Gene Regulation (25 points)

 
A prokaryotic cell can use three sugar sources, Sugar A, Sugar B, Sugar C. Sugar B and Sugar C are chemically related, but Sugar A is the preferred energy source. Three proteins, Gopherase 1, Gopherase 2 and Gopherase 3 code for enzymes that are necessary to break down Sugar B and Sugar C, but are not involved in the breakdown of Sugar A. The genes for these three enzymes are located in the Gopher operon. The table provides information about the regulation of the Gopher operon.
 

Sugar A
Sugar B
Sugar C
Level of Transcription

Present
Present
Present
0

Present
Absent
Present
0

Present
Present
Absent
0

Present
Absent
Absent
0

Absent
Present
Present
2

Absent
Absent
Present
1

Absent
Present
Absent
1

Absent
Absent
Absent
0

 
Below are two of the equations we generated in class to represent gene regulation.
Equation 1:          (1-R)(1+A)*S*P = T
Equation 2:          (1-R)(1+A)*TF1*TF2*TF3*TF4*TF5*P*C=T
Where R=Repressor, A=Activator, TF=Transcription Factor, S=Sigma, P=RNA polymerase, C=chromatin
 
1A. (2 points)Which of the two equations would you choose to modify to represent this situation? Explain why specifically referring to variables in the equation.
I would choose Equation _____________
Because
 
 
 
 
1B. (7 points) How would you modify the equation you chose to describe the regulation of the Gopher operon? Rewrite the equation and provide a key for any new variables you introduce. Be sure to use subscripts to indicate which sugar is controlling the regulatory proteins. Use A for Activator and R for Repressor. (e.g., AF would indicate that the Activator is under control of Sugar F.)
 
 
 
 
 
 
 
 
 
 
 
 
 
1C. (8 points) Explain your reasoning for why you made the modifications in 1B. If you did not change the equation or part of the equation, explain that as well. Make sure to cover the number of regulatory terms included (terms with R or A in them), and why the regulatory terms are structured the way they are (both why activator or repressor and why that mathematical representation (for example, if you were doing this for our class equation, you would be explaining why the term for the activator is A+1 and not 2A).
 
 
 
 
 
 
 
 
1D. (8 points) In a situation where Sugar B and Sugar C are present and Sugar A is absent, show what proteins are bound at the Gopher operon on the picture below and indicate the level and direction of transcription including approximation of transcription start and ending points.

Draw the proteins that are bound to the DNA and show where they are bound on the picture below.
Draw the proteins that are not bound to the DNA below the picture.
Indicate the level and direction of transcription with approximation of starting and ending points.

Label the regulatory proteins so it is clear which sugar is controlling their presence or absence and the role of the protein (e.g., AR would indicate that the Activator is under control of Sugar R). Proteins can be represented by circles or other shapes.
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Meiosis and Cell Reproduction (25 points)

 
Plants in the genus Arabidopsis are model organisms in biological research. The species Arabidopsis arenosa is a model organism for meiosis and autopolyploidy because it naturally occurs in both diploid (2n) and tetraploid forms (4n). Both types of plants undergo the same pattern of meiosis, producing eventual gametes with a ploidy half that of the parent cell. The species karyotype has 8 types of chromosome (n=8). For this question, assume that tetraploid plants have four homologs of each chromosome type.
 
2A. (2 points) Fill is the table below for diploid plants. If pairs are not present, enter a 0 or -.
 

 
G1
G2
Beginning of mitosis or meiosis
End of mitosis
End of meiosis I
End of meiosis II

# chromosomes
 
 
 
 
 
 

# homologous chromosome pairs
 
 
 
 
 
 

Ploidy (e.g. 2n)
 
 
 
 
 
 

# sister chromatid pairs
 
 
 
 
 
 

 
2B. (4 points) Fill is the table below for tetraploid plants. If pairs are not present, enter a 0 or -.
 

