RED DEER COLLEGE
BIOLOGY 217
INTRODUCTION TO CELL BIOLOGY
Winter 2014
Section E: Mon. Wed. Fri.
2:30 – 3:20
Room 1328
Section G: Mon. Tues. Thur. 11:00 – 11:50 Room 1439
Instructor:
Office:
Phone:
Email:
Will Marchuk
1607D
403-342-3110
[email protected] OR via Blackboard
Log into Blackboard - find this outline and READ
IT please! You are responsible for all the
information contained within. If you have ANY
questions or concerns, please see Will.
1.
Prerequisites: Biology 30 AND Chemistry 30. If you don’t have these prerequisites you should
discuss your options with the Department Chairperson immediately. Note: BIOL 217 is
not a prerequisite for BIOL 218. BIOL 217 and 218 can be taken in either term.
2.
Course Description:
This course is an introduction to cell structure and function. Major topics include the molecules and
structures that comprise prokaryotic and eukaryotic cells, cell membrane structure and function, the
mechanisms by which energy is harvested and used by cells, how cells reproduce, and how
information is stored and used within a cell via the processes of DNA replication, transcription, and
translation. Credit hours: 4.
3.
Learning Activities:
The nature of the course requires that the majority of the class material will be delivered by lecture,
but time is always available in every lecture for questions and class discussion. Most of the lecture
material will be available on-line via Blackboard (https://portal.rdc.ab.ca/cp/home/loginf). Course
material on-line via Blackboard (Bb) will play a major role in your learning activities.
4.
Learning Outcomes:
Biology 217 is primarily aimed at preparing students for senior level biology courses, not a survey
course for non-science students. With this in mind, the primary aim of this course is to cover the
material in such a way that each topic comes to a logical conclusion and provides some closure.
Laboratory exercises are designed to provide students with a basic understanding of how the
structure and function of cells is studied. Students who take no further biology courses should be
able to understand the material and use it for evaluating biological information that they may encounter
in other contexts. Throughout the course, students will be encouraged to develop and use analytical
and critical thinking skills.
5.
Texts / Primary References: (* Required)
1. *Reece, J. B. et al. 2011. Biology. 9th Ed. Hardcopy OR ebook. Redwood City, CA:
Benjamin/ Cummings. The ebook subscription is available at the College bookstore
OR online from numerous websites (CourseSmart, Amazon, eBay, Kijiji, etc.).
If you buy this book new you will have access to its website via:
http://www.campbellbiology.com
There is also a copy of the 8th edition on 24 hour reserve in the library. There is very little
difference between the two editions! If you can find a used version of the 8 th edition on line – buy
it. Amazon and eBay are two of many sites to find used AND new texts.
If you use an iPad, you may purchase your text from this link (much cheaper than the hard copy):
https://www.inkling.com/store/category/science/. This site also gives you the option of buying
individual chapters! Also, you may find the APP Notability of tremendous value if you use an iPad.
continued…
An interesting “take” on the education system:
http://www.theonion.com/video/in-the-know-are-tests-biased-against-students-who,17966/
-22. Marchuk, W. N. 2010-2011. Biology 217 Website on Blackboard (Bb). See Bb access procedures below.
3. *Biology 217 Laboratory manual
4. *How to write a scientific paper.
* Both of these resources are available on the Biol 217 Lab Bb course. Both are FREE.
6.
Laboratories:
Information on individual lab times and instructors will be posted separately. If you have any
questions or concerns regarding the laboratory – contact your assigned lab instructor (refer to the
RDC website or your timetable). A $20.00 “Materials Fee” has been charged to you as part of the
tuition of this course.
7.
Websites:
There are thousands of websites dealing biology. Here are several you may find interesting and
relevant. These sites will obviously lead you to many other related sites.
Will’s Bio. 217 Website`
https://portal.rdc.ab.ca
(see access procedure below)
Current science news
http://www.physorg.com
A list of great science/biology sites http://www.cod.edu/people/faculty/fancher/IntSites.htm
Great bio news site
http://www.sciencedaily.com/news/plants_animals/cell_biology/
New Scientist (great mag.)
http://www.newscientist.com/
Nature (another great mag.)
http://www.nature.com
A FREE online textbook
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/
8.
Blackboard (Bb) Log In Procedure:
1.
Open up a web browser – Google Chrome is BY FAR the best browser to use with Blackboard.
Windows Explorer is the WORST!
2.
Type in the address: https://portal.rdc.ab.ca (there is NO www) OR just go to the RDC website
http://www.rdc.ab.ca/ and click on “GET IN THE LOOP”.
3.
Type in your username and Password. Your username is your first initial followed by your last name
(all low case, no spaces). Your password is your birth date in YYMMDD format. For example, if your
birthday is July 6, 1999, your password is 990706. After your initial log in, you can change your
password if you wish.
4. Click on the specific course name to enter the course homepage.
If you are unable to log in, Email the College Helpdesk @: [email protected] or phone: 3423580 with the following information:




Your full name (first, middle, last) and student ID
Your birth date
The name, number, and section of the course you are trying to access
Your instructor’s name (if you have one)
Blackboard (Bb) has a great Mobile App (available
from iTunes) for your iPad or Smartphone.
