Download December 2009

Answer Key
1D
11B
21D
31A
41B
51B
61C
2D
12B
22B
32D
42D
52D
62A
3E
13D
23E
33B
43B
53E
63E
4E
14E
24C
34C
44E
54B
64D
5C
15D
25C
35D
45B
55C
65E
6A
16C
26E
36C
46D
56D
7C
17C
27A
37C
47B
57D
8B
18A
28B
38A
48ABCDE
58C
9C
19D
29B
39A
49A
59C
10CE
20A
30D
40ABCDE
50C
60E
1. Which of the following statements concerning proteins is CORRECT?
a. Proteins cannot be composed of multiple polypeptides.
b. Alpha helical structures are stabilized by hydrogen bonding between the carbonyl
oxygen and the amide hydrogen of amino acids on adjacent strands.
c. Formation of a peptide bond is via a hydrolysis reaction.
d. In parallel beta sheets, adjacent protein chains run in the same orientation.
e. Covalent bonds can be created from Van der Waals forces.
2. What is the CORRECT order of events during DNA replication on the lagging
strand?
(1) RNA primer synthesized by DNA primase.
(2) Separation of double-stranded DNA by helicase.
(3) Exonucleolytic proofreading by DNA polymerase.
(4) Excision of RNA, replaced by DNA.
(5) Nick sealing.
(6) Formation of a new phosphodiester bond by DNA polymerase.
(7) Binding of single-strand DNA binding proteins.
a.
b.
c.
d.
e.
2, 1, 7, 6, 3, 5, 4
2, 1, 6, 3, 4, 7, 5
1, 2, 7, 6, 3, 4, 5
2, 1, 7, 6, 3, 4, 5
2, 1, 4, 7, 6, 3, 5
3. Which statement is FALSE concerning mechanisms that ensure accuracy during
translation?
a. As it escorts an incoming aminoacyl tRNA to the ribosome, EF-Tu checks
whether the tRNA-amino acid match is correct.
b. At the A-site, if the codon-anticodon match between the tRNA and mRNA
template is correct, EF-Tu dissociates from the tRNA.
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c. Aminoacyl tRNA’s are in a bent conformation when bound to the GTP-form of
EF-Tu, which does not allow for incorporation of the amino acid into the growing
polypeptide chain.
d. At the A-site, rRNA in the small subunit of the ribosome forms a series of
hydrogen bonds with the codon-anticodon pair between the incoming tRNA, and
the mRNA template to determine if the basepairing is correct.
e. Incorrectly matched tRNA’s at the A-site whose anti-codon/codon interactions are
weaker tend to dissociate more slowly from the mRNA template than those which
are correctly basepaired.
4. Which of the following statements concerning hemoglobin is FALSE?
a. The same mutation causing sickle cell anemia is thought to be advantageous (in
heterozygotes) against malaria infection.
b. Each subunit of hemoglobin contains a heme group in the site that binds O2.
c. The disease sickle cell anemia is the result of a point mutation in the hemoglobin
gene.
d. Hemoglobin is composed of 4 subunits.
e. None of the above.
5. Which of the following statements concerning the ribosome is FALSE?
a. The ribosome is composed of a large and a small subunit.
b. The ribosome is composed of 2/3rds RNA and 1/3rd protein.
c. Ribosomal proteins are generally located in the interior, and rRNA’s on the
exterior of the ribosome.
d. The secondary structure of 23S rRNA is composed of 6 domains.
e. The entire 3D conformation of the large and small subunits have been
determined.
6. Which is NOT an example of splice site mutations causing abnormal processing of
the beta-globin primary RNA transcript in humans with the disease betathalassemia?
a. Mutations that cause exon rearrangements due to translational shifting of cryptic
splice sites.
b. Mutations that cause exon skipping due to destruction of a splice site.
c. Mutations that cause incorporation of new exons by the creation of new splice
sites.
d. Mutations that cause extensions of exons due to activation of cryptic splice sites.
e. None of the above.
7. What is TRUE concerning protein folding?
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a. Protein folding only occurs after the polypeptide has dissociated from the
ribosome.
b. The molten globule state does not have any of the secondary structures
contained in the final tertiary protein structure.
c. Molecular chaperones help proteins fold correctly.
d. Heat shock proteins tend to have an affinity for exposed hydrophilic patches on
incompletely folded proteins.
e. None of the above.
8. Which statement is FALSE concerning the processing and export of mature mRNA’s
from the nucleus?
a. Nuclear pore complexes are aqueous channels through the nuclear membrane
connecting nucleoplasm and cytosol through which successfully processed
mRNA’s are exported.
b. Improperly processed mRNA’s are retained in the nucleus where they are
degraded in nuclear endosomes.
c. Properly processed mRNA molecules can be distinguished by the lack of any
proteins involved in processing, such as snRNP’s.
d. Properly processed mRNA molecules have acquired cap-binding complexes,
exon junction complexes, and poly-A-binding proteins.
e. Initiation factors for protein synthesis do not associate with mRNA’s until after
they are exported from the nucleus.
