Appendix 4.1 - page 1
BIO 351-1, p. 1 of 4
Phycology: Evolutionary Theory of Endosymbiosis
Study Questions
1. All living organisms can be classified into one of the three domains: ______________,
___________________, or _________________. Which are prokaryotic? Which of the
two prokaryotic domains are most closely related to eukaryotes? Describe the differences
between prokaryotic and eukaryotic cells, and what the Evolutionary Theory of
Endosymbiosis states about how eukaryotes may have evolved.
2. Describe how an endosymbiotic relationship might develop if a hetertrophic organism
uptakes another organism in a food vacuole.
3. Describe the symbiotic relationship between the diatom Rhizosolenia and the
Cyanobacteria Richelia. Can each grow on its own? When is it most advantageous to
Rhizosolenia to participate in the symbiotic relationship?
4. Describe several other examples of modern endosymbiotic relationships involving
Cyanobacteria. For each relationship, describe the advantage to the Cyanobacteria, and
describe the advantage to the host.
5. Define primary endosymbiosis, and draw a diagram that illustrates primary
endosymbiosis. (See Fig. 7-2 in the textbook.)
6. Which three algal Phyla obtained their chloroplasts through primary endosymbiosis?
Was there a single endosymbiotic event that led to these separate Phyla, or three separate
primary endosymbiotic events?
7. If chloroplasts are obtained through primary endosymbiosis, how many membranes
should surround the chloroplast? Where does each membrane originate? Explain the
molecular difference between the membranes that surround the chloroplast in
Glaucophyta, and explain why this difference provides evidence for the evolutionary
theory of endosymbiosis.
8. In general biology class, you may have erroneously learned that the nucleus is where the
DNA is located. Is this entirely true? If eukaryotic organelles were once separate
organisms, would you expect that all of the DNA in a eukaryotic cell would be in the
nucleus?
9. Rubsico is crucial to photosynthesis. Describe its role in the Calvin Cycle. Also,
describe how the genes that code for the enzyme provide evidence that the chloroplast
and nuclear genome have become incorporated.
10. DNA molecules in the chloroplast and mitochondria are circular. How does that provide
molecular evidence for the evolutionary theory of endosymbiosis?
11. Chloroplasts and mitochondria contain their own transfer RNAs, ribosomes, and other
molecules needed to transcribe and translate their DNA into proteins. In addition, their
ribosomes are more sensitive to certain antibiotics (e.g. tetracycline & streptomycin) than
are the ribosomes in the cytoplasm of the cell in which these organelles are located.
Explain how this provides further evidence for the evolutionary theory of endosymbiosis.
12. Several of the above questions lead you through the molecular evidence that supports the
evolutionary theory of endosymbiosis. You can obtain the information that you need to
answer those questions from notes you took during lecture or from Chapter 7 in your
textbook. Keep in mind that on the final exam, I won’t ask questions like those above
that specifically point you to the answer. Instead, I’ll ask a general question, such as
Appendix 4.1 - page 2
BIO 351-1, p. 2 of 4
“Describe, in detail, the different types of molecular evidence that support the
evolutionary theory of endosymbiosis.”
13. Describe several examples of modern symbiotic relationships in which eukaryotic algae,
such as Chlorophytes or Dinoflagellates, live as endosymbiotes within the cells of
another organism. What is the advantage to the algal endosymbiont, and what is the
advantage to the host organism?
14. Coral depend upon endosymbiotic dinoflagellates called _____________________.
What makes zooxanthellae different from other dinoflagellates, and how is that difference
advantageous to the coral?
15. Some coral eggs do not contain cells of zooxanthellae. How do the juvenile animals
acquire the zooxanthellae? How does this provide evidence that endosymbiotic events
could originate as phagotrophy?
16. Explain how secondary endosymbiosis differs from primary endosymbiosis. For
example, Chlorarachniophytes obtained their chloroplasts through endosymbiosis of a
Chlorophyta alga. Is this an example of primary or secondary endosymbiosis? Be able to
draw a diagram of secondary endosymbiosis, beginning with primary endosymbiosis and
ending with secondary endosymbiosis. Include a vestigial nucleus in the chloroplast, as
occurs in Figure 7-4. However, unlike Fig. 7-4, include all of the chloroplast membranes
that you would expect would be present as a result of secondary endosymbiosis,
assuming, that none were lost over evoluationary time. In your drawing, indicate the
origin of each membrane.
17. Examine Fig. 7-24 and discuss the ultrastructural evidence that shows that
Chlorarachniopytes obtained their chloroplasts through secondary endosymbiosis.
18. Chlorachniophytes obtained their chloroplasts through the uptake of a Chlorophyta alga,
while Cryptomonads obtained their chloroplasts through the uptake of a Rhodophyta
alga. Are these examples of primary or secondary endosymbiosis? Why do multiple
endosymbiotic events among algae help explain why algae are not a monophyletic group?
19. Figure 7-23 in your textbook is a transmission electron micrograph of a dinoflagellate
alga that shows two vestigial nuclei in the chloroplast. This indicates that the
dinoflagellate obtained its chloroplast through ________________ endosymbiosis.
20. Dinoflagellates are incredibly diverse. Some species of dinoflagellates obtained their
chloroplasts through secondary endosymbiosis, and some obtained their chloroplasts
through tertiary endosymbiosis. Describe how tertiary endosymbiosis differs from
secondary endosymbiosis.
Evolution of Plants from Charophyceaen Algae:
1. Plants evolved from _________________, a Class of algae in the Phylum
_________________. Draw an evolutionary tree that includes Chlorophyta,
Charophyceae, and Embryophytes. Explain why Embryophytes and Charophyceae form
a monophyletic group.
2. Explain the difference between a trait that would be an ancestral plant of plants, vs. a trait
that would be a derived trait of plants. Indicate on the evolutionary tree that you drew
where an ancestral trait would have evolved, and where a derived trait would have
evolved. Would all embryophytes necessarily have a derived trait?
3. Coleochaetales and Charales are two “advanced” orders of Charophycean algae, meaning
that they are the last orders to evolve in the Charophyceaen group. Describe how the
Appendix 4.1 - page 3
BIO 351-1, p. 3 of 4
physical structure of each of these orders differs, but also describe how the structures of
both orders are relatively complex, as would be expected from the evolutionary
precursors of Embryophytes.
4. When the rare, little known species Entransia fimbriata was discovered to be in the order
Klebsormidiales, Martha Cook conducted a detailed study of the structure of this species.
What aspects of this species did she examine? Discuss the purpose of conducting such a
detailed analysis of this algal species.
5. Define Plasmodesmata, and describe their function in plants. Ultrastructural similarities
suggests that the plasmodesmata in embryophytes and in ___________ (name the
particular order of algae in the Charophycean algal group) have the same origin. What is
meant by ultrastructural similarities? Based upon this evidence, are plasmodesmata an
ancestral or derived trait? If plasmodesmata originated in Charophycean algae, would
you expect that all plants should have plasmodesmata? Why or why not?
6. Explain how plants reproduce via alternation of generations. In your description, explain
the role of the gametophyte in providing protection to the plant embryo, and explain the
role of placental transfer cells in transferring material between the gametophyte and the
developing sporophyte embryo.
7. Although some algae (e.g. Phaeophyta kelp) have alternation of generations,
Charophycean algae do not. However, all embryophytes have alternation of generations.
Therefore, is the particular type of alternation of generations that occurs in embryophytes
an ancestral trait, or is it a derived trait that evolved in early plants?
8. Choleochaete is not considered to have alternation of generations. Although it has a
haploid and diploid stage, only the __________ stage is multicellular. Choleochaete
undergoes sexual reproduction by _____________(isogamy or oogamy). In
Choleochaete, placental transfer cells transfer material between the _________, which is
___________ (diploid or haploid), and the_________, which is ___________ (diploid or
haploid).
9. Advanced Charophyceae (Coleochaetales and Charales), as well as all embryophytes,
have a phragmoplast during cytokinesis. Primitive Charophyeceae (e.g. Klebsormidiales
and Zygnematales), and other Chlorophyta have a phycoplast. Describe the difference
between a phragmoplast and a phycoplast, and explain the role of the phragmoplast
during cytokinesis.
10. In most embryophytes, the new cell plate begins its development in the cell center. (To
begin formation of the new cell plate, the Golgi vesicles carry molecules that will make
up the new cell plate to the cell center.) However, it was recently discovered that
cytokinesis in the flowering plant Arabidopsis exhibits polarized cytokinesis. What does
that mean?
11. Martha Cook examined cytokinesis in Coleochaete cells. Only cells on the outside of
Coleochaete divide. Describe the two ways that Coleochaete cells can divide. Draw a
colony of Coleochaete, illustrating dividing cells undergoing each type of cell division.
12. The Arabidopsis cells that were observed undergoing polarized cytokinesis had large
vacuoles. Why then, was Coleochaete an ideal Charophycean alga in which to look for
polarized cytokinesis?
13. Analyze the figures in Martha Cook’s paper, which I posted on Blackboard and will also
review in class on Mon. Dec. 10. Why was it necessary to take photos in several focal
planes? In other words, how might her interpretation of cytokinesis differed if she had
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BIO 351-1, p. 4 of 4
only examined one focal plane? Based on your experience looking at algae with the light
microscope, how are you able to view different focal planes in a 3-dimensional cell?
14. Examine the figures in Martha Cook’s paper, and be able to replicate her findings with
your own drawings.
15. Explain why the large vacuole in Coleochaete cells affects cytokinesis.
16. Based upon Martha Cook’s analysis of cytokinesis in Coleochaete, explain whether
polarized cytokinesis is an ancestral or derived trait. Based on your answer, discuss
whether you would you expect polarized cytokinesis to be widespread among plants or
whether you would expect it to occur only in Arabidopsis and close relatives of
Arabidopsis.
17. List two other ancestral traits (not discussed in the study questions above) that evolved in
Charophycean algae, and list two derived traits that Charophycean algae don’t have.
Appendix 4.1 - page 5
BIO 301-1, p. 1 of 3
Cell biology spring 2010 exam 2 review questions
Sections –
- Transport to cellular compartments – mitochondria – nucleus – ER – Golgi – lysosome and
the cell surface.
- Role of Glycosylation in signaling and folding.
- Transport vesicle formation and use.
- Mitochondria and mitochondrial energetics.
- Mitochondrial disease.
- Basic photosynthesis.
1. Describe the differences between signal sequences and signal patches.
2. Describe the structure and function of a nuclear pore complex.
3. How do nuclear localization signals work? What type of signal are they?
4. Describe nuclear import receptors.
5. Tell me everything about the RAN system
6. How do nuclear import and export receptors differ?
7. Describe how TOM works- what does it interact with? What signals does it use?
8. How does TIM work? How do the two work together?
9. What role does ATP play?
10. What is the role of hydrogen pumps in getting proteins into the mitochondria?
11. What role do the HSP 70’s play?
12. How do we get things between the mitochondrial membranes?
13. What happens if an import protein is defective?
14. Describe the ER in detail- how do the two compartments differ?
15. What is the difference between the two populations of ribosomes?
16. Detail how a protein gets into the ER.
17. What are the roles for the smooth ER? In what cell types would you expect to see more of
it?
18. How were signal sequences discovered?
19. How do start – stop signals work to get a protein thru the membrane multiple times?
20. What is Glycosylation and why is it important?
21. Describe trimming and its role in proper folding.
22. How do calnexin and calreticulin distinguish folded from incompletely folded proteins?
23. Detail what happens to improperly folded proteins.
24. Detail how Molecular mechanisms of membrane transport work.
25. Define coated vesicles and coated pits.
26. How does a coat function?
27. What are the differences between the three types of coats?
28. Describe in detail the formation and function of Clathrin coated vesicles. Don’t forget the
role of triskits, adaptins, hsp70 and dynamin.
29. How do COP-I and COP-II vesicles differ?
30. What are the roles of SARs and ARFs? What do they expose to anchor themselves?
31. What does GEF do?
32. Describe the entire snare cargo catching system.
33. How does botox work?
Appendix 4.1 - page 6
BIO 301-1, p. 2 of 3
34. What’s NSF? (besides what they put on your check when there is not enough money in
your checking account).
35. What are the roles of RABs?
36. How are Vesicular tubular clusters formed? What do they do?
37. Describe the retrieval cycle for escaped membrane bound proteins.
38. Explain in detail the KDEL system.
39. What’s the role of pH in retrieval?
40. Describe the entire snare cargo catching system.
41. Describe the structure of the Golgi? What happens here?
42. Describe the process of sugar modification?
43. Describe transport thru the Golgi in detail.
44. Describe Transport from the trans Golgi network to lysosomes especially the role for pH?
45. Describe that lead to degradation in the cell.
46. Describe Receptor-mediated endocytosis.
47. What is Autophagy and how does it work? Phagocytosis?
48. Describe the role of mannose 6 phosphate and its receptor.
49. Describe the regulated secretory pathway.
50. Describe how oxidative phosphorylation occurs.
51. Describe Transfer of electrons from NADH to Oxygen.
52. Why is biological oxidation more efficient than combustion for our needs?
53. How does ATP synthase work? In both forward and reverse directions.
54. What are the relative production yields of fats and carbs?
55. How does the ATP/ADP ratio act as a regulator?
56. Define and describe redox potential.
57. How are electron transported between respiratory complexes?
58. How does shape change drive proton pumps?
59. Describe the basis of mitochondrial disease.
60. Describe the structure and function of MT DNA.
61. How are fats for energy in the mitochondria?
62. What is MERF and what is its etiology?
63. What is MELAS and what is its etiology?
64. How can children of the same parents have different levels or types of mitochondrial
diseases?
65. List and describe the Mitochondrial compartments.
66. Describe in detail how use chemiosmotic coupling to harness energy. What are you doing
during this process?
67. Why are Mitochondria are often seen associated with microtubules?
68. Where and what happens in Glycolysis.
69. What are two types of fermentation that can occur? How do they differ? How does the
cell deal with their end products?
70. Differentiate between Anaerobic and aerobic energy sources in short and long term
exercise. What is going on in terms of mitochondrial function?
71. What is the role of glycogen in long period exercise and fat utilization?
72. Why is NAD+/ NADH used as an electron carrier? And how doe sit transfer energy?
73. Outline the Transfer of electrons from NADH to Oxygen.
74. What is Oxidative phosphorylation? What is the mechanism of Oxidative
phosphorylation? Where does it occur? What happens if it fails?
75. How does Proton motive force drive ATP formation?
Appendix 4.1 - page 7
BIO 301-1, p. 3 of 3
76. How does ATP drive proton motive force? I.e. how does F0F1 ATPase work? Why does
it need to be reversible?
77. How is efficiency and metabolic rate related? What are the roles for UCPs?
78. Define Redox Potential.
79. How do differences in Redox Potential move electrons thru the electron transport chain?
80. How efficient is this process?
81. What are the components of the respiratory chain? What is the role of Ubiquinone and
cytochrome c in this pathway? Why is kinetics involved?
82. What drives the activity of proton pumps?
83. What is the basis of mitochondrial disease? Why do mitochondrial diseases have such a
wide variety of symptoms?
84. What’s different between mitochondrial DNA and nuclear DNA?
85. Describe fatty acid oxidation – why is it more efficient?
86. What mutation is involved in MERF?
87. How van the same mitochondrial inherited diseases show different levels of severity and
different times of onset in different people- even in the same family?
88. Describe the data supporting some form of paternal mitochondrial inheritance.
89. Tell me absolutely everything about RuBisCO.
90. Describe the structure of the chloroplast – give reasons for each feature.
91. How and why are antenna complexes formed?
92. Describe the reasoning behind the uses of the various pigments found in the antenna
complexes and in the chloroplasts.
