Chapter 28 Regulation of Gene Expression
Multiple Choice Questions
1. “Housekeeping genes” in bacteria are commonly expressed constitutively, but not all of these genes
are expressed at the same level (the same number of molecules per cell). The primary mechanism
responsible for variations in the level of constitutive enzymes from different genes is that:
A) all constitutive enzymes are synthesized at the same rate, but are not degraded equally.
B) their promoters have different affinities for RNA polymerase holoenzyme.
C) some constitutively expressed genes are more inducible than others.
D) some constitutively expressed genes are more repressible than others.
E) the same number of mRNA copies are made from each gene but are translated at different rates.
2. Which of the following statements correctly describes promoters in E. coli?
A) A promoter may be present on either side of a gene or in the middle of it.
B) All promoters have the same sequence that is recognized by RNA polymerase holoenzyme.
C) Every promoter has a different sequence, with little or no resemblance to other promoters.
D) Many promoters are similar and resemble a consensus sequence, which has the highest affinity
for RNA polymerase holoenzyme.
E) Promoters are not essential for gene transcription, but can increase its rate by two– to three-fold.
3. The operator region normally can be bound by:
A) attenuator.
B) inducer.
C) mRNA.
D) repressor.
E) suppressor tRNA.
4. Small signal molecules that regulate transcription are not known to:
A) cause activator proteins to bind DNA sites.
B) cause repressor proteins to bind DNA sites.
C) directly bind to DNA sites.
D) prevent activator proteins from binding to DNA sites.
E) release repressor proteins from DNA sites.
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5. The diagram below represents a hypothetical operon in the bacterium E. coli. The operon consists of
two structural genes (A and B), which code for the enzymes A-ase and B-ase, respectively, and also
includes P (promoter) and O (operator) regions as shown.
When a certain compound (X) is added to the growth medium of E. coli, the separate enzymes A-ase
and B-ase are both synthesized at a 50-fold higher rate than in the absence of X. (X has a molecular
weight of about 200.) Which of the following statements is true of the operon described above?
A) All four genes (A, B, O, and P) will be transcribed into an mRNA that will then be translated into
four different proteins.
B) The 3‘ end of the mRNA from the operon will correspond to the left end of the operon as drawn.
C) The 5‘ end of the messenger from this operon will correspond to the right end of the operon as
drawn.
D) The repressor for this operon binds just to the right of A.
E) When RNA polymerase makes mRNA from this operon, it begins RNA synthesis just to the left
of gene A.
6. The diagram below represents a hypothetical operon in the bacterium E. coli. The operon consists of
two structural genes (A and B) that code for the enzymes A-ase and B-ase, respectively, and also
includes P (promoter) and O (operator) regions as shown.
When a certain compound (X) is added to the growth medium of E. coli, the separate enzymes A-ase
and B-ase are both synthesized at a 50-fold higher rate than in the absence of X (which has a
molecular weight of about 200). Which one of the following statements is true of such an operon?
A) Adding X to the growth medium causes a repressor protein to be released from the O region.
B) Adding X to the growth medium causes a repressor protein to bind tightly to the O region.
C) Synthesis of the mRNA from this operon is not changed by the addition of compound X.
D) The mRNA copied from this operon will be covalently linked to a short piece of DNA at the 5‘
end.
E) Two mRNA molecules are made from this operon, one from gene A the other from gene B.
7. Transcription of the lactose operon in E. coli is stimulated by:
A) a mutation in the repressor gene that strengthens the affinity of the repressor for the operator.
B) a mutation in the repressor gene that weakens the affinity of the repressor for the operator.
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C) a mutation in the repressor gene that weakens the affinity of the repressor for the inducer.
D) binding of the repressor to the operator.
E) the presence of glucose in the growth medium.
8. Protein amino acid side chains can hydrogen bond in the major groove of DNA, and discriminate
between each of the four possible base pairs. In which one of the following groups of amino acids
can all three members potentially be used in such DNA-protein recognition?
A) Ala, Asn, Glu
B) Arg, Gln, Leu
C) Asn, Gln, Trp
D) Asn, Glu, Lys
E) Glu, Lys, Pro
9. Which of the following base pairs can form a hydrophobic interaction with a protein in the major
groove?
A) A – T
B) G – C
C) T – A
D) C – G
E) Both A and C above
10. Which of the following base pairs have a potential H-bond acceptor in both the major and minor
grooves?