9. This question refers to transcriptional activation of a target gene by the estrogen
receptor. Place the following transcriptional activation events in the correct order:
(1) Recognition of the TATA promoter element by TFIID.
(2) Estradiol stabilizes the interaction between the estrogen receptor and the ERE.
(3) The interactions between core histones and promoter DNA are loosened.
(4) Recruitment of histone modifying enzymes.
(5) Phosphorylation of the C-terminal domain of RNA Polymerase II by TFIIH.
(6) Recruitment of RNA Polymerase II to the promoter.
a.
b.
c.
d.
e.
2, 3, 4, 1, 6, 5
3, 1, 2, 4, 5, 6
2, 4, 3, 1, 6, 5
1, 2, 3, 4, 5, 6
1, 2, 4, 3, 6, 5
10. In an experiment, the gene encoding the lac repressor protein was mutated so that it
encoded an abnormal repressor. The abnormal repressor was able to bind to the
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lac operator both in the presence or in the absence of allolactose. What effect would
you expect to see in bacteria carrying this mutation?
a. The bacteria would have difficulty growing in medium containing only glucose.
b. The lac operon would be induced in medium containing lactose but no glucose.
c. The CAP binding protein would bind to the CAP binding site when glucose was
absent.
d. In glucose and lactose, β-galactosidase levels would be higher than normal.
e. RNA polymerase would not be able to bind to the lac promoter.
11. A researcher isolated mRNA from 2 different cell types (hair follicle stem cells and
neural stem cells). The two transcriptomes were compared using the microarray
technique. The following graph summarizes the microarray data:
Which of the following statements is NOT a valid conclusion based on the data
shown in this graph?
a. There are fewer “gene 1” transcripts in neural stem cells than in hair follicle stem
cells.
b. “Gene 3” is expressed at a significantly higher level in hair follicle stem cells than
in neural stem cells.
c. Varying the expression level of “gene 2” potentially affects the developmental
fate of stem cells.
d. “Gene 3” could be a housekeeping gene such as TFIID.
e. The difference in transcript abundance for “gene 2” in these 2 cell types is
statistically significant.
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12. Which of the following would NOT be observed when normal bacteria are grown in
medium containing only lactose as a carbon source?
a.
b.
c.
d.
e.
CAP protein would be bound to CAP binding site.
The cAMP concentration in the cell would be low.
Lac permease concentration would be at a high level.
Allolactose would induce transcription of the lac operon.
The lac repressor would not be bound to the lac operator.
13. Which of the following is NOT a true statement about chromatin?
a. The positive charge of histones partially neutralizes the negative charge of DNA.
b. Heterochromatin is observed in interphase and tends to be transcriptionally
inactive.
c. Nucleosome structure is stabilized by hydrogen bonding between histones and
DNA.
d. Adjacent nucleosomes in euchromatin are tightly packed to prevent access of
basal transcription factors to DNA.
e. A nucleosome core consists of 8 core histone proteins and approximately 147
base pairs of DNA.
14. In a region of chromatin containing “gene X”, H3 N-terminal tails have been
covalently modified as shown in the figure below. Which of the following statements
about the effects of these modifications is NOT true?
a. It is more likely that RNA polymerase II will be recruited to the promoter of gene
X.
b. Covalent modification of lysine residues has reduced the positive charge of the
H3 tail.
c. It is likely that the chromatin in this region exists as euchromatin.
d. A code “reader-writer” complex likely transferred these modifications to adjacent
nucleosomes.
e. A histone kinase code “writer” was recruited to gene X by a gene regulatory
protein.
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15. If the antibody used in a chromatin immunoprecipitation (ChIP) experiment
recognized the glucocorticoid receptor, and the cells had been stimulated with
cortisol, which of the following components would NOT be expected in the results of
the ChIP analysis?
a. H2A
b. Histone acetyltransferase (HAT)
c. Glucocorticoid response element (GRE)
d. Hsp90
e. TFIID
16. You would like to identify all of the possible protein targets of a specific E3 ubiquitin
ligase. Which of the following techniques would provide this information?
a.
b.
c.
d.
e.
Chromatin immunoprecipitation
2-dimensional polyacrylamide gel electrophoresis
Yeast 2-hybrid assay
Western blot
Electrophoretic mobility shift assay
17. You would like to observe the sub-cellular localization of the p53 protein (a tumor
suppressor protein) in live cells. To do this, you decide to make a transgenic mouse.
