MOL 214

Final Exam
May 22, 2015

Your exam code number is:

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.

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 points each, 34 points total)

1. The primary stabilizing force of protein secondary structure is:

A. Ionic bonds
B. Covalent bonds
C. Van der Waals forces
D. Hydrogen bonds

2. The difference between a ribose and a deoxyribose sugar is:

A. The phosphate group attached to the 3’ carbon of the sugar

B. The hydroxyl group attached to the 2’ carbon of the sugar
C. The hydroxyl group attached to the 3’ carbon of the sugar
D. The phosphate group attached to the 5’ carbon of the sugar

3. How would a decrease in the processivity of DNA polymerase affect the replication of a cell’s
DNA?

A. The cell would no longer be able to perform discontinuous replication

B. The cell would replicate its DNA in the 3’ to 5’ direction
C. The cell would replicate its DNA much more slowly
D. The cell would no longer be able to effectively proofread during DNA replication

4. Which of the following choices correctly associates the sequence of (in this order):
the coding strand of the DNA, the corresponding mRNA, and the corresponding tRNA anticodon?

A. 5’-ATC-3’, 5’-AUC-3’, 3’-UAG-5’

B. 5’-ATC-3’, 5’-GAU-3’, 3’-CUA-5’
C. 5’-ATC-3’, 5’-GAU-3’, 3’-UAG-5’
D. 5’-ATC-3’, 5’-AUC-3’, 3’-CUA-5’

5. Which of the following events does NOT require base-pairing interactions?

A. Addition of an amino acid by a tRNA molecule

B. Recognition of intron-exon junctions by snRNPs
C. Addition of the poly-A tail
D. Elongation of the telomeres

6. In a polysome, which ribosomes will have synthesized the longest peptide chain at any particular
time?

A. The ribosomes nearest the 5’ end of the mRNA molecule

B. The ribosomes nearest the AUG codon of the mRNA molecule
C. The ribosomes nearest the 3’ end of the mRNA molecule
D. The ribosomes nearest the middle of the mRNA molecule

2
 Exam Code Number:___________

7. Which of the following statements is TRUE?

A. Only ER-bound ribosomes can bind signal recognition particle

B. Translation of the signal peptide occurs on free cytosolic ribosomes
C. A protein translated on ER-bound ribosomes is longer than the same protein translated
on free cytosolic ribosomes
D. ER-bound ribosomes only make proteins destined for the nucleus

8. Since steroid hormones bind to receptors inside the cell, which of the following is TRUE?

A. The receptor molecules are themselves lipids

B. The steroid/receptor complex can cross the nuclear membrane
C. Steroid receptors cannot bind to DNA
D. Steroid receptors activate transcription through phosphorylation

9. Below is shown a short sequence of DNA. Methylated cytosines are represented by “Cm”. If the
DNA containing this sequence is treated with sodium bisulfite and then PCR is performed, what
would you expect the resulting sequence to be?

5’-ATCGTCCmGAACmG-3’

A. 5’-ATTGTTCGAACG-3’
B. 5’-ATCGTCTGAATG-3’
C. 5’-ATTGTTTGAATG-3’
D. 5’-ATAGTCAGAAAG-3’

10. Which of the following statements best describes the difference between siRNAs and miRNAs?

A. siRNAs silence their gene targets by base-pairing with the sense strand, while miRNAs
silence their gene targets by base-pairing with the anti-sense strand
B. siRNAs act in the cytoplasm of the cell, while miRNAs act in the nucleus of the cell
C. siRNAs are processed from single-stranded RNAs that form a hairpin, while miRNAs are
processed from double-stranded RNAs
D. siRNAs originate primarily from external sources, while miRNAs originate from the
genome of the cell

3
 Exam Code Number:___________

11. Below are the results of an Ames test. All of the numbers provided in the table represent the
number of colonies present on plates that do not contain histidine. The column labels describe the
additional substances added to cultures of Salmonella bacteria. Based on the data below, which of
the following substances is likely to be a carcinogen?

A. Substance “B”
B. Substance “D”
C. Substances “A” and “C”
D. Substances “B” and “D”

12. How would a mutant in the EGFR protein that leads to constitutive activation and dimerization
of the receptor affect the Rb protein and the cell cycle?