ALL Bb course can be accessed via this QR Code
-39.
Assessment of Student Performance:
Throughout the term your abilities will be formally assessed in lecture by your performance on two
lecture exams and one cumulative final lecture exam. At the end of the term, these marks along with
your laboratory work will be the major determinant in assigning a letter grade reflecting your overall
performance. Refer to the chart on page 4 for how percentages are converted to a letter grade.
Lecture Portion totals 72% of course
(The following breakdown applies)
Two lecture Exams @ 16% each
- #1 near the 1st week of February
- #2 near the 1st week of March
(Specific dates will be announced in lecture one
week prior to exam)
Lab Portion totals 28% of course
The specific distribution of lab marks may
vary slightly from section to section. See
YOUR lab section outline for details.
PLEASE NOTE: You MUST pass the
lab component in order to receive
credit in this course.
One final Exam @ 40%
(Date to be announced by registrar)
Lecture exams will consist of a combination short answer and discussion-based questions.
There will be several very short unannounced “pop” quizzes throughout the term that may earn you
valuable “BANK” marks. If you skip class – you lose out. Details about these will be discussed in
class. All marks in the “bank” must be allotted by the last day of classes.
All grades will be assigned according to the Red Deer College grading system. See the Red Deer
College Calendar for specific details (http://www.rdc.ab.ca/Pages/default.aspx).
Deferred Exams: A student who has missed or will miss a final exam because of illness, domestic
affliction, or other compelling reason must apply to the registrar for a deferred final exam. Be
prepared to supply a letter from a medical doctor or other verification.
Supplemental Exams: If a student feels that s/he has not performed as well as expected on the final
exam, s/he may apply for a supplemental exam subject to the following conditions: 1) a fee will be
charged; and 2) each student is allowed to write a maximum of two supplemental exams per year.
You must apply to the registrar for a supplemental exam.
Please keep ALL marked assignments, quizzes, exams, and bank marks in a safe place. They
are proof of your academic performance should a discrepancy arise.
Academic Misconduct: Please become familiar with what constitutes academic misconduct, as well
as the consequences. Plagiarism involves submitting work in a course as if it were your own work.
Plagiarism may involve the act of submitting work in which some or all of the phrasing, ideas, or line of
reasoning are alleged to be the submitter’s own but in fact were created by someone else. My policy
is to assume that you are honest until you force me to conclude otherwise. A plagiarism detection
tool MAY be used in this course for any written assignments that might be submitted. The
complete RDC policy is available at: Academic misconduct policy
Midterm Feedback: Midterm feedback for this course will be available from the instructor following
marking of the first midterm examination (around the last week of February)
The RDC Final Examination Policy will be followed with respect to final examinations. Please review
this document (http://www.rdc.ab.ca/Pages/default.aspx) to ensure you understand the contents and
implications of the policy.
This course may be eligible for Prior Learning Assessment. Students should refer to the RDC Course
Calendar for a list of excluded courses.
Classroom Learning Resources may be available to students in alternative formats. Students should
refer to the RDC Course Calendar for these resources.
-4Students should be aware that Personal Counseling, Career, Learning and Disability Services are
provided by RDC (http://www.rdc.ab.ca/Pages/default.aspx). It is the student’s responsibility to
discuss their specific learning needs with the appropriate service provider.
PLEASE NOTE: For ALL in-class quizzes and exams, the following are NOT permitted:



Baseball-style hats
Electronic devices of ANY kind (e.g. computers, cell phones, iPods, iPads,
blackberries, dictionaries, translators, etc.) unless required for medical
reasons or for documented learning disabilities.
Anyone seen using an electronic device during any exam will receive an
automatic ZERO on the exam and asked to leave the exam.
Late Assignments/Missed Exams: Accommodations will be made for late assignments and/or
missed quizzes/exams ONLY when a letter, written and signed by a medical doctor, is provided.
A grade of ZERO will be assigned otherwise. The letter (hardcopy) must be submitted to the instructor
within one week from the date the exam was written or one week from the due date of the assignment.
In addition, only those students who have attended the majority of lectures prior to the exam will be
granted a make-up exam. Please contact your instructor if you have any questions or concerns
regarding these accommodations.
The following chart is used to convert percent grades to letter grades. PLEASE NOTE: This chart
applies to Will’s lecture section(s) only and MAY NOT apply to any other course at RDC. This
conversion scale is based on the Alberta Government’s Post Secondary Education Transfer Guide.
Performance Level
Exceptional Performance
A+
Approximate
%
Equivalency
96 – 100
Excellent Performance
A
A-
90 – 95
85 – 89
4.0
3.7
Good Performance
B+
B
80-84
75 – 79
3.3
3.0
B-
70-74
2.7
C+
C
64-69
60 – 63
2.3
2.0
C-*
(see below)
D+
D
56 – 59
1.7
53-55
50 – 52
1.3
1.0
F
0 – 49
0.0
Satisfactory Performance
Pass
Fail
RDC Grade
RDC
Grade
Points
4.0
C- is the minimum acceptable passing grade at the University of Alberta (if that’s
where you plan on going).
