can run through an exercise that skillfully shows how selective pressure can alter allelic frequencies in a population. It makes use of the example of mosquitoes and DDT presented in the book. Students can read about the increase in the DDT-resistance allele following DDT exposure in the text and then go to the CD-ROM and see it happen. One graph on the right side of the screen shows the frequencies of the different genotypes (homozygous dominants and recessives, heterozygotes) in the mosquito population; the other two show the allelic frequencies and mosqito population over time. These help the students to associate the pictorial results shown on the left side of the panel with the mathematical - graphical descriptions of the changes in population number and genetic makeup. You might want to write some questions related to the exercise that the students can do for an assignment. Ask them to explain what is happening. You could also use it as a quick animation during class to complement the lecture. Read More About It For topics related to this chapter, I have found the essays of Stephen Jay Gould and specifically the books in which his essays are collected to be excellent descriptions of how natural selection works. His essays are entertaining, literate, and informative. They are generally accessible to the non-scientist as well. Among the books you may want to consult are Ever Since Darwin, The Panda's Thumb, Hen's Teeth and Horses' Toes, Bully for Brontosaurus, Eight Little Piggies, Full House, and others. His books are readily available at your local bookstore. Supporting the Lab The topics in this chapter can be covered effectively in the lab. We have a population genetics lab exercise that we do each semester. We describe the Hardy-Weinberg principle to the class and explain the basic math. We break the problems in population genetics down into a few steps that need to be followed in order to solve such problems. The steps are as follows: (1) Determine the frequency of the recessive phenotype. (2) Determine the frequency of the double recessive genotype [the same as above in (1)]. (3) Determine the frequency of the recessive allele (square root of frequency of double recessive genotype). (4) Determine the frequency of the dominant allele (subtract the frequency of the recessive allele from 1.0). (5) You can use the frequencies of the alleles to calculate the expected frequencies of the homozygous recessive, homozygous dominant and heterozygote genotypes in the population. Then carry the students through some sample calculations/problems using this well-laid out procedure. We also do a simulation using pop-beads to demonstrate the Hardy-Weinberg principle. Students place 100 pop-beads (say 50 red and 50 white) in a beaker and mix them thoroughly. They then withdraw 40 pairs of beads from the beaker. Ask your students the expected ratio (it should be 1 : 2 : 1) and how many of the "offspring" should be homozygous dominant, heterozygous, and homozygous recessive (10 : 20 : 10). Most of your offspring will be close to the 1 : 2 : 1 ratio. Once they know the make-up of the newly produced generation, they should adjust the number of gametes in the beaker to reflect the allelic frequencies in the newly produced generation. This can be repeated for a number of generations. We usually do this with six groups per lab, with each group doing a few generations. Most of the time the allelic frequencies hover around 50% - 50%. In one or two cases, however, genetic drift usually occurs since the population size is so small. The exercise thus serves two functions. It demonstrates that the Hardy-Weinberg principle generally holds and it also demonstrates that genetic drift can happen as seen in the few cases where the ratio varies widely from 50%-50%. You can continue this exercise by simulating natural selection (say by favoring the survival of heterozygotes in your offspring and not favoring the homozygotes). This can be done by allowing all of the heterozygotes to survive and allowing 25% of the heterozygotes to "die" before reproducing. The number of gametes carrying each allele can then be adjusted accordingly and the next generation constructed. Over the generations, the allelic frequencies will be seen to vary. This demonstration is extremely effective but there is one difficulty. The math involved in figuring out the number of gametes that will appear in each generation is not difficult, but for those non-scientists who are apprehensive about math this will be difficult and perhaps anxiety-provoking. Lastly, part of the exercise is great fun. We spend some time going through a number of human traits (hitchhiker's thumb, left-handedness, widow's peak, mid-digital hair, etc.). Some of them are weird and the class gets a kick out of counting up how many of them are "mutants". They can calculate the frequencies for each trait (each trait will have a different frequency). They can use the Hardy-Weinberg principle and the procedure outlined above to calculate the allelic frequencies. This is an effective exercise and one that the students universally enjoy. Answers to Review Questions 1. Not all traits are determined by a single gene. Some are the result of the effects of a number of different genes, each with a number of different alleles; such traits are called polygenic or quantitative traits. The different combinations of alleles that can arise in such a situation will smooth out the forms of the trait over a continuum, usually defining a bell-shaped curve. If the influence of the environment on the expression of each allele is added to the mix, the bell curve will become even smoother. 2. A polygenic trait is one that is due to the simultaneous expression of two or more genes, while a monogenic trait is determined by the expression of only one gene. As the number of genes determining a trait increases, variation within a population changes from discrete categories to a smooth continuum. Height, weight, and growth rate are examples of polygenic traits. The traits Mendel studied like stem height and flower color in the pea are examples of monogenic traits. 3. A genetic locus is the specific chromosomal address of a gene, the fixed position occupied by one of the alleles or forms of that gene. The genetic locus is therefore the position of the gene; an allele is one of the forms of that gene. 4. All of the alleles found in a population of organisms are called the gene pool. A population is a group of organisms that occupy the same habitat and can interbreed. 5. In the Hardy-Weinberg equation, the letter p represents the frequency of the dominant allele, while the letter q represents the frequency of the recessive allele. The mathematical terms p2, 2pq, and q2 represent the frequencies of the homozygous dominant, heterozygous, and homozygous recessive genotypes, respectively. 6. When a population is in genetic equilibrium, the frequencies of its alleles for a particular gene or genes do not change from generation to generation. This means that forces like natural selection, emigration/immigration, small population size, non-random mating, and mutation are not acting to change allelic frequencies and that these frequencies will remain the same from generation to generation. In mathematical terms, genetic equilibrium means that p and q will remain the same from generation to generation. 7. When Hardy and Weinberg derived their mathematical principle describing genetic equilibrium, they assumed that populations are very large, that individuals within the population mate at random, that populations do not gain or lose individuals by emigration or immigration, that natural selection is not occurring, and that mutation is not occurring at a high enough rate to influence genetic variation. If one or more of the assumptions made by Hardy and Weinberg were incorrect, a population would most likely be prevented from reaching genetic equilibrium. 8. Since the double recessive phenotype (ww) makes up 16% (0.16) of the population, the frequency of the recessive w allele (q) would be the square root of 16% (0.16) or 40% (0.4). The frequency of the W allele (p) would be 100% - 40% (60%) or 1.0 - 0.4 (0.6). The frequency of heterozygotes in the population would be 2pq [(2)(0.6)(0.4)] or 0.48 (48%). 9. The heterozygote advantage is a circumstance where the heterozygote for a particular trait has a better chance to survive and reproduce than either of the two homozygotes. An example of heterozygote advantage is the gene for ОІ-hemoglobin. The normal allele for this gene is the HbA allele; the mutant allele is known as HbS. The homozygous dominant genotype HbA/HbA has normally functioning hemoglobin, but such individuals are susceptible to malaria. Homozygous recessive (HbS/HbS) individuals suffer from sickle-cell anemia, but are resistant to malarial infections, allowing them time to acquire immunity from later infections. Heterozygous individuals (HbA/HbS) have hemoglobin function that is essentially normal. However, under conditions of low oxygen tension, they can suffer relatively minor sickle-cell symptoms. They also are better able to survive malaria allowing them to acquire immunity from later infections. Thus, they derive the benefits of both alleles and the disadvantages of neither comprising a heterozygote advantage. 10. Microevolution comprises changes in population allelic frequencies. Macroevolution describes the larger-scale changes that lead to the origin of higher taxa or categories of organisms (like orders, families, and phyla). Most evidence indicates that the higher taxa that characterize macroevolution are formed by the accumulation of many small changes in gene frequencies at the population level. Thus, microevolution gives rise to macroevolution. 11. Directional selection is illustrated by the industrial melanism of the English speckled moth. When tree trunks were lighter and patchy, the lighter form of the speckled moth was favored. When trunks became darker because of industrial pollution, the population shifted relatively quickly to the darker form of the speckled moth. This form persisted until the environment was cleaned up. As the tree trunks got lighter, the population began to shift back toward the lighter form of the speckled moth. 12. In small populations, a chance change can lead to significant changes in alellic frequencies while the same change is less likely to have an effect on a larger population. For example, consider two populations, one consisting of ten individuals and one consisting of one hundred individuals. Assume that 10% of the individuals in each population carry a particular allele b of the B gene. Thus, one individual in the smaller population carries the allele while ten carry it in the larger population. While crossing the road, one member (10%) of the smaller population is struck and killed by a vehicle. If the individual killed by the vehicle was the one carrying the b allele, that allele will be removed from the population. If the larger population crosses the road and 10% of their population is killed by a vehicle, the most likely result is that nine of those killed will not carry the b allele, while one will. The b allele would still be found in 10% of the remaining population. Thus, there is a good chance that a small sample drawn from a larger population may not resemble the population from which it was drawn. 13. The founder effect occurs when there is a difference in the gene pool allelic makeup due to the initiation of a population by a small number of individuals. Bottlenecks occur when a population undergoes a temporary decline to low numbers from which survivors of all future generations are derived. They are similar in that future populations, in both cases, arise from a portion of a parent population. Also, in both cases, the portions of the population that establish the future generations do not have the same allelic frequencies as the parent population. In both cases, the allelic compositions of the portions of the population that establish a new population is determined by chance and not natural selection. Thus, both result in a decrease in genetic variation. They differ in the reason for the establishment of the new population. With the founder effect, the new population is established because a portion of the parent population leaves and sets up shop somewhere else. In the case of bottlenecks, the portion of the population that establishes a new population is what remains after a severe depletion of the parent population. 14. Gene flow is movement between populations that results in the introduction of alleles from one population to another via immigration or the loss of alleles from one population to another via emigration. It is more likely that gene flow will occur between two populations that overlap in time and space. It will be unlikely that much immigration/emigration will occur between populations on distant islands. However, two populations that overlap in time and space will allow many opportunities for emigration/immigration. 15. If populations do not conform to the Hardy-Weinberg principle, we can learn exactly how they differ from genetic equilibrium. Once this has been accomplished, we can then determine the factors responsible for those differences. CHAPTER 8 BIODIVERSITY: HOW DIVERSE IS LIFE? Lecture/CD-ROM Outline Overview I. Life on Earth is amazingly diverse - in the last 250 years, ~1.5 million different kinds of organisms have been described; many more have yet to be found A. 1950s - tropical biologists found many living things in tree tops; largely unknown since they rarely descended; found thousands of new species there 1. When fully cataloged, tropical ecosystems may add 15 million more species to life's list B. Deep oceans once thought to be wastelands also shown to have diversity 1. 1970s - rich biological communities found associated with ocean floor geologic vents 2. Vents spew hot, mineral-laden water that provides energy & nutrients to microbes 3. Unknown species of fish, crabs, clams, giant worms, etc. feed on microbes 4. Away from vents life is not teeming, but extensive & unique forms of life are present 5. Life also seen on sea mount tops & the thin transition layer between ice & water under pack ice C. Crawl spaces between soil particles - found lots of organisms (mesofauna); largely unnoticed 1. Too big for microscopes, too small to be noticed without them; now found everywhere 2. Their numbers & diversity appear to be extensive D. New organisms are being found thousands of feet deep in rock cracks, muds, & soils under lakes II. How many species on Earth? - estimates >100 million species A. Such diversity is a blessing - understanding how these organisms solve challenges of life is exciting, challenging, & awe-inspiring B. Also, a curse - describing, identifying, classifying, & naming these species is huge job 1. Data management system required is extensive & complicated 2. Data base also should be user-friendly & anybody should be able to get info in & out III. Such a system exists & comprises two branches of biology A. Taxonomy - the science of describing, classifying, & organizing organisms according to their similarities & differences B. Systematics - more interpretive approach; a study of evolutionary relationships among organisms IV. Steps in classification A. Group species according to shared characteristics; indicate ancestry; the more similar two species are, the more closely related they are - done by taxonomists B. But all organisms, no matter how dissimilar, share some characteristics; the study of similarities & differences & of evolutionary relationships sheds light on the origins of life How Do Biologists Keep Track of So Many Species?: History of Classification I. Biological system of classification is based on comparisons & hierarchical groupings, and is also somewhat arbitrary; took several hundred years to develop II. Prior to Darwin, classification was concerned with describing "natural order" A. Taxonomy traced back to Aristotle, as with so many other areas of biology 1. Arranged objects including animals into groups through series of "either-or" comparisons 2. Object is living or non-living, animal or plant, "blooded" or "non-blooded," etc. 3. Resulted in listing of animals by what was perceived to be a natural order leading progressively from simplest to most complex B. Theophrastus (his principal student) used similar "either - or" groupings to classify plants as trees or shrubs, subshrubs or herbs 1. Their classification system persisted with little change for nearly 1,500 years C. 14 th century - vast increase in exploration; most trips included a naturalist who described & collected specimens & brought them back to Europe for museums 1. For hundreds of years, collections grew, as did need to organize, classify & name organisms D. Dominant philosophy early on was that species were fixed & unchanging & could be arranged in some sort of natural order 1. Taxonomists' job is to describe species as accurately as possible to assist in accurate identifications & reveal life's natural order 2. Each species is seen as a separate type of life perfectly conceived 3. Descriptions tried to list each species' idealized characteristics; became species archetype 4. Perfect or archetypal rose had one set of characteristics, archetypal dog another; individual variations were largely ignored 5. Archetypes that shared a particular set of characteristics could be arranged together in groups E. At first, there was little agreement as to which characteristics should be chosen for grouping & how groups should be arranged 1. At 18th century start, there were many separate classification systems (some for plants; others for animals) 2. Organizationally, they had little in common & were largely incompatible; verge of chaos III. Carl von LinneВґ (1707 - 1778), Swedish botanist - enigmatic, maybe even eccentric; wrote carefully detailed plant, animal descriptions; obsessed with classification (even classified botanists) A. Brought simplicity, consensus to chaos in field; described >8000 species of plants & animals 1. To each, he assigned two Latinized names unique to each species (even Latinized his name to Carolus Linnaeus); this binomial nomenclature continues today 2. First name was the genus name; closely related forms could share it & be grouped together 3. Second name was the species name that distinguished between closely related forms B. Linnaeus recognized the need to organize species into higher taxonomic categories 1. Related genera (plural of genus) combined into orders which were combined into classes; the highest category was kingdom (two: plants & animals) 2. Did this as a matter of necessity; since he felt that there were too many genera to keep track of 3. Felt his descriptions of genera & species represented natural order but that orders & classes were largely artificial C. Linnaean system widely accepted into mainstream biology 1. Buffon (Linnaeus contemporary), Lamarck (Buffon's student), & Cuvier accepted & refined Linnaean system, concentrating on animals; others extended work with plants IV. After Darwin & Mendel, the emphasis shifted to ancestry of species - Darwin's theory of evolution caused reevaluation of the meaning of classification A. Before Darwin, species were fixed, immutable, perfect; sharing of characteristics was convenience to allow grouping B. Darwin viewed species differently & explained why characteristics were shared 1. Saw species as constantly, slowly changing; their sharing of characteristics makes sense since they share common ancestors 2. Species sharing most characteristics are most closely related 3. Dogs & wolves are closely related; cats & dogs less so (common ancestor farther back in time) C. Darwin's theory had little effect on taxonomists; archetype was replaced with type specimen (first specimen collected or representative specimen of given species) 1. Detailed description of type specimen defined essential characteristics of species; subsequent specimens measured against it 2. But after Darwin, individual differences in specimens were expected as a result of natural selection D. Mendelian & population genetics affected classification by stressing the importance of populations 1. Species were now seen as sets of individuals that could interbreed 2. Taxonomist's job now became to describe characteristics that differentiated one distinct population of a species from another 3. Type specimens were still collected but traits were expected to range through a predictable set of values How Do Biologists Keep Track of So Many Species?: Modern Tools of Classification I. Today, modern tools are yielding direct evidence of evolutionary relationships between species A. Species are now defined by the ability to interbreed, which is difficult & sometimes impossible to determine under natural conditions 1. Traditionally done by comparing structures & forms; assumed that if individuals are different, they won't interbreed; interbreeding criterion is not as straightforward as it sounds 2. Natural selection is not even-handed, populations change at different rates; the point at which they are different enough to be different species is difficult to tell B. Inferring evolutionary relationships is often difficult as well 1. Distantly related species may have similar traits if environments are similar - sharks (primitive fish), dolphins (mammals), icthyosaurs (extinct marine reptile); convergent evolution 2. Closely related species may differentiate (divergent evolution) - hummingbirds & ostriches II. Adjustments in classifying organisms are sometimes necessary A. Snow geese & blue geese were once thought to be separate species; inbreeding thought to occur with offspring thought to be sterile; not the case, so combined into one species 1. Blue forms & white forms are seen as color phases, individuals with different appearances B. Red foxes of Europe & America thought to be separate but American foxes interbreed with European & were probably European foxes released by settlers around 1750 III. New technologies in molecular biochemistry are making systematics more staightforward; relationships can be worked out by comparing proteins, RNAs, & DNAs A. Early efforts compared different species' cytochrome c - amino acid sequences compared 1. Since mutation rates were thought to be relatively constant, closely related species accrue fewer mutations 2. More distantly related species show greater cytochrome c variations B. Mitochondrial DNA, ribosomal RNA, & nuclear DNA comparisons as well C. Mostly, these techniques have led to few surprises - raditional taxonomists & systematists did their work well & it has passed another test of validity D. Ex.: first land vertebrates (early amphibians) were long thought to evolve from fish - which group? 1. Try to find which group of fish share the most characteristics with primitive tetrapods 2. Two distantly related candidates - lungfish (have lungs) & lobe-finned fish like Coelacanth (fins have tetrapod-type skeleton); lobe-finned fishes were favored over the years 3. rRNA comparisons suggest that lungfish sequences are closer to amphibians than that of lobefinned fishes - not settled yet; need more nuclear DNA & protein structure comparisons How Does the System Work?: Early Days I. Work of the taxonomist - put organisms into a series of hierarchical groups called taxa (taxon, sing.) A. Broadest groups contain the most organisms & they are broken into less inclusive groups which are subdivided even further until level of the individual species is reached B. All organisms within a particular taxon share certain characteristics C. Until recently, the choice of which characteristics to use for taxonomic comparisons was somewhat arbitrary & often involved analyses of homologous structures II. At first, there were thought to be only two kingdoms; now there are at least six A. From time of Aristotle to 20th century, organisms were divided into either plants or animals B. To be classified as a plant, the organism had to possess certain characteristics 1. Plants tend to be sessile (don't move around much) 2. Made of leaves that are generally green (photosynthetic & produce own food); also have stems & roots 3. Plant cells surrounded by thick walls C. Animals are generally more responsive (move around more than plants); their cells have no walls, they don't produce their own food III. Even this seemingly simple classification is not as simple as it sounds A. Where do you put: Fungi? - sessile, thick-walled cells but not photosynthetic; to group organisms together, don't need all characteristics of a given group so prioritize them 1. With fungi, thick cell walls were thought to be more important than mode of nutrition, so predominance of evidence suggested fungi were plants B. Bacteria also included as plants C. Where do you put Euglena? - had long flagella, no cell wall 1. In summer, it has well-defined chloroplasts, gathers at surface of ponds, & makes its own food 2. In winter, it loses chloroplasts & decomposes dead material 3. In summer, it acts like a plant; in winter, like an animal IV. Late 1960s - it was suggested that new kingdoms should be created to accommodate exceptions; five kingdom phase A. Kingdom Protista - includes Euglena & all similar one-celled organisms 1. Protists are eukaryotic cells (have organelles); some photosynthetic, some not 2. Some have thick walls, some do not B. Kingdom Monera - proposed to accommodate bacteria or single-celled prokaryotes C. Fungi - third new kingdom; proposed by R. H. Whitaker in 1969 V. Still exceptions - what about green algae?- most are single-celled, but many are not; multicellularity evolved in this group although it might have evolved independently in seaweeds (brown algae) A. Today, there are no single-celled brown algae, but some fossilized ones 1. Are they protists or plants? 2. Some consider them primitive plants, others protists like your text B. Existence of Archaebacteria, third cell type, creates special taxonomic problems 1. Where do they fit in? 2. A new taxonomic category larger than kingdoms was developed, the domain (most inclusive) How Does the System Work?: The Three Domains and Modern Classification I. There are three domains - Archaea & Bacteria both contain one kingdom but more could be added A. Domain Archaea - includes newly discovered cell types; contains one kingdom, the Archaebacteria (ancient bacteria with prokaryotic cells) B. Domain Bacteria - includes other members of old kingdom Monera; has 1 kingdom, the Eubacteria (true bacteria, prokaryotes) C. Domain Eukarya - includes all kingdoms & organisms composed of eukaryotic cells (protists, fungi, animals, plants) 1. Protists - single-celled & simple multicelled eukaryotes 2. Fungi - single- & multicelled eukaryotic, nonphotosynthetic organisms with thick-walled cells 3. Plantae - single- & multicellular eukaryotic, photosynthetic organisms with thick-walled cells 4. Animalia - multicellular, eukaryotic, nonphotosynthetic organisms with cells that have no walls II. Third cell type also creates problems for systematists - what are evolutionary relationships between domains? A. What does it mean that Archaea share more genes with Eukarya than with Bacteria? B. Which domain evolved first? III. Within each kingdom, there are many species, requiring additional categories A. All members of Domain Eukarya have one characteristic in common: cells eukaryotic so excludes Bacteria & Archaea; Eukarya contains millions of different species 1. Some single-celled, some multicellular; some have thick cell walls, some no cell walls 2. Multicellular organisms lacking cell walls are animals (Animalia) B. Animalia can be grouped further with each group a subdivision of the next larger taxon 1. Kingdoms divided into groups called phyla (botanists prefer divisions to group plants) like Phylum Chordata, that have legs, backbones, many of them so need more taxa 2. Phyla subdivided into classes: several classes of fish & several that live on land (one group is warm-blooded, with hair & mammary glands [Class Mammalia]) 3. Classes subdivided into orders, several in Mammalia, one including all monkeys, apes, & their relatives (Order Primate) 4. Orders subdivided into families; monkeys separated from great apes that belong to Family Hominidae including gibbons, orangutans, gorillas, chimpanzees, humans 5. Families divided into genera - humans are genus Homo; in the past, there were several human ancestors, known from fossils; they are species included in genus Homo, only one alive today 6. Example of species (distinct type of life) alive today is modern humans Homo sapiens (self, the wise); every species has similar set of taxa C. In particularly numerous groups (insects, certain plants), additional taxa are sometimes required 1. Formed using prefixes sub- (below) & supra- (above). 2. Between kingdom & phylum, taxonomists could have subkingdoms & supraphyla 3. Available for all taxonomic levels IV. Certain conventions used in writing scientific names A. All names are Latinized - not all taxa are listed but genus & species often are (always should be in biological writings) 1. Genus capitalized, species not 2. Scientific names italicized or underlined to distinguish them from other kinds of terms 3. In scientific writing, the second reference to the organism within a paragraph or so can be abbreviated (Escherichia coli abbreviated E. coli), but not the first time B. Biological system of classification is extremely useful to biologists 1. Can accommodate any number of species - newly discovered species can be fit into system by noting characteristics it shares with other organisms 2. System is arbitrary in selection of traits used for comparison 3. Ideally choose those that easily separate groups, irrespective of importance to organism (antenna knobs separate butterflies & moths) C. System is focused on interpretation 1. Taxa indicate evolutionary relationships (organisms sharing the same genus are closely related) 2. Those only sharing domains are distantly related 3. Relationships denote evolutionary history 4. If organisms stop sharing taxa ->stop sharing ancestors; jaguar & lion (common ancestor alive a few million years ago); both share common ancestor with E. coli dating back billions of years How Did Life Originate? I. Interest in life's origins is probably as old as humanity A. Ancient Greek/Roman scholars may have proposed spontaneous generation to answer the question B. Plagued Darwin who said, "Life may have originated in a warm, little pond."; ducked the question, implications of evolution on idea of spontaneous generation may not have been obvious II. Early speculations on the origins of life lacked experimental evidence - A. I. Oparin, Russian biochemist & J. B. S. Haldane, Scottish biochemist (1920s & 1930s) A. Reasoned Earth's early atmosphere was different from today's atmosphere 1. Atmospheres of other planets in solar system lacked free oxygen 2. Rocks on Earth's surface в‰Ґ3 billion or so years ago contained free iron, no rust (iron oxide) as would happen in O2 atmosphere; suggests there was no free O2 in the ancient atmosphere 3. Speculated on abundance of methane, ammonia, nitrogen, water vapor, maybe free hydrogen B. Envisioned a variety of energy sources on primitive Earth - earthquakes & lightning, ultraviolet light (no free oxygen so no ozone to keep UV out) 1. These energy sources working on atmospheric chemicals would stimulate chemical reactions 2. Speculated that amino acids (protein building blocks) would arise spontaneously; skeptics reasoned amino acid formation would have taken millions, maybe billions, of years III. Early experiments spontaneously produced organic compounds - Harold Urey, Univ. of Chicago & Stanley Miller, graduate student (1952) - built apparatus modeling Oparin-Haldane atmosphere A. Used electric sparks to simulate lightning in simulated atmosphere of methane, ammonia, hydrogen sulfide, & water vapor; water in flask simulated ocean 1. Water evaporated & condensed, simulating water cycle 2. In less than a week, the water turned cloudy вЂ”> amino acids had formed; repeated by others 3. Vary composition of gases & other conditions & get other carbon compounds (carbohydrates, lipids, DNA & RNA components, other amino acids) 4. Could make life's building blocks in proposed ancient atmosphere & it was easy & quick B. More circumstantial evidence accumulated 1. Astronomers found simple organic compounds in meteorites - some questioned the results, suggesting some kind of contamination, but compounds were found inside 2. Instruments remotely sensed methane deep in open space; carbon-based compounds are apparently common throughout the universe C. Then, astronomers & geologists were convinced that Earth's initial atmosphere could not have matched Oparin's & Haldane's model 1. Suggested a composition of mainly carbon dioxide, nitrogen, water vapor; still no free oxygen 2. Organic compounds would be much less likely to form 3. Some suggested that comets & meteorites brought Earth its first precursor carbon compounds D. Then more circumstantial evidence - fossils of ancient bacteria (3.5 billion years old) were found in western Australia (at least eleven different kinds of fossils found) 1. Suggested life must have evolved rapidly in something less than a billion years IV. The next step was to move beyond isolated carbon-based compounds - some complicated chemical reactions must have occurred spontaneously A. What are some possible scenarios? 1. When ocean tidal pools evaporate, salts & other impurities get highly concentrated; could have happened in ancient oceans, concentrating aminos, making protein formation more likely 2. Powerful electrostatic forces in bubbles would attract aminos, pull them close to each other; may allow proteins to form; if they burst, spew contents into air where other reactions occur 3. Iron pyrite crystals (fool's gold) & clay crystals (both are common on Earth's surface) could attract & concentrate aminos B. Over hundreds of millions of years, any, all, or similar processes could have filled oceans with proteins, carbohydrates, phospholipids, nucleotides 1. In such an early ocean, a kind of natural selection would favor certain molecules over others 2. Some molecules would be more stable & would persist; less stable ones would disappear 3. Chemical compound variety would decrease over time as more stable ones evolved & persisted V. Phospholipids arrange themselves into tiny bubbles covered by lipid bilayer resembling membrane A. Chemicals could be concentrated in bubbles; contents of one would differ from others 1. Some might contain proteins & other chemicals that would stabilize phospholipid membranes 2. These bubbles would persist aided by natural selection 3. Some might contain, by chance, proteins that could break down complicated chemicals to simpler ones, releasing energy B. Bubbles in ancient seas might fuse, mixing contents & capabilities; over time, more stable & complicated compositions would persist & thrive C. Eventually, they reach a level of complexity called protocells (not living); still can't reproduce, no DNA - how did it evolve & is DNA absolutely essentially? VI. Is DNA essential? - retroviruses have no DNA, genetic material is RNA; inside host, each virus has enough RNA to make a new generation of viruses; could RNA have done the same in protocells? A. Scripps Institute, La Jolla, CA (1993) found small molecule of synthetic RNA that within an hour began making copies of itself & the copies made more copies B. Then, copies began to change - evolve - acquiring new chemical characteristics, but not alive since it depends on a steady supply of preformed proteins C. In an ancient ocean filled with organic compounds, protocells might qualify as the first cells if they have: 1. RNA that can make copies of itself & evolve 2. RNA that could synthesize enzymes capable of breaking down other organic compounds 3. RNA that could synthesize enzymes capable of building & maintaining cell membranes D. Later, DNA could have evolved as method of conveniently & safely storing vital chemical information contained in cell RNA VII. These first cells evolved into the different cell types we see today A. Life appeared & forever changed the conditions of oceans 1. First cells would have been totally dependent on the ocean's preformed carbon compounds for nutrients; would have had no predators & nothing to control their populations 2. Numbers soared until nutrients were exhausted, then population would have crashed 3. These heterotrophic cells (cells incapable of producing their own food) would have been totally dependent on the ocean's nutrients for energy 4. Would also have made spontaneous generation of new organic compounds impossible; any free carbon compound would have been gobbled up B. Under these conditions, any cell with the ability to trap energy of sunlight & store it in relatively simple chemicals they produced would have advantages 1. Pigments absorb light energy (relatives of chlorophyll) 2. Cells that can produce chemicals that store energy are called autotrophs; their numbers soared 3. Similar cells evolved the ability to do the same thing using energy contained in certain inorganic chemicals found in or near the ocean - chemoautotrophs 4. Autotrophs proliferated as carbon-based soup played out C. Heterotrophs had to switch from dependence on soup to dependence on organic autotrophs 1. Heterotrophs would forever limit autotroph numbers 2. Autotrophs, by their presence or absence, would regulate heterotroph numbers 3. Led to capacity for balanced ecosystems; left fossils 3.5 billion years ago in the rocks of western Australia 4. A billion years later, some autotrophs evolved methods improving their ability to trap & store sunlight energy вЂ”> modern photosynthesis evolved 5. Numbers of these new autotrophs soared & as they did, a byproduct of photosynthesis, free oxygen, built up D. Most organisms of the ancient world found free oxygen intolerable 1. In oceans, organisms that built simple & complex organic compounds removed CO2 from the atmosphere 2. Latter day more advanced autotrophs removed most of the rest & replaced it with oxygen 3. The excess oxygen changed forever the chemical nature of the atmosphere to today's E. Other improvements in cellular efficiency evolved 1. First cells were necessarily simple in structure with few internal parts - prokaryotes 2. Between 2 & 1.5 billion years ago, a new kind of cell appeared in fossil record - eukaryotes 3. These had membranes on the inside producing compartments in which certain chemical reactions could be isolated from others 4. Cellular life then evolved into what we know today F. Cells (or their descendants) similar to those on Earth when O2 began to build up are still present 1. First O2 -intolerant heterotrophs are still here as Archaebacteria, confined to deep muds, inside carcasses, within intestinal tracts of more complicated organisms, in other O2 -free places 2. Chemoautotrophs are still here, too - found near volcanic vents deep in the ocean, in hot sulfur springs, & similar environments 3. Today's blue-green algae (cyanobacteria) must be similar to early prokaryotic autotrophs - still trap the energy of the sun & make it available to other organisms G. Lots of evolution occurred among eukaryotes - some are single-celled, some are multicelled; some are autotrophs, some are heterotrophs; some are plants, some are animals VIII. Within four billion years, life as we know it evolved A. Geologists & paleontologists - Earth first appeared ~4.6 billion years ago 1. Initially, it was much too hot to support complex chemicals of life 2. Earth had to cool considerably before life could appear B. Oldest known fossil cells (3.5 billion years ago [bya]) are far too complex to be the first cells 1. Thus, life must have first appeared between 4.6 & 3.5 billion years ago (probably about 4 bya) 2. For 2 billion years, ruled Earth as dominant forms of life вЂ”> evolved to tolerate every known aquatic & damp environment C. ~2.5 bya - photosynthetic cells formed & changed Earth's atmosphere from one dominated by CO2 to one dominated by oxygen D. ~2 bya - primitive eukaryotic cells evolved & were a more efficient cell type that allowed further evolutionary possibilities E. ~1 bya - multicellular organisms appeared; groups of cells living together was not new 1. Primitive prokaryotes form colonies of single cells that simply don't separate after division 2. Multicellularity evolved when some colonial cells specialized, concentrating on movement, food digestion, or reproduction; other cells became dependent on them for those functions F. ~600 million years ago - some multicellular organisms evolved hard parts (shells, skeletons, etc.) вЂ”> number & diversity of fossils increased G. By 500 million years ago -terrestrial Earth exploitation was in full swing вЂ”> diversity increased 1. Plants, animals, fungi, even some algae & bacteria become increasingly less dependent on watery environments for wetness and buoyancy 2. Life proliferated; some species persisted, little changed from their first appearance 3. Many others became extinct; replaced by new forms better adapted for environmental conditions How Diverse Is Life On Earth?: A Brief Look at the Archaea and Bacteria Domains I. Directly related to oldest organisms on Earth; have had lots of time to evolve & differentiate II. Thrive nearly everywhere - depths of ocean, deep in Earth, upper atmosphere, all surfaces, any body of water, anywhere that is the least bit damp A. Some depend on oxygen, others are indifferent to it, others find it toxic B. Some tolerate extreme heat, salinity, acidity, & combination of harsh environments C. Others are not very tolerant of harsh environments D. Incredibly numerous; number in healthy human's intestines > number of humans who ever lived III. Members of Archaea & Bacteria have several characteristics in common A. All are single-celled organisms; contain no nuclei & few other organelles except ribosomes (prokaryotic) B. Their DNA is contained in a single, twisted, circular chromosome floating free in cytoplasm C. All have relatively thick cell walls made of substances other than cellulose (unlike plants) D. Under intolerable environmental conditions, many form spores - lose most of cytoplasm, shrink, surrounded with thick cell wall, get metabolically inactive until conditions improve E. As spores, very light; float in air, move vast distances, & occur everywhere IV. Uses of bacteria - they are known for causing diseases but few do; some have positive uses and have been put to use by humans and, in some cases, other organisms A. Bacteria are used as sources of food B. They are used for the biological control of pests C. They are used as agents of fermentation D. They are used for the making of foods and and antibiotics E. Bacteria, along with fungi, are the main decomposers of dead organic matter & thus return nutrients to our environment V. Reproduction - mainly through simple cell division (binary fission); but rudimentary sexual reproduction occurs (conjugation); some bacteria do form colonies A. In conjugation, two cells form a cytoplasmic bridge (pilus) through which they pass at least a portion of one chromosome B. Some pick up stray genes from environment as a result of decomposition & feeding; most DNA is digested but sometimes DNAs are incorporated into genome & organisms gain new traits C. Characteristics that evolved in one organism are passed directly to another; distinction between species is blurred VI. Some are virtually immobile; others are equipped with one or more flagellae - whip back & forth pushing them along; others glide VII. Most Archaebacteria & Bacteria are heterotrophs (depend on other organisms for nourishment, i.e. as a source of organic molecules) A. Most are decomposers; when anything dies, bacteria & other decomposers attack B. Their powerful enzymes break down complex biochemicals into nutrients they absorb & use C. This is an invaluable ecological service; carcass nutrients are recycled & made available to others D. World of decomposers is highly competitive - must defend their carcass from others E. Some make & excrete powerful poisons only they can tolerate; most powerful known is made by Clostridium botulinum resulting in food poisoning; just protecting its nutrient source, living space VIII. A few Bacteria & Archaea are pathogens - cause diseases in nearly every other organism A. Pathogens are similar to decomposers, just start decomposition before victim dies B. Some excrete chemicals that destroy cells & tissues C. Others rob hosts of nutrients & may secrete toxic chemicals to ward off competitors; incidentally sickens or kills host; microbe doesn't care whether victim is host or carcass D. Pathogens are highly adapted to their harsh environment; living things fight back by creating environments hostile to most microbes IX. Other Archaea & bacteria live as mutualistic symbionts; form intimate partnerships with other organisms in which both benefit - examples: nitrogen fixation & intestinal populations A. All living things need a nitrogen source, most can not use gaseous nitrogen; some bacteria can transform free nitrogen into compounds (ammonia, oxides of nitrogen) - nitrogen fixation 1. Products can be used by other organisms; some plants, especially legumes (peas, beans, alfalfa) have symbiotic relationships with certain nitrogen-fixing bacteria 2. Legumes supply bacteria with places to live (root nodules) & with photosynthetic and other products in exchange for a steady supply of usable nitrogen B. Populations of E. coli bacteria reside inside the intestines of all healthy humans 1. They help us absorb water and & manufacture vitamins 2. Protect us - defend the space they occupy in our bodies from potentially harmful microbes 3. In return, we give them space, protection, habitable environment in which to live, & nutrients X. Some are autotrophs - make their own food; do not depend on other organisms for basic nutrients A. Microbial diversity in this group is extensive - blue-green algae use light for energy (chlorophyll); others use light but another pigment B. Some use energy sources other than light for energy like chemicals in hot springs or those coming out of underwater vents - chemoautotrophs XI. Come in four basic shapes - rods (bacilli), spheres (cocci), spirals (spirochetes), filaments; shape, color, & a few other traits form the basis of their taxonomy How Diverse Is Life On Earth?: The Phyla of the Archaea and Bacteria Domains I. Phyla of the Eubacteria - Cyanobacteria & Proteobacteria A. Cyanobacteria - named for their blue-green pigment; found in a variety of habitats (snow fields, frozen lakes, deserts, inside of rocks, hot springs) 1. More than 1,500 species; range from single cells to colonies 2. Account for 20% of the primary production in the seas B. Proteobacteria - the true bacteria 1. They display one of three body shapes: a sphere or coccus, a rod or bacillus, a spiral or helical shape (spirochetes) 2. Some are pathogenic & owe their pathogenic properties to components in their cell walls 3. Found in variety of habitats like the human gut, where they established a symbiotic relationship II. Kingdom Archaebacteria - prokaryotes that many believe are the most ancient group of living organisms; characterized by their ribosomal RNA, lipid structure, & certain enzymes A. Inhabit extreme environments such as hot springs, sea vents, boiling muds, volcanoes B. Originally placed with Monerans; now enjoy their own kingdom How Diverse Is Life On Earth?: A Brief Look at Domain Eukarya, Kingdom Protista I. Kingdom Protista - ~2 billion years ago, natural selection favored cells that could get more & faster energy from nutrients; eukaryotic cells evolved; what is a protist? A. Some protists are animal-like, some are plant-like, some are fungus-like - Euglena can alternate being either