Genetics Canadian 2nd Edition Hartwell

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MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.

1) Transcription in prokaryotes and eukaryotes is similar in that

A) both prokaryotic and eukaryotic proteins have identical affinities for DNA.
B) both are regulated by attachment of proteins to DNA adjacent to the gene being transcribed.
C) transcriptional machinery controls compaction and decompaction of chromatin.
D) the mRNA produced can undergo alternative splicing.
E) both are contained within the cell nucleus.
Answer: B

2) A regulatory protein that prevents transcription initiation not by recruiting corepressor but instead by
interfering with the function of activators is called ________.
A) basal factor
B) Negative regulator
C) direct repressor
D) indirect repressor
E) mediator
Answer: D

3) An initiation box contains which of the following pairs of bases?

A) A & C B) A & G C) C & G D) U & T E) A&T
Answer: E

4) Which of the following receptor transcription factors is an example of allostery in eukaryotes?

A) Gq protein
B) steroid hormone
C) Gs protein
D) peptide
E) polypeptide
Answer: B

5) Which of the following can recruit histone modifying enzymes to DNA resulting in heterochromatin
formation?
A) microRNA B) macroRNA C) siRNA D) miRNA E) piRNA
Answer: C

6) What is the name of the protein that insulators bind to?

A) TATA B) Poly A tail C) sxl D) initiator E) CTCF
Answer: E

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7) DNA methylation requires which of the following enzymes?
A) Polymerase I
B) Transferase
C) DNase
D) Ligase
E) Polymerase BII
Answer: B

8) The proteins that open local chromatin structure to allow gene transcription are called ________.
A) repressors
B) coactivators
C) heterodimers
D) negative regulators
E) enhancers
Answer: B

9) Heterochromatic regions are characterized by methylation on a ________ amino acid in histone

________.
A) Methionine, H2A
B) Tryptophan, H3
C) Tryptophan, H4
D) Lysine, H3
E) Methionine, H4
Answer: D

10) Zinc-finger peptide motifs are responsible for what aspect of protein function?
A) mRNA splicing
B) kinase activity
C) DNA replication
D) DNA binding
E) methylation
Answer: D

11) DNA sequences that serve as binding sites for proteins regulating transcription and are often found
adjacent to a gene are said to be
A) trans-acting.
B) transcription factors.
C) cross-reacting.
D) cis-acting.
E) origins of transcription.
Answer: D

12) The ________ is the cis-acting DNA sequence that serves as the binding site for RNA polymerase.
A) regulator B) promoter C) terminator D) initiator E) enhancer
Answer: B

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13) ________ are cis-acting DNA sequences that often function at a distance from the gene they are
regulating.
A) Promoter elements
B) Initiator elements
C) Terminator elements
D) Enhancer elements
E) Regulator elements
Answer: D

14) A cis-acting DNA sequence that modulates the basal rate of transcription of a gene is termed a(n)
A) promoter. B) initiator. C) repressor. D) enhancer. E) activator.
Answer: D

15) In generating a reporter construct to study gene regulation, the reporter gene introduced replaces
A) X-gal.
B) beta-galactosidase.
C) the cis-acting regulatory DNA sequence.
D) a random region of DNA.
E) the coding region of the gene being studied.
Answer: E

16) Mutations altering the amount of protein synthesized from a reporter construct occur most often in
which of the following sequences of DNA?
A) X-gal coding sequence
B) cis-acting DNA elements
C) the introns of the reporter gene
D) RNA polymerase II gene
E) the reporter gene
Answer: B

17) Mutations introduced into reporter constructs are used to study

A) the effects on cell function of expression of heterologous proteins.
B) Western blots.
C) protein-protein interactions.
D) the DNA sequences that are important for regulating gene expression levels.
E) colorimetric assays.
Answer: D

18) The gene products encoded by trans-acting elements perform their function by
A) physically associating with DNA polymerase.
B) regulating the expression of the gene from which they were transcribed.
C) the association of nucleotides with the elongating RNA transcript.
D) regulating the activity of telomerase.
E) associating with regulatory sequences distant from the gene from which they were transcribed.
Answer: E

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19) Trans-acting proteins that influence transcription are commonly referred to as
A) transcription factors.
B) enhancers.
C) tumour suppressors.
D) DNA polymerases.
E) promoter elements.
Answer: A

20) RNA polymerase I synthesizes ________ using a DNA template.

