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99:163 Medical Biochemistry Exam 2, Instructor-Dr. Wold October
9, 2009 Spivey & Watzke Auditoriums
During the Exam (8:30 - 10:20 am)
1. Select a seat leaving a space between individuals, turn off
cell phones, leave backpacks and other personal belongings at front
of auditorium.
2. Please fill in your student ID number (as well as your name)
on the Scantron form and fill in the dots using a number 2 pencil.
Extra pencils will be available.
3. You are welcome to use the bathroom during the exam. You must
leave your personal belongings, the exam and the Scantron form in
the exam room. Please let the instructor or TA know that you are
leaving the room. We reserve the right to restrict the number of
people leaving the room to one at a time.
4. If you believe you have detected a typographical error in a
question, please ask the instructors about it during the exam. Any
errors that are recognized will be corrected by placing a note on
the chalkboard in each auditorium.
Suggestions for approaching multiple-choice questions.
1. Try to identify the best (rather than perfect) answer from
the possible choices. 2. Think carefully about restrictive language
such as all, some, never, always, etc. 3. Try to limit the choices
and then guess (there is no penalty for incorrect answers).
After the Exam
1. If you finish prior to 10:20 am, please review your answers
and quietly turn in your Scantron form to the instructor or TA.
2. Voices in the hallways travel and may be distracting to other
students. Please wait until after all students are finished with
the exam at 10:20 am before discussing it.
3. You are welcome to keep the packet of exam questions after
you submit your Scantron form.
4. The Exam Key will be posted to the icon later in the day of
the exam. 5. Prior to noon on Monday, October 12-
If you believe you have found an error in the Exam Key, please
send a polite E-mail message to Dr. Wold ([email protected]).
Please include Biochem Exam in the subject line, and indicate the
relevant question(s) and foil(s) believed to be in error. If a
correction is needed, the key will be modified to allow more than
one answer to be counted as correct. Please note that I will not
reply to your email right away. I will not make any decisions on
changes to the key until I review all messages received by
Monday.
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1. Which of the following statements about the eukaryotic cell
cycle is true: a. DNA replication occurs in G1 phase. b. The G2/M
transition is regulated by a checkpoint. c. DNA repair only occurs
in S phase. d. RNA transcription occurs primarily in M phase. e. In
dividing human cells, G0 follows S phase.
2. Which of the following statements is false about activation
of a checkpoint in response to DNA damage?
a. RNA polymerase II encounters damage and terminates
transcription. b. Sensor proteins bind to sites of DNA damage. c.
Transducer kinases (ATM & ATR) are recruited to sites of DNA
damage and
activated. d. Transducer kinases phosphorylate effector kinases.
e. Effector kinases phosphorylate protein effectors to modulate
cell cycle and DNA
repair. 3. Which of the following statements about DNA or RNA is
false?
a. T base pairs with C b. purines base pair with pyrimidines c.
G and A base pair with pyrimidines d. purines base pair with U or C
e. A base pairs with U
4. Which of the following statements is true about triplex DNA
(H-DNA)? a. Triplex DNA can form with any sequence of DNA b.
Triplex DNA requires one strand be RNA c. Triplex DNA contains
Hoogsteen base pairs d. Triplex DNA only are most stable at high pH
where C is unprotonated e. Triplex DNA never forms in cells
5. Which of the following statements about histones is true? a.
Histones are not well conserved in evolution. b. Winding of DNA
around the histone octomer core of a nucleosome introduces
writhe into the DNA. c. Histones are basic proteins because they
contain a high percentage of glutamine
and asparagine. d. The only posttranslational modification of
histones is phosphorylation and
dephosphorylation. e. Histones have no role in packing DNA so it
will fit in the nucleus.
6. A double strand break in DNA is required to initiate
homologous recombination because: a. It will induce the G2-M
checkpoint. b. It is required to provide a 3 end that can invade a
homologous sequence. c. It provides a recognition site for
telomerase. d. It causes a high rate of mutations that promote
antibody diversity. e. It disrupts the structure of the chromatin
at the site of recombination.
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7. Which of the following is not a similarity between homologous
recombination and site-specific recombination?
a. Both processes have a 4-strand intermediate. b. Both
processes require breaking and rejoining DNA strands. c. Both
processes can change the sequence of the genome. d. Both processes
occur in both prokaryotes and eukaryotes. e. Both processes can
cause inversions or deletions of regions of the genome.
8. Which of the following statements about DNA replication
enzymes is true. a. DNA polymerases have high processivity because
they are covalently linked to
the template strand. b. At the replication fork, DNA helicases
utilize energy from ATP hydrolysis to
translocate along the newly synthesized strand. c. Primases must
add nucleotides to an existing a 3 OH group. d. Topoisomerases
release the links between parental DNA strands. e. DNA ligases do
not require a high-energy cofactor to form a phosphodiester
bond. 9. This week the 2009 Nobel Prize in Physiology was
awarded to Elizabeth Blackburn,
Carol Greider and Jack Szostak for their discovery of
telomerase. Which of the following statements about telomerase is
true?
a. Telomerase acts at both telomeres and centromeres. b.
Telomerase activates a checkpoint to prevent cell division if there
is damage to
the telomere. c. Telomerase extends the 3 end of eukaryotic
chromosomes to prevent
chromosome shortening. d. Telomerase expression decreases in
most human cells that go through the
Hayflick limit and become transformed (cancerous). e. Telomerase
acts at both the replication fork and at telomeres.
10. Two repair processes that are linked to DNA replication are
mismatch repair and translesion synthesis (error prone repair).
Which of the following statements about these repair processes is
false?
a. Mutations in genes involved in mismatch repair can cause
hereditary nonpolyposis colon cancer (HNPCC)
b. Translesion synthesis allows the replication fork to bypass
damage that would otherwise cause the replication fork to
stall.
c. Mismatch repair makes a transient gap in the newly
synthesized strand to remove the mismatch.
d. Mismatch repair occurs in both prokaryotes and eukaryotes. e.
