NOTE: THIS EXAM IS WORTH A TOTAL OF 125 POINTS

Part I: Choose the one BEST answer. Circle its letter. Read each question and all 5 choices carefully because more than one answer might seem correct at first glance. 1.5 points each  

1. Gene regulation in eukaryotes can be regulated by
a. effector molecules
b. molecules originating outside a cell
c. molecules that form complexes with cytoplasmic proteins, which then shuttle to the nucleus
d. signals that regulate processing of a primary transcript
e. all of the above

2. The addition of which of the following converts E. coli RNA polymerase core enzyme into the holoenzyme?
a. alpha subunit
b. beta subunit
c. sigma
d. rho
e. none of the above -- this is not how the core enzyme becomes the holoenzyme

3. If two organisms appear to be the same, except that one can tolerate higher temperatures than the other, what conditions should be used to study the gene(s) involved in temperature tolerance?
a. cool temperatures where both organisms thrive; use some other stressful condition (not temperature)
b. warm temperatures where both organisms thrive
c. very warm temperatures where one organism thrives but the other barely survives
d. hot temperatures where one organism survives but the other dies
e. extremely hot temperatures which kill both organisms, but one survives longer than the other 

4. Post-transcriptional processing of mRNA in eukaryotes includes
a. 5'-capping
b. splicing
c. changing the order of the internal sequences
d. a and b
e. all of the above 

5. A sequence of nucleotides that is found in many places, thought to have a common function is called
a. symmetrical
b. palindrome
c. hybrid
d. consensus
e. promoter

6. Imagine a norm of reaction graph. If an organism shows wide variation, that is, its variance generates a broad bell curve at any given condition, the norm of reaction line would tend to be _______ compared to an organism with a narrow bell curve.
a. steep
b. shallow
c. the same
d. more variable
e. can not tell from the information given 

7. Genetic equilibrium means
a. it is another term for being homozygous, breeding true
b. allele frequency in a population does not change from one generation to the next
c. phenotype frequency in a population does not change from one generation to the next
d. gene frequency in a population does not change from one generation to the next
e. a population is very large and mates randomly 

8. The Hardy-Weinberg formula can be used
a. to estimate allele frequency if phenotype frequency is known
b. to estimate phenotype frequency if allele frequency is known
c. a and b are true under all conditions
d. a and b are true only for populations in equilibrium
e. all of the above

9. Which of the following is a component of a eukaryotic RNA polymerase II promoter?
a. TATA box
b. CAAT box
c. GC-rich region
d. a and b
e. all of the above

10. Linker DNA is associated with
a. histone H1
b. all the histones
c. no histones
d. non-histone chromosomal proteins
e. any of the above may be true depending on gene activity 

11. "Fitness" is used in population and evolutionary genetics to mean
a. strength
b. probability that an organism will reproduce
c. probability that an organism will survive
d. ability to adapt to a changing environment
e. overall health 

12. Geographic partitioning of a population often results in speciation because
a. each group may adapt to its environment differently
b. each group may undergo genetic drift resulting in genotypic divergence
c. a and b are both possible or likely
d. such partitioning seldom if ever results in speciation
e. such partitioning can NOT result in speciation unless the new sites differ greatly 

13. Which of the following DNA sequences would NOT represent a palindrome?
a. 5' -ATATAT- 3'
b. 5' -GACCTG- 3'
c. 5' -GAGCTC- 3'
d. 5' -ATTAAT- 3'
e. 5' -AGTACT- 3' 

14. Positively charged proteins associated with eukaryotic DNA are
a. any histones
b. only nucleosome histones
c. all chromosomal proteins
d. there are no such proteins
e. all proteins are positively charged 

15. In eukaryotes, transcription can be regulated by
a. DNA sequence at the promoter
b. DNA sequence outside the promoter
c. DNA binding proteins
d. a and b
e. all of the above

16. Genes which are active are found in
a. euchromatin
b. heterochromatin
c. a and/or b
d. solenoids
e. any gene may be found in euchromatin or heterochromatin, but activity is not the deciding factor 

17. Enhancer sequences
a. encode enhancer-binding proteins which bind to and stimulate transcription at susceptible promoters
b. enhance transcription even when located far away from a promoter
c. are always found immediately upstream from a promoter
d. have highly conserved upstream consensus sequences
e. all of the above

18. In prokaryotes, transcription can be regulated by
a. DNA sequence at the promoter
b. DNA sequence outside the promoter
c. DNA binding proteins
d. a and b
e. all of the above 

19. If a DNA sequence is known, one can reliably infer the
a. RNA coding sequence
b. polypeptide's amino acid sequence
c. polypeptide function
d. a and b
e. none of the above
 

20. If an amino acid sequence is known, one can reliably infer the
a. DNA coding sequence
b. RNA coding sequence
c. polypeptide function
d. a and b
e. none of the above 

21. Genes which are not active are found in
a. euchromatin
b. heterochromatin
c. a and/or b
d. all genes are active
e. any gene may be found in euchromatin or heterochromatin, but activity is not the deciding factor 

II. [5 points each] Briefly explain your answers to selected multiple choice questions, as indicated. It is possible to earn credit here for good explanations, even if the multiple choice answer is incorrect, so be sure to express yourself clearly.  