A) rRNA B) tRNA C) snRNA D) mRNA E) dsRNA
Answer: A

21) tRNA molecules are transcribed by

A) DNA pol III.
B) RNA pol II.
C) DNA pol II.
D) RNA pol III.
E) RNA pol I.
Answer: D

22) Which of these is most important to ChIP (chromatin immunoprecipitation) technology?

A) an antibody that recognizes the DNA cis-element of interest
B) an antibody that recognizes a transcription factor of interest
C) an antibody that recognizes specific chromatin structures
D) an antibody that recognizes a nucleosome
E) an antibody that recognizes the promoter of interest
Answer: B

23) Which of the following is not true of enhancer DNA sequences?

A) They can be more than 10 kilobases from the gene they regulate.
B) They may contain multiple regulatory elements.
C) They may increase or decrease gene transcription levels.
D) They may be located upstream of a TATA box.
E) They contain the TATA box regulatory element.
Answer: E

24) A transcription factor that increases initiation of transcription by associating with an enhancer
element is termed a(n)
A) initiator.
B) activator.
C) super-repressor.
D) enhancer.
E) repressor.
Answer: B

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25) Theprimary function of basal transcription factors is to
A) activate RNA synthesis at origins of replication.
B) regulate activity of DNA polymerase II.
C) increase transcription by binding enhancer sequences.
D) repress transcription initiation of a particular gene.
E) assist in associating RNA polymerase with the promoter element.
Answer: E

26) ________ are basal transcription factors that associate with TBP to assist in initiating transcription
from eukaryotic class II genes.
A) TATAs
B) Jun and Fos
C) DNA-BPs
D) TAFs
E) Sxl and string
Answer: D

27) Proteinsthat consist of two identical polypeptide subunits are classified as

A) oligomers.
B) monomers.
C) diplomers.
D) heterodimers.
E) homodimers.
Answer: E

28) Theleucine zipper motif functions to

A) release leucines from misfolded transcription factors.
B) mediate the physical association of two polypeptides.
C) anchor transcriptional activator proteins to enhancer sequences.
D) integrate leucines and isoleucines into newly translated transcriptional activators.
E) open up proteins after transcription.
Answer: B

29) ________ are transcription factors that decrease transcriptional activity by associating with specific
enhancer elements or activator proteins.
A) TBPs
B) Regulators
C) Depleters
D) Repressors
E) Deregulators
Answer: D

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30) Which of the following is not a mechanism employed by repressor proteins to decrease transcription
of a specific gene?
A) The repressor binds to the activation domain of an activator, eliminating its ability to increase
transcription.
B) The repressor binds to RNA polymerase II, blocking its ability to associate with promoter
element.
C) The repressor binds to a DNA sequence in an enhancer, eliminating access to sequence by
activator.
D) The repressor associates with a promoter element, blocking RNA polymerase from binding
promoter element.
E) The repressor binds to DNA-binding domain of an activator, eliminating its ability to associate
with enhancer.
Answer: B

31) Mutations in the GAL80 gene in yeast result in the continuous expression of the GAL1, GAL7, and
GAL10 genes, even in the absence of galactose. This genetic evidence suggests that the GAL80 gene
product acts as a(n)
A) transcriptional repressor.
B) RNA polymerase.
C) promoter element.
D) transcriptional activator.
E) enhancer element.
Answer: A

32) The ________ is the repeating structural unit of chromatin, consisting of approximately 200 base
pairs of DNA and associated histone proteins.
A) regulosome
B) spliceosome
C) nucleosome
D) transcriptosome
E) enhanceosome
Answer: C

