Exam Code Number:____________________

MOL 214
EXAM 1
February 24, 2011

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Multiple choice questions (More than one answer may be correct – circle ALL correct
answers) (25 points)

1. If you add deoxyribose thymidine monophosphate in place of deoxyribose thymidine

triphosphate in a DNA replication reaction, what would happen?

A. Leading strand synthesis would not occur.

B. DNA synthesis would be unaffected
C. Lagging strand synthesis would not occur.
D. Primer synthesis would not occur.
E. Sugar backbone of DNA would be substituted

2. Which of the following features is common to both DNA replication and transcription?

A. Nucleotides are added to the 3' end of the newly synthesized strand
B. A sugar-phosphate bond is formed between the 3' hydroxyl and the 5' phosphate
C. Deoxyribonucleotides are incorporated into the growing sequence
D. Both RNA and DNA polymerase require oligonucleotide priming
E. Both RNA and DNA polymerase initiate at promoter sequences

3. A biochemist isolated and purified the molecules needed for DNA replication. When he added all
of the purified molecules to a sample of DNA, replication occurred but the DNA molecules formed
were defective. Each consisted of a normal DNA strand paired with segments of DNA a few
hundred nucleotides long. Which of the following has been left out of the mixture?

A. DNA Ligase
B. Helicase
C. Nucleotides
D. Polymerase
E. Magnesium

4. Which of the following could be a recognition sequence used by a type II restriction enzyme?

A. 5'-GAATTC-3'
B. 5'-ATAT-3'
C. 5'-ACAACA-3'
D. 5’-GCTGAT-3’
E. 3' -GGGTTT-5'

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5. Which of the following participate in transcription termination?

A. stem-loop sequences in mRNA

B. Rho
C. Multiple RNA polymerase molecules
D. Ribosomes
E. Promoters

6. Sigma factors

A. are used by both prokaryotes and eukaryotes

B. add specificity to RNA polymerase
C. bind to DNA
D. bind to RNA polymerase
E. are highly processive

7. To describe the genetic code as degenerate indicates that

A. mRNA is rapidly degraded

B. The code is not universal among organisms
C. Some amino acids have more than one codon
D. Frameshift mutations are tolerated
E. Stop codons may have corresponding tRNA molecules

8. The sequence of one strand of DNA is 5’-TCGATC-3’. The sequence of the complementary
strand would be

A. 5’-AGCTAG-3’
B. 5’-TCGATC-3’
C. 5’-CTAGCT-3’
D. 5’-GCTAGC-3’
E. 5’-GATCGA-3’

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9. Which of the arrow(s) in the diagram below best represents the position and direction of leading
strand DNA synthesis?

OriC

OriC

E. None of the arrows represent leading strand synthesis

10. If a closed circular piece of DNA contained many negative supercoils, how would this alter how
this DNA runs in an agarose gel?

A. It would run faster in the gel than the same DNA without supercoils
B. It would run slower in the gel than the same DNA without supercoils
C. The supercoils in the DNA would not make a difference
D. It is impossible to predict unless you know the exact number of supercoils
E. It would run as fragments on the gel due to the many nicks in supercoiled DNA

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Short Answer Questions

1. Numerous elegant studies were performed to identify the components of our genetic material.
Answer the following questions regarding those investigations.

a) Griffith’s experiments demonstrated transformation of an organism by genetic material using the

R and S strains of Streptococcus pneumonia. If the genetic material had been protein instead of
DNA, would the results of this experiment have been different? Please explain your answer. (3
points)

b) Hershey and Chase used radioactive isotopes of phosphorus (32P) and sulfur (35S) to demonstrate that
DNA is the genetic material passed onto the next generation. Why were these two isotopes chosen for their
experiment? (2 points)

c) Do the results from Hershey and Chase experiments distinguish between RNA or DNA as the
genetic material? Why or why not? (2 points)

d) Why was the blender step important in the Hershey and Chase experiments? (2 points)

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2. Here is a region of a eukaryotic chromosome. Replication starts near x. One strand of the DNA
has been labeled with heavy 15N, hence the capital letters, but all newly synthesized DNA in the
daughter cells will have normal N (lower case letters)

5’ aaaggg . . . . . . . x . . . . . ccctttggg 3’
3’ TTTCCC . . . . . . . X . . . . . GGGAAACCC 5’

That cell divides to make two daughter cells, which in turn divide to make four granddaughter cells.
Draw these chromosome sequences as they would look in the two daughter cells, clearly indicating
which contain the heavy and normal nitrogen. (4 points)

How many of the 4 granddaughter cells will contain DNA with heavy nitrogen? (2 points)

3. During DNA replication, the following nucleotide substitution occurred (underlined and in
bold):
5’- ATGGGTCACCTTGCCCGTCTTACTTGA-3'
3’- TACCCAGTGGAACGGGCAGAGTGAACT-5’

a) Which repair system will most likely correct this substitution? Briefly describe the mechanism.
(4 points)

b) The substitution is in the third codon position. Looking at the codon table at the end of the exam,
what kind of mutation is this nucleotide substitution? Is it deleterious to the cell? (2 points)