NOTE:
All examination papers and booklets are and shall remain the property of Red Deer College. In other
words, you don’t get to keep your midterm and final exam papers. Final exams are reviewable upon
request.
NOTE:
Jan 13 is the last day to register or add/drop courses for the winter term. March 19 is the LAST day to
withdraw from the winter term classes and receive a WD. April 9 is the last day of classes. Final
exam period is April 14 - 21 inclusive. It is your Responsibility to be available for the COMPLETE
final exam time period. Do not make any expensive vacation plans during the final exam period.
-510. Absences and tardiness:
You are strongly urged to attend and actively participate in all classes, as there is a very strong
correlation between attendance and grades. However, if you do miss a class, you should arrange to
borrow notes from other students in class because you are still responsible for all information
(including assignment due dates, etc.) covered in this class. If you miss an exam or assignment you
will receive a grade of zero unless you provide the instructor a written letter from a medical doctor
indicating that you were absent due to illness or a letter from you indicating domestic affliction.
BE ON TIME PLEASE. If you are more than 10 minutes late don’t bother coming to class. You will be rudely
interrupting the courteous students who were ON TIME and eager to learn!
11. Cell phone and computer use:
Cell phone use of any kind during lectures and exams is strictly prohibited. You will be asked to leave
the class if cell phone use becomes an issue. If you are asked to leave class, you must meet with your
instructor in person to discuss the issue BEFORE you are permitted to attend lecture again. To avoid
any problems - leave your phone in your locker!
Computer use in lectures is welcome – as long as it is being used for lecture purposes. Facebook,
Twitter, YouTube, email, games, porn, etc. are generally not relevant to lecture material in this course!
Those using computers for lecture purposes are asked to sit in the front row.
12. Consultation/Office hours:
My door is always open!!! Please feel free to stop by my office (1607D) anytime – if I’m in – we
can talk! If you would like to make a specific appointment, see me before or after class or email me.
13. Lecture Outline:* (numbers in brackets refer to chapters in the textbook*)
Topic 1
Biological organization; the classification of life; and science (portions of 1, 25, 26, 27)
Topic 2
The chemical context of life and the importance of water (2, 3) Self-directed
Topic 3
Macromolecules (4, 5)
Topic 4
OMITTED –W’14 term
Topic 5
Cell membranes (7)
Topic 6
Cell exteriors and intercellular junctions (6, 27)
Topic 7
Internal eukaryotic cell architecture (6)
Topic 8
Metabolism, energy, and thermodynamics (8)
Topic 9
Cellular respiration (anaerobic and aerobic) (9)
Topic 10
Photosynthesis (10)
Topic 11
Prokaryotic metabolism (26 & 27)
Topic 12
Eukaryotic cell division: Mitosis (12); Meiosis (Chapter 13) and cancer (18)
Topic 13
DNA structure and replication (16, 18)
Topic 14
Genes, the genetic code, and protein synthesis (17)
Topic 15
Bacterial genetics (18)
Topic 16
Acellular particles: viruses, bacteriophages; prions (Time Permitting) (19)
* As you can see this course is NOTHING like Biology 30. Please do not assume it is. We are interested in
cells in this course – not humans!
14. Learning Objectives*
 The following objectives are meant as a “guide” to your understanding of lecture material.
Exam questions will be based, in part, on your understanding of the learning objectives
provided and your ability to apply this understanding to specific applied scenarios.
 All learning objectives are subject to change. If any objectives are omitted or revised, you will
be notified in lecture or via email.
-6Topic 1. Biological themes; the classification of life, and science (portions of chapters 1, 6, 26, 27)
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Describe the FOUR unifying themes that pervade cell biology and explain how each helps to make sense out
of the enormity of biology.
Define life (as it pertains to cell biology)
Diagram the organizational hierarchy (levels of organization) in biology.
Use a specific biological example to explain the principle of emergent properties.
Explain why the continuity of life is based on DNA.
Provide a general overview of how energy and chemical energy flow through an ecosystem.
Explain why the cell theory is still a theory.
List three morphological traits that ALL cells share and explain why this commonality exists.
Distinguish between prokaryotic and eukaryotic cells and be able to compare and contrast the major features
of both cell types. (E.g. cell size and morphology, method of reproduction, chromosomal compliment,
metabolism, etc.)
Distinguish among the three Domains of life. List and distinguish among the three kingdoms of multi-cellular,
eukaryotic life.
Who devised the 3 Domain system of classification and why?
Explain the criteria the 5 kingdom system of classification is based on.
Discuss the significance of rRNA analysis with regards to the classification of life.
Discuss why it matters that we know what life is and how it is organized.
Define science; describe its unique characteristics and explain how science is used to solve specific
problems.
Use specific examples to compare and contrast mechanistic and vitalistic philosophies.
Distinguish between the scientific and colloquial use of the word "theory" and explain the problem with the
often heard statement “Oh, that’s just a theory”.
Explain how science has influenced YOU personally either socially, academically or economically. (Self directed)
Use a specific example to explain how science and technology relate to society. (Reading assign. Pgs. 24-25)
To understand the terminology that goes with biology, I suggest you start a word list (or a set of flashcards) of
terms/phrases that are new to you NOW and add to this list after each lecture
In addition to these general learning objectives, all questions posed in the Bb lecture notes are testable.