33) Theassociation of DNA with histones to form chromatin affects transcription by

A) decreasing basal transcription rates.
B) decreasing transcription of a few genes, while not influencing most others.
C) increasing transcription of a few genes, while not influencing most others.
D) increasing transcription of some genes and decreasing transcription of others.
E) increasing basal transcription rates.
Answer: A

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34) Regions of DNA are most sensitive to DNase digestion when
A) found at a recombination hotspot.
B) a cell is in G0.
C) the nuclei in which they are contained enter prophase.
D) they are free of histones.
E) they are maintained as chromatin.
Answer: D

35) TheDNase enzyme can be used in assays to identify regions of DNA that are
A) free of associated proteins.
B) unable to undergo transcription.
C) unable to undergo replication.
D) of the Z-DNA form.
E) associated with DNA polymerase.
Answer: A

36) Which of the following would be suggested by a DNase hypersensitive site?

A) The chromatin is in an open state and available for transcription.
B) Transcription terminates at this site.
C) No transcription occurs in this region of the chromosome.
D) It indicates a region devoid of (lacking) genes.
E) The DNA is highly methylated.
Answer: A

37) Hypercondensation of heterochromatin results in

A) hyperactivation of transcription.
B) reduced cell size.
C) DNA replication.
D) suppression of progression through metaphase.
E) transcriptional silencing.
Answer: E

38) DNA regions that are transcriptionally silenced by hypercondensation have often undergone a
modification of their cytosine residues termed
A) methylation.
B) integration.
C) phosphorylation.
D) dephosphorylation.
E) hyperoxidation.
Answer: A

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39) In yeast, the SIR protein complex physically interacts with histones H3 and H4 to cause
A) basal transcription.
B) transcriptional activation.
C) transcriptional silencing.
D) mRNA folding.
E) initiation of replication.
Answer: C

40) ________ is used to describe a situation in which a gene's expression pattern is dependent upon the
parent from whom it was inherited.
A) Spermatogenesis
B) Gender-specific RNA stability
C) Heterodimerization
D) Homodimerization
E) Genomic imprinting
Answer: E

41) A variation that does not involve a change in DNA sequence but can be passed from one generation
to another is a(n)
A) mutant chromosome.
B) replication origin.
C) Mendelian enhancer.
D) epigenetic condition.
E) enhancer trap.
Answer: D

42) InDrosophila females, Sxl protein associates with RNA transcribed from the ________ gene,
altering its splicing pattern.
A) sxl B) myc C) max D) sax E) SIR
Answer: A

43) Which of the following is not involved in RNA interference processes?

A) Dicer
B) Drosha
C) pre-miRNA.
D) RNA polymerase I
E) RISC
Answer: D

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44) All
of the following are associated with the formation of a functional miRNA except
A) stem-loop structures.
B) RNA pol II promoter.
C) lack of an open reading frame (ORF).
D) translation on ribosomes.
E) 5' GTP cap and 3' poly A tail.
Answer: D

45) Which of the following is not a mechanism for posttranslational modification controlling gene
function?
A) ubiquitination
B) phosphorylation
C) dephosphorylation
D) methylation
E) covalent attachment of small molecules to protein
Answer: D

46) Recessive mutations in the sxl gene in Drosophila are lethal in XX females because
A) recessive mutations indicate an increase in sxl activity.
B) recessive mutations are always lethal.
C) sxl is required for transcription of male-specific genes.
D) sxl functions as a repressor of male-specific dosage-compensation genes.
E) these mutations are the result of a loss of both X chromosomes.
Answer: D

47) Which of the following is not true of the mouse agouti Avy allele?
A) it is responsible for phenotypic variation
B) it is metastable
C) it is caused by a retrotransposon
D) it is recessive to all other alleles
E) it is an epiallele
Answer: D