 
G1
G2
Beginning of mitosis or meiosis
End of mitosis
End of meiosis I
End of meiosis II

# chromosomes
 
 
 
 
 
 

# homologous chromosome pairs
 
 
 
 
 
 

Ploidy (e.g. 2n)
 
 
 
 
 
 

# sister chromatid pairs
 
 
 
 
 
 

 
 
2C. (3 points) For your table in 2B for tetraploid plants, explain your reasoning for the numbers in the row on # sister chromatid pairs. You can use pictures in your explanation as well. (1-3 sentences each).
 
G1:
 
G2:
 
Beginning of mitosis or meiosis:
 
End of mitosis:
 
End of meiosis I:
 
End of meiosis II:
 
2D. (5 points) See the Exam 3 Assignment on Canvas to download a copy of the Morgan et al. 2020 article on meiotic evolution in autotetraplods. This research refers to the “numerous challenges” that new tetraploid A. arenosa plants might face and the strong selection likely present for mechanisms that promote stable meiosis. What is meant by stable meiosis and what challenges might tetraploid plants face in cell reproduction? In other words, what is the result of successful meiosis and what are the consequences if it doesn’t go right? (4-8 sentences. Your answer can refer to meiosis and tetraploids in general and doesn’t need to refer specifically to the article.)
 
 
 
 
2E. (3 points) In the research article (Morgan et al. 2020), the research focuses on prophase I and metaphase I during meiosis I. Why are these critical phases in meiosis? Why would they be the focus of meiosis evolution? Your answers to 2A and 2B may help you here. (2-6 sentences)
 
 
 
 
2F. (4 points) According to the research article (Morgan et al. 2020), describe ONE structural change that seems to have evolved that promotes stable meiosis. What potential problem in meiosis does the change address? Refer to the structure(s) involved in meiosis and what problem they might solve, not the genes that may be associated with the structure(s). Write in your own words, using minimal quotes from the article. No need to understand all parts of the article – focus on overall results. (3-6 sentences)
 
 
 
 
2G. (4 points) Some species of Arabidopsis can reproduce via self-pollination (akin to asexual reproduction) and cross-pollination (sexual reproduction). Why might self-pollination be advantageous in some circumstances? Consider that Arabidopsis is often considered a weed. Why might cross-pollination be advantageous in other circumstances? Think about the costs and benefits of asexual vs. sexual reproduction. (4-8 sentences)
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Inheritance (25 points)

In a different land and a different time, you are a dragon breeder. Giant green dragons with horns that breathe red fire and have wings fetch the most money. The inheritance pattern for these traits is shown in Table 1.
 
Table 1. Genotypes and phenotypes of different dragon traits

Trait
Homozygous Dominant
Heterozygous
Homozygous Recessive

Size
BB – big
Bb – big
bb – small

Color
GG – green
Gg – green
gg – blue

Horns
HH – horns
Hh – horns
hh – no horns

Fire
RR – yellow fire
Rr – yellow fire
rr – red fire

Wings
NN – wings
Nn – wings
nn – no wings

 
You have a male and female dragon with the valuable phenotype that you have recently bought to breed to produce more dragons with the valuable phenotype to sell.
Figure 1: The genotypes and phenotypes of the two dragons
The allele combinations and expected proportions produced by the male and female are shown in Table 2.
Table 2. Proportion of Sperm and Egg Types

Sperm Types
Proportion of Sperm Types
Egg Types
Proportion of Egg Types

rNgBH
.12
rNgBH
.02

rNgbh
.12
rNgbh
.02

rNgBh
.08
rNgBh
.03

rNgbH
.08
rNgbH
.03

rnGBH
.12
rnGBH
.02

rnGbh
.12
rnGbh
.02

rnGBh
.08
rnGBh
.03

rnGbH
.08
rnGbH
.03

rNGBH
.03
rNGBH
.08

rNGbh
.03
rNGbh
.08

rNGBh
.02
rNGBh
.12

rNGbH
.02
rNGbH
.12

rngBH
.03
rngBH
.08

rngbh
.03
rngbh
.08

rngBh
.02
rngBh
.12

rngbH
.02
rngbH
.12

3A. (3 points) Provide a mathematical model(s) or diagram(s) for calculating the proportion of the sperm or eggs. Use variables (not numbers, unless they would not change) and provide a key. Make sure the model meets our criteria for mathematical models of biological phenomenon.
 
