MOL 214

Exam 1
March 5, 2014

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Write this number on each

page of your exam.

DO NOT write everything you know about a topic, this will waste your time. If you provide more than one
answer for a question only your first answer will be graded.

If you need extra space, continue only on the back of the page that the question is written on. Clearly
label that you are using the back for your answer.

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I pledge my honor that I have not violated the honor code during this
examination.

Signature: __________________________________

Printed Name: ___________________________

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Multiple Choice Questions:

1. Which of the following statements about the newly synthesized strand of a human chromosome is
correct? (3)
(a) It was synthesized from a single origin solely by continuous DNA synthesis.
(b) It was synthesized from a single origin solely by discontinuous DNA synthesis.
(c) It was synthesized from a single origin by a mixture of continuous and discontinuous DNA
synthesis.
(d) It was synthesized from multiple origins solely by continuous DNA synthesis.
(e) It was synthesized from multiple origins solely by discontinuous DNA synthesis.
(f) It was synthesized from multiple origins solely by a mixture of continuous and discontinuous DNA
synthesis.
(g) It was synthesized from multiple origins by either continuous or discontinuous DNA synthesis,
depending on which specific daughter chromosome is being examined.

2. Which of the following statements does not describe both eukaryotic and prokaryotic transcription? (3)
(a) Promoter elements in the DNA sequence are required for polymerase binding.
(b) Proteins interact with the RNA polymerase and control its binding to DNA.
(c) RNA polymerase opens a double-stranded DNA molecule to expose the template strand.
(d) RNA polymerase can transcribe in either direction once it binds to a promoter sequence.
(e) None of above.

3. Which of the following is required for both splicing and transcription termination in eukaryotes? (3)
(a) A hairpin
(b) RNA polymerase II C-terminal domain
(d) snRNPs
(e) poly(A) polymerase
(f) a nuclease

4. In 2031, the newest Mars expedition returns with samples of

single-celled Martian life forms. You are running a laboratory that
is part of the consortium characterizing the proteome of the
creatures. Pictured is an amino acid present in proteins from the
Martian cells. You wish to study its chemical properties in earthly
cells. Which of the following amino acids do you think you could
most readily replace in a bacterial peptide with the least
perturbation? (3) (A chart of amino acid structures is given on the
last page of the exam)
(a) glycine
(b) histidine
(c) proline
(d) glutamic acid
(e) phenylalanine

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5. Which of the following types of bonds would you expect to form between the R groups of two polar,
charged amino acids? (3)
(a) disulfide bond
(b) electrostatic interaction
(c) hydrophobic interaction
(d) peptide bond
(e) hydrogen bond

6. Which of the following bonds/interactions is strongest? (3)

(a) ionic bond
(b) electrostatic interaction
(c) hydrophobic interaction
(d) peptide bond
(e) hydrogen bond

7. You are studying a membrane protein with four transmembrane alpha helices that assemble into a tight
bundle called a 4-helix bundle (illustrated above). Which of the following best describes the structure of
the 4-helix bundle? (3)
(a) A 4-helix bundle is an example of primary structure.
(b) A 4-helix bundle is an example of secondary structure.
(c) A 4-helix bundle is an example of tertiary structure.
(d) A 4-helix bundle is an example of quaternary structure.

8. Which of the following is the strongest prediction you can make about the transmembrane portion of this
4-helix bundle? (3)
(a) There will be mostly hydrophobic bases on the portions facing the outside of the bundle.
(b) There will be mostly hydrophilic bases on the portions facing the outside of the bundle.
(c) There will be mostly hydrophobic bases on the portions facing the inside of the bundle.
(d) There will be mostly hydrophilic bases on the portions facing the inside of the bundle.
(e) There will be mostly small side chains on the portions facing the inside of the bundle.

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Short Answer Questions

9. In the early 1900s scientists showed that chromosomes were the basis for inheritance, but the
predominant hypothesis was that proteins were the hereditary material. Why was this the
prevailing model? (4 pts)

10. A newly discovered protozoan has a genome that is 40% Adenine. What is the percentage of
Guanine? (2)

11. Griffith discovered a “transforming principle” based on experiments mixing heat-killed S and live
R bacterial strains. Two decades later, Avery MacLeod, and McCarty determined the identity of the
"transforming principle". What was the key evidence that they provided? (5)

12. One of the critical experiments showing that DNA was the hereditary material was performed by
Hershey and Chase using bacteriophage that infect E. coli. An important technological advance for
their experiment was the invention of the Waring blender. Why was this important for their
experiment? (5)

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13. Below is an illustration of the restriction maps of a plasmid vector and a molecule of DNA
containing a gene you wish to clone into the vector, as well as the specificities of several
restriction endonucleases available to you for the cloning experiment.

Which enzymes should be used to cut the vector, and which to cut out the gene of interest? (4)

14. Why is DNA helicase required for DNA replication in the cell but not for PCR or DNA sequencing?
(4)

15. Label the 5’ and 3’ ends of each parental DNA strand. (2)

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16. Three different types of nucleotides are shown below. For each molecule, specify whether DNA
polymerase could add the molecule to a strand of DNA that it is polymerizing. If your answer is no,
explain briefly why the molecule cannot be added. (4.5)

17. Could DNA polymerase extend a strand by adding deoxynucleotide triphosphates to molecules
ending with the structures shown below? Again, give a brief explanation for cases in which your
answer is no. (4.5)

18. Why can’t all DNA mutations be corrected by the proofreading activity of DNA polymerase? (4)

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19. Exposure of DNA to nitrous acid results in conversion of adenine to hypoxanthine. What type of
mutation would you classify this as? (3)
(a) Depurination
(b) Deamination
(c) Oxidation
(d) Thymidine dimer formation

The altered A base pairs with C (cytosine). Why is this a problem if there are still 2 hydrogen bonds
formed between the altered A and the C? (3)

20. You have managed to purify telomerase from a newly discovered protozoan. You test the enzyme
in a reaction with artificial telomeres and radioactive dGTP and run a gel to analyze the products.
Surprisingly, you find that the bands on the gel differ by 12 bases. Explain the property of your
telomerase that must be different from other known telomerases. (4)

21. Most of the cells in the human body are not replicating. What stage of the cell cycle are they in?
(2)

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22. In a project for your thesis, you’ve been studying the yeast cell cycle. You want to use Western
blotting to detect a cyclin and a CDK in a time course of an actively growing culture of yeast cells.
You intended to prepare two separate blots and apply an antibody to cyclin to one of them and an
antibody to CDK to the other, but you accidentally added both antibodies to one of your blots.
Which set of bands corresponds to the cyclin, and which to the CDK? (2)

Why was it necessary for you to perform a Western blot to identify these proteins instead of just
staining the SDS-polyacrylamide gel with protein dye? (3)

23. Walther Flemming was the first to observe chromosomes and describe mitosis. How is the
structural organization of chromatin during mitosis different from its organization during the G1
phase of the cell cycle? (4)

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24. Pictured above is the beginning of a bacterial transcription unit, including its promoter. Write out
the sequence of the first 6 bases of the mRNA transcript according to convention (4)

25. Based upon the results of DNA sequencing of the human genome, it is estimated that there are
around 25,000 genes in the human genome. However, the number of different types of proteins is
much higher than this. Why? (4)

26. Secondary structure is stabilized by hydrogen bonds between atoms of the polypeptide backbone
rather than between the side chains. How, then, do the side chains exert any influence over the
structure of a protein? (4)

27. Name two properties by which proteins can be separated. Provide a technique for each property
that can be used to separate proteins based on this property. (4)

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