What pieces of DNA should you ligate together to form the transgene that will be
injected into a mouse zygote?
a. The gene-specific control region of the p53 gene, a basal promoter, and the
protein-coding region of the GFP gene.
b. A basal promoter, the protein-coding region of the p53 gene, and the proteincoding region of the GFP gene.
c. The gene-specific control region of the p53, a basal promoter, the protein-coding
region of the p53 gene, and the protein-coding region of the GFP reporter gene.
d. The gene-specific control region of the p53 gene, a basal promoter, and the
protein-coding region of the p53 gene.
e. The gene-specific control region of the GFP gene, a basal promoter, and the
protein-coding region of the p53 gene.
18. What is the purpose of the GAL4 sequence included in the “bait” construct in the
yeast two-hybrid system?
a.
b.
c.
d.
To bind to the UAS sequence of the reporter gene.
To select for yeast that contain the reporter plasmid.
To provide a site for RNA polymerase II to bind.
To stimulate transcription of the reporter gene.
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e. To select for yeast that contain the bait and prey plasmids.
19. Transcriptional control of the Tryptophan (Trp) operon in E. coli is an example of
which class of gene regulation?
a.
b.
c.
d.
e.
Positive regulation with an inactivating ligand.
Negative regulation with a de-repressing ligand.
Negative regulation with an inactivating ligand.
Negative regulation with a co-repressing ligand.
Positive regulation with a co-activating ligand.
20. A researcher uses a binding site selection assay to identify the consensus DNA
sequence of the estrogen response element (ERE). The researcher then uses a
BLAST search to identify a list of genes that are responsive to estrogen. Which of
the following is not a concern with this method?
a. Only the ERE sequences within 500 base pairs of the basal promoter of a gene
are likely to be functional as transcriptional regulatory elements.
b. Some genes on the list could be due to random chance occurrence of the
consensus sequence in the genome.
c. Deletion analysis should be performed to test whether each predicted ERE is
necessary.
d. The list of genes could be incomplete because of nucleotide sequence variation
in the consensus ERE.
e. Sufficiency of each predicted ERE should be tested with a gain-of-function
experiment.
21. You extract nucleic acids from embryonic hindlimbs and forelimbs in order to
investigate Tbx4 expression in the embryo. Using a radioactively labeled DNA probe
that can hybridize with both Tbx4 RNA and DNA, you perform a Southern blot and a
northern blot. For the northern blot, you also perform an α-Tubulin (α-Tub) loading
control. The results are illustrated below. From the following list, choose the
possible explanation that is NOT supported by these results:
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a. The Tbx4 gene is present in cells of the forelimb and hindlimb.
b. A microRNA gene with sequence complementarity to Tbx4 mRNA is transcribed
in forelimb cells but not hindlimb cells.
c. In the hindlimb, two Tbx4 transcripts are present because of alternative splicing.
d. Tbx4 transcripts exist in the forelimb, but you used the promoter sequence from
the Tbx4 gene for your probe instead of the coding region.
e. In forelimb cells, the region of DNA including the Tbx4 gene contains methylated
CG dinucleotides.
22. A researcher obtains a set of target DNA sequences using a binding site selection
assay. However, the sequences appear random and cannot be aligned to define a
consensus binding site. Which one of the following is a possible explanation for this
result?
a. The antibody did not cross react with any proteins in the mixture containing
proteins and their bound DNA.
b. The radioactive DNA that migrated farthest toward the positive electrode of the
gel was excised and cloned.
c. The researcher forgot to add formaldehyde prior to lysing the cells.
d. The PCR reaction at the end of the procedure failed.
e. The protein that is precipitated by the antibody is not selective in the DNA
sequences it binds.
23. Which of the following statements does NOT accurately complete the following
sentence?
X-chromosome inactivation:
a. involves a repressive chromatin state that can be passed on to daughter cells
epigenetically.
b. involves specific covalent modifications to both the core histones and the DNA
itself.
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c. is a dosage compensation mechanism in females that ensures that genes from
only one X chromosome are expressed.
d. originates at the X-inactivation centre (XIC), which seeds and facilitates the
spread of heterochromatin over the length of the chromosome.
e. involves the synthesis of XIST proteins that coat the inactive X-chromosome and
promote the formation of heterochromatin.
24. Which of the following statements about packaging the bacterial genome into the
bacterial cell is TRUE?
a. Negatively charged polyamines neutralize the positive charge of the DNA.
b. Polyamines and other small proteins form nucleoids along the length of the
DNA.
c. The circular chromosome is condensed by DNA supercoiling.
d. Operons are regulated in part by chromatin state.
e. The genome is packaged into a 30nm structure.
25. Which of the following statements about packaging the human genome into
chromatin is NOT true?
a. ATP-dependent chromatin remodeling complexes can slide nucleosomes along
the DNA.
b. Active and inactive genes tend to occupy discrete territories within the interphase
nucleus.
c. A nucleosome consists of an octameric histone core and 147 nucleotides of
DNA.
d. Relatively unstructured N-terminal tails of histones protrude from nucleosomes.
e. Histone H1 and the positive charges of core histones are important to stabilize
chromatin structures.