A. The Rb protein would be hyperphosphorylated, and the rate of cell division would
increase
B. The Rb protein would not be phosphorylated, and the rate of cell division would increase
C. The Rb protein would be hyperphosphorylated, and the rate of cell division would
decrease
D. The Rb protein would not be phosphorylated, and the rate of cell division would
decrease

13. Why is the translocation of the myc gene from chromosome 8 to chromosome 14 characteristic
only of Burkitt’s lymphoma (a cancer involving B cells), and not of other cancers?

A. The translocation of chromosome 8 and 14 only occurs in B cells

B. Antibodies are only made in the B cells
C. Myc only promotes cell division in the B cells
D. B cells lack the necessary checkpoints to prevent cancer from occurring

4
 Exam Code Number:___________

14. Which of the following is true of an epigenetic modification?

A. It changes the sequence of the DNA

B. It occurs only at C-G base pairs
C. It is heritable
D. It occurs only in CpG islands

15. Which of the following alterations of a tumor suppressor gene would be most likely to lead to
cancer?

A. Hypomethylation of a CpG island at the promoter

B. Nonsense mutation in the codon for the 10th amino acid in the protein
C. A SNP in the coding region of the gene
D. Increased activity of a Histone Acetyltransferase in the region where the gene is located

16. A diploid cell contains 2 pairs of homologous chromosomes. Each pair of chromosomes is
heterozygous for a single allele (Aa and Bb, respectively). After meiosis, how many different
combinations of these alleles could be present in the daughter cells?

A. 2
B. 4
C. 8
D. 16

17. Below is shown a pedigree of a family, some of whom have been diagnosed with a genetic
disorder. Based on the information provided in the pedigree, what is the likelihood that the
individual in the final generation marked with a “?” will be affected by the disease?

A. 0%
B. 25%
C. 50%
D. 100%

5
 Exam Code Number:___________

Short Answer (116 points total)

1. (a) What is one way in which the separation of proteins by gel filtration chromatography
and SDS-PAGE are similar? (2 points)

(b) What is one way in which they are different? (2 points)

2. Although bacterial chromosomes contain a smaller number of nucleotides, some higher

eukaryotic species can actually replicate their DNA more quickly than a bacterial cell. Assuming
that the bacterial and eukaryotic polymerases are able to replicate approximately the same number
of nucleotides per second, what explains the ability of these eukaryotic cells to replicate their
chromosomes so quickly? (2 points)

3. Mutations can occur every time our DNA is replicated and our cells divide. (3 points)

(a) What is one negative consequence of these mutations?

(b) What is one positive consequence of these mutations?

6
 Exam Code Number:___________

4. DNA primers are used in both PCR and Sanger sequencing. In general, 2 different primers are
required for PCR, while only 1 primer is necessary for the Sanger sequencing reaction. Why are 2
different primers added to a PCR reaction, while only 1 primer is added to a Sanger sequencing
reaction? (2 points)

5. What are two components that must be present on a plasmid in order for it to be used as a
cloning vector? (2 points)

6. Describe how each of the following contributes to the structure of genomic DNA. (4 points)

(a) Overall positive charge of histone proteins:

(b) Supercoiling:

7. RNase P is a ribozyme that is known to convert pre-tRNA into tRNA. If RNase P was extracted
from cells and then heated above its Tm, would you expect that it would still perform this function?
Why or why not? (3 points)

7
 Exam Code Number:___________

8. A mutant eukaryotic RNA polymerase has been created that is missing part of the C-Terminal
Domain. The mutant protein is no longer able to be phosphorylated, and cells expressing this
mutant protein do not survive. Provide 2 reasons why these mutations would be lethal in vivo. (4
points)

9. Below is shown a diagram of a gene with introns and exons. What effect would the mutations
below have on the protein? (6 points)

(a) 3-base-pair deletion at the point marked by arrow “A”

(b) 1-base-pair deletion at the point marked by arrow “B”

(c) 1-base-pair deletion at the point marked by arrow “C”

8
 Exam Code Number:___________

10. A point mutation occurs upstream of the lac operon, in the CAP protein binding site. This
mutation prevents the CAP protein from binding to the DNA. (6 points)

(a) The cells containing this mutation are grown on media containing X-Gal. In the table
below, indicate the color of the colonies in the various growth conditions.

(b) Explain how changing the sequence of a binding site could affect the binding of a
protein to DNA.

