MOL 214

Exam 1
March 3, 2015

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Multiple Choice (2 pts. each):

1. Which of the following statements BEST explains why the element carbon forms so many
compounds?

A. Carbon readily forms covalent bonds with other carbon atoms

B. Carbon atoms have very high electronegativity
C. Carbon readily forms ionic bonds with other carbon atoms
D. Carbon atoms combine readily with oxygen

2. Which of the following BEST illustrates the importance of hydrophobic interactions to protein
folding?

A. Globular proteins are able to be denatured by increasing temperature

B. Nonpolar amino acid side chains are clustered in the interior of globular proteins
C. The formation of secondary structures, such as α helices and ß sheets
D. The formation of protein domains with specific functions

3. Which of the following is NOT an accurate description of a way that enzymes catalyze reactions?

A. Enzymes bind to the substrates and bring them into close proximity
B. Enzymes lower the activation energy of the reaction
C. Enzymes cause the substrates to look more like the transition state for a reaction
D. Enzymes contribute energy to the reaction

4. Which of the following BEST summarizes the antiparallel nature of DNA?

A. The nucleotides that make up DNA participate in complementary base pairing

B. The 5’ end of one DNA strand is adjacent to the 3’ end of a second DNA strand
C. The DNA helix is composed of two strands
D. The backbone of DNA is composed of phosphate groups and sugars
E. The bases of the DNA interact with each other through hydrogen bonding

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5. Consider the following ratios:

1. A/G
2. C/T
3. C/G
4. (A+C)/(G+T)
5. (A+G)/(C+T)
6. (A+T)/(G+C)

In double-stranded DNA, which of these ratios will always approximately equal 1?

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

6. All of the following statements apply to the Watson and Crick model of DNA except…

A. The two strands of the helix are held together by covalent bonds.
B. The distance between the strands of the helix is uniform.
C. The framework of the helix consists of sugar-phosphate units.
D. The two strands of the DNA form a double helix.
E. Purines form hydrogen bonds with pyrimidines.

7. In the image below, which regions would undergo lagging strand synthesis?

A. Strands A and B
B. Strands C and D
C. Strands A and D
D. Strand B and C

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8. Which of the following BEST explains the cause of the end replication problem?

A. The 3’-5’ exonuclease activity of DNA Polymerase III

B. The low processivity of DNA Polymerase I
C. The inability of DNA Polymerase III to begin DNA synthesis without a pre-existing 3’
hydroxyl group
D. The extension of the leading strand by telomerase

9. Which of the following BEST describes the reason why “restriction endonucleases” are so
named?

A. A restriction enzyme cuts DNA, and “restriction” is another word for cutting host DNA
B. A restriction enzyme confers resistance to a particular bacteriophage by cutting DNA
C. A restriction enzyme restricts the ability of other enzymes to catalyze reactions
D. A restriction enzyme only works at a particular temperature

10. Which of the following is NOT true of tandemly repeated DNA?

A. Tandemly repeated DNA can be used to identify individuals with great accuracy
B. Tandemly repeated DNA will reassociate more quickly than unique DNA after being
denatured and allowed to renature
C. Tandemly repeated DNA is commonly found within genes
D. Tandemly repeated DNA typically consists of short repeated sequences

11. Dideoxynucleotide triphosphates…

A. Have a hydroxyl group at the 3’ carbon
B. Have a hydroxyl group at the 2’ carbon
C. Prevent further chain elongation
D. Will not form a phosphodiester bond with the 5` nucleotide.

12. Where do the microtubules of the mitotic spindle originate?

A. at the centromere
B. at the centrosome
C. at a chromatid
D. at the kinetochore
E. at the telomere

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Short Answer:

1. The structure of an amino acid is shown below. Using the letters associated with the boxes
shown, indicate which part or parts (6 pts.)

(i) would be present at the N-terminus of a protein

(ii) would be present at the C-terminus of a protein

(iii) would be common among all amino acids

(iv) is specific to this amino acid

(v) would likely be most important for the formation of secondary structure

(vi) would likely be most important for the formation of tertiary structure

2. A number of common antibiotics are of a class known as “competitive inhibitors”. This means
that they inhibit their protein target (generally an enzyme) by binding to the target protein in the
same location as the normal substrate. These antibiotics “compete” with the normal substrate-
when they are bound to the target protein, the normal substrate is unable to bind, because the
antibiotic molecule is already bound. Thus, the enzyme is prevented from performing its normal
reaction. Why might it be less likely that a mutation would result in resistance to this type of
antibiotic? Explain your answer. (4 pts.)