48) Which of the following is true in twin studies of imprinting and epigenetics?
A) Twin studies are not useful in methylation because environment overwhelms heritability in
epigenetics
B) CpG methylation patterns are more similar in dizygotic twins than in monozygotic twins
C) Dizygotic twins have identical CpG methylation patterns
D) Monozygotic twins have identical CpG methylation patterns
E) CpG methylation patterns are more similar in monozygotic twins than in dizygotic twins
Answer: E

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 49) Which of the following is not true of pri-miRNA?
A) It may contain introns.
B) It is a substrate for Drosha in animal cells.
C) It is exported from the nucleus.
D) It is transcribed by RNA polymerase II.
E) It contains stem-loop structures.
Answer: C

50) What would be the most likely result of transferring the UTR (untranslated region) from one gene to
another?
A) The rate of transcription may be decreased.
B) The posttranslational modification may change.
C) The half-life of the mRNA may change.
D) The ubiquitination of the protein may change.
E) The binding of transcription factors may change.
Answer: C

TRUE/FALSE. Write 'T' if the statement is true and 'F' if the statement is false.

51) RNA interference is a process that regulates gene expression at the time of transcription.
Answer: True False

52) Homodimers contain two identical polypeptides.

Answer: True False

53) T In genomic imprinting, the "silencer" is sex-specific methylation of certain DNA sequences called
imprinting control regions (ICRs).
Answer: True False

54) Alternative splicing can generate different proteins.

Answer: True False

55) miRNA can destabilize mRNAs.

Answer: True False

56) piRNAs can facilitate histone modifications that inhibit transposable element transcription.
Answer: True False

57) Sxl protein can trigger a cascade of splicing.

Answer: True False

58) A nucleosome is made of a ball of histone proteins (two each of H2A, H2B, H3 only).
Answer: True False

59) Genomic imprints are reset during mitosis.

Answer: True False

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60) Recessive Sxl mutations that produce nonfunctional gene products have no effects in XY males.
Answer: True False

61) Cis-acting elements are DNA sequences that serve as attachment sites for DNA-binding proteins
that regulate the initiation of transcription.
Answer: True False

62) Trans-acting elements are genes located somewhere other than at the target gene and encode
proteins that regulate another gene.
Answer: True False

63) RNA polymerase III transcribes all protein-encoding genes.

Answer: True False

64) Enhancers are regulatory sites that are next to the promoter.
Answer: True False

65) Basal transcription factors bind to the promoters of all protein-encoding genes.
Answer: True False

66) In repressor quenching, a repressor protein binds directly to an activator protein.

Answer: True False

67) Genomic imprinting is an example of epigenetic alteration of DNA.

Answer: True False

68) The Sxl protein triggers a cascade of splicing affecting other transcripts besides its own.
Answer: True False

69) RNA interference is a posttranscriptional process for modulating gene expression in prokaryotes.
Answer: True False

70) Geneexpression can be modulated posttranscriptionally through micro RNAs (miRNAs) in

eukaryotes.
Answer: True False

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ESSAY. Write your answer in the space provided or on a separate sheet of paper.

71) GeneA is maternally imprinted while Gene B is paternally imprinted. A mother with Genes A and
B imprinted and a father with an imprinted Gene A have a daughter and a son. The children then
marry individuals known not to be imprinted for either gene. What is the imprint status of the
daughter and son respectively? If each marriage results in the birth of a daughter and a son, what
would you expect the imprint status of genes A and B to be for the grandchildren?
Answer: The mother is imprinted for Genes A and B but passes on only an imprinted Gene A (to all her
children). The father is imprinted for Gene A, but since this is a maternally imprinted gene, he
does not pass any imprint to his children. Therefore, both their children inherit an imprinted
Gene A and a Gene B that is not imprinted. The children of the daughter will be the only
grandchildren with imprinting, and then only on Gene A. The grandchildren from the son are
not imprinted for either Gene A or B.

72) Allsomatic cells in an individual have the same genetic content. Yet different cell types have
different functions. What allows two cells with identical DNA content to function differently?
Answer: Although DNA content is identical, different genes are expressed in different cells.