 
3B. (11 points) The mathematical model/diagram should apply to all calculations. To demonstrate that it works, explain how the model/diagram would be used to calculate the probability/proportion of rrNGBh sperm. Don’t just plug numbers in. Explain where those numbers came from referring to the following biological processes:

Segregation of alleles during meiosis
Independent assortment of chromosomes during meiosis
Genetic recombination

Remember to describe these processes in your explanation, not just repeat these phrases. Explain why you multiply or add.
 
 
 
 
3C. (11 points) Dragon buyers are fickle. The trendy dragon is now one that is small and blue has no horns, has wings and can breathe red fire as shown here:
 
Write the possible genotype(s) of this dragon:
 
 
Write a mathematical model for calculating the probability of producing any offspring genotype (include a key). Explain how this mathematical model represents the biological process of fertilization.
 
 
Use the mathematical model to make a determination of whether the dragon breeder will be able to make a living by breeding the male and female to produce the small blue dragon with wings and no horns that breathes red fire. Make sure you show how you would calculate the probability of producing this dragon. Show your work/explain your reasoning so that we can see how you derived your answer and where your numbers came from. (A pair of dragons produce 4 offspring every year.)
Work:
 
 
Can the dragon breeder make a living by producing the two dragons he already has to get the new trendy dragon? Explain your answer.
 
 
 
 
 
 
 
 
 
 

Animal Behavior (25 points)

Suppose you are a graduate student working on field research in the Serengeti National Park, Tanzania, studying a newly discovered apparently altruistic behavior seen in female African lions. It has been observed that female lions sometimes leave their pride group, on their own, to patrol their pride’s territory. If a neighbor lion from another pride is found, they will alert their pride-mates by roaring. Given what is currently known about lions and the basis of their social behavior, answer the following questions:
 
4A. (4 pts) What is the definition of altruism and why does this behavior fit this definition? Be specific, including information on what you learned about lions in class. (2-4 sentences)
 
 
 
 
4B. (3 pts) Kin selection is one hypothesis for the evolution of altruistic behavior. Applying Hamilton’s Rule, determine the level of relatedness required between lions to make this patrolling behavior advantageous, if the benefit (b) = 1.3 and the cost (c) = 0.39. Show a simple calculation.
 
 
 
 
 
 
4C. (4 pts) Does the value of relatedness from 4B suggest that kin selection could explain this behavior in lions? Explain. Consider what you know of the biology of a lion pride from class material, especially expected patterns of relatedness between females within a pride. (3-4 sentences)
 
 
 
 
 
 
4D. (7 points) Reciprocal altruism is another explanation for the evolution of altruism. What is reciprocal altruism and could this apply in this case for lions? Apply what you’ve learned in class about reciprocal altruism and lion behavior, and again use the values benefit (b) = 1.3 and cost (c) = 0.39. Consider the general context needed for reciprocal altruism to function. The GameBug simulator (http://ess.nbb.cornell.edu/) we used in class may be helpful here but is not required. (4-8 sentences)
 
 
 
 
 
4E. (7 points) Group selection is yet another explanation for the evolution of altruism. What is group selection and could this apply in this case for lions? Apply what you’ve learned in class about group selection and lion behavior, and again use the values benefit (b) = 1.3 and cost (c) = 0.39. Consider the general context needed for group selection to function. The GameBug simulator (http://ess.nbb.cornell.edu/) we used in class may be helpful here but is not required. (4-8 sentences)
 

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