93. What may be a common role for carotenoids in animal and plant systems? How does it
work in plants?
94. How do the 2 photo systems interact?
95. Describe the steps in Electron Flow through Photosystem II. Include the role of the
intermediaries.
96. Describe in detail the water splitting reaction. Why are so many photons needed to make
one oxygen? How does this help in battery charging?
97. Describe in detail the role of cytochrome bf.
98. What is the “special pair”? What are their roles? Where are they?
99. Describe electron flow and energy transfer in PSI.
100.
Compare and contrast the CF1-CF0 ATP synthase and the corresponding system
in mitochondria.
101.
What happens in Cyclic Electron Flow through Photosystem I? How does this
differ from the complete cycle? When and why is it used?
102.
How and why does Cyclic Photophosphorylation take place? What are the major
problems with Cyclic Photophosphorylation?
103.
What areof the three stages of the Calvin cycle?
104.
What are the immediate products of the RuBisCO reaction?
105.
How is RuBisCO affected by [CO2 ] and [O2 ]?
106.
How exactly does C4 differ from C3 carbon fixation?
107.
Describe in detail normal C3 fixation.
108.
Describe Crassulacean acid metabolism for carbon fixation.
109.
Compare Crassulacean acid metabolism and C3 and C4 metabolism.
110.
What happens in the oxidative phase of the Pentose Phosphate Pathway?
111.
Describe the roles of NADP+ and NADPH in the Pentose Phosphate Pathway.
112.
Why do we use both NAD+ & NADP+ ?
Appendix 4.1 - page 8
BIO-303
General Genetics
Exam 1 Study Guide
BIO 303-1, p.1 of 14
Terminology: Be sure you can define the following terms, and/or provide an example of each.
Gene
Chromosome
Chromatid
Centromere
Segregation
P1, F1 and F2 generations
Genotype
Genotypic ratio
Heterozygous
Recessive
Punnett Square
Dihybrid cross
Co-dominance
Variable Expressivity
Genetic anticipation
Gene Linkage
Crossing over
Haploid
Karyotype
Equational division
Mutant
Sex chromosome
Heterogametic sex
Bisexual
Monoecious
Dosage Compensation
Pedigree
Duplication
Paracentric Inversion
Nonreciprocal Translocation
Allele
Homologous chromosomes
Chromatin
Sister chromosomes
Independent assortment
Gamete
Phenotype
Phenotypic ratio
Homozygous
Dominant
Monohybrid cross
Back cross or Test cross
Epistasis
Penetrance
Genetic imprinting
Linkage group
Genome
Diploid
Reductional division
Wild-type
Autosome
Homogametic sex
Unisexual
Dioecious
Intersex
X-chromosome inactivation
Robertsonian Translocation
Pericentric Inversion
Reciprocal Translocation
Be sure you understand and can explain in detail the experiments done by,
Gregor Mendel
Sutton & Bovary
Frederick Griffith
Niremberg & Matthei
Avery, Macleod & McCarty
Mertz et al.
Hershey & Chase
T. H. Morgan
Watson & Crick
Correns, Devries & Tschermak
Schleiden & Schwann
Henking & Ruckert
Friedrich Mieschner
Rosalind Franklin
or, be sure you can describe/know what contribution they made to the field of genetics.
Appendix 4.1 - page 9
BIO-303
General Genetics
Exam 1 Study Guide
BIO 303-1, p.2 of 14
Indicate the chronological order of the following milestones of Genetics, with 1 being the earliest.
Note: this is not an exhaustive list of possible milestones of Genetics. Be sure to review the
notes for the first lecture for this question also.
Gregor Mendel proposes the basic laws of inheritance.
Schleiden & Schwann propose the cell theory of life.
Sutton & Bovari propose the chromosomal theory of inheritance.
First use of selection to improve crop yields.
Henking & Ruckert publish detailed descriptions of chromosome behavior during meiosis.
Watson & Crick propose the double helix model for the structure of DNA.
Mertz et al. report the identification of restriction endonucleases.
T. H. Morgan obtains the first experimental evidence supporting the chromosomal theory of
inheritance.
Avery, Macloed & McCarty provide the first experimental evidence that DNA is the genetic
material.
The Genetic Code is deciphered.
Sequencing of the human genome is completed.
The Watson & Crick model of a DNA molecule was based on data from biochemical studies and X-ray
diffraction analysis. For each of the following characteristics of DNA, indicate whether the
information came from biochemical (B) or X-ray diffraction (X) studies.
The amounts of the nitrogenous bases adenine (A) and thymine (T) in DNA are always equal.
The two strands of the helix are equally far apart along the length of the molecule.
The nitrogenous bases are located in the center of the helix.
There are approximately 10.4 base pairs per turn of the helix.
DNA is a linear molecule composed of four types of nucleotides.
Each nucleotide is composed of a sugar, a phosphate group, and a nitrogenous base.
Appendix 4.1 - page 10
BIO-303
General Genetics
Exam 1 Study Guide
BIO 303-1, p.3 of 14
In your own words, explain what restriction endonucleases are, and the importance of the discovery of
these enzymes to development of the field of molecular genetics.
Describe the stages of the cell cycle, and the events that characterize each.
Describe the events that characterize each stage of mitosis.
What are the various checkpoints in the cell cycle? Why are checkpoints important? What does each
checkpoint monitor?
Contrast the process of cytokinesis in animal and plant cells.
For the following statements indicate which ones are true for Meiosis (1) or Mitosis (2) or both (3)
a. Number of chromosomes in daughter cells remain same as parent
b. Takes place in somatic cells
c. Homologous chromosomes pair up
d. Spindle fibers form and extend towards the center of cell from the poles
e. DNA exchange takes place between non-sister chromatids of homologous chromosomes
f. Takes place only in reproductive cells
g. Parent cell undergoes two subsequent divisions
h. Homologous chromosomes pair up on equatorial plate
i. Amount of DNA is duplicated in the S phase
j. Cytokinesis (cytoplasm is split between daughter cells)
Mention at least one characteristic feature of the following steps of meiosis
Zygotene
Pachytene
Diplotene
Metaphase I
Anaphase I
Metaphase II
Anaphase II
Describe the stages of meiosis and the events that characterize each.
In a cell, two homologous dyads are seen, one at each the poles. (A) What stage of nuclear division is the
cell in? (B) In a meiocyte where 2n=32 how many bivalents will be visible?
Appendix 4.1 - page 11
BIO-303
General Genetics
Exam 1 Study Guide
BIO 303-1, p.4 of 14
Explain why meiosis leads to significant genetic variation while mitosis does not.
In what way(s) does the second division of meiosis differ from mitosis?
If an organism has a diploid number of 16 chromosomes, how many chromatids are visible at the end of
prophase of mitosis? How many chromosomes move towards each pole during anaphase?
There are 40 chromosomes in somatic cells of the white mouse (A) How many chromosomes does a mouse
receive from its dad (B) How many autosomes are present in a mouse gamete (C) How many sex
chromosomes are there in a mouse sperm?
How does the nucleus whose diameter is 5micron fit a 2meter long molecule of DNA?
In corn, the amount of DNA in several nuclei is measured based on UV light absorption. The measurements
were 0.7, 1.4 and 2.8. What cell types were likely used for the measurements?
If two chromosomes in a species karyotype have similar lengths and centromere placements, but are
not homologues, what is different about them? If you were a cytogeneticist, how would you
demonstrate that the chromosomes are not homologous?
Name one application of karyotyping in health sciences.
Tom and Mary got married and had a child who has a rare blood disorder. After performing karyotype on
the child doctors did not find any defects in the chromosomal structure. How can this phenomenon be
explained?
A round pea seed is germinated and the mature plant allowed to self-fertilize. Most of the seeds
produced are round, but some are wrinkled. What was the genotype of the original seed? What is the
expected ratio of round to wrinkled seeds.
Diagram a cross between a true breeding pea plant that produces yellow seeds (G/G) with one that
produces green seeds (g/g). Carry the cross out to the F2 generation. Answer the following questions:
What was the F1 genotype and phenotype?
Appendix 4.1 - page 12
BIO-303
General Genetics
Exam 1 Study Guide
BIO 303-1, p.5 of 14
What kinds of gametes could the F1 individuals produce?
What were the F2 genotypes and phenotypes, and in what ratios would you expect each to occur?
Diagram a cross between a true breeding pea plant that produces round seeds and purple flowers, with
one that produces wrinkled seeds and white flowers. (Round and purple are the dominant traits.) Carry
the cross out to the F2 generation. Answer the following questions:
What are the P1 genotypes?
What is the F1 genotype and phenotype?
What kinds of gametes will the F1 individuals produce?
What are the F2 genotypes and phenotypes?
What genotypic and phenotypic ratios are expected in the F2 progeny?
Diagram a cross between a true breeding pea plant that produces yellow seeds (G/G) and purple
flowers (W/W) with one that produces green seeds (g/g) and white flowers (w/w). Carry the cross out
to the F2 generation. Answer the following questions:
What was the F1 genotype and phenotype?
What kinds of gametes could the F1 individuals produce?
What were the F2 genotypes and phenotypes, and in what ratios would you expect each to occur?
Diagram a test cross of the F1 individuals from the question above, with the homozygous recessive
parent strain. What genotypes and phenotypes would you expect in the testcross progeny, and in what
ratios?
If you had a fruitfly with phenotype A, what test would you make to determine if it was Aa or AA? Explain
the different outcomes expected if the fly in question is AA or Aa.
If individuals of genotype AaBbCc are intercrossed:
How many different genotypes can occur in their progeny?
How many different phenotypes can occur in the progeny?
In a parental cross AABBCCDDEE X aabbccddee (A) how many different F1 gametes can be formed (B)
how many different genotypes are expected in the F2 (C) how many squares of a Punnett square would be
necessary to fit the F2 progeny?
What is the total number of gametes formed in the garden pea with chromosomal number 14, assuming
that at least one gene pair on each chromosome pair is heterozygous? What is the total number of possible
progeny with distinct phenotypes?
Appendix 4.1 - page 13
BIO-303
General Genetics
Exam 1 Study Guide
BIO 303-1, p.6 of 14
The lack of pigmentation is called albinism and in humans is the result of a recessive allele a and the
normal pigmentation is the result of its dominant allele A . Two normal parents have an albino child.
Determine the probability that (a) the next child will be an albino, (b) the next two children will be albino
(c) the chance of these parents producing two children – one albino and one normal?
The human condition albino is due to a recessive allele a. The dominant allele A is responsible for normal
pigmentation. Two normal individuals marry and have four albino children? How is this possible? Draw the
crosses to support your answer. What is the probability of this occurring?
The ability to taste the chemical Phenylthiocarbamate (PTC) is an autosomal dominant trait and the
inability to taste it is recessive. If a taster woman with a non taster father marries a taster man who in a
previous marriage had a non taster daughter what is the probability that their first child will be
a non taster girl
a taster boy
a non taster boy
In a breed of chickens brown feathers is governed by a recessive allele b and yellow feathers by its
dominant allele B. Determine the genotypic and phenotypic ratios expected from the following matings (A)
true breeding yellow X heterozygous yellow (B) heterozygous yellow X brown (C) true breeding yellow X
brown
Short hair in hamsters is governed by a dominant gene L and long hair by the recessive allele l . Black hair
results from the dominant genotype B_ and brown hair from bb (A) In a cross between a true breeding
short haired, black hamster and a true breeding short haired, brown hamster what genotype and
phenotypic ratios are expected among their progeny? (B) For the following cross LlBb X Llbb, what are the
phenotypes of the hamsters (i.e. the parents), what genotypes and phenotypes would you expect in their
progeny and in what ratios?
In tomatoes red fruit is dominant to yellow, oval shape is dominant to round and tall vine is dominant to
dwarf. A farmer has two pure lines, red, oval and dwarf, and yellow, round and tall. He wants to make a new
pure line that is yellow, oval and tall because there is higher demand for it. How should he do it? Show the
crosses he needs to make as well as how many progenies should be sampled in each case.
In shorthorn cattle, coat color may be red, roan (mix of red & white hairs), or white. Based on the
results of the following crosses, explain how coat color is inherited in cattle.
Red x red > all red progeny
White x white > all white progeny
Red x white > all roan progeny
Roan x roan > 1/4 red: 1/2 roan: 1/4 white
Appendix 4.1 - page 14
BIO-303
General Genetics
Exam 1 Study Guide
BIO 303-1, p.7 of 14
What are the genotypes of the parents and progeny in each cross from above?
A mother of blood group B has a child with blood group O. What are the possible genotypes of the mother
and the father?
In a maternity ward, four babies become accidentally mixed up. The ABO types of the four babies are
known to be O,A, B, and AB. The ABO types of the four sets of parents are determined. First, indicate
which baby(ies) could have been produced by each set of parents. Second, based on the process of
elimination, determine which baby is most likely the offspring of each set of parents. Note: in the second
part each baby can be assigned to only one set of parents and all four babies must be assigned to a set of
parents.
Parents
AB X O
AXO
AB X AB
OXO
Possible babies
Probable baby
A woman who is homozygous recessive for a mutation that causes deafness marries an unrelated man
who is also deaf because of homozygosity for a recessive mutation. They have a child whose hearing is
normal. Explain how this can happen. What genetic principle does this example illustrate?
In rats coat color is controlled by 2 independently assorting genes, producing 4 distinct colors,
A_B_ (gray), A_bb (yellow), aaB_ (black), and aabb (cream). A third gene determines whether fur
pigment is produced or not, C_ (pigmented), cc (no pigment, ie. white). What progeny genotype(s) and
phenotype(s) would be produced by the following crosses.
AAbbCC x aaBBcc
AaBbCc x AaBbcc
You cross a female fly having cinnabar (bright orange) colored eyes with a male who has brown eyes.
Both mutant eye colors are due to recessive alleles. The progeny of the cross have wild-type eye color.
You allow the F1 progeny to mate to each other, and in your F2 progeny you recover 340 flies with
wild-type eyes, 110 flies with cinnabar eyes, 115 flies with brown eyes, and 35 flies with white eyes.
How would you explain these results? Specifically think about, what are the genotypes of each
phenotypic class, and what is the likely source of the white eyed flies.
A cross of true breeding frogs that differ in regards to eye color (purple vs. green) and mating call
(uttering [rib-it rib-it] vs. muttering [knee-deep knee-deep]) produced F 1s that were all utters and had
Appendix 4.1 - page 15
BIO-303
General Genetics
Exam 1 Study Guide
BIO 303-1, p.8 of 14
blue eyes. Based on these results what can you postulate regarding the inheritance of these two traits
in frogs?
When the F1 frogs from the preceding cross were mated they produced F2 progeny in the following
ratio.
27/64 blue, utterer
12/64 green, utterer
9/64 purple, utterer
9/64 blue, mutterer
4/64 green, mutterer
3/64 purple, mutterer
a. How many gene pairs are involved in eye color and mating call in this species?
b. Of these, how many control eye color and how many control mating call type?
c. Assign gene symbols for all of the genes and indicate the genotypes of the P 1, F1 and F2
phenotypic classes.
Two normal looking fruit flies were crossed and in the progeny there were 404 females and 200 males.
What is unusual about this result?
Provide a genetic explanation for the anomaly.
Provide a test of your hypothesis.
The shape of carrots may be long (SLSL) , round (SRSR) or oval (SLSR). If long carrots are crossed to oval
carrots and the F1 is then allowed to cross at random among themselves, what phenotypic ratio is expected
among the F2 progeny?