73) Reporter constructsare used to identify and characterize DNA sequences that regulate the
expression levels of specific genes. What two DNA sequences are linked together to generate a
reporter construct?
Answer: Cis-acting regulatory sequences from the gene being studied and DNA sequence encoding the
reporter gene product.

74) What do the following two pedigrees illustrate?

Pedigree 1:

Pedigree 2:

Answer: Pedigree 1: paternal imprinting

Pedigree 2: maternal imprinting

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75) What's the role of activators in gene regulation?
Answer: 1. Activators help "recruit" the basal factors and pol II to core promoter sequences by interacting
directly with the components of this complex. This function is similar to that of most transcriptional
activators in bacteria. Positive regulators in bacteria like CRP stabilize the binding of RNA polymerase
to the promoter.
2. Activators recruit coactivators; these are proteins that open local chromatin structure to
allow gene transcription. Promoter DNA that is covered with nucleosomes is inaccessible to
basal factors. Thus, in order for a gene to be transcribed, the promoter DNA must be free of
nucleosomes.

76) Construct a diagram to illustrate how genomic imprints can reset during meiosis?
Answer:

77) Unlike prokaryotes, eukaryotes have three RNA polymerases. What are they and what does each do?
Answer: RNA polymerase I, II, and III are responsible for transcription of rRNA, mRNA and miRNA,
and tRNA and other small RNAs respectively.

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78) Each eukaryotic class II gene contains two kinds of essential DNA sequences. What are they?
Answer: All eukaryotic class II genes contain promoter and enhancer regions.

79) What is an enhanceosome?

Answer: The term enhanceosome is used to describe a multimeric complex of proteins and other small
molecules associated with an enhancer element.

80) How does chromatin structure regulate gene transcription?

Answer: Basic chromatin structure keeps eukaryotic transcription at a relatively low level. Remodelling
of chromatin can either completely silence or activate regional transcription. Hypercondensed
regions are silenced. Remodelling proteins can cause specific nucleosomes to unravel and
expose promoter regions in specific cells at specific times, which allows activation of some
genes.

81) Why is genomic imprinting considered an epigenetic alteration?

Answer: The methylation of CG dinucleotides within an imprinted region prevent RNA polymerase
from gaining access to the DNA and although the region is affected for the life of the
organism, the change is not encoded in the DNA and it is thus epigenetic, (outside the genes
but inherited).

82) Describe two modes of action by which RNA interference can modulate gene expression.
Answer: A perfect hybrid match between the miRNA and the target mRNA sequence results in cleavage of the
target mRNA and its rapid degradation by RNases.
A less than perfect match between the miRNA and the target mRNA sequence results in a lack of
cleavage by RISC. Subsequent attempts by ribosomes to translate the RISC-bound mRNA are blocked
by the RISC complex and translation is inhibited.

83) You are studying a brain region-specific mouse gene. You have cloned and sequenced the gene but
wish to identify the DNA sequences that direct the regional specificity. Describe an experimental
technique that would allow you to test this.
Answer: You could clone the upstream region, 5'UTR, introns and 3'UTR individually into reporter
constructs and make transgenic mice. The DNA segment responsible for the regulation of
regional expression would allow reporter gene transcription in the brain region of interest
while the other DNA sequences would not.

84) You have cloned and sequenced a new mouse gene and wish to know whether chromatin structure
may affect its transcription. You DNase treat and then run Southern analysis. In the mouse strain
with hypothetical phenotype A you detect your gene, but it is not detected in DNase treated samples
from the mouse strain with phenotype B. What do you suspect as the cause?
Answer: The detection of your gene on a Southern blot indicates that the genomic DNA for your gene
was protected by nucleosomes from DNase digestion and would therefore be inactive.
Conversely, when the gene is not detected on Southern analysis following DNase digestion,
the gene is not protected by chromatin structure and should therefore be active in vivo.

