Exam code number:________________________

MOL 214
Exam 1
March 1, 2012

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Multiple Choice (2 points each) Please choose only one answer for each question.

1. The melting temperature (Tm) of DNA is the temperature at which:

A) half of the bases in a double-stranded DNA sample have denatured.
B) all of the bases in a double-stranded DNA sample have denatured.
C) half of the phosphodiester bonds in a double-stranded DNA sample have denatured.
D) all of the phosphodiester bonds in a double-stranded DNA sample have denatured.
E) both A and C.
F) both B and D.

2. Which of the following statements about alpha helical structures is true?

A) Alpha helices are stabilized by phosphodiester bonds between amino acids that are four residues
apart.
B) Alpha helices are stabilized by hydrogen bonds between amino acids that are 10.5 residues apart.
C) DNA forms a right-handed alpha helix.
D) Alpha helices are a type of primary structure.
E) Alpha helices are always aligned in parallel to beta-sheets.

3. An enzyme that catalyzes dephosphorylation of a substrate is called a:

A) polymerase.
B) protease.
C) phosphatase.
D) kinase.
E) phosphorylase.

4. Which of the following statements is false about allosteric regulation?

A) Allosteric regulators activate enzymes.
B) Allosteric regulators inactivate enzymes.
C) Allosteric regulators bind to the enzyme’s active site.
D) Allosteric regulators can alter an enzyme’s conformation.
E) Allosteric regulators can interact with an enzyme reversibly.

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5. Which of the following is true about nucleosomes?

A) Nucleosomes are unwound by topoisomerase.
B) Nucleosomes are found in all three branches of life.
C) Histone octamers contain histones H2A, H2B, H3, H4, and the linker histone.
D) Nucleosomes are removed from the DNA by helicase.
E) DNA makes left-handed superhelical turns around histone octamers.

6. DNA polymerase delta:

A) is not very processive.
B) is responsible for leading strand synthesis.
C) is responsible for lagging strand synthesis.
D) primes DNA synthesis during replication and repair.

7. Which of the following correctly describes the order of events in DNA replication?
1) Primers are synthesized by primase.
2) Okazaki fragments are joined together by DNA ligase.
3) DNA is synthesized by polymerase.
4) DNA is unwound by helicase.
5) Primers are removed by nuclease.
6) Gaps are filled by polymerase.

A) 4, 3, 1, 2, 5, 6.
B) 4, 1, 3, 5, 6, 2.
C) 4, 1, 3, 2, 5, 6.
D) 4, 3, 6, 1, 2, 5.

8. Which of the following statements about DNA replication is true?

A) DNA primers are removed by a nuclease.
B) Okazaki fragments on the leading strand are joined together by DNA ligase.
C) Binding of DNA polymerase to the template strand is a rate-limiting step.
D) Clamp loader is not required for DNA replication in bacteria.

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9. Successive nucleotides of a DNA chain are joined by:

A) phosphodiester bonds between the 5’ carbon of one nucleotide and the 2’ carbon of the next.
B) glycosidic bonds between the 5’ carbon of one nucleotide and the 3’ carbon of the next.
C) hydrogen bonds between the complementary bases.
D) ionic bonds between the phosphate group of one nucleotide and the sugar group of the next.
E) phosphodiester bonds between the 3’ carbon of one nucleotide and the 5’ carbon of the next.

10. During DNA replication, new bases are added by polymerase:

A) 5’ to 3’ on the leading strand, 3’ to 5’ on the lagging strand.
B) 5’ to 3’ on the lagging strand, 3’ to 5’ on the leading strand.
C) 5’ to 3’ on both the leading and lagging strands.
D) 3’ to 5’ on both the leading and lagging strands.

Short Answer
1. Why is the peptide bond so rigid (2 points)?

2. What consequence does the rigidity of the peptide bond have for the structure of a polypeptide chain
(3 points)?

3. How do enzymes make reactions occur more rapidly (2 points)?

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4. Explain how isoelectric focusing can be used to separate proteins (5 points).