A) A – T
B) G – C
C) T – A
D) C – G
E) All of the above
11. Which of the following base pairs have a potential H-bond donor in both the major and minor
grooves?
A) A – T
B) G – C
C) T – A
D) C – G
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E) All of the above
12. The DNA binding motif for many prokaryotic regulatory proteins, such as the lac repressor, is:
A) helix-turn-helix.
B) homeobox.
C) homeodomain.
D) leucine zipper.
E) zinc finger.
13. Protein structural motifs often have general functions in common. Which one of the following motifs
is known to be involved in protein dimer formation but not in direct protein-DNA interactions?
A)
-barrel
B) Helix-turn-helix
C) Homeodomain
D) Leucine zipper
E) Zinc finger
14. Which of the following statements about regulation of the lac operon is true?
A) Glucose in the growth medium decreases the inducibility by lactose.
B) Glucose in the growth medium does not affect the inducibility by lactose.
C) Glucose in the growth medium increases the inducibility by lactose.
D) Its expression is regulated mainly at the level of translation.
E) The lac operon is fully induced whenever lactose is present.
15. The binding of CRP (cAMP receptor protein of E. coli) to DNA in the lac operon:
A) assists RNA polymerase binding to the lac promoter.
B) is inhibited by a high level of cAMP.
C) occurs in the lac repressor region.
D) occurs only when glucose is present in the growth medium.
E) prevents the repressor from binding to the lac operator.
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16. Consider the lac operon of E. coli. When there is neither glucose nor lactose in the growth medium:
A) CRP protein binds to the lac operator.
B) CRP protein displaces the Lac repressor from the lac promoter.
C) the repressor is bound to the lac operator.
D) RNA polymerase binds the lac promoter and transcribes the lac operon.
E) the operon is fully induced.
17. A regulon is a(n):
A) group of related triplet codons.
B) network of operons with a common regulator.
C) operon that is subject to regulation.
D) protein that regulates gene expression.
E) ribosomal protein that regulates translation.
18. The tryptophan operon of E. coli is repressed by tryptophan added to the growth medium. The
tryptophan repressor probably:
A) binds to RNA polymerase when tryptophan is present.
B) binds to the trp operator in the absence of tryptophan.
C) binds to the trp operator in the presence of tryptophan.
D) is a DNA sequence.
E) is an attenuator.
19. Which one of the following statements about the transcription attenuation mechanism is true?
A) In some operons (e.g., the his operon), attenuation may be the only regulatory mechanism.
B) Sequences of the trp operon leader RNA resemble an operator.
C) The leader peptide acts by a mechanism that is similar to that of a repressor protein.
D) The leader peptide gene of the trp operon includes no Trp codons.
E) The leader peptide is an enzyme that catalyzes transcription attenuation.
20. Which of the following statements is true of the attenuation mechanism used to regulate the
tryptophan biosynthetic operon in E. coli?
A) Attenuation is the only mechanism used to regulate the trp operon.
B) One of the enzymes in the Trp biosynthetic pathway binds to the mRNA and blocks translation
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when tryptophan levels are high.
C) The leader peptide plays a direct role in causing RNA polymerase to attenuate transcription.
D) Trp codons in the leader peptide gene allow the system to respond to tryptophan levels in the cell.
E) When tryptophan levels are low, the trp operon transcripts are attenuated (halted) before the
operon’s structural genes are transcribed.
21. Attenuation in the trp operon of E. coli:
A) can adjust transcription of the structural genes upwards when tryptophan is present.
B) can fine-tune the transcription of the operon in response to small changes in Trp availability.
C) is a mechanism for inhibiting translation of existing (complete) trp mRNAs.
D) results from the binding of the Trp repressor to the operator.
E) results from the presence of short leader peptides at the 5‘ end of each structural gene.
22. By increasing the spacing between sequence 1 and sequence 2 in the leader peptide of the trp operon
of E. coli, attenuation compared to the normal sequence is:
A) unchanged.
B) increased.
C) always decreased.
D) only decreased in the absence of Trp.
E) Cannot be determined from the information given.
23. By mutating selected bases in sequence 3 in the leader peptide of the trp operon of E. coli, attenuation
compared to the normal sequence is:
A) unchanged.
B) only increased in the presence of Trp.
C) always increased.
D) decreased.
E) Cannot be determined from the information given.
24. RecA protein provides the functional link between DNA damage and the SOS response by displacing
the LexA protein from its operator sites on the SOS genes. RecA does so by:
A) associating with polymerase holoenzyme to help it remove LexA from operator.