animal- or plant-like B. Characteristics shared by protists - most are unicellular, lack tissues, seldom demonstrate cell specialization; all are eukaryotic II. An overview of the Protista - Algae A. Autotrophic, trap light with chlorophyll found in chloroplasts; found in almost all naturally occurring aquatic environments where they perform essential ecological functions 1. In the open waters of oceans, lakes, ponds, slow-moving rivers, & streams, floating algae (phytoplankton) convert sunlight into usable energy 2. Some algae are bacteria, others are simple plants, many are protists B. Closer to shore, the importance of green plants as photosynthesizers increases III. Protozoans (first animals) - heterotrophs, single-celled eukaryotes; no cell walls, no chloroplasts, no chlorophyll; commonly found in fresh & marine waters & muds; most are highly mobile A. There are tiny grazers feeding on algae, tiny carnivores feeding on bacteria & other protists, & tiny scavengers feeding on dead material & contributing to decomposition B. A few are parasites causing serious diseases in animals - in humans, malaria, African sleeping sickness, amebic dysentery IV. Slime molds - heterotrophic protists; fascinating life cycles A. Start life as single-celled, free-living organisms resembling ameboid protozoans (move by pseudopods) but can at times organize selves (free-living cells) into multicellular organisms B. Acellular or plasmodial slime molds - cells aggregate, nuclei divide repeatedly; resulting multinucleated masses (plasmodia) stream through the soil feeding on bacteria & cellular debris 1. If moisture or nutrients are lacking, aggregates break up, form fruiting bodies resembling tiny mushrooms вЂ”> form spores (by sexual reproduction) that withstand hostile environments C. Cellular slime molds spend most of life as amoeboids; when the environment is hostile, they aggregate into sluglike forms that move rapidly in search of better conditions 1. Occasionally form tiny mushroomlike fruiting bodies when they reproduce sexually 2. Could place them in Protista, Fungi, or Animalia вЂ” for now Protista How Diverse Is Life On Earth?: The Phyla of Kingdom Protista I. Protistan phyla: Plant-like phyla A. Euglenophya - unicellular, move by means of two flagella; have flexible outer covering 1. May be either animal-like or plant-like 2. Their relationship to other organisms & their role in evolution are the center of controversy B. Pyrrophyta - many are fiery red; also known as dinoflagellates; about 1,000 species 1. Many are unicellular, but some form colonies 2. Most are marine & found in warm seas where they compose the major component of plankton 3. Some produce toxins & can be poisonous to humans; contribute to dangerous red tides C. Chrysophyta - the golden algae & diatoms; photosynthetic & compose the largest portion of photosynthetic organisms in plankton 1. Critical for marine food chains 2. Some have thick & often beautiful cell walls made of silicon dioxide 3. When they die, they settle to the ocean floor & create huge sediments, which become sedimentary rocks D. Phaeophyta - brown algae; often quite large; many referred to as kelp; all are multicellular 1. Have flagellated reproductive cells 2. Photosynthetic & contain fucoxanthin (brown pigment) in addition to chlorophyll 3. About 1,500 species of brown algae E. Rhodophyta - red algae; ~ 4,000 species; mostly marine; have both unicellular & multicellular forms; have no motile cells; photosynthetic 1. Red pigment in red algae absorbs blue light which penetrates to a greater depth in the ocean than other colors 2. Allows red algae to photosynthesize at greater depths than other algae F. Chlorophyta - green algae; ~7,000 species; all are photosynthetic with cell walls made of cellulose 1. There are unicellular, multicellular, & colonial forms; some are flagellated 2. Believed to be the evolutionary link to modern plants 3. For example, Volvox forms colonies of cells that resemble a multicelled organism II. Protistan phyla: Animal-like phyla A. Sporozoa - unicellular; lack means of independent locomotion; all cause disease & spend at least part of their life cycle inside the cells of a host species; malaria is a disease caused by a sporozoan 1. Depend on other organisms to carry them from host to host 2. Their life cycles & reproduction are often complex B. Zoomastigina - the flagellates; move by means of one to several flagella; unicellular, some are freeliving, others are symbiotic, some are pathogenic 1. Reproduction usually by binary fission 2. Important human diseases caused by this group - African sleeping sickness, sexually transmitted diseases, Giardia C. Sarcodina - demonstrate characteristic amoeboid movement by extending temporary cytoplasmic extensions (pseudopodia); therefore, they have no fixed shape 1. Amoeba may be shelled (radiolarians) or naked 2. Marine Sarcodina shells - so plentiful that they are main components of some marine sediments D. Ciliophora - the ciliates; move by means of cilia; unicellular & can reproduce asexually by binary fission or sexually by conjugation 1. Common in both fresh & marine waters 2. Feed there on bacteria, algae, & other protistan or scavenge on dead plants or animals III. Protistan phyla: Fungus-like phyla A. Oomycota - the water molds; consist of branched mycelia; have chitin or cellulose cell walls 1. Produce flagellated spores; in sexual stage, produce oospores 2. Some are parasitic; ~680 species of water molds B. Acrasiomycota - the cellular slime molds; vegetative form is unicellular & moves by pseudopodia 1. These amoeba-like cells form aggregates & develop into multicellular pseudoplasmodia 2. These pseudoplasmodia eventually develop fruiting bodies & produce spores; ~70 species C. Myxomycota - plasmodial slime molds; originally classified as fungi; ~500 species 1. Spend part of their life cycle as thin, streaming, multicellular plasmodia 2. Plasmodia creep along decaying material 3. Form spores in sporangia & have motile reproductive cells How Diverse Is Life On Earth?: A Brief Look at Domain Eukarya, Kingdom Fungi I. Important in ecosystem function & human society, rusts, blights, yeasts, mushrooms A. Major traits - all eukaryotic, mostly multicellular; heterotrophic, either saprotrophic or parasitic; often possess a fibrous network of hyphae (called mycelia) 1. Thick cell walls are not made of cellulose but chitin (more commonly found in exoskeletons) 2. Reproduce by means of spores that are produced sexually or asexually; cells are usually haploid, but they have a brief diploid period 3. Fungi are decomposers & can attack virtually all organic matter; cause most plant diseases; attack crops & stored foods; some also cause human diseases of the lungs & skin B. Previously considered plants that lost chloroplasts & photosynthesis; now have their own kingdom C. Also include yeasts which are single-celled & microscopic; most are multicellular & macroscopic II. Multicellular fungi that start life as tiny spores may persist for years & be carried very far from origin A. When conditions become favorable, spore cells divide rapidly; typically, several threadlike structures (hyphae) grow out in several directions from spore B. As they grow, cells release enzymes that break down organic compounds in environment into absorbable nutrients; soon nutrients near hyphae are exhausted C. By then, hyphae tips grow into a new territory with new nutrients; sent back to older cells D. Older cells lose walls & membranes between adjacent cells, maybe facilitating nutrient transfer E. Except for tip cells, hyphal mass (fungal mycelia) becomes multinucleated protoplasmic mass III. Reproduction in Fungi A. Most reproduction in fungi is asexual 1. Yeasts reproduce by simple cell division or budding 2. Hyphae breaking off of multicellular fungi simply grow through mitosis into new individuals 3. Many fungi form fruiting bodies that produce & release asexual spores B. Although most never do, others resort to sexual reproduction, at least occasionally 1. Typically, gametes form zygotes that immediately undergo meiosis, grow into new individuals 2. Unlike animals (only gametes are haploid), all cells of these mature fungi are haploid IV. Especially in terrestrial ecosystems, fungi are important decomposers competing with bacteria A. Recycle vital nutrients upon which other organisms depend; fungi are extensive & numerous 1. Example: ~10% of cells in a tree are alive at any one time, rest are dead; once dead, up to 30% of tree mass may be living fungal hyphae (tree more alive when dead than when alive) B. Also primary decomposers of dead leaves; soil beneath feet is laced with hyphae that decompose organic matter, individual mycelium may be meters long C. Competition between bacteria & fungi is keen; fungi produce poisons they can tolerate that discourage competitors & predators; basis of much of the antibiotic industry 1. Use fungal poisons to kill pathogens without endangering patients (ex.: penicillin) V. Some soil fungi have abandoned decomposer life style to form symbiotic relationships with other organisms (ex.: mycorrhizal associations formed with trees) A. Fungal hyphae surround tree root hairs & extend out into neighboring soil; in exchange for photosynthetic products (especially glucose) 1. Mycorrhizal fungi provide trees with soil nutrients & water; sometimes, healthy tree growth totally depends on healthy associations with symbiotic fungal partners B. Lichens are product of another symbiotic relationship involving fungi & blue-green algae 1. Typically, lichens grow on rocks, tree trunks, or at high latitudes & altitudes (harsh environments in which soil nutrients are lacking or unavailable) 2. Algae provide lichens with photosynthetic products 3. Fungi provide protection, anchorage; release powerful chemicals that etch nutrients out of rock 4. Sometimes, symbioses are so intimate that individual algal & fungal cells aren't distinguishable VI. Some fungi are parasites, especially on plants A. Farm crops particularly susceptible because crops in large fields & tightly packed populations rusts, blights, smuts are best known & most loathed by farmers B. Humans have fungal diseases: athlete's foot, ringworm, vaginal yeast infections VII. Also provide important human foods - certain kinds of fungi convert soy beans into soy sauce & along with specific bacteria, milk into cheese (little spots in blue cheese are edible mold) A. Yeasts produce alcohol & CO2 during cellular respiration B. In bread making, this CO2 is used to raise the dough while alcohol boils off during baking C. In beer & wine making, alcohol is preserved while gas is vented off How Diverse Is Life On Earth?: The Phyla of Kingdom Fungi I. Zygomycota - produce spores called zygospores; includes common bread mold, Rhizopus A. Other members of this genus attack plants such as strawberries B. Important economically; fungi such as Phytopthora; can destroy important food crops such as potatoes, resulting in widespread hunger II. Ascomycota - the sac fungi; reproduce sexually by means of ascospores, produced in sacs (asci) A. Members of this phylum include brewer's or baker's yeast (Saccharomyces cerevisiae), truffles (Tuber melanosporum ), morels (Morchella esculenta) B. Members of Ascomycota are the most common type of fungi found in lichens, a commensalistic relationship with algae III. Basidiomycota - the club fungi; represented by about 16,000 species A. Sexual reproduction is by basidiospores produced on a basidium B. Include such fungi as the mushrooms, jelly fungi, coral fungi, bird's nest fungi, stinkhorns IV. Deuteromycota - the imperfect fungi; so-called because no sexual stage has been observed A. Reproduction resembles that of Ascomycota so they are thought to have evolved from them B. Members of this group responsible for such ailments as athlete's foot, ringworm, candidal yeast infections C. Most famous belong to genus Penicillium, from which we get penicillin How Diverse Is Life On Earth?: A Brief Look at Domain Eukarya, Kingdom Plantae I. General traits of Kingdom Plantae A. Eukaryotic cells are surrounded by thick cell walls, multicellular, autotrophic, green due to chlorophyll-containing chloroplasts that photosynthesize; have alternation of generations life cycle B. Extremely diverse in structures (leaf shapes, types of pigments, number of petals, etc.); no agreement where to place algae (text puts them in Protista; some put them in Plantae) II. Among the first organisms to live out of water - barriers overcome to move from water to land A. All cells must have water - in H2 O, surrounded by it; on land, it is limited; cell walls resist its loss B. Gravity (especially for large organisms) - in H2 O, organisms float; on land, need support - cell walls along with turgor pressure (internal pressure of H2 O against cell walls) resists gravity 1. Extensive root systems in most successful plants provide anchorage 2. Thick cell walls & extensive root systems have allowed some terrestrial plants (redwoods) to be the largest organisms that ever lived C. All cells must have nutrients & oxygen - in water, just wait until both come by in solution; on land, must seek out both - roots facilitate nutrient & water uptake D. Organisms are most vulnerable in gamete stage, such problems are minimized in H2 O (spew gametes into H2 O & they find each other); on land, would expose gametes to threat of drying out 1. Could surround gametes with thick protective shells, but how would they unite? III. In near-shore fresh water environments, submerged, floating, & emergent plants assume ecological roles played by floating algae in deep-water environments A. Through photosynthesis, make sun's energy available to other organisms B. In fresh water, green algae (principally as phytoplankton) are primary energy producers, a role assumed by brown & red algae near the shore in oceans C. Mosses, ferns, gymnosperms (naked seed plants), flowering plants - land environment energy producers & for humans, too (everything we eat is flowering plant or animal that eats them) How Diverse Is Life On Earth?: The Divisions of Kingdom Plantae I. Bryophyta - include mosses, liverworts, hornworts; seen in variety of environments (moist to very dry) A. Lack the vascular tissues & supportive tissues found in more advanced groups of plants B. Gametophyte is the most dominant stage of their life cycle C. Thought to have diverged from ancestor common to vascular plants; perhaps it was green alga II. Lycophyta - club mosses; represented by about 1,000 species; vascular plants A. Have dominant sporophyte in their life cycle; most are found in tropical areas, but also are conspicuous in temperate environments B. Two main genera - Lycopodium & Selaginella (may appear to die during drought conditions but comes alive again when it rains) III. Sphenophyta - horsetails; vascular plants; represented by only one living genus, Equisetum A. Found world-wide in moist areas; its rhizomes grow rapidly & are poisonous to livestock B. If cut up rhizomes to get rid of them, only find that many new plants grow from fragments C. Epidemal tissues of horsetails are very rough & have been used as polishing devices IV. Psilophyta - whisk ferns; simplest vascular plants because they lack true roots and leaves A. Get name because of highly branched stems that give them the appearance of whisk brooms B. Two living genera: Psilotum (found in subtropical regions of U. S. & Asia) & Tmesipteris (restricted to Pacific islands) V. Pterophyta - ferns; largest group of seedless vascular plants; primarily tropical, but some found in temperate & desert areas; some, like Marattia, have large leaves reaching 4.5 meters wide A. Ecology of ferns is well studied since some can be rather noxious weeds B. When forests are burned to establish pasture land, ferns can quickly become pests due to rapidly dividing rhizomes VI. Cycadophyta - cycads; ~140 species; only 2 species are native to U. S., both belong to genus Zamia A. Many cycad species face extinction & remain only in cultivated gardens B. Have palmlike leaves & therefore bear no resemblance to other living gymnosperms (conebearing plants), but they are gymnosperms & produce seeds in cones VII. Ginkgophyta - ginkgos; ancient group of plants (>80 million years old) with one surviving species A. Broad-leaved deciduous trees that bear naked seeds B. Mature seeds look like plums & have a nauseating odor; they are delicacy in some parts of world VIII. Gnetophyta - small, bizarre-looking group of seed plants; some, like Ephedra , are used as stimulating medicinal teas; species E. sinica contains chemicals similar to human neurotransmitters A. Welswitschia mirabilis maybe most bizarre-appearing of them; looks more like someting out of a science fiction movie than a real plant B. Found only in southwestern Africa IX. Coniferophyta - conifers; mostly evergreen plants; most abundant of cone-bearing plants A. Members of genus Pinus are are the most abundant trees in the northern hemisphere B. One representative of bristlecone pines (P. longaeva) thought to be >4,725 years old C. Other members: yews, spruces, redwoods, cypresses, junipers X. Anthophyta - angiosperms (flowering plants); ~235,000 species 1. Their phylogeny is next to impossible to determine; molecular phylogeny may help 2. Don't know how flowers evolved, evolutionary history of monocots & dicots, where flowering plants first evolved How Diverse Is Life On Earth?: A Brief Look at Domain Eukarya, Kingdom Animalia I. Kingdom Animalia - all are multicellular, eukaryotic heterotrophs, lacking thick cell walls; diverse group of organisms A. Evolutionary trends found within the animal kingdom 1. Development of symmetry 2. Formation of a body cavity (coelem) 3. Fate of the first opening in the embryo B. Biologists differ in their opinions as to how animals arose 1. Some believe that single-celled protists came together to form colonies which then gave rise to multicellular animals 2. Others think that large multinucleated protists gave rise to multicellular animals when plasma membranes surrounded each nucleus, thus forming individual cells II. Animals generally respond much more quickly to sudden changes in immediate environments A. Animals move around more than other multicellular organisms; evolution has developed structures that facilitate movement: legs, wings, surface muscles that change shape (jellyfish) B. Include three phyla of worms (flat, round, segmented) that lack limbs; limblessness is popular body plan & not restricted to worms (snakes, eels) C. Not all animals are motile - sponges & mollusks (mussels, barnacles) stay put most of their lives III. Structure & organization of animals is generally more fixed than other multicellular organisms A. All mammals have four limbs; all insects have six limbs B. Plants grow a little bit each year whenever conditions warrant throughout lives; animals have spurts of growth when young, little or no growth when adults C. Most have predictable body plans; individuals of particular group all have roughly same shape (sponges are exception) 1. Animal bodies tend to be symmetrical; most bilaterally (left side is a mirror image of the right) 2. Some radially symmetrical (jellyfish, adult spiny-skinned animals) - any number of lines can be passed through body dividing right & left mirror images IV. All terrestrial organisms face problems associated with limited water - animal cells quickly lose water when exposed to dry air A. Solution is animal tissues are bathed in water & bodies are surrounded with impervious barrier: shell, hard outer skeleton, waterproof skin B. Extracellular water is high in dissolved sodium chloride (salinity approaches that in sea water) C. Animals carried their ocean with them V. Animals made H2 O-land transition several times during evolutionary history - snails, slugs (mollusks) became terrestrial independent of insects (jointed-legged animals) & amphibians (back-boned animals) VI. Many evolutionary trends in animals involved refinement of physiological systems (more extensive in animals) A. Nervous systems non-existent in simple sponges but becomes netlike in jellyfish, ladderlike in flatworms, cord with off-branching lateral nerves in others B. Brains do not appear until segmented worms, then become increasingly complex & are most complex in backboned animals How Diverse Is Life On Earth?: The Phyla of Kingdom Animalia I. Porifera - sponges; most primitive of animal phyla; multicellular, but cells are loosely held together A. Lack symmetry & do not have defined tissues or organs B. Most species are marine, but there are a few freshwater species C. Water continually enters & exits sponges from which they filter out nutrients D. Their skeletons are composed of spicules that are left behind when they die II. Cnidaria - have radial symmetry & unlike Porifera have defined tissues A. Get their name from stinging cells (nematocysts) that they use for protection & capture of prey B. Many, like Portuguese man-of-war, are harmful to humans C. Most have two distinct forms in their life history: hydra & sea anenomes are examples of polyp form; other form is called medusa or jellyfish III. Platyhelminthes - flatworms; possess bilateral symmetry; lack a body cavity (coelem) but do have distinct tissues; also demonstrate cephalization or formation of distinct head region A. Tapeworms & flukes are parasitic B. Responsible for a variety of diseases in humans & other animals IV. Nematoda - roundworms; most abundant animals on Earth; found in every possible environment A. Have bilateral symmetry & possess false body cavity (pseudocoelem) B. Many are parasitic & responsible for intestinal diseases (pinworm, hookworm, trichinosis, elephantiasis in humans) C. Others are found free living in soil, marine, & freshwater habitats V. Mollusca - over 60,000 species; share two characteristics вЂ” muscular foot on ventral surface & mantle that secretes calcium carbonate to make shell A. Have a coelem & along with annelids & arthropods, are protosomes (first opening in embryo - the blastopore, becomes the mouth) VI. Annelida - first animals to demonstrate true segmentation A. Body segments represent repeating units with own excretory, nervous, & circulatory structures B. Have bilateral symmetry & a coelem; protosomes (like molluscs & arthropods) C. Found in a variety of habitats & may be quite large & colorful VII. Arthropoda - named for their jointed appendages; make up largest phylum in terms of species A. Bilateral symmetry & coelem; protostomes like molluscs & annelids B. Covered by hardened exoskeleton containing chitin; must be shed for individual to grow C. Also undergo metamorphosis from immature stages to distinct adult stages VII. Echinodermata - bilateral symmetry as larvae & radial symmetry as adults A. Have coelem but are like chordates in that their first embryonic opening forms an anus; second opening becomes the mouth (deuterostome) B. Use a series of tube feet for locomotion & for grasping prey C. Have the ability to regenerate lost parts & can form new adult from small fragment VIII. Chordata - like echinoderms, possess bilateral symmetry, coelem, & are deuterostomes A. No matter how distinct the adult form, all chordates at some time in development possess supportive rod (notochord), dorsal tubular nerve cord, gill slits, postanal tail B. Many theories regarding evolution of chordates C. Some early ancestors of chordates include living species like tunicates & Amphioxus Where Are We Now? I. Taxonomy & systematics are currently two of the most active, exciting areas of biology - why? II. New technologies used by systematists that allow more precise determinations of relationships between species A. Using biochemistry techniques, systematists can now determine: 1. The order of amino acids in proteins 2. The order of nucleotides in ribosomal RNA & mitochondrial DNA 3. Sequences of partial and complete genomes of organisms B. These are the most basic levels at which existing species become new ones 1. Species with similar protein & nucleic acid structures are assumed to be more closely related than those with dissimilarities 2. Because the rate at which mutations change these factors is thought to be constant, the length of time the two species have been evolutionarily separated can be estimated III. Growing awareness that biological classification is only just beginning has stimuated an increased interest in the field A. 100 million species estimated on the planet; only 1.5 million described B. New species are found each day; opportunities to do so may continue through most of next century IV. Sense of urgency in the field; human activities particularly in the tropics are negatively affecting biodiversity A. Some believe we may be heading for new mass extinction (loss of millions of species) 1. Species becoming extinct every day, some even before they are described 2. Will stay unknown unless they leave fossils 3. Their importance to ecosystems will never be fully appreciated; contribution to human welfare & biosphere will be forever lost 4. Some may contain cures for human diseases, may be new human foods, or produce otherwise useful products B. Taxonomists are urged to to go into areas where extinctions may be occurring most rapidly in efforts to catalog species & save remnant populations before they are lost Analogies, Anecdotes and Illustrations Where Is Life Found? In introducing the topic of biodiversity to your class, you might want to include a brief description of the unexpected places where life has been found. This gives an idea of the kinds of extreme conditions in which life can evolve and/or survive. The text outlines a couple of these: the geothermal vents on the ocean floor, the tops of sea mounts, the thin transition layer between the ice and water under the pack ice in the Arctic and Antarctic Oceans, and the crawl spaces between soil particles. Remind your students of the conditions under which life appears to have evolved on the planet: no oxygen, a noxious atmosphere, high temperatures. Also, remind them of the recent reports of bacteria-like formations in the Mars rocks found in Antarctica. Add to that the discovery that bacteria that had escaped the sterilization procedures usually applied to American spacecraft on an unmanned lunar lander had survived on the lunar surface under extreme conditions for years. When the piece containing the bacteria was returned to Earth, they were cultured and grew on the culture dish. Grocery Store Analogy The book uses an excellent analogy for the classification system. The authors liken the classification system used to organize the living world to that used in a grocery store. Items in a grocery store are grouped in sets (Meats), subsets (chicken, pork, beef), sub-subsets (breasts, thighs, wings, etc.), etc. This is a hierarchical system. See if your students can think of other examples. If they can, it means that they understand the concept. If they have trouble, ask some leading questions to guide them. Other possible examples are the organization of books in a library, book stores like Borders or Barnes and Noble with their sections of books and organization within those sections, video stores, etc. Carolus Linnaeus Carl von LinneВґ is an interesting man. You may enhance the interest of your students by telling them about some of his eccentricities. Many years after his death, he was widely considered to be narrowminded. Mayr describes him as a complex person, full of contradictions. His methodology was exacting and practical and he had great literary powers. He was a numerologist and in his later years, he was considered to be a bit of a mystic. His descriptions of organisms were exacting. He lived in Holland and visited Germany, France, and England but spoke only Swedish and Latin. He was so obsessed with classification that he even elaborately classified botanists. He became so consumed with his Latinized naming system that he Latinized his own name to Carolus Linnaeus. He was a real character. Remembering the Classification System: Mnemonic Devices The easiest way to remember the order of taxa in the classification scheme is to devise a mnemonic device that helps the student remember it. It is simple and time-honored and satisfies the students' tendencies to want to memorize things. The good news is that this is a good time to apply that technique. I'm usually not a fan of memorization but it does, at times, come in handy. This is one of those times. The mnemonic devices that seem to be most effective are those that are at least slightly off color. Students love them. While it is probably over the top to use a mnemonic device for everything, certain things cry out for them. Using such a device with the taxa is one of those things. There are a couple of well-known devices, one of which is King Philip Came Over For Great Sex. This one, of course, was created before domains were recognized so now we must add another word at the beginning (Dear King Philip Came Over For Great Sex). If you find the last word in this one offensive, other "S" words should be easy to come by (spaghetti, salmon, strudel, etc.) To include divisions in the device, you could alter it as follows: Dear King Philip O' Day Came Over For Great Sex. O'Day stands for "or Division." You could also make up one of your own. I made up a fairly nonsensical one but it accomplishes its purpose (Dreadful Kings Prevaricate or Deceive, Cleverly Overlooking Fine Good Subjects). How Important Are Decomposers? I try to emphasize the importance of decomposers to the living world. I can make the point in a number of ways, but I try to do it in ways that will attract the attention of my students. I ask them if they have ever driven past the same animal lying dead by the side of the road on successive days. I ask them what happens to the roadkill. They undoubtedly will have noticed that the corpses disappear at a surprisingly rapid rate. I also tell them that they can occasionally see this process happening in time-lapse photography on programs shown on the Discover Channel or the Learning Channel or other science television programs. I point out that this disappearance is largely the work of decomposers. I also tell my students that if it were not for decomposers, the lecture hall in which they sit would be filled with corpses that reach up to their necks. This may be a bit of an exaggeration, but it gets the point across. I then ask them how this decomposition benefits them in other ways. Immediately or after some leading questions, someone answers that the decomposition allows for the recycling of the molecules found in the carcasses so they can be altered and reused by other organisms. Lichens as Indicators of Pollution A number of organisms have been used as indicators of pollution. Among them are lichens. They are apparently so sensitive to environmental shifts that they will die off when environmental pollution becomes too severe. On the other hand, when measures have been taken to reverse the effect of pollution, the reappearance of lichens and other equally sensitive species suggests that clean-up efforts are succeeding. Point this out to your students. If you wish, use it to spur discussion of environmental issues. Try to examine the issues from both sides, those for and against preservation of the environment (remember that some people do not believe that there is a problem). Such discussions might best be run in seminars associated with the class in attached laboratory sessions. Turgor Pressure Turgor pressure is the build-up of internal pressure in plant cells through the pushing of water against plant cell walls. The function of this pressure is to make plant cells sturdy and allow them to withstand the pull of gravity. It is largely turgor pressure that allows plants like trees, coleus, and other plants to stand up and resist gravity. Root systems help, too, especially for larger plants like the giant redwoods. A good example of how turgor pressure can work is a fire hose. In most cases, students can see them in their dormitories folded up behind a window, where they can be obtained in case of fire. They may also have seen them on television or in person at the scene of a fire. Ask your students, what these hoses are like before being filled with water. They are heavy and somewhat floppy. Then ask the class what happens when they fill with water. The build-up of pressure against the thick, reinforced walls of the hose make it hard. The hoses become so hard, in fact, that if the firemen do not have a good grip on them before the water is turned on, the hoses will move around rapidly, possibly hitting firemen and breaking some bones. You can remind students of the movie Roxanne in which Steve Martin plays a fire chief. There are some scenes in the movie showing the training of his rather inept volunteer fire-fighting force. The hoses can be seen whipping around when their grip is not secure. In one vignette, a firefighter is shown holding on to a hose while he is in the air in front of a second story window. The hose has picked him up and waved him around. While somewhat exaggerated for comedic effect, this is an example of turgor pressure at work. The same force is missing from plants that have not been recently watered. The water in these plants has been depleted and the plants wilt and droop as a result. Ask your students where the water has gone. If they have been paying attention, they will realize that water, along with carbon dioxide, is a reactant in photosyhthesis and that it has been used up during that process. When the plants are watered again, the supply of water to the plant cells is replenished, pressure builds up in the cells of the plant and it stands up, relieving its wilted state. The Echinoderms: Our Closest Relatives Among the Animal Phyla? We are members of the phylum Chordata. In all the other phyla in the Animal kingdom, to which one are we most closely related? Demonstrating considerable hubris, many of us believe that the chordate and, specifically, humans are the most advanced and successful phylum. If we were to decide on our closest relatives in the animal kingdom, we might choose the insects which have the most animal species or some of the other phyla. The phylum that most would not pick first as our closest relatives would be the Echinodermata, the phylum of the sea urchin and the starfish. Yet, the Echinoderms, in the eyes of most experts, are our closest relatives for the simple reason that we along with the Echinoderms are the only phyla who are deuterostomes. During the embryonic development of the chordates and echinoderms, the mouth opening forms second. In the molluscs, the arthropods and annelids, the mouth opening forms first; they are protostomes. Due to this difference, they are more distant relatives to the chordates than are the echinoderms. Make this point to your students. Ask them what they think the answer is and why before you tell them. The correct answer may impress them more that way. Sample Test Questions. Multiple Choice, Conceptual, and Open-Ended Questions From the Text 1. What is the approximate number of species presently described in the Fall of 1999? a. 15 million b. 150,000 c. 1.5 million d. 100 million e. 3 billion 2. What features of ocean floor vents allow them to support such rich biological communities? a. They spew hot water into the environment d. The vents spew hydrochloric acid b. They spew mineral-laden water into the environment e. a and b c. The vents poison clams and worms 3. What do hot water and minerals released at ocean floor vents provide for the microbes that live there? a. They provide energy c. They provide nutrients e. b and c b. They provide light d. a and c 4. What are mesofauna? Mesofauna are small organisms that live in the crawl spaces between soil particles. They are too big to be studied adequately with microscopes and too small to be noticed without them. Now that they are known they are being studied at a very high rate. Their numbers and diversity appear to be extensive. 5. What is the approximate number of species presently thought to be living on Earth? a. 15 million b. 150,000 c. 1.5 million d. 100 million e. 3 billion 6. The science of describing, classifying, and organizing organisms according to their similarities and differences is ________. a. systematics b. evolution c. taxonomy d. toxicology e. systemetology 7. The study of evolutionary relationships among organisms is _________. a. systematics b. evolution c. taxonomy d. toxicology e. systemetology 8. What was the basis of the first system of classification developed by Aristotle? Aristotle's system of classification was based on a series of "either-or" comparisons, such as classifying things as animal or plant, blooded or non-blooded, etc. 9. What is an archetype? Taxonomists constructed lists that included the idealized characteristics of a particular species. This list of characteristics for a particular species became its archetype. This list came to be the definition of a perfect representative of the species in question. 10. Who is responsible for the binomial nomenclature that is used to name organisms today? a. Carl von LinneВґ b. Aristotle c. Carolus Linnaeus d. Charles Darwin e. a and c 11. What effect did the discoveries of Mendel and Darwin have on taxonomy? Before Darwin, species were viewed as fixed, immutable, and perfect. It was felt that the shared characteristics of organisms in the living world were a convenience supplied to allow proper grouping of organisms. After Darwin, species were seen as constantly and slowly changing. The shared characteristics of different organisms could now be explained in a different way. They now reflected the common ancestry of such organisms. The more closely related such organisms were, the more characteristics they shared. More distantly related organisms share fewer traits. However, this did not change the taxonomists job very much. The archetype was simply replaced by the type specimen, the first specimen collected or the representative specimen of a given species. Before Darwin, individual differences in specimens were ignored; after Darwin, such differences were expected and considered to be a result of natural selection. Mendelian and population genetics affected taxonomists by stressing the importance of populations. Species were now defined by the ability of organisms in a population to interbreed. The taxonomist's job now became to describe characteristics that differentiated one distinct population of a species from another. 12. Comparing which of the following things with new biotechnology techniques has made systematics more straightforward? a. proteins b. lipids c. a, d, and e d. RNAs e. DNAs 13. The general name for the hierarchical groups into which taxonomists place organisms is ________. a. taxis b. taxa c. classes d. orders e. taxonomics 14. The first classification of organisms into plants and animals was done by ________. a. Archimedes b. Paracelsus c. Aristotle d. Linnaeus e. Theophrastus 15. What features of Euglena made it difficult to classify? It had long flagellae like an animal cell would have and no cell wall, again a feature suggesting it is an animal cell. In the summer, it has a well-defined chloroplast, gathers at the surface of ponds and makes its own food, just like a plant would. In the winter Euglena loses its chloroplast and drops to the muddy bottom of the ponds where it decomposes dead material to obtain nutrients, suggesting an animal nature again. 16. What was the solution to the inconsistencies inherent in the long-standing two kingdom classification system? In the late 1960s, it was suggested that new kingdoms should be created to accommodate exceptions to the two kingdom system. The result was a five kingdom system. One of the new kingdoms was the Protista which would include Euglena. Protists are eukaryotic cells and single celled organisms. Some are photosynthetic and some not. The bacteria which were at one time classified as plants were placed in a kingdom with all of the other single-celled prokaryotes, the Monera. The Fungi, previously classed as plants, were placed in the third new kingdom. 17. Assuming that the change to a five kingdom classification made sense, why has a new taxonomic layer been added to the system? Despite the improvements wrought by the five kingdom system, exceptions still existed. The green algae are a problem for the five kingdom system; some are unicellular, some are not. The placement of brown algae (seaweeds) is questionable. There are no living single-celled brown algae, but there are some fossilized ones. Today, some consider them to be primitive plants; others consider them to be protists. Furthermore, the discovery of a new type of cell, the Archaebacteria, created problems for taxonomy. The result has been the development of a new taxonomic category larger than kingdoms, the domain. 18. Describe the basic organization of the new taxonomic system that incorporated the new taxonomic category, the domain. Presently, three domains have been proposed. The domain Archaea includes the newly discovered cell types and contains one kingdom, the Archaebacteria. The domain Bacteria includes the other members of the old kingdom Monera and also has one kingdom, the Eubacteria. The third domain, the Eukarya, includes all of the kingdoms and organisms composed of eukaryotic cells (protists, fungi, animals, and plants). 19. Kingdoms are divided into ________. a. phyla b. classes c. subdomains d. a and e e. divisions 20. Which of the following taxonomic groups can be found between the kingdom and phylum level? a. supraphylum b. suprakingdom c. subkingdom d. subphylum e. a and c 21. Which of the scientific names below is in the proper format? a. Homo Sapiens b. Escherichia coli c. lumbricus terrestrius d. Gallus gallus e. b and d 22. On what basis did Oparin and Haldane suggest that the Earth's early atmosphere was different from today's? The atmospheres of the other planets in the solar system lacked free oxygen. They assumed the same was true of the atmosphere of the primitive Earth. Furthermore, rocks on the Earth's surface about 3 bya contained free iron and no iron oxide as would have been the case in an oxygenrich atmosphere. 23. Which energy sources below may have been present on the early Earth and might have worked on atmospheric chemicals to stimulate chemical reactions? a. lightning b. ultraviolet light c. infrared light d. microwaves e. a and b 24. The first cells on the planet almost certainly lived off of the nutrients that had built up in the oceans since they were incapable of producing their own food. Such cells are called _________. a. chemoautotrophs b. autotrophs c. heterotrophs d. deutertrophs e. soupotrophs 25. What was the significance of Urey and Miller's experiment? Miller and Urey duplicated in a glass vessel the composition of the atmosphere on the primordial Earth and arranged it so the atmospheric mixture could be sparked with electricity to simulate lightning. Water in the flask simulated the ocean. In less than a week, the water turned cloudy and was found to contain amino acids. Others repeated their experiment with slightly different conditions and made other organic chemicals important to life. This suggests that such important biochemicals could have been produced on the primitive Earth given the long period of time available for the reactions to occur. 26. What circumstantial evidence supported the findings of Urey and Miller? Astronomers have found simple organic compounds deep inside meteorites. Instruments have also been able to sense remotely methane deep in open space. This suggests that carbon-based compounds are common throughout the universe. Furthermore, 3.5 billion year old fossils containing fossils of ancient bacteria have been found in western Australia. This suggests that life must have evolved rapidly in something less than a billion years. 27. Why is it thought that RNA may have been the genetic material of the first living organisms on Earth? In 1993, workers at the Scripps Institute found a small molecule of synthetic RNA that could make copies of itself. The copies could also make copies of themselves. Eventually, it was demonstrated that the copies could change or evolve. If protocells acquired RNA that could make copies of itself and evolve and RNA that could synthesize enzymes capable of breaking down other organic compounds and building and maintaining cell membranes, they could be considered the first cells. Later, DNA could have evolved as a method of conveniently and safely storing vital chemical information contained in cellular RNA. RNAs have also been found that can catalyze chemical reactions. 28. Eventually, cells arose that could harness light energy and use it to produce chemicals that store energy. Such cells are called ________. a. chemoautotrophs b. autotrophs c. heterotrophs d. deutertrophs e. soupotrophs 29. _________ evolved the ability to harness the energy contained in certain inorganic chemicals found in or near the ocean. They also used this energy to produce chemicals that stored the energy they had acquired. a. Chemoautotrophs b. Autotrophs c. Heterotrophs d. Deutertrophs e. Soupotrophs 30. What byproduct of photosynthesis changed the Earth and led to the decline of the earliest forms of life on the planet? How did it cause that decline? Photosynthesis produced oxygen as a byproduct while using up carbon dioxide in the atmosphere. Thus, oxygen built up. The earliest organisms on the Earth were actually oxygen-intolerant. For them, it was poisonous. Thus, they were forced out of regions of the Earth where oxygen was plentiful. These were Archaebacteria; they are still present on the Earth but they are confined to deep muds, inside carcasses, within the intestinal tracts of more complex organisms, and in other oxygen-free places. They continue to survive in such areas. 31. The oxygen-intolerant organisms present when oxygen began to build up in the atmosphere are represented on the planet today by the _________. a. Archons b. Eubacteria c. Eukarya d. Archaebacteria e. Protista 32. About 600 million years ago, the number and diversity of fossils increased. What event triggered that increase? Some multicellular organisms evolved hard parts like shells and skeletons. This made it easier for fossils to form. 33. Which domain is directly related to the oldest organisms on Earth? a. Eukarya b. Archaea c. Eubacteria d. b and c e. a and b 34. You look at an electron micrograph of two bacteria. They are side-by-side and connected by a structure called a pilus. What is the process in which the bacteria are engaged? a. binary fission c. conjugation e. b and c b. a rudimentary form of sexual reproduction d. sporulation 35. Which of the activities below occurs during the formation of spores by bacteria living under intolerable environmental conditions? a. loss of most of cytoplasm c. shrinkage e. a, c, and d b. a gain of cytoplasm d. decrease in metabolic activity 36. What structure do bacteria use to help them move? a. cilia b. one or more flagellae c. tiny feet d. pseudopodia e. secreted slime forms 37. What kind of organisms can make powerful poisons that only they can tolerate? a. decomposers b. pathogens c. Fungi d. bacteria e. all of the above 38. Why do bacterial and fungal decomposers make powerful poisons? The world of decomposers is a highly competitive one. Decomposers must defend their carcasses from other decomposers so they make and secrete powerful poisons that only they can tolerate. They do this to protect their nutrient source and living space. In what way are pathogens similar to decomposers? Pathogens are simply decomposers that begin to decompose their host before the victim dies. Some of them excrete chemicals that destroy cells and tissues. Others rob hosts of nutrients and may secrete toxic chemicals to ward off competition. These chemicals incidentally sicken or kill the host. The microbe doesn't care whether a victim is a host or a carcass. 