Mutations in translesion synthesis proteins can cause Fanconis
Anemia.
11. Why does DNA contain thymine instead of uracil? a. Because
uracil wont hydrogen bond to adenine b. Because thymine is less
sensitive to UV damage c. So that deamination of cytosine can be
detected as a form of damage and be
repaired by base excision repair d. So that the deamination of
cytosine can be detected as a form of damge and be
repaired by mismatch repair e. Because uracil induces kinks in
helical structure of DNA
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12. Which of the following is the best statement describing
types of chemical modifications of DNA?
a. Ultraviolet radiation in sunlight can cause interbase
crosslinks between adjacent pyrimidine residues.
b. Chemical modification of DNA can alter base pairing. c. The
glycosidic bond between deoxyribose and purine can
spontaneously
hydrolyze in the aqueous environment in the nucleus. d. Reactive
oxygen species produced by mitochrondria during electron transport
can
modify either bases or the phosphodiester backbone of DNA. e.
All of the above are true.
13. You are doing a research project on a novel, primitive
unicellular eukaryote, called HKI. You find that this organism has
a very small genome and contains only one RNA polymerase. This
suggests that the process of transcription in this organism is more
like prokaryotes than eukaryotes. If this is the case, which of the
following statements is most likely to be correct about HKI
transcription?
a. HKI RNA polymerase will have a C-terminal domain (CTD). b.
HKI mRNA will be polyadenylated. c. HKI RNA polymerase will contain
a 3 to 5 exonuclease used for proofreading. d. HKI RNA polymerase
will terminate at sequences that contain a hairpin followed
by a string of A residues. e. HKI RNA polymerase does not need
sigma factor to bind to
promoter/transcription start sites. 14. Which of the following
techniques would be the best way to determine whether or not
the HKI genome contains introns? a. Use restriction
endonucleases to make a map of the genome. b. Compare the sequences
in a HKI genomic DNA library to those in a HKI cDNA
library. c. Isolate 20 fragments from an HKI genomic DNA library
and use these fragments
to probe the restriction endonuclease digest of the full genome
in a Southern blot. d. Use mass spectrometry to determine the
protein sequence of 10 of the most
abundant proteins in HKI and compare the predicted gene
sequences to similar sequences in other organisms.
e. Isolate mRNA from HKI, label the pool of mRNA and then
determine the average size of the RNA using gel
electrophoresis.
15. Assume that the results from the experiment described in the
previous question demonstrates that HKI has introns and exons.
Which of the follow statements is most likely to be true for
HKI?
a. HKI will have small nuclear ribonuclear proteins (snRNPs). b.
The length of the initial RNA transcripts in HKI will be shorter
than the final
mRNA. c. The introns will act as primers during DNA replication.
d. The introns will be cleaved by poly-A polymerase in HKI. e. The
introns will be bound by a rho-like factor during splicing.
16. Which of the following proteins does not function primarily
in the eukaryotic nucleus? a. RNA polymerase II b. RISC complex c.
TATA binding protein d. Poly(A) polymerase e. DNA polymerase
delta
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17. The first part of the sequence of the E. coli tryptophan
operon mRNA is shown below.
Assume that you are analyzing an E. coli strain (X) that has a
mutation in the tryptophan operator site so that the only
regulation of this operon is by attenuation. You compare tryptophan
mRNA levels in strain X to a mutated strain X that also has a
mutation that changes the leucine codon* (CUG) in the leader
peptide into a termination codon (UAG). Which statement best
describes the expected change in mRNA levels that will be observed
in the mutated strain?
a. Decrease levels of tryptophan mRNA under all growth
conditions. b. Decrease levels of tryptophan mRNA under conditions
of limiting tryptophan. c. Increase levels of tryptophan mRNA under
all growth conditions. d. Increase levels of tryptophan mRNA under
conditions of limiting tryptophan. e. Increase levels of tryptophan
mRNA under conditions of abundant tryptophan.
18. Initiation of RNA polymerase II transcription requires all
of the following except? a. TATA-binding protein (TBP) b. TFIIH c.
Upstream regulatory sequences d. An open chromatin structure e.
Dephosphorylation of the C-terminal domain of RNA polymerase
II.
19. Which of the following is the best statement describing the
general role of chromatin remodeling or functions of chromatin
remodeling complexes?
a. Chromatin remodeling can cause the conversion of
heterochromatin to euchromatin and vise versa.
b. Chromatin remodeling complexes primarily cause
post-translational modifications on histone H1.
c. Chromatin remodeling complexes are usually small with a
single enzymatic activity.
d. Euchromatin is the default state of human genome and
heterochromatin is only present because of the constant action of
chromatin remodeling complexes.
e. None of the above statements are true.
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20. Which of the following properties best describes most
eukaryotic transactivating factors? a. They are only composed of a
DNA binding domain and a protein interaction
domain. b. They primarily interact with modified histones in
chromatin. c. They primarily interact with DNA, the basal
transcription complex and co-
activators. d. They usually function independently of any other
protein complexes. e. They primarily function by displacing
repressors from the promoter region.