NOTE*:
 Unless otherwise indicated by your instructor, you are responsible for ALL learning objectives
provided. Because of time constraints, some material may not be covered in lecture. You are,
however, still responsible for this material. In most cases the information can be easily found in
the text, in the on-line Biology 217 lecture notes or other suggested readings or lecture
handouts.
 “Reading assignments” are JUST THAT! It is YOU’RE responsible to find the appropriate pages in
the text or on-line and READ!!! Reading assignments are testable.
 “Self-directed assignments” are totally up to you. Often, you may just have to “THINK” about
what I’m asking and be prepared to present your point of view. All self-directed assignments
are testable.
Topic 2. The chemical context of life and the importance of water (portions of chapters 2, 3, 5)
We will NOT be going over much of Topic 2 in lecture. Instead, you will be completing a “self-directed learning
experience”. This is a fancy way of basically saying – “You learn it on your own”!! The suggested chapters in the
text (listed above) and the completed lecture notes on Bb will provide you all the information you need to complete
your task. I suggest Google would NOT be the first route to take in this exercise.
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List the eight elements that make up over 99% of ANY cell and explain WHY these eight are needed in such
large amounts.
Compare and contrast the three main types of chemical bonds: covalent, ionic, hydrogen. (e.g. relative bond
strength, behavior of the electrons involved).
Explain why a water molecule is polar and capable of bonding with four neighboring water molecules.
Explain the importance of water being a polar molecule.
List the five unique chemical properties of water.
Discuss the biological implications (relevance) of the five unique properties of water (from objective #5).
Explain why water never has a pH of 7.0?
Explain how the dissociation of water is the basis of the pH scale and explain how the pH of a solution may
change.
Use a balanced chemical equation to explain how acid precipitation forms from an excess of carbon dioxide in
the atmosphere.
Briefly describe the four levels of protein structure.
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Use a specific example to explain what exactly a protein is and why proteins are so sensitive to a decrease in
pH (increase in H+)
Briefly discuss the cause and effect of ocean acidification.
Be able to correctly answer ALL questions posed in the attached notes.
In addition to these general learning objectives, all questions posed in the Bb lecture notes are testable.
Topic 3. Macromolecules (and a bit if biochemistry) (chapters 4, 5)
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Explain how carbon’s electron configuration explains its ability to form large, complex and diverse organic
molecules.
Describe how carbon skeletons may vary, and explain how this variation contributes to the diversity and
complexity of organic molecules.
Briefly explain why life is said to be “carbon-based”.
List the four major classes of macromolecules and be able to distinguish between monomers and polymers
Draw diagrams to illustrate condensation and hydrolysis reactions.
Use specific examples to distinguish between catabolic & anabolic reactions, and endergonic & exergonic
reactions.
Distinguish between monosaccharides, disaccharides, and polysaccharides and provide a specific example
and function of each.
Describe the formation of a glycosidic linkage (bond).
Distinguish between the glycosidic linkages found in starch and cellulose. Explain why the difference is
biologically important.
Describe the building-block molecules, structure, and biological importance of triglycerides (fats and oils),
phospholipids, and steroids.
Distinguish between saturated and unsaturated fats.
Explain chemically why olive oil is liquid at room temperature whereas butter is solid at room temperature.
Distinguish between cis and trans fat molecules and discuss the heath aspects of these molecules.
(Reading assignment)
Discuss the biological relevance of the amphipathic nature of phospholipids.
Explain how cholesterol and phospholipid molecules help to maintain membrane fluidity.
Explain how a peptide bond forms between two amino acids.
Explain what determines protein structure and why protein structure is so important to cell biochemistry.
Explain how the primary structure of a protein is determined.
Name two types of secondary protein structure. Explain the role of hydrogen bonds in maintaining secondary
structure.
Explain how weak interactions and disulfide bridges contribute to tertiary protein structure.
Use a specific example to explain how a protein may become denatured and be able to explain the biological
relevance of protein denaturation.
List the major components of a nucleotide, and describe how these monomers are linked to form a nucleic
acid.
Distinguish between: pyrimidine and purine; nucleotide and nucleoside; ribose and deoxyribose; 5 end and 3
end of a nucleotide.
Compare and contrast RNA with DNA with regards to chemical composition, location, and function.
In addition to these general learning objectives, all questions posed in the Bb lecture notes are testable.
Topic 4. OMITTED – W’14 term
Topic 5. Cell membranes (chapter 7)
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List at least five specific functions of cell membranes.
Discuss the evidence for the fluid mosaic model of membrane structure.
Explain the meaning of the statement that phospholipids and most other membrane constituents are
amphipathic molecules.
Explain how the fluid mosaic model of membrane structure explains each experimental finding:
a. Actual membranes adhere more strongly to water than do artificial membranes composed only of
phospholipids.
b. Membranes with different functions may differ in type and number of membrane proteins.
c. Membrane proteins are not very water-soluble.
d. EMs of freeze-fracture membrane preparations shows protein particles interspersed in a smooth matrix.
