Chapter 17—Gene Regulation in Eukaryotes
Fill in the Blank
1. ______________________ are encoded by DNA distant from the gene being regulated,
and often function as DNA-binding proteins.
Ans: Trans-acting factors (transcription factors)
Difficulty: 1
2. ______________________ are DNA sequences, often found near the 5' end of the
regulated gene, to which proteins bind, thus regulating the transcription of the gene.
Ans: Cis-acting elements
Difficulty: 1
3. Trans-acting factors that function to increase the level of expression of a gene are termed
___________________________.
Ans: transcriptional activators
Difficulty: 2
4. Trans-acting factors that function to decrease the level of expression of a gene are termed
___________________________.
Ans: transcriptional repressors
Difficulty: 2
5. The mechanism of transcriptional repression in which trans-acting repressor proteins bind
to an activator protein, thus preventing the activator from activating transcription is
termed __________________. Repressors that function using this mechanism mediate
their effect by binding to either the ________________________ domain or
_________________________ domain of the activator protein.
Ans: quenching, Transcriptional activation, DNA-binding
Difficulty: 3
6. A single strand of nucleotides that is complementary to an mRNA is termed a(n)
___________________ sequence.
Ans: antisense
Difficulty: 2
7. Numerator and denominator elements regulate sex-determination in Drosophila. If the
ratio of numerator homodimers to numerator/denominator heterodimers is high, the
________________ gene will be expressed, generating a fly with ___________________
sexual characteristics.
Ans: sxl, female
Difficulty: 3
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8. ______________________ is a small protein that is covalently attached to polypeptides
in long chains, targeting the tagged peptide for degradation. The large, multienzyme
complex that functions to degrade these tagged polypeptides is termed a
___________________.
Ans: ubiquitin, proteosome
Difficulty: 3
Multiple Choice
9.
A)
B)
C)
D)
E)
Transcription in prokaryotes and eukaryotes is similar in that:
transcriptional machinery controls compaction and decompaction of chromatin.
the mRNA produced can undergo alternative splicing.
both prokaryotic and eukaryotic proteins have identical affinities for DNA.
both are contained within the cell nucleus.
both are regulated by attachment of proteins to DNA adjacent to the gene being
transcribed.
Ans: E
Difficulty: 3
10.
A)
B)
C)
D)
E)
Most decisions controlling the amount of gene product synthesized are made during:
termination of replication.
transport of mRNA to the cytoplasm.
initiation of transcription.
alternative splicing.
regulation of translation.
Ans: C
Difficulty: 2
11.
A)
B)
C)
D)
E)
Zinc-finger peptide motifs are responsible for what aspect of protein function?
kinase activity
DNA binding
mRNA splicing
DNA replication
methylation
Ans: B
Difficulty: 2
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12. DNA sequences that serve as binding sites for proteins regulating transcription and are
often found adjacent to a gene are said to be:
A) cross-reacting.
B) cis-acting.
C) trans-acting.
D) origins of transcription.
E) transcription factors.
Ans: B
Difficulty: 2
13. The __________________________ is the cis-acting DNA sequence that serves as the
binding site for RNA polymerase.
A) promoter
B) terminator
C) enhancer
D) regulator
E) initiator
Ans: A
Difficulty: 1
14. ______________ are cis-acting DNA sequences that often function at a distance from the
gene they are regulating.
A) Promoter elements
B) Terminator elements
C) Enhancer elements
D) Regulator elements
E) Initiator elements
Ans: C
Difficulty: 2
15. A cis-acting DNA sequence that modulates the basal rate of transcription of a gene is
termed a(n):
A) repressor.
B) activator.
C) promoter.
D) enhancer.
E) initiator.
Ans: D
Difficulty: 2
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16. In generating a reporter construct to study gene regulation, the reporter gene introduced
replaces:
A) -galactosidase.
B) a random region of DNA.
C) the cis-acting regulatory DNA sequence.
D) X-gal.
E) the coding region of the gene being studied.
Ans: E
Difficulty: 3
17. Mutations altering the amount of protein synthesized from a reporter construct occur most
often in which of the following sequences of DNA?
A) The reporter gene.
B) Cis-acting DNA elements.
C) X-gal coding sequence.
D) RNA polymerase II gene.
E) none of the above
Ans: B
Difficulty: 3
18.
A)
B)
C)
D)
E)
Mutations introduced into reporter constructs are used to study:
the DNA sequences that are important for regulating gene expression levels.
the effects on cell function of expression of heterologous proteins.
colorimetric assays.
protein-protein interactions.