39. What is a mutualistic symbiont? A mutualistic symbiont is an organism that forms an intimate partnership with other organisms in which both organisms benefit. 40. How does the association of some plants with nitrogen-fixing bacteria benefit the plants? Most living organisms including plants are unable to use gaseous nitrogen as a nitrogen source. Some bacteria can transform free nitrogen into compounds like ammonia and oxides of nitrogen that can be used as a nitrogen source. An association between plants and these bacteria provides these nitrogencontaining compounds for the plants. 41. Organisms that use chemicals in hot springs or those coming out of volcanic ocean floor vents as sources for energy to make their own food are called _______. a. chemoautotrophs b. chemoheterotrophs c. a and e d. photoheterotrophs e. photoautotroph 42. Another name for floating algae in the open waters of oceans, lakes, ponds, and other bodies of water is ___________. a. bugs b. phytoplankton c. photoplankton d. protozoids e. slime molds 43. What response do cellular slime molds make when their environment becomes hostile? Under hostile conditions, the amoeboid cells of cellular slime molds aggregate into sluglike forms that move rapidly in search of better conditions. Occasionally, they form tiny mushroomlike fruiting bodies when they reproduce sexually. 44. Threadlike structures that grow out in several directions from a spore under favorable conditions as a result of rapid cell division are called ________. a. mycelia b. celluloids c. hyphae d. fungofoids e. a and c 45. Older cells of a hyphal mass often lose the cell walls and membranes between adjacent cells leading to the formation of a multinucleated protoplasmic mass called the _______. It is thought that this change in the older cells facilitates nutrient transfer. a. mycelia b. celluloids c. hyphae d. fungofoids e. a and c 46. Which kingdom contains organisms that respond most quickly to sudden changes in their immediate environments? a. Plantae b. Archaea c. Animalia d. Fungi e. b and c 47. What kingdom consists of eukaryotic cells surrounded by thick cell walls? Plantae or Fungi. What kingdom consists of heterotrophic eukaryotic cells with thick cell walls made of chitin? Fungi. 48. In which kingdom other than Fungi is chitin found? Animalia. What role does it play in that kingdom? It is a major component of the exoskeletons of insects, lobsters, and crabs. 49. What kingdom consists of autotrophic eukaryotic cells with thick cell walls? Plantae. 50. Which kingdom does not contain organisms that possess cell walls? Animalia. Probably most Protista do not have cell walls, but the algal protists do. 51. Why do plant cells generally not exhibit amoeboid movements? Amoeboid movement would not normally occur in plant cells because the cell wall would prohibit it. Multiple Choice, Conceptual, and Open-Ended Questions From the CD-ROM 1. Of the classification schemes described in Section 8.1 (Classification) of the CD-ROM, which one(s) are the most valid for natural organisms? The two based on physiological characters, like the characteristics of the heart, and the biochemical characters, like the DNA fingerprint, would be the most applicable to natural species. The classification based on the number of body segments would also be useful and while less obvious than the first two (number of spots and body color), it still can be determined by mere observation of the organisms. 2. What was the reason for classifying organisms into the kingdom Monera? The Monerans were different from the other organisms in one major respect. They were prokaryotes and contained no internal membrane systems. The only membrane they had was the cell membrane itself. This set them apart from the plants and animals whose cells contained membrane-bound organelles. The bacteria had often been classified as plants prior to this, because they possessed cell walls like plants even though the walls were composed of different materials. 3. Why was the kingdom Protista eventually originated? The kingdom Protista was created to accommodate eukaryotic organisms that possessed characteristics of both animals and plants. Rather than make the difficult decision of placing them in one or the other of those kingdoms, they were placed in a kingdom of their own. 4. In the animation located in Section 8.2 of the CD-ROM (The History of Classification), it is mentioned that the kingdom Fungi was created to accommodate organisms previously classified as plants that did not photosynthesize. The animation shows that this new kingdom also took some of its member organisms from another kingdom. Which kingdom was it? The Protista. 5. Aside from making humans sick, which most of them do not do, bacteria have been put to what uses? Bacteria have been used as sources of food, for the biological control of pests, as agents of fermentation, and for the making of foods and antibiotics. Bacteria, along with fungi, are the main decomposers of dead organic matter. They thus function to return nutrients to our environment. 6. Which kingdom is thought to contain cells that closely resemble the first living cells on the planet and are believed to be the most ancient group of living organisms? a. Archaebacteria b. Eubacteria c. Protista d. Fungi e. Eukarya 7. How is the environment generally occupied by the organisms referred to in Question 6 above described? The Archaebacteria usually inhabit particularly extreme environments that resemble those of the early Earth and appear to be an ancient group of bacteria. 8. Evidence from which discipline has provided evidence that a more inclusive level of classification than the kingdom is required? Molecular biology. 9. Which phylum includes the blue-green algae? a. Archaebacteria b. Eubacteria c. Proteobacteria d. Cyanobacteria e. Archaea 10. What phylum includes the bacteria that inhabit the human gut? a. Archaebacteria b. Eubacteria c. Proteobacteria d. Cyanobacteria e. Archaea 11. The organisms that are typified by the extreme environments like hot springs and sea vents that they generally occupy are members of what kingdom? a. Archaebacteria b. Archaea c. Proteobacteria d. Cyanobacteria e. Fungi 12. What invaluable ecological service do decomposers perform? When anything dies, bacteria and other decomposers attack the dead organism and break down the complex biochemicals of which it is made into nutrients. These nutrients in these carcasses are thus recycled and made available to others. 13. Which phylum of the Eubacteria is typified by photosynthetic organisms? Cyanobacteria. 14. What phylum contains organisms that are typically unicellular and move by means of two flagella? At times, they may be either plant-like or animal-like in nature. Euglenophyta. 15. Which organisms are generally known as dinoflagellates and are associated with red tides? a. Chrysophyta b. Euglenophyta c. Pyrrophyta d. Phaeophyta e. Rhodophyta 16. Chrysophyta a. compose the largest portion of photosynthetic plankton d. b and c b. are known as diatoms e. a and b c. are associated with red tides 17. Rhodophyta contain a red photosynthetic pigment different from the more common green photosynthetic pigment. What is the functional reason for the red pigment? The red pigment of the Rhodophyta absorbs blue light which penetrates to greater depths in the ocean than other colors of light. Thus, the Rhodophyta can photosynthesize at greater depths than other algae. 18. Which Protistan phylum is thought to be the evolutionary link to modern plants? The Chlorophyta. 19. The organisms that cause malaria are members of what animal-like Protistan phylum? Sporozoa 20. Organisms from the phylum Zoomastigina cause which of the following diseases? a. African sleeping sickness c. many sexually transmitted diseases e. a, b, and c b. Giardia d. Herpes 21. Amoeboid movement by extending pseudopodia is associated most prominently with which phylum? a. Ciliophora b. Sarcodina c. Zoomastigina d. Sporozoa e. b and c 22. What locomotory apparatus is typical of the Ciliophora? Cilia. What type of sexual or quasi-sexual reproduction do the Ciliophora perform? Conjugation. 23. Which phylum is usually known as the cellular slime molds and has members that move via pseudopodia? The Acrasiomycota. 24. Members of which of the following phyla have cell walls made of cellulose or chitin? a. Plantae b. Oomycota c. Myxomycota d. Acrasiomycota e. a and b 25. Briefly describe the major traits of the kingdom Fungi. The Fungi are characterized by cells possessing cell walls of chitin and reproduction by sexually- or asexually-produced spores. Cells of the Fungi are usually haploid but may have brief diploid periods. They are decomposers and can attack virtually all organic matter. They cause most plant diseases, attack crops and stored foods, and can cause human diseases of the lungs and skin. 26. Which phylum of Fungus is most likely to be the one that includes the Fungus that caused the famous and historically important Irish potato famine of the 1800s? The famine played a role in the emigration of many Irish people to the United States. It is most likely that the fungus that caused the Irish potato famine was a member of the phylum Zygomycota. 27. The production of what food products largely depends on members of the phylum Ascomycota? a. cheese b. bread c. beer d. b and c e. a and b 28. The Deuteromycota are known as the imperfect fungi for what reason? They are called the imperfect fungi, because thus far no sexual stage has been observed in these organisms. 29. Which phylum contains the genus from which we get penicillin? The Deuteromycota. 30. The Bryophyta contain the ______. a. club mosses b. liverworts c. hornworts d. b and c e. a, b, and c 31. What phylum includes the whisk ferns, usually considered to be the simplest vascular plants? a. Bryophyta b. Psilophyta c. Sphenophyta d. Pterophyta e. Rhizomata 32. Why are the Psilophyta called the simplest vascular plants? They are called the simplest vascular plants, because they lack true roots and leaves. 33. Which phylum comprises the largest group of seedless vascular plants? The Pterophyta. 34. Cone-bearing seeds are seen in a. gymnosperms b. Cycadophyta c. Ginkgophyta d. a and b e. Pterophyta 35. When I was in college, the freshman quad was populated with trees that would periodically drop seeds with a nauseating odor. Of which phylum were they likely to be members? a. gymnosperms b. Cycadophyta c. Ginkgophyta d. a and b e. Pterophyta 36. Which of the following is not a group of flowering plants? a. Anthophyta b. Coniferophyta c. Cycadophyta d. Ginkgophyta e. b, c, and d 37. WhatвЂ™s another name for a multicellular, eukaryotic heterotroph and of what kingdom is such an organism a member? Such an organism is an animal of the Kingdom Animalia. 38. What are two hypotheses that might explain the evolution of animals? Some biologists believe that single-celled protists came together to form colonies which then gave rise to multicellular animals. Alternatively, others think that large multicellular protists gave rise to multicellular animals when plasma membranes surrounded each nucleus, thus forming individual cells. 39. The functional part of a sponge that was used for cleaning before synthetic sponges came along is composed of what part of the sponge? a. their cytoplasm b. their skin c. their skeleton d. c and e e. spicules 40. What do Cnidarians use for protection and capture of prey? a. stinging cells b. numatocycts c. nematocysts d. a and c e. protocysts 41. Cephalization is first seen in which phylum? The phylum Platyhelminthes. 42. Which phylum in the kingdom Animalia includes the most abundant animals on Earth? a. Porifera b. Platyhelminthes c. Mollusca d. Arthropoda e. Nematoda 43. What feature(s) is (are) common to the Mollusca? a. muscular digit on ventral surface c. muscular foot on ventral surface b. muscular foot on dorsal surface d. mantle that secretes calcium carbonate e. c and d 44. What do the following phyla have in common - Mollusca, Arthropoda, Annelida? a. The first opening in their embryos is an anus d. They are protostomes b. The second opening in their embryos is a mouth e. c and d c. The second opening in their embryos is an anus 45. Which phylum exhibits the first true segmentation? Annelida. 46. Which phylum is the largest in terms of species? a. Mollusca b. Nematoda c. Arthropoda d. Chordata e. Echinodermata 47. Which phyla make use of chitin on their exterior surface? a. Mollusca b. Arthropoda c. b and e d. Echinodermata e. Fungi 48. Why do many biologists consider the Echinodermata to be more closely related to the Chordata than the Arthropoda or the Annelida? The Echinodermata and Chordata alone are deuterostomes; their mouth openings form second dring their embryonic development. 49. What features do all chordates have in common? All chordates, at some time in their developmental process, possess a supportive rod or notochord, a dorsal tubular nerve cord, gill slits, and a postanal tail. Using BioInquiry in Large Classes Integrating Components into the Lecture Section 8.1 of the CD-ROM contains an interesting exercise demonstrating the difficulties in classifying organisms. You should encourage your students to attempt it. Obviously, in nature there would be many more organisms with which to deal. The exercise demonstrates that often the easiest traits to observe may be the ones that are least useful in classifying organisms accurately. The third classification scheme involving the number of body segments is somewhat less obvious than the first two classification schemes but yields somewhat less information than the last two. In the exercise, the last two and best methods for classifying the organisms are the classification by physiological characters (structure of the heart) and by biochemical characters (DNA fingerprint). Both of these techniques would require closer examination of each organism (dissection or DNA technology) but the effort would yield more useful information. The exercise skillfully makes this point. Section 8.2 of the CD-ROM (The History of Classification) contains an effective animation that explains in clear terms the progress from a two kingdom classification system to the present three domain, six kingdom system. If students are having trouble understanding the present classification system and its origin, suggest this animation to them. There is very little on the CD-ROM in Section 8.3 that deals with the origin of life, but the website contains some information on the controversial aspects of the origin of life. Section 8.4 of the CD-ROM contains brief descriptions of the major phyla/divisions in the living world along with pictures of some representative species in each phylum. This is a useful tool for informing your students of the extent of diversity in the living world. Have them go through it at home and take note of the major features of each of the phyla/divisions covered. The pictures give an excellent pictorial view of the range of diversity of the organisms in each phylum. It may also be useful to incorporate the CD-ROM into a lab exercise dealing with diversity. Read More About It There are a number of books that students might find informative on the topics of diversity and the origin of life. Edward O. Wilson's The Diversity of Life is excellent. He describes the process of evolution and its role in creating the astonishing diversity of life on the planet. He also outlines the evidence suggesting a decline of planetary diversity that is projected to reach 20% by the year 2020. He proposes potential strategies for slowing or stopping this decline and perhaps even enhancing diversity. For sheer description of the diversity of life on Earth, I suggest any of David Attenborough's books: Life on Earth, The Living Planet, The Trials of Life, The First Eden, and The Life of Birds. He describes the variety of life on the planet vividly and the books each contain beautiful photographs of the organisms he describes. You may wish to recommend tapes of his television series as well. For descriptions and opinions on the origin of life on the planet, you or your students may wish to consult a couple of other books as well. A somewhat older book, Cosmos by Carl Sagan, deals with the origin of life among other things. Tapes of the television series are also available from most video stores. A new book, The Fifth Miracle: The Search for the Origin and Meaning of Life by Paul Davies, addresses the issue of the origin of life. He examines the role of the bombardment of the Earth by comets and asteroids in the origin and evolution of life. He discusses the Mars rock that is reputed to contain the fossilized remains of bacteria-like life forms that may have evolved on the Red Planet over 3.5 billion years ago and remarks on its implications to the story of the origin of life on Earth. This is a fascinating and eminently readable book. Supporting the Lab We have have utilized a number of different laboratory exercises to demonstrate diversity in the living world. Museum labs work quite well if your department has an adequate number of preserved specimens. The lab can be peppered with questions that students should be able to answer by looking at the specimens. Section 8.4 of the CD-ROM, as mentioned above, is a tour of the major phyla in the different kingdoms complete with descriptions of important features and photographs of representative examples of each phylum or division. Sections 8.1 and 8.2 of the CD-ROM deal with the concept of classification and adequately make the point about the difficulties involved with such classification schemes. Section 8.2 specifically addresses the movement from the two kingdom system to the present six kingdom, three domain system that is presently acccepted by most investigators. You may also wish to use dichotomous keys in a laboratory exercise to key out the organism on display in the laboratory. This will give students a pretty good idea about how successful classification schemes work. Answers to Review Questions 1. About 1.5 million different kinds of organisms have been found and described in the last 250 years. That number is likely to rise substantially in the near future. Educated guesses suggests that there may be greater than 100 million species living on Earth. As we look in places previously ignored, new species are being discovered on a daily or weekly basis. 2. Taxonomy is the science of describing, classifying, and organizing organisms according to their similarities and differences. Systematics is also involved with describing, classifying, and organizing but takes a more interpretive approach focusing on the evolutionary relationships among organisms using those similarities and differences as a guide. Taxonomy is thus a first step in systematics. A higher number of similarities between two organisms would suggest a higher degree of relatedness between the two organisms. 3. Hierarchical systems are systems in which the things being classified are aranged into sets and subsets and even sub-subsets, etc. For example, the set "Meats" could be subdivided into "Chicken," "Beef," "Pork," etc. Further, the subset "Chicken" could be subdivided further into "Whole Chickens" and "Chicken Parts," which could be further subdivided into "Thighs," "Breasts," "Drumsticks," etc. Comparative systems are systems that are based on similarities and differences. It is these comparisons and the assessment of their similarities and differences that allow their proper placement in the hierarchical system. 4. Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species 5. By convention since the time of Linnaeus, all names are Latinized. Also by convention, all of the taxa are not generally listed, while the genus and species taxa names usually are. In fact, it is deemed necessary for genus and species names to be present in biological writings. The genus name is always capitalized, while the species name is not. Furthermore, scientific names are italicized or underlined to distinguish them from other kinds of terms. This explains why Homo sapiens is written the way it is. 6. Biological classification was first used to give some order to the living world. Life on Earth is so diverse and there are so many species that they cry out for some organization. It is an attempt to group together organisms with common traits. Initially, before Darwin, its purpose was to describe "natural order." The perception was that there was a natural order leading progressively from the simplest to the most complex organisms. Perhaps they thought that by properly ordering the living world they could gain insight into the thinking of God. After Darwin and Mendel, the classification schemes began to be used to address the question of the relatedness of different species. Nowadays, the classification system is focused on interpretation. Taxa indicate evolutionary relationships between organisms. When organisms share more taxa, they are more closely related. If they share only domains, they are distantly related. 7. The three domains are the Archaea, the Bacteria, and the Eukarya. The Archaea consist right now of one kingdom, the Archaebacteria. The Archaebacteria are prokaryotes and have no membrane-bound organelles. They are unlike the other prokaryotes; they are methane producers, are able to tolerate conditions with extreme salt concentrations, and are resistant to heat and acid. They break down organic matter in extreme and anaerobic environments. The Bacteria also include one kingdom, the Eubacteria, and include the rest of the prokaryotic living world. The Eukarya include all of the eukaryotic kingdoms: Animalia, Plantae, Fungi, and Protista. These organisms have cells that contain membrane-bound organelles. They are for the most part multicellular as well, unlike either of the other two domains. 8. It became necessary to create more kingdoms than just the plants and animals, since there were a number of organisms that could not easily be placed in one kingdom or the other. For example, Euglena had properties of plants (chloroplasts and photosynthesis) and animals (flagellae and acquisition of nutrients during part of the life cycle in a manner reminiscent of animals). Fungi had cell walls but no chloroplasts. Bacteria were grouped with plants even though they are prokaryotes while plants are eukaryotes. 9. Humans are in the domain Eukarya, the kingdom Animalia, the phylum Chordata, the class Mammalia, the order Primate, the family Hominidae, the genus Homo, and the species sapiens. 10. Most investigators believe that life began in the oceans. They speculate that the molecules necessary for life built up in the oceans and eventually found their way inside protocells that evolved into living cells. It is thought that lightning and ultraviolet light would work on atmospheric chemicals to form biologically important molecules, which would then drop into the oceans. Other scenarios suggest that evaporation of tidal pools concentrated salts and other impurities. Amino acids might become so concentrated in this way that the formation of proteins would be more likely. It has also been proposed that powerful electrostatic forces in bubbles would attract amino acids, pull them into close proximity possibly allowing protein formation. If the bubbles burst, they would spew their contents into the air where other reactions would occur. Alternatively, iron pyrite or clay crystals could attract and concentrate amino acids promoting protein formation. Biologically important chemicals also have been formed in space and it has been speculated that some of the chemicals essential for life on Earth may have come to the planet in comets and meteorites. Finally, some have suggested that life on Earth began in space and that perhaps the first life on Earth evolved on another planet. Life might then have been carried here in meteorites like the Mars rock. Bacteria have been shown to survive in the harsh conditions of space. Bacteria from Earth survived for some time on a lunar probe on the moon's surface. 11. Earth first appeared about 4.6 billion years ago, at which point the Earth was still too hot to support the complex chemicals of life. Before life could appear, Earth needed to cool considerably. Between 4.6 and 3.5 billion years ago (probably about 4 billion years ago), the first life appeared. For this to happen, the oceans had to fill up with nutrients like proteins, carbohydrates, nucleotides, and carbohydrates. The phospholipids, at some point, self-assembled into a lipid bilayer forming bubbles that could concentrate certain chemicals. Those that were best suited for their environment would be selected for by natural selection. They could also fuse with other bubbles forming more stable structures. Eventually, they reached the level of protocells but were not alive until they became associated with genetic material, most likely RNA that could perform both the coding function and replication of DNA and enzymatic activity. Eventually, DNA took over for RNA as the genetic material, since it could conveniently, safely, and stably store the genetic information. The oldest known fossilized cells are in rocks that are 3.5 billion years old. The primitive life thus formed ruled the planet for about 2 billion years and then about 2.5 billion years ago photosynthetic organisms arose and changed the Earth's atmosphere by removing CO2 and building up oxygen in the atmosphere. About 2 billion years ago, primitive eukaryotic cells evolved and by 1 billion years ago multicellular organisms appeared. About 600 million years ago, some multicellular organisms evolved hard parts after which the number and diversity of fossils increased. By 500 million years ago, exploitation of the Earth was in full swing with plants, animals, fungi, algae, and bacteria evolving. Life proliferated; some organisms became extinct while new species arose. 12. All of the bacteria are single-celled organisms that contain no nuclei and few other organelles except for ribosomes. Their DNA is contained in a single, twisted, circular chromosome floating free in the cytoplasm. All of them have relatively thick cell walls made of substances other than the cellulose that is found in plant cell walls. Under intolerable environmental conditions, many form spores. At this time, they lose most of their cytoplasm, shrink, and become surrounded by an especially thick cell wall. They also become metabolically inactive until conditions improve. As spores, they become very light, float in the air, and move vast distances. They mostly reproduce by simple cell division (binary fission) but can participate in a rudimentary form of sexual reproduction (conjugation). Some bacteria can pick up stray genes from the environment. Some are virtually immobile while others are equipped with one or more flagellae that serve to move them along. Most are heterotrophs and most of these are decomposers, but some are autotrophs that use light or chemicals as sources of energy to make their own food. A few of them are pathogens as well. Some bacteria of both the Archaea and the Eubacteria domains live as mutualistic symbionts. 13. All protists are eukaryotic cells that possess membrane-bound organelles; this the major characteristic held in common by all of the protists. They are mostly single-celled and simple multicelled organisms. Also, most of the protists live in aquatic or damp environments. They all tend to reproduce asexually. The three major groups of protists are the algae, the protozoans, and the slime molds. The algae are autotrophic and perform photosynthesis while the protozoans are predominantly, if not totally, heterotrophic and slime molds are totally heterotrophic. Most of the algae and protozoans are singlecelled creatures. The slime molds start life as single cells, resembling ameboid protozoans, but they can organize themselves into multicellular organisms. Some protozoans can act as parasites and cause serious diseases in animals: for example, malaria, African sleeping sickness, and amebic dysentery. Algae and slime molds generally do not. Slime molds exhibit more complex life cycles than do the other two groups as well. 14. Fungi are all eukaryotic cells surrounded with thick walls, made of chitin rather than the cellulose found in plant cell walls. They are mostly multicellular; all are heterotrophic and either saprotrophic or parasitic. Most are important in ecosystem function; some are important to human society. Most reproduction in fungi is asexual by means of spores that are produced asexually or sexually; sexual reproduction occurs occasionally, but is relatively rare. Most fungi play the role of decomposers in the ecosystems they occupy, but a few have established symbiotic relationships. 15. Lichens are the product of a symbiotic relationship involving fungi and blue-green algae. They typically grow on rocks, tree trunks, or at high latitudes and altitudes. The algae provide lichens with photosynthetic products and the fungi provide protection and anchorage. They also release powerful chemicals that are capable of etching nutrients out of rock. In some cases, the symbioses in lichens are so intimate that individual algal and fungal cells are not distinguishable. 16. Plants are made of eukaryotic cells and are surrounded by thick cell walls made of cellulose. They are generally multicellular, autotrophic, and possess chlorophyll-containing chloroplasts that photosynthesize. This accounts for their essentially universal green color. Their life cycles are usually typified by an alternation of generations. The green algae are the primary energy producers in fresh water; near the shore in the oceans the brown and red algae fulfill this function. The mosses, ferns, gymnosperms (naked seed plants), and flowering plants are the other major plant divisions. The Bryophyta lack the vascular and supportive tissues found in more advanced groups of plants. The Lycophyta have a dominant sporophyte in their life cycle. Under drought conditions, their two main genera may appear to die, but come alive again when it rains. The Sphenophya are represented by only one living genus; they are the horsetails and their epidermal tissues are so rough that they have been used as polishing devices. Cutting up their rhizomes to get rid of them is not productive, since many new plants grow from their fragments. The Psilophyta are the simplest of all the vascular plants since they lack true roots and leaves. The Pterophyta are the largest group of seedless vascular plants and are primarily tropical. The Cycadophyta are unusual in that they are the only gymnosperms (cone-bearing plants) to have palmlike leaves and thus bear no resemblance to other living gymnosperms. The Ginkgophyta possess mature and naked seeds that look like plums and are distinguished by their overpowering nauseating odor. The Gnetophyta typically are a small, bizarre-looking group of plants and they can be easily distinguished by their bizarre appearance. The Coniferophyta are mostly evergreens and are thus easy to distinguish; they also are cone-bearing plants. The Anthophyta or angiosperms are the flowering plants, a trait which makes them relatively easy to distinguish. 17. All animals are multicellular, eukaryotic heterotrophs that lack the thick cell walls typical of other kingdoms. Animals are also generally more responsive to sudden changes in their immediate environments. Animals move around more than members of the other kingdoms. Their structures and organization are generally more fixed than other multicellular organisms. Most have predictable body plans with individuals of a particular group all having the same shape. Sponges are the exception to this rule. Most animals are bilaterally symmetrical (flatworms, roundworms, segmented worms, chordata, arthropods). Some are radially symmetrical (coelenterates). The Porifera (the sponges) are the most primitive animal phylum. Unlike the other animal phyla, they lack any type of symmetry and do not have defined tissues or organs. Their skeletons are composed of spicules that are made of calcium carbonate. The Cnidarians are typified by stinging cells called nematocysts that they use for prey capture and protection. The Platyhelminthes possess bilateral symmetry but lack a coelem (a body cavity). They also are the lowest phylum to exhibit cephalization. The Nematoda are the most abundant animals on Earth. They are bilaterally symmetrical and have a false body cavity, a pseudocoelem. The Mollusca are typified by the fact that they are protostomes like only two other phyla (Annelida and Mollusca) and they share two characteristics, a muscular foot on the ventral surface and a mantle that secretes calcium carbonate to make a shell. The Annelida are the first organisms to demonstrate segmentation, they are bilaterally symmetrical with a coelem and they are protostomes. The Arthropoda are distinguishable by their hardened, chitin-containing exoskeleton which must be shed in order for growth to occur. They also undergo metamorphosis from immature stages to distinct, adult stages. The Echinodermata larvae are bilaterally symmetrical, but they exhibit radial symmetry as adults. Like the Chordata, they are deuterostomes (mouth opening forming second in the embryo). They use a series of tube feet for locomotion and grasping prey. They are also one of only a few phyla with the ability to regnerate lost parts. In fact, they can form a new adult from a small fragment. Finally, the Chordata are distinguished by the possession at some time in development of a supportive rod, the notocord, a dorsal tubular nerve cord, gill slits, and a postanal tail. 18. Some members of all of the kingdoms have made the move from water to land, even including a few of the Archaebacteria that live in deep muds, inside carcasses, and in the intestinal tracts of some organisms. CHAPTER 9 BIOENERGETICS: HOW DO ORGANISMS ACQUIRE AND USE ENERGY? Lecture/CD-ROM Outline Overview I. Every living organism requires a constant supply of energy to stay alive A. Ultimately, the energy comes from the sun B. If organisms fail to replenish energy they use, they die & deteriorate until they are indistinguishable from the environment II. It was long thought that energy of life was somehow different from other forms of energy in the Universe; life was thought to be defined & characterized by a special vital force A. "Vital force" thought to follow its own set of rules different from the rules governing energy flow in the inanimate world B. Now know that energy in all forms is the same in living and nonliving worlds - rules governing it apply universally How Does Energy Behave in the Universe? I. The energy of life is not unique - for centuries, the idea of a special life energy (vital force) was widespread A. Virtually every culture had a name for it, all roughly translated "breath of life" 1. ch'i - Chinese 2. ruh - Arabs 3. prana - Indians 4. pneuma - Greeks B. Connection between breathing & life is an ancient one 1. Exchange of gases with the environment is part of the conception of what it means to be alive & an outward sign of metabolism (a fundamental process of life) 2. Metabolism includes all of the chemical reactions that occur in cells C. Result of metabolism - organic substances are made or converted to other organic molecules 1. With many conversions, energy is transformed 2. Some of that energy can be used to do the work of living 3. Metabolism & chemical reactions that constitute it are the means by which organisms extract & use energy to stay alive; it is a unique feature of life II. Energy can take different forms, but it is always conserved A. Word "energy" introduced in 1807 (relatively late) 1. Before that, physicists carefully studied different forms of energy (especially heat & mechanical energy of objects in motion) 2. Idea that heat, movement, light, etc. were manifestations of the same thing, energy, was new 3. Energy now is the term used to denote anything that can do work B. Work can have many definitions 1. Physicist - work is done when force is applied to an object and the object moves 2. Biologist - work is done when something is moved (muscle) or something is made (protein, DNA); bioelectrical work (nerve cell carries signal); biological work (gradient produced, etc.) C. Late 19th century - different forms of energy shown to be interchangeable (via mechanical devices) 1. Light could be converted to heat; motion converted to electricity 2. When one energy form was converted to another, total energy always added up to the same amount 3. Led to the formulation of natural law that is one of the most important ideas in understanding energy - First Law of Thermodynamics (Law of Conservation of Energy) 4. Statement - energy may change form, but it may neither be created nor destroyed (there is as much energy in the universe now as there ever was or will be) 5. Ignore Einstein's interchangeability of mass & energy - it is not seen in living systems D. It soon became apparent that living organisms can no more create energy from nothing than can mechanical devices - energy for life comes from radiant heat & light of the sun E. Realization that living organisms obeyed First Law was the beginning of the end of vitalism 1. Life was no longer exempt from the laws of the universe 2. But First Law does not tell us the direction that energy spontaneously moves & changes III. In any energy transformation, entropy increases A. Ice cube in a cup of hot tea вЂ”> soon ice cube melts, leaving a cup of lukewarm tea 1. At first in cup, some areas have concentrated heat energy & some have less energy (ice cube) 2. Spontaneously, energy becomes more randomly distributed, more disordered 3. Illustrates Second Law of Thermodynamics - changes always occur in a direction in which the energy of the universe becomes more disordered B. Physicists have a name for the amount of disorder in the universe вЂ”> entropy 1. Systems with high entropy are highly disordered; those with low entropy are highly ordered 2. The greater the entropy of the system, the more difficult it is to distinguish one part of the system from another C. In theory, Second Law says that entropy will continue to increase until every area of the universe has exactly the same amount of energy & exactly the same composition as any other area 1. Given enough time, entropy will reach its maximum вЂ”> no ordered regions in the universe 2. Every area of the universe will be indistinguishable from every other area; should be a long time coming D. Tough to picture this, but can picture small parts of the universe where entropy is maximized 1. Called this situation equilibrium (condition of maximum entropy) 2. The Second Law says that without an infusion of energy from an outside system, all systems spontaneously move closer to equilibrium at all times 3. When a system reaches equilibrium, no more changes occur unless it gets energy from outside IV. How then is life possible? A. Questions about life 1. Does the organization of living things violate the Second Law? 2. Do life-filled ecosystems violate the Second Law? 3. Life moves away from equilibrium, why is the Second Law not violated? A. Answer - every time life imposes order on a small part of universe, there is an even greater increase in entropy somewhere else 1. In the case of life, entropy increases are traced to the burning of the sun 1. As living things utilize energy, there is a constant conversion of useful energy into useless energy (heat) 2. Contributes to amount of disorder in the universe B. Life is an uphill struggle; living organisms must do biological work to keep the forces of the universe from dismantling highly ordered bodies & driving them toward equilibrium 1. Requires a constant supply of energy, but many organisms cannot get it directly from the sun 2. Some can; photosynthetic organisms capture light energy from the sun & use it to build highenergy organic molecules from low-energy inorganic precursors - called autotrophs 3. If it cannot photosynthesize (heterotrophs), it must eat organic molecules built by autotrophs 4. Energy used for work of living is stored in chemical bonds between atoms in food C. Autotrophs make food -> both autotrophs & heterotrophs have access to the rich source of energy How Is Energy Transformed in the Biosphere?: Oxidation I. Fire is an example of energy transformation - as chemical bonds between atoms in fire's fuel break, light & heat are released rapidly A. Living things carry out similar processes, but do not give off all energy B. They capture energy that is released & use it to do biological work II. Animal respiration, like fire, is oxidation A. For centuries, it was thought that flammable substances contained a substance called phlogiston 1. Phlogiston supposedly flowed into the air when substances were burned -> heat & light were a manifestation of that movement - championed by Joseph Priestley B. 1770s - Priestley put candle under a bell jar вЂ”> found that in an enclosed space, flame made air unfit to support fire вЂ”> flame went out 1. A mouse under a bell jar died much as the flame died; mouse made air unfit for breathing 2. Put candle & mouse under the same bell jar вЂ”> both died 3. He concluded rightly that burning changed air in the jar in the same way that breathing did, but felt that both the mouse & flame filled the jar with the poison phlogiston (not as convincing) C. Antoine Laurent Lavoisier - disproved phlogiston theory; reasoned that if burning object emits phlogiston, then as it burns, weight should decrease 1. If carefully accounted for all fire products, the opposite happened; the total weight increased 2. Concluded that burning does not add phlogiston to the air, but instead removes something from the air 3. Called that something oxygen (mice & flames take it from the air, making it unfit for animals) 4. First to recognize that fire & breathing are both forms of burning (both consume oxygen) 5. Later found that oxygen from air combines with fuel carbon & hydrogen to form CO2 & H2O 6. Called process oxidation (chemical reaction in which oxygen is combined with another substance; also a reaction in which oxygen is added to compound, atom, or hydrogen) 7. Oxidation also defined as a situation in which electrons are removed from a compound or atom D. Equation for chemical reaction representing oxidation: C6H12O6 + 6 O2 вЂ”> 6 CO2 + 6 H2O 1. C6H12O6 - glucose; good starting fuel since cellulose from wood is a glucose polymer & also a monomer in starch & other carbohydrates consumed as food 2. O2 - molecular oxygen gas; during reactions, CвЂ”H bonds are broken & new CвЂ”O & HвЂ”O bonds are formed III. When most such bond rearrangements occur, there is energy transformation A. Sometimes, energy is absorbed from the environment to form new bonds B. Sometimes, energy is released to do work (such energy that is doing work or causing an effect on matter is called kinetic energy) C. Before fuel molecules are oxidized, however, they contain a different kind of energy (potential energy, energy that is stored or inactive) 1. Wood & food contain potential energy & can exert no effect on matter until they are oxidized 2. When oxidized, their potential energy is converted to kinetic energy & can be used to do biological work (food) or give off heat & light (wood) IV. Chemical bonds are interactions between electrons of different atoms; the energy of chemical bonds is stored in the bonds' electrons; this energy can be released in a controlled or uncontrolled fashion A. Uncontrolled release of energy from bond electrons (ex.: direct mixture of hydrogen & oxygen gas) вЂ”> explosion would destroy the living organism B. Controlled release of energy - in living cells, water is formed as a result of glucose metabolism 1. High-energy electrons are passed down electron transport chain instead of being transferred directly to oxygen to form water 2. Transport molecules extract energy from electrons in a stepwise fashion 3. Electrons pass from one transport molecule to the next until they ultimately combine with O2 & hydrogen to form H2 O; some of this energy is used to make ATP & some is lost as heat V. Thus, during cell metabolism, electrons & their energy are removed from one molecule & transferred to another (oxidation-reduction reaction) A. Electron energy is transferred by these electron transport molecules B. Molecules that gain electrons are said to be reduced; those that lose electrons become oxidized VI. Two main differences between fire and food (metabolism) A. Fire is a chaotic process that oxidizes everything in its path; metabolism is an organized series of individual reactions in which only specific fuel molecules are oxidized B. Fire releases excess energy as heat & light; living organisms stay at or close to the same temperature even though they are constantly doing oxidation reactions 1. Metabolism captures the energy of oxidation in other potentially useful chemical bonds 2. Main example of energy-capturing molecule is adenosine triphosphate or ATP How Is Energy Transformed in the Biosphere?: Enzymes I. Metabolism - efficient, highly specific; after meal, blood is filled with glucose (major digestion product) A. To burn glucose like wood would create much heat & light & damage the organism 1. So organism extracts it in a controlled manner that can be captured for biological work & that will maintain constant temperature 2. Cells break high-energy glucose down to low-energy CO2 & water by steps to enhance the chance of capturing energy B. Must be highly efficient so not much energy is lost as heat (form that cannot be used); heat energy quickly becomes disordered increasing entropy of living system C. Process is highly specific - reactions only involve appropriate fuel molecules, not others in the cell 1. Do not want to destroy any of the carefully constructed organic molecules of cell structure 2. Must burn fuel, not cellular machinery D. Specificity & efficiency - achieved by enzymes (proteins that catalyze [speed up] metabolic steps) II. Enzymes speed up chemical reactions but cannot force reaction to go in a direction inconsistent with laws of thermodynamics A. Some reactions that appear to be inconsistent with the Second Law occur quite readily вЂ” how? 1. Large energy-rich compounds are made from smaller, energy-poor compounds 2. Organisms can couple seemingly unfavorable reactions with favorable reactions that provide energy to make unfavorable reactions happen 3. Some reactions that are highly consistent with the Second Law don't proceed (paper oxidizes very slowly) B. Favorable reactions may need a bit of a push to get them started 1. Before new chemical bonds can be made, must break old ones 2. Overall reaction represents net decrease in energy, but the first step (breaking bonds) is an energy barrier preventing realization of equilibrium (barrier is called activation energy) 3. Example: match to start paper burning, raises overall energy of paper molecules C. Example: glucose molecules need help past the activation barrier as well 1. Enzyme joins a single glucose molecule & stretches & bends the chemical bonds until the energy of activation is made lower 2. Enzymes thus work by lowering activation energy III. Properties of enzymes and enzyme-catalyzed reactions A. The Induced Fit Model of the enzyme active site and enzyme action 1. Shape of enzyme changes when substrate binds to it 2. Allows reactants (substrates) to interact and be chemically transformed into product 3. After reaction is complete, product is released and enzyme resumes initial shape B. Temperature and enzyme activity 1. As temperature increases from 0В°C, molecular motion increases & enzyme activity increases 2. At higher temperatures, the weak interactions can no longer hold the enzymes into their effective shape вЂ”> they denature; since shape is so important to their function, activity drops 