21. In class, we discussed a mutation in the DEC2
transcriptional repressor that was found in a family that seemed to
need less sleep that normal. Transgenic mice carrying this mutant
allele had a longer active cycle than control mice. A two channel
microarray study is planned to try to determine which genes are
expressed differently in the brains of mice carrying the mutant
allele of DEC2. This experiment will start with RNA isolated from
the brains of a control mouse and a DEC2 mutant mouse. The
following statements describe steps in this experiment. Which step
is incorrect or not appropriate?
a. The two RNA samples are used to make two cDNA pools. b. The
two cDNA pools are labeled with different fluorescent labels. c. A
mouse microarray is obtained that contains 32,000 probes
complementary to
known mouse genes bound at defined locations on a large glass
slide. d. Two samples are hybridized to separate mouse array slides
and the level of
hybridization compared between the two slides. e. Analysis of
the resulting data will provide the relative expression levels of
all of
the genes on the array. 22. There are three codons in the
standard genetic code that usually function to terminate
translation (UAA, UAG, UGA). Which of the following is false
about terminator codons?
a. Mutations that change an amino acid codon into a termination
codon are called missense mutations.
b. Terminator codons do not interact with standard tRNAs. c. An
open reading frame is a sequence in DNA or RNA that does not
contain any
terminator codons. d. In humans, a rare specialized serine tRNA
incorporates selenocysteine at some
UGA codons. e. Mitochondria in some organisms use a non standard
codon to terminate
translation. 23. Aminoacyl-tRNA synthetases are important for
charging tRNA with the proper amino
acids. Which of the following statements about aminoacyl-tRNA
synthetases is true? a. The energy used by aminoacyl-tRNA
synthetases to couple an amino acid to a
tRNA comes from hydrolysis of two molecules of GTP. b. One major
source of specificity of the charging reaction comes from binding
the
proper amino acid. c. Aminoacyl-tRNA synthetases recognize the
correct tRNA by interacting with the
anticodon. d. Aminoacyl-tRNA synthetases are part of the
ribosome. e. None of the known aminoacyl-tRNA synthetases have
editing or proofreading
activity to increase the accuracy of charging.
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24. Which of the following statements describes a similarity
between initiation of protein synthesis in prokaryotes and
eukaryotes by ribosomes?
a. Both usually initiate at multiple different start codons on a
message. b. Both do not require any high-energy cofactors (e.g.
ATP, GTP) for initiation. c. In both an assembly of the large and
small ribosome subunits binds to the mRNA. d. Both use AUG as a
start codon. e. Binding of the mRNA to the ribosome is directed by
base pairing between a
ribosomal RNA and a specific sequence in the mRNA. 25. Which of
the following statements about peptide bond formation on the
ribosome is
true? a. The ribosome only requires mRNA, aminoacyl-tRNAs and
nucleotide cofactors
(GTP & ATP) to form a new peptide bond. b. The nascent
polypeptide chain is bound to the A site while the next
incoming
aminoacyl-tRNA binds to the P site. c. Specificity of the
incoming aminoacyl-tRNA is regulated by a two-step binding
reaction and requires GTP hydrolysis. d. The ribosome proofreads
each aminoacyl-tRNA to make sure the proper amino
acid is attached before synthesizing a peptide bond. e. None of
the other four answers are correct.
26. Which of the following statements is true about protein
folding? a. Proteins predominantly fold after detaching from the
ribosome. b. Because the information needed for folding is in the
primary sequence, all
proteins fold correctly by themselves. c. Protein folding only
occurs in the cytoplasm. d. The final folded structure of a protein
determines to which part of the cell (which
organelle) it is transported. e. Molecular chaperones require
ATP hydrolysis to promote proteins folding into
their native structure. 27. Pick the best answer for this
sentence: DNA sequencing
a. is used in DNA fingerprinting. b. requires the experimenter
to know the source of the DNA. c. methodology will work equally
well on RNA and DNA. d. is usually automated and highly efficient.
e. always requires separating the DNA on by gel elecrophoresis.
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Answer Key Exam #2 - 99:163 2009
1. B 2. A 3. A 4. C 5. B 6. B 7. E
8. D 9. C 10. E 11. C 12. E 13. D 14. B
15. A 16. B 17. E 18. E 19. A 20. C 21. D
22. A 23. B 24. D 25. C 26. E 27. D
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Practice Questions for Medical Biochemistry Wold Lectures -
September, 2010
1. Which of the following is usually NOT a constituent of DNA a.
phosphate (PO4) b. the purine Guanine c. the pyrimidine Uracil d.
the purine Adenine e. deoxyribose
2. Twist is best described by: a. The rotation of a base
relative to the orientation of the deoxyribose in degrees b. The
number of times the two strands pass around each other in the DNA
helix. c. The number of times the two strands pass around each
other in three-
dimensional space. d. The total number of times the two strands
pass around each other. e. The mobility of the DNA in agarose gel
electrophoresis
3. B-form DNA a. is unaffected by pH. b. has a major and a minor
groove. c. can form with one RNA and one DNA strand. d. always has
writhe. e. All of the above.
4. The action of a eukaryotic type II topoisomerase on a
negatively supercoiled DNA molecule causes
a. the linking number to change by multiples of 1. b. a
transient break in one DNA strand. c. unwinding of the B-form DNA.
d. a change in the writhe of the DNA molecule. e. All of the
above
5. Which of the following properties is NOT true of histones? a.
Histones form a dodecamer complex that binds DNA non-specifically.
b. Histones have an amino acid content that includes a high
proportion of lysine
and arginine. c. Histones are the core components of the
nucleosome d. Histone get modified after translation on both N- and
C-terminal tails e. Histone modifications can regulate gene
transcription
6. Which of the following statements about replication proteins
is FALSE? a. DNA polymerases require a primer for synthesis. b. DNA
helicases translocate along ssDNA and separate the two strands in
the
helix. c. Single-stranded DNA binding proteins prevent secondary
structure in ssDNA. d. Sliding clamp proteins stabilize the protein
complex at the origin of replication
until priming can occur. e. DNA ligase is important in the
processing of Okazaki fragments.
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7. DIFFERENT mechanism in prokaryotic and eukaryotic DNA
replication. a. Okazaki fragment processing b. Processivity of
replicative DNA polymerases c. Primer synthesis for Okazaki
fragments d. Regulation of initiation of replication at origins on
chromosomes. e. Separation of the parental DNA strands at the
replication fork
8. Conversion of DNA damage to a mutation REQUIRES: a. the
modification to break the DNA strand. b. DNA replication of the
modified base. c. the modification to not be recognized by the
cellular repair machinery. d. the modification to be recognized by
the cellular repair machinery. e. the cellular check points to be
disrupted.