A mutant allele in mice causes a bent tail. Six pairs of mice were crossed. Their phenotypes and those of
the progeny are given below. N=normal phenotype, B=bent phenotype. Deduce the mode of inheritance of
this phenotype.
Cross
Parents
Progeny
1
Fem.=N Male=B
Fem=all B
Male=all N
2
Fem = B Male=N
Fem=male=1/2B, 1/2N
3
Fem = B Male=N
Fem= all B Male=all B
4
Fem= N Male= N
Fem=all N
Male=all N
5
Fem=B
Male=B
Fem=B
Male=B
6
Fem=B
Male=B
Fem=B Male=1/2B, 1/2N
Wherever not mentioned consider all males/females to be of the same genotype e.g. Fem=N means all
females are normal
Is the phenotype recessive or dominant?
Autosomal or sex-linked?
What are the genotypes of all parents and the progeny?
Appendix 4.1 - page 16
BIO-303
General Genetics
Exam 1 Study Guide
BIO 303-1, p.9 of 14
The flowery fowl is much admired by farmers because of its looks but unfortunately it does not breed
true, when two flowery are intercrossed, they always produce 50 percent flowery, 25percent normal, and
25 percent with peculiar woolly feathers that soon fall out, leaving the birds naked.
Give a genetic explanation for these results, showing the genotypes of all phenotypes, and provide a
statement of how your explanation works.
If you wanted to mass-produce flowery fowls for sale, which types would be best to use as a breeding
pair?
An allele A that is not lethal when homozygous causes rats to have yellow coats. The allele R of another
gene that assorts independently produces a black coat. Together A and R produce a gray coat whereas a
and r produce a white coat. A gray male is crossed with a yellow female and the F1 is 3/8 yellow, 3/8 gray,
1/8 black and 1/8 white. What are the genotypes of the parents?
Cats with shortened legs are called ‘flatbush’. When flatbush are mated to normal cats they produce
Flatbush and normal cats with equal frequency. When Flatbush are mated to Flatbush they produce two
Flatbush to one normal. Crosses between normal cats produce only normal progeny. How can you explain
these results? Make sure you show the crosses that would support your hypothesis.
A wheat variety with colored seeds is crossed to a colorless strain producing an all-colored F1. In the F2,
1/64 of the progeny has colorless seeds (A) How many pairs of genes control seed color? (B) What were
the genotypes of the parents and the F1 (use your own symbols for the genes)
A dog breeder crosses a male Black Lab with a female yellow Lab. All of the puppies from all three
litters are black. Based on these preliminary results, which trait would you predict is dominant and
which is recessive assuming coat color is a monogenic trait? What would you predict is the genotype of
the puppies? If a male from one litter and a female from a second litter are bred when they reach
maturity, what would you predict for their offspring? That is, what would be the possible coat colors
and what probability would you predict for obtaining a puppy having a particular coat color. (4 pts)
You do the F1 cross described above in question 6. That is, you cross F1 males and females. A total of
32 F2 puppies are produced. The coat colors of the puppies are as follows: (6 pts)
18 black : 12 chocolate : 2 yellow
Based on this result what changes you would make to your hypothesis (assumptions and predictions
from question 6) regarding the inheritance of coat color in labrador retrievers?
What is the source of the chocolate coat color? What are the possible genotypes for each of the coat
colors? Note, your revised hypothesis must be consistent with the results obtained for both the F1 and
F2 generations.
Appendix 4.1 - page 17
BIO-303
General Genetics
Exam 1 Study Guide
BIO 303-1, p.10 of 14
A dog breeder crosses a male Black Lab with a female white Lab. All of the puppies from all three
litters are chocolate (brown). Based on these preliminary results, what can you tell me about
inheritance of coat color in Labrador retrievers? What would you predict is the genotype of the each
of the parents and of the puppies? If a male from one litter and a female from a second litter are
bred when they reach maturity, what would you predict for their offspring? That is, what would be
the possible coat colors and what probability would you predict for obtaining a puppy having a
particular coat color.
You do the F1 cross described in the question above. That is, you cross F1 chocolate males and females.
A total of 32 F2 puppies are produced. The coat colors of the puppies are as follows:
12 chocolate : 8 white : 6 black : 6 yellow
Based on this result what changes you would make to your hypothesis (assumptions and predictions
from the first part of the question) regarding the inheritance of coat color in labrador retrievers?
What is the source of the yellow and white coat colors? What are the possible genotypes for each of
the coat colors?
Note, your revised hypothesis must be consistent with the results obtained for both the F1 and F2
generations.
The images below show the four common colors of Budgerigars (Budgies or parakeets), blue, green,
yellow & white (albino). It is known that at least two genes are involved in feather color, the B-gene
that controls production of a blue pigment and the Y-gene that controls production of a yellow pigment.
When green Budgies are mated to each other, each of the four colors are observed among their
progeny, with green being most common, blue and yellow being less common and about equal to each
other, and the albinos being least common. Based on this information, how would you explain the
inheritance of feather color in this species?
Appendix 4.1 - page 18
BIO-303
General Genetics
Exam 1 Study Guide
BIO 303-1, p.11 of 14
Following up on the previous question, among the progeny of the green Budgies you also observe that
the blue Budgies fall into two distinct classes based on the intensity of the feather color, bright blue
(red arrow) and pale blue (yellow arrows). Assuming that there are just two genes involved in
determining feather color in Budgies, how would you explain the difference in the two classes of blue
Budgies? Be sure your answer is consistent with your answer from the preceding question.
Appendix 4.1 - page 19
BIO-303
General Genetics
Exam 1 Study Guide
BIO 303-1, p.12 of 14
What pattern of inheritance is shown in the pedigree below. Indicate below the symbol, the predicted
genotypes of individuals I-1, I-2, II-2, II-3, II-4, II-6, II-7, III-2, & III-4. Note: On the exam
the details of the pedigree may be different. Be sure you understand how to interpret
pedigrees in general, not just this specific pedigree.
I
II
III
1
2
3
4
5
6
7
8
Pattern of inheritanceIf individuals III-3 and III-6 married, what is the probability that they would have an affected child?
If individuals III-3 and III-7 married, what is the probability that they would have an affected child?
Describe the major difference(s) in sex determination and male fertility between Drosophila and
humans. What is the evidence to support this?
The graph below shows the effect of temperature on sex development in a species of turtle. Based on
this table, at what temperature range would you expect to see approximately equal numbers of males
and females? At what temperature range would you expect to see mostly male turtles? At what
temperature range would you expect to see mostly females developing? Be sure you are able to
explain the other 2 graphs on page 109 as well.
Appendix 4.1 - page 20
BIO-303
General Genetics
Exam 1 Study Guide
BIO 303-1, p.13 of 14
What is the current hypothesis regarding the basis for temperature dependent sex development in
some reptiles and turtles. Explain in detail how the hypothesis would account for the data shown in the
graph above.
Explain why calico and tortoiseshell cats are almost invariably female.
How could you account for a calico cat that is male?
Explain the difference between each of the following sets of terms.
Aneuploidy & euploidy
Monosomy & trisomy
Autopolyploid & allopolyploid
What is the evidence that Down Syndrome and other aneuploidies are more often the result of
nondisjunction during oogenesis rather than during spermatogenesis?
What evidence indicates that humans with aneuploid karyotypes occur at conception but are usually
inviable?
A girl with Turner syndrome also expresses the X-linked trait hemophilia, as did her father. In which
of her parents did nondisjunction occur to produce this result? Explain your reasoning.
A boy with Kleinfelter syndrome is born to normal appearing parents, except that the father has an Xlinked skin condition called anhidrotic extodermal dysplasia (AED). The mother’s skin appears normal.
The boy has patches of normal skin and patches of abnormal skin characteristic of AED. In which
parent did nondisjunction occur to produce this result? Explain your reasoning. Be sure to include
explanation regarding what Kleinfelter’s is and how you would account for the boy’s patches of normal
and AED type skin.
Explain the difference between paracentric inversion & pericentric inversion.
If an individual is heterozygous for a paracentric inversion, what would be the consequences if a
crossover occurred between the homologues (during meiosis), within the inverted region of the
chromosome? What effect would this have on the individual in which the crossover occurred?
If an individual is heterozygous for a pericentric inversion, what would be the consequences if a
crossover occurred between the homologues (during meiosis), within the inverted region of the
chromosome? What effect would this have on the individual in which the crossover occurred?
Appendix 4.1 - page 21
BIO-303
General Genetics
Exam 1 Study Guide
BIO 303-1, p.14 of 14
Inversions are said to “suppress crossing over”. Is this technically correct? If not, explain what
effect inversions have on crossing over.
Explain the difference between reciprocal and non-reciprocal translocations.
When two plants belonging to the same genus but different species are crossed, the F 1 hybrid is more
viable, and has more ornate flowers than either parent. However, the hybrid is also sterile and can
only be propagated by vegetative cuttings. Explain why the hybrid is sterile. How could a plant
geneticist attempt to reverse the sterility of the hybrid?
The primrose Primula kewensis, has 36 chromosomes that are similar in appearance to the
chromosomes of two related species, P. floribunda (2n = 18) and P. verticillata (2n = 18). How could P.
kewensis arise from these related species? In genetic terms, how would you describe P. kewensis?
The first two pregnancies for a couple result in late term stillbirths. The reproductive histories of
both families, over 3 generations, showed a pattern of frequent miscarriages, stillbirths and
malformed babies that died shortly after birth in the husband’s family. There was no history of
miscarriages or other reproductive problems in the wife’s family. The husband has a karyotype done,
which shows that he has the normal number of chromosomes. What are the most likely causes of the
frequent miscarriages etc. in the husband’s family?
A young woman who is normal in appearance and intelligence has a child with Down syndrome.
Karyotypes of the woman and her child reveal that the woman has 45 chromosomes while her Down
syndrome child has 46. Explain how this could occur.
Appendix 4.1 - page 22
BIO 305-3, p. 1 of 2
General Ecology Study Questions for Chapter 11: Competition
Lecture Outline:
• Define competition and resource.
• Exploitative vs. interference competition.
• Competitive exclusion principle
• Lokta-Volterra equations
– Zero population growth isoclines represent stable population sizes (when population is
not growing or decreasing)
– Show that competing species coexist more easily when they use resources differently.
• Three reasons that could prevent competitive exclusion from occurring.
– Disturbance prevents competition from proceeding to its conclusion.
– Environmental instability can alter which species is superior.
– Resource partitioning and/or character displacement can reduce competition.
Study Questions
1. Define competition. Then, explain why each factor in the definition is important. Why must the
two species be competing for the same resource? Why must the resource be limiting in order for
competition to occur? Give a several examples of what can be considered to be “harm.”
2. Explain how a resource is different from a physical factor, and give several examples of each.
3. Fig. 11.4 shows competition between two diatom genera: Asterionella and Synedra. Use the data
in that figure to answer the following questions.
a. Define carrying capacity. Which diatom genus has the highest carrying capacity when
grown alone?
b. For what resource are the two genera competing? Which genus uses that resource more
efficiently? Use the data in Part 1 of Fig. 11.4 to support your answer.
c. When grown together, which genus outcompetes the other? Is it the genus with the
higher carrying capacity when grown alone? Or, is it the genus that uses the resource
more efficiently? Explain.
4. Explain how exploitative competition differs from interference competition.
5. Is the competition between Asterionella and Synedra an example of exploitative competition or
interference competition? Explain.
6. Does Fig. 11.6 show an example of exploitative competition or interference competition?
Explain.
7. For what resource is Semibalanus competing with Chthalamus (Fig. 11.8)? Why does each need
this resource, and why is the resource limiting in the environment in which these barnacles live?
8. Which barnacle (Semibalanus or Chthalamus) competes more effectively for the limiting
resource? With that in mind, why is the superior competitor not present at the top of the intertidal
zone? Explain how this example demonstrates that abiotic and biotic factors interact to determine
species distributions.
9. Describe the competitive exclusion principle and explain why the word “complete” is important
in the principle. Which figure illustrates the competitive exclusion principle: Fig. 11.10D or
11.10E?
10. Explain why P. caudatum and P. bursasaria (Fig. 11.10E) are able to coexist, while P. aurelia
and P. caudatum (Fig. 11.10D) are not.
11. Even though P. caudatum and P. bursasaria (Fig. 11.10E) are able to coexist, does the
competition between the two species affect their carrying capacities? Explain.
12. Explain how the Lotka-Volterra competition equation (p. 249) differs from the logistic growth
equation (p. 211). (You don’t need to memorize these two equations, but if I show either or both
on the exam, you will need to be able to explain what each term of each equation means and how
the equations differ from one another.)
Appendix 4.1 - page 23
BIO 305-3, p. 2 of 2
13. Use the Lotka-Volterra equations to complete the following.
a. If α increases, dN1/dt will ___________ (choose increase, decrease, or remain the same).
b. If N2 decreases, dN1/dt will __________ (choose increase, decrease, or remain the same).
c. If α decreases, dN2/dt will __________ (choose increase, decrease, or remain the same).
d. If K2 increases, dN2/dt will __________ (choose increase, decrease, or remain the same).
14. Define zero population growth isocline.
15. The equations for the N1 and N2 zero population growth isoclines can be determined when dN1/dt
and dN2/dt ___________________ (choose: >0, <0, or =0).
16. From the equation dN1/dt = r1N1 (1–(N1 + αN2) / K1), we know that dN1/dt =0 when
_________________ = 0.
17. In class, we solved the equation 1–(N1 + αN2)/K1 = 0 for N2 (as explained in Box 11.2 on p.
250). The result can be expressed as an equation for a line, y=mx+b, with N 1 as x and N2 as y.
What is the slope of the line? What is the y-intercept? How does this equation for a line compare
to Fig. 11.12a?
18. From the equation dN2/dt = r2N2 (1–(N2 + αN1) / K2), we know that dN2/dt =0 when
_________________ = 0.
19. Solve the equation you wrote in #18 for N2. Then, write the equation in the form of an equation
for a line (y=mx+b). Finally, compare that equation to the line graphed in Fig. 11.2b. (If you
have trouble, refer to Box 11.2 on p. 250 for help.)
20. Zero population growth isoclines:
a) Explain why the equation K1>K2/α (Fig. 11.13a) allows you to determine which of the results
occurs.
- competitive exclusion of species 1 (species 2 “wins”)
- competitive exclusion of species 2 (species 1 “wins”)
- coexistence
b) Do the same for K2>K1/α (Fig. 11.13b).
c) What if both K1>K2/α and K2>K1/α occur (Fig. 11.13c)?
d) What if K1 < K2/α and K2 < K1/α (note the < signs, unlike the > signs in questions a-c), as in
Fig. 11.13d?
21. Coexistence of species:
a) Coexistence of two species can occur when conditions are as in the equation below. Explain
the meaning of each term in the equation.
b) If two species use resources similarly, then α and α should be close to ____ (fill in: 0 or 1).
For example, imagine that α = α = 0.90. Then, K1/K2 must be between _________ and
__________ for coexistence to occur. (Understand how to use the equation and be able to
perform similar calculations on the exam.)
c) If two species use resources differently, α and α should be close to ____ (fill in: 0 or 1).
Imagine that α = α = 0.05. Then, K1/K2 must be between _________ and __________ for
coexistence to occur. Is this range greater or smaller than the range for question b above?
d) Based upon your answers to questions a-c, is coexistence of species more likely when species
use resources similarly or when they use resources differently? Explain why the different
ranges for K1/K2 allow you to draw this conclusion.
e) Why were Paramecium. caudatum and P. bursasaria (Fig. 11.10E) able to coexist, and how
does the answer to that question relate to your answer to question d?