3. Temperature optimum is the temperature at which the enzyme exhibits its highest activity C. pH & enzyme activity - enzyme activity is influenced by pH 1. Enzymes are held into their shapes by weak interactions between composite amino acids 2. Changes in pH affect charges on amino acids (R groups, terminal amino, & carboxyl groups) 3. Alteration of charges will change the shape of the enzyme & thus its activity 4. pH at which enzyme works best is called pH optimum; activity normally drops on either side of the pH optimum 5. pH of environment within which enzyme normally works will usually match pH optimum IV. Enzyme inhibitors - molecules that slow down or stop enzyme-catalyzed reactions A. Competitive inhibition - occurs when molecule resembling substrate binds to enzyme active site 1. Prevents binding of substrate and thus prevents the reaction 2. Normal activity usually returns when a competitor is removed or replaced by normal substrate B. Noncompetitive inhibition - inhibitor binds to a site other than the active site (allosteric site) 1. Results in change in enzyme shape & prevents binding of substrate 2. Tends to be less readily reversible than competitive inhibition V. Metabolic efficiency - first hallmark of enzyme-catalyzed reactions A. Most efficient reaction either captures as much energy as possible from energy-yielding reactions or spends as little energy as possible to catalyze a reaction that consumes energy 1. Energy released can be captured in form of ATP or 2. Use ATP to drive thermodynamically unfavorable reactions B. Energy from glucose released stepwise, a little at a time (as many as 25 reactions) - only that way can energy be captured efficiently so that it can be used elsewhere in the cell 1. Each reaction results in a short-lived compound that occurs at a point in the pathway somewhere between starting point & end; called metabolic intermediates 2. As long as overall energy change from original reactants to products is favorable, the process will occur spontaneously & yield energy C. Energy-consuming reactions also occur in small steps 1. Easier to supply energy to drive energy-consuming process a little at a time 2. Cellular metabolism characterized by metabolic pathways (sequences of enzyme-catalyzed reactions in which product of one reaction serves as reactant of the next) 3. Often the pathways are linear, but they can be circular, they can interconnect with each other, or they can be branched 4. If branched, product of one reaction can go in either of 2 or more subsequent directions depending on the needs of the cell at any particular time VI. Metabolic specificity - second hallmark of enzyme-catalyzed reactions A. Given enzyme only binds to a specific kind of molecule (its substrate) - one or a few at most B. No side reactions with enzymes 1. Different enzymes catalyze each of chemical reactions of metabolism 2. For each step, only the appropriate substrate reacts C. Cells contain thousands of enzymes shuttling various organic substances from one form to another & changing the concentrations of cell constituents in response to the demands of life How Is Energy Transformed in the Biosphere?: ATP, The Energy Currency of Life I. ATP is assembled by energy-yielding metabolic pathways of the cell & is broken down to drive energy-consuming pathways; main energy currency molecule in living organisms A. Adenosine triphosphate (ATP) is modified ribonucleotide containing three phosphates & adenine 1. Adenosine with one phosphate is found in RNA along with three other nucleotides (U, G, C) B. ATP was first isolated from rabbit muscle by a German biochemist in 1929 1. Eventually found in virtually all living tissue 2. Soon implicated in almost every metabolic pathway, either as a source of energy or as a product II. Adenosine is a combination of nitrogen-containing base (adenine) & 5-carbon sugar A. When adenosine is not part of RNA chain, it can connect with one phosphate to make adenosine monophosphate (AMP) or with two phosphates (adenosine diphosphate; ADP) B. Third phosphate on ATP can be broken off relatively easily leaving ADP & one phosphate 1. Packet of energy is released at the same time that can be captured & used 2. Removal (loss) of phosphate is called dephosphorylation C. When phosphate is added to ADP driven by energy released from metabolic pathways, ATP is formed; called phosphorylation D. Cell contains a finite amount of adenosine that cycles between ADP & ATP 1. When rested & well fed, most of your adenosine is ATP 2. As you move or exercise, ADP becomes more plentiful, but you constantly replenish ATP by breaking down fuels like glucose E. Living things do conserve extra energy for emergencies - starch, oils, glycogen, fat 1. ATP not accumulated in great abundance 2. Energy of these storage products is first converted to ATP before it can be tapped III. Other nucleotide-based compounds shuttle hydrogen - three other pairs of compounds cycled in metabolism (NAD+/NADH, FAD/FADH2, NADP+/NADPH) A. NAD+, FAD & NADP+ can each pick up H atoms & electrons from one metabolic intermediate to become NADH, FADH2 or NADPH 1. Later relinquish those hydrogens (& electrons) to different H (electron) -accepting molecules again becoming NAD+, FAD & NADP+ B. Breaking of CвЂ”H bonds & formation of OвЂ”H & CвЂ”O bonds when breaking down glucose does not occur directly 1. H's (& electrons) are transferred from organic fuels to H (electron) carriers e.g. NAD+ to NADH 2. These molecules relinquish their H's (electrons) to O to form H2O (also an indirect process) C. In biosynthetic pathways where new CвЂ”H bonds are made, NADPH takes H to site of synthesis 1. H's (electrons) are transferred from NADPH to carbon there to make new proteins, lipids, etc. How Do Organisms Use Energy?: Overview of Cellular Respiration I. Cellular respiration is the name given to metabolic pathways in which cells harvest the energy from the metabolism of food molecules A. Glucose breakdown is one of the main pathways of cellular respiration B. Glucose breakdown occurs in cells as a continuous sequence of >25 steps grouped into 3 stages 1. Glycolysis 2. Krebs cycle 3. Electron transport system II. Glycolysis - universal energy-harvesting process of life; most widespread metabolic pathway in the living world, common to every living thing & similar or identical in every type of cell; very primitive A. Probably evolved early in life's history - may have been present in the first living cell & passed on to all successful progeny of that first cell B. Glycolysis (means "sugar splitting") 6-C sugar glucose is split in half to make two 3-C compounds 1. Hydrogens are also stripped from carbons 2. Energy of broken bonds is captured & there is a net yield of 2 ATPs 3. Unlike the next two stages, it occurs in the cytoplasm of the cell & requires no organelles 4. Also uses no oxygen so sometimes it is called the anaerobic (not requiring oxygen) pathway of cellular respiration III. Krebs cycle - aerobic (require oxygen); both occur in the mitochondria; Krebs completes breakdown of glucose to single carbon molecules A. Takes derivatives of two 3-C glycolysis products, breaks them apart & strips Cs of their H atoms B. Leaves behind six CO2 molecules C. Does not require O2 but is prelude to the next cell respiration stage in which O2 is required IV. Electron transport system (ETS) - both glycolysis & Krebs cycle transfer H atoms from Cs of glucose to molecules of NAD+ to make NADH A. Extracts more energy by transferring those H atoms from NADH to oxygen making water B. ETS is a eries of enzymes that transfers H from NADH to O2, step by step, & captures energy released in the process 1. Energy is captured when ADP & phosphate are joined to make ATP 2. Because the process requires oxygen it is sometimes called oxidative phosphorylation 3. During this process, oxygen we breathe in is consumed, converted really, to water How Do Organisms Use Energy?: Glycolysis I. Consider a marathon runner who has eaten some carbohydrates prior to a race; use muscle cell as example (but could occur in any cell) A. Net overall reaction of glycolysis (see below) 2 ATP 2 ADP C6 H 1 2 O6 Glucose 2 C3 H 6O3 2 NAD+ Pyruvic Acid 2 NADH B. Starting fuel is 6-C glucose (C6H12O6) & end result is 2 molecules of 3-C pyruvic acid (pyruvate) 1. 2 ATPs & 2 NADHs are formed 2. Each step in the pathway is catalyzed by a single, highly specific enzyme 3. Splitting of glucose into 2 pyruvates occurs in nine separate steps with at least nine different metabolic intermediates & the help of at least nine enzymes II. When oxygen is limited, lactic acid fermentation takes over - if demands on the muscles exceed the capacity of the lungs & circulatory system to deliver O2, glycolysis can deliver ATP anaerobically A. Two problems with anaerobic metabolism 1. 2 ATPs per glucose glycolysis supplies are enough for a short sprint, but cannot be maintained for long - only organisms with low energy demands can survive on glycolysis alone 2. In the absence of oxygen, glycolysis converts all of the limited NAD+ to NADH; when there is no more NAD+ available, glycolysis stops B. Problem solutions 1. Problem A.1. solution - stop & rest or slow down until metabolism switches back to aerobic 2. Problem A.2. solution - fermentation C. When O2 is limited, glycolysis does not end with pyruvate but includes additional 10th step designed to regenerate NAD+ to NADH 1. H is taken away from NADH & added back to pyruvic acid regenerating NAD+ & making lactic acid (lactic acid fermentation) 2. Lactic acid cannot enter Krebs & ETS; it accumulates in the muscles & the corresponding acidity gives the person a sensation of fatigue D. When O2 is available again (lungs & circulatory system catch up), glycolysis products are shunted to mitochondria for further oxidation & better ATP yield III. The steps in glycolysis A. Starts with glucose energized by addition of phosphate & energy from ATP -> glucose phosphate B. Glucose phosphate is rearranged to fructose phosphate which is then energized by second ATP to form fructose diphosphate - first 2 steps result in the net loss of 2 ATP molecules C. Fructose diphosphate splits into two 3-C molecules 1. From this step on, each reaction occurs twice for each molecule of glucose metabolized 2. Cell now starts to replenish ATP molecules used earlier & adds more to the ATP supply D. Each 3-C molecule receives phosphate from the cytoplasm 1. Each molecule is oxidized by the transfer of hydrogen and electrons to NAD+ (oxidized NAD) 2. Produces reduced NAD (NADH) - source of future energy extraction 3. When this NADH enters ETS, 3 ATPs are produced but there is only a net gain of 2 ATPs since 1 ATP is used to get this NADH from cytoplasm into mitochondrion where the ETS is E. Phosphate is removed from each of 3-C molecules & transferred to ADP to form ATP - net gain of ATP is now 0; the cell has broken even F. Remaining phosphate is removed from each of the 3-C molecules & transferred to ADP 1. Results in formation of two molecules of pyruvate (glycolysis end product) 2. Net gain of 2 ATPs for all of glycolysis How Do Organisms Use Energy?: Krebs Cycle I. Fatty acids & amino acids can also be metabolized to make ATP A. In a marathon, glucose & glycogen stores in the muscles are depleted after a few miles 1. Runner must switch to burning fatty acids released into blood from adipose tissue 2. All three major foodstuffs (carbohydrates, lipids, proteins) are ultimately oxidized by enzymes of mitochondria constituting Krebs cycle & ETS 3. Must be prepared by other metabolic pathways like glucose is prepared by glycolysis B. Thus, Krebs cycle is the central pathway in cellular metabolism II. Pyruvate from glycolysis moves into mitochondria where enzyme-run reaction prepares it for Krebs cycle - this transitional step accomplishes three things, all with one large mitochondrial enzyme A. Hydrogen atoms are stripped from pyruvic acid & transferred to NAD+ to make NADH B. A carbon atom is removed from 3-C pyruvic acid & is lost as CO2 C. Resulting 2-C compound is attached to a large carrier molecule (coenzyme A or CoA); when 2-C fragment is attached to CoA, the complex is called acetyl CoA III. What goes into the Krebs cycle & what comes out? - for every acetyl CoA that donates 2 Cs to Krebs cycle (one turn of cycle); important to remember that cycle turns twice for every glucose molecule A. In - one 2-C compound, 3 NAD+s, 1 FAD, 1 ADP plus one phosphate; chemical energy enters pathway in form of acetyl CoA (double above for both turns of cycle) B. Out/turn - 3 NADHs, one FADH2, 1 ATP (or its energetic equivalent) & 2 CO2s; chemical energy leaves the Krebs cycle in the form of ATP, NADH, FADH2 (last two used to make ATP in ETS) 1. 3 NAD+s pick up H's from Krebs cycle intermediates to become NADHs 2. FAD also picks up H's during the course of the cycle to make FADH2 C. Krebs cycle enzymes and intermediates are dissolved in fluid within the mitochondria (matrix) 1. With the right combination of substrates, enzymes, cofactors (nonprotein substances that help enzymes function), NAD+, FAD, ADP, & PO4-, glycolysis, Krebs can happen in a test tube 2. ETS & ATP synthesis require the presence of intact mitochondria IV. Steps in Krebs cycle A. Preparation for the Krebs cycle - both pyruvates from glycolysis enter the mitochondrion 1. Lose a C atom that joins with oxygen to form carbon dioxide 2. Results in the formation of an acetyl (2-C) group B. Each of the 2-C acetyl groups is oxidized & then joins with coenzyme A to form acetyl CoA electrons from the acetyl group are used to reduce NAD+ to form NADH C. Each acetyl CoA then joins with 4-C oxaloacetate to form citrate - the beginning of Krebs cycle & these reactions occurring in the mitochondria D. Subsequent reactions result in the removal of 2 Cs that join with oxygen to form 2 CO2 s E. Further reactions result in the formation of new ATP, only one made directly during Krebs cycle F. Subsequent reactions result in the production of 3 molecules of NADH & one molecule of FADH2 ; the final product of the Krebs cycle is oxaloacetate; ready to start another turn of cycle How Do Organisms Use Energy?: Electron Transport I. Electron transport - the biggest release of energy comes when NADH & FADH2 pass Hs (& electrons) to O2 to make water A. As with other metabolic pathways, energy release is stepwise but unlike others B. ETS & ATP synthesis depend on the mitochondrial membrane II. Understanding of mitochondrial structure is essential to understanding electron transport - large organelles are surrounded by two membranes that differ biochemically A. Smooth outer membrane forms boundary between mitochondria contents & the rest of cell fluids; has large protein-lined pores (porins) that allow most small substances to pass freely in & out B. Inner membrane has deep folds (cristae) - no porins, but rich in other proteins, many of which are part of the energy-transforming machinery 1. Effective barrier against small substance movement between matrix & intermembrane space 2. Barrier plays important role in storing energy and making ATP C. Components of ETS are enzymes grouped into four large complexes, deeply integrated into inner mitochondrial membrane 1. H's from NADH & FADH2 are split into atomic components (electron & proton for each H) 2. Electrons from NADH & FADH2 are shuttled through the complexes to ultimately join with O2 & other protons on the inside of the mitochondrion to make water 3. Protons from NADH & FADH2 meanwhile are released into space between the 2 membranes D. Each of the four complexes contain several different components, each capable of picking up one or two electrons & passing them to the next component 1. Substrate that enters ETS is H taken from NADH & FADH2, not electrons 2. In ETS, H electrons are stripped away from their protons & shuttled from carrier to carrier on four complexes; as they are passed they go from a high energy state to a low energy state 3. At the same time, protons are deposited between the two membranes; effectively pumped from matrix to intermembrane space by energy from electrons 4. At the end of the ETS, electrons pass to O2 & with two protons from the matrix, form water 5. ETS has formed a gradient of protons across the inner mitochondrial membrane III. ATP is made using energy from the proton gradient - not at equlibrium, so gradient can do work; very similar to hydroelectric dam A. Steep proton gradient contains potential energy; force of diffusion drives protons inward to matrix 1. Inner mitochondrial membrane, however, prevents their movement 2. To tap this source of potential energy, need a passageway through membrane & a coupling mechanism to do work B. Mitochondria have it, a large, lollipop-shaped enzyme embedded in the membrane 1. Lollipop stick (F0 subunit) - hollow cylinder forms an opening in the mitochondrial membrane through which only protons can pass; allows them to flow in direction diffusion pushes them 2. Sphere (F1 subunit) sits atop hole, readily binds to both ADP & P; as protons move through the hole, their energy of passing pushes ADP & P together to make ATP C. This mechanism of ATP synthesis is called chemiosmosis & differs from other ways that the cell makes ATP 1. In glycolysis & Krebs cycle, P is directly connected to metabolic intermediates of pathways, then transferred to waiting ADP 2. Chemiosmosis - ATP synthesis is indirect since it is coupled to proton movement down the gradient D. Big ATP payoff from cellular respiration is realized in the inner mitochondrial membrane 1. For each glucose entering glycolysis that is fully oxidized, 36 ATPs are formed 2. ATP is used to power all kinds of biological work in humans & all other living things 3. Among the most widespread metabolic pathways in the living world; depends on an outside source of metabolic fuel (food) IV. Details of oxidative phosphorylation - energy is extracted from each of ten reduced NAD molecules (NADH) & each of two reduced FAD molecules (FADH2 ) A. These reduced coenzymes are formed during glycolysis, acetyl CoA formation, & Krebs cycle B. Each NADH & FADH2 releases a pair of electrons to ETS 1. Each electron pair is transferred from a higher energy level to a lower energy level 2. In the process, energy is released that can be used to make ATP - 3 ATP for each NADH; 2 ATPs for each FADH2 3. Finally, electrons & hydrogen ions combine with oxygen to form water How Do Organisms Acquire Energy?: Photosynthesis - An Introduction I. Photosynthetic organisms make organic molecules from simple low-energy compounds (CO2 & H2O) A. They supply the food & oxygen other organisms need to survive B. Organic chemicals contain far more potential energy than either CO2 & H2O вЂ”> extra energy comes from sunlight II. Photosynthesis uses light energy to make food A. Jan Baptista van Helmont, Flemish chemist (1660) вЂ“ tested the idea that all of the raw material for plant growth is found in soil 1. Grew a willow tree in a pot of soil for five years, carefully weighing the pot each year 2. Tree grew tall & sturdy, gaining 150 pounds of living tissue 3. Soil lost only a few ounces, thus soil did not provide nourishment for the tree 4. Concluded that the tree used daily H2O he gave it to fuel growth; without it, the tree would die B. Van Helmont was half right, plant did need H2O; but energy of H2O is not enough to fuel life C. Joseph Priestley (1770s) вЂ“ grew plant under jar 1. As long as the plant & jar were kept in the light, plant grew until all CO2 in jar was exhausted 2. If put mouse & plant in jar together, both lived & grew for longer time than either could alone; mouse provided CO2 for plant & plant provided O2 for mouse D. A few years later, light's role was recognized вЂ“ it is essential for the formation of organic molecules from CO2 & H2O 1. Process was called photosynthesis (literally "put together with light") 2. Photosynthesis is the process by which some organisms can make organic compounds from simple inorganic compounds using energy from the sun 3. Animals depend on O2 produced by plants in light & on carbon-containing materials they make E. On a global scale, carbon, hydrogen, & oxygen move back & forth between autotrophs & heterotrophs without being used up or destroyed; overall process is called carbon cycle III. Pigments absorb the energy of light A. Light is a form of electromagnetic radiation - such radiation occurs in a vast spectrum of sizes & energies: shorter wavelength radiation has more energy than longer wavelength radiation 1. X-rays - example of short-wave, high-energy electromagnetic radiation 2. Heat, microwaves, radio waves are long-length, lower-energy radiation 3. One small region of the spectrum is visible to our eyes (visible spectrum or light) 4. There are differences in visible spectrum wavelengths that the brain interprets as colors 5. Only a few colors of light provide energy upon which life on Earth ultimately depends B. Most photosynthetic organisms are green; they are green because they contain pigments 1. Pigments are molecules that absorb some wavelengths of light & reflect others 2. In green plants, the most important pigment is chlorophyll (a complex organic molecule that absorbs light in blue & red parts of the spectrum, but reflects green light) C. Grind green leaves & extract chlorophyll in alcohol, then study its ability to absorb light 1. Aim blue light at extracted chlorophyll вЂ”>chlorophyll strongly fluoresces (light is briefly absorbed, then emitted at a different wavelength 2. Chlorophyll absorbs the energy of blue light, raising some of the chlorophyll molecules to a higher energy level 3. Separated from other parts of the plant, energized electrons have nowhere to go & fall back to their original levels (some of this energy is lost as heat, some is lost as fluorescent light) 4. Because some energy is converted to heat, lost light has less than total energy absorbed (thus its wavelength is longer [lower energy] than that of light originally absorbed) 5. In intact plants, there is almost no fluorescence; instead, the electrons are energized & sent along metabolic pathways that ultimately capture energy in the form of organic compounds D. First two forms in which light energy is captured are ATP & NADPH (relative of NADH) 1. To make ATP & NADPH (light required; absorbed light energy is used to make them); made in the first phase of photosynthesis вЂ” light-dependent reactions 2. ATP & NADPH are used as energy sources to make carbohydrates in second phase of photosynthesis, which is independent of light 3. This second phase is called the Calvin-Benson cycle or light-independent reactions) How Do Organisms Acquire Energy?: The Light-Dependent Reactions I. Before light reactions can be understood, chloroplast structure must be understood A. Chloroplasts are large, green, membrane-bound organelles that are the site of photosynthesis 1. Surrounded by two membranes (inner & outer) 2. Have a third membrane system within internal space (stroma) - arranged in disk-shaped sacks (thylakoids) B. Two important features of the internal structure 1. The thylakoid membranes contain light-harvesting photosynthetic pigments & enzymes that capture the energy of light-energized electrons 2. Internal membranes define space (lumen) that is separate from the rest of the stroma II. What happens during light reactions? вЂ“ chlorophyll is contained in light-gathering units called Photosystems I and II (absorb slightly different wavelengths of light); the steps in the process A. Chlorophyll in plants (Photosystem I) absorbs blue & red light & reflects back the green light 1. Blue & red light energy boosts certain electrons from chlorophyll to higher energy levels 2. In this excited state, electrons are passed to an electron transport molecule (acceptor) in the thylakoid that readily accepts them 3. Electrons can only be passed when they are highly energized (oxidation-reduction reaction) B. Electrons pass down electron transport chain (enzymes) embedded in thylakoid membrane until finally used to reduce NADP+ (picks up proton) to NADPH on thylakoid membrane stromal side 1. Could continue until all the chlorophyll in Photosystem I (PS I) is oxidized, but this does not happen 2. Chlorophyll is missing electrons & without them it is highly unstable, so other electrons replace those lost from PS I (see below) 3. At first, it was thought that the replacement electrons came from O2 ; now it is known that they come from the chlorophyll of Photosystem II (PS II) C. Chlorophyll in PS II also absorbs light energy that raises its electrons to a higher energy level 1. As in PS I, excited electrons are transferred from chlorophyll to an electron transport molecule (acceptor) 2. Electrons are passed through a series of electron carriers along the electron transport chain to PS I where they replace electrons used to reduce NADP 3. Replacement of electrons allows for synthesis of more reduced NADP (NADPH) D. During transport of electrons from PS II to PS I some energy is harnessed to produce ATP 1. Step by step, electrons are passed from one carrier to another giving up a little bit of energy with each step; carriers capture that energy to be used later to make ATP 2. Along the way, carrier molecules move more protons from the stroma to the thylakoid lumen E. Eventually, chlorophyll from PS II is oxidized; it must get replacement electrons, but from where? 1. PS II & its chlorophylls readily react with molecules in the vicinity that can fill the void 2. One such molecule is always in abundance вЂ” water 3. Unstable chlorophyll is powerful enough to strip electrons away from water molecules 4. Water from the lumen of the thylakoid is broken into its components: electrons for chlorophyll, electron-deficient H+ ions (lone protons), & one atom of oxygen (O) 5. Protons remain in the thylakoid lumen (used in other metabolic reactions or to create proton gradient across thylakoid membrane) 6. Oxygen diffuses out into the surrounding air after joining with another oxygen atom to form O2 , it is the source of our atmospheric oxygen F. Light-dependent reactions continue as long as there is a supply of electrons - depends on presence of a light source & water for supply of electrons 1. At the end of the path, electrons are passed to NADP+ to make NADH in addition to the production of oxygen & accumulation of protons inside the lumen (a form of stored energy) G. Energy of light has thus been captured in two forms 1. The synthesis of NADPH from NADP+ 2. Proton gradient across the thylakoid membrane - cannot be used directly to make food; must first be converted to ATP by chloroplast ATP synthase III. Chloroplast ATP synthase - makes ATP in way very similar to what happens in mitochondria A. Structures of the chloroplast & mitochondrial ATP synthases are so similar that they probably evolved from a common ancestor protein (molecular cousins) 1. Both bring ADP & phosphate close together B. Chemical bond is formed between them when the protons are allowed to flow past these two compounds through a protein-lined hole in the membrane 1. As they move, the gradient is dissipated & ATP is formed IV. Completes light-dependent, photosynthetic pathway reactions - together, reactions are called noncyclic photophosphorylation since the electrons follow a linear, noncyclic pathway from H2 O to NADPH A. As long as the sun shines, NADPH (via reduction of NADP+) and ATP are produced B. Overall equation - 2 H2O + 2 NADP+ + ADP + phosphate light> O2 + 2 NADPH + ATP V. Cyclic photophosphorylation вЂ“ alternate route A. Noncyclic photophosphorylation makes a bit more NADPH than ATP, but Calvin-Benson cycle in which NADPH & ATP are used to make carbohydrate requires 3 ATPs for every 2 NADPHs 1. Plants compensate for the difference between supply & demand for these products by using an alternate pathway 2. It generates a proton gradient to make ATP, but generates neither NADPH nor oxygen B. Depending on the need for ATP, electrons can bypass NADP+ & be passed back to the chlorophyll molecule from which they were originally derived 1. Many of the steps responsible for moving protons across thylakoid membrane still occur 2. Proton gradient is still created; thus the pathway can capture enough energy to convert ADP to ATP, but the electrons end up exactly where they started 3. Since the electrons end up where they began, the process is called cyclic photophosphorylation C. Archaebacteria use a version of cyclic photophosphorylation to make ATP & for them, it supplies enough ATP to sustain life VI. For autotrophs (other than Archaebacteria), cyclic & noncyclic photophosphorylation combination is followed by light-independent reactions A. Fix carbon from low energy CO2 into high-energy organic molecules via the Calvin-Benson cycle How Do Organisms Acquire Energy?: The Light-Independent Reactions I. Melvin Calvin & A. A. Benson learned each of the steps of carbon fixation because of two important research tools developed in the late 1940s & early 1950s A. Radioactive carbon (14C; carbon-14) - could add to mash of plant cells in form of 14CO2 B. Paper chromatography - used to separate small organic compounds from a mixture II. Calvin & Benson were interested in following carbon atoms from CO2 through each single step as they were incorporated into sugar A. Used green alga (Chlorella) cultures & exposed them to radioactive CO2 B. Exposed some cultures for several minutes & others for just a few seconds 1. Cells were killed & C-containing compounds were separated using paper chromatography 2. Radioactive compounds had incorporated 14CO2; they were metabolic intermediates of photosynthesis 3. Found that first compound to incorporate 14CO2 was 3-C acid called phosphoglycerate (PGA) C. Later studies showed that CO2 actually first combined with 5-C compound called ribulose biphosphate (RuBP) to make 6-C sugar 1. That sugar immediately splinters into two 3-C PGAs 2. Later, radioactive carbon was found in two other 3-C compounds - one shunted from chloroplast stroma to the cell cytoplasm where it is made into sugar III. Steps in light-independent reactions A. CO2 joins with RuBP forming an unstable 6-C molecule that breaks into two 3-C PGA molecules 1. This first step in Calvin-Benson cycle is catalyzed by enzyme called ribulose biphosphate carboxylase (Rubisco) 2. Rubisco brings carbon into the biosphere (carbon fixation) B. Using ATP & NADPH from light-dependent reactions as energy sources, two PGA molecules undergo a series of reactions 1. These reactions lead to the formation of two molecules of glyceraldehyde phosphate (GAP) C. Some GAP is used to produce 6-C carbohydrate molecules & the RuBP needed for additional Calvin-Benson cycles 1. Constant GAP supply is available as long as CO2 & RuBP are available 2. Two GAP molecules are needed for every 6-C carbohydrate made 3. 6-C carbohydrates undergo further reactions & may eventually become glucose D. Through a series of complex reactions, other GAP molecules are rearranged to produce an additional RuBP, completing the cycle; ATP from light-dependent reactions is used in the process IV. About Rubisco - arguably, Rubisco is the most important enzyme on Earth A. It is certainly the most abundant (it is estimated that there are 22 pounds of Rubisco for every person on Earth) B. Rubisco is remarkably slow & not very efficient as enzymes go 1. Only capable of fixing about three molecules of CO2/second (most enzymes work at thousands of times per second) 2. Rubisco slows in the presence of oxygen (product of light-dependent reactions in chloroplast) C. Agronomists are working hard to improve speed & efficiency of this critical enzyme upon which all life depends Where Are We Now? I. Some unwanted byproducts of cell metabolism reactions may contribute to physical deterioration that accompanies aging - one product of aerobic metabolism especially, the free radical A. Free radicals are varieties of atoms or molecules that are very unstable & highly reactive 1. In nonradical molecules, electrons that orbit an atom's nucleus occur in pairs, making them stable 2. A free radical is a molecule or atom that has a single, unpaired electron in its outermost orbit B. Free radical will steal an electron from neighboring molecule to even out the number of electrons in its outer shell 1. This transforms the neighboring molecule into a free radical which may, in turn, steal an electron from yet another neighbor 2. Sets in motion a kind of biological chain reaction 3. For the most part, such electron exchanges are highly controlled & damage is prevented II. In some metabolic reactions, particularly those involving oxygen, free radicals escape A. Body has two ways of dealing with dangerous free radicals 1. Certain compounds in the body can act as antioxidants; they can absorb the extra electron from oxygen radicals & convert these radicals into harmless products (beta-carotene, selenium) 2. Cells make an enzyme (superoxide dismutase) that converts harmful radicals into harmless products; found in all organisms that have been studied B. Some think that age-related symptoms (wrinkles, arthritis, loss of flexibility, diseases like cancer & degenerative diseases of the nervous system) result from accumulated free radical damage 1. 1993 - researchers discovered that a large proportion of afflicted individuals carried mutation that causes the defective form of superoxide dismutase C. Cannot stop the formation of free radicals because they are a normal part of our metabolism 1. Can increase intake of compounds that can act as antioxidants 2. Diet rich in fruits & vegetables has lots of zinc, selenium, beta-carotene, vitamins A, C, & E (all shown to have antioxidant properties) Analogies, Anecdotes and Illustrations Transmutation of Energy I explain transmutation of energy to my students using the following example, an amusing one to them, especially not long after the first exam. I ask them to picture me perched on the ledge of the molding above the blackboard. I tell them that there would be energy stored in my body by virtue of its position perched on the ledge (potential energy). I then ask the class what would happen if I stepped off of my perch. They, of course, realize that I would start moving toward the floor. The potential energy my body possessed by virtue of its position on the ledge was being converted into energy of motion (kinetic energy). I then explain that as my body strikes the floor, kinetic energy is converted to the energy of sound (thump), the energy that breaks some bones, the energy that may dent the floor, etc. I try to play it for laughs to make the point. The End of the Universe In explaining entropy to my students, I talk to my students about one of the possible ends of the universe вЂ” entropic doom. If the universe does not contain enough mass to cause it to collapse back upon itself, the universe may continue to expand until it attains maximum randomness or disorder. At that point, equilibrium will be attained throughout the universe and it may simply wink out. I also tell them that if the universe collapses back upon itself into a single point, sometimes referred to as the Big Crunch, it may be followed by a Big Bang. Should this happen repeatedly the universe could be described as an oscillating universe. This means that there may have been any number of Big Crunches and Big Bangs. I point out that science fiction has dealt with this issue. I mention that some have suggested that the collapse of the universe might result in time running backwards which, if true, may mean that the students will have to listen to the same lecture again вЂ” backwards. I recommend the book The World at the End of Time by Frederick Pohl that describes entropic doom quite strikingly (interesting story, too). A relatively new book Cosm by Gregory Benford describes the life of a universe created in a laboratory. How Can Students Remember the Meaning of Oxidation and Reduction? Students often have trouble remembering the meanings of oxidation and reduction and the significance of these reactions. First, emphasize for your students that electrons are, for all intents and purposes, synonymous with energy. When a molecule like NAD picks up an extra electron, it has been reduced and, by virtue of picking up an energetic electron, has itself become more energetic. Conversely, a molecule that has lost an electron to another molecule has lost energy. How can students keep the meanings (terminology) of reduction and oxidation straight? Once students understand that reduction means the addition of electrons, ask them what happens to the charge on a molecule that has been reduced. Since they should know that electrons have a negative charge, they should understand that the addition of an electron to such a molecule would lower or reduce its charge. Therefore, it is easy to remember that the addition of an electron to a molecule should be called reduction because it reduces the charge of the molecule. Oxidation is not as easy to remember. However, if one recalls that oxidation is the opposite of reduction, then it becomes easy to remember that oxidation is the loss of an electron. How Is Energy Stored in ATP? After I have described the structure of ATP to my students, I like to explain to them how energy is stored within that structure. At the time, I have a transparency of ATP projected on the screen. I ask the class what the charge on a phosphate group is. Usually, they come up with the correct answer вЂ” negative. I then ask them to imagine what would happen if the bond between the terminal phosphate and the second phosphate on ATP were broken. You might have to ask leading questions to make the point. Of course, since phosphates are negatively charged, if the high-energy bond is broken, the two negatively charged phosphates will be repelled from each other and they will fly apart. Conversely, ask them what will happen if you tried to reattach the departed phosphate to ADP. Since the end of ADP and the phosphate group are both negative, it will take an expenditure of energy to reattach the phosphate group. To illustrate just how much energy might be required, remind your students what happens if they try to push the North ends of two magnets together. It is literally impossible to do. Attaching two negatively charged phosphates would be similarly difficult. I often have my students participate in a small demonstration to get the idea across. I have two volunteers come to the front of the class and designate them phosphate groups. After establishing the negative charge of phosphate groups, I ask them what would happen if I tried to push them together. They get the idea that I would have trouble pushing them together because of the repulsion. I ask them what would happen if I were able to connect them with a bond (I have them hold hands). They usually realize without help that they would try to get as far apart as the bond connecting them will allow. I ask them what will happen if that bond is broken. They, of course, say that they would separate quite quickly. I sometimes add the example of a child in a grocery store holding his/her parent's hand as they head to the check-out line. The child suddenly notices the candy in the lane that the parent has chosen to avoid and strains in that direction. I ask the class what will happen if the parent lets go. These examples effectively illustrate how energy can be stored in the high-energy bonds attaching the two end phosphate groups on ATP. Finally, ask your class why the phosphate attached directly to the ribose of ATP is not attached by a high-energy bond. The answer, of course, is that this last phosphate is attached directly to a structure that lacks a negative charge (the ribose). Consequently, it is not attached by a high-energy bond like the two terminal phosphate groups. The Mitten-to-Glove Analogy for the Induced Fit Model I suggest the following analogy to illustrate the Induced Fit Model of the enzyme active site. I ask students if they have ever tried to put a glove on a small child's hand. Most have. I remind them that it is relatively difficult to get a child's hand into such a glove. Just when you think you've got all the fingers where they belong, one moves. This goes on seemingly forever. I have the class consider a potentially marvelous invention. What if there were a mitten with a place for the thumb and a compartment for the other four fingers that would change to a five-fingered glove as soon as the thumb and other four fingers were properly located within the mitten? In this example, the mitten is induced to fit the child's hand just like the enzyme's active site changes to fit the substrate better after it binds. Analogy for Enzymes One analogy often used to illustrate an enzyme is a bricklayer. Imagine that a you have a construction company and you hire a number of bricklayers, each of whom has essentially identical skills in terms of laying bricks. These bricklayers can be described as very specialized. They may only be capable of laying the traditional orange bricks; other types of bricks are beyond their skills as bricklayers. This would illustrate the specificity of enzymes. Ask the class what would happen to the rate of building a wall if you doubled the number of bricklayers. Of course, the rate would double. Ask the students what would happen if the temperature increased. As the temperature got too high, the work on the wall would slow down as the heat began to weaken the bricklayers. One could add to the scenario that lower temperatures slowed the work as well because the bricklayers are all bundled up to keep warm, thus cutting down their efficiency. This adequately demonstrates temperature optimum. Perhaps pH optimum could be illustrated with the somewhat gruesome example of changing the bricklayers' environment by making it more basic or more acidic than it would normally be. The noxiousness of these extreme environments would certainly slow the reaction rate. How Does an Enzyme Lower the Activation Energy? I have used an analogy that effectively illustrates how enzymes lower activation energy. When I was an undergraduate, movie prices began to climb to prohibitive levels and attendance at movie theaters dropped off significantly. Soon, a new type of movie theater began to appear around the country, the dollar movie. A number of movie theaters began to show second-run movies for the low, affordable price of $1. Attendance at these theaters skyrocketed and actually forced first-run movie theaters to offer bargain matinees. The elevated prices are analogous to the activation energy for a particular reaction. As those prices went up, the attendance (analogous to enzyme reaction rate) went down. The lowering of prices (decreasing the activation energy) increased attendance just as an enzyme lowers the activation energy of the reaction it catalyzes, resulting in an increased reaction rate. Fermentation and the Marathon I have long used an illustration of fermentation similar to the one used in the BioInquiry text. The tale of the long-distance runner is an excellent one. It can begin with the pasta dinner the night before many marathons, when the runners eat pasta to top of their glycogen reserves in preparation for the next day. Ask your students why. I would hope that they can make the connection between the glucose in starch (pasta) and the glucose to be stored in glycogen prior to the race. I often tell them stories of my years living near the Boston Marathon route. For years, I lived along the Boston Marathon route between the 20 and 22 mile mark. This happens to be a place where ambulances tended to wait because people tended to drop out quite often in this area. Usually, if people made it through this point, they would make it to the end. Presumably, people who were in not quite good enough shape would run out of their reserves somewhere within this two mile stretch. Contributing to this would be people whose muscles were not getting adequate oxygen supplies. Exercise, in addition to building muscle mass, enhances blood flow and oxygen supply to the muscles. If oxygen supply to the muscles is great enough, the runner will get 36 ATPs from the vast majority of glucose molecules used as fuel. If the oxygen supply is less than adequate, they will be running anaerobically for a greater percentage of the time and will thus get only two ATPs per glucose from a larger percentage of their glucose fuel molecules. Consequently, they will exhaust their fuel faster and possibly drop out of the race sooner. The Economics of Fermentation It might be valuable to point out that fermentation is an economically important process if it is not immediately obvious to your students. Fermentation in plant material and with baker's and brewer's yeast is responsible for many alcoholic beverages and baking. The products of fermentation in these organisms are ethanol and CO2. Ethanol, of course, is the alcohol that is formed during fermentation in the production of wine, beer, and other beverages. Fermentation is also responsible for the rising of bread and cakes during baking. Fermentation producing lactic acid is responsible for food products like cheese and other dairy products that come from fermentation. Teaching Glycolysis, Krebs Cycle, and Respiration I use an approach similar to the one suggested by the BioInquiry text, but I do not resist giving the students a little more detail. Emphasis is on the number of carbons in the molecules of these metabolic pathways. While I often mention the names of these compounds, I do not require my students to remember their names or their structures. I make available to my students computer rendered drawings of the pathways (glycolysis, Krebs cycle, electron transport, etc.). I use transparencies of these same drawings while lecturing about the pathways so that my students can take notes right on the drawings. Those drawings can be seen at the end of this section of the Manual. Use them however you like, or not at all. Make sure while you are teaching the pathways that you emphasize where in the cell each occurs and how they connect together. Point out where the reactants in the overall reaction for respiration are used up and where the products are made. Point out the similarities and differences between respiration and photosynthesis after you have covered both processes. You may want to foreshadow some of these similarities and differences before you cover the second process, no matter which one you cover second. Allow me to express a word about the order of coverage of photosynthesis and respiration. Textbooks seem to be split about which approach to use. I have heard passionate arguments for both approaches as well. Logistically, I have found it easier to talk about glycolysis and respiration first. Once I have explained electron transport in respiration, describing the pathways in photosynthesis always seems easier. On those occasions when I have taught photosynthesis first, it has not made it easier to teach respiration afterwards. I cannot explain the reason for this and it may simply be me, but for what it is worth, those are my two cents. Nucleotides: They Are Everywhere in These Pathways I emphasize for my students something that was never emphasized in my own education. I realized it one day after I had been teaching this material for a number of years. It was one of those epiphanies a teacher often gets in the middle of teaching. Nucleotides are everywhere in these energy-producing and -utilizing pathways. Quite often, we do not emphasize that ATP, the energy currency of the cell, is a nucleotide. We simply mention its name and that it is the energy currency of the cell and leave it at that. One day, it dawned on me that relatives of ATP show up in these pathways all the time. I began stressing that for my students. I point out that nucleotides do things other than carrying or helping to express the genetic code. NAD, NADP, FAD, Coenzyme A, and ribulose biphosphate are all relatives of