26. In a microarray experiment, red and green fluorescent dyes were used to label the
mRNA populations isolated from two different eukaryotic cell types. mRNA from
neurons was labeled red and mRNA from epithelial cells was labeled green. The
two labeled mRNA populations were mixed and hybridized to a single microarray
chip. Which of the following is true of the data obtained from DNA microarray
analysis?
a. Microarray spots that appear green indicate that the gene had equivalent
transcript abundance in the two RNA populations.
b. The proteomes of the two cell populations can be inferred from the microarray
data.
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c. The microarray analysis will likely reveal that the transcriptome is static and
identical in the two cell types.
d. Genes with increased transcript abundance in epithelial cells relative to neural
cells could be recognized by their red fluorescence on the chip.
e. This technique can potentially monitor differences in the level of mRNA
corresponding to every gene in the genome.
27. Which of the following statements about the histone code is NOT true?
a.
b.
c.
d.
e.
Specific lysine residues can be monoacetylated, diacetylated or triacetylated.
Specific serine residues are targets of histone kinases.
Specific lysine residues can be either acetylated or methylated, but not both.
All of the core histones contain lysine residues that are targets for acetylation.
Both the globular domain and N-terminal tails of core histones are targets for
covalent modifications.
The following figure represents a pair of silver-stained 2-dimensional gels. For
simplicity, most of the proteome is not illustrated. For the 2D gel on the left, proteins
were isolated from a tumor cell line, and for the 2D gel on the right, the proteins were
isolated form a normal control cell line. Use this figure to answer the following two
questions.
28. Which of the following is NOT a valid conclusion based on the 2D gel on the left.
a. Proteins were separated by isoelectric focusing in dimension 1.
b. Protein Y migrated toward the positive pole in both dimensions 1 and 2.
c. Protein X has a higher molecular weight than protein Y.
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d. At low pH, protein Y is more positively charged than protein X.
e. In dimension 2, negatively charged SDS molecules caused protein Y to unfold.
29. Which of the following possibilities is NOT supported by the 2D gels shown above?
a. Protein Z is poly-ubiquitinated in normal cells, but not tumor cells.
b. Protein Z is sequestered in the cytoplasm of normal cells by Hsp90, but its
conformation allows nuclear import in tumor cells.
c. The mRNA encoding protein Z forms a stem loop in its 3’ UTR that is recognized
by nuclear retention proteins, and this stem loop is cleaved in tumor cells.
d. A micro-RNA that represses translation of Z in normal cells is not expressed in
tumor cells.
e. In normal cells, the poly-A tail of the mRNA encoding gene Z has been removed
by endonucleolytic cleavage.
30. Which of the following potential targets for mutation are LEAST likely to alter the
phenotype of a cell, tissue or organism?
a. Nucleotide substitution in the splicing branch point of an intron.
b. Single nucleotide insertion in the protein coding region.
c. Nucleotide substitution in a consensus transcription factor binding site that
changes one of the invariant bases.
d. Nucleotide substitution in the DNA linking the basal promoter and the gene
regulatory region.
e. Deletion of a nearby chromatin barrier sequence.
31. A grad student makes a new antibody by expressing a protein kinase in E.coli,
purifying the protein, and injecting this antigen into a rabbit. The grad student
performs a western blot on proteins isolated from cultured neural cells using the new
antibody for the first time. The grad student identified three proteins with different
molecular weights that were clearly labeled on the western blot. Which of the
following explanations for this result is NOT possible?
a. The protein kinase mRNA was the target of a small interfering RNA.
b. The antigen recognized by the primary antibody is not specific to the protein
kinase.
c. Post-translational modifications of the protein kinase affect its migration in the
polyacrylamide gel.
d. The new antibody was not tested using immunoprecipitation.
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e. Various isoforms of the protein kinase are formed by alternative splicing.
32. A scientist is characterizing chromatin organization from a novel organism from outer
space. From the following list of results from the alien, choose the item that is the
most similar to the majority of eukaryotes on earth.
a. The alien genome is condensed approximately 1000-fold through the action of
topoisomerases.
b. The alien nuclosome core is an octamer comprising pairs of histones H1, H2,
H3A and H3B.
c. Wrapping of alien DNA 1.7 times around the histone core is stabilized by 142
covalent bonds between the DNA and histone core proteins.
d. Some alien histone core proteins can be covalently modified on their N-terminal
or C-terminal tails.
e. Acetylation of alien DNA is associated with a euchromatic chromatin state.
33. You are analyzing the differences and similarities between chromatin isolated from a
euchromatic region of an active X-chromosome compared to a heterochromatic
region of an inactivated X-chromosome. Both X chromosomes are from a female
mammal. Which of the following would you NOT expect to observe?
a. Chromatin from the inactive X-chromosome contains hypoacetylated core
histone H3 and H4 tails.
b. The X-inactivation center (XIC) of the inactive X-chromosome is transcriptionally
repressed.
c. Chromatin from the inactive X-chromosome contains XIST RNA.
d. Methylated DNA was isolated from chromatin from the inactive X-chromosome.
e. A specific Lysine residue is methylated in the tail of core histone H3 isolated from
the inactive X-chromosome.