Describe the fluidity of the components of a cell membrane and explain how membrane fluidity is influenced by
temperature and membrane composition.
Explain how cholesterol/phytyosterols help to maintain membrane fluidity as temperatures change.
Distinguish between peripheral and integral membrane proteins and provide a specific example of each.
Explain the role of membrane carbohydrates in cell-cell recognition.
Explain HOW cell membranes are selectively permeable. How exactly is selectivity determined?
Explain how hydrophobic molecules cross cell membranes.
Distinguish between channel proteins and carrier proteins.
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Explain how aquaporins facilitate the passage of water through membranes.
Define diffusion. Explain why diffusion is a passive and spontaneous process.
Explain why a concentration gradient of a substance across a membrane represents potential energy.
Distinguish between solutions that are hypertonic, hypotonic, and isotonic to cell contents.
Define osmosis and predict the direction of water movement based on differences in solute concentrations.
Explain how transport proteins facilitate diffusion.
Distinguish between osmosis, facilitated diffusion, and active transport. Provide specific examples of each.
Use a specific example to explain the process of cotransport.
Explain how large nonpolar molecules are transported across a cell membrane.
Use a specific example to explain how vesicular (bulk) transport across a cell membrane works.
Use specific examples to distinguish between exocytosis and receptor-mediated endocytosis.
In addition to these general learning objectives, all questions posed in the Bb lecture notes are testable.
Topic 6. Cell exteriors and intercellular junctions (chapters 6, 27)
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Describe the basic structure and function of a bacterial cell wall.
Compare the similarities and differences between Gram positive and Gram negative cell walls.
Discuss the medical relevance of bacterial cell walls (both Gram positive and Gram negative).
State the function(s) of each of the following prokaryotic features:
a. Capsule (glycocalyx)
b. fimbriae
c. sex pili
d. peptidoglycan
e. LPS layer
f. Porin proteins
What is a biofilm and what advantages does it provide to bacterial cells.
Describe the basic structure and functions (at least two) of plant cell walls.
Describe the basic structure of the extracellular matrix (ECM) in animal cells and its primary functions (at least
two).
Briefly describe three different examples of ECM discussed in lecture.
Name the intercellular junctions found in plant and animal cells and list the function of each type of junction.
Explain why the cell wall and ECM can’t be impermeable to metabolites.
List three aspects of cell structure that best reveal the evolutionary unity of cells?
In addition to these general learning objectives, all questions posed in the Bb lecture notes are testable.
Topic 7. Internal eukaryotic cell architecture (chapter 6)
This lecture topic is a TAKE-HOME ASSIGNMENT. Please see Pg. 7.1 on Bb for details.
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Explain the advantages of compartmentalization in eukaryotic cells.
Describe the structure and function of the nuclear envelope, including the role of the pore complex.
Briefly explain how the nucleus controls protein synthesis in the cytoplasm.
Explain the role of the nucleolus in protein synthesis.
Distinguish between free and bound ribosomes in terms of location and function.
List the components of the endomembrane system, and describe the structure and function of each
component.
Compare the structure and functions of smooth and rough ER.
Explain the significance of the cis and trans sides of the Golgi apparatus.
Name three different kinds of vacuoles, giving the function of each kind.
Briefly describe the energy conversions carried out by mitochondria and chloroplasts.
Describe the structure of a mitochondrion and explain the importance of compartmentalization in
mitochondrial function.
Distinguish among amyloplasts, chromoplasts, and chloroplasts.
Identify the three functional compartments of a chloroplast. Explain the importance of compartmentalization
in chloroplast function.
Describe the evidence that mitochondria and chloroplasts are semiautonomous organelles.
Explain the roles of peroxisomes in eukaryotic cells.
Describe the functions of the cytoskeleton.
Compare the structure, monomers, and functions of microtubules, microfilaments, and intermediate
filaments.
Explain the structure and role of centrioles and basal bodies.
Explain how the ultrastructure of cilia and flagella relate to their functions.
In addition to these general learning objectives, all questions posed in the Bb lecture notes are testable.
-9Topic 8. Metabolism, energy, and thermodynamics (chapter 8)
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Define metabolism and explain why cells need energy.
Use specific examples to explain the role of catabolic and anabolic pathways in cellular metabolism.
List the SIX main kinds of cellular work. Explain in general terms how cells obtain the energy to do cellular
work
Distinguish between kinetic and potential energy. Provide specific examples of each.
Distinguish between a closed and an open system. Explain why an organism is considered an open system.
What is thermodynamics and explain the first and second laws of thermodynamics in your own words.
Explain why highly ordered living organisms do not violate the second law of thermodynamics.
Write and define each component of the equation for free-energy change.
Use specific examples to explain the difference between spontaneous chemical reactions and nonspontaneous reactions.
Distinguish between exergonic and endergonic reactions in terms of free energy change.
Define oxidation and reduction.
Explain in general terms how redox reactions are involved in energy exchanges.
Explain why metabolic disequilibrium is one of the defining features of life.
Describe the structure of ATP and identify the major class of macromolecules to which ATP belongs.
Be able to distinguish between the three ways ATP can be synthesized.
Explain how ATP performs cellular work.
Explain what an enzyme is and describe the function of enzymes in biological systems.