ATP. The Performing Arts and Scientific Accuracy or Why Can't They Handle the Truth? I have a few pet peeves. One of them is when playwrights and screenwriters get the science wrong in their works. One such example is the movie A Few Good Men. Other than the mistake I will mention, it is a fine movie. The marine, around whose death the pivotal trial in the movie is centered, died of a condition called lactic acidosis. Lactic acidosis is a metabolic disorder that leads to an abnormal buildup of lactic acid in the blood and spinal fluid. The effect of this buildup is to make the blood, spinal fluid and tissues too acidic. It may be inherited or acquired and can be life-threatening. It can lead, in a number of patients, to nerve and muscle damage and may lead to problems in thinking, talking, walking, and balancing. In the movie, if I recall correctly, it is described as a condition that results from the patient burning oxygen. Well, gee, don't we all do that. Now don't get me wrong, it is a minor point with respect to enjoying the movie, but wouldn't it be better to define it correctly. At any rate, I tell my students about this 'mistake,' define lactic acidosis for them, and urge them to look for other such errors just for the fun of it. Star Trek in its various incarnations has some great ones. I am a fan of all of the series and movies, but I wince every time I hear them make such a mistake. Where Do Fats and Proteins (Amino Acids) Feed into Glycolysis and Krebs Cycle? One of the drawings that follows at the end of this section emphasizes the points at which breakdown products of lipids and proteins feed into glycolysis and Krebs cycle. It is simplified but makes the point as does the book. I also point out that amino acids lose their amino groups before the remaining carbon skeleton enters glycolysis-Krebs cycle. Ask your students where the amino groups go. They are toxic if the concentrations rise to too high a level (ammonia), so most of them combine with CO2, another waste product, to form urea that ends up being excreted in the urine. Do not forget to mention that the fats are more efficient at storing energy per unit weight than are the carbohydrates. Ask the students why fats are not used as more immediate sources of energy. The answer is, of course, that the carbohydrates are able to be metabolized more quickly than are the fats. While less efficient in terms of driving ATP production, they are easier to mobilize. When the carbohydrates run out, there has been enough time to mobilize the fats for ATP production. You may want to inform the students of the role of acetyl CoA in the synthesis of fatty acids and weight gain. If there is too much carbohydrate in the diet, excess acetyl CoA may build up. There is more of it than can feed into Krebs cycle so the excess is channeled into fatty acid synthesis. Also point out that weight loss cannot occur unless the overweight person burns up his/her available carbohydrates and breaks into the more efficient lipid stores. Electron Transport: The Bucket Brigade The bucket brigade has been an effective analogy for electron transport. Bucket brigades used to be used to fight fires. A line would form at a fire with one end near a source of water and the other near the fire. Buckets would be filled at the water source and passed down the line until the person closest to the fire would toss the water in his bucket onto the conflagration. The bucket would then be passed back up the line for a refill. In passing down the line, water would invariably be spilled from a bucket since everyone was hurrying. The electron transport system is similar. Electrons enter the system with high energy and with each hand-off down the pathway, they lose some. Sometimes the energy is sufficient to drive the production of ATP. Chemiosmosis The analogy used in the book of a hydroelectric dam is tremendously effective in describing chemiosmosis. One can do no better than portraying the hydrogen ions as water trapped behind the dam (inner mitochondrial membrane). The passage of the water (hydrogen ions) through the turbines (ATP synthase) down its concentration gradient with the accompanying production of electricity (ATP) works perfectly as an example and is one that seems to stick with the students. You can also deal with the formation of the gradient. Point out that the electron transport molecules come in two varieties: those that carry electrons alone and those that carry hydrogen ions and electrons. When an electron is passed to an ETS molecule that also binds protons/hydrogen ions, a proton is picked up from the mitochondrial matrix. When such a molecule passes its electron off to another ETS molecule that binds only electrons, it must divest itself of the proton it picked up earlier and this it does. However, it dumps the proton into the space between the two mitochondrial membranes, not back into the matrix where it originally obtained the proton. The result is that passage of electrons down the electron transport chain resulted in the pumping of protons across the inner mitochondrial membrane, thus setting up a powerful electrochemical gradient. The energy used to accomplish this was the energy stored in the electrons that entered the ETS. The Light-Dependent Reactions: An Exercise in Problem Solving I like to teach the light-dependent reactions as an exercise in problem solving. First, I teach cyclic photophosphorylation using the drawings I have included in this chapter. I explain what the photosystems are and how they work. Then, starting with the photosystem, I describe light striking the photosystem and exciting an electron to the point that it is passed off to an acceptor molecule outside the photosystem. I then describe the electron flow that brings the electron back to the photosystem from which it originated (the cyclic flow) and emphasize the production of ATP as the electrons travel down the electron transport chain. Ask the students why this process is called cyclic photophosphorylation. They are often scared of this huge vocabulary word. Break it down for them piece by piece to explain the name. It is called "cyclic" because of the cyclic electron flow; "photo' because it is driven by light, and "phosphorylation" because a phosphate group is added to ADP to make ATP. Next, I take on noncyclic photophosphorylation. I start with Photosystem I and talk about the absorption of light by the photosystem, the excitation of the electrons, and their passage to the acceptor molecule (X). I point out that in noncyclic photophosphorylation one of two things can happen to the electron bound to X. First, the electron could pass down the pathway leading back to the photosystem from which it originated (cyclic photophosphorylation pathway) or it can go down another pathway leading to NADP+ where it reduces NADP+ to NADPH. After I remind them what NADPH is used for in the light-independent reactions, I ask my students what problem has been created at Photosystem I. After a little prodding at most, someone figures out that the photosystem will run out of electrons and that if this happens photosynthesis will come to a screeching halt. I ask them how this problem can be solved. Looking at the drawing on the overhead projector, they figure out that the second photosystem supplies electrons to replace those missing from Photosystem I. I point out that this solves the problem with Photosystem I. I ask them if there is another problem. They figure out that Photosystem II now lacks electrons. I ask them how that problem is solved. Someone invariably suggests a third photosystem. I ask them why that is impractical They realize quickly that an infinite series of photosystems would be needed. I ask leading questions to get to the point about what a better source of electrons might be. It is not too difficult to get them to realize that there could be no better source than the most plentiful molecule on the Earth: water. Finally, I make sure they understand the products of noncyclic photophosphorylation. I ask them to characterize the two pathways and urge them to learn the similarities and differences between them. I also make sure they understand that the noncyclic pathway includes within it the cyclic pathway and ask them what the evolutionary significance of that fact is. C3 and C4 Photosynthesis BioInquiry does not cover C3 and C4 photosynthesis in great detail. You may wish to add to the coverage, however. It illustrates the kinds of adaptations that organisms must make to survive in the environments in which they find themselves. C3 photosynthesis refers to the first stable product of the Calvin-Benson cycle, phosphoglycerate (a 3-carbon molecule). Organisms that perform C3 photosynthesis do quite well in temperate environments but have problems when the climate becomes hotter and drier. The reason for this is related to the ability of oxygen to inhibit the action of Rubisco. In hot, dry climates, plants tend to keep closed the stomata located on the undersides of their leaves. These are openings into the leaf interior that facilitate the exchange of gases located inside the leaves with those in the surrounding atmosphere. When open, however, the stomata allow enhanced water loss in addition to gas exchange. The plant responds by keeping the stomata closed much more in hot, dry climates. Consequently, the oxygen produced by photosynthesis builds up in the air spaces within the leaf and since the cells that fix CO2 out of the atmosphere are exposed to the oxygen, Rubisco is inhibited. Photosynthesis slows and the plant's growth slows measurably. You may wish to guide students through this story asking leading questions as you go. To illustrate the concept, ask the students what happens to their lawns in the dry part of July. I realize that this question will not work everywhere, but I live in the Northeast. When July comes, my frequency of mowing goes way down. Next, make the point that some plants have "figured" out away to circumvent this problem somewhat. They have changed their biochemistry and anatomy a bit and have come up with a solution that allows them to thrive in climates that would severely hamper the C3 plants mentioned above. They carry out C4 photosynthesis. They sequester the cells performing C3 photosynthesis (the bundle sheath cells containing Rubisco) in a cylinder surrounding the plant's vascular tissues. Surrounding that cylinder is another made of mesophyll cells. This cylinder seals off the first one from the air spaces inside the leaf so that the Rubisco inside the bundle sheath cell cylinder is not affected by elevated oxygen concentrations inside the leaf. In cross section, this arrangement of cells looks like a wreath, a feature that gives the anatomy its name, Krantz (German for wreath) anatomy. The mesophyll cells in the outer cylinder fix CO2 out of the atmosphere and attached it to a 3-carbon molecule (phosphoenol pyruvate; PEP) producing a 4-carbon molecule (oxaloacetate вЂ” ask them where they have heard of this before), hence the designation C4 photosynthesis. The enzyme that adds CO2 to PEP is called PEP carboxylase; it is not inhibited by the high levels of oxygen found in plants living in hot, dry climates. Consequently, these plants can continue to fix CO2 from the atmosphere under conditions that would prevent C3 plants from doing so. Once fixed, the CO2 is shuttled to the bundle sheath cells where it is released from the shuttle molecule and sent into the Calvin-Benson cycle by attachment to RuBP through the action of the uninhibited Rubisco. Examples of plants that perform C4 photosynthesis are sugar cane, maize (corn), and crab grass. Ask students if they now understand why crab grass does so well on their lawns during the summer. You may also wish to mention another strategy used by other plants to get around the same problem. This strategy, adopted by a number of succulents like "ice plants" and many cacti, is to perform the light-dependent reactions during the day, storing up the products of the reactions. At night, when it is cooler and the risk of desiccation is lower, the carbon fixation occurs. These plants are called CAM plants. The name comes from crassulacean acid metabolism after the plant family Crassulaceae, in which the process was first discovered. Drawings of Respiration and Photosynthesis On the following eleven pages there are drawings of the pathways and processes of cellular respiration and the light-dependent and light-independent reactions of photosynthesis. Feel free to use them in your class as transparencies and/or handouts for your students. I have used them in the past and found them to be quite useful. My students take notes all over the handouts and it seems to help them comprehend the material. ENERGY PRODUCTION IN LIVING ORGANISMS NH 2 I. Important Molecules C A. N C N CH HC C N N OHO P OO P O O OO P O O 5' C H 1' O 3' H 2' } Adenosine AMP - Adenosine Monophosphate ADP - Adenosine Diphosphate ATP - Adenosine Triphosphate ATP = Adenosine P P ADP = Adenosine P P AMP = Adenosine P ATP + H 2 O 1. 2. 3. 4. P ADP + P + ENERGY Downhill reaction Spontaneous Energy released - в€†G ADP + P + ENERGY 1. 2. 3. 4. } Adenine Uphill reaction Not spontaneous Energy required + в€†G ATP + H 2 O Ribose B. Nicotinamide Adenine Dinucleotide (NAD) NH 2 C N N N N ADENOSINE (Adenine Base in RNA) 5' CH 2 P H O S P H A T E O O HO -O P 2' OH O Phosphate group added here in NADP O -O P O C O NH 2 O N 5' CH 2 NICOTINAMIDE + O HO RIBOSE 2' OH H H C O N NH 2 + H C 2H + O N + R Oxidized Form (NADo x ) NH 2 + H+ + R Reduced Form (NAD re ) C. Nicotinamide Adenine Dinucleotide Phosphate (NADP) Phosphate group added to adenosine substituent of NAD at the 2' C of ribose (see above). GLYCOLYSIS AND KREBS CYCLE P R E P A R A T O R Y C6 Glucose ATP ADP C6 S T E P S P ATP ADP C6 P 2 C3 P P PGAL (Phosphoglyceraldehyde) O X I D A T I O N F O R M A T I O N NADo x NAD re 2 Pi 2 C3 P 2 C3 P 2 C3 P P 2 ADP 2 ATP 2 H 2O O W F I T A H T P 2 ADP 2 ATP 2 C3 Pyruvate NAD re NADo x 2 C2 + NADre NAD o x 2 C3 Lactic Acid 2 CO2 In animals and some microorganisms Alcohol In plants (most) and many microorganisms Krebs (TCA) Cycle 4 CO2 2 ATP 6 NAD re 2 FAD re KREBS CYCLE (CITRIC ACID CYCLE) C3 (2 molecules of pyruvic acid for every one original glucose molecule) Pyruvic Acid NADox C2 NAD r e CO2 Acetyl CoA ~ H-C-C S - CoA + H O2 Citric Acid HS - CoA H2 O C6 C4 Oxaloacetic Acid H2 O C6 NADr e 2H Isocitric Acid NADox C4 NAD r e FAD r e Malic Acid C6 2H 2H NADox Oxalosuccinic Acid C6 FAD ox Fumaric Acid ATP ADP NADox NADr e 2H C4 GTP GDP CO 2 О± - Ketoglutaric Acid CO 2 C5 HS - CoA HS - CoA C4 H2 O C4 Succinyl Coenzyme A Succinic Acid 1 turn of cycle yields: 1 ATP 1 FAD re 3 NADre P i 2 turns of cycle /molecule of glucose 1 NADre for every pyruvate shuttled to the Krebs Cycle ATP Tally Sheet Summary of Energy Yield from 1 Glucose Molecule Note: NADre and FADre donate electrons to the electron transport system (ETS) Each NADre made yields 3 ATPs from the ETS. Each FADre made yields 2 ATPs from the ETS. PROCESS DIRECT YIELDS Glycolysis (in cytoplasm) FINAL YIELD OF ATP 2 ATPs ----------------------------------------------> 2 ATPs 2 NADre x 3 ATP = 6 ATP But 2 ATP used to transport electrons across mitochondrial membrane (6 - 2 = 4)------------> 4 ATPs _________________________________________________________________________________ Respiration (in mitochondrion) A. Pyruvate to Acetyl CoA (twice) 2 NADre x 3 ATP = 6 ATP ----------------------> B. Krebs Cycle 2 ATP ----------------------------------------------> 2 ATPs 6 NADre x 3 ATP----------------------------------> 18 ATPs 2 FADre x 2 ATP ----------------------------------> 4 ATPs FINAL TOTAL 6 ATPs 36 ATPs RELATIONSHIP OF PROTEIN AND FATS TO CARBOHYDRATE METABOLISM Proteins Amino Acids Fats Polysaccharides Simple Sugars Glycerol Fatty Acids PGAL Pyruvic Acid NH 3 Acetyl CoA Krebs (Citric Acid) Cycle RESPIRATORY ELECTRON TRANSPORT CHAIN NAD r e re NADox FP ox ADP + Pi ATP re Q ox re ox cyt b, c1 ADP + P i ATP re cyt c ox re ox cyt a, a 3 ADP + Pi ATP 1/2 O2 H 2O R E D U C I N G P O W E R O F E L E C T R O N S PQ re Cyt f re PC re 2 ATP 2 ADP + 2 Pi CYCLIC PHOTOPHOSPHORYLATION ox ox ox LIGHT re X 4e- ox P700 Reactive Molecule or Reaction Center Antenna Molecule R E D U C I N G P O W E R O F E L E C T R O N S 2 H 2O re 4 e- (To medium) + 4H O2 Q ox 4 e- ox PQ re Energy LIGHT ox Cyt f re 2 ADP + 2 P i 2 ATP re PC ox re X ox re Fd ox Non-Cyclic Pathway 4 e- P700 Reaction Center Photosystem I Cyclic Pathway NON-CYCLIC PHOTOPHOSPHORYLATION Photosystem II P680 Reaction Center re FP ox LIGHT + From medium 2 NADPo x + 4 H 2 NADP r e THE CALVIN - BENSON CYCLE: THE THREE-CARBON PHOTOSYNTHETIC PATHWAY Cycle Starts Here From Light Reactions 6 ATP 6 molecules of phosphoglycerate (PGA) 3 Carbons 6 ADP (6 x 3 Carbons) 3 molecules CO2 6 molecules of diphosphoglycerate (3 x 1 Carbon) (6 x 3 Carbons) 6 NADPr e 3 molecules of Ribulose Diphosphate (3 x 5 Carbons) 6 NADPo x 6 molecules of glyceraldehyde phosphate (6 x 3 Carbons) 6 ATP 6 ADP From Light Reactions 5 molecules of glyceraldehyde phosphate (5 x 3 Carbons) 1 molecule of glyceraldehyde phosphate (1 x 3 Carbons) 6 Carbon Sugar (Glucose) Other Sugars or Polysaccharides C 4 PHOTOSYNTHESIS CO 2 C4 NADPre NADPo x C3 AMP PEP Mesophyll Cell ATP NADPo x C4 C3 Calvin Cycle CO2 NADPre PGAL C5 C6 Glucose Bundle Sheath Cell Sample Test Questions Multiple Choice, Conceptual, and Open-Ended Questions From the Text 1. The idea that the energy used by living organisms is somehow unique and different from energy in the inanimate world is called: a. equilibrium b. entropy c. vitalism d. metabolism e. vital force 2. The name for the collected chemical reactions that occur in cells is: a. heterotrophism b. metabolism c. vitalism d. equilibrium e. b and d 3. Which statement below is consistent with the First Law of Thermodynamics? a. Energy cannot be eaten. d. Energy can be neither created nor destroyed. b. Energy can be created and destroyed. e. Energy is not interconvertable. c. The universe tends toward randomness. 4. Which of the following is an example of the First Law of Thermodynamics? a. gasoline powering a car's movement d. electricity stored in a battery b. an ice cube melting e. water freezing c. a thrown ball 5. According to the Second Law of Thermodynamics, energy will ______become more randomly distributed during a process. a. spontaneously b. with an energy input c. not d. non-spontaneously e. never 6 What realization marked the beginning of the end of vitalism? The realization that living organisms obeyed the First Law of Thermodynamics, that they could no more create energy from nothing than could mechanical devices, was the beginning of the end of vitalism. 7. Entropy is a term that describes: a. the amount of disorder in the universe b. the amount of heat in the universe c. the amount of randomness in the universe d. a and c e. the amount of energy in the universe 8. At what point does a living organism attain equilibrium? A living organism attains equilibrium when it dies. When an organism no longer obtains energy from its surroundings (in the form of food), it will die. A system that is getting no energy from its surroundings will spontaneously move toward equilibrium. 9. How can living organisms maintain order in their area of the universe and still obey the Second Law of Thermodynamics? When life imposes order on a small part of the universe, there must be an even greater increase in entropy elsewhere in the universe. 10. Which of the following did Priestley think happened when a flammable material burned? a. The material gave off a substance he called oxygen. b. A substance called phlogiston flowed into the air. c. A substance called phlogiston combined with what remained of the burned material. d. There were huge explosions. e. Oxygen combined with the flammable material. 11. What would happen if a mouse were placed in a bell jar? a. The mouse grows. c. The mouse dies. e. The bell jar expands. b. The mouse eats. d. The bell jar implodes. 12. A chemical reaction in which oxygen is combined with other substances is called: a. reduction b. oxygenation c. dehydration d. oxidation e. condensation 13. What is taken from the atmosphere and added to burned materials? a. phlogiston b. nitrogen c. hydrogen d. krypton e. oxygen 14. Which of the following is an example of kinetic energy? a. a thrown baseball c. the energy stored in the bonds of gasoline b. a rock at the top of a hill d. the energy stored in glucose e. c and d 15. Lavoisier conducted a study of the effect of burning on flammable materials. He did so by keeping careful account of all of the products of the fire. Which of the following statements reflect what he learned from his study? a. He discovered that the burned material had gained weight. b. He concluded that burning did not add phlogiston to the air. c. He concluded that burning removed something from the air. d. He recognized that fire and breathing are both forms of burning. e. all of the above 16. Which of the following is an example of potential energy? a. a thrown baseball c. a moving train b. a rock at the top of a hill d. the energy stored in glucose e. b and d 17. How is metabolism different from uncontrolled oxidation like that seen when paper is burned? Metabolism is both more efficient and more specific than is uncontrolled oxidation. It is more efficient in that the energy is not released all at once as happens when a material is burned. In metabolism, the energy is released a bit at a time which allows it to be captured and stored in molecules like ATP and NADH. Metabolism is more specific in that it is mediated by enzymes that catalyze each step in the process. Enzymes typically act on a limited number of substrates since their active sites can only bind to substances that have a shape allowing them to fit in the active site. The relationship between an enzyme and its subtrate is a very specific one. 18. Living organisms clearly carry out some reactions that are unfavorable. This seemingly runs counter to the Second Law of Thermodynamics. How do living organisms manage to get around this seeming contradiction? Organisms can couple seemingly unfavorable reactions with favorable reactions that provide energy to make the unfavorable reactions happen. 19. Why do some seemingly favorable reactions occur very slowly or not at all? Favorable reactions may possess an energy barrier that prevents a reaction from occurring as fast as might seem likely at first glance. In such a reaction, only those substrate molecules with extremely high energy may possess enough energy to surmount this barrier, the activation energy. At any given moment, the number of substrate molecules possessing sufficient energy is only a small percentage of the total. Therefore, the rate at which substrate can be converted to product is correspondingly low. 20. Enzymes work by: a. raising the activation energy, thus increasing reaction rates b. lowering the activation energy, thus increasing reaction rates c. making a thermodynamically unfavorable reaction favorable d. making a thermodynamically favorable reaction unfavorable e. b and c 21. What molecule below is often used used to drive thermodynamically unfavored reactions? a. ATP b. ADP c. GDP d. glucose e. O2 22. Short-lived compounds that occur at a point in a metabolic pathway somewhere between the starting point and the end are called: a. metabolic interjections c. metanephric homologs e. internecines b. metastatic intermediates d. metabolic intermediates 23. Metabolic pathways can be: a. linear b. circular c. all of the other answers d. branched e. interconnected 24. In what form do living organisms conserve energy for emergencies? a. fats b. oils c. starch d. ATP e. a, b, and c 25. Metabolic specificity is reflected in the ability of enzymes to: a. bind to one or a few products at most d. destroy substrates b. bind to one or a few substrates at most e. denature at high temperature c. catalyze thermodynamically favorable reactions 26. Which of the following molecules are adenine-containing nucleotides? a. ATP b. ADP c. a, b, and d d. FAD e. GTP 27. Why must oxidation reactions always be accompanied by reduction reactions? If a molecule has been reduced, it has picked up an electron. Since electrons do not generally float freely in the cytoplasm of a cell, the electron that was picked up had to have come from some other molecule. Since that molecule lost an electron, it was oxidized. Therefore, every time there is a reduction reaction, it must be accompanied by an oxidation reaction. 28. What metabolic pathway is common to virtually every living thing and similar or identical in every type of cell? a. Krebs cycle b. electron transport system c. glycolysis d. a and c e. light reactions 29. Which pathway is known as the anaerobic pathway of cellular respiration? a. glycolysis b. Krebs cycle c. electron transport system d. photosynthesis e. a and b 30. In what form do carbon atoms leave the Krebs cycle? a. CO b. CO2 c. glucose d. CH4 e. a and b 31. What is meant by oxidative phosphorylation? Oxidative phosphorylation is the addition of a phosphate group to ADP to form ATP via a process that requires oxygen. Specifically, it refers to the production of ATP by the electron transport system. 32. Which of the following compounds is a breakdown product of cellular respiration? a. CO b. CO2 c. O2 d. b and e e. H2O 33. What are two problems with anaerobic respiration or fermentation? The first problem with anaerobic respiration or fermentation is that only two ATPs are produced per glucose as compared to the 36 ATPs per glucose when respiration runs aerobically. The second problem is that during glycolysis running anaerobically, all of the limited NAD+ is converted to the reduced form (NADH). Since NAD+ is depleted in the absence of O2, eventually glycolysis would be brought to a halt when NAD+ runs out. 34. What is the product of anaerobic respiration in animals? a. ethanol b. CO2 c. lactic acid d. ATP e. c and d 35. What causes the sensation of fatigue that someone who has exercised more strenuously than usual feels? Such a person has probably run glycolysis in his/her muscles anaerobically. Thus, lactic acid has built up in their muscles. The increased acidity in the muscles leads to the sensation of fatigue. 36. You homogenize a sample of rat liver and separate portions of the preparation into the following fractions: cytoplasmic fraction, nuclear pellet, mitochondrial membranes, and mitochondrial matrix (soluble material inside the mitochondrion). In which fraction will you find the following: a. glycolytic enzymes - cytoplasmic fraction. b. Krebs cycle enzymes - mitochondrial matrix c. electron transport system - mitochondrial membranes 37. In what form do living organisms conserve energy for emergencies? a. fats b. oils c. starch d. ATP e. a, b, and c 38. What supplies the energy used to synthesize ATP in the mitochondria? The electron transport system transports H ions across the inner mitochondrial membrane from the matrix to the intermembrane space using energy obtained from high energy electrons moving down the ETS. 39. Cyanide is a non-competitive inhibitor of the electron transport chain. How does it kill a person? Once it inhibits a molecule in the ETS, the chain will be blocked at that point. The ETS will back up causing all of the NAD to be tied up in the reduced form, Glycolysis will be blocked because of the requirement for NAD+ and the organism poisoned with cyanide will be unable to make ATP. Since ATP is needed for an organism to do the bulk of its biological work, it will die. 40. Why does a lack of oxygen kill someone? If no oxygen is present, the electron transport system will be unable to pass its electrons to oxygen. Thus, all of the electron transport molecules will be in their reduced forms and the whole ETS will back up. If the entire ETS is reduced as would happen in the absence of oxygen, reduced NAD will be unable to pass its electrons to the ETS. Soon, all of the cellular NAD will be in the reduced form; there will be no NAD+ left. Since NAD+ is required for glycolysis, in the absence, glycolysis will not occur. The organism would die because it would be unable to make any ATP at all. 41. What is the reason for the folded cristae in the inner mitochondrial membrane? The enzymes of the electron transport system and ATP synthase are located on the cristae membranes. Folds in the inner mitochondrial membrane increase the surface area inside the mitochondria and provide more surface area to house the ETS enzymes and ATP synthase. Thus, the folding increases the capacity for ATP synthesis in the mitochondria. 42. How do protons reenter the mitochondrial matrix during oxidative phosphorylation? Protons flow down their electrochemical gradient back into the mitochondrial matrix through the hollow F0 subunit of ATP synthase. The movement of these protons down their gradient thus drives the production of ATP. 43. The process by which a proton gradient is constructed in mitochondria is called: a. chemistry b. chemiharmonics c. osmosis d. chemiosomosis e. fermentation 44. Van Helmont grew a willow tree in a pot for five years and carefully weighed the pot each year. He found that while the tree gained 150 pounds of living tissue, the soil only lost a few ounces. What did van Helmont conclude? He concluded that the tree had used its daily supply of water to fuel its growth. As circumstantial evidence, he argued that without the water, the tree would have died. Was he right? Why or why not? He was half right. The tree did need water, but the energy that it can supply is not enough to fuel life's chemical processes. A few years later, it was demonstrated by others that light and CO2 were also required for photosynthesis. 45. A graduate student decides to reproduce the experiments of Joseph Priestley. He places a plant in a sealed jar. The plant grows for a while and then stops. Next, he places a mouse in another jar. It survives a while and then dies. What can the graduate student do to prolong the lives of the mouse and the plant while they reside in a sealed glass jar? The simplest way to prolong the lives of the mouse and the plant in the sealed jar would be to put them both in the sealed jar together. The plant had stopped growing because its supply of CO2 was exhausted. The mouse had died because it ran out of oxygen. By placing them in the jar together, the mouse produces CO2 that the plant can use and the plant produces O2 for the mouse to breathe. Thus, since they both fulfill the other's needs, they both survive longer. 46. Assume that you expose a pigment that fluoresces in the visible light range to green light. Which color below is the fluorescence likely to be? a. violet b. indigo c. red d. green e. b and d 47. What color of light below would be most likely to be absorbed by chlorophyll? a. green b. blue c. red d. b and c e. a and b 48. What color of light is most likely to drive photosynthesis? a. green b. blue c. red d. b and c e. a and b 49. The internal disk-shaped sacks of membrane seen in electron micrographs of chloroplasts and surrounding a space are called: a. thylakoids b. cristae c. stroma d. matrix e. dipthongs 50. What evidence suggests that cyclic photophosphorylation is a relatively ancient pathway? A pathway that appears to be a version of cyclic photophosphorylation has been found in Archaebacteria. They use the pathway to make ATP and for them, it supplies enough ATP to sustain life. The presence of cyclic photophosphorylation in Archaebacteria, a fairly ancient organism, suggests that this pathway has been around for a very long time. 51. The light-independent reactions of photosynthesis were once referred to as the dark reactions while the light-dependent reactions were called the light reactions. Why have the names been changed? The old names were confusing. The name 'light reactions' was correctly interpreted to mean that the reactions required the presence of light. However, people would often assume that the 'dark reactions' required darkness. This is incorrect. The dark reactions can occur in either light or darkness as long as supplies of NADPH and ATP are adequate. 52. Where in chloroplasts are the photosynthetic pigments located? a. the inner membrane b. the outer membrane c. cristae d. thylakoids e. stroma 53. Chloroplasts are purified from a spinach plant and separated into the following fractions: inner chloroplast membrane, outer chloroplast membrane, thylakoid membranes, stroma. Where do the following substances located? a. Calvin-Benson cycle enzymes вЂ“ stroma b. photosynthetic pigments вЂ“ thylakoid membranes c. chlorophyll - thylakoid membranes d. chloroplast ATP synthase вЂ“ thylakoid membranes e. electron transport chain вЂ“ thylakoid membranes 54. In which locations have lollipop structures been visualized in the electron microscope? a. inner mitochondrial membrane c. thylakoid membrnae e. outer mitochondrial membrane b. inner chloroplast membrane d. a and c 55. What research tool was instrumental in unraveling the Calvin - Benson cycle? a. paper chromatography c. radioactive carbon e. gas chromatography b. radioactive phosphorus d. a and c 56. To what molecule does Rubisco attach CO2? a. phosphoglycerate c. ribulose biphosphate b. phosphoglyceraldehyde d. a and b e. pyruvate 57. In hot, dry climates, plants are often forced to close their stomata, openings on the underside of their leaves, to prevent themselves from drying out. They are no longer able to release the oxygen byproduct of photosynthesis to the atmosphere and, consequently, oxygen builds up in air spaces within the leaf, while carbon dioxide levels decrease. Which of the following things will happen? a. Rubisco activity will increase c. carbon monoxide will be released e. b and d b. Rubisco activity will decrease d. Rubisco will denature 58. How do free radicals set in motion a biological chain reaction? Free radicals will steal electrons from neighboring molecules, thus creating another free radical that may steal an electron from yet another neighbor. Free radicals, particularly those involving oxygen can escape and cause damage. 59. Which of the methods below is used to deal with dangerous free radicals in the body? a. denaturation of peroxide c. superoxide dismutase e. b and c b. antioxidants d. peroxidase 60. What kinds illnesses and maladies are thought to be caused by accumulated free radical damage? A number of age-related symptoms are thought by some to be caused by free radicals among them wrinkles, arthritis, loss of flexibility, and diseases like cancer and degenerative diseases of the nervous system. Multiple Choice, Conceptual, and Open-Ended Questions From the CD-ROM 1. When a living organism uses energy, some of it is always lost in what form? a. light b. motion c. magnetism d. heat e. sound 2. How does heat lost to the environment during living processes help organisms to obey the Second Law of Thermodynamics? Heat lost to the environment during life's processes contributes to the amount of disorder in the universe. 3. What is meant by the Induced Fit Model of enzyme action and its active site? It is now known that enzymes work by binding substrates to the active site. After initial binding, the shape of the enzyme and possibly its active site changes. The result is an increase in the affinity of the enzyme for its substrate. the enzyme binds the substrate more tightly and/or moves reactive R groups into position to catalyze the desired reaction. The enzyme to a degree folds up around the substrate. It is induced to fit the substrate, hence the name. 4. What would be the result of the uncontrolled release of energy stored in an organism's supply of glucose? So much energy would be released at once that the organism would probably be severely injured and perhaps killed. 5. How does the way in which living organisms pass electrons to oxygen to form water differ from what happens when those electrons are passed from hydrogen to oxygen to form water? The direct passage of the electrons from hydrogen to oxygen to form water releases the stored energy all at once. Living organisms pass the electrons down a chain of electron transport molecules so that the energy is extracted from them in a stepwise fashion. Some of that energy can be captured and stored in molecules like ATP and NADH. 6. A molecule that has _______ electrons is said to be ________. a. gained, reduced b. lost, oxidized c. gained, oxidized d. lost, reduced e. a and b 7. Why is the mechanism by which enzymes attach to their substrates referred to as the Induced Fit Model of enzyme action? When the substrate binds to the enzyme active site, the enzyme changes its shape improving the fit between the enzyme active site and the substrate. The enzyme is induced to fit the substrate better. When the product(s) of the reaction leave(s), the enzyme returns to its initial shape. 8. Enzyme-catalyzed reactions exhibit a temperature optimum because: a. low temperatures slow down molecular motion d. a and c b. low temperatures speed up molecular motion e. b and c c. high temperatures denature proteins 9. What causes enzyme activity to decrease at higher temperatures? At higher temperatures, the additional molecular motion brought on by the increased temperature overcomes the weak interactions that are largely responsible for maintaining the enzyme's functional shape. Thus, the enzyme denatures, losing its shape and, because of this loss, losing its activity. 10. What is the temperature optimum of the enzyme in the exercise in Section 9.2 of the CD-ROM? a. 35В°C b. 55В°C c. 37В°C d. 37В°F e. 0В°C 11. What are the pH optima of enzymes 1 and 2, respectively, in the pH optimum exercise of Section 9.2 of the CD-ROM? a. 4.3, 10 b. 10, 4.3 c. 6.5, 7 d. 8, 5 e. 4, 9 12. What kind of molecule is ATP? a. a ribonucleotide b. a phospholipid c. a carbohydrate d. a protein deoxyribonucleotide e. a 13. How can altered pH affect the activity of an enzyme? a. At pHs above the pH optimum, the enzyme will denature. b. At pHs below the pH optimum, the enzyme will denature. c. At a pH equal to the pH optimum, the enzyme will denature. d. At pHs below the pH optimum, enzyme activity will increase. e. a and b 14. Which of the following pHs would most likely be the pH optimum of an enzyme that works in the small intestine or stomach of the human digestive tract? a. 9.3 b. 3.2 c. 7.2 d. 11.6 e. 13.2 15. A substrate X is converted to a product Y by an enzyme. A molecule P resembles X, but cannot be converted to Y by the enzyme. What happens to the rate of Y production by the enzyme, if P and X are mixed in the test tube in roughly equal amounts as compared to what happens when the enzyme is incubated solely with X? a. Y production increases. c. The amount of X decreases. e. b and d b. Y production is inhibited. d. P binds to the enzyme active site often. 16. What kind of inhibitor would an inhibitor that resembles the substrate for an enzyme-mediated reaction most likely be? Why? Such an inhibitor would most likely be a competitive inhibitor. A competitive inhibitor works by temporarily occupying the enzyme active site and preventing access to that site by the substrate. If a substrate cannot reach the enzyme active site, it will not be converted to product. To occupy the enzyme active site, an inhibitor would have to be somewhat similar in shape to the enzyme's normal substrate. 17. What would be the most likely way to reverse the effect of a competitive inhibitor? a. Heat the enzyme. c. Degrade the substrate. e. b and c b. Increase substrate concentration. d. Increase product concentration. 18. An effective inhibitor of enzyme action in no way resembles the enzyme's normal substrate. Which of the following statements is most likely to be true? a. The inhibition could be reversed by increasing substrate concentrations. b. The inhibitor binds to a site other than the active site. c. The inhibitor binds to the enzyme's allosteric site. d. The binding of inhibitor alters the shape of the enzyme in a way that decreases its efficiency. e. b, c, and d 19. What would be the effect of a molecule that binds irreversibly to the allosteric site of an enzyme? a. The enzyme would be temporarily disabled. d. The enzyme's activity would increase. b. The enzyme would be permanently disabled. e. The substrate binds permanently to the enzyme. c. The enzyme would denature. 20. The removal of a phosphate group from ATP: a. results in the production of ADP and a phosphate group. b. consumes energy c. releases energy d. requires energy e. a and c 21. After an organism has fed, in what form will most of its adenosine be? a. ATP b. ADP c. NAD+ d. AMP e. ACG 22. Why are the first couple of steps of glycolysis often referred to as the pump-priming or preparatory steps for glycolysis? In the first couple of steps of glycolysis,two ATPs are actually used up to start the process going. These ATPs will eventually be recovered and additional ones made during the final steps of glycolysis. 23. What is the net gain in ATPs per glucose obtained from glycolysis? a. 0 b. 36 c. 2 d. 24 e. 4 24. What molecule is the end product of glycolysis? a. oxaloacetate b. acetyl CoA c. CO2 d. pyruvate e. water 25. How many carbons from one glucose molecule actually enter Krebs cycle? a. 4 b. 0 c. 6 d. 3 e. 5 26. Carbons that are lost while the carbons from pyruvate are being conveyed to the Krebs cycle are disposed of in what form? a. CO b. glucose c. CO2 d. ATP e. none of the above 27. What molecule donates carbons derived from pyruvate to the Krebs cycle? a. pyruvate b. acetyl CoA c. oxaloacetate d. NAD+ e. NADH 28. What molecule is produced first when carbons from pyruvate enter the Krebs cycle? a. oxaloacetate b. acetyl CoA c. CO2 d. ATP e. citric acid 29. How many carbons are there in the first product in the Krebs cycle? a. 14 b. 4 c. 2 d. 6 e. 3 30. Why is the Krebs cycle called a cycle? The Krebs cycle is a circular pathway of reactions. Two carbons from pyruvate via acetyl CoA are added to the four carbon oxaloacetate to make the six carbon citric acid. At the end of the cycle of reactions, oxaloacetate is regenerated and will join to another acetyl group from acetyl CoA. 31. What molecule donates electrons to the electron transport system? a. NAD+ b. NADH c. b and e d. FAD e. FADH2 32. How many ATPs would be produced if 5 molecules of NADH donated electrons to the electron transport system? 15 ATPs. How many ATPs are produced when 4 FADH2 molecules donate electrons to the electron transport system? 8 ATPs. 33. Why does the NADH produced during glycolysis result in a net gain of two ATPs while reduced NAD molecules produced in the mitochondria result in a net gain of three ATPs a piece? The NADH molecules produced during glycolysis are made in the cytoplasm. The electron transport system is found in the inner mitochondrial membrane. The glycolysis-derived NADH molecules must move into the mitochondria in order to donate their electrons to the electron transport system. There is an energy cost of one ATP to get the NADH into the mitochondrion. Since three ATPs are produced when NADH donates its electrons to the electron transport system, there is a net gain of two ATPs when a glycolysisderived NADH donates its electrons to the ETS. 34. What are the first two forms in which the energy of light is captured during photosynthesis? a. ADP, ATP b. NADPH, ATP c. NADPH, NADP+ d. NADP+, NADPH e. ADP, NADPH 35. In which stage of photosynthesis are NADPH and ATP used to produce carbohydrates? The lightindependent reactions. In which stage of photosynthesis are ATP and NADPH made? The lightdependent reactions. 36. Assume that you can measure the pH in the lumen of the thylakoid disks and the stroma of the chloroplast. In which compartment should the pH be lower as the light-dependent reactions of photosynthesis progress? Since the light-dependent reactions pump protons (H+ ions) from the stroma of the chloroplast to the thylakoid lumen, the concentration of H+ ions will rise in the thylakoid lumen. Thus, the pH in the thylakoid lumen should be lower in the thylakoid lumen than it is in the stroma. 37. Why would it be impractical to replace with electrons from another photosystem the electrons lost by Photosystem II in replenishing the missing electrons in Photosystem I? If a third photosystem was used to replace the electrons lost from Photosystem II, another photosystem might be needed to replace its electrons. This could go on almost infinitely. It is better to use an almost inexhaustible supply of electrons like those in water. 38. What are the products of noncyclic photophosphorylation? a. NADP+ b. NADPH c. ATP d. O2 e. b, c, and d 39. A scientist is studying photosynthesis in a spinach plant, and he is trying to determine where the oxygen given off by the spinach plant comes from. He labels the carbon dioxide exposed to the plant with radioactive oxygen and then analyzes the plant material and gas given off from the plant to determine the location of the radiolabeled oxygen. In what molecule does the radiolabel appear? a. phosphoglycerate b. carbohydrates c. gaseous oxygen d. water e. a and b 40. How many light absorption events are required to lift an electron from the energy content typical of electrons in water to the much higher energy content of electrons stored in NADPH? It takes two light absorption events to lift electrons from the energy content of electrons in water to the energy content typical of electrons stored in NADPH, one event for each of the two photosystems. Why are this many events required? Why is one light absorption event not enough? None of the light that can be absorbed by chlorophyll contains enough energy to lift the electrons from the level found in water to the level found in NADPH in just one step. Thus, two absorption events are necessary. 