Block 2

1. Which of these is not a function of reverse transcriptase?

a. Proofreading
b. RNA degradation
c. RNA dependent DNA synthesis
d. DNA dependent DNA synthesis
2. Fill in this chart for lactose operon
Glucose Level Lactose Level Transcription of lac
operon?
Why
High High
High Low
Low High
Low Low


3. Which of the following statements is true about attenuation and the tryp codon?
a. At high concentrations of tryp, 2:3 hairpin forms
b. At low concentrations of tryp 2:3 hairpin forms
c. The leader peptide is rich hydroxylated proline
d. Attenuation occurs at the transcriptional level
4. Which of these is not a human protein/DNA interaction?
a. Zinc Finger
b. HMG-Box Motif
c. Leucine Zipper
d. Helix turn Helix
e. Helix Loop Helix
5. At high concentrations of iron
a. Ferritin is actively transcribed, Transferrin is not
b. Transferrin is actively transcribed, Ferritin is not
c. Both are actively transcribed
d. Neither are actively trasncribed
6. What is the sequence of the original DNA for the control? Just do the first 10 bases
a. CGGCTATCAG
b. GCCGATAGTC
c. AAATTACATG
d. TTTAATGTAC

7. A circular plasmid contains a number of RE sites. Cuts at each of these sites makes
the fragments shown in the chart. Draw out the plasmid.
EcoR1 2.0 Kb, 4.0 Kb
HindIII 0.5Kb, 5.5Kb
BamH1 1.0Kb, 1.0Kb, 4Kb
EcoR1 +BamH1 1.0Kb, 3.0Kb
HindIII+EcoR1 0.5Kb, 2.0Kb, 3.0Kb
EcoR1 +HindIII+Bam H1 0.5Kb, 1.0Kb, 2.0Kb


8. What test is this? What does it show you?

a. Southern: expression of globin gene
b. Northern: evidence of splicing
c. Western: differential protein expression
d. Eastern: lipid expression in different organelles
9. Match the correct vector with insert size (kbp)
a. Plasmid
b. Bacterial Artificial Chromosome
c. Yeast Artificial Chromosome
d. Bacteriophage
i. <300
ii. <2000
iii. <15
iv. <23
10. Describe what each of these elements in a mammalian expression vector are used
for.
a. Ampicillin
b. Neomycin
c. SV40 ori/enhancer/polyA
d. pUC ori
e. Myc Epitope
f. Pcmv
11. Which of the following is not a true statement about RNAi?
a. RNAi is a mechanism that inhibits gene expression by either destroying
mRNA or by inhibiting translation
b. DICER is the catalytic subunit of Argonaut
c. Humans generally undergo translation inhibition pathway, but can also
under destruction pathway by adding dsRNA
d. RISC stands for RNA-induced silencing complex

12 . A third-year medical student joins a laboratory that studies gene regulation. The
laboratory uses bacteria to study gene expression and metabolic regulation after exposure
to toxic compounds. The goal is to generalize the observations seen in prokaryotic cells in
response to the toxins and to compare the response to eukaryotic cells. Which of the
following statements is true regarding prokaryotic and eukaryotic genomes?
(A) They are both diploid.
(B) They both organize and compact their DNA with histones.
(C) They both have short repetitive DNA sequences throughout their genome.
(D) They both organize their genes into operons.
(E) They both use the same genetic code to convert codons to amino acids.

13. One colony of bacteria is split into two Petri plates: one plate with growth medium
containing glucose and all 20 amino acids and one medium with one sugar (lactose) and
one nitrogen source (NH4 +). Which of the following statements is correct concerning the
cells growing in the second medium?
(A) cAMP levels will be lower than cells growing in the presence of glucose.
(B) CAP protein (cAMP-binding protein) will be bound to the lac promoter.
(C) The lac repressor will be bound to the lac operator.
(D) RNA polymerase will not bind to the trp promoter.
(E) Attenuation of transcription of the trp operon will increase

14. A 13-year-old boy has is brought to the emergency room by his parents because he
develops severe diarrhea and vomiting for several days. He had recently eaten
undercooked seafood. After a battery of tests it is discovered that he has extremely high
levels of cyclic AMP and is diagnosed with Cholera. Which of the following mechanisms
might be the result of Cholera Toxin?
(A) Producing cGMP
(B) Binding to an intracellular receptor
(C) Activating of Apoptosis mechanism
(D) Adenylate cyclase locked into stimulatory state
(E) Causing phosphorylation of Tyrosine Residues



15. A 44 year old woman sees her oncologist to discuss her cancer treatment. She is placed
on a medication which inhibits estrogen synthesis in an effort to control tumor growth. The
medication which her physician put her on most likely

(A) Activates attenuation due to low Trp levels inside the cell
(B) Binds to Adenylyl Cyclase preventing downstream binding of CREB to the CRE
(C) Competitively binds to the estrodial site on the estrogen receptor preventing
transcription
(D) Binds to DNA and prevents RNA Pol from attaching
(E) Causing phosphorylation of Tyrosine Residues