22. Review Fig. 11.14. Normally, which plant species is competitively superior? Why was that
species no longer able to competitively exclude the other plant species after 1983?
23. Explain why environmental instability can prevent competitive exclusion from occurring.
24. Explain why resource partitioning could eventually lead to character displacement. Use the
example of the finches in Fig. 11.18 to support your answer.
Appendix 4.1 - page 24
BIO
340:
Molecular
Biology
(Lab
Manual)
Spring
2010
Site Directed Mutagenesis based on Quick Change Mutagenesis (Stratagene protocol) Introduction of mutation in proteins begins at the DNA level. For this introduction to take place, we first examine the
amino acids that will be undergoing some mutation within given protein sequence in RpBphP2 (P2) in red light
photoreceptors. This mutation will allow us to analyze any possible important role of that certain amino acid in a certain
protein.
I . Design forward and reverse primers that contain desired mutation.
A. Obtain protein sequence of the Protein RpBphP2 through NCBI webpage (PUBMED)
- Go to www.ncbi.nlm.nih.gov website
- Scroll down to search “Gene” and type for “ Rpa3015”.
- Click on the coding region (colored red) on Genomic Region, Transcripts, and Products
- Click “FASTA” to view just the protein sequence (or)
Click “GENPEPT” to view the protein sequence and click on “CDS” to view nucleotide sequence.
- Repeat the same search for “Rpa3016”
B. Locate the amino acid desired within P2 DNA and Protein Sequence.
- Multiply the number indicating location of amino acid within the sequence by three to find the number of
bases coding for that amino acid in the DNA Sequence.
Example:
His 255 in P2 [255 x 3= 765 Therefore bases from 763 to 765 code for amino acid His 255]
C. Select a DNA segment of 25 to 45 base length
Bases coding for amino acid to be changed should be located at the middle of the segment.
(NOTE: Genetic codes that translate to alanine are gct,gcc,gca, and gcg. Choosing “gct” is more desired as it has
the least number of base change with the last base matching the wildtype. Also, it is preferred to have a high
number of g and c bases in both ends of the segment for better annealing)
Example:
His 255 in P2 (teal) to Alanine (red)
Wildtype:
gtctcgcccg tccatctgga atacatg
Mutant: gtctcgcccg tcgctctgga atacatg
D. Make forward and reverse primers of 5’-3’ from mutant segment.
Example: (from changing His 255 in P2 to Ala)
5’ gtctcgcccg tcgctctgga atacatg
3’ cagagcgggc agcgagacct tatgtac
5’ catgtat tccagagcga agggcgagac
3’
5’
3’
(forward) [bases 751- 777]
(reverse)
(reverse in 5’-3’ direction)
E. Submit primers in 5’-3’ direction to Oligoanalyzer
- Go to www.idtdna.com website
- Click for OligoAnalyzer
- Copy and paste segment in the box and hit “analyze”
1
|
P a g e Maria
Yebra
and
Emina
A.
Stojkovic,
Ph.D.
Appendix 4.1 - page 25
BIO
340:
Molecular
Biology
(Lab
Manual)
Spring
2010
Site Directed Mutagenesis based on Quick Change Mutagenesis (Stratagene protocol) Example of result:
OLIGO ANALYZER RESULTS
Dilution
Resuspension
SEQUENCE:
5'- GTC TCG CCC GTC GCT CTG GAA TAC ATG -3'
COMPLEMENT:
5'- CAT GTA TTC CAG AGC GAC GGG CGA GAC -3'
LENGTH:
27
GC CONTENT: 59.3 %
MELT TEMP: 64.2 ºC
MOLECULAR
WEIGHT:
8227.4 g/mole
EXTINCTION
COEFFICIENT:
245800 L/(mole·cm)
nmole/OD260:
4.07
µg/OD260:
33.47
(Note: The recommended melting temperature is not lower than 62 ºC. For later PCR purposes the
Annealing temperature will have 5 ºC lower from this melting temperature calculation by the
OligoAnalyzer).
Now repeat all the steps for Rpa3016 (gene coding for RpBphP3). Only this time you are looking at D216 and Y272
residues. We need to make following mutations D216H, D216K, D216R, Y272F, Y272S, Y272H. Each team will design
primers for only one of these mutations.
2
|
P a g e Maria
Yebra
and
Emina
A.
Stojkovic,
Ph.D.
Appendix 4.1 - page 26
BIO
340:
Molecular
Biology
(Lab
Manual)
Spring
2010
Site Directed Mutagenesis based on Quick Change Mutagenesis (Stratagene protocol) II. Polymerase Chain Reaction
The wild type plasmid from E. coli should be isolated as it will serve as the template. The isolate plasmid will then
undergo the three steps of polymerase chain reaction for amplification.
•
•
•
Increase of temperature (95 °C) to denature the plasmid vector making it single strand. (denature)
Temperature will be decreased to 5°C lower than melting temperature of the primer containing mutation
(annealing)
Temperature will be increased to 70°C allowing DNA polymerase to elongate the primers with the mutation.
(extension)
3
|
P a g e Maria
Yebra
and
Emina
A.
Stojkovic,
Ph.D.
Appendix 4.1 - page 27
BIO
340:
Molecular
Biology
(Lab
Manual)
Spring
2010
Site Directed Mutagenesis based on Quick Change Mutagenesis (Stratagene protocol) This results with nicked circular strands. As this process occurs the mutant plasmid are increasing in quantity while the
wild type plasmid is at same initial amount.
Thermal Cycling Protocol:
1. Prepare control reaction
5µl of 10 x reaction buffer
2µl (10ng) of pWhitescript 4.5-kb control plasmid (5ng/µl)
1.25 µl (125 ng) of oligonucleotide control primer #1
1.25 µl (125 ng) of oligonucleotide control primer #2
1µl of dNTP mix
39.5 µl of ddH2O to final volume of 50 µl
1µl of PfuTurbo DNA polymerase
2.
Prepare sample reaction
5µl of 10 x reaction buffer
X µl (5-50 ng) of dsDNA template
X µl (125 ng) of oligonucleotide primer #1
X µl (125 ng) of oligonucleotide primer #2
1 µl of dNTP mix
ddH2O to final volume of 50 µl
1µl of PfuTurbo DNA polymerase
3. Run control reaction for 18 cycles with 5 minutes of extension time.
4. Cycle each reaction using cycling parameters and adjust segment 2 according to type of mutation desired [single
amino acid changes =16 number of cycles]
Segment
Cycles
1
1
12
to
2
18
Temperature
Time
95°C
30
seconds
68°C
95°C
55°C
30
seconds
1
minute
1
minute/kb
of
plasmid
length
5. Place reaction on ice for 2 minutes to cool down to less than or equal to 37°C.
Checkpoint: Perform DNA Gel Electrophoresis [using 10 µl of product on 1% agarose gel ]
III. Separation of Mutant Plasmids from Wildtype Plasmids
In order to examine any effect of a certain mutation, the wild plasmid needs to be removed from the mixture. This allows
us to look at more valid results examining the difference that occur when a mutation is introduced and the important
function of the wild type amino acid in that structure. The wild type plasmid is methylated as it was initially extracted
4
|
P a g e Maria
Yebra
and
Emina
A.
Stojkovic,
Ph.D.
Appendix 4.1 - page 28
BIO
340:
Molecular
Biology
(Lab
Manual)
Spring
2010
Site Directed Mutagenesis based on Quick Change Mutagenesis (Stratagene protocol) from the bacteria. The mutant plasmid is not methylated. It is this difference that can make it possible to remove plasmids
not containing the mutation. To do this we use a restriction enzyme Dpn1 that would specifically cleave methylated DNA.
- Add 1 µl of Dpn1 restriction enzyme to amplification reaction below mineral oil using small pipet tip
- Pipette solution up and down gently to mix solution
- Place reaction mixtures in microcentrifuge for 1 minute
- Incubate reaction immediately for 1 hour at 37°C for parental dsDNA digestion.
- Mutant plasmid following Dpn1 digest will be placed in DHα cells.
IV. Transformation
The mutant plasmids would be taken up by cells by electroporation.
Preparation of Electrocompetent Cells (E. coli)
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Prepare L-broth : 10 g of Bactotryptone, 5 g of Bacto yeast extract, 5 g NaCl ; dissolve in 1.0 L water
Autoclave L-broth
Prepare 10% (v/v) Glycerol: 12.6 g glycerol in 90 ml of water. Then autoclave.
Obtain 1/100 volume of fresh overnight E. coli culture and inoculate in 1L of L-broth in 4 L conical flask
Grow cells at 37°C shaking at 300 rpm to an optical density of .5 to .7
Place cells in ice for 5 minutes. (Note: keep cells in ice water bath in all steps before adding cells)
Transfer cells to cold centrifuge bottle
Centrifuge at 4000 x g for 10 minutes at 4 °C
Carefully discard all of the supernatant.
Resuspend pellet gently in 5ml of ice-cold filter sterilized DIH2O using pipette.
Add up to 1L of ice-cold filter sterilized DIH2O.
Centrifuge solution at 4000 x g for 10 minutes at 4 °C. Carefully remove all the supernatant.
Resuspend pellet gently in 5 ml ice-cold filter sterilized DIH2O.
Add up to 500ml of ice-cold filter sterilized DIH2O.
Centrifuge solution at 4000 x g for 10 minutes at 4 °C. Carefully remove all the supernatant
Resuspend pellet in 10 ml of ice-cold 10% glycerol.
Transfer all of the solution to a 15ml conical tube.
Centrifuge solution at 4000 x g for 15 minutes at 4 °C. Carefully remove all the supernatant
Resuspend cell pellet in 0.5 ml of ice-cold 10% glycerol with cell concentration to be about 1 -3x 1010 cells/ml
Store suspension in aliquots of 40 µl into 1.5 ml eppendorf tubes at -80°C in freezer.
Electroporation protocol (Micropulser):
•
•
•
•
•
•
Prepare plain LB medium
Thaw cells
Place each sample in a 1.5 ml microfuge tube and electroporation cuvettes on ice
Mix 40 µl of cell suspension with 1 to 2 µl of DNA and incubate on ice for 1 minute
Set Micropulser to “Ec1” when using 0.1 cm cuvettes or “Ec2” “Ec3” when using 0.2 cm cuvettes
Transfer cell mixture to cold electroporation cuvette and tap suspension to the bottom.
5
|
P a g e Maria
Yebra
and
Emina
A.
Stojkovic,
Ph.D.
Appendix 4.1 - page 29
BIO
340:
Molecular
Biology
(Lab
Manual)
Spring
2010
Site Directed Mutagenesis based on Quick Change Mutagenesis (Stratagene protocol) •
•
•
•
•
•
Place cuvette in chamber slide and push the slide into chamber till cuvette is between contacts in chamber base.
Pulse once
Remove cuvette from chamber and immediately add 200µl of LB medium with no antibiotics to cuvette.
Gently resuspend cells using Pasteur pipette.
Transfer cell suspension to 17 x 100 mm polypropylene tube
Incubate tube for 1 hour, shaking at 225 rpm at 37°C.
Plate on selective medium - 200µl (Kanamycin)
VI Isolation of Mutant Plasmid:
A.
•
•
•
Preparation of the cells
Spread the cells in an LB agar plate containing the antibiotic (same antibiotic that the mutant plasmid contains).
Inoculate a 1 to 10 ml LB medium with a single isolated colony
Incubate overnight at 37 ºC in shaking incubator.
B. Production of a Cleared Lysate
• Centrifuge from 1-5 ml (high number plasmid) or 10 ml (low number plasmid) of bacterial culture to 5 minutes at
10,000 x g.
• Remove supernatant and excess media
• Transfer the cell pellet in a 1.5 ml microcentrifuge tube
• Resuspend by pipetting 250 µl of Resuspension solution.
• Add 250 µl of Cell Lysis Solution and mix by inverting tube 4 times.
• Incubate from 1 to a maximum of 5 minutes or until the cell suspension becomes clear
• Remove partial clearing of lysate
• Add 10 µl of Alkaline Protease Solution and mix by inverting tube 4 times.
• Incubate tube at room temperature for 5 minutes.
• Add 350 µl of Wizard Plus SV Neutralization Solution and immediately mix by inverting 4 times.
• Centrifuge the bacterial lysate at maximum speed 14,000 x g for 10 min. at room temperature.
C.
•
•
•
•
•
•
•
•
•
•
•
•
Centrifugation Protocol
Insert one Spin Column into a 2 ml Collection tube for each sample.
Transfer 850 µl of clear bacterial lysate (without white precipitate) to the prepared spin column.
Centrifuge supernatant at 14,000 xg for 1 minute at room temperature.
Remove spin column from tube and discard flowthrough from collection tube.
Reinsert spin column to collection tube.
Add 750 µl of Column Wash Solution (diluted with 95% ethanol) to spin column
Centrifuge at 14,000 x g for 1 minute at room temperature.
Remove spin column from tube and discard flowthrough from collection tube.
Reinsert Spin Column to Collection tube.
Repeat the wash using 250 µl of Column Wash Solution (diluted with 95% ethanol)
Centrifuge at 14,000 x g for 2 minutes at room temperature.
Transfer the Spin Column without the column wash solution to a 1.5 ml microcentrifuge tube.
6
|
P a g e Maria
Yebra
and
Emina
A.
Stojkovic,
Ph.D.
Appendix 4.1 - page 30
BIO
340:
Molecular
Biology
(Lab
Manual)
Spring
2010
Site Directed Mutagenesis based on Quick Change Mutagenesis (Stratagene protocol) •
•
•
•
Elute plasmid DNA using 100 µl of Nuclease-Free Water to Spin Column.
Centrifuge tube at 14,000 x g for 1 minute at room temperature.
Remove the 1.5 ml microcentrifuge tube and discard Spin Column.
Store 100 µl of eluted DNA with 11 µl of 10x TE buffer. Cap microcentrifuge tube and store at -20 °C or below.
Checkpoint: Perform a DNA gel electrophoresis to see if there is any presence of the DNA plasmid and no RNA
contamination.
VII. Sequence Plasmid DNA and confirm mutation:
Send product to sequencing facility.
VIII. Electroporation to BL21 cells.
After confirmation take mutant plasmid and place into the BL21cells (protease deficient). This plasmid has HO
gene (Ampicillin) to convert heme to biliverdin. See instructions from part V (Transformation).
Electroporation protocol (Micropulser):
•
•
•
•
•
•
•
•
•
•
•
•
Prepare plain LB medium
Thaw cells
Place each sample in a 1.5 ml microfuge tube and electroporation cuvettes on ice
Mix 40 µl of cell suspension with 1 to 2 µl of DNA and incubate on ice for 1 minute
Set Micropulser to “Ec1” when using 0.1 cm cuvettes or “Ec2” “Ec3” when using 0.2 cm cuvettes
Transfer cell mixture to cold electroporation cuvette and tap suspension to the bottom.
Place cuvette in chamber slide and push the slide into chamber till cuvette is between contacts in chamber base.
Pulse once
Remove cuvette from chamber and immediately add 200µl of LB medium with no antibiotics to cuvette.
Gently resuspend cells using Pasteur pipette.
Transfer cell suspension to 17 x 100 mm polypropylene tube
Incubate tube for 1 hour, shaking at 225 rpm at 37°C.
Plate on selective medium - 200µl (Kanamycin)
7
|
P a g e Maria
Yebra
and
Emina
A.
Stojkovic,
Ph.D.