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3. Below is a diagram of a transmembrane protein embedded in a phospholipid bilayer. Label the

transmembrane domain with the type(s) of amino acids (nonpolar, polar, or charged) that you’d
expect to find in each region within the boxes shown. (3 pts.)

4. Bacteriophage do not possess histones. If they did, how would this affect the results of Hershey
and Chase’s experiment, which identified DNA as the hereditary material? Explain your answer. (4
pts.)

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5. Below is shown the data from Meselson and Stahl’s experiment to investigate DNA replication.
For each generation, (0, 1, and 2), diagram what the DNA molecules found in each band would look
like. For each generation, be sure to label each of the strands as either “new” or “old” AND either
“15N” or “14N”. (6 pts.)

6. For each of the following proteins, describe the function AND describe how the process of DNA
replication would be impaired if a cell did not make that protein. (10 pts.)

(a) Primase

(b) DNA polymerase 3’ to 5’ exonuclease activity

(c) DNA Helicase

(d) Clamp Protein

(e) Topoisomerase

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7. Blackburn and Grieder were able to show that a synthetic telomere

sequence was elongated in the presence of Tetrahymena cell extract. The gel
that was produced from this experiment is shown to the right, and a
“laddering” of the bands is evident. What is the significance of the distance
between the bands in the “ladder”? (3 pts.)

8. (4 pts.)

(a) What is one way that DNA can be mutated by substances or processes that do not
naturally exist in our bodies?

(b) What is one way that DNA can be mutated by substances or processes that exist
naturally in our bodies?

9. Compare and contrast the process of DNA replication in cells and through PCR. (6 pts.)
(a) Describe two ways in which the processes are similar.

(b) Describe two ways in which they are different.

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10. In a bacterial species like E. coli, scientists use the following nomenclature to indicate the
presence or absence of a restriction enzyme and an enzyme that methylates the DNA (a
methyltransferase):

“RB+” indicates the presence of a restriction enzyme of type “B”, while “R-“ indicates the
absence of a restriction enzyme.

“M+” indicates the presence of a methyltransferase, while “M-“ indicates the absence of a
methyltransferase.

(a) The chart below lists a number of phages, as well as a number of bacterial strains that the
phages could infect. Fill in the chart with an “I” if you believe a successful infection will occur for
that combination of phage and bacteria and “N” if you believe it is unlikely that infection would
occur. (8 pts.)

(b) There are strains that lack a restriction endonuclease, but possess a methyltransferase (R-,M+)
and strains that lack both (R-,M-). However, there are no strains that lack a methyltransferase, but
possess a restriction endonuclease (R+,M-). Propose a hypothesis explaining this observation.

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11. Your labmate is trying to express a human gene in E. coli, in order to make enough of the
protein to perform further biochemical studies. She cloned her gene into the plasmid using EcoRI.
She then selected 3 different colonies from the plate containing antibiotic where her original
transfection/transformation was plated and isolated plasmid from all 3. Then, she digested a
sample of each plasmid with XbaI and performed gel electrophoresis, in order to confirm that the
gene had been cloned into the plasmid correctly. Surprisingly, after digestion, each of her samples
created a different pattern on the gel. The locations of restriction enzyme sites in the plasmid and
the insert and the results of the gel are shown below.

(a) What is the most likely explanation for each of the patterns observed for each of the 3
samples? (6 pts.)

(b) What color would you have expected each colony to be if the cells were grown on plates
containing X-GAL? (3 pts.)

(c) Which of the 3 plasmids should she use for her future experiments? (2 pt.)

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12. Using the gel below, draw the pattern you would expect to result from a Sanger sequencing
reaction in which the given dNTPs or ddNTPs were incorrectly added to the reaction tube with
primers, template DNA, and polymerase. For simplicity’s sake, assume that, after the sequence to
which the primer binds, the sequence is the following: 5’-CAGCTAT-3’. Also, assume that you are
performing a Sanger sequencing reaction as it was originally performed, using a gel and radioactive
ddNTPs, instead of fluorescent ddNTPs. (4 pts.)

(a) all 4 types of ddNTPs, no dNTPs

(b) ddATP and dCTP, dGTP, and dTTP

13. At which stage(s) of mitosis are chromosomes composed of two chromatids? (2 pts.)

14. In 1-2 sentences, explain why nucleosomes are so important to eukaryotic cells. (2 pts.)

15. Explain what would happen to the cell cycle in a cell that was missing the anaphase-promoting
complex and why? (3 pts.)

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