Western blots.
Ans: A
Difficulty: 2
19. The gene products encoded by trans-acting elements perform their function by:
A) associating with regulatory sequences distant from the gene from which they were
transcribed.
B) regulating the expression of the gene from which they were transcribed.
C) the association of nucleotides with the elongating RNA transcript.
D) physically associating with DNA polymerase.
E) regulating the activity of telomerase.
Ans: A
Difficulty: 2
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20.
A)
B)
C)
D)
E)
Trans-acting proteins that influence transcription are commonly referred to as:
DNA polymerases.
tumor suppressors.
enhancers.
transcription factors.
promoter elements.
Ans: D
Difficulty: 1
21.
A)
B)
C)
D)
E)
RNA polymerase I synthesizes _________ using a DNA template.
dsRNA
mRNA
tRNA
snRNA
rRNA
Ans: E
Difficulty: 2
22.
A)
B)
C)
D)
E)
The transcription and processing of rRNA molecules takes place in:
the cytoplasm.
Golgi bodies.
the nucleolus.
the nuclear envelope.
ribosomes.
Ans: C
Difficulty: 1
23.
A)
B)
C)
D)
E)
F)
tRNA molecules are transcribed by:
DNA pol I.
DNA pol II.
DNA pol III.
RNA pol I.
RNA pol II.
RNA pol III.
Ans: F
Difficulty: 2
24.
A)
B)
C)
D)
E)
The promoter of nearly all eukaryotic genes contains a(n):
RNA polymerase binding region.
TATA box.
initiation site.
b and c only
a, b and c
Ans: E
Difficulty: 2
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25.
A)
B)
C)
D)
E)
Which of the following is not true of enhancer DNA sequences?
They contain the TATA box regulatory element.
They retain function if their nucleotide sequence is inverted.
They can be more than 10 kilobases from the gene they regulate.
They may increase or decrease gene transcription levels.
They may contain multiple regulatory elements.
Ans: A
Difficulty: 3
26. A transcription factor that increases initiation of transcription by associating with an
enhancer element is termed a(n):
A) initiator.
B) activator.
C) repressor.
D) enhancer.
E) super-repressor.
Ans: B
Difficulty: 2
27.
A)
B)
C)
D)
E)
The primary function of basal transcription factors is to:
repress transcription initiation of a particular gene.
assist in associating RNA polymerase with the promoter element.
increase transcription by binding enhancer sequences.
activate RNA synthesis at origins of replication.
regulate activity of DNA polymerase II.
Ans: B
Difficulty: 2
28. _____________ are basal transcription factors that associate with TBP to assist in
initiating transcription from eukaryotic class II genes.
A) TATAs
B) DNA- BPs
C) TAFs
D) Jun and Fos
E) Sxl and string
Ans: C
Difficulty: 2
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29. _______________ motifs function to promote the DNA-binding activity of many
transcriptional activator proteins.
A) ABP
B) Zinc finger
C) Basolateral
D) Leucine zipper
E) Medial cleft
Ans: B
Difficulty: 2
30.
A)
B)
C)
D)
E)
Proteins that consist of two identical polypeptide subunits are classified as:
monomers.
oligomers.
heterodimers.
homodimers.
diplomers.
Ans: D
Difficulty: 2
31.
A)
B)
C)
D)
E)
The leucine zipper motif functions to:
mediate the physical association of two polypeptides.
anchor transcriptional activator proteins to enhancer sequences.
release leucines from misfolded transcription factors.
integrate leucines and isoleucines into newly translated transcriptional activators.
open up proteins after transcription.
Ans: A
Difficulty: 3
32. _________________ are transcription factors that decrease transcriptional activity by
associating with specific enhancer elements or activator proteins.
A) Deregulators
B) Depleters
C) Regulators
D) Repressors
E) TBPs
Ans: D
Difficulty: 2
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33. Which of the following is not a mechanism employed by repressor proteins to decrease
transcription of a specific gene?
A) The repressor associates with a promoter element, blocking RNA polymerase from
binding promoter element.
B) The repressor binds to the activation domain of an activator, eliminating its ability to
increase transcription.
C) The repressor binds to DNA-binding domain of an activator, eliminating its ability to
associate with enhancer.
D) The repressor binds to a DNA sequence in an enhancer, eliminating access to sequence by
activator.
E) The repressor binds to RNA polymerase II, blocking its ability to associate with promoter
element.
Ans: E
Difficulty: 4
34.