Appendix 4.1 - page 31
BIO 352-1, p. 1 of 1
Aquatic Biology (BIO 352): Nitrogen Cycle Activity
Name: ___________________
Be sure to explain the reasoning behind your answers. Answers that explain how a process occurs and
the scientific reasons why a process occurs will obtain more points than incomplete answers.
1. Label 1-2 arrows in the diagram of the N cycle below for each of the following processes: a)
denitrification, b) nitrogen fixation, c) nitrification, d) ammonification, e) nitrate ammonification, and f)
nitrogen assimilation. (You should label a minimum of one arrow for each of letters a-f.)
2. Define chemolithoautotrophic bacteria. In your definition, specify the energy source, electron donor,
and carbon source, and whether these bacteria occur in oxic or anoxic water.
3. Define anaerobic heterorganotrophic bacteria. In your definition, specify the energy source, electron
donor, and carbon source, and whether these bacteria occur in oxic or anoxic water.
4. Explain why chemolithoautotrophic bacteria and anaerobic heterotrophic bacteria are both most
prevalent at the oxic-anoxic interface in a lake, rather than at the top of the water column or at the bottom
sediments.
5. Label one arrow in the diagram of the N cycle below that illustrates a process conducted by g)
chemolithoautotrophic bacteria and h) anaerobic organoheterotrophic bacteria. (You should label one
arrow for letter g and one arrow for letter h.)
Appendix 4.1 - page 32
Instructor: Emina A. Stojković
Pymol Assignment
50 points
Bio 362-Biochemistry
Summer, 2009
Structure and mechanism of phytochrome photoconversion
This writing assignment is intended to summarize structure and function of the assigned
phytochrome by answering 4 questions that are listed below. Answer each of the listed
questions in 300 words or less. Questions 1 and 4 are worth 10 points and questions 2 and
3 are worth 15 points. You should keep in mind that your audience has general
knowledge of the subject.
Pymol assignment is due at the end of the class period (4pm) on Tuesday, July 7th
(digital copy via email). Late assignments will not be accepted. If you cannot
complete the assignment in the assigned time period just email me partial assignment in
order to receive partial credit.
This assignment should take a couple of hours of work. You are expected to reproduce
a couple of structure figures from the assigned research article (posted on Bb in the
scientific research article folder) and email me two documents – I. ms word
document with answers to each question and II. the final structure images in the ppt
file format. There are two research articles posted in the scientific research article folder
and you should check first the pdf document titled pymol assignment of phytochrome
structures to determine which research article you should use as your reference.
Remember to include the link to the pdb file that you will use for analyzing structure of
your phytochrome.
This assignment is formal and as such you are expected to provide names of members of
your lab team and page #’s on each page. You need to submit one copy of the pymol
assignment for you and your lab partner. You are only allowed to work on this
assignment with your lab partner. If your lab partner does not show up, you have to work
on your own. You are not allowed to communicate your work to the rest of class during
the assigned time period. The only materials that you can use as a reference are your
personal laptops and your lab notebooks.
Note: I strongly recommend that you prepare your structure figures first before
answering each question. If your molecule is an oligomer, make sure to reduce the
numbers of monomers present in order to accomplish clear structure figures as
presented in the research articles.
Questions:
1.
How does the structure of your phytochrome differ from RpBphP3 (P3) structure
that we studied during our first computer lab. Focus on domain composition of the
proteins, chromophore orientation and photoconversion properties of each of the proteins.
2.
Provide your first structure figure and briefly explain the highlights of that figure.
Students working on Cph1 structure have to reproduce 1B figure (without background
gray shade) from the assigned research article. Students working on PaBphP structure
have to reproduce figure 1A.
1
Appendix 4.1 - page 33
Instructor: Emina A. Stojković
Pymol Assignment
50 points
Bio 362-Biochemistry
Summer, 2009
3.
Provide your second structure figure and briefly explain the highlights of that
figure. Students working on Cph1 structure have to reproduce figure 3C while students
working on PaBphP structure should reproduce figure 2B (2C instead of 2B for those
whose names were highlighted with a *).
4.
In your opinion, which amino acid residues play a key role in determining
photoconversion properties of your phytochrome? List three (provide name and number
based on the primary protein sequence) and explain your reasoning.
2
Appendix 4.2 - page 1
BIO 301-1, p. 1 of 3
Cell biology spring 2010 exam 2 review questions
Sections –
- Transport to cellular compartments – mitochondria – nucleus – ER – Golgi – lysosome and
the cell surface.
- Role of Glycosylation in signaling and folding.
- Transport vesicle formation and use.
- Mitochondria and mitochondrial energetics.
- Mitochondrial disease.
- Basic photosynthesis.
1. Describe the differences between signal sequences and signal patches.
2. Describe the structure and function of a nuclear pore complex.
3. How do nuclear localization signals work? What type of signal are they?
4. Describe nuclear import receptors.
5. Tell me everything about the RAN system
6. How do nuclear import and export receptors differ?
7. Describe how TOM works- what does it interact with? What signals does it use?
8. How does TIM work? How do the two work together?
9. What role does ATP play?
10. What is the role of hydrogen pumps in getting proteins into the mitochondria?
11. What role do the HSP 70’s play?
12. How do we get things between the mitochondrial membranes?
13. What happens if an import protein is defective?
14. Describe the ER in detail- how do the two compartments differ?
15. What is the difference between the two populations of ribosomes?
16. Detail how a protein gets into the ER.
17. What are the roles for the smooth ER? In what cell types would you expect to see more of
it?
18. How were signal sequences discovered?
19. How do start – stop signals work to get a protein thru the membrane multiple times?
20. What is Glycosylation and why is it important?
21. Describe trimming and its role in proper folding.
22. How do calnexin and calreticulin distinguish folded from incompletely folded proteins?
23. Detail what happens to improperly folded proteins.
24. Detail how Molecular mechanisms of membrane transport work.
25. Define coated vesicles and coated pits.
26. How does a coat function?
27. What are the differences between the three types of coats?
28. Describe in detail the formation and function of Clathrin coated vesicles. Don’t forget the
role of triskits, adaptins, hsp70 and dynamin.
29. How do COP-I and COP-II vesicles differ?
30. What are the roles of SARs and ARFs? What do they expose to anchor themselves?
31. What does GEF do?
32. Describe the entire snare cargo catching system.
33. How does botox work?
Appendix 4.2 - page 2
BIO 301-1, p. 2 of 3
34. What’s NSF? (besides what they put on your check when there is not enough money in
your checking account).
35. What are the roles of RABs?
36. How are Vesicular tubular clusters formed? What do they do?
37. Describe the retrieval cycle for escaped membrane bound proteins.
38. Explain in detail the KDEL system.
39. What’s the role of pH in retrieval?
40. Describe the entire snare cargo catching system.
41. Describe the structure of the Golgi? What happens here?
42. Describe the process of sugar modification?
43. Describe transport thru the Golgi in detail.
44. Describe Transport from the trans Golgi network to lysosomes especially the role for pH?
45. Describe that lead to degradation in the cell.
46. Describe Receptor-mediated endocytosis.
47. What is Autophagy and how does it work? Phagocytosis?
48. Describe the role of mannose 6 phosphate and its receptor.
49. Describe the regulated secretory pathway.
50. Describe how oxidative phosphorylation occurs.
51. Describe Transfer of electrons from NADH to Oxygen.
52. Why is biological oxidation more efficient than combustion for our needs?
53. How does ATP synthase work? In both forward and reverse directions.
54. What are the relative production yields of fats and carbs?
55. How does the ATP/ADP ratio act as a regulator?
56. Define and describe redox potential.
57. How are electron transported between respiratory complexes?
58. How does shape change drive proton pumps?
59. Describe the basis of mitochondrial disease.
60. Describe the structure and function of MT DNA.
61. How are fats for energy in the mitochondria?
62. What is MERF and what is its etiology?
63. What is MELAS and what is its etiology?
64. How can children of the same parents have different levels or types of mitochondrial
diseases?
65. List and describe the Mitochondrial compartments.
66. Describe in detail how use chemiosmotic coupling to harness energy. What are you doing
during this process?
67. Why are Mitochondria are often seen associated with microtubules?
68. Where and what happens in Glycolysis.
69. What are two types of fermentation that can occur? How do they differ? How does the
cell deal with their end products?
70. Differentiate between Anaerobic and aerobic energy sources in short and long term
exercise. What is going on in terms of mitochondrial function?
71. What is the role of glycogen in long period exercise and fat utilization?
72. Why is NAD+/ NADH used as an electron carrier? And how doe sit transfer energy?
73. Outline the Transfer of electrons from NADH to Oxygen.
74. What is Oxidative phosphorylation? What is the mechanism of Oxidative
phosphorylation? Where does it occur? What happens if it fails?
75. How does Proton motive force drive ATP formation?
Appendix 4.2 - page 3
BIO 301-1, p. 3 of 3
76. How does ATP drive proton motive force? I.e. how does F0F1 ATPase work? Why does
it need to be reversible?
77. How is efficiency and metabolic rate related? What are the roles for UCPs?
78. Define Redox Potential.
79. How do differences in Redox Potential move electrons thru the electron transport chain?
80. How efficient is this process?
81. What are the components of the respiratory chain? What is the role of Ubiquinone and
cytochrome c in this pathway? Why is kinetics involved?
82. What drives the activity of proton pumps?
83. What is the basis of mitochondrial disease? Why do mitochondrial diseases have such a
wide variety of symptoms?
84. What’s different between mitochondrial DNA and nuclear DNA?
85. Describe fatty acid oxidation – why is it more efficient?
86. What mutation is involved in MERF?
87. How van the same mitochondrial inherited diseases show different levels of severity and
different times of onset in different people- even in the same family?
88. Describe the data supporting some form of paternal mitochondrial inheritance.
89. Tell me absolutely everything about RuBisCO.
90. Describe the structure of the chloroplast – give reasons for each feature.
91. How and why are antenna complexes formed?
92. Describe the reasoning behind the uses of the various pigments found in the antenna
complexes and in the chloroplasts.
93. What may be a common role for carotenoids in animal and plant systems? How does it
work in plants?
94. How do the 2 photo systems interact?
95. Describe the steps in Electron Flow through Photosystem II. Include the role of the
intermediaries.
96. Describe in detail the water splitting reaction. Why are so many photons needed to make
one oxygen? How does this help in battery charging?
97. Describe in detail the role of cytochrome bf.
98. What is the “special pair”? What are their roles? Where are they?
99. Describe electron flow and energy transfer in PSI.
100.
Compare and contrast the CF1-CF0 ATP synthase and the corresponding system
in mitochondria.
101.
What happens in Cyclic Electron Flow through Photosystem I? How does this
differ from the complete cycle? When and why is it used?
102.
How and why does Cyclic Photophosphorylation take place? What are the major
problems with Cyclic Photophosphorylation?
103.
What areof the three stages of the Calvin cycle?
104.
What are the immediate products of the RuBisCO reaction?
105.
How is RuBisCO affected by [CO2 ] and [O2 ]?
106.
How exactly does C4 differ from C3 carbon fixation?
107.
Describe in detail normal C3 fixation.
108.
Describe Crassulacean acid metabolism for carbon fixation.
109.
Compare Crassulacean acid metabolism and C3 and C4 metabolism.
110.
What happens in the oxidative phase of the Pentose Phosphate Pathway?
111.
Describe the roles of NADP+ and NADPH in the Pentose Phosphate Pathway.
112.
Why do we use both NAD+ & NADP+ ?
Appendix 4.2 - page 4
BIO 150-4, p. 1 of 3
BIO 150- Analysis of a Primary Research Paper
Goals:
- Understand the difference between primary and secondary literature.
- Analyze a primary research paper given to you by your instructor to understand the type of
information included in each section (abstract, introduction, methods, results, discussion,
acknowledgements, and literature cited sections).
- Relate the introduction, methods, results, and discussion sections to the information you write in
your lab notebooks.
- Obtain your lab report assignment. You lab reports will include all the parts of a primary
research paper that you learned about today!
How does primary literature differ from secondary literature?
Primary literature includes research articles that describe original scientific research conducted by
the author(s) of the article. Research methods are described (usually in a methods section), and data is
presented (usually in a results section). Primary research articles are subjected to a peer-review process
before they are published in a scientific journal. Before the article is published, the editor of a scientific
journal sends the article to “peers,” other scientists who review the article to determine if the research is
worthy of publication. For example, research that didn’t follow the scientific method would have a
difficulty being published!
Secondary literature does not describe original research, but summarizes the results of previous
research. Your textbook is an example of secondary literature. You may also see articles in scientific
journals called “review” articles. A review article summarizes the results of a large number of primary
research articles. For example, the article “The horseshoe crab, Limulus polyphemus: 200 million years of
existence, 100 years of study” summarizes research conducted on the horseshoe crab for the past 100
years. It is published in a journal, Reviews in Fisheries Science, that only publishes review articles.
Analyzing the sections of a primary research paper:
Most primary research papers are separated into the following sections: abstract, introduction,
methods, results, discussion, acknowledgements, and literature cited sections. You will analyze the
content of each section of a primary research paper, “Effects of blood extraction on the mortality of the
horseshoe crab, Limulus polyphemus.”
The Introduction section contains
- background information necessary to understand the research topic
- justification of the necessity of the research
- the research objectives, or purpose
1. In your opinion, what are the two most important pieces of background information given in the
introduction section? Explain why you feel each piece of information is crucial for understanding
the research topic. Did others at your table choose similar or different pieces of information?
2. What reason(s) are given in the introduction section as to why this research is necessary?
3. What is the independent variable?
4. What is the dependent variable?
5. Note that the introduction section ends with a statement of the research objective(s). Rewrite the
research objective(s) statement in your own words.
1
Appendix 4.2 - page 5
BIO 150-4, p. 2 of 3
The Methods section contains a description of the methods and equipment, so that
- readers understand how the research objectives were tested
- someone else could repeat the research.
- irrelevant info that would not affect results is not included.
6. When, where, and how were specimens collected?
7. Name each piece of equipment mentioned.
8. Name two factors mentioned in the methods section that were kept constant across the
experiment.
9. Do you feel that the research required significant skill, equipment, or training? Explain.
The Results section presents the research results
- without discussing what the results mean
- data is presented in table and/or graph format
- the content of each table and/or graph is summarized in the text, so that the “main gist” of the
data could be understood without referring to that table or graph.
10. Every table has a table heading and every graph (figure) has a figure caption that describes the
contents. What important information is included in the table heading at the top of Table 1?
11. In your own words, summarize the data presented in Table 1.
12. How does your summary compare to the summary in the text of the results section? How would
you improve their summary?
The Discussion section
- gives a scientific explanation for the data
- discusses problems or potential limitations of the current research study
- compares the data to previously published research
- gives suggestions for future studies research
- gives conclusions, or summarizes the implications of the results
13. Describe data from two previous research studies mentioned in the discussion section, and how
that data differs from the data obtained in this research study.
14. Describe four limitations of this research study that are discussed by the authors.
15. What additional suggestions do you have for future research studies?
16. Mortality in 1997 due to fisheries: Commercial fisheries caught _________ pounds of horseshoe
crabs in 1997. Assuming that an average horseshoe crab weights 4 pounds, calculate the number
of horseshoe crabs killed by commercial fisheries in 1997.
17. Mortality in 1997 due to biomedical companies: Biomedical companies bled ________
horseshoe crabs in 1997, and returned them to the ocean. Based upon the results of this research
study, calculate the number of horseshoe crabs expected to have died in 1997 due to the bleeding
process.
18. Based on your answers to #15 and #16, did the fishery or biomedical industry cause the most
deaths of horseshoe crabs? What conclusions can thus be drawn about the most important factor
causing horseshoe crab decline?