9. Which of the following definitions is the most precise
description of double-strand break repair via homologous
end-joining?
a. A repair pathway that fixes errors that occur during DNA
replication. b. A repair pathway that fixes errors with some loss
of genetic information. c. DNA repair that only occurs after
S-phase. d. General recombination with the break resulting from DNA
damage. e. A repair pathway in which proteins including Ku and DNA
protein kinase
(DNA-PK) bind DNA ends and then promote ligation to recreate a
continuous DNA strand.
10. The human genome contains which of the following classes of
DNA sequence: a. Exons b. Sines c. Lines d. Retrotransposons e. All
are found in the human genome
11. Which of the following is NOT a common property of E. coli
RNA polymerase? a. RNA polymerase synthesizes RNA in a 5 to 3
direction. b. RNA polymerase transiently unwinds the DNA. c. RNA
polymerase binds a sigma factor to initiate transcription. d. RNA
polymerase can usually transcribe either either a DNA or an RNA
template. e. RNA polymerase can initiate synthesis without a
primer.
12. Eukaryotic RNA polymerase II has a C-terminal domain (CTD)
that is involved in a number of processes in transcription. Which
of the following is NOT TRUE for the CTD?
a. It interacts with the polyadenylation complex. b. It
interacts with the complex that adds the cap to the 5 end of the
RNA
transcript. c. It interacts with the spliceosome through snRNPs.
d. It interacts with transcription mediator complexes. e. It
interacts with the DNA at the promoter.
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13. snRNAs in eukaryotic cells
a. provide the purine that carries out the initial nucleophilic
attack during the splicing of RNA polymerase II transcripts.
b. recognize the splice junctions during splicing of RNA
polymerase II transcripts. c. hydrolyze ATP during splicing. d.
interact with tRNAs during translation. e. can function without
proteins.
14. HIV differs from most other retroviruses because a. it kills
the cells it infects. b. it has a reverse transcriptase that does
not have a 3 to 5 proof-reading
exonuclease. c. it initially expresses its viral proteins as a
polyprotein. d. it passes through a double stranded DNA
intermediate. e. its replication is inhibited by nucleotide
analogues.
15. Which of the following regulatory motifs or proteins DO NOT
bind to DNA? If a motif is specified, consider the function of the
motif only.
a. Leucine zipper motif b. Helix-turn-helix motif c. Lac
repressor d. Zinc-finger proteins e. Catabolite activator protein
(CAP)/cAMP repressor proteins (CRP)
16. Chromatin remodeling a. opens up the structure to allow DNA
binding proteins to bind to target sites. b. is caused by changes
in the modifications on histone tails. c. is catalyzed by the
Swi/snf complex. d. results in a stable chromatin structure. e. all
of the above.
17. Which of the following steps does NOT occur in activation of
a majority of genes in eukaryotic cells?
a. Binding of TATA-binding protein (TBP) to a TATA sequence. b.
Interaction of mediator complexes with the basal transcription
machinery. c. Small molecules/metabolites interaction with protein
repressors causing reduced
binding to UAS sequences. d. Transactivators binding to the DNA
near the promoter. e. DNA looping allows distant sites to act on
the promoter.
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18. Gal4 protein is a transactivator from yeast that activates
the expression of genes involved in
galactose metabolism. Gal4 is composed of a zinc-finger domain,
a coiled-coil domain and an acidic activator domain. Suppose a
yeast strain was created that did not contain wild-type Gal4
protein but instead had a recombinant Gal4 protein in which the
Gal4 activator domain was replaced with the acidic activation
domain of GCN4. (GCN4 is a yeast transcriptional activator protein
that stimulates the expression of genes involved in amino acid
biosynthesis and is induced by amino acid starvation.) Predict what
would happen to the expression of the two classes of genes listed
in the table if this strain is grown in media with galactose. (In
the table: = no induction, ++ = induction, + = weak induction.)
Galactose metabolism genes
Amino acid biosynthesis genes
a. b. ++ c. + d. ++ ++ e. None of the above
19. Wobble base-pairing refers to a. degeneracy in the genetic
code. b. a mechanism by which some tRNA synthetases can charge
several related tRNA
molecules. c. the property by which a single tRNA anticodon can
interact with several
different related codons. d. the mechanism by which a mutant
suppressor tRNA can bind and cause the
insertion of an amino acid at a termination codon. e. alternate
base pairing found in triplex DNA.
20. In transcriptional attenuation that occurs in the Tryptophan
operon, a. translation regulates the rate of transcription
termination. b. transcription regulates the rate of translation
termination. c. transcription undergoes a frame shift to allow the
expression of certain genes. d. pauses in translation regulate mRNA
degradation. e. pauses in transcription allow rho dependent
termination.
21. Which of the following processes do NOT contribute to the
overall accuracy of translation? a. Amino acid coupling to tRNA by
aminoacyl-tRNA synthetases. b. Editing (hydrolase) activity in
aminoacyl-tRNA synthetases. c. Recognition of the tRNA by
aminoacyl-tRNA synthetases. d. Binding of the aminoacyl-tRNA to the
A site of the ribosome. e. Peptide bond formation by peptidyl
transferase in the ribosome.
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22. Which of the following statements is true?
a. Proteins usually fold completely before they are transported
to the lumen of the Endoplasmic Reticulum.
b. Some neurological diseases are caused by accumulation of
aberrantly folded proteins.
c. All proteins require molecular chaperones for proper folding.
d. Ubiquitin binds to unfolded proteins and targets them for
degradation. e. Glycosylation of proteins occurs in the
cytoplasm.