A)
B)
C)
D)
E)
The Myc transcription factor functions to increase transcription in specific cell types by:
associating with Ras to form heterodimers.
forming Myc-Myc homodimers.
associating with Max for form heterodimers.
dissociating with Fos-Jun heterodimers.
enhancing formation of Max-Max homodimers.
Ans: C
Difficulty: 3
35.
A)
B)
C)
D)
E)
The Myc protein is synthesized only in cells that are:
in G0.
virally infected.
proliferating.
cancerous.
dormant.
Ans: C
Difficulty: 3
36. Which of the following protein dimers are unable to associate with a DNA enhancer
element?
A) Jun/Jun
B) Fos/Jun
C) Max/Max
D) Myc/Myc
E) Myc/Max
Ans: D
Difficulty: 4
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37. Why do Max/Max homodimers convert to Myc/Max heterodimers in the presence of Myc
protein?
A) Myc has a higher affinity for Max than Max has for Max.
B) Myc more tightly associates with DNA, thus recruiting Max monomers to the enhancer.
C) The enhancer element being regulated only associates with Myc/Max heterodimers.
D) Max is rapidly degraded in the presence of Myc.
E) Myc/Myc homodimers are rapidly degraded in the presence of Max.
Ans: A
Difficulty: 4
38. 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) promoter element.
C) enhancer element.
D) transcriptional activator.
E) RNA polymerase.
Ans: A
Difficulty: 4
39. A(n) _____________________ is a cis-acting DNA sequence that functions to regulate a
cluster of two or more related genes.
A) TBP
B) promoter element
C) transcriptional activator
D) derepressor
E) locus control region
Ans: E
Difficulty: 2
40. A locus control region (LCR) associated with its complete transcription factor complex is
referred to as a(n):
A) transcriptosome.
B) regulosome.
C) nucleosome.
D) enhanceosome.
E) spliceosome.
Ans: D
Difficulty: 2
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41. Eukaryotic cells are able to carefully regulate precise levels of transcription in specific
genes encoding structural proteins through:
A) complex enhancer elements that can associate with multiple activator and repressor
proteins.
B) production of different types of RNA polymerase.
C) regulation of the expression of many different transcription factors.
D) a and c
E) a, b, and c
Ans: D
Difficulty: 3
42. The ________________ is the repeating structural unit of chromatin, consisting of
approximately 200 base pairs of DNA and associated histone proteins.
A) transcriptosome
B) regulosome
C) nucleosome
D) enhanceosome
E) spliceosome
Ans: C
Difficulty: 1
43.
A)
B)
C)
D)
E)
The association of DNA with histones to form chromatin affects transcription by:
increasing basal transcription rates.
decreasing basal transcription rates.
increasing transcription of a few genes, while not influencing most others.
decreasing transcription of a few genes, while not influencing most others.
increasing transcription of some genes and decreasing transcription of others.
Ans: B
Difficulty: 2
44.
A)
B)
C)
D)
E)
Regions of DNA are most sensitive to DNAase digestion when:
they are free of histones.
they are maintained as chromatin.
the nuclei in which they are contained enter prophase.
a cell is in G0.
found at a recombination hotspot.
Ans: A
Difficulty: 2
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45.
A)
B)
C)
D)
E)
The DNAase enzyme can be used in assays to identify regions of DNA that are:
unable to undergo transcription.
associated with DNA polymerase.
unable to undergo replication.
of the Z-DNA form.
free of associated proteins.
Ans: E
Difficulty: 3
46.
A)
B)
C)
D)
E)
Hypercondensation of heterochromatin results in:
hyperactivation of transcription.
suppression of progression through metaphase.
DNA replication.
transcriptional silencing.
none of the above
Ans: D
Difficulty: 2
47. DNA regions that are transcriptionally silenced by hypercondensation have often
undergone a modification of their cytosine residues termed:
A) hyperoxidation.
B) methylation.
C) dephosphorylation.
D) phosphorylation.
E) integration.
Ans: B
Difficulty: 2
48.
A)
B)
C)
D)
E)
In yeast, the SIR protein complex physically interacts with histones H3 and H4 to cause:
mRNA folding.
transcriptional silencing.
transcriptional activation.
basal transcription.
initiation of replication.
Ans: B
Difficulty: 3
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49. _______________ is used to describe a situation in which a gene's expression pattern is
dependent upon the parent from which is was inherited.
A) Genomic imprinting
B) Spermatogenesis
C) Heterodimerization
D) Homodimerization
E) Gender-specific RNA stability
Ans: A
Difficulty: 2
50. A variation that does not involve a change in DNA sequence but can be passed from one
generation to another is a(n):
A) enhancer trap.