41. If a scientist presents a plant with water possessing a radiolabeled oxygen atom and monitors the plant material and gases given off by the plant, where is the radiolabeled oxygen detected after a few minutes of exposure to light and the consequent photosynthesis? a. carbon dioxide b. gaseous oxygen c. carbohydrates d. phosphoglycerate e. c and d 42. What are the products of cyclic photophosphorylation? a. NADP+ b. NADPH c. ATP d. O2 e. b, c, and d 43. The following statements apply to photosynthesis, cellular respiration, both processes, or neither process. Indicate which process is referred to in each statement by writing either P, C, PC or N in the blank before each statement. __ P __ a. Uses carbon dioxide as a reactant. _ C__ b. Electron transport system produces water. _ C__ c. Occurs in all cells. __ PC d. Generates molecules having carbon skeletons of varying lengths useful in other cellular pathways. __ PC e. Contains a cyclic biochemical pathway that alters carbon skeletons. ___ N_ f. ADP generated by donation of phosphate groups from high energy phosphorylated molecules (substrate level phosphorylation) ___ P __ g. Produces oxygen as a byproduct. ___ C__ h. During this process, six-carbon molecules are converted to 4-carbon molecules _ PC _ i. Some of the reactions involved occur in a milieu sometimes called the matrix __ PC _ j. Uses reduced coenzymes as sources of energy __ PC _ k. Uses ATP as a source of energy __ PC _ l. Produces ATP at some point in the process. ___ N_ m. DNA replicated as part of process __ P ___ n. Chemiosmosis occurs Using BioInquiry in Large Classes Integrating Components into the Lecture A few of the animations/exercises in Chapter 9 of the CD-ROM will be helpful in demonstrating the essential points of bioenergetics. Section 9.2 of the CD-ROM contains effective animations that illustrate the workings of the Induced Fit Model of the enzyme active site. It shows clearly how the active site is altered to fit the substrate(s) more snugly after binding is completed, returning to its somewhat less complementary shape after the reaction has ended. This section also contains exercises in which the student is asked to conduct an experiment to determine the optimum temperature for a hypothetical enzyme. The student selects different temperatures at which the enzyme's activity is tested, and s/he can, with a little ingenuity, zero in on the temperature that yields the best activity and type that value into the designated space to see if the correct result has been obtained. The exercise on pH optimum requires a little less ingenuity but demonstrates that the activity of enzymes may vary with pH and that different enzymes may work effectively over widely variant ranges of pH. The animations depicting the mechanisms of action of competitive and noncompetitive inhibitors are particularly effective and could be shown during lecture if the technology is available. Alternatively, it could be shown in a laboratory setting or the students could be urged to view it at home on their own time. Section 9.2 also contains panels that clarify the structure of ATP and demonstrate the cycling of ATP to ADP and back to ATP again. Further animations/illustrations emphasize the difference between the controlled release of energy seen in an electron transport chain and the uncontrolled, explosive release of energy seen when hydrogen and oxygen gas combine to form water. Section 9.3 of the CD-ROM take the student virtually step-by-step through glycolysis, Krebs cycle, and electron transport with explanations and thought-provoking questions accompanying each overlay in the composite drawing. These could be used during the lecture/lab, or students could use them as a study tool at home. Also, feel free to print out, use, and distribute the drawings of ATP, NAD, glycolysis, Krebs cycle, cyclic and noncyclic photophosphorylation, etc. that are included in this chapter of the Instructor's Manual. Section 9.4 of the CD-ROM covers the light-dependent and -independent reactions of photosynthesis and the Calvin-Benson cycle. Again, these processes are dealt with in a step-by-step fashion with relevant commentary and questions accompanying each step. Students can follow the electron and molecule flow with simplified drawings. The approach with noncyclic photophosphorylation is the one I prefer in which the process starts with Photosystem I and emphasis is placed on solving the problem of the electrons missing from the chlorophylls of the photosystem when they have been stored temporarily in NADPH. Once again use them in the lecture/lab setting if you prefer or suggest the students view the vignettes at home to reinforce what they have heard in lecture. One particularly cute feature is the fact that the succession of panels illustrating the Calvin-Benson cycle have no end; they keep going. It is a cycle after all. See if your students can make the connection. Read More About It For more detailed coverage of bioenergetics, I suggest the book Bioenergetics by Albert Lehninger. It is somewhat old now but it explains the flow of energy in cells quite well. The science fiction books mentioned in the Analogies section above that discuss entropy are excellent as well and entertaining (Cosm by Gregory Benford and The World at the End of Time by Frederick Pohl). Supporting the Lab As a supplement to the lab portion of the course, you may wish to show your students (or ask them to review) the CD-ROM animations concerning enzyme-substrate interactions, temperature, and pH optimum and enzyme inhibition. These would be a good lead-in to labs involving investigations of enzyme activity. The same is true of the CD-ROM items on respiration and photosynthesis. A good lab exercise and one that impresses the students is the extraction of chlorophyll from spinach or from some other plant. If you shine ultraviolet light on the extracted chlorophyll, it fluoresces a beautiful deep red color. You can also run a paper chromatogram of the extracted chlorophyll. In short order, you will see a number of pigments separated on the chromatogram. Answers to the Review Questions 1. I will not agree to patent the invention. The first law of thermodynamics states that one form of energy can be converted to other forms of energy, but it also states that enegy can be neither created nor destroyed. An invention that required no fuel would have no source energy and it would be unable, according to the first law, to create anew the energy it required. Mechanical devices cannot create energy from nothing. Therefore, such an invention would be impossible and unworthy of a patent. 2. A perpetual motion machine would also not be awarded a patent. Perpetual motion machines, by definition, will keep moving forever without an infusion of energy. Without an infusion of energy, the motion in the perpetual motion machine would move toward equilibrium, that is, it would run down and eventually stop. Motion would be considered a change and when equilibrium is attained, no further changes should be possible without an infusion of energy. 3. Entropy is the name for the amount of disorder in the universe. Equilibrium is the condition of maximum entropy. When a system has attained maximum entropy, when it is as random as it can be, it has reached equilibrium. When equilibrium has been reached, no more changes can occur unless energy is obtained from the outside. 4. Lavoisier reasoned that if breathing and fire added phlogiston to the air during burning, then the weight of the material being burned should decrease. Lavoisier carefully accounted for all of the products produced during burning and compared their weight to the weight of the material before it was burned. He found that the weight had actually increased and concluded that burning does not add phlogiston to the air but that instead it removes something from the air adding it to the burned material. He called the material removed from the air oxygen. Both burning and breathing thus remove oxygen from the air. Both fire and metabolism are given the general name oxidation. 5. Vitalism suggested that living organisms did not have to obey the laws of the universe like the First Law. After experimentation with living organisms, it quickly became apparent that living organisms are no more able to create energy from nothing than are mechanical devices. It was found that the energy for life comes directly or indirectly from the radiant heat and light of the sun. The realization that living organisms obeyed the First Law (the Law of the Conservation of Energy) was the beginning of the end of vitalism. It meant that life was no longer exempt from the laws of the universe. Living organisms also obey the Second Law of Thermodynamics by increasing the randomness of the part of the universe outside the system of the living organism. Thus, while order within the living organism increases (entropy decreasing), the remainder of the universe outside the living organism exhibits a larger increase in entropy. Thus, the sum of entropy both inside and outside the living organism is positive, satisfying the requirements of the Second Law. The increased entropy of the surroundings is largely due to the conversion of useful energy into useless energy (heat), which then contributes to the disorder in the rest of the universe. 6. Enzymes do not make reactions occur that would not normally occur. Many reactions are favored thermodynamically, but still run very slowly. Those that do run slowly do so because there is an input of energy required before these reactions can be carried out at significant rates. The amount of energy required for this purpose is referred to as the activation energy. Enzymes speed up reactions that are thermodynamically favored by overcoming this activation energy. If a reaction is not thermodynamically favored, an enzyme cannot cause it to occur; it is referred to as nonspontaneous and will occur only after a significant input of energy. 7. A fire, once started, will generally burn anything that it touches. It speeds up the oxidation of paper raising the overall energy of all of the paper molecules. Metabolic oxidation, on the other hand, is selective about what is being oxidized. The cell generally burns fuel molecules like glucose and not cellular machinery like proteins and DNA. Enzymes which are responsible for catalyzing all reactions in the cell, including oxidative reactions are extremely specific with respect to the substrates on which they can act. For each step in metabolic oxidation, only the appropriate substrate reacts. Oxidation of glucose by fire releases the energy stored in glucose all at once resulting in the emission of significant amounts of heat and light. This would not be good for a living organism since the heat and light given off would be likely to damage a living organism severely. Living organisms are much more efficient in extracting energy from glucose. Living organisms enhance their specificity either by capturing as much energy as possoble from oxidative reactions or by spending as little energy as possible to catalyze reactions that consume energy. When glucose is oxidized in the cell, energy is released from it in a stepwise fashion, a little bit at a time. At particular points in that sequence, some of the energy that is released is captured and stored in ATP or other similar molecules. While some energy is given off as heat during such a process, the process harnesses energy much more efficiently than does a fire. 8. A number of small steps in metabolism facilitates a more efficient capture and storage of energy than could occur if the energy were released in one big step. 9. Reactions that are thermodynamically favorable may occur very slowly or seemingly not at all. The reason for this is that most reactions have an energy barrier, the activation energy, that must be surmounted before the reaction can be completed. This is the energy required to break bonds which is usually the first step in such chemical reactions. Very few substrate molecule, at any given time, have an energy content sufficient to surmount the activation energy. Thus, such reactions occur at very low rates. 10. The forms of the four compounds that have the highest energy are ATP, NADH, FADH, and NADPH. 11. Glycolysis is widely considered to be the first metabolic pathway to evolve for a few reasons. First, it is a universal energy-harvesting process of life and has been shown to be the most widespread metabolic pathway in the living world. It is common to every living thing and is similar or identical in every type of living cell and thus appears to be very primitive. It is thought that it may have been present in the first living cell and then may have been passed on to all successful progeny of that first cell. 12. When yeast are living anaerobically, they depend on glycolysis for energy. Humans are multicellular organisms unlike yeasts and have higher ATP requirements than do yeasts. Thus, the elevated efficiency of aerobic respiration (18 times the ATP production per glucose) over anaerobic respiration is needed to fulfill the higher energy requirements of humans. While humans can survive for a time under anaerobic conditions, their energy requirements are so high that they will die without the oxygen that allows them to produce ATP more efficiently. 13. Glucose goes into glycolysis and it carries all of the chemical energy entering the pathway. At the end of glycolysis, there are two pyruvate molecules for every glucose that entered glycolysis. Furthermore, there is a net gain of two ATPs for every glucose molecule metabolized. Finally, two reduced NADH molecules are produced for every glucose molecule. They will be used in the electron transport system to make ATPs if oxygen is available. At the end of glycolysis, portions of the energy originally stored in glucose can be found in the ATPs, reduced NADH molecules, and pyruvate molecules produced by glycolysis. 14. At the end of glycolysis, the six carbons that entered the pathway in glucose are found in the two 3-C pyruvate molecules produced at the end of glycolysis. At the beginning of the Krebs cycle, four of the six carbons are found in intermediates of the Krebs cycle, specifically citric acid. Citric acid is produced when two carbons from pyruvate are donated to oxaloacetate (a four carbon molecule) to produce citric acid, a six carbon molecule. In accounting for the products from one glucose molecule, two pyruvates (a 3-carbon molecule) must be considered together. The two carbons from the original glucose that do not enter the Krebs cycle are given off as CO2. At the end of Krebs cycle, four of the carbons are still in Krebs cycle; the others have been given off as CO2. 15. The inner mitochondrial membrane is analogous to the dam. The H+ ions (protons) concentrated between the two mitochondrial membranes is analogous to the water behind the dam. The turbine in a hydroelectric dam is analogous to the mitochondrial ATP synthase. 16. Chlorophyll in solution absorbs the blue light and some of its electrons are boosted to higher energy levels. In an intact chloroplast, the electrons would travel down the electron transport system eventually ending up in NADPH. However, when chlorophyll is in solution, the connections that convey the electrons to NADPH are not present. Consequently, the electrons drop back to their original lower energy level. Most of the energy is re-emitted as red light, which is longer-wavelength, lower-energy light than the blue light that was originally absorbed by the chlorophyll. The missing energy was lost as heat and explains why the re-emitted light was not the same color as the light that had been absorbed. 17. The light-dependent reactions cannot occur in a test tube using only the plant cells' juices. The reason for this is that the pigments that absorb the light and the electron transport system are located in the thylakoid membranes. Furthermore, intact thylakoid membranes are required in order to set up the proton gradient between the thylakoid lumen and the stroma of the chloroplast that is used to produce ATP. Finally, the chloroplast ATP synthase enzyme that synthesizes the ATP is embedded in the thylakoid membranes as well and extracts the energy from the proton gradient as the protons move back into the stroma from the thylakoid lumen. 18. Noncyclic photophosphorylation makes more NADPH than ATP. The light-independent reactions (the Calvin-Benson cycle) that make carbohydrates actually require more ATP than NADPH (three ATPs for every two NADPHs). Plants compensate for this difference in supply and demand for ATP by using an alternate pathway, cyclic photophosphorylation, to make more ATP. Like noncyclic photophosphorylation, it generates a proton gradient between the thylakoid lumen and the stroma, but it does so without generating NADPH or oxygen. Furthermore, the electrons that move through the electron transport system end up exactly where they started, hence the name cyclic photophosphorylation. Finally, the Archaebacteria use a version of cyclic photophosphorylation to make ATP. For them, it supplies enough ATP to sustain life. The ancient heritage of the Archaebacteria and their reliance on this cyclic pathway suggest that it may be very ancient, maybe one of the earliest metabolic pathways. Noncyclic photophosphorylation is also most likely an evolutionary offshoot of cyclic photophosphorylation. 19. Rubisco (ribulose biphosphate carboxylase) fixes gaseous CO2 out of the atmosphere and attaches it to a sold 5-carbon skeleton (ribulose biphosphate). Without it, plants could not manufacture the food they need to sustain their lives and the lives of all of the organisms that depend on plants directly or indirectly for their nourishment. 20. The chloroplast and mitochondrial ATP synthases are called "molecular cousins" because they probably evolved from a common ancestor protein. Their structures and functions are thus very similar. CHAPTER 10 ANIMAL PHYSIOLOGY: HOW DO ORGANISMS RESPOND TO CHANGE? Lecture/CD-ROM Outline Overview I. Changes in an organisms' external & internal environments must be tolerated, adjusted to, & compensated for A. Such changes can be predictable or unpredictable, short-term or long-term B. They can also occur simultaneously II. There are nearly as many different responses as there are species but there are patterns to them III. Once life moved from the water to the land, it followed two divergent, but parallel, paths A. Autotrophy вЂ“ led to flowering plants (see Ch. 12 for their physiology) B. Heterotrophy вЂ“ led to birds & mammals (see Ch. 11 for human physiology as an example of quintessential, highly adapted terrestrial animal) IV. Closely related species have similar physiological processes вЂ“ example: desert kit & Arctic foxes A. Kidneys of both are similarly adapted to conserve & recycle water (lacking in the desert & frozen and unavailable in the Arctic) B. Both use ears to regulate body temperature 1. Kit fox ears are huge & radiate unwanted body heat to their slightly cooler environments 2. Ears of Arctic fox are small, fur covered, too well insulated to lose much needed body heat to consistently colder environment What Are the Underlying Principles of Physiology?: Introduction I. All multicellular organisms evolved from single-celled organisms A. Generally, when bacteria reproduce, cells divide & separate to lead independent existences 1. Often daughter cells do not separate; they stay connected as do their offspring 2. Single cell becomes a long string of cells, a colony вЂ“ multicellular entity, but not multicellular organism; if any cell of colony is separated from the rest, it can live independently B. This independence is not true of the cells of multicellular organisms 1. Except for gametes, no shark cell can exist under natural conditions independent of other shark cells вЂ“ different kinds of shark cells depend on other cell types for what they can do 2. Mutual interdependence among cells distinguishes multicellular organisms from colonies II. Multicellular organisms are also distinguished by certain features & responses: A. The cells of multicellular organisms are hierarchically organized B. Multicellular organisms are more than the sum of their parts C. Multicellular organisms function best within stable internal environments D. Feedback systems control many physiological processes What Are the Underlying Principles of Physiology?: Cells of Multicellular Organisms Are Hierarchically Organized I. Multicellular organisms are more than simple masses of interdependent cells; their cells are instead highly organized; one layer builds into the next (cells вЂ”> tissues вЂ”> organs вЂ”> organ systems) II. Cells are organized into tissues вЂ“ groups of similar cells performing a similar function; number of tissues depends on organism complexity (jellyfish вЂ“ only a few; humans - >200); examples: A. Epithelial tissues вЂ“ cover surfaces throughout the body (inside & out); protect what they cover; typically reproduce rapidly to replace those damaged by injury or disease; three general types 1. Columnar вЂ“ column-shaped 2. Cuboidal - cube-shaped 3. Squamous вЂ“ flattened B. Connective tissues вЂ“ found throughout body; usually reproduce much more slowly than epithelial tissue; usually composed of living cells surrounded by non-living matrices; functions vary 1. Fibrous connective tissue вЂ“ forms tendons which bind muscles to bones or ligaments that bind bones to other bones 2. Loose connective tissue вЂ“ forms delicate sheets throughout the body that surround & protect other parts & fill spaces 3. Cartilage & bone вЂ“ connective tissues that form skeletons 4. Blood вЂ“ connective tissue that transports materials around the body C. Muscle tissues вЂ“ highly contractile; reproduce more slowly than epithelial tissue; major function is to move internal parts or, along with bones, to move the body as a whole; three types 1. Striated вЂ“ associated with body movements 2. Smooth вЂ“ associated with movements of internal body parts 3. Cardiac- associated with the heart D. Nerve tissues вЂ“ found throughout the body; especially numerous in brains & nerve cords; normally in birds & mammals, nerve tissue cells lose the ability to reproduce prior to birth 1. Primary function is to relay information from external & internal environments to the brain, process that & other information, & relay messages from the brain to all internal body parts III. Tissues, in turn, are organized into organs вЂ“ complex system of tissues that work together to perform common functions; they are the obvious parts of the body A. The stomach is an organ surrounded by connective tissue; contains smooth muscles, nerves, other connective tissues, & blood vessels (also made of different tissue types mentioned above) B. Forearm & skin are also organs IV. Organs are organized into organ systems вЂ“ physiologists focus most of their attention on functioning organ systems V. Organ systems are organized into individuals What Are the Underlying Principles of Physiology?: Multicellular Organisms Are More Than the Sum of Their Parts I. In multicellular organisms, parts work together seamlessly вЂ“ many organ systems may be involved in one process (example: arm movement involves muscles, skeleton, nerves) A. More complex actions involve more systems вЂ“ example: you are hungry so you eat an apple 1. Nerves of the stomach inform the brain that the stomach is empty helping, you decide you are hungry 2. Muscles, nerves, bones are used to pick up the apple, bite, chew, & swallow it 3. Other nerves tell it food is coming, stimulating muscle cells to increase contractions & other stomach cells to release gastric juices 4. Still other nerves dilate blood vessels to bring more blood & oxygen to the stomach & intestines in anticipation of increased activity & eventual nutrients 5. Pancreas monitors blood sugar levels вЂ“ if high, releases hormones telling the liver to store glucose from the apple; if low, other hormones stimulate glucose release into blood for energy 6. Generating energy for all this activity requires O2; supplied courtesy of respiratory system B. All of these systems act & react to each other & the situation in seamless & integrated fashion вЂ“ no single system can handle this simple task alone II. Physiologically, multicellular organisms are synergisms (systems that are more than the sum of their parts) A. Tough to study physiology of whole individuals вЂ“ too complex to contemplate as a single unit B. Thus, the approach has been reductionist вЂ“ break the complexity into small, manageable units that can be more conveniently studied 1. Later, after we understand how the components work, we can put them back together & see how the system functions as a unit 2. Study physiology system by system, but do not forget that they interact synergistically What Are the Underlying Principles of Physiology?: Multicellular Organisms Function Best Within Stable Internal Environments I. Often, an organism's coping with external & internal environments is geared to provide either: A. Survival or 1. Need for survival is obvious; all must cope with predators, elusive nutrients, limited space, competitors, etc. 2. Those that can successfully cope may get enough excess energy, nutrients, & other resources to be able to reproduce вЂ”> they pass individual characteristics on to offspring B. Nearly constant internal conditions - maintenance of nearly constant internal conditions is homeostasis ("steady state"); it is less obvious but equally important need 1. All organisms do their best within a rather narrow range on internal conditions (body temperature, blood glucose levels, water) 2. Maintaining homeostasis in ever-changing environment often involves considerable effort II. Examples of homeostasis A. Snakes are cold-blooded (ectothermic or poikilothermic) animals - heat & thus their body temperature is absorbed from their environment 1. Early on a cool morning, snakes are likely to be found basking on sunny rocks, soaking up the sun -> it warms their internal temperature to get it within optimal ranges 2. Later, as the day warms, snakes seek shade to avoid overheating 3. They regulate their internal temperatures to keep within a rather narrow range by their behavior B. Snakes that fed the night before received a shot of nutrients including glucose as the meal digested 1. All their cells need glucose to fuel activities, but too much in blood has serious consequences 2. Function of the snake's liver is to store glucose 3. Over the next several days, it gradually releases glucose, first to the blood, then to the cells so that there is always enough, but never too much C. Humans & other warm-blooded (endothermic or homeothermic) animals - body temperature is generated internally 1. Maintaining near constant internal temperatures in ever-changing thermal environments is much more complex 2. Involves both behavioral & physiological processes What Are the Underlying Principles of Physiology?: Feedback Systems Control Many Physiological Processes I. Homeostasis is a considerable challenge - organisms must constantly monitor environments & respond correctly to changes with a goal of keeping near constant internal conditions; controlled by feedback II. Feedback loops - used extensively by organisms to help maintain homeostasis (involved in both nervous & endocrine systems) A. Have three major necessary components вЂ“ receptors, control center, effectors B. How do they work? - model being presented is similar to that used by living organisms to help regulate physiological processes 1. Stimuli from an organism's environment are triggers for feedback loops - touch, temperature changes, changes in the chemical makeup of blood, etc. 2. Feedback loop regulates the internal condition of an organism; the condition must be maintained within a certain optimal range; feedback loop helps to maintain this optimum 3. Receptors respond to various stimuli to which the organism may be exposed from its external & internal environments; transfer information to the control center 4. In the control center, information perceived & relayed by receptors is processed 5. Also in the control center, decisions are made as to which stimuli the organism should respond to & what the right response is; may receive many pieces of info for any single process 6. Effectors (like muscles & glands) receive instruction from the control center; only those effectors that are needed respond to instructions from control center 7. Response is governed by the activity of effectors, but they received their instructions from the control center, which responded to stimuli received by receptors 8. As a result of each process in the loop, the internal conditions are maintained or returned to the optimal state; feedback loop is complete C. Two kinds of feedback systems - positive & negative III. Positive feedback - example: microphone on stage connected to speakers; some examples of human activities controlled by positive feedback - hysteria, childbirth, sexual arousal A. If the microphone is too sensitive, it may begin to pick up & broadcast background sounds вЂ”> system begins to whine 1. The more sound it picks up, the louder it broadcasts 2. The louder it broadcasts, the more it picks up, until someone grabs it or pulls the plug B. Positive feedback leads to increasing instability (ever louder noise) & some kind of climactic event 1. Positive feedback enhances or intensifies a process 2. Receptors, control centers, & effectors are also involved C. Human example: some of the events during childbirth (labor) - events begin as the baby enters the birth canal 1. Labor contractions force the baby into the birth canal & begin the birth process; may last for several hours 2. As baby enters birth canal, cervix becomes distended; serves as stimulus for further responses 3. Specialized nerve cells in the uterus (receptors) sense stretching of cervix & uterus & send nerve impulses to the brain (control center) 4. Brain then triggers hypothalamus & pituitary to release more oxytocin (hormone necessary for labor) which travels in the blood to the uterus 5. Uterine muscles (effectors) are stimulated to contract at a greater rate than before (response) 6. Due to the contractions, the baby is pushed farther into the birth canal; at this time, birth is near 7. Cervix & uterus stretch further; has the positive effect of stimulating the release of more oxytocin (positive feedback) 8. Oxytocin release continues until the baby is born; birth terminates positive feedback system IV. Negative feedback - more often seen & more useful to the organism, generally leads to stability; example: home thermostat A. Thermostat is usually found at a place in the home interior that experiences minimal temperature change вЂ”> it senses temperature & controls the furnace 1. If the temperature falls below the predetermined critical temperature (set point) вЂ”> furnace is turned on 2. When the temperature gets above a set point вЂ”> furnace is turned off 3. Thermostat measures only a portion of house's total heat energy; if the temperature in an isolated bedroom is freezing cold & thermostat is warm вЂ”> furnace is not turned on B. Called negative feedback since when the house gets cold, the thermostat causes it to warm; used to slow down, shut off, or reverse a physiological process & return it to an optimal condition C. A human example of negative feedback - maintenance of nearly constant internal temperature 1. Small portion of the hypothalamus is the body's thermostat, located on the floor of the brain about midway between the ears, & richly surrounded with blood vessels 2. Hypothalamus monitors blood temperature; like a thermostat, it measures only a small portion of the body's total heat 3. If blood at the hypothalamus is only a few tenths of a degree below body set point there (~1В° warmer than that under tongue) вЂ”> signals body to shiver, draw in limbs, get restless, etc. 4. When the body gets too warm, the hypothalamus causes the body to sweat 5. These functions, too, are controlled by feedback systems, more complex than a thermostat D. Another human example - college student taking an exam 1. Stress begins - walk into the room where the exam will take place -> blood pressure increases 2. Blood pressure rises - blood pressure is a force exerted by the blood onto walls of blood vessels; an increase in heart rate causes an increase in blood pressure 3. Increase in blood pressure serves as a stimulus perceived by specialized nerve cells (receptors) located in the walls of certain arterioles; cells send signals to the control center (brain) 4. Brain functions as the control center & processes information sent to it by the receptors; interprets thisinformation & sends the appropriate information to the effectors 5. Heart rate decreases - nerve impulses from the brain go to the heart (act as effector); heart responds by beating more slowly, arterioles also dilate, resulting in decreased blood pressure 6. As the heart beats more slowly, it lowers the blood pressure &the amount of blood going to the arterioles & arteries 7. As blood pressure drops, the body returns to optimal condition (negative feedback control) What Are the Underlying Principles of Physiology?: Five Additional Points I. Ultimately, all physiological processes are cellular phenomena A. Nutrients are first absorbed by cells in the small intestine B. Force that moves nutrients from the intestines to other cells of the body are contractions of heart muscle cells that pump blood C. Plasma membranes of cells are of particular importance to physiologic processes - hormones fasten onto the target cells by seeking out specific plasma membrane proteins D. Nutrients & wastes enter & leave cells through the membranes II. Generally speaking, there is a relationship between form & function A. With some exceptions, the shape & structure of the organ, tissue, or cell is related to its function 1. Nerves connect various parts of the body with the brain & other nerves вЂ”> long, thread-like form facilitates function 2. In more complex organisms, the digestive system is long & hollow, which facilitates its functions as a processor of food & collector of nutrients B. Relationship between form & function is a result of evolution 1. As natural selection favors those individuals with adaptive traits, it favors cells, tissues, organs, & organ systems best suited for specific functions 2. In a sense, natural selection molds form to fit function C. Surface-to-volume ratio - often partially responsible for determining the form & function of cell; larger organisms comprise more cells & not larger ones 1. Materials enter & leave cells across the plasma membrane 2. The greater the surface area of this membrane, the more rapidly the cell can exchange substances 3. As a cell increases in size, its volume increases more rapidly than its surface area 4. Bigger cell uses materials & produces wastes more rapidly than it can exchange them with its environment 5. By making smaller cells to encompass the same volume, surface-to-volume ratio remains high (see CD-ROM exercise 10.1) III. Tolerable ranges of internal & external conditions often vary from one organism to another A. Certain species of algae do best in nearly boiling hot springs 1. Others thrive in snow where environmental temperatures are consistently at or below freezing 2. Neither can tolerate the temperatures that are optimal for the other B. Within species, there may be similar individual differences - among humans, certain individuals are better able to cope with cold than others IV. Evolution often results in increasing complexity, but not always A. Example: digestive system 1. Those of simple animals like the jellyfish are considerably less complex than those of more advanced animals such as chordates 2. Free-living flatworms (more advanced than jellyfish, less advanced than chordates) have digestive systems of intermediate complexity B. Exceptions: not common; but there are cases of evolution leading to simplicity rather than complexity 1. Tapeworms are closely related to & obviously evolved from free-living flatworms 2. But they lack digestive systems altogether V. Plants are structurally and physiologically less complex than animals A. The most advanced plants (flowering plants) basically consist of only three organ systems (roots, shoots, leaves) comprised of roughly a dozen tissues B. Chordates have eight principal organ systems & >200 tissue types C. Despite their great differences in complexity, both plants & animals have been equally successful in coping with changing environments How Do Organisms Acquire and Process Nutrition and Wastes?: Digestion in Bacteria, Protists, & Fungi I. Each organism is intimately & continuously connected to our external environments; in fact, each one is totally dependent on its surroundings A. Need energy obtained directly or indirectly from the sun вЂ” or, in rare exceptions, from the Earth 1. Energy is stored in nutrients that provide raw materials for growth, maintenance, other functions 2. Nutrients come from the atmosphere, the Earth, or both B. All organisms вЂ” all cells вЂ” continuously require water C. As organisms consume energy & process nutrients, they produce potentially toxic wastes that go back into the environment where they become another organism's nutrients II. Bacteria, Protists, & Fungi excrete enzymes to break down complex compounds & obtain nutrients A. Nutrients required by bacteria, protozoan protists, & fungi are not readily available 1. These organisms are mostly decomposers or pathogens, living on the carcasses or bodies of larger plants or animals 2. Initially, a victim's compounds are much too large to go through decomposer cell walls & membranes 3. First, they must be broken down into simpler compounds that can be transported into cells B. As needed, bacteria & fungi produce & secrete enzymes into the environment to accomplish this 1. Complex compounds are digested outside of cells 2. Carbohydrates are broken down into simple sugars, proteins into amino acids, fats into fatty acids & glycerol How Do Organisms Acquire and Process Nutrition and Wastes?: Digestion in Multicellular Animals I. Some animals are active hunters; others are more passive & wait for prey to come to them A. Still, regardless of how food is found, there is always a close relationship between structures used for nutrient acquisition & how they function B. Each of the processes involved is regulated by some control process вЂ”> result is maintenance of homeostasis II. Methods of nutrient acquisition A. Tentacles of Hydra which contain stinging cells (nematocysts) are used to capture prey; Hydra belongs to phylum Cnidaria which are characterized by the presence of stinging cells 1. Nematocysts (cnidoblasts) are released when Hydra comes in contact with its prey; they contain toxins that render the prey helpless & paralyzed until it can be processed as food 2. Using its tentacles, the Hydra moves food into the opening of its gastrovascular cavity 3. Once inside the cavity, food is processed & nutrients are absorbed by cells of the animal B. Some organisms live inside another organism, resulting in benefits to both - termite gut symbiosis 1. Relationship between termites & organisms living in their guts is symbiosis (living together) 2. This particular form of symbiosis is called mutualism, since organisms benefit from each other 3. Termites feed on wood, but cannot digest components of wood 4. The microorganisms can; they provide the enzymes necessary to allow termites to digest wood III. Multicellular animals have digestive systems with which to obtain nutrients A. Ingest portions of external environment B. Internally break down complex compounds into simpler ones & absorb useful nutrients C. Return unused portions to the environment IV. Digestive systems show an evolutionary sequence from simpler animals (sponges) through most complex (birds, mammals); perhaps, more than any other physiological system A. Sponges вЂ“ do not really have a digestive system; flagellated cells lining their internal spaces create currents that suck water into & through their bodies (filter-feeding) 1. Food items are picked up by endocytosis & digested intracellularly 2. Smaller compounds diffuse into cells or are picked up by active transport B. Jellyfish & flatworms вЂ“ have digestive systems with only one opening 1. Food swallowed into a large cavity, much branched in flatworms 2. Digestive enzymes secreted into the cavity break down complex compounds into simpler ones that can be absorbed 3. After a time, undigested material & metabolic wastes are expelled through mouth into the environment C. Roundworms a complete digestive systems (& rest of animal phyla, too), tubes equipped with two openings (mouth & anus) 1. Roundworm system is a simple tube, uniform throughout its length; swallowed food moves along the tube & mixes with enzymes 2. Usable nutrients are absorbed, undigested material goes out of anus as feces 3. Complete digestive system allows the processing of more than one meal at a time; as nutrients from one meal are absorbed farther along the tube, new meal can be swallowed at the head D. Segmented worms вЂ“ digestive tube runs the length of the body & is divided into a series of specialized regions: pharynx, esophagus, crop, gizzard, intestine 1. Food passes along the tract, is chewed, stored, digested, absorbed, then excreted (assembly line) E. Mollusks, arthropods, vertebrates вЂ“ these digestive systems are further refined 1. Have long, differentiated tubes that also process food in assembly-line fashion 2. Unlike segmented worms, digestive tubes are coiled & twisted, their lengths are much greater than the length of the animal as a whole; allows for more complete & efficient digestion 3. Accessory organs (livers, gall bladders, pancreases) appear & enhance digestion further V. Some animals establish symbiotic (intimate) relationships with other organisms to improve their chances of obtaining nutrients A. Some corals house green algae whose photosynthetic products feed both coral & algae B. Animals that feed on cellulose need particular assistance вЂ“ cellulose is abundant in many ecosystems as a major component of algal & plant cell walls 1. Few organisms make enzymes able to break down cellulose into simple sugars that diffuse across cell membranes; major exception - assorted bacteria & protozoa that can digest it 2. Cows, rabbits, termites вЂ“ support large numbers of symbiotic microbes in their digestive tracts C. Humans have intestinal symbionts вЂ“ benign strains of Escherichia coli crowd our large intestines, help absorb water, & produce certain vitamins, among other functions How Do Organisms Acquire and Process Nutrition and Wastes?: Animals Use Respiration to Obtain the Gases They Need I. Most organisms need a reliable O2 source for respiration, must get rid of CO2, the respiration waste product A. There are exceptions вЂ“ Archaea & some primitive fungi (yeasts) find O2 toxic 1. In initial Earth atmosphere (no O2), life forms evolved totally intolerant of this most reactive of elements 2. Their direct descendants are still intolerant вЂ“ live in bottom muds, carcasses, intestinal tracts, & other environments where O2 can be avoided II. How do organisms obtain O2 & get rid of CO2? вЂ“ short answer is by diffusion A. For single-celled & smaller multicelled organisms вЂ”> nothing else is needed 1. Jellyfish & flatworms get fairly big without a need for specialized respiratory systems 2. With large internal spaces & body shape (in flatworms), none of their internal cells are very far from the environment; O2 diffuses in & CO2 out to meet cellular needs B. In more advanced organisms, the need grew for a specialized, efficient respiratory system to assist diffusion вЂ“ why? 1. The organisms became larger & bulkier 2. Their activity levels & thus their energy requirements increased 3. Their bodies became covered with impermeable coverings (bark, shells, cuticle, scales, bony plates, skin) C. Among animals, there are basically three types of respiratory systems 1. Skin - the outer body covering 2. Gills - outpocketings of tissue that work best in water 3. Lungs - inpocketings of tissue that work best in air D. All of these respiratory systems share two characteristics 1. Extensive surface areas 2. Thin, moist cell layers that facilitate diffusion E. Evolutionary relationships between respiratory systems is much less straightforward than with digestive systems; in fact, may have evolved independently at least three times in terrestrial animals III. Many invertebrates & some vertebrates (amphibians) breathe through their skin A. Small blood vessels (capillaries) bring blood rich in CO2 & deficient in O2 close to the skin's surface where gas exchange takes place by diffusion B. In most frogs & salamanders, respiration through the skin is only a backup system 1. It meets their needs during periods of inactivity (during hibernation) 2. With increased activity, needs increase & lungs or gills become essential 3. One large group of salamanders have neither gills nor lungs; they respire only through skin 4. For skin to work as a respiratory organ, skin must be kept moist IV. Primitive gills, complex outpocketings of tissue that hang out in the water, are especially common in aquatic insect larvae & some salamanders A. Salamanders - gills consist of thin coverings & thin blood vessels; diffusion in & out is straightforward 1. Problems arise because these delicate tissues are unprotected & difficult to move 2. Gill movement becomes necessary as immediately surrounding water gets deficient in O2 & CO2 builds up B. Aquatic mollusks & fish - gills are internalized & covered with protective body parts creating immediate problem of how to move replenishing water at least periodically in past gills 1. Clams use ciliated tissues to move water through incurrent siphons, past gills, & out through excurrent siphons 2. Water also passes mouths, excretory pores, reproductive pores, & anuses from which clams obtain food & into which they deposit wastes & gametes C. Squids & octopuses - suck water into mantle cavities, where gills are located D. Highly active sharks & bony fish (e.g. tuna) - water flows in through continuously open mouths, past gills, & out through gill slits (several in sharks; only one large one in bony fish) 1. Most bony fish continuously gulp water, forcing it past gills & out through gill slits 2. In this way, they supply gill with fresh water during periods of relative inactivity 3. In all these animals, as refreshed water passes over gills, O2 diffuses in & CO2 diffuses out V. Lungs are the respiratory tissue of choice among terrestrial animals - big problem is the need to protect respiratory tissues from drying out A. Lungs are protected from drying out, since they are internal structures into which air enters through one or relatively few openings, but this only minimizes water loss 1. Replenishing water lost through respiratory surfaces is the continuous price paid by all terrestrial organisms B. Most primitive lungs (terrestrial snails & primitive arthropods) - simple internal spaces connected to the surface by openings; no muscles move gases in & out; rather, oxygen diffuses in & CO2 out C. Insects - have tracheae (complex systems of tubes leading from external world to internal body regions) 1. External openings of tracheae (spiracles) are found mainly on the insect's abdomen 2. Gas exchange takes place in the smallest of these tubes usually located furthest from spiracles 3. In most insects, flow is passive as gases diffuse in & out 4. In more active insects (e.g. grasshoppers) muscles pump air in & out of the trachea D. Pulmonary lungs of vertebrates (lungfish, amphibians, reptiles, birds, mammals) - there are special muscles that move air in & out 1. Muscles of the mouth region in fish & amphibians 2. Rib muscles in reptiles 3. Both rib muscles & air sacs in birds 4. Rib muscles & diaphragms in mammals E. Lungs of lungfish & amphibians - structurally rather simple, consisting of little more than simple sacs & connecting tubes (larger trachea & smaller bronchi) F. Internal structure is much more complex in birds & mammals 1. Lungs of birds are connected to internal spaces that increase buoyancy (useful when flying) & work like bellows, pumping air into lungs 2. In both birds & mammals, lungs are composed of myriad small pockets, alveoli, that vastly increase surface areas through which gaseous exchanges take place How Do Organisms Acquire and Process Nutrition and Wastes?: Circulatory Systems Move Nutrients, Gases, and Other Materials Through the Bodies of Complex Animals I. Once materials from the outside environment are acquired/internalized & processed, next problem is to distribute them to needy cells & tissues of animal; often some kind of circulatory system is involved A. The heart is a specialized organ that pumps fluids in animal circulatory systems; there is no single type of heart found among animals B. Heart & circulatory systems evolved in conjunction with other systems, like respiratory system C. How has circulation been handled in the animal world? (see below) II. Small animals have little need for special circulatory systems A. Sponges - flagellated cells circulate water throughout their internal spaces; allows exchange of nutrients for metabolic wastes & O2 for CO2, using nothing more than diffusion & osmosis B. Jellyfish & flatworms 1. Digestive systems are large or complexly branched internal spaces 2. Thus, no cell is far removed from either its external environment or the internal digestive system, so materials & gases are exchanged by diffusion & osmosis III. Larger, more complex animals - moving materials through their bodies is a challenge A. Internal cells are so far away from the external environment that simple diffusion will not suffice B. Segmented worms - special transport systems carry nutrients & O2 from environment to cells & metabolic wastes like CO2 to environment from cells (major circulatory system functions) C. Basically