34. Which of the following statements is FALSE?
a. The DNA recognition motif of some gene regulatory proteins consists of a betasheet secondary structure that fits into the major groove of the DNA.
b. DNA-protein interactions generally consist of about 20 weak interactions that
together ensure specificity and strength of the interaction.
c. Gene regulatory proteins “read” the DNA minor groove because it provides the
maximum amount of information from functional groups in the DNA.
d. R-groups of gene regulatory proteins interact with hydrogen bond donors and
acceptors, hydrogen atoms, and methyl groups of DNA bases.
e. Many gene regulatory proteins recognize DNA as dimers.
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35. A researcher identified a short DNA sequence matching the consensus
glucocorticoid response element (GRE) by in silico analysis. The GRE consensus
sequence is located 500 nucleotides upstream of an uncharacterized gene (gene B).
Which of the following statements is TRUE?
a. The researcher can conclude that Gene B transcription is activated when the
GRE is bound by a glucocorticoid receptor dimer in the presence of cortisol.
b. The DNA region containing the predicted GRE should be deleted from a reporter
transgene to test whether it is sufficient for reporter gene transcription.
c. The DNA region containing the predicted GRE should be ligated to a reporter
transgene containing a basal promoter to test whether it is necessary for reporter
gene transcription.
d. The DNA region containing the predicted GRE should be used in an
electrophoretic mobility shift assay with glucocorticoid receptor proteins that have
been treated with cortisol.
e. The predicted GRE is too close to the basal promoter to easily form the DNA
loop involved in transcriptional activation.
36. Which of the following statements concerning DNA binding motifs is FALSE?
a. The Trp repressor contains two helix-turn-helix DNA binding motifs that
recognize a two segment recognition motif separated by a short nucleotide
spacer.
b. A C2H2 zinc-finger motif consists of two Cysteine residues and two Histidine
residues coordinated by a single zinc ion.
c. Zinc finger motifs interact with the major groove using specific R-groups from
their antiparallel beta sheet.
d. The Helix-loop-helix motif is responsible for both dimerization and DNA binding.
e. Leucine zippers consist of two α-helices that each bind to one half of a symmetric
DNA sequence.
37. You want to isolate proteins from a cell lysate that are able to bind to the short DNA
sequence “GGGCCC”. You used a two-step DNA affinity chromatography method,
as discussed in lecture. At the end of the protocol, you expected the final eluate to
contain proteins that recognized your DNA sequence, but no proteins were present
in the final eluate. Why might this be the case?
a. The missing proteins are still bound to the second column because the final
buffer should have been low-salt and you used high-salt instead.
b. You conducted the protocol properly, but your DNA fragment contains a
sequence only recognized by a basal transcription factor.
c. Your DNA fragment does contain a gene regulatory sequence, but the cells you
used to isolate total cellular proteins did not express the relevant gene regulatory
protein.
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d. You conducted the protocol properly, but none of the proteins used at the
beginning of the assay are able to bind to DNA.
e. All of the above are correct.
38. Which of the following statements about nuclear import of proteins is FALSE?
a. The hydrolysis of ATP to ADP is part of the cycle related to the transport of
proteins into the nucleus.
b. Nuclear localization signals are rich in the positively charged amino acids Lysine
and Arginine.
c. Gene regulatory proteins can be sequestered in the cytoplasm by inhibitor
proteins such as Hsp70.
d. Cells contain various nuclear import receptor proteins that recognize the nuclear
localization elements of a subset of cargo proteins.
e. The nuclear pore complex blocks the passive diffusion of large macromolecules.
39. Which of the following statements about eukaryotic transcriptional activator or
repressor proteins is FALSE?
a. Eukaryotic gene repressor proteins prevent transcription by physically competing
with RNA Polymerase for binding to the promoter region.
b. Eukaryotic gene repressor proteins can recruit histone methyltransferase to
modify histones.
c. Eukaryotic gene repressor proteins can mask the activation surface of a gene
activator protein by direct protein interaction.
d. Eukaryotic gene activator proteins can lead to histone code modifications that
recruit TFIID to the basal promoter.
e. Eukaryotic gene activator proteins can recruit histone acetyltransferases to
modify histones.
40. Because of its sequence similarity to the fly Eyeless transcription factor, you
hypothesize that the vertebrate Pax-6 protein acts as an eye selector gene (or
master control gene) in mice. Assuming your hypothesis is CORRECT, which of the
following predictions is TRUE?
a. Deleting the Pax-6 gene from the mouse genome should cause loss of eyes,
since Pax-6 is expected to be necessary for eye development.
b. The Pax-6 promoter region should contain regulatory DNA sequences that are
necessary for reporter gene expression in the embryo where eyes will develop.
c. Pax-6 protein is expected to be cytoplasmic in the embryonic cells that will
develop into the eyes.
d. Expressing the Pax-6 gene in mouse limb buds should cause extra eyes to
develop, since Pax-6 is expected to be sufficient for eye development.