16. A research fellow is studying Trp Regulation. While running an experiment with a
colony of prokaryotes she is asked by one of her technicians how attenuation causes
hairpin formation and how this regulates transcription. The researcher explains that

(A) The lack of Trp in the cell causes the ribosome to stall on the second peptide
sequence thereby causing a hairpin to form between sequences 3 and 4 allowing
transcription to occur
(B) The lack of Trp in the cell causes the ribosome to stall on the Open Reading Frame
before sequence 2 allowing a hairpin to form between sequences 2 and 3 and
causing RNA Pol to fall off (Rho Independent Termination)
(C) The lack of Trp in the cell causes the Ribosome to stall on the second sequence
allowing a hairpin to form between sequences 3 and 4 causing RNA Pol to fall off
(Rho Independent Termination)
(D) The lack of Trp in the cell causes the ribosome to stall on the Open Reading Frame
before sequence 2 allowing a hairpin to form between sequences 2 and 3 preventing
RNA Pol from falling off.

17. Two second year medical students are studying for their Step I exams when one asks
the other to explain how the Lac Operon represses transcription. The student explained to
her classmate that

(A) The lac operon will be turned off when Glucose is present and Lactose is present due
to the fact that Glucose generates high cAMP levels in the cell and thus allowing the
activator to bind and inducing the repressor by high levels of Allolactose
(B) The lac operon is turned on when Glucose and lactose are both present because
Glucose lowers cAMP levels causing the activator to bind and dissociating the
repressor with high Allolactose levels
(C) The lac Operon is turned on when no glucose is present but Lactose is because
absence of glucose allows for high cAMP levels and high Allolactose levels this
allowing the activator to bind and inducing the repressor
(D) The lac Operon is turned off when no glucose is present but Lactose is because
absence of glucose allows for high cAMP levels and high Allolactose levels this
allowing the activator to bind and inducing the repressor


18. Which of the following statements is true regarding prokaryotic RNA Polymerase?
A. It has both proofreading and helicase activity
B. Strength of binding to the DNA is determined by the consensus sequence
C. Prokaryotes have 3 different types
D. It needs a primer

19. What will not affect the rate of transcription?
A. The spacing between the consensus sequences
B. The distance of the consensus sequence from +1
C. Negative supercoiling by Topoisomerase
D. The spacer sequences


20. What is true about Rho dependent termination of transcription??
A. It can unwind double stranded DNA
B. It is an ATP independent mechanism
C. It binds at the termination site
D. It is unique to prokaryotes

21. What is required for the Rho independent mechanism??
A. Strong A-U bonding to make Hairpin and weak GC bonding in RNA/DNA hybrid
B. Strong A-U bonding in RNA/DNA hybrid and weak GC bonding to make Hairpin
C. Weak AU bonding to make Hairpin and strong GC bonding in RNA/DNA hybrid
D. Weak AU bonding in RNA/DNA hybrid and strong GC bonding to make Hairpin


22. What is the purpose of U2 snRNP in splicing?
A. It binds to the 5 splice donor site and undergoes two transesterification reactions.
B. It binds to the branch site A making a reactive OH capable of starting a
nucleophilic attack
C. It binds to the 3splice acceptor site and joins with U5 in order to bring the two
ends together
D. It binds to the 5splice acceptor site and joins with U5 in order to bring the two
ends together

23. What enzyme is responsible for the addition of the poly-A tail?
A. guanylyltransferase
B. S-adenosylmethionine
C. guanine-7- methyltransferase
D. polyadenylate polymerase

24. Which of the following is not an enzymatic activity of Reverse Transcriptase?

A. DNA dependent RNA synthesis
B. RNA degradation
C. DNA dependent DNA synthesis
D. RNA dependent DNA synthesis

25. How has staphylococcal bacteria formed resistance to Erythromycin?
A. It binds to the 23S rRNA site
B. It has converted a single guanine in the 23S rRNA so erythromycin cannot bind
C. It has converted a single adenosine in the 23S rRNA so erythromycin cannot bind
D. Erythromycin has converted a single guanine in the 23S rRNA so staphylococcal
bacteria cannot bind





































Answers

1. A
2.
Glucose Level Lactose Level Transcription of lac
operon?
Why
High High No No cAMP
High Low No No camp, repressor
bound
Low High Yes Lots of cAMP,
repressor is
unbound
Low Low No High camp but
repressor remains
bound


3. B
4. E
5. A
6. D
7.

X is EcoR1
Y is HindIII
BamH1 cuts should be around the X on the right. 1Kb on each side.


8. B
9. A iii, B i, C ii, D iv
10:
a. Ampicillian : selection in bacteria
b. Neomycin: selection in eukaryotes
c. SV40 ori/enhancer/polyA: needed for neomycin synthesis in eukaryotic cells
d. pUC ori: ORI in bacteria
e. Myc Epitope: allows protein to be purified from all other proteins
f. Pcmv: where transcription for the gene of interest starts

11. D
12. E
13. B
14.D
15.C
16. D
17. C
18.B
19.D
20.D
21.D
22.B
23.D
24.A
25.C