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Answer Key
Testname: UNTITLED11

1) B
2) D
3) E
4) B
5) C
6) E
7) B
8) B
9) D
10) D
11) D
12) B
13) D
14) D
15) E
16) B
17) D
18) E
19) A
20) A
21) D
22) B
23) E
24) B
25) E
26) D
27) E
28) B
29) D
30) B
31) A
32) C
33) A
34) D
35) A
36) A
37) E
38) A
39) C
40) E
41) D
42) A
43) D
44) D
45) D
46) D
47) D
48) E
49) C
50) C
15
Answer Key
Testname: UNTITLED11

51) FALSE
52) TRUE
53) TRUE
54) TRUE
55) TRUE
56) TRUE
57) TRUE
58) FALSE
59) FALSE
60) TRUE
61) TRUE
62) TRUE
63) FALSE
64) FALSE
65) TRUE
66) TRUE
67) TRUE
68) TRUE
69) FALSE
70) TRUE
71) The mother is imprinted for Genes A and B but passes on only an imprinted Gene A (to all her children).
The father is imprinted for Gene A, but since this is a maternally imprinted gene, he does not pass any
imprint to his children. Therefore, both their children inherit an imprinted Gene A and a Gene B that is not
imprinted. The children of the daughter will be the only grandchildren with imprinting, and then only on
Gene A. The grandchildren from the son are not imprinted for either Gene A or B.
72) Although DNA content is identical, different genes are expressed in different cells.
73) Cis-acting regulatory sequences from the gene being studied and DNA sequence encoding the reporter
gene product.
74) Pedigree 1: paternal imprinting
Pedigree 2: maternal imprinting
75) 1. Activators help "recruit" the basal factors and pol II to core promoter sequences by interacting directly with the
components of this complex. This function is similar to that of most transcriptional activators in bacteria. Positive
regulators in bacteria like CRP stabilize the binding of RNA polymerase to the promoter.
2. Activators recruit coactivators; these are proteins that open local chromatin structure to allow gene
transcription. Promoter DNA that is covered with nucleosomes is inaccessible to basal factors. Thus, in
order for a gene to be transcribed, the promoter DNA must be free of nucleosomes.

16
Answer Key
Testname: UNTITLED11

76)

77) RNA polymerase I, II, and III are responsible for transcription of rRNA, mRNA and miRNA, and tRNA
and other small RNAs respectively.
78) All eukaryotic class II genes contain promoter and enhancer regions.
79) The term enhanceosome is used to describe a multimeric complex of proteins and other small molecules
associated with an enhancer element.
80) Basic chromatin structure keeps eukaryotic transcription at a relatively low level. Remodelling of
chromatin can either completely silence or activate regional transcription. Hypercondensed regions are
silenced. Remodelling proteins can cause specific nucleosomes to unravel and expose promoter regions in
specific cells at specific times, which allows activation of some genes.
81) The methylation of CG dinucleotides within an imprinted region prevent RNA polymerase from gaining
access to the DNA and although the region is affected for the life of the organism, the change is not
encoded in the DNA and it is thus epigenetic, (outside the genes but inherited).

17
Answer Key
Testname: UNTITLED11

82) A perfect hybrid match between the miRNA and the target mRNA sequence results in cleavage of the target mRNA
and its rapid degradation by RNases.
A less than perfect match between the miRNA and the target mRNA sequence results in a lack of cleavage by RISC
Subsequent attempts by ribosomes to translate the RISC-bound mRNA are blocked by the RISC complex and
translation is inhibited.
83) You could clone the upstream region, 5'UTR, introns and 3'UTR individually into reporter constructs and
make transgenic mice. The DNA segment responsible for the regulation of regional expression would
allow reporter gene transcription in the brain region of interest while the other DNA sequences would not.
84) The detection of your gene on a Southern blot indicates that the genomic DNA for your gene was
protected by nucleosomes from DNase digestion and would therefore be inactive. Conversely, when the
gene is not detected on Southern analysis following DNase digestion, the gene is not protected by
chromatin structure and should therefore be active in vivo.

18