5. How do polyclonal antibodies differ from monoclonal antibodies (4 points)?

6. The Griffith experiment demonstrated that something from the pathogenic R-form of Streptococcus
pneumoniae could transform the non-pathogenic S-form to enable it to kill mice. Predict if a mouse
will live or die if injected with the following mixtures (5 points).

a. live S + heat killed R

b. live R + heat killed S

c. live R + heat killed S + DNase

d. live R + heat killed S + protease

e. live S + live R + DNase

7. When bacteria are dividing rapidly, DNA polymerase cannot synthesize DNA fast enough to keep
pace with cell division. How is this problem solved (2 points)?

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8. To complete your thesis, you need to purify Carolina Blue Fluorescent protein (CBP) from an E. coli
cell lysate. When active, CBP emits the most beautiful color in the world. You begin the
purification by running the lysate over an ion exchange column. Next, you pool several beautiful
blue-colored fractions from this column and run them over a gel filtration column. The elution
profile of the gel filtration column is pictured below. Your advisor asks you to analyze samples from
the major peaks using SDS-PAGE. The coomassie-stained gel is pictured below, with the molecular
weight (MW) size standard indicated to the left of the gel.

MW= protein size standard.

a. Which peak contains proteins with a larger molecular weight (2 points)?

b. Which peak do you suspect contains CBP (2 points)?

c. In a rush to get to the bar, you forget to write down which samples are loaded into which lanes of
the gel. Name one technique you could use to determine which one of the bands in the gel is
CBP (2 points)?

9. Name and briefly describe the two general ways that cells regulate protein activity by proteolysis (4
points).

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10. Hershey and Chase performed a famous experiment to demonstrate that DNA was the hereditary
material.
a. What radioactive labels were used in this experiment and why were they used (4 points)?

b. How did they ensure that they were monitoring only newly made phage after they infected
bacteria with radiolabeled phage (2 points)?

c. What would Hershey and Chase have observed if protein was the hereditary material (2
points)?

11. Meselson and Stahl demonstrated that DNA replication was semi-conservative. Pictured below is
actual data from their experiment. Describe the setup behind this experiment.
a. Why were the cells first grown in 15N and then switched to 14N (3 points)?

b. Why is there only one band in generation 0 (1 point)?

c. Why are there two bands in generation 2 (3 point)?

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12. Pictured below is the domain organization of an unfolded transmembrane protein. The boxed H-
domains are composed of hydrophobic amino acids. If you know that the N-terminus is found in the
cytoplasm, draw the expected structure of this transmembrane protein in the membrane below (3
points).

13. What kind of secondary structure do transmembrane domains typically adopt (1 point)?

14. The origin of DNA replication is a distinct site. What is the base composition typically found at an
origin? Why is this the case (3 points)?

15. Describe the experiment approach used by Stanley Prusiner to demonstrate that proteins are the
infectious agent that cause Scrapie. How would his results have differed if DNA is the infectious
agent (4 points)?

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16. How do infectious proteins like prions cause disease (3 points)?

17. Describe an experimental strategy to purify DNase protein from a cell extract of E. coli. How could
you be sure that your final product is pure? How could you be sure that it specifically targets DNA
for degradation (4 points)?

18. Control of the cell cycle is extremely important. DNA synthesis must be coordinated with the timing
of cell division. What is the name of the enzyme that controls this critical process? How does
activity of this protein change as the cell progress through G1 (growth), S (synthesis), and M
(mitosis) phases (3 points)?

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19. What feature of the double-stranded DNA helix suggested to Watson and Crick a mechanism by
which DNA could be replicated (2 points)?

20. A scientist engineered a new form of DNA polymerase I that can bind to the sliding clamp. How does
this change affect the function of the polymerase (2 points)?

21. Answer the following questions about the structure of DNA.

a. Why does it make sense that the phosphates are on the outside of the DNA chain (2 points)?

b. Why does it make sense for the bases to be stacked in the center (2 points)?

c. Some DNA binding proteins bind to a specific DNA sequence. What feature(s) of the DNA
helix allow(s) amino acid side chains to bind to specific bases in the DNA (3 points)?

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