2
Appendix 4.2 - page 6
BIO 150-4, p. 3 of 3
In the Acknowledgements section, the authors thank those who
- provided equipment or facilities, access to sample sites, etc.
- helped with planning the research, collecting samples or data, etc.
- read drafts of the article and made suggestions for improvement
- paid for the research
19. Who helped design the research study?
20. What is the name of the institution (or unit) that provided necessary facilities?
21. Who paid for this research, and why would they be interested in the research results?
In the Literature Cited section, complete citations are given for all sources mentioned in the text of the
paper.
Note that complete citations for research articles are written in the following format.
Authors’ names, year of publication, title of article, title of scientific journal in which it was
published, volume number of that journal, issue number (in parentheses), page number range.
22. Write out the complete citation for the research article you just read, in correct format. (Look at
the Berkson and Shuster citation in the literature cited section as an example of the format to
follow.)
23. Read the first paragraph of the introduction section and note that the author states that the
horseshoe crab fishery has been increasing rapidly. What sources does the author cite as
providing evidence for that statement?
24. Read the Novitsky citation in the literature cited section, and note that it is a single-author
citation. Then, find the Novitsky citation in the Introduction section. What is the proper way to
refer to single-author citations in the text of the paper?
25. Read the Berkson and Shuster citation in the literature cited section, and note that it is a citation
with two authors. Then, find the Berkson and Shuster citation in the Introduction section. What
is the proper way to refer to a citation with two authors in the text of the paper?
26. Read the Loveland citation in the literature cited section and note that it has more than two
authors. Then, find the Loveland citation in the Introduction section. What is the proper why to
refer to a citation with more than two authors in the text of the paper? (Note: “et” is latin for
“and”- it’s not an abbreviation, so it doesn’t have a period. The reason that “al.” has a period is
that it is an abbreviation for “others.”)
The Abstract is simply a short summary of the research paper. Even though it appears at the beginning
of a research paper, we’re analyzing the abstract last because it is written last! The abstract contains the
most important information from each section of the paper, so it can’t be written until the entire paper is
finished.
27. The abstract contains seven sentences. Number each sentence from 1-7.
For each numbered sentence, determine if the information in that sentence came from the
introduction, methods, results, or discussion sections.
(Note: you don’t have to refer to the rest of the paper to answer this question! Once you
understand the type of information that belongs in each section, you can read any sentence and
know where that information came from.)
3
Appendix 4.2 - page 7
BIO 305-4, p. 1 of 2
Searching for and analyzing a primary research paper (10 points)
You will search the scientific literature using three different databases (Biological Abstracts,
Medline, Google Scholar). Instructions for searching these databases and obtaining articles you find
in your search are on the next page. You will use the same keyword (choose a keyword or phrase
related to the topic of the research you will conduct at Mary Mix McDonald Woods) to see how many
matches (articles) you get from each database. You will then choose one primary research paper and
answer some questions to evaluate it.
How does primary literature differ from secondary literature?
Primary literature includes research articles that describe original scientific research conducted by
the author(s) of the article. Research methods are described (usually in a methods section), and data is
presented (usually in a results section). Primary research articles are subjected to a peer-review process
before they are published in a scientific journal. Before the article is published, the editor of a scientific
journal sends the article to “peers,” other scientists who review the article to determine if the research is
worthy of publication. For example, research that didn’t follow the scientific method would have a
difficulty being published!
Secondary literature does not describe original research, but summarizes the results of previous
research. For example, you may see articles in scientific journals called “review” articles. A review
article summarizes the results of a large number of primary research articles. If the word “review”
appears in the title or abstract, the article is probably not a primary research article.
Type the answers to questions 1-4 (or copy and paste) into the Comment Box.
1) What keyword or phrase did you use for all three databases?
2) How many articles did you find with those keywords in Biological Abstracts? How many in Medline?
How many in Google Scholar? Elaborate on why you think there are differences in the number of
articles each database provided.
3) Select one primary research paper that has background information relevant to your Mary Mix
McDonald Woods research project or data to which you may be able to compare your data. Write the
COMPLETE citation of the paper. Use the same style as used in the literature cited sections of
Heneghan et al. 2002 or Heneghan et al. 2007.
4) Evaluate the primary research article by answering the following questions. Please label your
answers as 5-a) through 5-g). Write all answers entirely in your own words. (Do not quote or copy
any text from the paper.)
a. Summarize the reasons the authors give to explain why their research is necessary or important.
b. Restate the research objectives in your own words.
c. Do the research methods described in this paper require significant skill, equipment or training?
Justify your answer.
d. Choose one table or graph in the paper and summarize the data presented in that table or graph.
What can be concluded from that data?
e. Describe three citations used in the discussion section. Why did the authors include them? How are
the citations used? For example, are they used to provide more information relevant to the paper or
to support the results? Do they contradict the study’s findings?
f. Read the acknowledgements section to determine how the research was funded. Do you believe
that the funding source may have interfered with the research conclusions, or not? Explain.
g. If you were conducting a follow-up study, what would you do differently? Can you think of any
problems or flaws in the research that would have to be rectified? Did the research results raise
additional questions that need to be addressed?
h. Attach a .pdf copy of the article using the “attach document” feature when you submit this
assignment via Blackboard.
Appendix 4.2 - page 8
BIO 305-4, p. 2 of 2
Searching for primary research articles in the ecological literature
1. Biological Abstracts is a database of the biological literature. You can reach this database on-campus
from the library’s website by clicking “B” in the Database A-Z tab in the library webpage. Otherwise:
a. Click on:
http://apps.isiknowledge.com/BIOABS_GeneralSearch_input.do?product=BIOABS&search_mode=Gene
ralSearch&SID=1AfK4L@EdF3Okf2PbOF&preferencesSaved=&highlighted_tab=BIOABS
b. Type your search word in the Keyword box for Topic. Note that you can also search by other
categories such as author, publication name, etc. Note: if you type several words, the database will only
search those terms as a complete phrase. If you want to obtain more articles, separate each word with the
word “and.”
f. If you don’t obtain as many articles as you need, or if you don’t obtain appropriate articles, try
changing your keywords.
g. Click on a title to read the abstract.
h. If an abstract seems interesting, click on the “Find it at NEIU” symbol to see if you can get a
copy here.
i. If you can’t get a copy here, request it via Interlibrary Loan (see instructions below- it takes 23 days to receive via ILL, so don’t do at the last minute).
2. The Medline database also contains ecological abstracts, but it’s mostly for medical articles. Go to
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi
3. You can also search for papers in Google Scholar: http://scholar.google.com/schhp?ie=UTF8&hl=en&tab=ws Click on Advance Scholar Search so you can then click on the “Biology, Life Sciences,
and Environmental Science” box to narrow your results
Requesting an article via ILL
•Go to http://library.neiu.edu/
•Click on “Interlibrary Loan” near the top of the page (under “Quick Links & Searches”).
•You will need the 14-digit number from your ID card.
•Under “New Request,” choose “article.”
•Enter the information.
•The article will be sent as a .pdf file to your neiu e-mail address.
Appendix 4.3 - page 1
BIO 150-5, p. 1 of 2
Identifying Patterns and Exploring &Analyzing Data
Almost all biological research requires the collection, analysis and interpretation of data: data are required
to establish that a particular pattern or phenomenon exists, and are required to test hypotheses about the
underlying cause of the pattern. The way that we collect data and test hypotheses falls under the broad
heading of experimental design. In this lab, your quest is to design an experiment that will let you
discover ecological patterns in student bodies, collect and summarize the data to establish whether any
patterns exist, propose hypotheses that could explain the patterns, and propose experiments that would let
you test the hypotheses.
I will provide you with a variety of measuring devices used by biologists to measure organisms. Working
in groups of 4-6, I want you to come up with a number of characteristics of student bodies that can be
measured (discreetly and without causing physical or psychological discomfort) and compared among
groups of students. As a class, we will discuss each group’s choices.
The measuring devices I will provide include:
1) dial calipers (to measure the thickness or diameter of relatively small things with a high
degree of precision)
2) plastic rules and meter sticks (for less precise measurements of length)
3) 30-m or 50-m reel tape measures
4) diameter tapes (d-tapes; used to estimate the diameter of objects that are approximately
circular in cross section)
Often, patterns that biologists work with (or look for) are differences between two or more groups (e.g.,
between sexes, between groups of organisms occupying different habitats, or between groups of
organisms subjected to different experimental treatments). The "groups" of students that I want you to
compare are the sexes (males vs. females), as there are many examples in nature in which one sex is
larger, more colorful, or has body parts that exhibit different size-proportionalities (allometries).
Examples of things that you may decide to measure might include (but are not limited to): height,
forearm diameter, calf diameter, leg length, or head diameter.
Once you have chosen two characteristics to measure, you will collect data as a class, and look for
patterns among the data (differences between males and females). We will then look at a number of ways
of presenting and analyzing the data to see whether, in fact, males and females differ for each of the
characteristics measured, and that you can use to look for correlations between some of the traits
measured. Examples of ways of summarizing, presenting and analyzing data that we will discuss in the
coming weeks include:
1) generating histograms: look for differences in frequency distributions
2) generating scatterplots: plot values of two variables against each other on x,y plot; look for
correlations between variables
3) calculating central tendencies (means, averages, or medians)
4) calculating estimates of variability (standard deviations, variances, standard errors)
5) generating bar charts using means and standard errors; look for differences in means of
groups
6) conducting t-tests to determine whether the means of two groups differ significantly from each
other
7) conducting correlation tests in to determine whether two variables are significantly similar to
one another (correspond with one another).
Appendix 4.3 - page 2
BIO 150-5, p. 2 of 2
Once a pattern has been identified, the interesting questions become: What is the cause of the difference?
or What is the value of having that trait in a particular environment? and How can we test the hypotheses
that we generate to explain the differences? Thus, for the last part of this exercise, you will come up with
reasonable hypotheses that could account for or explain any differences we find between males and
females in the class, and propose experiments that could be done to test these hypotheses. For these parts
of the lab, you should pretend that you are dealing with wild animals that you are observing in nature,
rather than the domesticated animals you are observing in an artificial habitat.
Write down search terms related to the measurements you collected today:
Eventually, you will write a primary research paper about your data, with abstract, introduction, methods,
results, and discussion sections. As part of the discussion section, you will compare your data to other
primary research papers. You will use a biological database called Biological Abstracts to identify
appropriate research, and a program called Endnote Web to help organize the research papers you find.
An assignment (posted on Blackboard) in which you practice using Biological Abstracts and Endnote
Web is due next week. When searching for papers in Biological Abstracts, you will use appropriate
search terms related to the data you collected today. Listen to instructions for developing search terms
and write down possible search terms that you can use to complete the Biological Abstracts and Endnote
Web assignment.
________________________________
__________________________________
________________________________
__________________________________
________________________________
__________________________________
Complete your lab notebook entry. Each section should include the following.
Introduction
 Your hypothesis.
 The scientific reasons behind your hypothesis. In other words, what were the reasons that you
developed your hypothesis? What is the potential significance of your data?
Methods
 Precise descriptions of what was measured on each individual, how it was measured and the
degree of precision to which it was measured (e.g., "to the nearest 0.01g");
Results
 Neat, well-organized and clearly labeled table(s) containing all data that was collected and an
indication of who collected it (you? another member of your group? members of another
group?);
Discussion
 Can you think of any ways in which the data we collected in our quest for pattern may have been
biased? How could we control for these possible sources of bias? (Note: "Sources of bias" are
not the same as "sources of error." A biased data set is one that is not representative of the real
group being examined.)
 In coming up with hypotheses that could explain differences between males and females, I asked
you to pretend that we were wild animals found in a natural environment (such as the African
savanna). In fact, we no longer live under those conditions. Can you think of any adaptive
values in our current environment that might exist for the differences you observed?
 How could knowing that two (or more) variables are strongly correlated with each other help in
designing experiments utilizing a species, or in collecting data on a species? (Consider the fact
that some measurements are easier to make than others, and that, all things considered, we always
want to minimize the effort involved in collecting data.)
Appendix 4.3 - page 3
BIO 305-3, p. 1 of 2
General Ecology Study Questions for Chapter 11: Competition
Lecture Outline:
• Define competition and resource.
• Exploitative vs. interference competition.
• Competitive exclusion principle
• Lokta-Volterra equations
– Zero population growth isoclines represent stable population sizes (when population is
not growing or decreasing)
– Show that competing species coexist more easily when they use resources differently.
• Three reasons that could prevent competitive exclusion from occurring.
– Disturbance prevents competition from proceeding to its conclusion.
– Environmental instability can alter which species is superior.
– Resource partitioning and/or character displacement can reduce competition.
Study Questions
1. Define competition. Then, explain why each factor in the definition is important. Why must the
two species be competing for the same resource? Why must the resource be limiting in order for
competition to occur? Give a several examples of what can be considered to be “harm.”
2. Explain how a resource is different from a physical factor, and give several examples of each.
3. Fig. 11.4 shows competition between two diatom genera: Asterionella and Synedra. Use the data
in that figure to answer the following questions.
a. Define carrying capacity. Which diatom genus has the highest carrying capacity when
grown alone?
b. For what resource are the two genera competing? Which genus uses that resource more
efficiently? Use the data in Part 1 of Fig. 11.4 to support your answer.
c. When grown together, which genus outcompetes the other? Is it the genus with the
higher carrying capacity when grown alone? Or, is it the genus that uses the resource
more efficiently? Explain.
4. Explain how exploitative competition differs from interference competition.
5. Is the competition between Asterionella and Synedra an example of exploitative competition or
interference competition? Explain.
6. Does Fig. 11.6 show an example of exploitative competition or interference competition?
Explain.
7. For what resource is Semibalanus competing with Chthalamus (Fig. 11.8)? Why does each need
this resource, and why is the resource limiting in the environment in which these barnacles live?
8. Which barnacle (Semibalanus or Chthalamus) competes more effectively for the limiting
resource? With that in mind, why is the superior competitor not present at the top of the intertidal
zone? Explain how this example demonstrates that abiotic and biotic factors interact to determine
species distributions.
9. Describe the competitive exclusion principle and explain why the word “complete” is important
in the principle. Which figure illustrates the competitive exclusion principle: Fig. 11.10D or
11.10E?
10. Explain why P. caudatum and P. bursasaria (Fig. 11.10E) are able to coexist, while P. aurelia
and P. caudatum (Fig. 11.10D) are not.
11. Even though P. caudatum and P. bursasaria (Fig. 11.10E) are able to coexist, does the
competition between the two species affect their carrying capacities? Explain.
12. Explain how the Lotka-Volterra competition equation (p. 249) differs from the logistic growth
equation (p. 211). (You don’t need to memorize these two equations, but if I show either or both
on the exam, you will need to be able to explain what each term of each equation means and how
the equations differ from one another.)
Appendix 4.3 - page 4
BIO 305-3, p. 2 of 2
13. Use the Lotka-Volterra equations to complete the following.
a. If α increases, dN1/dt will ___________ (choose increase, decrease, or remain the same).
b. If N2 decreases, dN1/dt will __________ (choose increase, decrease, or remain the same).
c. If α decreases, dN2/dt will __________ (choose increase, decrease, or remain the same).
d. If K2 increases, dN2/dt will __________ (choose increase, decrease, or remain the same).
14. Define zero population growth isocline.
15. The equations for the N1 and N2 zero population growth isoclines can be determined when dN1/dt
and dN2/dt ___________________ (choose: >0, <0, or =0).