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4. For each of the following proteins, explain what its function is AND describe where the process
of DNA replication would get stuck if a cell did not make that protein.(10 points)

DNA polymerase δ 5’ – 3’ polymerizing activity

DNA polymerase ε 3’ to 5’ exonuclease activity

DNA Helicase

Clamp protein

Topoisomerase

5. Why does DNA polymerase delta need to be more processive than DNA polymerase alpha? (2
points)

What allows DNA polymerase delta to be more processive? (2 points)

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6. Name each functional group that belongs at the positions indicated by the boxes. You do not
need to draw out the chemical structures, but just name the groups.
(3 points)

7. You are working as a scientist in a Biotechnology company on developing new anti-cancer

agents targeting telomerase.
a) Why are telomerases a good target for anti-cancer therapy?(3 points)

b) Would there be side effects with treating a cancer patient with an anti-telomerase
therapeutic agent? If so, what? If not, why? (3 points)

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8. You are working in a lab as a graduate student before the automated sequencing machine (using
fluorescent dyes) was invented. Your project is to sequence a gene, so you use radioactive
primers and perform gel electrophoresis of the DNA synthesis (sequencing reaction) products.
For the following DNA segment shown below, and using the primers indicated, how many
different sized radioactive fragments would you detect on the gel? Write out the sequence of
these fragments.

5'-AAAAAAAACTGAATTACGAGGGGGGGG-3'
3’-TTTTTTTTGACTTAATGCTCCCCCCCC-5’

a) If you use a primer with the sequence 5'-CCCCCCCC-3' and you added ddATP? (4 points)

9. Transcription of double-stranded DNA in prokaryotes and eukaryotes is a complex process.

Answer the following question regarding transcription.

5’-CTGGGCCACAAGTGCATATAAGTGAGGTAGGGATCAGTTGCTCCTCAGAATACAGCTTACATTTGCTTCTTGA-3’
3’-GACCCGGTGTTCACGTATATTCACTCCATCCCTAGTCAACGAGGAGTCTTATGTCGAATGTAAACGAAGAACT-5’
*
a) A molecular biologist cloned part of a gene shown above from Drosophila. Which RNA
polymerase is responsible for transcribing this gene? Briefly describe an experiment that would
prove that the polymerase you answered was in fact responsible for transcribing this gene. (3 points)

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5’-CTGGGCCACAAGTGCATATAAGTGAGGTAGGGATCAGTTGCTCCTCAGAATACAGCTTACATTTGCTTCTTGA-3’
3’-GACCCGGTGTTCACGTATATTCACTCCATCCCTAGTCAACGAGGAGTCTTATGTCGAATGTAAACGAAGAACT-5’
*

b) The bottom strand of DNA is used as the template for transcription and the site at which
transcription starts is indicated by the symbol *. What is the sequence of the RNA transcript that is
made from this DNA template? Please indicate the 5’ and 3’ end. (3 points)

c) In the DNA sequence shown above, which proteins recognize and bind the underlined promoter
sequence in eukaryotes? (2 points)

d) The molecular biologist suspects other promoter elements in the gene above. Briefly describe an
experiment that she can perform to prove it has promoter elements that affect transcription? (3
points)

e) What RNA structure plays a role in termination in termination?(1 point)

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10. You are a new graduate student starting your research in a lab that works on cancer biology.
Numerous studies have implicated the role of Gene X in the development of breast and ovarian
cancer in 5% of patients. The first thing you are asked to do is to clone this gene from human
epithelial cells into a plasmid. So you extract DNA from epithelial cells and decide to PCR amplify
Gene X in order to clone into a plasmid. The sequence of Gene X is shown below along with the
restriction endonuclease sites available. (EcoRI-boxed and BamHI-underlined) and the lengths of
the DNA when cut with these endonucleases.

a) Design two primers to amplify Gene X, including the first and the last base pair in the amplified
product. The primers should be 8 nucleotides in length. Label the 5’ and 3’ ends of each primer. (4
points)

b) What is the expected frequency that an 8 nucleotide long primer would likely to bind a specific
sequence in the genome? (Formulate your answer in a way that doesn’t require a calculator).
Assume that all bases occur at equal frequency in the genome. (2 points)

c) Once you have the amplified region of Gene X, you want to develop a strategy to clone this
region into the plasmid shown on the next page using the multiple cloning sites (MCS) on the
plasmid. Which enzyme(s) would you use to clone Gene X into the plasmid shown on the next
page? (2 points)

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d) Now you want to determine which orientation Gene X is inserted within the plasmid. The size of
the plasmid alone is 3.0 kb. The fragment from BamH1 to the MCS is 0.5kb. The HindIII to
BamH1 fragment is 0.5 kb.
Which enzyme would you use to digest the plasmid to prove the orientation of Gene X? For each of
the possible orientations, on the gel below, show the fragments as they would run on an agarose gel.
Be sure to label the fragment sizes. Indicate the direction of DNA mobility. (6 points)

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