Download Problem set 7

Problem set 7 - BIOC 441
Multiple Choice:
1.
What is the nitrogenous base found on the last common precursor in the biosynthesis of
AMP and GMP?
A)
B)
C)
D)
E)
2.
6-mercaptopurine.
Hypoxanthine.
Adenine.
Guanine.
5-aminoimidazole-4-(N-succinylcarboxamide).
Which of the following statements about Sanger sequencing of DNA is correct?
A)
B)
C)
D)
E)
Sanger sequencing relies on chemical cleavage of template DNA strands into
small fragments.
Sanger sequencing reactions require the presence of radiolabeled, but not
unlabeled deoxynucleotide triphosphates.
Sanger sequencing reactions require the presence of both radiolabeled and
unlabeled deoxynucleotide triphosphates.
Sanger sequencing reactions require the presence of deoxynucleotide
diphosphates.
Sanger sequencing requires GTP (the RNA nucleotide).
3.
Pick the BEST statement about DNA topoisomerases.
A)
DNA topoisomerases do not change linking number.
B)
All topoisomerases change linking number in increments of ±1.
C)
All topoisomerase II inhibitors work equally well on bacteria and eukaryotes.
D)
All topoisomerases require ATP.
E)
The reaction cycle of all topoisomerases involves an intermediate in which DNA
is covalently attached to a Tyr residue in the enzyme active site.
4.
Which of the following (A-C) is required for continuous synthesis of
deoxyribonucleotides from riboncleotides?
A)
Thioredoxin.
B)
Thioredoxin Reductase.
C)
FADH2.
D)
ALL of the above (A-C) are required.
E)
NONE of the above (A-C) are required.
5.
What is this thing?
A)
Thymidine.
B)
Uracil.
C)
Cytosine.
D)
5-methylcytosine.
E)
Cytidine.
6.
Which one of the following does NOT act as a chain terminator for DNA, RNA, or
protein synthesis?
A)
B)
C)
D)
E)
F)
7.
What is the most common cause of mutations that are subsequently corrected by DNA
polymerase proofreading sites (= 3´to 5´exonuclease sites)?
A)
B)
C)
D)
E)
8.
Puromycin.
2´, 3´-dieoxyguanosine triphosphate.
2´-deoxyguanosine triphosphate.
3´-deoxyguanosine triphosphate.
Acyclovir (after its conversion from prodrug to active drug).
UV photodamage.
Intercalating toxins.
Residual radiation from the Chernobyl accident.
Oxidizers.
Spontaneous keto/enol and amide/imidic acid interconversion in template DNA.
Which of the following functions (A-C) resides within the bacterial primosome?
A)
DNA polymerase.
B)
DNA ligase.
C)
Endonuclease.
D)
ALL of the above (A-C).
E)
NONE of the above (A-C).
9.
We set up test tube reactions containing ATP, GTP, leucine, and the cognate aaRS and
tRNA for leucine. To each of four replicate reactions we add one of the nucleotides
shown. Which one (A-D) acts as the strongest competitive inhibitor of tRNA[Leu]
aminoacylation?
A)
B)
C)
D)
E)
10.
Which of the following statements best describes wobble codons?
A)
B)
C)
D)
E)
11.
The wobble base may be in any position 5'-X-Y-Z-3´.
The wobble base in an mRNA codon may contain inosine.
Wobble pairing can occur only when the tRNA anticodon contains inosine.
Wobble pairing increases the speed of protein synthesis.
Wobble pairing increases the error rate of protein synthesis.
Which of the following types of interaction is most important in maintaining the stable
folded structure of a tRNA molecule?
A)
B)
C)
D)
E)
12.
A.
B.
C.
D.
None of the above (A-D) would act as a competitive inhibitor of aminoacylation.
Salt bridges.
Disulfide bonds.
Isopeptide bonds
Hydrogen bonding between base pairs.
Base stacking interactions.
Which of the following statements (A-D) about origins of DNA replication is false? Or
are all of the statements true (E)?
A) A single bacterial origin can fire (initiate replication) more than one time per cell
cycle.
B) A single eukaryotic chromosome can contain hundreds of separate origins.
C) Replication licensing is the process through which eukaryotic origins are prevented
from firing multiple times in one cell cycle.
D) At both bacterial and eukaryotic origins, replication is bidirectional, with two
replication forks moving away from from each origin in opposite directions.
E) ALL of the above answers (A-D) are true.
13.
Which of the following statements best describes eukaryotic RNA polymerase II?
A) RNAP II requires a primer for initiation.
B) RNAP II directly recognizes the sequence 5´-TATA-3´.
C) Phosphorylation of the RNAP II C-terminal domain is required for efficient capping,
splicing, and polyadenylation of mRNA transcripts.