B) bending LexA operator DNA to force dissociation of LexA repressor.
C) binding to LexA protein to weaken directly its affinity for operator sites.
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D) causing self-cleavage of LexA, thus inactivating its binding to operator.
E) competitively binding to LexA operators and serving as an activator.
25. An example of coordinate control is the down-regulation of ribosomal RNA synthesis in response to
amino acid starvation, which will cause synthesis of ribosomal proteins to be limited. What is the
correct order of the following events that participate in the signaling process?
1. Binding of stringent factor to the ribosome
2. Formation of the unusual nucleotide ppGpp
3. Formation of the unusual nucleotide pppGpp
4. Binding of uncharged tRNA in the ribosomal A-site
A) 1, 4, 2, 3
B) 1, 4, 3, 2
C) 4, 1, 2, 3
D) 4, 1, 3, 2
E) 4, 2, 1, 3
26. Which of the following is not true regarding the regulation of transcription in prokaryotes by RNA?
A) Small RNAs can disrupt local hairpins that prevent ribosome binding.
B) Small RNAs require a protein chaperone to facilitate RNA-RNA base pairing.
C) Riboswitches are often found in the 5-untranslated region of genes.
D) Each riboswitch can bind an assortment of small metabolites.
E) Riboswitches can affect either transcription of translation.
27. Which one of the following statements about eukaryotic gene regulation is correct?
A) Large polycistronic transcripts are common.
B) Most regulation is positive, involving activators rather than repressors.
C) Transcription and translation are mechanistically coupled.
D) Transcription does not involve promoters.
E) Transcription occurs without major changes in chromosomal organization.
28. Which one of the following statements about eukaryotic versus prokaryotic gene regulation is not
correct?
A) Access to eukaryotic promoters is restricted by the structure of chromatin.
B) Most regulation is positive, involving activators rather than repressors.
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C) Larger and more multimeric proteins are involved in regulation of eukaryotic transcription.
D) Transcription and translation are separated in both space and time.
E) Strong promoters in eukaryotes are generally fully active in the absence of regulatory proteins.
29. Which one of the following does not contribute to the activation of transcription in eurkaryotes?
A) SWI/SNF chromatin remodeling proteins
B) Histone acetyltransferases
C) Histone methylases
D) Histone deacetylases
E) Alterations in histone content
30. Which of the following is a DNA sequence?
A) Coactivator
B) Corepressor
C) Enhancer
D) Inducer
E) Transactivator
31. Which one of the following types of eukaryotic regulatory proteins interacts with enhancers?
A) Basal transcription factors
B) Coactivators
C) Repressors
D) TATA-binding proteins
E) Transactivators
32. Which one of the following does not interact with mediator?
A) TATA box
B) TATA binding protein
C) CTD of RNA polymerase
D) TFIIH
E) Modification and remodeling enzymes
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33. Which one of the following is not involved in steroid hormone action?
A) Cell surface receptors
B) Hormone-receptor complexes
C) Specific DNA sequences
D) Transcription activation and repression
E) Zinc fingers
34. Gene silencing by RNA interference acts by of the target gene.
A) inhibiting transcription
B) inhibiting translation
C) inhibiting splicing
D) degradation of the mRNA
E) inhibiting polyadenylyation
35. Which one of the following classes is expressed in the unfertilized egg and is involved in directing the
spatial organization of the Drosophila embryo early in development?
A) Gap genes
B) Homeotic genes
C) Maternal genes
D) Segment polarity genes
E) Segmentation genes
36. Which one of the following classes of genes is involved in specifying the localization of organs in the
Drosophila embryo?
A) Gap genes
B) Homeotic genes
C) Maternal genes
D) Segment polarity genes
E) Segmentation genes
37. In the development of the fly Drosophila, homeotic genes:
A) are transcribed during egg production; their mRNAs lie dormant in the egg until it is fertilized.
B) determine the number of body segments that will form.
C) are expressed late and determine the detailed structure of each body segment.
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D) generally have no introns.
E) are not translated into proteins.
38. Which of the following is false?
A) Unipotent cells can develop into only one type of cell or tissue.
B) Pluripotent cells can develop into a complete organism.
C) Multipotent bone marrow cells can develop into different types of blood cells.
D) Totipotent cells can develop into any kind of tissue.
E) Totipotent, unipotent, multipotent, and pluripotent are all types of stem cells.