23. Which of the following techniques would not be used in one
or both of the types of DNA
fingerprinting? a. DNA sequencing b. Restriction endonuclease
cleavage c. Southern blotting d. PCR amplification e. Gel
electrophoresis
24. Which of the following statements is NOT true? a. Type II
restriction endonucleases cut DNA at specific sequences. b. Type II
restriction endonucleases are a useful tool for cloning DNA
sequences. c. Type II restriction endonucleases can be used to make
a genomic DNA library. d. Type II restriction endonucleases usually
cut methylated DNA. e. Type II restriction endonucleases can
produce DNA ends with short single
stranded overhangs. 25. DNA microarrays
a. can determine the stability of thousands of RNAs in a cell at
the same time. b. rely on northern (RNA:DNA) hybridization. c.
compare two different samples from cells or tissues. d. can usually
be analyzed by visual inspection. e. can be used to determine the
changes in the genome of a specific tumor.
26. hich of the following classes of proteins can contribute to
the development of cancer? a. Growth factors b. Signal-transduction
proteins c. DNA repair proteins d. Transcription factors e. All of
the above
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27. In the Watson-Crick model for the DNA double helix (B form)
the AT and GC base pairs
share which one of the following properties? a. The distance
between the two glycosydic (base-sugar) bonds is the same in
both
base pairs, within a few tenths of an angstrom. b. The molecular
weights of the two base pairs are identical. c. The same number of
hydrogen bonds is formed between the two bases of each
pair. d. The plane of neither base pair is perpendicular to the
axis of the helix. e. The proton-binding groups in both base pairs
are in the charged or ionized form.
28. The action of a type I topoisomerase on a negatively
supercoiled DNA molecule causes a. Changes in the linking number of
a DNA molecule b. A transient break in one DNA strand c. Changes in
the Writhe of the DNA d. The DNA to become relaxed e. All of the
above
29. Which of the following processes contribute to the
compaction of DNA in a eukaryotic cell? a. DNA binding to histones
b. Arrangement of histones into 30 nm fibers c. Attachment of the
DNA to a chromosomal scaffold d. Post translational modification of
nucleosomes e. All of the above
30. An Okazaki fragment is a: a. fragment of DNA resulting from
endonuclease action. b. fragment of RNA that is a subunit of the
30S ribosome. c. piece of DNA that is synthesized in the 3' ! 5'
direction. d. segment of DNA that is an intermediate in the
synthesis of the lagging strand. e. segment of mRNA synthesized by
RNA polymerase.
31. At replication forks in E. coli: a. DNA helicases make
endonucleolytic cuts in DNA. b. DNA primers are degraded by
exonucleases. c. DNA topoisomerases make endonucleolytic cuts in
DNA. d. RNA primers are removed by primase. e. RNA primers are
synthesized by primase.
32. Which of the follow DNA repair pathways only corrects errors
that occur during S-phase? a. Mismatch repair b. Nucleotide
Excision Repair c. Base Excision Repair d. Direct reversal of
damage by O6-methlyguanine DNA methyltransferase e. Nonhomologous
End Joining
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33. Unlike bacteria, eukaryotic chromosomes need multiple DNA
replication origins because:
a. eukaryotic chromosomes cannot usually replicate
bidirectionally. b. eukaryotic genomes are not usually circular,
like the bacterial chromosome is. c. the processivity of the
eukaryotic DNA polymerase is much less than bacterial
enzyme. d. their replication rate is much slower, and it would
take too long with only a
single origin per chromosome. e. they have a variety of DNA
polymerases for different purposes, and need a
corresponding variety of replication origins. 34. .When
bacterial DNA replication introduces a mismatch in a
double-stranded DNA, the
methyl-directed repair system: a. cannot distinguish the
template strand from the newly replicated strand. b. changes both
the template strand and the newly replicated strand. c. corrects
the DNA strand that is methylated. d. corrects the mismatch by
changing the newly replicated strand. e. corrects the mismatch by
changing the template strand.
35. In base-excision repair, the first enzyme to act is: a. AP
endonuclease. b. Dam methylase. c. DNA glycosylase. d. DNA ligase.
e. DNA polymerase.
36. Which of the following statements about site-specific
recombination is not true? a. Site-specific recombination is
catalyzed by enzymes called recombinases and/or
transposases b. Site-specific recombination is necessary for
generating antibody diversity in
mammals c. Site-specific recombination can cause insertion or
deletion of DNA sequences d. Site-specific recombination can cause
inversion of DNA sequences e. Site-specific recombination initiates
with a double strand break in DNA
37. Which of the following statements about genes is true: a. A
gene can direct the synthesis of a protein or a RNA. b. Genes are
continuous DNA sequences. c. All sequences in the genome that
contain genetic information are genes. d. The structure of genes is
the same in prokaryotes and eukarotes e. The number of genes in an
organism correlates with the size of its genome.
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38. Which one of the following is true about the genetic
code?
a. All codons recognized by a given tRNA encode different amino
acids. b. It is absolutely identical in all living things. c.
Several different codons may encode the same amino acid. d. The
base in the middle position of the tRNA anticodon sometimes
permits
wobble base pairing with 2 or 3 different codons. e. The first
position of the tRNA anticodon is always adenosine.
39. RNA polymerase: a. binds tightly to a region of DNA
thousands of base pairs away from the DNA to
be transcribed. b. can synthesize RNA chains de novo (without a
primer). c. has a subunit called " (lambda), which acts as a
proofreading ribonuclease. d. separates DNA strands throughout a
long region of DNA (up to thousands of
base pairs), then copies one of them. e. synthesizes RNA chains
in the 3' ! 5' direction.
40. Splicing of introns in eukaryotic nuclear mRNA primary
transcripts requires: a. a guanine nucleoside or nucleotide. b.
endoribonucleases. c. polynucleotide phosphorylase. d. RNA
polymerase II. e. small nuclear ribonucleoproteins (snurps).
41. Which of the following DNA sequences is not generally
required for initiation of transcription in eukaryotes.
a. TATA box b. Up-element c. Upstream activator sites d.
Enhancers e. Inr sequence
42. Which of the following enzymes does not belong: a. DNA
Polymerase delta b. Telomerase c. HIV reverse transcriptase d. RNA
polyerase II e. DNA polymerase lambda
43. Which of the following best describes splicing of RNA
polymerase II transcripts a. Splicing initiates when a 2OH from an
andenosine attacks the 5splice site b. A proteins in the
spliceosome contains the active site to catalyze splicing c.