D) Enhancer-binding activator proteins stimulate transcription by directly contacting
RNAP II.
E) ALL of the above answers (A-D) are TRUE.
14.
Choose the best statement about the RNAP II C-terminal domain (CTD).
A) As RNAP II leaves the promoter, the CTD becomes heavily phosphorylated.
B) As RNAP II leaves the promoter, the CTD becomes heavily methylated.
C) The covalently modified CTD binds capping enzyme and other factors that
process the nascent RNA transcript.
D) Both answers A and B are correct.
E) Both answers A and C are correct.
15.
Which of the following statements best describes covalent modification of
histones?
A)
B)
C)
D)
E)
The N-terminal tails of histone proteins are often acetylated.
The N-terminal tails of histone proteins are often phosphorylated.
The N-terminal tails of histone proteins are often methylated.
The N-terminal tails of histone proteins are often ubiquitylated.
All of the above answers (A-D) are correct.
16. Which of the following statements best describes the ribosomal small subunit?
A) It contains the peptidyltransferase center.
B) It has the intrinsic capacity to specify which amino acids correspond to
specific codons.
C) It is made entirely of RNA.
D) It controls sequential pairing of codons and anticodons in a specific reading
frame.
E) The small subunit binds to the mRNA only after the large subunit has bound
to the initiation codon.
17. Which of the following answers best describes tRNA molecules?
A) tRNA molecules have stereospecific surfaces that directly bind specific
amino acids for aminoacylation.
B) tRNA molecules do NOT have stereospecific surfaces that directly bind
specific amino acids for aminoacylation.
C) Aminio acids are esterified to the 5´ terminus of a tRNA to form an aa tRNA.
D) A and C.
E) B and C.
18. Which of the following answers (A-D) best describe aminoacyl tRNA synthetases?
A) All aaRS enzymes must carry out two distinct synthetic operations.
B) All aaRS enzymes contain a proofreading site.
C) aaRS enzymes are multifunctional: each aaRS can conjugate several
different amino acids to the correct cognate tRNA molecules.
D) tRNA synthetases do NOT contact the anticodon surfaces of tRNA
substrates.
E) None of the above answers (A-D) is correct.
19. You set up an in vitro (test-tube) protein synthesis reaction. The tube contains all
the stuff needed: ribosomes, initiation and elongation factors, and aa-tRNA
molecules for all twenty amino acids. The mRNA consists entirely of U and C
nucleotides in random order. Assume that initiation does not require aatRNA[fMet].
Which amino acids (answers A-D) are polymerized into the resulting
polypeptide?
A)
B)
C)
D)
E)
Phe, Pro.
Phe, Ser, Leu Pro.
Phe, Leu, Ile, Met, Val
Ser, Pro, Thr, Ala.
None of the above.
20. Which of the following statements does not describe heterochromatin?
A)
B)
C)
D)
E)
The DNA in heterochromatin is heavily methylated.
The DNA in heterochromatin is heavily acetylated.
The histones in heterochromatin are heavily methylated.
The DNA in heterochromatin is generally not transcribed.
The DNA in heterochromatin is relatively condensed.
21. Which of the following statements (A-D) best describe wobble anticodons?
A) They are found in mRNA molecules.
B) They are found in ribosomal RNA molecules.
C) Wobble bases (W) always occur in the position 5'-W-X-Y-3' within the
anticodon.
D) The wobble base is always an inosine (I) base.
E) NONE of the above answers (A-D) describe wobble anticodons.
22. What are the functions of eIF4 complex?
A) To bind the 7-methylguanosine cap.
B)
C)
D)
E)
To bind the poly-A tail.
To help the ribosome locate the first AUG codon.
To bind the Shine-Delgarno sequence.
Answers A and B and C.
23. An mRNA molecule isolated from a human cell is exactly 500 nt long. How many
atoms of phosphorus does it contain?.
A)
B)
C)
D)
E)
499.
500.
501.
502.
503.
24. Which of the following antibiotics has an effect most similar to the normal function
of RF1 or RF2?
A)
B)
C)
D)
E)
Chloramphenicol.
Tetracycline.
Puromycin.
Macrolides.
Etoposide.
25. The "fragment transfer reaction" was used to obtain evidence for which of these
biochemical phenomena?
A)
B)
C)
D)
E)
Post-transcriptional 3´ CCA to tRNA acceptor stems.
Post-transcriptional 5´ cap addition to eukaryotic mRNA molecules.
Non-templated poly-A tail addition to eukaryotic mRNA molecules.
Purely RNA-catalyzed peptidyltransfer.
Purely RNA-catalyzed Group I intron excision.
26. Bacterial IF-2 has which of the following properties (A-D)?
A)
B)
C)
D)
E)
Binds aaRS.
Binds tRNA anticodon.
Interacts with P site.
Translocates mRNA in small subunit.