16. From the equation dN1/dt = r1N1 (1–(N1 + αN2) / K1), we know that dN1/dt =0 when
_________________ = 0.
17. In class, we solved the equation 1–(N1 + αN2)/K1 = 0 for N2 (as explained in Box 11.2 on p.
250). The result can be expressed as an equation for a line, y=mx+b, with N 1 as x and N2 as y.
What is the slope of the line? What is the y-intercept? How does this equation for a line compare
to Fig. 11.12a?
18. From the equation dN2/dt = r2N2 (1–(N2 + αN1) / K2), we know that dN2/dt =0 when
_________________ = 0.
19. Solve the equation you wrote in #18 for N2. Then, write the equation in the form of an equation
for a line (y=mx+b). Finally, compare that equation to the line graphed in Fig. 11.2b. (If you
have trouble, refer to Box 11.2 on p. 250 for help.)
20. Zero population growth isoclines:
a) Explain why the equation K1>K2/α (Fig. 11.13a) allows you to determine which of the results
occurs.
- competitive exclusion of species 1 (species 2 “wins”)
- competitive exclusion of species 2 (species 1 “wins”)
- coexistence
b) Do the same for K2>K1/α (Fig. 11.13b).
c) What if both K1>K2/α and K2>K1/α occur (Fig. 11.13c)?
d) What if K1 < K2/α and K2 < K1/α (note the < signs, unlike the > signs in questions a-c), as in
Fig. 11.13d?
21. Coexistence of species:
a) Coexistence of two species can occur when conditions are as in the equation below. Explain
the meaning of each term in the equation.
b) If two species use resources similarly, then α and α should be close to ____ (fill in: 0 or 1).
For example, imagine that α = α = 0.90. Then, K1/K2 must be between _________ and
__________ for coexistence to occur. (Understand how to use the equation and be able to
perform similar calculations on the exam.)
c) If two species use resources differently, α and α should be close to ____ (fill in: 0 or 1).
Imagine that α = α = 0.05. Then, K1/K2 must be between _________ and __________ for
coexistence to occur. Is this range greater or smaller than the range for question b above?
d) Based upon your answers to questions a-c, is coexistence of species more likely when species
use resources similarly or when they use resources differently? Explain why the different
ranges for K1/K2 allow you to draw this conclusion.
e) Why were Paramecium. caudatum and P. bursasaria (Fig. 11.10E) able to coexist, and how
does the answer to that question relate to your answer to question d?
22. Review Fig. 11.14. Normally, which plant species is competitively superior? Why was that
species no longer able to competitively exclude the other plant species after 1983?
23. Explain why environmental instability can prevent competitive exclusion from occurring.
24. Explain why resource partitioning could eventually lead to character displacement. Use the
example of the finches in Fig. 11.18 to support your answer.
Appendix 4.3 - page 5
BIO 150-6, p. 1 of 7
DISPENSING LIQUIDS, PART 1
BIO 150
GOALS:
-
Review the metric system.
Learn to correctly use electronic balances
Learn to record data collected in lab in a proper lab notebook entry with introduction,
methods, results, and discussion sections.
Estimate the number of drops in 1 mL of water.
INTRODUCTION:
Many activities you will undertake in biology labs will require that you be able to dispense
various volumes of liquids accurately and quickly. For example, if you are running DNA on a gel, you
will first have to digest the DNA using very small volumes (microliters, or µL) of restriction enzymes
(nucleases); at the other extreme, you may decide to do an experiment in ecology in which you water
plants with solutions containing different concentrations of salt, and need to be able to mix 100-liter
batches of each solution.
This week, you will learn to estimate small amounts of volume by determining the average
number of drops (dispensed using a dropper and bulb) in 1 mL. Next week, you will be introduced to a
variety of devices designed to accurately and precisely dispense different quantities of solutions, reinforce
the relationship between the mass and volume of water, and help you to understand the accuracy (and
precision) with which you can dispense volumes using the different devices. Before beginning, it is
important to review metric units used to measure mass (weight) and volume.
REVIEW OF THE METRIC SYSTEM:
Volumes of liquids are measured in units of liters, including L, mL, µL, and nL. One mL (milliliter) is
equivalent to 1 cc (cubic centimeter).
1 L (liter) = _________ mL (milliliters)
1 L = _________ mL
1 mL = _________ L (microliters)
1 mL = _________ L
1 L = _________ nL (nanoliters)
1 L = _________ L
1 nL = _________ mL
1 L = _________ L
1 mL = _________ cc (cubic centimeter)
Mass (or weight) of an object or a volume of material is measured in units of grams, including kg, g,
mg, µg, and ng.
1 kg (kilogram) = _________ g (grams)
1 g = ___________ kg
1 g = ________ mg (milligrams)
1 g = _________ mg
1 mg =
_________ g (micrograms)
1 mg = _________ g
1 kg = _________ mg
1 g = _________ mg
1 g = _________ g
1 g = _________ g
1 g = __________ ng
1 ng = _________ g
Density is the relationship between mass and volume. It is useful to know the density of pure water.
1 mL pure water has a mass of ________ g
1 L pure water has a mass of _________ kg
Density of pure water can be expressed as __________ g/mL, __________ g/cc, or __________ kg/L.
Practice converting between metric units:
5 L = ________________ mL
0.5 g = _______________ mg
60 L = ______________ mL
500 mL = ______________ L
0.007 mg = ____________g
0.75 mL = ______________L
8 kg = ________________ mg
54 ng = _____________ g
789 nL = _______________mL
4.26 kg = _______________ g
5.3 g/mL = ______________kg/L
65 g/cc = _____________g/mL
Appendix 4.3 - page 6
BIO 150-6, p. 2 of 7
PROPER USE OF THE ELECTRONIC BALANCE:
Although you may encounter other kinds of balances and scales, we will be using digital
electronic balances in order to weigh (or more accurately, to determine the mass of) things in lab.
Steps for using the electronic balance:
1. Place balance on a solid surface. The balance must be on a solid, stable surface, away from any
strong drafts. (The balances are very sensitive to vibrations. When using a balance, never learn
on the table.)
2. Level the balance before plugging it in or turning it on. Most balances have a bubble-level and
two or more adjustable feet that can be turned to raise or lower one side or corner of the balance.
Shorten all of the legs as much as possible and then raise legs one at a time until the bubble is
perfectly centered in the ring of the level. If you move the balance after having leveled it, you
may have to re-level it.
3. Turn on the balance after it is leveled. The balance may have to be turned on for a few minutes
before the reading becomes stable.
4. Zero the balance before weighing any samples. If you are weighing your samples in a container,
you may also set the container on the balance before you zero (tare) the balance. Then, when
weigh the container with the substance, the weight of the container will automatically be
subtracted.
5. Note: Pay attention to the maximum capacity of the balances that you use. It is very important to
NOT exceed the capacity of the balance. Also, add objects gently to the weighing pan. Doing
otherwise can damage a balance permanently.
CONDUCTING THE LAB EXERCISE:
You will determine the average number of drops (dispensed using a dropper and bulb) in 1.0 mL
of pure (deionized) water (DI H2O). As you complete this exercise, you will record your data in a proper
lab notebook entry, with introduction, methods, results, and discussion sections.
Develop a hypothesis:
Before you begin, think about how many drops that you expect should be in 1 mL of water.
Write a hypothesis in the form of a testable statement. The hypothesis should be written in the
introduction section of your lab notebook. (The introduction also includes a brief description of the
purpose of the lab exercise.)
Steps for conducting the lab exercise: You will now test your hypothesis by collecting data!
1. Make sure that the electronic balance is on a stable surface and is leveled (see above).
2. Place a beaker on the balance and zero the balance.
3. Leaving the beaker on the balance, add drops of DI water until the balance reads 1.00 g (or as
close as 1.00 g as possible without going over). Record the number of drops in a table in your lab
notebook (see below).
4. Repeat steps 2-3 another 5 to 10 times. Each time, another person at your table should add the
drops of DI water.
5. When you are finished, determine the average number of drops in 1 mL of water and estimate the
volume of a single drop of water.
Recording your data in a table:
When recording data in the results section of your lab notebook, you should always record data in
table format. Before beginning any lab exercise, take time to read through the instructions so that you
know the type of data that you will collect. Make an appropriate table in your results section before
beginning the lab exercise, in which you will record your data.
Appendix 4.3 - page 7
BIO 150-6, p. 3 of 7
For this particular exercise, an effective data table might look like this:
Title of table: Number of drops (dispensed using a dropper and bulb) in 1.0 mL of DI H 20.
Initials of person dispensing drops
# drops in 1.0 mL DI H20
Add rows as necessary, as group
will repeat exercise 5-10 times…
An additional way in which you can ensure that you make the best possible use of your time in
the lab (and to ensure that you actually complete everything that will be expected of you in a given lab
period) is to divide the labor among the members of your lab group. A good way of dividing labor during
a lab exercise is to assign one person the task of recording the data into their lab notebook, and then have
everyone else copy the data after class or after all of the data have been collected. (It is also good
practice for the person recording the data to repeat out loud the numbers that they are entering, in order to
verify that they heard and wrote down the correct numbers.)
COMPLETING YOUR LAB NOTEBOOK ENTRY:
Remember that a proper lab notebook entry contains introduction, methods, results, and
discussion sections.
 The introduction should contain a brief description of the purpose of the lab and your hypothesis.
 The methods section should briefly describe the methods you performed. Specify the equipment used
as you describe the methods.
 The results section should contain your data, in table format.
 In the discussion section, interpret the meaning of your data.
- Was your hypothesis supported or refuted by your data? Explain.
- How could this data be used? For example, what is the estimated volume of one drop of water?
- Were there limitations to the experiment as you conducted it? If you could do the experiment
again, what aspect of the methods would you change?
- Think ahead- write a new hypothesis that should be tested next, and explain why data obtained by
testing this hypothesis would be useful.
Appendix 4.3 - page 8
BIO 150-6, p. 4 of 7
DISPENSING LIQUIDS, PART 2
BIO 150
GOALS:
.
- Distinguish and name the different types of devices used to dispense liquids, and
understand when to use and how to correctly use each device.
- Understand the difference between accuracy and precision.
-
INTRODUCTION:
Last week, in BIO 150 and in BIO 201, you used equipment designed to dispense small amounts
of volumes (glass droppers and micropipettors). This week in BIO 150, you will be introduced to a
variety of devices designed to accurately and precisely dispense larger volumes. You will learn the
variety of equipment available, when to use each particular type, and how to accurately use each type. In
addition, you will learn the difference between accuracy and precision. This lab requires that you know
how to convert units of mass, volume, and density in the metric system.
ACCURACY VS. PRECISION:
Accuracy refers to your ability to obtain the correct measurement (how close your measurement is to the
expected value). Precision refers to your ability to obtain repeatable measurements. You can be precise
without being accurate.
Accuracy: If you are dispensing 5.0 ml samples of water accurately, the mass of each sample
should be 5.0 g; if you are dispensing the samples inaccurately, the mass of each one may be
something more or less than 5.0 grams.
Precision: If you are dispensing the samples precisely, each sample should have approximately
the same mass (whether you are dispensing them accurately or not), and if you are dispensing
them imprecisely, the samples will vary in mass.
DEVICES FOR DISPENSING VOLUMES OF SOLUTIONS:
Beakers –flat-bottomed, straight-sided, relatively broad vessels with a flared top and a pouring spout;
available in a range of sizes from 5ml to several liters; may be marked with graduations to indicate
approximate volumes; made of glass, Nalgene or other materials.
Erlenmeyer flasks –flat-bottomed vessels with a tapered shape and a straight neck; available in a range
of sizes from 5ml to several liters; may be marked with graduations to indicate approximate volumes;
made of glass, Nalgene or other materials.
Graduated cylinders –tall, narrow vessels with straight sides, a broad base and a pouring spout;
available in a range of sizes from 5ml to 2 liters or more; marked with graduations indicating precise
volumes (usually in increments of 0.1ml or 1ml, depending on the size of the cylinder); made of
glass, Nalgene or other materials.
Volumetric flasks (glass) – rounded vessels with a flattened base and narrow elongated stem; the stem is
marked with a line that indicates when the flask contains the volume of liquid that the flask is
calibrated to hold; available in a range of sizes, but each size can only be used to accurately dispense
a single volume of liquid; made of glass.
Appendix 4.3 - page 9
BIO 150-6, p. 5 of 7
Volumetric pipettes (used with a pipette pump) – long, slender tubes with a bulge in the middle; the
tube above the bulge is marked with a line that indicates when the pipette contains the volume of
liquid that it is calibrated to hold; available in a range of sizes, but each size can only be used to
accurately dispense a single volume of liquid; made of glass.
(Serological) Pipettes – long, slender, straight-sided tubes marked with graduations indicating precise
volumes in increments that vary with the total volume that the pipette is capable of holding; may be
designed to be filled up to a graduation marked “0” and then emptied until it reads the volume that
has been dispensed, or may be designed to read the volume of liquid that has been drawn up into the
pipette (and then that volume is emptied completely); liquids are drawn up into the pipette and
dispensed from it using a pipette pump (see next); made of glass or plastic.
Pipette pump – a device that is attached to the end of a pipette and used to generate suction that draws a
liquid up into the pipette; releasing the suction then allows the liquid to flow out of the pipette.
Available in a variety of flavors: the ones you will most likely be using are either (a) rubber bulbs
with squeeze-activated valves that allow the user to create and release suction and a stem into which
the end of a pipette is inserted, or (b) plastic handles with a rubber sleeve into which the end of the
pipette is inserted and a geared stem that you raise with a thumbwheel in order to create suction or
lower in order to dispense the liquid.
Micropipettors (used with disposable tips) – used with disposable tips to dispense small volumes (11000l, to the nearest 1l) of liquids; more information about these will be provided elsewhere.
Burette – like a pipette, but liquids are dispensed through a stopcock, and the volume of liquid dispensed
is determined by subtraction of the initial reading from the final reading; used for doing titrations;
made of glass, stopcocks can be Teflon or glass
Pasteur pipettes with bulbs – slender, thin-walled tubes with a long tapered tip and a rubber bulb that is
squeezed in order to draw up and dispense liquids
Glass droppers with bulbs – slender, thicker-walled tubes with a short-tapered tip and a rubber bulb that
is squeezed in order to draw up and dispense liquids
VOLUME IS MEASURED AT THE BOTTOM OF THE MENISCUS:
When most liquids are placed in a container, capillary action will draw the liquid that is in contact
with the walls of the container up the sides. This causes the surface of the liquid to become curved (or
cresent-shaped), and forms the “meniscus”. When determining the volume of the liquid in a container,
you must always look at where the bottom of the meniscus is, you must be holding the container perfectly
level (in the case of a pipette, this means that it must be perfectly vertical), and you must have your eyes
at the same level as the meniscus. In some cases, failing to do all of these things may make little
difference, but in other cases (and in some experiments) the error that you introduce may be enough to
create problems.
Appendix 4.3 - page 10
BIO 150-6, p. 6 of 7
CONDUCTING THE LAB EXERCISE:
In order to determine the accuracy and precision with which you can dispense liquids, and the
accuracy and precision of a variety of devices that can be used to dispense them, you will dispense (and
determine the mass of) a given volume of a solution using several of the devices described above. Half
the class will dispense 10-mL samples of one solution, and the other half will dispense 5-mL samples of a
second solution. One of the solutions will simply be water, and the other will be something other than
just water (but harmless); one of your tasks will be to determine which solution is which.