Why must the cytoplasm be extremely crowded for enzymes to function optimally?
Explain why an investment of activation energy is necessary to initiate a spontaneous reaction.
Explain how enzyme structure determines enzyme specificity.
Explain the induced-fit model of enzyme function.
Describe the mechanisms by which enzymes lower activation energy.
Explain how substrate concentration affects the rate of an enzyme-catalyzed reaction.
Explain how temperature, pH, cofactors, and enzyme inhibitors can affect enzyme activity.
Use a specific example to explain the principle of competitive inhibition.
In addition to these general learning objectives, all questions posed in the Bb lecture notes are testable.
Topic 9. Cellular respiration (anaerobic and aerobic) (chapter 9)
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Explain why cells need energy to perform work.
In general terms, distinguish between fermentation and cellular respiration.
Write the summary equation for cellular respiration. Write the specific chemical equation for the degradation
of glucose.
Define oxidation and reduction (repeat).
Explain in general terms how redox reactions are involved in energy exchanges.
Describe the role of NAD+ in cellular respiration.
In general terms, explain the role of the electron transport chain in cellular respiration.
Name the three stages of cellular respiration and state the region of the Euk. cell where each stage occurs.
Describe how the carbon skeleton of glucose changes as it proceeds through glycolysis.
Explain why ATP is required for the preparatory steps of glycolysis.
Identify where substrate-level phosphorylation and the reduction of NAD + occur in glycolysis.
Describe where pyruvate is oxidized to acetyl CoA, what molecules are produced, and how this process links
glycolysis to the citric acid cycle.
List the reactants and products of the citric acid cycle. Explain why it is called a cycle.
Describe the point at which glucose is completely oxidized during cellular respiration.
Distinguish between substrate level phosphorylation and oxidative phosphorylation.
In general terms, explain how the exergonic “slide” of electrons down the electron transport chain is coupled
to the endergonic production of ATP by chemiosmosis.
Explain why ATP synthase is considered a molecular rotary motor.
Explain where and how the respiratory electron transport chain creates a proton gradient. Explain why this
gradient is described as a proton motive force.
Summarize the net ATP yield from the oxidation of a glucose molecule by constructing an ATP ledger.
Explain why it is not possible to state an exact number of ATP molecules generated by the oxidation of a
molecule of glucose.
Distinguish between fermentation and anaerobic respiration.
State the basic function of fermentation.
Compare the fate of pyruvate in alcohol fermentation and lactic acid fermentation.
Compare the processes of fermentation and cellular respiration with regards to overall chemical efficiency.
Distinguish between obligate and facultative anaerobes.
Describe how food molecules other than glucose can be oxidized to make ATP.
Explain how glycolysis and the citric acid cycle can contribute to anabolic pathways.
In addition to these general learning objectives, all questions posed in the Bb lecture notes are testable.
- 10 Topic 10. Photosynthesis (chapter 10)
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In general terms, explain the flow of energy and nutrients through an ecosystem.
Briefly explain how the laws of thermodynamics apply to the flow of energy through an ecosystem.
Explain the intimate chemical relationship between cellular respiration and photosynthesis.
Describe the structure of a chloroplast, listing all membranes and compartments.
Write a summary equation for photosynthesis.
Explain van Niel's hypothesis and describe how it contributed to our current understanding of photosynthesis.
Describe the evidence that supported his hypothesis. (Reading Assignment)
In general terms, explain the role of redox reactions in photosynthesis.
Describe the two main stages (the light Rxs and carbon fixation) of photosynthesis in general terms.
Describe the relationship between an action spectrum and an absorption spectrum. Explain why the action
spectrum for photosynthesis differs from the absorption spectrum for chlorophyll a.
List the wavelengths of light that are most effective for photosynthesis.
Explain what happens when a solution of chlorophyll a absorbs photons. Explain what happens when
chlorophyll a in an intact chloroplast absorbs photons.
List the components of a photosystem and explain the function of each component.
Explain why water is essential for a photosystem to function.
Trace the movement of electrons in linear (noncyclic) electron flow and explain the function(s) of this electron
flow
Describe the similarities and differences in chemiosmosis between oxidative phosphorylation in mitochondria
and photophosphorylation in chloroplasts.
State the function of each of the three phases of the Calvin cycle.
Describe the role of ATP and NADPH in the Calvin cycle.
Know what reactants go into the Calvin cycle (and where they came from) and what products come out (and
where they go)
List the possible fates of photosynthetic products.
Briefly explain the contributions Peter Mitchell and Melvin Calvin made to our understanding of how cells
transform light energy into chemical energy.
In addition to these general learning objectives, all questions posed in the Bb lecture notes are testable.
Topic 11. Prokaryotic metabolism (chapters 25, 27)
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Explain why it might be said that the history of life on Earth is one long “age of prokaryotes”.
Discuss the reasons why Prokaryotes are “Masters of Adaptation”.
Describe how prokaryotes carry out photosynthesis and cellular respiration when they lack
compartmentalized organelles such as chloroplasts and mitochondria.
What specific structural features (physiological and morphological) allow Prokaryotes to adapt and survive?