11. You are interested in understanding which genes in liver cells are controlled by glucocorticoids
(steroid hormones), and further, how the expression of these genes is changed in the presence of
glucocorticoids. You have at your disposal liver cells in cell culture, reverse transcriptase,
fluorescent dNTPs, purified glucocorticoids, radioactive dNTPs, SDS-PAGE and agarose gels, and
microarrays. (8 points)

(a) What experiment would be the best way to investigate this question?

(b) Briefly (in 2-3 sentences) describe what experimental and control samples you would
use to perform the experiment.

9
 Exam Code Number:___________

(c) Briefly (in 2-3 sentences) describe your anticipated results from your proposed
experiment and how these results would help you to answer your research question.

12. Choose two of the terms listed below: (8 points)

Methylation, Acetylation, Enhancers, Transcription Factors

(a) Describe how each of the two terms you chose can regulate transcription.

(b) Describe how the two terms you chose work together to regulate transcription.

10
 Exam Code Number:___________

13. A patient has arrived at your clinic with symptoms resembling those of a condition called
hemochromatosis. Patients with this condition absorb and store more iron than normal. After
confirming that this patient has wild-type hemoglobin, you perform the following tests: a northern
blot to examine your patient’s ferritin and transferrin mRNAs before and after the patient receives
treatment to lower their iron levels, an SDS-PAGE gel to determine levels of IRE-Binding Protein,
Ferritin protein, and Transferrin protein in your patient before and after treatment to lower their
iron levels, and a gel-shift assay with your patient’s IRE-binding protein and their ferritin and
transferrin mRNAs. The results are shown below: (12 points)

(a) What can you conclude from the northern blots? Is this what you would expect if the
system was functioning normally?

(b) What can you conclude from the protein levels provided in the table? Is this what you
would expect if the system was functioning normally?

11
 Exam Code Number:___________

13. (cont):

(c) What can you conclude from the gel-shift assays? Is this what you would expect if the
system was functioning normally?

(d) Propose an explanation for the observed results, including a description of the mutation
that is likely present in this patient and responsible for their symptoms.

14. Briefly describe 2 reasons that cells in primary cell culture reach the plateau phase and senesce.
(4 points)

15. (a) Briefly (1-2 sentences) describe how the symptoms of the hereditary and non-
hereditary forms of retinoblastoma differ. (3 points)

(b) How did these differences lead Knudson to propose the two-hit hypothesis? (3 points)

12
 Exam Code Number:___________

16. Below is shown a pedigree of a family with hereditary retinoblastoma. The mother and father
in the bottom right-hand region of the pedigree (generation III) are concerned about the health of
their 4 young children, and decide to have them all pre-emptively tested for the presence of Rb
mutations, before any of them have developed tumors. A northern blot for the Rb mRNA was
performed on cells from each child and is also shown below. (5 points)

(a) Based on the data shown, which of the children are more likely to develop
retinoblastoma?

(b) Explain your answer in part (a).

17. Complete the following table by determining whether the cell cycle would proceed in each of
the following situations. Write a “+” if cell division would occur and a “-“ if cell division would not
occur. (6 points)

13
 Exam Code Number:___________

18. How does the process of apoptosis prevent the development of cancer? (2 points)

19. What would be the effect of a deletion of the Xic region of an X chromosome? (4 points)

(a) in a male offspring?

(b) in a female offspring?

20. Explain why Prader-Willi and Angelman Syndromes may develop in children of either sex, but
can only be inherited from a parent of a particular sex? (4 points)

14
 Exam Code Number:___________

21. The images below are from an organism with 4 chromosomes. Label each of the following
images as occurring during mitosis or meiosis, the phase of mitosis/meiosis that is pictured, and
whether the cell is “n” or “2n”, and “c”, “2c” or “4c” at the end of the pictured phase. (9 points)

22. Describe how each of the following contributes to increasing the genetic variability of a species.
(8 points)

(a) Chromosome segregation:

(b) Crossing over:

(c) SNPs:

(d) DNA polymerase:

15
 Exam Code Number:___________

23. (a) Briefly describe one way that trisomy of the 18th chromosome might increase the
expression of a gene located on the 8th chromosome. (2 points)

(b) Briefly describe one way that trisomy of the 18th chromosome might decrease the
expression of a gene located on the 12th chromosome. (2 points)

16