Short Answer Questions
39. Usually, a mutation in the promoter region of an operon causes reduced levels of synthesis of the
proteins encoded by that operon. Occasionally, a mutation in the promoter region actually causes
increased levels of synthesis. Can you suggest a plausible explanation?
40. Describe and contrast positive regulation and negative regulation of gene expression.
41. Define operon and polycistronic mRNA.
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42. Match the molecule with its role in the lac operon. Note that a given molecule may have more than
one role.
Molecule Function
(a) Galactose (1) Substrate of
-galactosidase enzyme
(b) Glucose (2) Product of
-galactosidase enzyme
(c) IPTG (3) Inducer of lac operon
(d) Lactose
43. Match the protein or structural feature on the left with one appropriate description on the right.
____ Activator (a) A positive regulator
____ Helix-turn-helix (b) A negative regulator
____ Leucine zipper (c) Facilitates transcription only when bound to a signal
____ Repressor molecule
____ Zinc finger (d) A DNA-binding structural motif found in many
prokaryotic regulatory proteins
(e) A structural feature involved in protein-protein interactions
between some regulatory protein monomers
(f) A protein that dissociates from DNA when bound to a
signal molecule
(g) A DNA-binding structural motif found in many eukaryotic
regulatory proteins
44. E. coli cells are placed in a growth medium containing lactose. Indicate how the following
circumstances would affect the expression of the lactose operon (increase/decrease/no change).
(a) Addition of high levels of glucose
(b) A Lac repressor mutation that prevents dissociation of Lac repressor from the operator
(c) A mutation that inactivates
-galactosidase
(d) A mutation that inactivates galactoside permease
(e) A mutation that prevents binding of CRP to its binding site near the lac promoter
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Pages: 1159–1160, 1165–1166 Difficulty: 2
45. Draw a simple map of the lactose operon indicating the relative positions of promoter, operator, CRP–
binding site, repressor gene (I), and the structural genes of the operon (A, Y, Z). Indicate where the
CRP protein binds within this operon. When it is bound to this site, does the CRP protein have a
positive or negative effect on gene expression in this system?
46. Briefly explain (a) why there is a lag in cell growth when bacteria are switched from a medium
containing glucose to one containing lactose. (b) When the growth medium contains both lactose and
glucose, what proteins will be bound to the lac operon regulatory region? (c) If only lactose is in the
growth medium, what proteins will be bound to the lac operon regulatory region?
47. In prokaryotes such as E. coli, many operons that encode enzymes involved in amino acid
biosynthesis begin with a sequence coding for a leader peptide. This peptide has no known enzymatic
function and is rich in the amino acid that is synthesized by the enzymes coded for in the operon.
What is the function of this leader peptide?
48. The SOS response in E. coli is triggered by extensive damage to the cell’s DNA and increases the
capacity for repairing such DNA. What molecular events bring about expression of the SOS genes?
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49. Explain how synthesis of ribosomal proteins in E. coli is regulated at the level of translation.
50. Match each of the operons with the type(s) of regulation present in that operon. Note that a given
type can be used more than once, or not at all; also, a given operon may have more than one type of
regulation.
Operon Type or Regulation
(a) lac (1) Activation
(b) trp (2) Repression
(c) SOS (3) Attenuation
(4) DNA rearrangement
51. Describe three different mechanisms by which riboswitches can modulate mRNA.
52. Describe briefly the relationship between chromatin structure and transcription in eukaryotes.
53. Define each in one to two sentences: (a) heterochromatin; (b) euchromatin; (c) chromatin
remodeling.
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54. Describe in one or two sentences the role of each of the following types of proteins in the regulation
of gene expression in eukaryotes: (a) basal transcription factors; (b) transactivators; (c) coactivators.
55. DNA-binding transactivating proteins often possess a domain separate from their DNA-binding
domains that serves as a docking site for interactions with the transcription complex, coactivators,
corepressors, or even chromatin remodeling proteins, to regulate gene transcription. Describe three
known kinds of such domains, and provide an example of each.
56. Describe briefly the process by which steroid hormones affect gene expression.
57. What are three mechanisms of translational repression that are known to exist in eukaryotes?
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58. Large numbers of micro-RNAs (miRNAs), also known as small temporal RNAs (stRNAs), have now
been discovered in higher eukaryotes. Describe their characteristics and general function.
59. Describe briefly the general role of the protein products of each of the following types of genes in the
embryonic development of the Drosophila: (a) maternal genes; (b) segmentation genes; (c) homeotic
genes.
60. Name and contrast the four different types of stem cells found in humans.