Explain why prokaryotes are unable to grow in very salty or sugary foods, such as cured meats or jam.
State the function(s) of each of the following prokaryotic features: (REPEAT OBJECTIVE)
a. capsule
b. fimbriae
c. sex pilus
d. nucleoid
e. plasmid
f. endospore
Explain why Prokaryotes possess more metabolic diversity than in ALL Eukaryotes combined.
Distinguish, with prokaryotic examples, among the following nutritional types: photoautotrophs,
chemoautotrophs, photoheterotrophs, and chemoheterotrophs. List the source of carbon and energy for
each.
Distinguish among obligate aerobes, facultative anaerobes, and obligate anaerobes.
Discuss the “problem with oxygen”. (READING ASSIGNMENT)
Define nitrogen fixation and provide a general chemical equation for this process.
Explain the importance of nitrogen fixation to life on Earth.
Discuss the FIVE ecological roles (niches) Prokaryotes play.
Define bioremediation. Describe two examples of bioremediation involving prokaryotes.
Explain why some Archaea are known as extremophiles. Describe the distinguishing features of extreme
halophiles and extreme thermophiles.
Discuss the metabolism and environmental significance of methanogens.
In general terms, describe the role of chemoheterotrophic and autotrophic prokaryotes in the cycling of
chemical elements between the biological and chemical components of ecosystems.
Distinguish among mutualism, commensalism, and parasitism. Provide an example of a prokaryote partner
in each type of symbiosis.
Identify two specific ways prokaryotes have affected you positively today and two specific ways prokaryotes
have affected you negatively today. (SELF DIRECTED)
In addition to these general learning objectives, all questions posed in the Bb lecture notes are testable.
- 11 Topic 12. Eukaryotic cell division: Mitosis (chapter 12); Meiosis (Chapter 13) and cancer (chapter 18)
Mitosis
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Briefly compare cell division in prokaryotes and eukaryotes.
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Explain how cell division functions in reproduction, growth, and repair.
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Describe the structural organization of a prokaryotic and eukaryotic genome.
4.
Describe the major events of eukaryotic cell division that enable the genome of one cell to be passed on to
two daughter cells.
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List the phases of the cell cycle and describe the sequence of events that occurs during each phase.
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List the phases of mitosis and describe the events characteristic of each phase.
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Explain why DNA must be condensed and uncondensed during cell division and explain the role of histones in
these processes.
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Describe the changes in the mitotic spindle during each phase of mitosis.
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Define cytokinesis and compare this process in animals and plants.
10. Briefly explain how the cell cycle is regulated and explain what occurs in checkpoints G1 and G2
11. Describe the internal and external factors that influence the cell cycle control system.
12. Explain how the abnormal cell division of cancerous cells escapes normal cell cycle controls.
Meiosis
13. Explain in general terms how traits are inherited from parents to offspring.
14. Describe how the chromosome number (chromosomal compliment) changes throughout the human life
cycle.
15. List the FOUR functions meiosis plays (its MORE than just reduction division).
16. Distinguish between the following pairs of terms:
Asexual and sexual reproduction
Binary fission and mitosis
Mitosis and meiosis
Somatic cells and gametic cells
Haploid and diploid
Chromosome and chromatid
17. Explain how haploid and diploid cells differ from each other. State which cells in the human body are diploid
and which are haploid.
18. Explain why fertilization and meiosis must alternate in all sexual life cycles.
19. Distinguish between the three life cycle patterns characteristic of eukaryotes, and name one organism that
displays each pattern. (READING ASSIGNMENT)
20. In general terms, describe the phases of meiosis I and meiosis II and describe the events characteristic of
each phase.
21. Describe the process of synapsis during prophase I and explain how genetic recombination occurs.
22. Discuss the significance of genetic recombination.
23. Describe three events that occur during Meiosis I but not during Mitosis
24. Explain how independent assortment, crossing over, and random fertilization contribute to genetic variation in
sexually reproducing organisms.
25. In addition to these general learning objectives, all questions posed in the Bb lecture notes are testable.
Topic 13. DNA structure and replication (chapters 16, 18)
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Explain why researchers originally thought protein was the genetic material.
Explain how the experiments performed by the following scientists provided evidence that DNA is the genetic
material: (READING ASSIGNMENT)
a.
Frederick Griffith
b.
Oswald Avery, Maclyn McCarty, and Colin MacLeod
c.
Alfred Hershey and Martha Chase
d.
Erwin Chargaff
Explain how Watson and Crick deduced the structure of DNA and describe the evidence they used. Explain
the significance of the research of Rosalind Franklin.
Describe the structure of DNA. Explain the base-pairing rule and describe its significance.
Describe the semiconservative model of replication and the significance of the experiments of Matthew
Meselson and Franklin Stahl.
Describe the process of DNA replication, including the role of the origins of replication and replication forks.
Explain the role of DNA polymerases in replication.
Explain what energy source drives the polymerization of DNA.
Distinguish between the leading strand and the lagging strand.
Explain how the lagging strand is synthesized even though DNA polymerase can add nucleotides only to the
3’ end. Describe the significance of Okazaki fragments.
Explain the roles of DNA ligase, primer, primase, helicase, topoisomerase, and single-strand binding
proteins, pol I, and pol II.