None of the above answers (A-D) is correct.
27. A growing E. coli cell assembles as many as 1,000 new 70S ribosomes (large +
small subunit) a minute. If we count only the proteins actually incorporated into
these ribosomes, how many new proteins must the cell synthesize per second,
just to make proteins that will be component parts of the new ribosomes?
Choose the best approximate answer.
A)
B)
C)
D)
E)
30.
100.
300.
1,000.
3,000.
28. Which of the following factors is needed for bacterial ribosome disassembly
following termination?
A)
B)
C)
D)
E)
Ef-G.
GTP.
ATP.
A and B.
A and B and C.
29. RNA splicing is important in most eukaryotes. Which of the following statements
about splicing is incorrect?
A) Splicing involves removal of introns and ligation (joining) of exons.
B) Splicing of RNAP II transcripts from a single gene can yield different mRNA
products in brain versus lung cells.
C) Splicing occurs in the cytoplasm, not the nucleus.
D) Most splicing reactions are controlled by a SNURP complex called the
spliceosome.
E) Certain RNA molecules can splice themselves without any assistance from
protein.
30. Which of the following are substrates of aminoacyl-tRNA synthetase enzymes?
A)
B)
C)
D)
E)
tRNA.
GTP.
ATP.
A and B.
A and C.
Short answer:
31.
Eukaryotic chromosomes have many origins of replication. For a chromosome with 100
origins.
a. At what stage of the eukaryotic cell cycle are these origins licensed?
b. What is licensing?
c. How does the cell ensure that each origin is licensed once and only once per cell
cycle?
d. How many replication forks will these 100 origins initiate?
e. Do all origins "fire" -- initiate replication -- at the same moment?
f. What happens when replication forks initiated from two different origins collide with
one another?
32.
What enzymatic activities does primase consist of?
33.
What enzymes involved in replication of a bacterial chromosome require ATP (vs.
dATP)? What do these enzymes do?
34.
When the MGMT pathway is employed, what is the approximate cost (in ATP
equivalents) expended to remove a single methyl group from a guanosine residue? Why
is this the case? (By the end of the course you should be able to calculate a reasonably
precise answer to this question, not merely an approximate one).
35.
List at least three different events that can lead to DNA damage.
a. Describe the kinds of mutations that arise in response to these events.
b. Describe the major repair pathways used to deal with these forms of DNA damage.
36.
Describe how the bacterial mismatch repair pathway preferentially repairs the more
recently synthesized of the two DNA strands.
37.
List three diseases that can arise from deficiencies in DNA repair genes.
38.
Would some human genes involved in DNA repair be considered tumor suppressors or
antioncogenes? Why?
39.
Compare and contrast the functions of DNA methylation in bacterial cells versus human
cells.
40.
Draw the structure of two typical products of DNA resulting from UV photodamage.
41.
Describe the function of the mediator complex.
42.
What GTFs are directly involved in formation of the RNAP II open complex? What do
they do?
43.
In human cells, the GTF TFIIH functions not only in transcription, but in DNA repair.
What might it do in this context?
44.
Describe what enahncer sequences in DNA do, and how they promote transcription.
45.
Draw the linkage of the 7-methylguanosine cap on an mRNA molecule.
a. How and when is it added to mRNA molecules?
b. What is the function of the cap?
c. Imagine that a small molecule toxin was discovered that prevents cap addition. What
would you expect to happen in cultured cells upon addition of this toxin?
46.
About mRNA splicing:
a. What two nucleotides are always found at the 5' end of an intron?
b. What two nucleotides are always found at the 3' end of an intron?
c. Draw a cartoon of the lariat structure. Show on your diagram the linkage that closes the
lariat, and identify the residues in parts a and b above.
This is not a study question so much as it is a thing to think about.
This plot shows the cost of sequencing DNA, in dollars per base. Each tick on the Y axis marks a
10× decrease in cost. The X axis shows time in years.
Today you can sequence about 10 million bases for a dollar, and it's getting cheaper really fast.
Sequencing is getting cheaper a lot faster than microprocessors get cheaper. Think of the first
iPod you saw, now think of the iPhone4. DNA sequencing technology is improving much faster
than that.
If this trend continues (most specialists think costs will continue to plummet), getting your
genome sequenced will within a few years become one of the cheapest tests that a doctor — or a
government — can run. We're talking cheap-like-a-blood-test cheap, most likely within ten years
or so.
Most people who think hard about this stuff assume that by the time most of you are, say, 35,
almost everyone in the industrialized world will have had their genome sequenced. This is
exponential change. As with the polio vaccine, cell phones, and the internet, there will be a
moment where adoption will go from almost no one to almost everyone, seemingly overnight.
The social, political, and economic implications are immense, and this will all happen because of
a half century of advances in biochemistry.