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e. Pax-6 gene regulatory sequences should be sufficient to drive GFP expression
from a basal promoter in embryonic eyes.
41. Adding a polyubiquitin chain to a target protein to mark it for proteasomal
degradation is a multi-step process. Which of the following is part of that process?
a. An E2 ubiquitin-activating enzyme primes itself with ubiquitin using energy
released by ATP hydrolysis.
b. E1 transfers ubiquitin onto the cysteine side chains of E2 ubiquitin conjugating
enzymes.
c. An E2/E3 ubiquitin ligase recognizes an E1 protein and attaches a single
ubiquitin molecule to E1.
d. E1 ubiquitin ligase begins a new polyubiquitin chain on the target protein to be
degraded.
e. The carboxy terminus of ubiquitin is initially activated though a high-energy
phosphodiester linkage to an R-group from the ubiquitin activating enzyme E2.
42. Which of the following is an example of epigenetic inheritance?
a. Gene A has a mutation that changes the amino acid sequence of its nuclear
localization signal.
b. Monozygotic twins have the same eye color because they inherited the same
alleles.
c. Embryonic stem cells can be forced to differentiate into various cell types by
exposing them to different extracellular signals.
d. The promoter region of gene A is methylated, and this methylated state is
maintained in both daughter cells following mitosis.
e. Allelic variation can affect phenotype by altering the function of enzymes.
43. Which of the following statements about post-transcriptional regulation of gene
expression is FALSE?
a. In Drosophila females, the Sex-lethal protein blocks a regulated splice site in the
transformer mRNA.
b. The poly-A tail of an mRNA can be shortened by a deacetylating nuclease
(DAN), increasing mRNA stability.
c. A single transcript can produce two different protein isoforms by skipping an
optional exon during splicing.
d. Ribosomes can use different AUG codons in a single mRNA to translate proteins
with different N-termini.
e. A sequence in the 3’ untranslated region of some transcripts results in their
retention in the nucleus, preventing translation.
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44. The influenza virus has a single-stranded RNA genome. Which tests could be
performed by Health Canada to determine if the flu virus is present in cells isolated
from the respiratory tract of a pig that shows flu symptoms?
a. A western blot to detect viral RNA-dependent RNA polymerase.
b. A northern blot to detect transcripts encoding viral Hemagglutinin.
c. A Southern blot to detect the viral genome after it inserts into a host
chromosome.
d. The tests described in a, b, and c would show the presence of the virus.
e. The tests described in a and b (i.e. not c) would show the presence of the virus.
45. Which of the following statements regarding dsRNA-mediated gene silencing or
RNA interference is FALSE?
a. The presence of double stranded RNA in a cell recruits a protein complex
containing the Dicer RNase enzyme.
b. Perfect base pairing between a micro-RNA and target mRNA is required for
translational inhibition and mRNA degradation.
c. The RISC complex uses a single-stranded small interfering RNA to identify and
repress target RNAs.
d. Dicer cleaves double stranded RNA into small interfering RNAs that are about 23
nucleotides in length.
e. Small RNA molecules can target DNA methylation to genes in the nucleus and
silence transcription.
46. Which of these statements regarding protein folding is FALSE?
a.
b.
c.
d.
Misfolded proteins can be recognized by the E3 component of ubiquitin ligases.
Denatured or abnormal proteins are degraded by the proteasome.
Repeated cycles of Hsp70 binding and release help the target protein to re-fold.
Incorrectly folded proteins are isolated in the capped hydrophilic barrel of Hsp70
chaperones.
e. Refolding of proteins by Hsp60 is an energy-dependent process involving
hydrolysis of ATP.
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47. Which of the following statements concerning the yeast 2-hybrid system is TRUE?
a. The Leu gene encodes an enzyme that acts as a reporter indicating when the
“bait” and “prey” fusion proteins interact and activate transcription.
b. If two proteins that normally interact in vivo are unable to enter the nucleus in
yeast cells, this is likely to give rise to a false negative result.
c. A false positive result may arise if the prey protein has a transcriptional activation
domain and it does not normally interact with the bait protein in vivo.
d. The His gene is used as a reporter gene to indicate the efficiency of
transformation of the “prey” plasmid.
e. A Gal4 protein containing a DNA-binding domain and a transcriptional activation
domain is expressed from a plasmid containing the Trp gene as a selectable
marker.