Define “antiparallel” and explain why continuous synthesis of both DNA strands is not possible.
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Explain the roles of DNA polymerase, mismatch repair enzymes, and nuclease in DNA proofreading and
repair.
Compare a bacterial chromosome and a eukaryotic chromosome.
Describe how the packing of chromatin changes during the course of the cell cycle.
In addition to these general learning objectives, all questions posed in the Bb lecture notes are testable.
Topic 14. Genes, the genetic code, and protein synthesis (chapter 17)
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Briefly explain how information flows from gene to protein.
Distinguish between transcription and translation.
Define the “Central Dogma” and discuss whether this idea is ever violated?
Explain the difference between exons and introns.
Distinguish between the “one gene-one enzyme” hypothesis and the “one gene-one polypeptide” hypothesis
and explain why the original hypothesis was changed.
Explain how RNA differs from DNA. (REPEAT)
Compare where transcription and translation occur in bacteria and in eukaryotes.
Define “codon” and explain the relationship between the linear sequence of codons on mRNA and the linear
sequence of amino acids in a polypeptide.
Why is the genetic code described as being a triplet code?
Explain why polypeptides begin with methionine when they are synthesized.
Explain what it means to say that the genetic code is redundant and unambiguous.
Explain how RNA polymerase recognizes where transcription should begin. Describe the role of the
promoter, the terminator, and the transcription unit.
Explain the general process of transcription, including the three major steps of initiation, elongation, and
termination.
Explain how RNA is modified after transcription in eukaryotic cells.
Define and explain the role of ribozymes. What three properties allow some RNA molecules to function as
ribozymes?
Describe the functional and evolutionary significance of introns.
Describe the structure and function of tRNA.
Explain how tRNA is joined to the appropriate amino acid.
Describe the structure and functions of ribosomes.
Describe the process of translation (including initiation, elongation, and termination) and explain which
enzymes, protein factors, and energy sources are needed for each stage.
Describe the significance of polyribosomes.
Explain what determines the primary structure of a protein and describe how a polypeptide must be modified
before it becomes fully functional.
Describe what determines whether a ribosome will be free in the cytosol or attached to the rough
endoplasmic reticulum.
Trace the “life history” of a protein – any protein (your choice – e.g. histamine, lysozyme, porin) from its gene
to its site of synthesis to its final site of action.
In addition to these general learning objectives, all questions posed in the Bb lecture notes are testable.
Topic 15. Bacterial genetics (chapter 18)
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Compare the major genetic differences between Prokaryotes and Eukaryotes. (READING ASSIGNMENT –
See page 15-1)
Prokaryotes (bacteria) are often considered very primitive life forms compared to Eukaryotes. Be able to
argue against this belief.
Discuss the genetic reasons why Prokaryotes (bacteria in particular) are considered “masters of adaptation”.
Define horizontal gene transfer (HGT) and discuss its importance to bacteria survival.
Discuss the role of Transformation, Conjugation, and Transduction in bacterial genetics.
Explain the adaptive advantage of bacterial genes grouped into an operon.
Using the trp operon as an example, explain the concept of an operon and the function of the operator,
repressor, and corepressor.
Explain how repressible and inducible operons differ and how those differences reflect differences in the
pathways they control.
Describe how the lac operon functions and explain the role of the inducer, allolactose.
Distinguish between positive and negative control. Give examples of each from the lac operon.
In addition to these general learning objectives, all questions posed in the Bb lecture notes are testable.
- 13 Topic 16. Acellular particles: viruses, bacteriophages; prions (Time Permitting) (chapter 19)
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List and describe the structural components of viruses.
Explain why viruses are obligate intracellular parasites.
Explain how a virus identifies its host cell.
Describe bacterial defenses against phages.
Distinguish between the lytic and lysogenic reproductive cycles, using phage  as an example.
Which viral genes are expressed during the prophage stage? Explain the significance of prophage gene
expression in the lysogenic cycle and to viral disease.
Describe the reproductive cycle of an enveloped virus.
Describe the reproductive cycle of an HIV retrovirus.
List some characteristics that viruses share with living organisms and explain why viruses do not fit our usual
definition of life.
Define and describe mobile genetic elements. Explain why plasmids, transposons, and viruses are all
considered mobile genetic elements.
Describe the evidence that viruses probably evolved from fragments of cellular nucleic acids. (READING
ASSIGNMENT)
Explain how viral infections may cause disease.
Describe the three processes that lead to the emergence of new viral diseases.
What is a prion and explain how prions may act as a transmissible pathogen.
Discuss the similarities and differences between viruses and prions?
In addition to these general learning objectives, all questions posed in the Bb lecture notes are testable.
It is the student’s responsibility to be familiar with the information contained in this outline and to clarify any areas of con cern
with the instructor.
Students should refer to the Student Dispute, Appeal and Misconduct Processes Policy and Standard Practi ce
(http://www.rdc.ab.ca/Pages/default.aspx) should questions or concerns about the course outline not be resolved directly with
the instructor.
Any changes to this course outline will be made in consultation with the students in attendance and must be approved by the
chairperson.
17 December 2013
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Chair’s Signature