Splicing rearranges genes to simplify RNA transcripts d. Splicing
does not require energy because all the reactions are exchange
reactions e. Splicing can occur without proteins.
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44. Small signal molecules (like cAMP in the lac operon) can do
which of the following in regulating bacterial gene expression:
a. provide input to the regulatory process that depends on the
nutritional/energy status of the cell
b. increase repressor binding to operator sites c. reduce
repressor binding to operator sites d. increase activator binding
to its binding site e. all of the above
45. Which of the following eukaryotic complexes/proteins is most
likely to cause global changes in the regulation of gene
expression?
a. An enhancer binding protein b. The concentration of a basal
transcription factor c. A chromatin remodeling complex d. A general
transcriptional mediator e. A transcriptional repressor
46. Which of the following processing events does not occur with
tRNAs in eukaryotic cells? a. Cleavage of the 3 terminus b. CAP
addition to the 5 terminus c. Methylation of some bases d.
Deamination of some bases e. Splicing of intron(s)
47. Complete the following sentence: The genetic code a. has one
start codon and two stop codons b. is universal in all organisms on
earth c. is not degenerate d. allows a single sequence to have
encode multiple genes e. has variable word length
48. Pick the best ending of the following sentence: In
initiation of translation in eukaryotes a. the small ribosome
subunit initially binds to the first AUG in the mRNA b. only GTP is
hydrolyzed c. uses a specialized tRNA d. assembles the two subunits
of the ribosome before binding tRNA e. binds the initiator tRNA in
the A-site
49. Pick the statement that is NOT CORRECT about the Polymerase
Chain Reaction (PCR). a. PCR amplifies DNA segments geometrically
b. PCR is usually done using heat stable DNA polymerases c. PCR
requires two primers that are complementary to the ends of the
target DNA d. PCR can synthesize DNA with high fidelity e. PCR
requires DNA ligase
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50. Which of the following statements is FALSE about Molecular
chaperones?
a. Molecular chaperones mostly function during heat shock
conditions. b. Molecular chaperones require ATP hydrolysis to
function c. Molecular chaperones help some proteins fold as they
are being synthesized d. Molecular chaperones help some proteins
refold after they are denatured e. Molecular chaperones interact
with unfolded regions on proteins
51. Cyclin-dependent kinases play a critical role in regulating
the cell cycle. As such they are subjected to multiple levels of
regulation. Which of the following is NOT a mechanism that human
cells use to regulate cyclin-dependent kinases?
a. Modulation of the cellular levels of cyclins. b.
Phosphorylation of the cyclin-dependent kinase. c. Regulation of
the synthesis of cyclin-dependent kinases by growth factors. d.
Binding of GTP to an allosteric site on the kinase. e. Binding of
protein inhibitors to the cyclin-cdk complex.
52. Cancer is a family of diseases that are characterized by
abnormal cell proliferation. Which of the following statements BEST
describes a property of cancer cells?
a. Cancer cells have normal cellular checkpoint activation. b.
Cancer development requires mutation of both copies of a
proto-oncogene to an
activated form. c. Cancer is usually derived from a single cell
that has multiple mutations. d. Cancer will only occur if an
individual inherited at least one copy of a mutant
allele of a tumor suppressor gene. e. Cancer occurs when cells
fuse abnormally.
53. ene X encodes a functional transcriptional regulator
(protein X) that increases p21 protein levels in cells. What is the
LIKELY effect of constitutively increasing gene X expression in
cancerous tissue within patients who suffer from Li-Fraumeni cancer
syndrome? (Patients with this syndrome inherited one defective
allele of p53 from a parent.)
a. No effect since p53 is already mutated in this syndrome. b.
There will be increased activation of the G1 checkpoint. c. There
will be decreased activation of the G1 checkpoint. d. The effect of
the p53 mutation will be enhanced; the cancer will become
metastatic. e. There will be a decrease in the stability of p21
protein.
54. Experiments are done to understand the mechanism by which
protein X regulates the expression of p21. Which of the following
statements is LEAST LIKELY to describe a possible mechanism by
which protein X is activating p21 transcription.
a. Protein X is a ribosomal protein. b. Protein X modulates the
activity of the SWI/SNF complex. c. Protein X binds the coactivator
complex, Mediator. d. Protein X requires zinc ions to function. e.
Protein X binds to a specific class of enhancer.
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55. There is a cell line in which gene X has been knocked out
using cre/lox gene replacement. mRNA from the knock-out cells and
from the parental line (with intact gene X) are isolated and
subjected to microarray analysis to try to understand the effect(s)
of protein X on gene expression. Which of the following statements
is FALSE about this experiment?
a. cDNAs are made from both mRNA samples and each sample is
labeled with a different fluorescent tag linked to a dNTP.
b. The microarray contains thousands DNA sequences from human
genes. c. The two samples are hybridized to the DNA microarray. d.
After quantitation, the absolute number of RNA molecules present in
the
knockout cells is determined for all of the DNA sequences in the
microarray. e. Computerized analysis will be required to determine
which of the differences
observed are significant. 56. Base pairing of nucleic acids is
critical for many processes in cells and in the laboratory.
Which of the following statements about base pairing is FALSE?
a. G-C and A-T base pairs have similar geometry. b. G-C and A-T
base pairs have similar thermal stability. c. Base pairing is
important for formation of tertiary structure in tRNA and rRNA. d.
Base pairing directs the specificity of RNA silencing by microRNAs.
e. Base pairing occurs in the formation of triplex DNA.
57. Which of the following is CORRECT regarding LINES, SINES,
and retroviruses? a. LINES and SINES are thought to be derived from
retroviruses. b. LINES and SINES may produce active viral particles
whereas integrated
retroviruses do not. c. LINES, SINES, and retroviruses all have
open reading frames (ORFs). d. LINES and SINES are found
exclusively in genes whereas retroviruses randomly
integrate into the genome. e. LINES, SINES, and retroviruses
occur rarely in the genome.
