MOL 214

Exam 1
March 3, 2015

Your exam code number is:

Write this number on each Answer Key
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.

Remember to write legibly, if we can’t read it, we can’t grade it!

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

Signature: __________________________________

Printed Name: _______________________________

 Exam Code Number:______________
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

2
 Exam Code Number:______________
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

3
 Exam Code Number:______________
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

4
 Exam Code Number:______________
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 C (1 pt.)

(ii) would be present at the C-terminus of a protein A (1 pt.)

(iii) would be common among all amino acids A, B, C (1 pt.)

(iv) is specific to this amino acid D (1 pt.)

(v) would likely be most important for the formation of secondary structure A, C (1 pt.)

(vi) would likely be most important for the formation of tertiary structure D (1 pt.)

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.)

No credit, given in question- Competitive inhibitors bind to the same binding site on the protein as the normal
substrate

1 pt.- The mutation would cause a conformational change in the enzyme.

1-2 pts.- As we discussed in class, both the shape of the binding site and interactions between the protein and the
molecule or protein it binds to are important.

Full credit (4 pts.)- It could be difficult to obtain a mutation that altered the shape of the binding site in such a way
that the substrate could still bind, while the competitive inhibitor could not. A mutation that impairs binding of the
competitive inhibitor is likely to also impair the binding of the normal substrate, because they bind in the same
site, which would also prevent the enzyme from functioning.
5
 Exam Code Number:______________

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.)
Polar and/or Charged (1 pt.)

Nonpolar (1 pt.) Polar and/or Charged (1 pt.)

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.)

1 pt.- If bacteriophage had histones, they would likely have been injected into the bacterial cell with the
DNA

2 pts.- Histones are protein, so the histones would have contained radioactive sulfur. The DNA would have
contained radioactive phosphorous. Radioactive sulfur would have been injected into the bacterial cells as
part of the histones, while radioactive phosphorous would have been injected as part of the DNA, so the
bacterial cells would have been radioactive in both cases.

1 pt.- This would have made it impossible for Hershey and Chase to identify DNA as the hereditary material.

Common Mistakes:

-1 pt. for no explanation of labels (radioactive sulfur or phosphorous)

-2 pts. for no explanation of the answer

6
 Exam Code Number:______________
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.)

1 pt.- Diagram

2 pts.- Correct association of 15N with old

and 14N with new

1 pt./generation (3 pts. total)- Correct

labeling of old & new strands

For left band in generation 2, also

accepted 1 “old” 14N strand and one “new”
14N strand

Common Mistakes:
-1 pt. for failing to correctly
associate 15N with old and & 14N
with new for some strands

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: 1 pt.- Creates RNA primer that provides 3’ –OH for DNA Pol to start replication
1 pt.- Unlikely that replication would be able to begin, although replication forks could form
Common Mistakes: -.5 pts. for not specifying that Primase creates RNA primer, -.5 pts. for
saying that primers are needed to tell DNA Pol where to begin replication

(b) DNA polymerase 3’ to 5’ exonuclease activity 1 pt.- removes incorrectly paired bases during
replication
1 pt.- Many more mistakes in the replicated DNA
Common Mistakes: -.5 pts. for describing mismatch repair

(c) DNA Helicase 1 pt.- unwinds the DNA helix

1 pt.- Unlikely that replication would be able to begin

(d) Clamp Protein 1 pt.- Binds to the polymerase and holds it on the DNA strand being replicated
1 pt.- DNA Pol would be much less processive, and would likely fall off the DNA
relatively quickly, making replication less efficient/take much longer

(e) Topoisomerase 1 pt.- Relieves tension of supercoiling as helix is unwound

1 pt.- Helix might reach a point where tension prevents it from opening any further,
strands could break or be damaged due to tension from supercoiling

Common Mistakes: -.5 pts. for various errors in description of enzyme functions or effect on the cell

7
 Exam Code Number:______________
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.)

1 pt.- The ladder occurs because the telomerase is adding repeats to the telomere

2 pts.- The distance between the bands is equal to the number of base pairs in each
telomere repeat.

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?

2 pts.- Any of the following: UV radiation: Thymidine/Thymine Dimers, Nitrosamines: Alkylation,

Ionizing Radiation: Oxidation, Additional answers given credit

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

2 pts.- Any of the following: Water can cause Depurination, Water can cause Deamination, DNA
Polymerase sometimes makes mistakes that are missed in proofreading, Additional answers given
credit

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.

1.5 pts. each (3 total)- Two of the following possible answers: Both require primers, Both require
polymerase, Additional answers also given credit

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

1.5 pts. each (3 total)- Two of the following possible answers: Separation of strands is through
heating in PCR, but helicase in the cell, Primers are DNA in PCR, but RNA in the cell, Replication in
PCR is of a specific region of the DNA, but in the cell, all of the DNA is replicated, Additional answers
also given credit

8
 Exam Code Number:______________
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.)

I N I

I I I

I N I

.5 pts.- Each box in the chart

(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.

1.5 pts.- Methyltransferases prevent cleavage of the bacterial chromosome by methylating the bacterial DNA,
which prevents the endonucleases from cleaving the host chromosome

2 pts.- In strains that possess a restriction endonuclease, but lack a methyltransferase, there is no way to prevent
the restriction endonuclease from cleaving the host chromosome. Thus, those cells will die virtually immediately.

9
 Exam Code Number:______________
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.)

2 pts.- Sample 1: The desired insert is cloned correctly into the plasmid

2 pts.- Sample 2: No insert was cloned into the plasmid

2 pts.- Sample 3: An incorrect insert was cloned into the plasmid (likely bigger than desired insert)
Common Mistakes: No credit for suggesting that 2 genes of interest were cloned into the
vector (this would have resulted in 3 bands on the gel)

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

1 pt.- Sample 1: White

1 pt.- Sample 2: Blue

1 pt.- Sample 3: White

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

2 pts.- Sample 1 plasmid

10
 Exam Code Number:______________
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

1 pt.- Correct # of bands (1)

1 pt.- Correct location (near bottom)

(b) ddATP and dCTP, dGTP, and dTTP

1 pt.- Correct # of bands (1)

1 pt.- Correct location (near bottom or

slightly above “Mistake (a)” band, as
described)

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

1 pt.- Prophase, 1 pt.- Metaphase

Common Mistakes: Deductions for additional incorrect stages

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

2 pts.- Wrapping of DNA around the nucleosomes is the first step in packaging the DNA so that it can fit into
the nucleus

Common Mistakes:
-1 pt. for partial description (for example, including only “fitting into the nucleus”)

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

2 pts.- It would get not be able to progress beyond M phase.

1 pt.- The APC is required to degrade cyclin so that the cell can progress beyond mitosis.

Common Mistakes:
-1 pt. for “the chromatids will not separate”
-2 pts. for “the chromosome will not separate”

11