1. Multiple choice #18: give an example of each process or component (which occurs)  

2. Multiple choice #15: give an example of each process or component (which occurs) 

3. Explain or demonstrate your answer for multiple choice #6

4. Explain your choice for multiple choice #3. Use a norm of reaction graph to illustrate what is occurring

III. Point values as assigned. Choose sufficient questions to answer to TOTAL 75 points. You may answer up to80 points or use the "write your own" for the final "extra credit" 5 points. 

1. [10 points] Your text states that knowledge of the molecular components forming chromosomes is essential to the understanding of the function of genetic material. To explain this statement, specifically explain: 

a. how the organization of genetic material is different in prokaryotes and eukaryotes, and the implications of this structure on gene regulation in these two groups, and

b. what else is important about chromatin structure (beyond DNA sequence) and how chromatin structure affects gene regulation in eukaryotes. 

2. [10 points] If we were to look at two different cell types in a single organism, we would find the same genomic DNA, but different genes would be expressed to yield the two distinct tissue phenotypes. Briefly explain what chromatin components are involved in determining the tissue-specific gene activity, and the experimental basis for this model. -- or (in other words) -- How can the expression of related genes be coordinated in eukaryotes? How might it be possible to express a particular gene as a member of one group of genes under one set of conditions but with a different group of genes under another set of conditions. Contrast the eukaryotic model of coordinated gene expression with what you know about prokaryotic regulation.

3. [5 points] Describe the eukaryotic RNA pol II promoter. Where is sequence important? If there is a region where sequence is not important, explain what is important there. How do you think these 2 types of regions are used - why are they important in their own ways? 

4. [5 points] What is genetic drift? Explain why genetic drift is more likely (more significant) as population size decreases. Is this always bad? Explain why or why not (or circumstances in which it would be disadvantageous, circumstances in which it would be advantageous) 

5.[10 points] a. What is the Hardy-Weinberg Law, or describe genetic equilibrium?

b-d. The Hardy-Weinberg Law is based on three premises. For each, explain (or illustrate) why it is important -- why equilibrium, as described, requires these 3 conditions.

6. [10 points] Two people of normal phenotype have had a child with Gaucher disease, a lethal recessive trait.

If they have 7 more children, what is the probability that ....                                                                ⁿp_x = [ n! (p^x)(q^n-x) ] / [ x!(n-x)! ]

a) their next child will be afflicted?

b) the next three and last two will be normal but the third and fourth will be afflicted?

c) they will have the same number of boys and girls when they are finished? 

d) they will have exactly one more child with Gaucher disease? 

e) they will have no more children with Gaucher disease and all of the 7 new children are boys?

7. [10 points] For the following populations (each is independent) give the values of p & q, and state whether the population is in Hardy-Weinberg equilibrium [where p = freq(A); q = freq(a) alleles, respectively] :

8. [5 points each part] If you needed to devise a vector, you would need to incorporate several functional components, depending on the desired use for the vector. List the typical important components for the following vector categories or uses: Explain your choices. Where might you look for DNA with these functions (give an example of a DNA region with each function). You may choose functions from the following list:  

a. DNA amplification to produce large quantities of some DNA of interest (for a sequencing study, for example) 

b. expressing a protein for mass production (like insulin for replacement therapy) 

c. testing the importance of individual base pairs or sequences on promoter activity  

d. specific gene product which is expressed only under certain physiological conditions (for replacement gene therapy, for example)

9. [10 points] Referring to the graph:

a. Explain how this information could be used to help devise conditions for a study of this system   

b. Indicate what conditions you would use - and why (this answer may be merged with part (a)  

c. Is this system likely to be an experimental organism, human, or could be either? Explain. 

10. [10 points] In beasts discovered on a newly discovered moon, you observe that there are about three times as many beasts with long eyelashes as there are with short eyelashes. (isn't it wonderful how geneticists get to travel?)  

a. Assuming that eyelash length is determined by a single gene with two alleles, are you justified in concluding that the long eyelash allele is dominant to the short eyelash allele? Why or why not? 

b. What is an alternative interpretation? 

c. Briefly state how one could demonstrate which conclusion is more likely [hint: how can you demonstrate dominance if it exists?]

11. Free choice [5 pt] What question were you expecting that was not asked? Write your own question & answer it.Please ask yourself something you can answer well!! Credit will depend on value of question as well as answer.