58. Which of the following is FALSE regarding DNA topology? a.
Linking number (L) cannot change unless DNA strands are broken. b.
B-form DNA has +1 twist (T) for every 10.4 base pairs. c. DNA with
a writhe (W) of zero is termed relaxed. d. Binding of DNA to
histones in the presence of a type I topoisomerase changes the
writhe (W) of DNA. e. Cruciform DNA preferentially forms upon
overwinding the DNA.
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59. DNA replication requires the concerted action of multiple
proteins to accurately duplicate genomic DNA. Which of the
following statements about DNA replication in eukaryotes is
TRUE?
a. DNA replication initiates at a single unique site on each
chromosome. b. The accuracy of DNA synthesis by classical DNA
polymerases is the only
mechanism for ensuring that DNA replication is accurate. c. It
is necessary for a clamp-loading complex to topologically link the
sliding
clamp, PCNA, to the DNA to make the replicative DNA polymerase
highly processive.
d. RNA primers are removed by base excision repair after the
lagging strand has been ligated to form a continuous strand.
e. Initiation of eukaryotic replication is regulated by (i)
cyclin-dependent kinases (cell cycle dependent kinases) and (ii)
protein complexes forming at sites of initiation but (iii) not by
degradation of initiation proteins.
60. Which of the following MOST ACCURATELY describes the
function of a type I topoisomerase?
a. Can link (catenate) or unlink (decatenate) two DNA molecules.
b. Changes linking number (L) in units of 2. c. Has a catalytic
mechanism that causes a transient break in one strand of DNA. d.
Function only on positively supercoiled DNA. e. Is directly
affected by the mutation that causes Li-Fraumeni cancer
syndrome.
61. A patient presents with a large, darkly colored, irregularly
shaped skin blemish on her shoulder. The patient sunbathes
extensively in the summer and used tanning salons during the
winter. Upon thinking back to Medical Biochemistry, you remember
that thymidine dimers are commonly formed by excess exposure to UV
light. Which of the following is TRUE regarding thymidine
dimers?
a. They form as cyclobutane rings between the two consecutive
purine bases. b. Fixing this type of DNA damage requires
recombinational repair. c. Nucleotide excision repair would be
unlikely to help fix this type of DNA
damage. d. This type of DNA damage is repaired less efficiently
in patients with Xeroderma
Pigmentosum. e. DNA ligase is not required to fix this type of
DNA damage.
62. Which of the following definitions is the MOST PRECISE
description of double strand break repair via recombinational
repair?
a. A repair pathway that directly rejoins the broken DNA with
some loss of genetic information at the site of the break.
b. A repair pathway that only occurs during DNA replication c. A
repair pathway in which a Holliday junction is formed between the
broken
DNA and a homologous DNA molecule. d. A repair pathway in which
the damage is removed by a specific glycosylase. e. A repair
pathway that requires the action of a translesion DNA
polymerase.
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63. Which of the following is FALSE regarding V-J
recombination?
a. Some DNA is permanently lost in these cells. b.
Transesterification catalyzed by an internal A residue causes the
loss of the
intervening DNA segments. c. The reaction is error-prone. d. The
function is to maximize immunologic recognition of diverse
foreign
molecules. e. V-J recombination is essential for normal immune
function.
64. While doing scientific research during the summer between
your M1 and M2 year of medical school, you decide to pulse-label
some living human cells with radioactive uridine triphosphate. You
fractionate the different types of nucleic acid from these cells.
Which of the following fractions will have the MOST
radioactivity?
a. Ribosomal RNA b. Messenger RNA c. Transfer RNA d. Genomic DNA
e. Mitochondrial DNA
65. Which of the following statements describing genomic
libraries and library screening is FALSE?
a. A genomic library is usually made by digesting genomic DNA
with a restriction endonuclease.
b. A genomic library will contain both exon and intron
sequences. c. The library can be screened using colony
hybridization d. A synthetic oligonucleotide to a known gene
sequence can be used to screen the
library. e. It is only possible to screen a library for a gene
using a probe that is
complementary to the template strand of that gene. 66. Which of
the following statements is TRUE about bacterial RNA
polymerase?
a. Binding of the RNA polymerase to a promoter is mediated by
the sigma subunit binding to the UP element.
b. RNA polymerase synthesizes an RNA transcript that has an
identical sequence to the template strand (except for U
substituting for T).
c. RNA polymerase synthesizes RNA in a 5 to 3 direction from a
DNA template and requires a primer.
d. RNA polymerase synthesizes an RNA transcript that is
complementary to the coding strand.
e. Initially forms an inactive complex on the DNA called a
closed complex. Which of the following statements is the MOST
ACCURATE comparison of initiation of
prokaryotic RNA polymerase (RNAP) and eukaryotic RNA polymerase
II (Pol II)? a. RNAP initiates at specific sites called promoters
while Pol II does not initiate at
specific sites. b. Both RNAP and Pol II initiate at specific
sites called promoters and only Pol II
undergoes a conformational change from closed to open
conformation prior to initiation of transcription.
c. RNAP binds to promoters in the absence of any cofactors other
than a sigma subunit while Pol II requires the action of multiple
and often diverse factors to form a stable complex at a
promoter.
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d. RNAP always requires the rho (#) factor to terminate
transcription at a specific sequence while Pol II does not
terminate at specific sites.
e. Both RNAP and Pol II have a repeated amino acid sequence at
the C-terminus of the catalytic subunit that is phosphorylated and
used to regulate activity.
68. Primary transcripts of eukaryotic nuclear mRNA are spliced
and modified after transcription and before translation. Which of
the following is FALSE about splicing?
a. Splicing can be different in different tissues. b. Splicing
of mRNA primary transcripts requires multiple snRNAs (small
nuclear
RNAs). c. Alternate splicing can occur in the same cell type. d.