48. Which of the following definitions is TRUE?
a. The “proteome” is the entire complement of proteins expressed by a cell, tissue
or organism; proteomes can be characterized with 2D gel electrophoresis.
b. The “genome” refers to the complete, unique set of hereditary material in a cell;
genomes can be characterized by whole-genome shotgun sequencing.
c. The “metabolome” describes the complete and very dynamic set of smallmolecule metabolites produced by a cell, tissue or organism.
d. The “transcriptome” is the complete set of RNA transcripts that can possibly be
expressed in a cell; transcriptomes can be inferred from genome sequences.
e. All of the above are correct.
49. You have joined a lab as a new summer research student and have been asked to
purify DNA from D. melanogaster (fruit fly). You decided to use two different
protocols that yielded the following results:
•
•
Protocol A gave an A260:A280 ratio of 1.9
Protocol B gave an A260:A280 ratio of 1.2
Which of the two protocols resulted in a more pure DNA sample (the sample least
contaminated with proteins), and according to what you have learned in BIO240,
which step may have been used/removed to obtain this result?
a. A chloroform-isoamyl alcohol step was used in Protocol A to yield a purer DNA
sample.
b. A chloroform-isoamyl alcohol step was removed in Protocol A to yield a purer
DNA sample.
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Answer Key
c. A chloroform-isoamyl alcohol step was used in Protocol B to yield a purer DNA
sample.
d. A chloroform-isoamyl alcohol step was removed in Protocol B to yield a purer
DNA sample.
e. An A260:A280 ratio can only be used to determine DNA concentration and
cannot be used to determine DNA purity.
50. You need to perform a PCR reaction but realized that you have run out of Taq DNA
polymerase. Out of desperation, you decided to use a different polymerase, Baq
DNA polymerase. Baq DNA polymerase functions most efficiently at 78ºC instead of
the regular 72ºC for Taq DNA polymerase. Which step(s) of the PCR protocol do you
need to change in order for Baq DNA polymerase to function most efficiently?
The temperature(s) of:
a. denaturation needs to be changed to 78ºC.
b. annealing needs to be changed to 78ºC.
c. extension needs to be changed to 78ºC.
d. denaturation and extension need to be changed to 78ºC.
e. denaturation and annealing need to be changed to 78ºC.
51. A 21Kb linear piece of DNA was cut with the restriction enzymes BamHI and HindIII
alone and in combination, and produced the following fragments. Which of the
following is the CORRECT restriction map?
BamHI: 6Kb, 7Kb, 8Kb
HindIII: 10Kb, 11Kb
BamHI + HindIII: 3Kb, 4Kb, 6Kb, 8Kb
BamHI
HindIII
BamHI
a.
8Kb
BamHI
b.
6Kb
c.
4Kb
HindIII
4Kb
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4Kb
3Kb
BamHI
3Kb
BamHI
HindIII
3Kb
6Kb
8Kb
HindIII
8Kb
6Kb
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Answer Key
BamHI
d.
6Kb
HindIII
BamHI
3Kb
4Kb
HindIII
BamHI
8Kb
HindIII
e.
8Kb
3Kb
6Kb
4Kb
52. Which of the following is TRUE?
a. Nucleosides have three major components: a base, a sugar, and a phosphate
group.
b. In double stranded DNA there are three hydrogen bonds between the bases,
adenosine and thymine.
c. A-DNA is the most common DNA helix structure found in human cells.
d. Amphiphilic beta sheets contain sequences of alternating hydrophobic and
hydrophilic amino acids.
e. The primary structure of a protein is dictated by the hydrogen and disulfide bonds
between amino acids.
53. Which of the following is true about bioinformatic tools?
a. ClustalW compares one known sequence against a data base of sequences.
b. The BLASTn query sequence must be a protein sequence in Fasta format.
c. When performing a BLAST search, a subject sequence with a high E value is
desirable.
d. BLAST and ClustalW are different graphical user interfaces that were designed
to perform the same bioinformatic task.
e. In a BLAST search, the E value of a subject sequence can increase as the size
of the data base increases.
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Answer Key
54. What is the correct order of DNA isolation steps to be used with wheat germ?
i.
ii.
iii.
iv.
v.
vi.
vii.
a.
b.
c.
d.
e.
Deproteinize DNA
Acetylate histones
Rupture nuclear envelope and dissociate histone and non-histone proteins
Separate nuclei from cellular components
Rupture cell wall and plasma membrane
Chelate divalent cations needed by DNAses
Precipitate DNA
v, iii, v, iv, ii, vi, vii
v, iv, iii, vi, i, vii
iii, v, iv, i, vi, ii, vii
iii, iv, ii, vi, v, i, vii
v, i vi, iii, iv, ii, vii
55. Which of the following is TRUE concerning detergents?
a.
b.
c.
d.
e.
Detergents are less soluble than lipids in water.
Detergents are large amphiplastic molecules.
Their polar ends can be either ionic or non-ionic.
At high concentrations above a threshold, they form monomeric micelles.
SDS is an example of a weak uncharged detergent.
56. Which of the following statements regarding A, B and Z-DNA is CORRECT?
a.
b.
c.
d.
e.