two types of circulatory system 1. Open circulatory system - found in arthropods, blood periodically leaves blood vessels, bathes tissues, & is recollected into the vessels 2. Closed circulatory system - found in many other animals, including humans; blood never leaves the blood vessels D. In more complex animals, the circulatory system carries products made by the animals' cells & tissues (hormones, disease-fighting proteins, and cells) IV. Circulatory systems have three major components: vessels, blood, & hearts; each evolved from rather simple components in primitive worms to highly complex ones in chordates V. The evolution of the heart - how does the heart differ from fish through mammals? A. Heart of a typical fish contains two chambers (an atrium & a ventricle); fish use gills to exchange oxygen & CO2 with the environment 1. Circulation is accomplished by one circuit through the heart 2. Atrium receives blood from systemic capillaries (high in CO2 & low in O2 ) 3. Blood is then pumped by the ventricles to the gills where CO2 is removed & O2 is added 4. Oxygen-rich blood then flows from the gills to cells & tissues of fish B. Amphibian heart contains three chambers (two atria & one ventricle); there are two atria, because there are two circuits of circulation: one from lungs & the other from the rest of the body 1. There is some mixing of oxygen-rich & oxygen-poor blood in the single ventricle 2. In addition to using the circulatory system for gas exchange, many amphibians also exchange gases across skin surface C. Reptile heart is very similar to that of amphibians in that there are two atria & one ventricle 1. In reptilian heart, the ventricle is partially separated into two chambers 2, As with amphibians, there is a mixing of oxygen-rich & oxygen-poor blood in the ventricle 3. However, when blood leaves the ventricle, it is first channeled to the pulmonary system & then secondarily to the systemic system 4. This increases the possibility of O2 -poor blood going to lungs instead of into systemic system D. Mammalian heart has four complete chambers: two atria & two ventricles 1. Blood from the body enters the right atrium & is pumped to the lungs by the right ventricle 2. Blood from the lungs enters the left atrium & is pumped to the body by the left ventricle 3. During human fetal development, lungs do not function for gas exchange 4. A hole in the wall between the two atria allows blood to pass from the right atrium into the left atrium, thus bypassing the pulmonary system How Do Organisms Acquire and Process Nutrition and Wastes?: Animals Must Maintain Proper Water Balance I. Water is a precious necessity - all minerals & chemicals required by an organism must be dissolved in water in order to move into cells, but too much of a good thing can be bad A. In too much water, needed nutrients become too dilute & acquiring them becomes difficult, if not impossible B. Not much an organism can do to to control the amount of water in its environment, but can control water in its internal environment II. Proper concentrations of solutes & water in an animal's body fluids quite often differ from those in the environment A. Diffusion & osmosis constantly tend to minimize these imbalances - this creates a major problem for most animals B. Mechanisms used to overcome the problem depend partly on evolutionary history & environment 1. Generally, mechanisms available to vertebrates are more advanced than those in invertebrates 2. Problems experienced in salt water differ from those in fresh water & those on land III. Cells & tissues of many marine invertebrates & in sharks & rays are isotonic to environments (concentrations of solutes & water inside matches the concentrations outside) A. They are osmotically balanced & experience no net increase or decrease in water B. Often, this balance is achieved by controlling amino acid concentration within cells 1. By reducing amino acid concentrations slightly (perhaps by protein synthesis), cell voids H2O 2. Increasing amino acid concentrations has the opposite effect C. Some marine invertebrates (like spiny-skinned echinoderms) are isotonic since they lack the ability to regulate any individual ions -> H2O & solute concentrations balances that of the environment IV. Other marine invertebrates live in hypertonic environments - solute concentration is higher (& water lower) in the environment than in the tissues A. Show marked concentration gradients between the tissues & the environment of at least a few solutes; often differences related to their environments & individual life styles 1. Jellyfish Aurelia regulates its sulfate ions at levels considerably below those of its environment 2. Sulfate is a relatively heavy ion & reducing its concentration in tissues reduces overall density, making animal more buoyant 3. Many marine arthropods that have the ability to move quickly show lower than environmental magnesium concentrations (this ion decreases muscular activity) B. Most marine vertebrates (especially bony fish) also live in hypertonic environments 1. Tend to lose water by osmosis through the gills (rest of the body is protected from water loss by scales, skin, or layers of slime) & in their urine 2. Replace lost water by drinking copious quantities of water, creating a problem of elimination of accompanying solutes 3. Gills rid fish of some solutes by active transport; others concentrated in, voided with urine V. Generally, brackish & fresh water invertebrates live in hypotonic environments (solute concentrations highest in their tissues) & show lower overall solute concentrations than marine counterparts A. Lessens diffusion & osmotic gradients; simplifies the challenge of maintaining balance with the environment B. Since environment is hypotonic, they tend to gain water & lose solutes 1. Excess water is generally voided by special excretory organs - kidneys in vertebrates & similar structures in invertebrates 2. Keeping proper amount of solutes is more of a problem - usually, these are recaptured from the environment by active transport through gills or intestines C. Fresh water fish face the same problems as invertebrates вЂ”> they live in hypotonic environments & tend to gain water 1. Water enters by gills & is eliminated by the kidneys 2. Typically, urine is highly diluted; still some solutes are lost in this manner 3. Some lost solutes are replaced in food they eat, by their normal digestion, & active transport 4. Gills both lose solutes by diffusion & recover them by active transport VI. Terrestrial animals face a double-edged problem with respect to water - water is limiting in terrestrial habitats & because of chronic dryness, the tendency to lose water is intensified A. Animals lose water through evaporation from skin & respiratory surfaces & in feces, urine, or special secretions B. To obtain water, they drink it, soak it up through skin, extract it from food (even driest grain is over half water), or metabolize it (product of respiration) C. Terrestrial animals have five ways in which they can reduce water loss 1. Seek out moist environments - earthworms do best in damp soil; frogs, salamanders, & many invertebrates live close to water, easing the necessity of maintaining moist skin 2. Seek habitats where humidity is high (lowers evaporation losses) - burrows in soil or wood, under logs or rocks, in leaf litter; often teem with invertebrates & more than a few vertebrates 3. Some are active mainly at night when humidity is highest 4. Body coverings protect them from H2O loss (snail shells; arthropod exoskeletons; reptile scaly skin; bird feathers, impermeable skin; many insects, a few amphibians - waxy secretions) 5. Animals in driest environments (meal worms in dry flour to desert mammals like kangaroo rats) often have special mechanisms (reduce H2O loss in feces, concentrate wastes in urine) How Do Organisms Acquire and Process Nutrition and Wastes?: Organisms Must Get Rid of Metabolic Wastes I. Cellular metabolism produces waste compounds that must be disposed of A. One of the most serious ones is ammonia, a nitrogen-containing compound made when proteins & amino acids are metabolized; ammonia is highly poisonous & most cells must get rid of it quickly B. Other waste compounds are not particularly toxic, but their buildup could interfere with normal cellular processes C. If nothing else, accumulation of these compounds could cause osmotic imbalances II. Individual cells & small organisms rely solely on diffusion to get rid of unwanted wastes III. Marine sponges, jellyfish, tapeworms, & spiny-skinned animals have no special excretory organs & depend entirely on diffusion of wastes through body surfaces IV. Larger organisms - metabolic waste disposal is a more complex challenge, special excretory systems are needed; apparently excretory organs evolved three separate times - worms, mollusks, vertebrates A. Flat- round- & segmented worms have numerous open or closed tubes that may be simple or branched; collect wastes & fluids & eventually dispose of them through numerous pores B. Mollusks have paired excretory organs, tube-like affairs that collect wastes & dump them into the mantle cavity & ultimately into the environment C. Insect excretory systems consist of Malpighian tubules, two to several hundred tubules that lie in the body cavity & open into the intestine V. Much more is known about how these insect systems work than other invertebrate excretory systems A. Waste products, especially uric acid, enter tubules from the body cavity by active transport, simple diffusion, & osmosis; once in the intestine, uric acid precipitates into semi-solid material 1. Much water & some solutes are reabsorbed; what remains is excreted along with feces B. Insects that eat mainly fresh vegetation that is high in water content produce copious amounts of watery wastes C. Insects that eat primarily dry food produce little waste water 1. Extreme among insects are meal worms like Tenebrio that eat nothing but dry flour, yet receive all the water they need 2. Meal worms are extremely efficient at reabsorbing water VI. Vertebrates have kidneys to get rid of their metabolic wastes; to function properly, kidneys depend primarily on four processes - diffusion, osmosis, active transport, filtration How Do Organisms Monitor Their Environments and Move From Place to Place?: Introduction I. External environments are frequently challenging so organisms have evolved mechanisms with which to minimize, avoid, work with, or overcome such challenges A. Predators & competitors come & go B. Surroundings become too hot, too dry, or contaminated C. Gravity imposes limits on how large organisms can become & how efficiently they can move II. Organisms have four options in the face of such challenges A. Isolate themselves within thick shells or similar structures B. Seek shelter C. Adjust to changing conditions D. Move to more favorable environments III. Each option has limits A. Isolation cannot be so extreme that organisms lose complete contact with the environment B. Organisms can stay sheltered only so long; must eventually at least seek nutrients C. Adjustments to environmental changes often take time & require that environments change slowly IV. Often these options work against each other - thick body coverings protect but also impede movement; sometimes, however, they work together How Do Organisms Move From Place to Place?: Microbes, Thick Cell Walls and Movement I. Organisms move for a variety of reasons - to seek shelter, escape harm, find more favorable environments, etc. II. Early on, bacteria evolved thick cell walls as barriers that hold the environment at bay - these thick cell walls also hold water, nutrients, & other chemicals within cells A. Bacteria are also surprisingly mobile - their flagellae & ability to glide (not well understood) provide movement B. Ability to move rapidly even with thick cell walls appears to be helped by their small size which in watery surroundings minimizes gravity & maximizes buoyancy C. Compared to those of other microbes, bacterial flagellae are relatively short, thin, & stiff 1. They rotate at the base, close to where they join the cell wall 2. As they rotate, the tips spin like propellers, pulling the bacteria from place to place III. Many protistan algae share thick cell walls & methods of movement with their bacterial ancestors A. They glide or use flagellae, but their flagellae are structurally quite different from those of bacteria B. Typically, protistan algae are found in aquatic environments where gravity effects are minimized IV. Protozoan protists have no cell walls & are even more highly mobile (unlike bacteria & algae); basically four groups of protozoa differentiated by their means of locomotion A. Zoomastigina - move by flagella (structurally, functionally similar to those of algae); ex.: Euglena B. Ciliophora - move by cilia (like numerous, short flagellae); 1000s cover the surface, beat in unison to produce rapid complex motion (back, forward, twists, spirals typical); ex.: paramecia C. Sarcodina - amoeboid protozoans; move by means of pseudopodia (false feet) 1. Cytoplasm streams in particular direction, forming first a bulge that becomes foot-like extension into which rest of cytoplasm streams 2. Pseudopodia do not last long; new ones form whenever amoeba adjusts direction of movement 3. Amoebas are often larger in size & thus their movements are slower 4. Most live in bottom muds & damp soils, but some live suspended in water 5. Due to their size, gravity should be a problem, but they evolved silicon dioxide (glass) or calcium carbonate shells (gas-filled or with elaborate spines); hold them suspended D. Sporozoa - have lost all means of locomotion; all are parasites, depend on other organisms to carry them from place to place How Do Organisms Move From Place to Place?: Movement in Animals I. Animals are generally quite sensitive & highly responsive to environmental change A. Typically they are highly mobile (this ability is used to distinguish animals from plants) B. Animals retained & built on methods of movements inherited from protozoan-like ancestors; ciliated & flagellated tissues are found in all animal phyla 1. Sperm are flagellated 2. Ciliated tissues move eggs through reproductive systems, foreign objects out of respiratory system, & are associated with many animal sensory systems 3. Cilia along ventral (belly) surface propel free-living flatworms in smooth, gliding movements 4. Amoeboid cells are ambulatory tissues in many animals like sponges, where they apparently transport materials from the digestive system to other cells 5. In vertebrates, amoeboid cells comprise white blood cells & fight disease II. For most animals, movements require additional specialized tissues, muscles (cells rich in proteins actin & myosin) arranged as fibers A. When actin & myosin interact, they slide over each other which, in effect, contracts cell B. In order to produce motion, muscles must be connected to something 1. Typically, long fibrous muscles are connected to other body parts by connective tissue 2. One end of the muscle is anchored, the other is connected to the part of the body that the muscle is intended to move C. One of the simplest types of gross muscle movement is seen in roundworms 1. Longitudinal muscles run length-wise & are attached at various places along cylindrical bodies 2. Contracting muscles along one side shortens cylinder on that side only; twists worm into a "C" 3. If, as those muscles relax, those on the opposite side contract -> worm is twisted into a backward "C" 4. If the muscles of the anterior (head) end are contracted opposite those of the posterior (tail) end вЂ”> the body undulates in "S" shape, first in one direction, then in the other 5. H2O-filled cavity within the worm's body keeps it from collapsing; H2O incompressibility provides a type of skeleton (hydrostatic); useful to soft-bodied animals (& soft tissues) 6. This simple motion requires careful coordination, timing of muscle action (by nervous system) D. Two important points in the roundworm example (typical of all multicellular organisms) 1. Muscles only contract; they do not push 2. Different sets of muscles work as antagonists (one set moves part of the worm's body in one direction, while another set moves it in the opposite direction) E. Earthworms have longitudinal muscles whose antagonists are circular muscles that run around the body associated with each body segment 1. When longitudinal muscles contract, the worm's body shortens 2. When circular muscles contract, the worm's body lengthens 3. Bristles on ventral surface point toward tail, dig into substrate, keep the worm moving forward III. ~600 million years ago, some multicellular animals evolved hard parts (shells & skeletons) A. Advantages & disadvantages 1. Hard parts offer great protection from a variety of environmental challenges 2. Hard parts also contributed to animal movement вЂ”> convenient places for muscles to attach 3. On debit side, hard parts are heavy & difficult to move B. Some of the first animals to evolve shells were mollusks (clams, mussels, snails) 1. Whenever environments become threatening, the shells are closed with special muscles 2. Not all shells are obvious (in slugs, squids, octopuses, very small ones) -> minimizes weight, sacrifices tissue protection, but still provides convenient sites for key muscle group attachment 3. These mollusks have much greater mobility than their more fully shelled counterparts C. Much of the success of arthropods (most successful animal phylum) is due in large part to their exoskeletons (external skeletons) 1. Exoskeleton provides great protection & nearly an infinite number of potential sites on which to anchor muscles 2. As a result, various arthropods swim, walk, fly, jump, & burrow on legs, wings, & fins; other appendages become pinchers, claspers, antennae, mouth parts 3. Movements of all these appendages are controlled with delicate, complex muscle groups fastened at strategic locations to the exoskeleton 4. Exoskeletons are heavy & impose rather severe limits as to how large arthropods can become D. In most chordates, particularly vertebrates, skeletons are internal 1. The cost of endoskeletons is that more soft tissue is directly exposed to the environment 2. Benefit is that they weigh less & are easier to move, permitting individuals of larger size 3. Endoskeletons facilitate growth, but still provide numerous attachment sites for muscles which facilitate complex body movements; ex.: human How Do Organisms Monitor Their Environment?: Introduction I. In order to live successfully in ever-changing, often unpredictable, potentially dangerous environments in which resources are limiting & competition keen, organisms need information II. Three questions are constantly important A. What is the current state of the environment? B. What changes are taking place? C. What adjustments need to be made, internally & externally, to adapt to these changes? III. For multicellular organisms, the questions are equally valid for external surroundings & internal conditions IV. Two physiologic systems are devoted to answering these questions A. One is chemical - the only system available to microbes, fungi, & plants B. The other is cellular - the nervous system found in animals How Do Organisms Monitor Their Environment?: Chemical Monitoring & Hormones I. Microbes & fungi may monitor and respond to their environments chemically A. The most primitive environmental monitoring system is chemical - all cells probably respond to their environments chemically - ex.: microbes assess the presence or absence of lactose chemically 1. Some microbes respond to sudden lactose introduction into the environment by making correct enzymes with which to digest it 2. When the lactose is no longer present вЂ”> the enzyme is no longer made B. Certain microbes practice a form of primitive sexual reproduction; cells come together & form cytoplasmic bridge (pilus) between them & exchange nuclear material 1. How does the microbe know it is contacting the appropriate partner? - surface proteins in the cell membrane are apparently key 2. If surface proteins are compatible, partners are appropriate; if not microbes move on C. Fungal mold Philobus is particularly common in cow pastures where it feasts on feces 1. After a time, fruiting bodies form, stalks that spew spores up to 2 meters - not a random event 2. Photosensitive cells control the growth of stalks so that they point toward the sun (away from ground), ensuring that the spores are spewed well away from the parent cow patty 3. Control agent is probably a chemical sensitive to light that controls stalk growth 4. Spores land on grass, are eaten by another herbivore; some survive trip through digestive system & are deposited to start over again II. Hormones - important in chemically-based monitoring & control systems in animals (endocrine system) A. Hormones monitor & control functions that, compared to nerves, happen slowly over a period of several days or weeks - growth, maturity, reproduction, many metabolic functions B. Many hormones made by humans & other vertebrates are also found in invertebrates & protists 1. Adrenaline (involved in human fight or flight responses) & endorphins (natural pain killers) are found in protozoans 2. Insulin (controls human blood sugar levels) & cholecystokinin (controls human gall bladder activity) are found in many invertebrates C. We do not know what these hormones do in protists & invertebrates; their presence suggests: 1. Vertebrate hormones, even human ones, are ancient in origin; they inherited their hormones from ancestors, but they have redefined the physiological contexts in which they are useful 2. Life is conservative; a chemical found useful by one organism is likely to be useful to another III. Hormones often work together to control complex animal phenomena (ex.: insect metamorphosis) A. Ecdysone controls molting in arthropods; as they mature, they outgrow their exoskeletons, which periodically must be shed & new ones grown 1. In insects, each life stage between molts is an instar; insects may go through several before becoming adults 2. Later instars not only grown & molt but take on adult characteristics such as wings & the ability to reproduce B. Maturation is controlled by juvenile hormone - its presence in early instars inhibits maturation & maintains larval condition; in later instars, it is not secreted & maturation occurs (pupa forms) IV. Hormonal control can be complicated - in humans, five interacting hormones control blood sugar levels & female reproductive activities involve no less than seven interacting hormones How Do Organisms Monitor Their Environment?: Introduction to the Nervous System I. Animals have nervous systems A. For animals, quick adjustment to environmental conditions is often essential to survival - nervous systems have evolved to handle this B. Vertebrates - billions of neurons, the basic cellular unit of nervous system, connect all parts of the body with the animal's brain 1. Brain assesses sensory inputs from the animal's internal & external environments & initiates appropriate responses 2. How animals respond to perceived environmental changes is often controlled by motor nerves that carry information from the brain to the body II. Most animals have the same modes of sensing as humans - touch, site, hearing, taste, smell; some have additional sensory systems A. Lateral line system in fish that senses pressure B. Facial pits of some snakes that sense infrared radiation C. Special skin receptors in certain fish (e.g. electric eels) & amphibians that detect electric fields III. As with the digestive system, animal nervous system evolution is a study of increasing complexity How Do Organisms Monitor Their Environment?: Evolution of the Nervous System I. Sponges, thought to be the simplest, most ancient of animals lack nervous systems altogether; yet their cells & tissues are still able to communicate A. On the inside of their bodies, specialized, flagellated cells (collar cells) create currents that suck water in through myriad incurrent pores 1. Water circulates through the sponge's body & exits out through a few larger excurrent pores 2. As water travels through the body, nutrients & O2 are extracted by cells & wastes, CO2, & gametes are added for removal from body B. If you place weak acids or other potentially dangerous substances just outside the sponge, they will start to enter 1. Flagellae stop, reverse direction, & throw the noxious substance out, protecting the sponge 2. How the sponge detects noxious substances & controls flagella is not well understood 3. Cells of the sponge are coordinated without the benefit of a nervous system II. Jellyfish & relatives - have primitive a nervous system consisting of a net-like pattern of neurons that control muscles A. Unlike more complex animals, impulses in jellyfish nerves flow in both directions B. Control pulsing movements of medusal (bell-shaped) jellyfish & complex crawling movements of polyp (barrel-shaped) jellyfish C. Nothing like a brain in these animals, but the number of nerves increases near the mouth III. Free-living flatworms like Planaria have ladder-shaped nervous systems running the length of their otherwise unsegmented bodies A. Where the legs of these ladders meet the rungs, knobs of neurons, called ganglia, form B. Near worm head end, ganglia connected to eyespots are unusually large - precursors of brains C. Flatworms learn to find food in a simple T-maze, simplest animals for which learning is shown IV. Segmented worms (e.g. earthworms) have a single nerve cord running the length of their bodies close to the ventral surface A. In every body segment, lateral nerves branch off, controlling muscle & other organ activities in that segment B. At the anterior (head) end, enlarged ganglia in several segments form a proper brain V. Invertebrates more complex than segmented worms have basically the same kind of nervous system A. Lateral nerves regularly branch off of the ventral nerve cord B. As an animals's complexity increases, so does that of its lateral nerves & especially its brain VI. Vertebrates have the most complex nervous system of all, especially their brains A. Pattern is basically the same as in advanced invertebrates, lateral nerves regularly branch off of a central nerve cord; brain is located near the head end B. In vertebrates, the nerve cord runs near the dorsal (back) surface How Do Organisms Reproduce?: Introduction I. Purpose of life is to reproduce - life can persist only through reproduction A. Only species that can consistently produce enough offspring to replace losses due to disease, predation, accidents, aging, etc. can persist B. Those that do not become extinct II Individuals that are alive today came into existence through some form of reproduction A. Their parents were successful in the sense that not only did they survive for a time, but they also garnered enough resources & energy to be able to produce offspring & the offspring survived B. Evolution tells us that these offspring tend to possess characteristics appropriate to their particular environments C. Soon it will be the offspring's turn to pass genes & characteristics on to the next generation, etc. in successful species III. Two kinds of reproduction: asexual (does not require gametes) & sexual (utilizes gametes, reproductive cells, that unite to form a zygote) A. Some cells simply split in two B. Others have complex courtship & reproductive strategies that may last for several hours How Do Organisms Reproduce?: Asexual Reproduction Is The Most Common Method I. Under favorable environmental conditions, other activities curtailed while cell divides in two A. In prokaryotic cells & some protists, process is called binary fission; mitosis in all others 1. Process forms two identical cells 2. Can be a very rapid process & may occur every 20 minutes or less 3. Many of these organisms can also reproduce by sexual reproduction B. In some bacteria, single-celled protists, & single-celled fungi, resultant cells immediately separate & become totally independent organisms 1. Those cells that fail to separate become colonies of individuals joined by shared sides 2. Even in colonies, each individual cell is capable of independent existence II. Some animals also reproduce by asexual reproduction A. Starfish fragments regenerate into complete adult starfish B. Hydra bud off new individuals; grow from the surface of an adult; these buds enlarge & then detach and become free-living organisms C. Asexual reproduction also occurs in plants (Ch. 12) III. All organisms, no matter how sophisticated, depend, at least partially, on asexual reproduction A. Mechanism by which single-celled zygotes (fertilized gametes) become multicellular adults B. Through mitosis, multicellular animals replace lost tissues 1. Lizards regrow lost tails 2. Salamanders replace lost leg C. Humans have lost much of the ability to replace lost parts 1. Nerve cells have totally lost the ability to reproduce (undergo mitosis) long before birth 2. Other human tissues can reproduce by mitosis - replace stomach lining each day, make 180 trillion new red blood cells/day How Do Organisms Reproduce?: An Introduction to Sexual Reproduction I. Sexual reproduction evolved among bacteria, protists, & fungi A. Many microbes are not totally dependent on asexual reproduction; ex.: conjugation - simplest form of sexual reproduction; seen in bacteria B. Cytoplasmic bridge (pilus) develops between two individuals through which one-way exchange of genetic material occurs; well-studied in lab, not much known about it in nature C. In an evolutionary sense, this is the birth of sexual reproduction II. Overview of sexual reproduction in eukaryotes - formation of gametes begins the process; gametes then unite to form a zygote, which proceeds to divide A. Gametes - haploid, unite to form a diploid zygote; unlike animals & other organisms, plant gametes are a product of mitosis & not meiosis 1. Characteristics of gametes vary from organism to organism 2. In animals & plants, some gametes (usually the male gamete) have locomotive structures B. Division results in multicelled diploid organism - involves the addition of new cells & also changes that give cells their unique properties III. In eukaryotes, reproduction becomes very complex; almost as many different patterns as there are species; but the patterns reduce to three major life cycle themes A. Diploid cycle - most familiar, seen in all animals & some protists & algae 1. All cells of an organism are diploid except for gametes, which remain single-celled haploid entities until fertilization 2. Resultant zygote develops into a new individual, diploid except for its gametes B. Haploid cycle - frequently seen in fungi & some algae; throughout most of their lives, organisms are comprised of haploid cells 1. Often budding & other types of asexual reproduction results in new haploid individuals 2. When they reproduce sexually, a limited number of cells from two individuals merge, fuse nuclei, & become diploid 3. Often immediately undergo meiosis & resulting haploid spores are dispersed, usually by wind or water, to grow into new haploid individuals C. Alternating cycle - all plants & some algae; typically two distinct generations 1. Haploid gametophyte (gamete-producing) 2. Diploid sporophyte (spore-producing) - cells undergo meiosis & become spores that grow into female & male gametophytes that, in turn, produce gametes that fuse & grow into sporophytes 3. In algae & primitive plants (mosses, ferns) - two generations occur in completely separate individuals 4. In more advanced plants, the two generations occur in the same individual; gametophyte is greatly reduced but is still a multicellular entity How Do Organisms Reproduce?: Marine and Aquatic Invertebrates I. Sexual reproduction in water is relatively easy вЂ“ no drying of gametes; big problem is timing A. As gametes, organisms are virtually defenseless & very vulnerable, especially to drying out reproducing in water minimizes this problem 1. Many aquatic organisms spew gametes into the environment where they must find each other to allow fertilization 2. Timing is everything & gamete release is far from random B. In most cases, all individuals of a particular species are reproductively active at the same time вЂ”> release gametes together on cue II. Why are water species reproductively active at the same time; what is the cue for coordinated gamete release? A. Simultaneous release of gametes has two advantages 1. Facilitates fertilization, since sperm & eggs are able to unite & be available at the same time 2. Foils predators (floods market); by the time predators detect & respond to so much food, event is over; enough successful fertilizations to perpetuate the species, but predators can anticipate B. In tropical sponges, jellyfish, squid, clams, & others, it appears to be a lunar cycle 1. Every 28 days, all individuals of a given species release gametes 2. Each species has its own phase of the cycle to respond to - some release when the moon is full, others during a new moon, still others somewhere in between C. Away from the tropics, timing & release of gametes is more complex 1. Gametes are released only during certain times of the year, typically warm months 2. Within this time span, precise gamete release is again correlated to the phases of the moon III. Among aquatic organisms, there is considerable variation in the amounts of yolk (sources of energy & nutrients for developing embryos) eggs contain A. Eggs of many spiny-skinned animals contain virtually no yolk B. Those of other invertebrates have considerable yolk C. All manners of variation between the extremes How Do Organisms Reproduce?: Invertebrates on Land I. Many animals successfully reproduce on land вЂ“ independently, several animal groups (segmented worms, mollusks, arthropods, & chordates [vertebrates]), acquired the ability to survive on land II. Each followed similar evolutionary paths A. Each group originated in the ocean & evolved successively in brackish water (estuaries, salt water marshes), fresh water (rivers, lakes, especially wetlands), & finally terrestrial habitats B. Each also evolved mechanisms to protect gametes & developing young from rising dryness III. Many segmented worms are hermaphroditic (both male & female reproductive systems) A. Mating usually involves two individuals exchanging sperm which each stores internally for a time B. After a time, each individual develops a collar-like structure around the outside of the body near the head end into which eggs & sperm are eventually released 1. Thus, after true copulation, fertilization occurs externally 2. Later, the collar is shed as a cocoon in which subsequent development takes place C. No larval stages; what hatches is essentially a miniature adult IV. Mollusks represented on land by terrestrial snails & slugs вЂ“ largely hermaphroditic & exchange sperm during mating; external fertilization occurs immediately A. Eggs contain considerable yolk to nourish developing embryos B. Development is direct (no larval stage) C. Often, embryos have numerous cilia that circulate the internal contents of the egg, bringing nutrients & oxygen to & wastes away from embryo D. Most terrestrial mollusks keep eggs in their mantle cavity; others lay them immersed in bag of slime in damp soil or rotting vegetation V. Arthropod reproduction has many variations; exceptions are the rule; a reflection of their success вЂ“ example: insects, the most successful arthropods A. Insect eggs have little yolk 1. In some primitive insects, female gametes/eggs are nourished by the cells that surround them 2. In more advanced insects, a mature egg contains several germ cells, most of which become support cells that nourish the primary egg cell B. Typically, insect eggs are surrounded & protected by a shell containing a terminal pore through which sperm gain access C. Fertilization is internal to female's body; sperm is transferred either in liquid form or as a sperm packet picked up by or injected into female How Do Organisms Reproduce?: Vertebrates I. Vertebrates вЂ“ a significant key to their success was the evolution of amniote eggs in which the embryo is encased in a thick, fluid-filled sac & protected from drying out II. Primary problem of the developing embryo is securing nutrients & getting rid of accumulating, potentially toxic metabolic wastes without drying out A. In marine environments, such problems are minimized since the developing embryo is surrounded by nutrient-rich sea water; nutrients & water diffuse in & wastes out with little or no effort B. Some marine fish eggs are relatively simple вЂ“ little more than female gamete surrounded by gelatinous coat through which sperm (or its nucleus), nutrients, H2O, wastes easily penetrate C. Other fish eggs (especially those of fresh water fish), have considerable yolk (nutrient- & energyrich material upon which developing embryo feeds during early development) III. Mating among aquatic vertebrates is even more complex in terms of timing than in invertebrates A. Less responsive to lunar cycles, more responsive to place, time of year, presence of suitable mates B. Typically, at a specific place & time of year, male & female fish meet - one or both choose a location & construct a nest (from scrape in sand/gravel to elaborate structure of seaweed, etc.) 1. After suitable & appropriate courtship behaviors, female releases eggs into the nest & male releases sperm into the nest as well 2. In some cases, resulting zygotes are immediately ignored or zygotes are buried or nests are otherwise closed; sometimes offspring are protected by one or both parents IV. Fish eggs are vulnerable to predators & other environmental hazards, so development is usually fast A. After only a few days, fish larvae hatch, can swim, get food, seek shelter, & avoid at least some predators V. Reproduction among amphibians often resembles fish reproduction; reproductively, they are a complex group, variations on what is normal are common & fascinating A. Most are still dependent on water as a medium for reproduction 1. At appropriate places & times, females & males approach; males often attach to females for a period of time (a few minutes to several days); as eggs laid in H2O, sperm are released 2. Whole salamander populations may gather in masses of individuals releasing gametes into H2O B. Amphibians usually lay eggs in or near fresh water, which has limited nutrients; in addition to their protective layers, eggs carry large quantities of yolk 1. Compared to fish, amphibian development takes longer 2. Larvae (tadpoles) hatch with huge, distended bellies crammed with yolk remnants that continue to feed it after hatching 3. As yolk is consumed, larvae become increasingly able to secure their own food VI. Reptiles - first truly terrestrial vertebrate group; key factor to success is evolution of the reptilian egg A. Leathery shells, resist H2O loss & yet are permeable to O2 & CO2, surround & protect the contents 1. Inside, large masses of yolk contain sufficient energy & raw materials to ensure that when the young hatch, they will be small versions of adults, fully responsive to the environment 2. As yolk amount suggests, compared to fish, development is slow (needed for nutrition, energy) B. Soon after fertilization, a series of membranes form & surround the embryo; liquids they contain provide additional layers of protection 1. One membrane forms a sac, which accumulates & isolates wastes 2. Additional layers of protein material (egg white) surround & protect the embryos 3. Such eggs are still susceptible to the environment's worst вЂ“ predators, direct sunlight, flooding C. Usually buried in loose soil or laid beneath rocks/logs 1. Alligators & some lizards protect sites where they are laid 2. Some snakes keep them inside their body until they hatch вЂ”> give birth to living young VII. Which came first вЂ“ the chicken or the egg? вЂ“ the egg did; birds including chickens simply borrowed & made minor modifications to the reptilian egg (leathery shell became brittle) VIII. Mammals also initially borrowed reptilian egg A. Today, only two species of egg-laying mammals exist 1. Platypus & spiny anteater - both from Australia; essentially similar to reptilian eggs 2. After hatching, additional nourishment is provided by thefemale's mammary glands B. Marsupials did away with the mammalian egg entirely 1. Embryos are retained inside the female's body for a time 2. Born at a very early embryonic stage, usually when only a few millimeters or centimeters long 3. First task is to crawl from the birth canal to the outside of the female's body & on up to a special abdominal pouch (marsupium) where the mammary glands are located 4. The mammary glands provide the fetuses with nutrients & energy C. Placental mammals further protect embryos & fetuses 1. Egg structure with its membranes & fluids but without shells is retained inside the female body 2. Some surrounding membranes are modified into a placenta, a structure that firmly attaches to the embryo & later attaches the fetus to the female's uterus 3. Placental blood vessels flow beside the female's blood vessels & from the female, nutrients, O2, & other substances pass to the fetus 4. Wastes (CO2, etc.) pass the other way to be disposed of by the female's kidneys & lungs 5. Thus protected & provided for, fetuses remain inside the female body until at least minimally able to withstand external environment How Do Organisms Reproduce?: Development I. Compared to plants, animal growth & development is considerably more complex & widely studied A. Much is known about various patterns of animal embryonic development; patterns are generally variations on a theme 1. Initially, there are significant increases in the cell number (through mitotic events called cleavages) with little or no overall growth in size; in fact, individual cells get much smaller 2. Next comes the early appearance of organ systems 3. Then, further refinement of the organ systems & significant growth; invariably starts at the head end & proceeds toward the tail end 4. Often, there is a considerable lag between anterior & posterior development B. Example: marsupials вЂ“ at birth, they have fully functional heads & forelimbs while the hind legs are still in limb bud stage II. Early cleavage stages are complicated by the amount of yolk eggs contain A. Sea urchins contain little yolk so early cleavages are straightforward and simple B. Frog eggs contain considerable yolk 1. First two cleavages (mitotic) of the zygote begin almost immediately after fertilization & result in four cells, each roughly the same size with equal amounts of cytoplasm & yolk 2. Third cleavage occurs off center, producing four smaller cells containing most of the active cytoplasm & four larger cells containing most of the yolk 3. This divides the embryo into 2 regions: the animal pole & the vegetal pole; thereafter, cleavage occurs more frequently toward the animal pole which becomes the developing embryo 4. During initial divisions, there is very little increase in the embryo volume so cells get smaller 5. In time, a hollow ball of cells forms (blastula); cells can move between its surface & interior 6. Cells begin to differentiate; result is cells that take on unique characteristics & become different from the cells from which they came; development moves to tadpole stage and then adult frog C. Reptile & bird eggs contain even more yolk вЂ“ new individual starts off as an insignificant blob floating on yolk sea; cleavages occur here, avoiding the yolk entirely III. Yolk is important to most developing animals A. Organisms developing from eggs with little yolk get nourishment from their watery environments 1. Their development is typically rapid, and they become independent as soon as possible B. Vertebrates require more development time & their eggs contain increasing amounts of yolk C. The most advanced mammals nourish developing young with mammary glands, placentas, or both; no significant amounts of yolk IV. Growth & development in arthropods is complicated by their exoskeleton - in insects, two patterns of growth & development occur A. Some follow typical pattern of arthropod development вЂ“ hatch as miniature adult, but without wings or reproductive organs & then undergo a series of molts before becoming adults B. Others exhibit complete metamorphosis - worm-like larvae hatch (caterpillars, grubs, maggots) 1. After a series of molts, they go into a period of inactivity (pupate) & emerge completely transformed into a new organism 2. Caterpillars become moths or butterflies, grubs become beetles, maggots become flies 3. Often their dietary preferences change V. Insect metamorphosis - under control of various hormones & involves recognizable stages A. As in amphibians, cleavage begins in insects following the formation of a zygote 1. Differentiation results in specialization of cells 2. Some insects complete metamorphosis over several seasons, others during one season 3. Larvae or caterpillar feed to build up reserves for further development (destructive) 4. Stop feeding & move to pupa or molt; changes occur inside the pupa building adult structures B. Under hormonal control - hormones made in specialized cells are controlled by negative feedback 1. It is essential that certain hormone concentrations are available during various metamorphosis stages 2. If not вЂ”> abnormal development or development could be terminated VI. Freshly hatched fish & reptiles are essentially miniature adults - fully capable of independent existences (find food, avoid predators); those successful at both grow, reach adult size, & reproduce VII. Growth & development of amphibians is complicated since they are only partially transformed from aquatic to terrestrial life styles A. Typically, what hatches is an aquatic creature equipped with gills, a streamlined body shape, a flattened, paddle-like tail, & no other limbs (tadpole); does not resemble an adult 1. After a time (a few days to over a year), larvae undergo a metamorphosis in which they lose gills & gain lungs, lose tails & gain legs, otherwise become adapted for terrestrial life 2. Many change their dietary preferences; typically stop being herbivores & become carnivores 3. Another period of growth occurs before sexual maturity is reached B. Amphibian group is complex & many exceptions to typical pattern are known 1. Salamanders keep their tails 2. Some larvae become reproductively capable & fail to metamorphose further 3. Others grow limbs, keep gills, & continue to be aquatic as adults VIII. Two patterns of post-hatching growth & development in birds A. A few (waterfowl, shorebirds, some waders, chicken-like birds) follow an essentially reptilian pattern 1. Hatchlings are miniature adults to the extent that they can immediately leave nest, recognize food, & secure it B. Most lack feathers & are initially dependent on adults for protection from predators, wetness, & cold; others are even less well developed at hatching (blind, featherless, helpless) 1. For several weeks, they are totally dependent on adults for food & protection from predators, rain, & excessive heat or cold 2. In essence, they undergo much of their later stages of embryonic development after hatching IX. All mammals are helpless at birth, totally dependent on adults for nourishment & protection A. For all baby mammals, initial nourishment is provided by female's mammary glands B. Even after weaning (occurs after a few weeks to months), adults continue to either bring food to young or take young to food C. Some baby mammals get immediately beyond initial helplessness 1. Within only a few hours, the young of hoofed animals are able to run almost as fast as adults 2. Newborn whales are brought to the surface for their first breath, but are soon able to swim with adults, find the surface, & breathe independently D. For other mammals, development is slower 1. Unique in mammals, much of what they need to know is learned from close associations with parents & adults, like ...... 