ATP hydrolysis does not appear to be required for the RNA cleavage
or ligation
steps in the spliceosome. e. Messenger RNAs are the only type of
RNAs that have introns and are spliced.
69. Chromatin structure is very important in regulating gene
expression patterns. Which of the following is TRUE of
chromatin?
a. Histone acetylation and phosphorylation are not reversible.
b. Histone deacetylases repress transcriptional activity. c.
Chromatin remodeling is usually a spontaneous process (does not
require ATP). d. Histone modifications most commonly occur on
histone H1. e. Histones are small, hydrophobic proteins.
70. Transcription in eukaryotes is largely regulated by positive
transcriptional regulators, including a number of leucine zipper
proteins. Which of the following is NOT characteristic of leucine
zipper proteins?
a. Dimerize via an aliphatic interface rich in leucine residues
b. Bind DNA by forming a sliding clamp around the nucleotide
backbone c. Can form either homo- or heterodimers d. Both proteins
in a dimer interact with DNA. e. Activate transcription by
affecting binding or activity of RNA polymerase II.
71. Which of the following is FALSE about the genetic code? a. A
missense mutation changes the sequence of the DNA and the amino
acid
encoded by the DNA. b. An open reading frame is a series of
codons without stop codons. c. A silent mutation changes the
sequence of the DNA without changing the amino
acid sequence encoded by the DNA. d. All DNA in the human body
uses exactly the same genetic code. e. Translation of
homoribopolymers results in homopolypeptides.
72. Transcription and translation are coupled in prokaryotes.
Which of the following statements is FALSE about prokaryotic
transcription and translation?
a. Prokaryotic transcription is often regulated by repressors
binding to operators and blocking RNA polymerase binding.
b. In the tryptophane operon the cellular level of tryptophane
charged aminoacyl tRNA helps regulate tryptophane mRNA levels.
c. A mRNA molecule has only one ribosome bound and translating
protein at a time. d. Prokaryotic translation initiates by an
interaction between the 16S ribosomal RNA
and a specific sequence in the message just up-stream from the
AUG. e. Prokaryotic mRNA can contain multiple open reading frames
(i.e. is
polycistronic).
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73. Peptide bond formation occurs in the ribosome. Which of the
following statements is TRUE?
a. The ribosome only requires mRNA, aminoacyl-tRNAs and
nucleotide cofactors (GTP & ATP) to form a new peptide
bond.
b. The nascent polypeptide chain is bound to the P site while
the next incoming aminoacyl-tRNA binds to the A site.
c. Specificity of the incoming aminoacyl-tRNA is regulated by a
two-step binding reaction and requires GTP hydrolysis. This is the
only GTP hydrolyzed during the synthesis of a peptide bond
d. The ribosome proofreads each aminoacyl-tRNA to make sure the
proper amino acid is attached before synthesizing a peptide
bond.
e. None of the other four answers are correct. 74. molecular
techniques are listed with a molecule or reaction that is important
in that
technique. Choose the INCORRECTLY matched pair. a. Sanger DNA
sequencing, dideoxynucleoside triphosphates b. DNA fingerprinting,
variable number tandem repeat sequences (VNTRs) c. Cloning DNA
fragments, DNA ligase d. PCR, extension from a 3 phosphate e.
Restriction endonuclease digestion, sequence-specific DNA-cleavage
reaction
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75. A short fragment of protein X (discussed in questions
53-55), has a partial amino acid sequence determined by
multidimensional mass spectrometry. Two polypeptides are
determined: Fragment L (Met-Lys-Tyr-Cys-Ile-Asn) and Fragment P
(Ser-Arg-Leu-Cys-Gly-Pro). Using your knowledge of the structures
of the amino acids, translation and the genetic code (shown at
right), which of the following statements is CORRECT regarding the
two fragments?
a. The potential coding sequences for Fragment L are less
degenerate than those for Fragment P.
b. The potential coding sequences for Fragment P are less
degenerate than those for Fragment L.
c. At pH 7, Fragment P is more positively charged than Fragment
L.
d. At pH 7, Fragment L is more positively charged than Fragment
P.
e. Fragment P is more likely to be a signal peptide than is
Fragment L. 76. Which of the following statements is true about
protein synthesis?
a. All proteins fold properly during translation. b. RNA editing
can cause premature termination of translation by changing an
amino acid codon to a stop codon. c. A frameshift that occurs
during translation always results in premature
termination of the polypeptide chain. d. Proteins destined to be
localized within the plasma membrane are synthesized in
the Golgi complex. e. Poly-ubiquitination of proteins (addition
of multiple ubiquitin molecules to lysine
residues on the protein) targets the protein for extra-cellular
secretion. 77. A human gene (G) is discovered that, when expressed,
directly blocks production of
protein Z from gene Y. Which of the following is LEAST LIKELY be
true for gene G? a. Gene G may encode a reverse transcriptase. b.
Gene G may affect the production of protein from RNA. c. Gene G may
not encode for a protein. d. Gene G may encode a transcriptional
repressor that interacts with gene Y. e. RNA from gene G may
interact with the RISC complex.
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Practice Questions for Medical Biochemistry Wold Lectures
September, 2010
Answer Key 1. C 2. B 3. B 4. D 5. A 6. D 7. D 8. B 9. D 10. E
11. D 12. E 13. B 14. A 15. A 16. E 17. C 18. B 19. C 20. A 21.
E
22. B 23. A 24. D 25. C 26. E 27. A 28. E 29. E 30. D 31. E 32.
A 33. D 34. D 35. C 36. E 37. B 38. C 39. B 40. E 41. B 42. D
43. A 44. E 45. C 46. B 47. D 48. C 49. E 50. A 51. D 52. C 53.
B 54. A 55. D 56. B 57. A 58. E 59. C 60. C 61. D 62. C 63. B
64. A 65. E 66. E 67. C 68. E 69. B 70. B 71. D 72. C 73. B 74.
D 75. A 76. B 77. A