B) replication origin.
C) Mendelian enhancer.
D) mutant chromosome.
E) epigenetic condition.
Ans: E
Difficulty: 3
51. In Drosophila females, Sxl protein associates with RNA transcribed from the
________________ gene, altering its splicing pattern.
A) sax
B) max
C) sxl
D) myc
E) SIR
Ans: C
Difficulty: 4
52.
A)
B)
C)
D)
E)
Loss of the poly-A tail associated with eukaryotic mRNAs results in:
rapid translation of the transcript.
elongation of the transcript.
decreased translation initiation on the transcript.
rapid degradation of the transcript.
the addition of a new polyA sequence to the transcript.
Ans: D
Difficulty: 2
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53.
A)
B)
C)
D)
E)
The half-life of an mRNA transcript can be increased by:
increasing RNA polymerase activity.
decreasing the rate at which the transcript is synthesized.
increasing the length of the polyA tail on the transcript.
decreasing RNA polymerase activity.
increasing the translation rate on the transcript.
Ans: C
Difficulty: 3
54. A change in nucleotide sequence that occurs after transcription and RNA splicing is
termed:
A) mRNA polishing.
B) post-translational modification.
C) methylation.
D) mRNA editing.
E) polymerase mutagenesis.
Ans: D
Difficulty: 2
55. Which of the following is not a mechanism for post-translational modification controlling
gene function?
A) ubiquitination
B) methylation
C) phosphorylation
D) dephosphorylation
E) all are post-translational modifications
Ans: B
Difficulty: 4
56.
A)
B)
C)
D)
E)
Recessive mutations in the sxl gene in Drosophila are lethal in XX females because:
sxl functions as a repressor of a male-specific dosage of compensation genes.
recessive mutations indicate an increase in sxl activity.
these mutations are the result of a loss of both X chromosomes.
sxl is required for transcription of male-specific genes.
recessive mutations are always lethal.
Ans: A
Difficulty: 3
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57. ___________________ are short sequences of DNA of a predetermined sequence that are
synthesized in vitro.
A) Northern blots
B) cDNAs
C) Exotranscripts
D) Ribonucleases
E) Oligonucleotides
Ans: E
Difficulty: 2
58. Which of the following is not a difficulty encountered by molecular biologist attempting
to develop oligonucleotide therapies from treatment of cancer?
A) The oligonucleotides are much larger than antibodies and proteins.
B) Oligonucleotides of differing lengths are effective against different genes.
C) Short oligonucleotides are often complementary to more than one gene.
D) Oligonucleotides may adversely affect critical internal organs.
E) Oligonucleotides have decreasing specificity as the number of nucleotides they contain
decreases.
Ans: A
Difficulty: 4
Matching
In the problem below, match each of the enzymes with the protein function
a. Synthesizes tRNAs and other small RNA molecules.
b. Post-translationally modifies proteins by phosphorylating specific amino acids.
c. Digests DNA molecules.
d. Digests RNA in DNA/RNA hybrid molecules.
e. Generates RNA molecules that become functional components of ribosomes.
f. Modifies cytosines in CG dinucleotides, often resulting in transcriptional silencing.
g. Generates long ribonucleotide sequences composed only of adenines for attachment to 3' ends
of many mRNAs.
h. Synthesizes RNA molecules that encode polypeptide sequences.
59. Ribonuclease H
Ans: d
Difficulty: 2
60. Poly-A polymerase
Ans: g
Difficulty: 2
61. Kinase
Ans: b
Difficulty: 2
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62. RNA polymerase I
Ans: e
Difficulty: 1
63. RNA polymerase II
Ans: h
Difficulty: 1
64. RNA polymerase III
Ans: a
Difficulty: 1
65. DNAase
Ans: c
Difficulty: 2
66. Methylase
Ans: f
Difficulty: 3
Match each of the proteins with the correct protein function
a. Becomes covalently bound to specific proteins, thus targeting those proteins for destruction.
b. Binds to specific enhancer elements to control mating type in yeast.
c. Functions in association with other proteins to control gene expression by regulating chromatin
structure.
d. Forms homodimers that bind specific enhancers to repress transcription in terminally
differentiated cells.
e. Activates transcription of galactose metabolizing genes in yeast.
f. Assists in binding of RNA polymerase II to promoter elements.
g. Marker protein that fluoresces green when exposed to specific wavelengths of light.
h. Represses expression of yeast galactose metabolizing genes by quenching a transcriptional
activator protein.