The first set of students will dispense 5-mL samples of their solution using:
25-mL graduated cylinder
5-mL volumetric pipette
5-mL pipette
The second set of students will dispense 10-mL samples of their solution using each of the following
devices:
25-mL Erlenmeyer flask (filled to the 10mL line)
10-mL graduated cylinder
10-mL volumetric pipette
5-mL pipette
Before you begin, write a hypothesis in the introduction section of your lab notebook:
When you write your hypothesis, consider the following. Which group of students (those measuring 5mL or 10-mL) do you believe will obtain the most accurate measurements? Which group of students do
you believe will obtain the most precise measurements? Which of the pieces of equipment do you believe
will most accurately and precisely measure the desired volumes?
Collecting your data:
Because one of the objectives is to determine accuracy and precision with which you are able to dispense
your samples, it will be necessary to dispense several samples using each device. In order to collect all of
your data as efficiently as possible, it is worth considering the strategy that you use to dispense and weigh
several samples in succession. Although it would be perfectly reasonable to weigh the empty beaker into
which you will be dispensing your samples, record its mass, dispense your first sample into it, weigh the
beaker and the sample it now contains, record the mass, determine the difference in mass (in order to
determine the weight of the sample), empty the beaker, and repeat the process for each subsequent sample
… it would be far more efficient to avoid having to repeatedly record masses and repeatedly empty the
beaker. So … we will ask you to use the following protocol:
1.
2.
3.
4.
5.
6.
7.
8.
Make sure that your balance is on a steady surface, away from drafts, and is leveled.
Place the empty beaker on the balance.
Zero the balance.
Remove the beaker and dispense your sample into it.
Place the beaker (containing the sample) back on the balance.
Record the mass of the sample in your lab notebook, and the unit (g).
Zero the balance.
Repeat steps 4-7 (in bold) for each subsequent sample, until you have dispensed the given volume
a total of five times using each device.
Appendix 4.3 - page 11
BIO 150-6, p. 7 of 7
Remember that you should always record your data in table format when possible. For this
particular exercise, an effective data table might look like this:
Example of title: Mass (g) of 10-mL samples of “Solution A” dispensed using the given measuring
devices.
Sample #
1
2
3
4
5
25 ml Erlenmeyer
flask
Measuring device
10 ml graduated
10 ml volumetric
cylinder
pipette
5 ml pipette
How can you determine whether the liquid you measured (solution “A” or solution “B”) was water or
another liquid? If another liquid, do you have ideas as to what the liquid might be? (Hint: Calculate the
density of your measurements.)
Completing your lab notebook entry:
Remember that a proper lab notebook entry contains introduction, methods, results, and
discussion sections.
 The introduction should contain a brief description of the purpose of the lab and your hypothesis.
 The methods section should briefly describe the methods you performed. Specify the equipment used
as you describe the methods.
 The results section should contain your data, in table format.
 In the discussion section, interpret the meaning of your data.
- Was your hypothesis supported or refuted by your data? Explain.
- Was the liquid that you measured water or another solution? Explain how you know the answer
to this question.
- Were there limitations to the experiment as you conducted it? If you could do the experiment
again, what aspect of the methods would you change?
- Think ahead- write a new hypothesis that should be tested next, and explain why data obtained by
testing this hypothesis would be useful.
Appendix 4.3 - page 12
BIO 360-1, p. 1 of 2
Vert. Physiology Lab #1 - Tutorial
I would like you to do two figures for this lab. They will be due at the beginning of the next
lab period. The first figure should be done in Excel and the second should be done in MS Word.
Figures should be in black & white or grey scale (no color) and the graph should not be filled (i.e.,
should not have a grey background). Your figures must not be identical to any one else’s figures.
Figure 1: Pulse Rate
 This figure should be done in Excel.
o Record your pulse rate according to the experimental protocol for several
seconds.
o Save your data as a text file.
o Open the text file, copy the data, and paste it into Excel.
o Create an XY scatter plot of the data in a new Excel page.
o Resize, refine, and manipulate the graph until it is appropriately configured
for publication in a scientific journal.
o Add a text box to the page and create an appropriate caption for the figure.
Include descriptive statistics of your pulse rate (mean, range and standard
deviation) based on at least ten data points.
o Add a second, small text box in the lower right corner of the page with your
ID in it.
Figure 2: Pulse Rate at Various Data Sampling Rates
 This figure should be dome in MS Word.
o Complete the “Adjusting the Sampling Rate” exercise as described.
o Select the appropriate waveforms and go to WINDOWS > ZOOM
WINDOW.
o Go to EDIT > COPY ZOOM WINDOW.
o Open MSWord and Paste the ZOOM WINDOW into Word.
o Use text boxes to overlay and/or re-label the graph as necessary to produce a
publication quality figure.
o Create an appropriate caption for the figure that includes descriptive statistics
of your pulse rate (as described above).
o Add your ID to the bottom right corner of the page.
Also see:
Making Graphs with Excel
http://qrc.depaul.edu/StudyGuide/MakingGraphsWithExcel.htm
Making Graphs with Excel (PDF)
http://www.gulllakecs.org/Technology/Making%20Graphs%20with%20Excel.pdf#search='making%20graphs%20with%20Excel'
Making Scientific Graphs with Microsoft Excel
http://www.howe.k12.ok.us/~jimaskew/excelgra.htm
Excel Graphing Tutorial
http://www.ocf.berkeley.edu/~ufourcc/Excel%20Graphing%20Tutorial.htm
Appendix 4.3 - page 13
BIO 360-1, p. 2 of 2
Vert. Physiology Lab #8 Assignment
Reflexes & Reaction Time
I would like you to do figures and data analyses as needed for this lab. They will be due at
the beginning of the next lab period. The figures should be done in Excel or any other graphing
program and have an appropriate, detailed, explanatory caption.
Exercise 1: The Stretch Reflex
 Complete this exercise as explained in the manual on each member of your team.
Write a description of 1) the subjective experience of how the Jendrassik manoeuvre
affects the knee jerk reflex and 2) the neural organization that must exist for the
phenomena to occur.
Exercise 3: Reflexive Contraction of the Palmis Brevis
 Complete this exercise and as explained. Write a description of the reflex from a
subjective and objective point of view. Describe and illustrate the muscular/neural
anatomy underlying the reflex and why it can be elicited by pressure.
Exercise 4-8: Reaction Times
 Complete the exercises as explained. However, you should collect 50 data points for
each person in your group, for each exercise. Graph the individual reaction times
across the 50 trials for each member of your group for each experiment and describe
the pattern of changes, if any, that occur over trials.
 This set of experiments should yield 5 line graphs, each of which has one line for
each member of your group. Each graph might look something like this (except the
X axis would be 1-50):
Time (sec)
Reaction Time
8.00
7.00
6.00
5.00
4.00
3.00
2.00
1.00
0.00
Student 2
Student 1
1
3
5
7
9
11
13
15
Trials

In your captions for the figures (1) be sure that you incorporate the answers to the questions
in the lab manual and (2) give some explanatory comments regarding why there are or are
not differences within and/or between experimental results.
Appendix 4.4
BIO 351-2, p. 1 of 1
Oral presentation of the results of a primary research paper
Carefully choose what you will present in order to remain within the 10-min. time limit. Practice
to make sure that you can really present your information without exceeding your time limit!
Item
Points
possible
Title Slide (authors’ names, journal
name, publication year)
Importance of research (give some
background information to explain
why this research was necessary)
1
Specific research objectives
(don’t just list them- explain them
to audience)
How were methods similar & how
were they different from methods
we’ve used in lab or on field trips?
Thorough explanation of data in
two tables and/or graphs.
- Explain slowly and in detail,
so that those who’ve never
seen the graph or table can
follow your explanation.
- Explain what is represented by
each axis, symbol, etc.
Explain pattern of data.)
Explanation of conclusions that
can be drawn from data,
explaining how that data relates
to the research objectives.
What additional or unanswered
questions does this data lead you to
think of? How would you go
about conducting a research project
to answer those questions?
Effectiveness of visual aids. For
example:
- Text clear, simple, and easily
read from back of room
- No more text than needed
- Graphs and/or tables annotated
to highlight important aspects
- Slides with graphs and/or
tables not to “busy” for
audience to follow data
(generally, only 1 graph or
small table per slide.
Delivery (eye contact, pacing,
enthusiasm)
Giving thoughtful, honest answers
to questions
2
TOTAL
OTHER COMMENTS:
2
1
6
2
1
2
2
1
20
Points
obtained
Comments
Appendix 4.5 - page 1
Biology M.S. Thesis students in last 5 years (completed) – in chronological order
Student
Research Advisor
Kennedy,
Kathy
Tessalee, Eli
R.G.Rawlins (Rush
Memorial)
S. Mungre
Rowan, Karen
Waikel
Jackson, Pete
Kasmer
Jones,
Moneen
Kasmer
Bowman,
Tracy
Puryear
Jackson, Erin
R.G.Rawlins (Rush
Memorial)
Hay, Marsha
Kimble
Lyke, Martha
J. Dubach
(Brookfield Zoo)
Pollack,
Kathy
Kasmer
Qureshi,
Ahmed
Thomas
Webster,
Katherine
P.
Schreckenburger
(Loyola
University)
J. Dubach
(Brookfield Zoo)
Santonastaso,
Trent
Advisor
of record
Waikel
Kimble
Kimble
Stojković
Kasmer
Thesis Title
Optimizing the embryo culture system
in an in vitro fertilization laboratory.
Apoptotic effect of manganese and
cobalt on neuronal PC12 cell.
The effect of differentiation on the
expression of multidrug resistance
proteins in murine keratinocytes
Temporal and spatial vegetation
dynamics in a remnant oak savanna:
Middlefork Savanna, Lake County,
Illinois.
Intraguild predation between the larvae
of an indigenous and introduced species
of ladybird beetle (Coleoptera:
Coccinellidae) when prey are not
limiting.
The effects of methotrexate and
leukovorin on survival and the
developing spinal cord, brain, and head
regions in ICR mice.
Development of a microbicidal sperm
wash for use in ART with HIV-infected
males
Hemocyanin in Limulus polyphemus
protein variation in trilobites with age.
Molecular genetic analysis of African
lion (Panthera Leo) population
structure in Etosha National Park.
Restoration of the eastern prairie
fringed orchid (Platanthera
leucophaea): natural pollinators and the
abundance of larval host plants.
Effects of 1% ethanol supplementation
on fission rates, mortality rates, and
longevity in aging Paramecium
tetraurelia cells.
Antibiotic susceptibility testing of
clinically significant nondiphtheriae
Corynebacterium species.
Population structure of wild raccoons
(Procyon lotor) from various habitat
types across the Chicago area using
molecular techniques.
Defense
date
May 2006
July 2006
August
2006
August
2006
December
2006
August
2007
April 2008
December
2008
December
2008
May 2009
August
2009
December
2009
December
2009
Appendix 4.5 - page 2
Biology M.S. Thesis students in last 5 years (in progress)
Student
Sara Rose
Advisor
J. Olfelt
Camille Belpedio
S. Mungre
Nawaf Habib
Laura Ybarra
S. Mungre
M. Kimble
Luiza Przewodnikowska
T. Puryear
Thesis topic
Genetic diversity of apples in outhwestern Asia. (defended in
April 2010)
Monitoring stress and resiliency building in animal-assisted
therapy dogs (canis familiaris). (defended in April 2010)
Role of advanced glycation products in apoptosis of PC12 cells.
Relating brain development to behavior in mice (Mus
musculus) exposed to different levels of folinic acid during
gestation.
Effects of methotrexate toxicity and varied folate analog
supplementation on cranial facial development in the ICR
mouse.
Library Thesis Students:
In addition to the students listed below, three additional students received credit for BIO 497 (Library
Thesis), but in reality they were allowed to register and do a review paper, due to a lack of available grad
level courses.
Completed:
Rory Klick- library thesis on the effects of deer on native vegetation in forest preserves.
In progress:
Nadia Ahmed- working with one of the ecologist at Brookfield Zoo on a project related to evaluating
the practicality of combining bison in for prairie restoration and meat production.
Samira Kahn- will be working with a professor at Northwestern on project related to improving the
nutritional quality of school lunches.
Appendix 4.6 - page 1
3-Year Assessment Plan for the Undergraduate Curriculum
YEAR 1:
 Choose a departmental assessment coordinator, who will lead the 3-year effort to develop
a system to continuously assess departmental learning outcomes.

Choose coordinators for core courses (BIO 150, 201, 202, 301, 303, and 305).
Responsibilities of coordinators for core courses will include a) arranging regular
meetings between faculty teaching different sections of the same core course to facilitate
regular communication, b) providing prep sheets to the prep staff for common labs, c)
gathering assessment materials to give to the departmental assessment coordinator, and d)
spearheading efforts to expand the use of instructional technology when appropriate (e.g.
utilizing computer-based course materials or bioinformatics resources).

For each core course, faculty teaching that course will work together to decide upon
common learning outcomes, assessment instruments, and textbook, so that students
taking different sections of the same core course will gain similar knowledge and skills.

We will compile a library of assessment instruments currently used in courses throughout
the program, to serve as a resource for faculty developing assessment instruments and for
upcoming discussions about how courses complement or build upon one another.

We will discuss the departmental learning outcomes to determine if any revisions need to
be made before assessment of those outcomes begins in year 2. For example, suggestions
have been made to add the following two learning outcomes to the undergraduate
program.
- SLO 2c. Apply biological knowledge to evaluate important issues that impact
society. (Students are more apt to remember biological information if they realize
its relevance. Also, applying biological knowledge will increase critical
observational, thinking, and reasoning skills.)
- SLO 1d. Apply information learned in cognate areas (chemistry, math, and
physics) to better understand biology. (Adding this statement to our departmental
learning outcomes explains the importance of the required cognate courses. It
will also encourage us to better integrate cognate material into biology courses.
Although we currently do a good job integrating chemistry content into courses,
we need to work further to improve integration of math and physics concepts into
appropriate courses.)

We will implement the requirement for all students in capstone courses each semester to
take the MFT exam. To encourage students to take the MFT exam seriously, we will a)
give the exam during the second week of the semester, before students are distracted by
studying for exams, b) enter students who score highly (e.g. in the top 50% of NEIU
biology) in a drawing to win a gift certificate to Amazon.com.
YEAR 2:
 The departmental assessment coordinator will work with faculty teaching core courses to
determine which departmental learning outcomes would be best assessed by each core
course.
Appendix 4.6 - page 2

For each core course, faculty will develop assessment instruments (e.g. grading rubrics
for assignments or exam questions) for at least two departmental learning outcomes.

The assessment instruments in development will be tested in each section of the core
course to determine where revisions are necessary.

We will begin a departmental discussion about developing standard expectations for
assignments commonly applied across courses, such as lab notebook entries, lab reports
written in the style of a primary research paper, and oral presentations.
YEAR 3:
 We will begin systematic use of the assessment instruments developed and tested during
year 2. Faculty will use the assessment instruments each semester and give the data to
the departmental assessment coordinator.

Now that learning outcomes and assessment instruments have been developed for each
core course, we will begin a departmental discussion of how core courses and electives
complement and build upon one another. Deficiencies in student learning, as revealed
by the previous two years of MFT, will supply important information to our discussion.
We will revise learning outcomes for individual courses and the curriculum as a whole
accordingly.

As we evaluate the curriculum as a whole, we will consider whether our current course
requirements are preparing our undergraduate students to effectively compete with
graduates from other universities. Many institutions require biology majors to take
Calculus I and/or II, Organic Chemistry II, and Biochemistry. We currently do not
require those courses of our students, which may place them at a disadvantage.

We will consider implementing additional assessment instruments. For example, several
faculty use mid-semester surveys to obtain feedback from students. We will also
consider Student Assessment of Learning Gains (SALG, www.salgsite.org) surveys.