2. What food to eat, where to get it, where to seek shelter, how & where to avoid predators, & how to interact with others of their species 3. As time passes, young become more & more self-sufficient until finally they disperse 4. Process can take considerable time вЂ” typically in humans 18 to 20 years Where Are We Now? I. Study of plant & animal physiology has lagged behind study of human physiology - three trends in recent decades have tended to narrow these gaps in understanding A. Physiology of plants & animals is an innately interesting biological topic 1. Since early days of biology, relatively small under-supported group of dedicated biologists are drawn to this study 2. Through their efforts, much of what we know has been documented 3. Work continues & expands B. Certain procedures & experiments in physiology are done more easily on animals than on humans 1. Many intrusive procedures are not permitted on humans 2. Surgeons hone skills on test animals 3. Only later, are results of such efforts extrapolated & extended to humans 4. Much of what we know about human physiology was first discovered through studies of rats, pigs, monkeys, & rabbits 5. Animals are also used to test drugs for side effects & toxicity of many new products & pollutants 6. Question raised - to what extent are animal responses typical of those occurring in humans? C. In recent decades, the kinds of products that animals & plants provide to humans has moved beyond food, clothing, & companionship 1. Soon genes of one organism will be able to be transplanted into genomes of other organisms 2. Microbes are being used to produce human proteins (insulin) 3. Adult sheep & cattle have been cloned from somatic cells; eventually, they will be infused with new genes & used to produce drugs, hormones, & other useful proteins 4. Pigs may be used to grow human organs for transplant (their physiology is quite similar) these would be less likely to be rejected; early results are promising II. Procedural questions for all of this seem answerable with a little more time & effort A. But there are ethical questions 1. Is a pig heart the same as a human heart? 2. Does a pig have rights or interests? 3. What if pigs harbor benign virus that in humans becomes virulent? 4. Could transgenic transplants trigger another AIDS virus? B. To answer these & other questions we need to know as much about animal physiology as about human physiology Analogies, Anecdotes and Illustrations Epithelial and Connective Tissues I often tell my students about the classification of epithelial tissues. It does not take a long time, and there are really only two criteria to which they need to pay attention. First, epithelia can be classified on the basis of the number of cell layers. An epithelium composed of a single cell layer is called a simple epithelium. If there is more than one cell layer in an epithelium, it is called a stratified epithelium. These epithelia can also be classified on the basis of the shape of the cells in their uppermost layer. If the cells in the uppermost layer of the epithelium are flattened, it is a squamous epithelium. If the cells in the top layer are cube- or dice-shaped, it is a cuboidal epithelium. Finally, the third type of epithelium, a columnar epithelium, has cells in its top layer that are column-shaped (taller than they are wide). Usually when an epithelium is being classified, both classification schemes are used together. Thus, an epithelium consisting of one cell layer in which the cells are flattened would be a simple squamous epithelium. You may also wish to give them a taste of the significance of these different types of epithelia in terms of their function. This is an example of the relationship between structure and function. The best example of this is the simple squamous epithelium of the alveoli in the lungs. Ask your students why the flattened cells of a squamous epithelium would be important in the alveoli and why columnar or cuboidal cells would be less well suited. The answer is, of course, that oxygen and CO2 must be exchanged with the blood across the walls of the alveoli. The exchange would work best if the cells across which these gases must move were as thin as possible. Cuboidal or columnar epithelia would be too thick to facilitate efficient exchange. Other epithelia do not fall under this classification scheme. Transitional epithelia appear to be multilayered with the top layer of cells looking very bulbous sometimes and fairly flattened at other times. This particular epithelium is found in places like the urinary bladder. The epithelium has the bulbous cells in the top layer when the urinary bladder is relatively undistended. If the bladder is full or nearly so, these same cells would appear to be somewhat flattened. Another interesting special case is an epithelium referred to as a pseudostratified epithelium. A pseudostratified epithelium is one that consists of a single cell layer that looks like multiple cell layers. Stories about different epithelial tissues help illustrate the relationship between strucutre and function. They are relatively simple and not that hard for students to understand. Further structure-function examples can be gleaned from the connective tissues. The fibrous connective tissues of tendons and ligaments have fibers oriented in one direction alone. That direction corresponds to the direction of force normally experienced by the tissue. Ligaments and tendons tear when the force to which they are exposed comes from a direction other than the one for which they are designed. I have been to basketball games where a player planted his leg to go up for a layup, and he tore a ligament for this reason. It was not pretty. In contrast, loose areolar tissue possesses fibers that run literally in all directions. This tissue experiences force from a number of directions and the fibers are oriented accordingly. Other connective tissue (elastic connective tissue) contains elastic fibers that can stretch and recover. They are coiled like tiny springs and act like springs. Such tissue is found in the pinna of the ear and in arteries. These fibers allow the flexibility of the outer ear, the fact that you can fold it up and it will bounce back. As the heart forces blood into arteries, they expand. The elastic fibers help the arteries recover their original diameter when the bolus of blood from the contraction of the heart has passed. In older people, the fibers lose some of their ability to recover after the arteries have expanded; this can cause health problems. Use other examples if you choose. When you are telling your students about these tissues, ask leading questions. Try to get them to think about the advantages of certain types of fibers and their placement. Ask them how these tissues are suited to their functions via elements of their structure. Get them to think. The Importance of Osmosis, Diffusion, and Surface Area to Physiology I think it is essential to stress for your students the importance of the simple principles of osmosis and diffusion (to which they were introduced earlier in the semester) in the physiological processes that they usually learn about much later. There is a tendency for students to "learn" about these and other principles (usually by memorization) and then forget them. Thus, when such principles are mentioned later on, the students act as if they have never before heard of the concepts. My colleagues and I refer to this behavior as a "core dump." To teach this material, set up situations (hypotonic, isotonic, hypertonic, dry environments, etc.) and then ask the students what they mean for the creature and what problems such environments present. Once the problem has been established, ask them how it could be solved, what strategies would work, and which ones would not. Ask them what other problems the solutions might cause. I feel that such a problems approach is an effective one. Students, especially non-majors, do not seem to think in terms of survival problems organisms might have, perhaps because the survival challenges that most of them face are relatively tame. If you keep punching away at these principles, they begin to anticipate where you are going. That suggests to me that they are learning the material. The same applies to the importance of surface area and the tricks that organelles and organism use to maximize it. A partial list includes cristae in mitochondria, stacks of thylakoid disks in chloroplasts, the RER, the branching and alveoli of the respiratory system, branching in the digestive system, etc. If you ask the question enough times in enough different ways, the point gets through. One cannot overestimate the value of repetition in teaching such material. Muscle Contraction: How Molecules Work Together to Accomplish Something? I have often thought that one of the best examples, if not the best, of molecules working together to accomplish a task is muscle contraction. I usually cover this in much more detail than the text does, when I have the chance, but you could use your own judgment about how detailed you want to get. You could just talk about the fact that actin and myosin filaments slide over one another. Or you could describe what myosin filaments look like and describe how they reach out with their ATPase heads and grab actin filaments causing the filaments to slide over one another. You could talk about the roles of calcium and the troponin molecules that bind the calcium in the contraction of muscle. If you would like to go a bit deeper, you could tell them where the calcium comes from (the sarcoplasmic reticulum) and how it is released. When I have the opportunity (and the time), I like to follow this process from the nerve impulse traveling down the motor neuron to the stimulus traveling along the transverse tubule system of the muscle cell to the sarcoplasmic reticulum receiving the stimulus and the resultant release of calcium ions into the cytoplasm and its subsequent binding to troponin that lifts tropomyosin off of actin filaments exposing myosin binding sites on those same filaments. I have, of course, barely sketched here what happens. What I like about this story is that it is a fairly easily understandable sequence of events, a cascade in which one event triggers the next from the beginning to the end of the process. You can also decide the degree of detail that suits your particular purposes. Some Reproduction Is Stranger Than Fiction There are a number of examples of organisms that reproduce in strange ways. There is a type of salamander that apparently has no males. Instead, it mates with a closely related species of salamander whose sperm activates the egg to develop, but makes no hereditary contribution to the resulting embryo. This development without a real fertilization is called parthenogenesis. Other species can also reproduce parthenogenetically. There are several species of parthenogenetic aphids in which the hatched egg gives rise to several generations of asexually reproducing females. In the autumn, however, a type of female is produced whose eggs can develop into males and sexually reproducing females. These organisms can mate and the eggs that are produced have the ability to overwinter successfully. In the spring, these eggs hatch giving rise to a new generation of asexually reproducing females. Ask your students how this can happen without changing the number of chromosomes in the species вЂ“ a major no-no. It turns out that the diploid number is maintained, because the egg releases only one polar body during meiosis (instead of the normal two). Thus, the egg ends up with the normal diploid number of twelve chromosomes. Even more crazy is how the switch is made to females that can give rise to both female and male embryos. These females undergo meiosis and make two different kinds of eggs. In female-producing eggs, six pairs of chromosomes enter the single polar body; this results in an egg with twelve chromosomes that develops into a sexually reproducing female. Male вЂ“producing eggs send an extra chromosome pair to the polar body and have only ten chromosomes; this egg develops into a sexually-reproducing male. During meiosis, the male parcels its ten chromosomes out so that each meiotic event gives rise to equal numbers of sperm with four and six chromosomes. The sperm with four chromosomes degenerate. The sperm with six chromosomes can fertilize the eggs containing six chromosomes, thus producing embryos that will become asexually reproducing females. (For more detail on this process, check Scott Gilbert's Developmental Biology textbook.). These stories are good just to show your students that reproduction does not always go simply and illustrates that there are always exceptions to rules in biology. I am sure that you have run across similar unusual situations in your career. Use them in your teaching. This is the kind of stuff that really grabs student interest because it is so weird. Sample Test Questions Multiple Choice, Conceptual, and Open-Ended Questions From the Text 1. What were the two pathways that life followed once it moved from the water to the land? Autotrophy (organisms that made their own "food" molecules like flowering plants) and heterotrophy (animals that must consume food - plants or animals) are the two pathways that life followed when it moved from water to land. 2. Why would two foxes like the desert kit fox and the Arctic fox that live in such different climates both have kidneys similarly adapted to conserve and recycle water? Despite the fact that the Arctic has water in its frozen form everywhere and the desert has very little water available because it is so dry, water is, for all intents and purposes, equally unavailable in both environments. Thus, creatures that live in the desert and those that live in the Arctic, must all conserve water in any way that they can. Their kidneys, therefore, are specialized for water conservation and recycling. 3. What feature of kit foxes helps them regulate their body temperature? a. huge ears b. small, fur-covered ears c. good insulation d. autotrophy e. efficient kidneys 4. What word or phrase correctly describes a colony of bacteria? a. multicellular organism c. prokaryotic b. multicellular entity d. eukaryotic e. b and c 5. What distinguishes multicellular organisms from colonies of bacteria? The most important distinguishing characteristic is that the cells of multicellular organisms exhibit mutual interdependence. If a bacterial cell is separated from a colony, it can live independently. The same is not true of a cell from a multicellular organism (except for gametes). In addition, the cells of multicellular organisms are hierarchically organized. Multicellular organisms are more than the sum of their parts; they are synergisms. Multicellular organisms also function best within stable internal environments. Finally, feedback systems control many of their physiological processes. 6. You are studying tissues in the lab and in the microscope, and you observe a layer of cells on the outer surface of one of the tissues. The cells in the layer are flattened. What words below comprise an accurate description of the tissue you observed? a. squamous connective c. squamous epithelium e. striated muscle b. cuboidal epithelium d. cuboidal connective 7. Which of the arrangements below is the correct hierarchy for the cells of a multicellular organism from the largest to the smallest unit? a. cells, tissues, organs, organ systems, individuals b. individuals, organ systems, organs, tissues, cells c. individuals, organ systems, organs, cells, tissues d. cells, tissues, organs, individuals, organ systems e. cells, organs, tissues, organ systems, individuals 8. Which tissue is characterized by slow rates of cell division and is usually composed of living cells surrounded by a non-living matrix? a. cartilage b. bone c. connective tissue d. a, b, and c e. muscle 9. What tissue's major function is the movement of internal parts or movement of the body as a whole? a. cartilage b. bone c. connective tissue d. a, b, and c e. muscle 10. What type of tissue loses the ability to reproduce prior to birth? a. cartilage b. bone c. nerve tissue d. muscle tissue e. a and c 11. Why is it difficult to study the physiology of whole individuals? Individuals are too complex to contemplate as a single unit. Consequently, biologists usually approach the study of physiology in a reductionist fashion. They break the complexity into small, manageable units that can be more conveniently studied. It is hoped that later, after the operation of the components is understood, we will be able to put them back together and see how the system functions as a unit. 12. The maintenance of nearly constant internal conditions is referred to as: a. homeopathy b. homeotic c. staticity d. homeostasis 13. Cold-blooded animals are also known as: a. endothermic b. ectothermic c. homeothermic 14. Endothermic organisms a. maintain constant temperatures b. generate heat internally e. hyperion d. poikilothermic c. generate cold externally d. generate heat externally 15. Which term below is most closely associated with homeostasis? a. reproduction b. feedback c. homosexuality d. elasticity e. b and d e. a and b e. phlogiston 16. Which of the following is an example of positive feedback? a. maintenance of constant temperature d. constantly changing neural inputs b. constant blood glucose levels e. a and b c. sexual arousal 17. Which form of feedback control is most often seen and most useful to an organism? Negative feedback is seen more often than positive feedback in living organisms and is, in general, more useful. 18. What is the general effect of negative control systems? The general effect of negative feedback systems is to lead to stability in the system. 19. What type of enzyme inhibition is most likely to be involved in a feedback loop? a. competitive inhibition c. reversible inhibition e. b and c b. noncompetitive inhibition d. irreversible inhibition 20. What feature of nerve cells makes them particularly well suited to their purpose of connecting various parts of the body with the brain and other nerves? a. their long, thread-like form c. their inability to run anaerobically e. a and c b. their compact cell body d. their ability to run aerobically 21. What cell organelle is important to physiological processes because of its ability to interact with hormones and to facilitate the passage of nutrient and wastes? a. nucleus b. nucleolus c. plasma membrane d. nuclear membrane e. mitochondria 22. What is the source of the nutrients that provide raw materials for the growth and maintenance of organisms, among other functions? a. the atmosphere b. the Earth c. other organisms d. a and b e. a, b, and c 23. What is the fate of potentially toxic wastes from organisms that are released back into the environment? a. they evaporate c. they disintegrate e. they pollute b. they become nutrients for other organisms d. they denature 24. Why can't the compounds in the victims of decomposers or pathogens enter these organisms immediately? a. They are too large to pass through decomposer/pathogen cell walls. b. They are too small to pass through decomposer/pathogen cell walls. c. They are too large to pass through decomposer/pathogen cell membranes. d. They are too small to pass through decomposer/pathogen cell membranes. e. a and c. 25. How do bacteria and fungi digest the compounds of their victims? a. They produce and denature digestive enzymes. b. They secrete acid to digest these compounds. c. They produce and secrete digestive enzymes. d. They produce and secrete mitochondria. e. c and d 26. How do sponges get food items into their cells to facilitate digestion? a. exocytosis b. locomotion c. apoptosis d. endocytosis e. ingestion 27. What type of feeding is typical of sponges? a. extrusion b. filter-feeding c. ingestion 28. How do smaller molecules get into sponge cells? a. diffusion b. osmosis c. active transport d. extracellular digestion d. a and c e. engorging e. sipping 29. What is the major difference between the digestive systems of jellyfish and that of roundworms? The digestive system of roundworms is a complete digestive system; it has two openings, a mouth and an anus. The digestive system of a jellyfish is not complete; it has only one opening through which food enters the digestive system and through which wastes exit. 30. What feature of digestive systems first evolved in the segmented worms? a. specific digestive enzymes d. a flat digestive system b. division of the digestive system into specialized regions e. a smooth digestive system c. a twisted digestive tube 31. The coiling and twisting of the digestive systems in mollusks, arthropods, and vertebrates is said to increase their efficiency. How does the twisting and coiling do that? The twisting and coiling of digestive systems allows much longer digestive systems to fit within the bodies of these organisms. The increased length provides increased surface area over which nutrient absorption can occur. This makes the process much more efficient. 32. Where do Archaea and other oxygen-sensitive organisms often live? a. bottom muds c. intestinal tracts of other organisms b. carcasses d. hydrothermal vents e. all of the above 33. The relationship between cows and their intestinal microbes is described as symbiotic. Both the cows and the intestinal microbes benefit from the relationship. What is the benefit to each type of creature? The cows acquire the ability to digest cellulose. This allows them to eat grass and other plants in order to obtain their nutrient material. The intestinal microbes benefit by getting protection and a readily available nutrient supply. The cow walks around and obtains the nutrients. The microbes do not have to go looking for their nutrients; they are delivered by the cow. 34. What is the major mechanism by which single-celled and smaller multicelled organisms obtain O2 and get rid of CO2? a. infusion b. diffusion c. active transport d. facilitated diffusion e. osmosis 35. For what reasons, do more advanced organisms require a more specialized, efficient respiratory system to assist diffusion? Diffusion requires an assist in more advanced organisms, because they are larger and bulkier. Their activity levels and thus their energy requirements are increased. Their bodies also become covered with impermeable coverings like bark, shells, cuticle, scales, horny plates and skin. 36. Why is diffusion effective in smaller, multicelled organisms like jellyfish and flatworms? Despite the fact that they are fairly large, they do not need specialized respiratory systems. They have large internal spaces and, in the case of flatworms, a flat body shape. These features mean that no internal cell is very far from the environment. Consequently, O2 can diffuse in easily and CO2 can diffuse out easily as well. 37. Which of the following is a type of respiratory system found in animals? a. skin b. gills c. lungs d. a, b, and c e. wattle 38. What are two characteristics common to all respiratory systems? They have extensive surface areas and they consist of moist cell layers that facilitate diffusion. 39. How does skin work as a respiratory organ? Small blood vessels called capillaries bring blood rich in CO2 and deficient in O2 close to the skin's surface where gas exchange takes place by diffusion. 40. Describe primitive gills and the organisms that possess them and point out the problems that their structure can cause. Primitive gills are found in aquatic insect larvae and some salamanders. They are complex outpocketings of tissue that hang out in the water. They consist of thin coverings and thin blood vessels. Diffusion in and out of these structures is straightforward. Problems arise because these delicate tissues are unprotected and difficult to move. Gill movement becomes important and necessary as the water immediately surrounding the organism gets deficient in O2 and as the CO2 builds up. 41. What problem arises when gills are internalized? When gills are internalized and covered with protective body coverings, it immediately becomes difficult to move replenishing water at least periodically in past the gills. 42. Why do most bony fish continuously gulp water? Gulping water continuously forces it past gills and out through the gill slits. In this way, they can supply gills with fresh water during periods of relative inactivity. 43. What is the major advantage realized from internalized lungs in terrestrial organisms? a. prevents twisting of the tissue c. allows the tissue to dry out e. it is easier to get rid of CO2 b. prevents lungs from drying out d. supplies lungs with more oxygen 44. How can gases get into the small tracheae tubes inside insects where gas exchange takes place? a. passive flow involving diffusion d. a and c b. osmosis e. water carries air in c. muscles pump air in and out of tracheae 45. What important feature distinguishes pulmonary lungs from most of the more primitive insect "lungs"? a. special muscles move air in c. a and b e. the surfaces are thicker b. special muscles move air out d. the lung surfaces are moist 46. What advantage does the presence of small pockets called alveoli confer on the lungs of birds and mammals? a. increased surface area c. moist surfaces e. a and c b. decreased surface area d. dry surfaces 47. Why do small animals have little need for circulatory systems? Small organisms are small enough that no cell is far enough from the external environment to prevent or hamper osmosis and diffusion from adequately carrying out gas exchange, getting rid of wastes, and acquiring nutrients. Sponges have flagellated cells that circulate water throughout their internal spaces, allowing an exchange of nutrients for metabolic wastes and O2 for CO2. Jellyfish and flatworms have digestive systems that are large and/or complexly branched so that no cell is far removed from either its external environment or the internal digestive tract. 48. Distinguish between open and closed circulatory systems. In open circulatory systems, blood periodically leaves blood vessels, bathes tissues, and is recovered into the vessels. In a closed circulatory system, the blood never leaves the blood vessels. 49. Why do sharks and rays experience no net increases or decreases in water content? a. They are isotonic to their environment. d. They are osmotically balanced. b. They are hypotonic to their environment. e. a and d c. They are hypertonic to their environment. 50. Which of the following stresses is placed on marine organisms that live in a hypertonic environment? a. They tend to lose water to the environment. b. They tend to gain water from the environment. c. They pick up solutes present at lower concentrations in their environment. d, They pick up solutes present at higher concentrations in their environment. e. a and d 51. What mechanisms do marine organisms living in hypertonic environments use to alleviate the excess water they pick up? They replace lost water by drinking copious amounts of water. They also concentrate their urine so that they lose as little water as possible when urinating. What problem does the solution to that above present to these organisms? When they drink copious amounts of water, they also gain many solutes with the water since it is hypertonic. What strategies do these organisms employ to solve the problem introduced by the solution to the first problem? They use active transport at the gills to get rid of some of the unwanted solutes. Other solutes are concentrated in and voided with the urine. 52. Which of the following is experienced by organisms living in an environment that is hypotonic to their internal bodily fluids? a. They tend to gain water from their environment. d. a and c b. They tend to lose water to their environment. e. b and c c. They tend to lose solutes to their environment. 53. How are the problems introduced by a hypotonic environment dealt with by the organisms that populate it? In these organisms, excess water is generally voided by special excretory organs, kidneys in vertebrates and similar structures in invertebrates. The urine produced is usually very diluted. Solutes lost to the environment are recaptured from the environment by active transport through the gills or intestines. Some lost solutes are replaced in food these organisms eat, by their normal digestion, and by active transport. 54. What problems do terrestrial organisms have with respect to water? a. Water is limited in terrestrial environments. d. b and c b. Water is too plentiful in terrestrial environments. e. a and c c. They tend to dry out in terrestrial environments. 55. How do terrestrial organisms acquire water? a. They drink it. c. They extract it from food. b. They soak it up through their skin. d. They produce it during metabolism e. all of the above. 56. How do terrestrial organisms lose water to the environment? a. They lose water through evaporation from skin. b. They lose water through evaporation from the respiratory system. c. They lose it in feces and urine. d. They lose it in special secretions. e. all of the above. 57. What is the source of the nitrogen that appears in ammonia, one of the most serious toxic wastes produced by cellular metabolism? a. proteins and amino acids b. carbohydrates c. lipids d. nucleic acids e. a and b 58. Upon what processes do kidneys depend to get rid of their metabolic wastes? a. diffusion b. osmosis c. active transport d. filtration e. all of the above 59. In what ways can organisms meet the challenges from the external environments in which they live? a. Isolate themselves within thick shells and other similar structures. b. Seek shelter. c. Adjust to changing conditions. d. Move to more favorable environments. e. all of the above. 60. Bacteria are surprisingly mobile despite their thick cell walls. Many scientists believe that this relates to their small size. How would their small size help to make them more mobile? a. It minimizes the effect of gravity. d. a and e b. It allows them to diffuse. e. It maximizes their buoyancy. c. It provides them with a propulsion system. 61. How does the movement of bacterial flagellae differ from the standing wave form movement of eukaryotic flagellae? a. Flagellae in bacteria act like springs. d. Bacterial flagellae are denser. b. Bacterial flagellae rotate at their base. e. Bacterial flagellae are more buoyant. c. Bacterial flagellae assemble and disassemble. 62. Which of the following are appendages used by Protistans for movement? a. cilia b. flagellae c. pseudopodia d. bristles e. a, b, and c 63. Which appendages of Protistan origin are also found in the cells of vertebrates? a. cilia b. flagellae c. pseudopodia d. bristles e. a, b, and c 64. Which of the following proteins plays an important role in muscle contraction in vertebrates? a. actin b. myosin c. ATP d. a and b e. a, b, and c 65. Which name below would be a good name for the model that describes the mechanism of contraction seen in muscles? a. Sliding Filament Model c. Contracting Filament Model e. Spring Load Model b. Slippery Shoes Model d. Contracting Actin Model 66. What will happen if the longitudinal muscles of a roundworm on one side of the worm contract? Contracting the longitudinal muscles along one side of a roundworm shortens the cylinder of the roundworm on that side alone, causing the worm to twist into a "C." 67. What advantages below have exoskeletons conferred upon insects? a. protection b. attachment sites for nerves c. attachment sites for muscles d. a and b e. a and c 68. What keeps a roundworm's body from collapsing? a. an exoskeleton c. a hydrostatic skeleton b. an endoskeleton d. a calciferous skeleton e. b and d 69. What is the effect on an earthworm's body when its circular muscles contract? Its body lengthens. What is the effect of contracting the longitudinal muscles? The body shortens. The circular and longitudinal muscles of an earthworm are an example of what kind of muscle arrangement seen in organisms with more developed muscular systems? Muscle antagonists. 70. What evidence suggests that the hormones found in vertebrates may have a long evolutionary history? a. Some hormones found in vertebrates are also found in the soil. b. Some hormones found in vertebrates are also found in protozoans. c. Some hormones found in vertebrates are also found in invertebrates. d. Some hormones found in bacteria are also found in protozoans. e. b and c 71. Ecdysone controls a. molting in insects b. molting in clams c. maturation in insects d. maturation in earthworms e. puberty in humans 72. In terms of rapidity of response, which is faster вЂ” the endocrine system or the nervous system? The nervous system is faster and makes rapid responses to stimuli. The nervous system controls activities like hitting a baseball, smacking at a biting mosquito, driving a car, etc., things that a hormone would be too slow to accomplish. The endocrine system responds to stimuli over a much longer period of time. Hormones generally control functions and processes that happen slowly over a period of several days or weeks. Examples of processes controlled by hormones are growth, maturity, reproduction, and many other metabolic functions. 73. Juvenile hormone controls a. molting in insects b. molting in clams c. maturation in insects d. maturation in earthworms e. puberty in humans 74. What organism is the simplest organism for which the ability to learn has been demonstrated? a. sea urchin b. jellyfish c. flatworm d. roundworm e. reptiles 75. What is the method of reproduction that results in the highest degree of variability? a. adipterous b. sexual c. conjugation d. asexual e. homozygous 76. In some bacteria, protists, and single-celled fungi, cells undergoing asexual reproduction sometimes do not separate and thus remain attached. What is such a grouping of cells called? a. cell story b. colony c. bacteria d. bacteriophage e. cell group 77. What is the most common form of reproduction? a. asexual reproduction b. sexual reproduction c. meiosis d. mating e. a and c 78. Which cells in humans have lost the ability to divide? a. cells of stomach lining b. skin cells c. liver cells d. nerve cells e. red blood cell precursors 79. What is the name of the structure that is the cytoplasmic bridge between bacterial cells involved in conjugation? a. capillary b. vein c. pilus d. DNA tube e. a and c 80. What is the most common reproductive cycle seen in animals? a. alternating cycle b. diploid cycle c. haploid cycle d. a and c e. all of the above 81. Organisms exhibiting which reproductive cycle(s) have cells or tissues that do not contain homologous pairs of chromosomes? a. alternating cycle b. diploid cycle c. haploid cycle d. a and c e. all of the above 82. Gametophytes a. are haploid b. are diploid c. produce gametes d. produce spores e. a and c 83. Sporophytes a. are haploid b. are diploid c. produce gametes d. produce spores e. b and d 84. In which plants do the two generations of an alternating reproductive cycle appear in different individuals? In algae and primitive plants like mosses and ferns, the two generations of the alternating reproductive cycle appear in completely separate individuals. In which plants do the two generations of the alternating reproductive cycle occur in the same individual? In more advanced plants, the two generations of the alternating reproductive cycle occur in the same individual. In plants in which both generations appear in the same plant, which of the two generations predominates? In these plants, the sporophyte generation predominates; the gametophyte generation appears as a multicellular entity, but is greatly reduced. 85. What is the greatest danger faced by gametes? The greatest danger faced by gametes is drying out. 86. What often serves as the cue for the shedding of gametes into the water in tropical sponges, jellyfish, squids, and other organisms that mate in water? a. solar cycle b. lunar cycle c. daylight d. magnetic fields e. electric fields 87. What factors below influence the timing of mating in aquatic vertebrates? a. specific time of year c. appropriate courtship behaviors b. specific place d. all of the above e. a and b 88. What is the purpose of yolk in the eggs of organisms? The purpose of yolk in an egg is the nourishment of the developing embryo. It is a source of energy and nutrients. 89. Why do the eggs of spiny-skinned marine animals generally have little yolk? The ocean waters in which they live contain ample nutrients making the presence of yolk less essential. Furthermore, these embryos develop fairly quickly to the point where they can seek their own food so very little yolk is required to support their development. 90. What is an hermaphrodite? An hermaphrodite is an organism that possesses both male and female reproductive systems. 91. Why do insect eggs tend to have little yolk? Female gametes (eggs) in insects tend to be nourished by the cells that surround them. In some insects, the egg case contain a number of presumptive egg cells initially, but usually all but one of these cells become support cells that nourish the primary egg cell. 92. What is a key to the success of land vertebrates? A significant key to the success of land vertebrates was the evolution of amniote eggs in which the embryo is encased in a fluid-filled sac and protected from drying out. 93. Why are the problems of developing embryos in terms of securing nutrients and getting rid of potentially toxic metabolic wastes minimized in marine environments? In marine environments, the developing embryo is surrounded by nutrient-rich sea water. Nutrients and water enter and wastes leave the developing embryo with little or no effort. 94. Frog eggs are laid in water, why do they require more yolk than marine fish eggs? Amphibians lay their eggs in or near fresh water; marine fish lay their eggs in sea water. Compared to the fish, frog development takes longer. Furthermore, the fresh water in which they develop contains limited nutrients so the yolk is needed to compensate for the lack of nutrients in the water. Eggs laid in sea water are surrounded by a significant amount of nutrients and therefore less yolk is needed to support development. 95. What are the three kinds of mammals with respect to the development of their offspring and describe each type briefly? The egg-laying mammals (platypus and spiny anteater) lay eggs that closely resemble reptilian eggs. After hatching, the offspring obtain nourishment from the female's mammary glands. The fetuses of marsupials are retained inside the female's body for a time. They are born at an early embryonic stage and complete their development in a pouch (marsupium) in which they receive nourishment from the mammary glands. Placental mammals complete the development of their fetuses in the uterus. A placenta is formed that connects the developing fetus to the female's uterus. Placental blood vessels obtain nutrients and O2 from the mother's bloodstream and conveys metabolic wastes to the female's bloodstream. Subsequently, these wastes are disposed of by the mother's kidneys and lungs. 96. What is the result of early cleavage stages in embryos in which the zygote undergoes rapid mitosis with no growth between each successive mitotic event? a. The cells get bigger. c. The cells change their shape. e. a and c b. The cells get smaller. d. The cells stay the same size. 97. What is the effect on cleavage of high concentrations of yolk? a. Cleavage slows down. c. It has no effect. b. Cleavage speeds up. d. It stops cleavage completely. e. It shrinks the nucleus. 98. Cleavages occur more frequently toward the ______ pole of the frog embryo. a. vegetal b. north c. south d. animal e. vegetable 99. In arthropods, worm-like larvae that go through a series of molts, go into a period of inactivity called pupation and then emerge as a completely transformed organism. This is a description of the process of: a. mitosis b. meiosis c. endometriosis d. metamorphosis e. metastasis 100. A major part of post-birth development that in some mammals can take years is called: a. stenosis b. apoptosis c. metamorphosis d. halitosis e. learning Multiple Choice, Conceptual, and Open-Ended Questions From the CD-ROM 1. What are the three major components of feedback loops of any type? Every feedback loop must include a receptor of some type that monitors an organism's external and internal environment. There must also be a control center in each feedback loop that processes information perceived by the receptors. It also makes decisions about what the appropriate response should be and sends out signals, notifying the effectors, the third component of the system, that produce responses to the stimuli received by the receptors and processed by the control center. 2. Which of the following would normally act as an effector in a feedback loop? a. gland b. muscle c. brain d. a and b e. spinal cord 3. In what way does the brain, the hypothalamus, and the pituitary, the control center(s) operating during childbirth, tell the uterus that it needs to keep contracting? The hypothalamus and pituitary secrete the hormone oxytocin into the blood. Oxytocin travels in the bloodstream to the uterus where it stimulates the muscles of the uterus to contract, intensifying labor in the process. 4. Occasionally, labor will slow down almost to a stop. Doctors may then be forced to induce labor by injecting a synthetic version of what chemical into the mother? a. cortisol b. oxytocin c. cholesterol d. prolactin e. progesterone 5. To what does the word "positive" in positive feedback refer? Positive feedback keeps a response going in the same direction as it was going initially; it enhances and intensifies the already existing response. 6. What is the reason for using the word "negative" to describe negative feedback? Negative feedback is used to slow down, shut off, or reverse a physiological process and return it to an optimal condition. 7. Positive feedback leads to increasing instability in a system and is often exemplified by intensification of the response. How then could the response in a positive feedback system be terminated? Give an example. To terminate a positive feedback loop, the stimulus must somehow disappear. At first glance, this might seem difficult to achieve, since in positive feedback, the stimulus is repeatedly intensified. In childbirth, it is the baby pressing against and distending the cervix and stretching the uterus that serves as a stimulus to continue the contractions leading to birth. The stimulus for further contractions will stop once the child is born, since there will be no further stretching of the uterus and pressure against the cervix. Once this happens, the contractions should stop as well,with the possible exception of delivery of the placenta. Thus, birth itself terminates the stimulus and the positive feedback system. 8. Assume that substance M is a product of a metabolic pathway. When concentrations of M rise to a certain level, M binds to and inhibits the enzyme that converts the first reactant in the pathway to the pathway's first product. What will be the effect of this inhibition on the amount of M present in the cell? Since high amounts of M inhibit the enzyme catalyzing the first reaction in the pathway, the reaction producing M at the end of that pathway will also be inhibited. Since M is probably being used up in the course of normal metabolism and the reaction that produces M is inhibited, the amount of M in the cell should decrease. What will happen when the amount of M drops below a certain point? When the amount of M drops below a certain point, M that is bound to the enzyme leaves it and the enzyme is reactivated. Eventually, the concentration of M will begin to increase since the reaction sequence that produces it is largely uninhibited. What kind of enzyme inhibition is involved in the process described above? Noncompetitive inhibition. What is the overall effect of the mechanism on the concentration of M in the cell? The amount of M should remain fairly constant. If M concentrations rise too high, its synthesis is inhibited. If the concentration drops too low, M production increases. The mechanism leads to stability in the concentration of M. Of what kind of feedback is this mechanism an example and why? Since the effect of the mechanism is to stabilize the amount of M and since the effect of the mechanism is to slow down and reverse the physiological process described returning M concentrations to optimal conditions, this is an example of negative feedback. 9. When blood pressure is too high, what effectors receive signals from the brain to correct the situation and what do they do? a. The heart beats more slowly. c. Arterioles dilate. e. Arterioles constrict. b. The heart rate speeds up. d. a and c. 10. Where are the receptors that monitor blood pressure located? a. in the walls of venules c. in the walls of veins b. in the walls of arterioles d. in the walls of the heart e. a and b 11. What is the surface area : volume ratio for a cuboidal cell with a side 1 Вµ in length? The surface area : volume ratio for this cell is 6.0. The surface area is 6 Вµ2; the volume is 1 Вµ3. What is the surface area : volume ratio for a cuboidal cell with a cell 4 Вµ in length? The surface area of this cell is 16 Вµ2 x 6 or 96 Вµ2; the volume is 64 Вµ3. The surface area : volume ratio is 1.5. How could you divide the 4 Вµ cuboidal cell up into cells of equal size that will maintain the surface area : volume ratio of the 1 Вµ cuboidal cell? Dividing the 4 Вµ cuboidal cell into 64 1 Вµ cuboidal cells would preserve the desired surface area : volume ratio of the 1 Вµ cuboidal cell. 12. The tentacles of Hydra contain specialized cells that are used to capture prey. What are they called? a. stinging cells b. nematocysts c. a and b d. stingocysts e. blastocytes 13. Why is the decrease in surface area : volume ratio a problem for bigger cells? Bigger cells use materials and produce wastes more rapidly than they can exchange these materials with the environment. As a cell gets bigger, there is more living material to support and less surface area to aid in that support. 14. What is the name of the cavity into which a Hydra moves food in order to digest it? a. gastric bundle b. gastrovascular cavity c. stomach d. gut e. gastroenterus 15. Termites eat wood, but lack the enzymes necessary to digest its components (like cellulose). They solve this problem by populating their guts with microorganisms that possess the enzymes that allow them to digest wood. What word describes the relationship between termites and these microorganisms? a. b and d b. symbiosis c. chemiosmosis d. mutualism e. parasitism 16. Once nutrients have been acquired and processed, they must be distributed around the organism. What organ system is responsible for this task in larger organisms? a. respiratory system b. circulatory system c. immune system d. excretory system e. a and b 17. What organ is responsible for propelling fluids through the body for the purpose of distributing nutrients and oxygen and collecting waste products? a. lungs b. arteries c. veins d. venules e. heart 18. What other organ system is most closely associated with the circulatory system? a. respiratory system c. reproductive system e. a and d b. endocrine system d. excretory system 19. How many circuits through the heart are required to complete a cycle of circulation in a fish? a. 2 b. 0 c. 1 d. 3 e. 4 20. In a fish, where does the blood go after it leaves the gills? After leaving the gills, the blood travels to the tissues and cells of the fish to which it delivers oxygen and from which it collects carbon dioxide. 21. At what point is the blood in a fish least oxygenated? a. as it enters the ventricle c. as it enters the atrium b. as it enters the right vent