67. Gal4
Ans: e
Difficulty: 3
68. TBP
Ans: f
Difficulty: 2
69. Ubiquitin
Ans: a
Difficulty: 2
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70. 2 repressor
Ans: b
Difficulty: 3
71. GFP
Ans: g
Difficulty: 1
72. Max
Ans: d
Difficulty: 3
73. Gal80
Ans: h
Difficulty: 3
74. SWI
Ans: c
Difficulty: 4
True or False
75. cis-acting elements are DNA sequences that serve as attachment sites for DNA-binding
proteins that regulate the initiation of transcription.
Ans: True
Difficulty: 1
76. Trans-acting elements are genes located somewhere other than at the target gene and
encode proteins that regulate another gene.
Ans: True
Difficulty: 1
77. RNA polymerase III transcribes all protein-encoding genes.
Ans: False
Difficulty: 2
78. Enhancers are regulatory sites that are next to the promoter.
Ans: False
Difficulty: 2
79. Basal transcription factors bind to the promoters of all protein-encoding genes.
Ans: True
Difficulty: 1
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80. In repressor quenching, a repressor protein binds directly to an activator protein.
Ans: True
Difficulty: 1
81. The max gene is expressed at all times.
Ans: True
Difficulty: 1
82. A locus control region acts in cis at a long distance.
Ans: True
Difficulty: 1
83. One function of chromatin is to increase transcription to a high basal level.
Ans: False
Difficulty: 2
84. Genomic imprinting is an example of epigenetic alteration of DNA.
Ans: True
Difficulty: 1
Short Answer
85. All somatic 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?
Ans: Although DNA content is identical, different genes are expressed in different cells.
Difficulty: 2
86. Reporter constructs are 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?
Ans: Cis-acting regulatory sequences from the gene being studied, and DNA sequence
encoding the reporter gene product.
Difficulty: 3
87. Unlike prokaryotes, eukaryotes have three RNA polymerases. What are they and what
does each do?
Ans: RNA polymerase I, II, and III are responsible for transcription of rRNA, mRNA,
and tRNA and other small RNAs respectively.
Difficulty: 2
88. Each eukaryotic class II gene contains two kinds of essential DNA sequences. What are
they?
Ans: All eukaryotic class II genes contain promoter and enhancer regions.
Difficulty: 3
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89. What is an enhancesome?
Ans: The term enhancesome is used to describe a multimeric complex of proteins and
other small molecules associated with an enhancer element.
Difficulty: 3
90. How does a Locus Control Region regulate a cluster of genes?
Ans: Like an enhancer, the LCR functions by binding to transcription factors with
activation domains. Unlike most enhancers, however, the LCR-transcription factor
complex interacts sequentially with other transcriptions factors at cis-regulatory
regions that are directly adjacent to each gene in the cluster.
Difficulty: 4
91. How does chromatin structure regulate gene transcription?
Ans: Basic chromatin structure keeps eukaryotic transcription at a relatively low level.
Remodeling of chromatin can either completely silence or activate regional
transcription. Hypercondensed regions are silenced. Remodeling proteins can
cause specific nucleosomes to unravel and expose promoter regions in specific cells
at specific times, which allows activation of some genes.
Difficulty: 3
92. Why is genomic imprinting considered an epigenetic alteration?
Ans: 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).
Difficulty: 4
Experimental Design and Interpretation of Data
93. 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.
Ans: 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.
Difficulty: 4
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94. Describe the results you would expect on Northern and Western analyses if a hypothetical
gene was up-regulated at the transcriptional level in response to the presence of zinc.
How would your results differ if zinc acted to reduce the turn-over of the protein?
Ans: In the presence of zinc, Northern analysis would show more mRNA (a darker band)
for the gene in comparison to controls without zinc. Western analysis should also
detect more protein present in the presence of zinc if no other regulation changes
occurred. In the latter case where zinc was known to effect protein turnover, there
should be no difference in band intensity between control and zinc treated sample
on the Northern blot but an increase in protein detected on the Western blot.
Difficulty: 3
95. You have cloned and sequenced a new mouse gene and wish to know whether chromatin
structure may effect 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?
Ans: 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.
Difficulty: 4
96. Gene A is maternally imprinted while Gene B is paternally imprinted. A Mom with
Genes A and B imprinted and a Dad 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
for the grandchildren.
Ans: Mom is imprinted for Gene A and B but only passes on an imprinted Gene A (to all
her children). The Dad is imprinted for Gene A but since this is a maternally
imprinted gene, he does not pass any imprint to his children. Therefore, all four
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 grandsons are not imprinted for either Gene A or B.
Difficulty: 4
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