A-DNA has a right-handed helix formed under high salt conditions.
The major and minor grooves of all three forms of DNA are identical.
B-DNA has a right-handed helix formed under dehydrating conditions.
Z-DNA is characterized by a left-handed helix formed under high salt conditions.
Z-DNA is a right-handed helix formed when there are many C-G pairs.
57. Loading dye is added to DNA samples before loading the sample onto an agarose
gel. Which of the following is NOT a function of the loading dye?
a. The loading dye makes the sample more dense than the running buffer and thus
“pulls” the sample into the wells.
b. The loading dye helps visualize the sample while loading.
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Answer Key
c. The loading dye can be used as a reference point while running the gel.
d. The loading dye contains ethidium bromide that will enable the nucleic acids to
be visualized with UV light.
e. The bromophenol blue in the loading dye will travel towards the positive end of
the gel.
58. The accession number:
a. summarizes the number of occurrences of each base code in the subject
sequence.
b. cites all the literature containing data reported in a GenBank entry.
c. is the unique and unchanging code assigned to each GenBank entry.
d. is dependent on the length of the matched portion of the query sequence.
e. changes as newer sequences are added to the PubMed database.
59. Which of the following statements regarding DNA, RNA and protein stabilizing forces
is INCORRECT?
a. Hydrogen bonding stabilizes formation of alpha-helices and B-sheets in proteins.
b. DNA and RNA backbones are negatively charged and can form ionic bonds with
positively-charged ions.
c. Van der Waals forces are not involved in stacking interactions between DNA and
RNA base pairs.
d. Hydrogen bonding occurs between complementary base pairs of DNA double
helices.
e. Hydrophobic interactions stabilize DNA, RNA and protein structures because
water forces non-polar surfaces together to minimize their disruptive effects on
hydrogen bonding of water.
60. If you were making a 50 µl PCR reaction using 5X PCR buffer, how much PCR
buffer should you add to the tube?
a.
b.
c.
d.
e.
2.5 µl
5.0 µl
25 µl
1U
10 µl
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Answer Key
61. There are several reasons for comparing a protein sequence of unknown function
with protein sequences of known function. All of the following statements are true
EXCEPT:
a. X-ray crystallography has already revealed the structure of many proteins.
b. Proteins with the same structure often perform the same biochemical function.
c. Discovery of homologous sequences and structures via bioinformatic analysis
means that direct experimentation is unnecessary.
d. Predictions of protein structures have been based on data from NMR
spectroscopy and our knowledge of the physical forces that act on atoms.
e. Bioinformatic analyses can make the design of experiments on proteins of
unknown function more efficient.
62. A sample of DNA is digested using Xba1 and BamH1. The sample is then run on a
gel along with a molecular weight (MW) ladder. Possible restriction maps using bp
units are shown below.
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Answer Key
Sample
MW
Ladder
Xba BamH
(1)
500 500
2000bp
1500bp
1000 bp
Xba
1500
BamH
500
Xba
(2)
1000
1500
Xba BamH
500
Xba
(3)
500 bp
500 500
1000
500
Xba
(4)
1500
500
Which of the following restriction maps shown above could represent the DNA
sample?
a.
b.
c.
d.
e.
1 and 4 only
2 and 3 only
4 only
3 only
1, 2, 3, and 4
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Answer Key
63. What mechanism have bacteria evolved to prevent the digestion of their own DNA
by restriction nucleases?
a. Bacterial DNA is a single stranded, circular plasmid that is glycosylated at the
restriction sites to prevent cleavage.
b. Bacteria produce enzymes that chelate divalent cations that are required for
nuclease activity.
c. Bacterial DNA is circular therefore they do not possess the palindromic
sequences recognized by the restriction nucleases.
d. Bacteria evolved restriction nucleases that only produce staggered cuts, while
their DNA only has blunt ended recognition sites that are acetylated.
e. Bacterial DNA is methylated at or near restriction sites to prevent cleavage.
64. Which of the following statements regarding restriction enzymes used in Lab 5 is
CORRECT?
a. A restriction buffer is used together with the enzyme to provide a chelating
medium necessary for optimal nuclease function.
b. The recognition sequences are similar to palindromes because the sequence is
the same for the Okazaki fragments used for synthesis of the leading and lagging
strands.
c. The CITES database contains a listing of restriction enzyme recognition sites.
d. The majority of restriction enzymes recognize either four or six base pair
sequences.
e. The restriction enzymes used in Lab 5 are commonly referred to as restriction
exonucleases because they cleave nucleic acids from the ends of DNA.
65. All of the following could affect migration of a nucleic acid fragment within an
agarose gel EXCEPT:
a.
b.
c.
d.
e.
Mass of the fragment.
Percentage agarose in the gel.
Voltage and/or current used.
Whether the fragment was single or double-stranded.
Whether the fragment originated from a prokaryote or a eukaryote.
END OF TEST
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