Chapter 16—Gene Regulation in Prokaryotes
Fill in the Blank
1. The names of the two individuals winning the Nobel Prize for discovering the lac
operon were __________________ and ___________________.
Ans: Jacob, Monod
Difficulty: 1
2. Mutations in either of two sites will produce a constitutive phenotype. These two sites
are ____________ or ______________.
Ans: Repressor, Operator
Difficulty: 2
3. The process by which a specific molecule stimulates the synthesis of a given protein is
called _________________.
Ans: Induction
Difficulty: 1
4. A regulator that physically blocks the DNA binding site of RNA polymerase is called a
_______________ regulator.
Ans: Negative
Difficulty: 1
5. A genetic unit that consists of several genes coding for proteins, an operator (o) and a
promoter (p) is termed an _____________.
Ans: operon
Difficulty: 1
6. Walter Gilbert purified the lac repressor and showed that it actually has two sites for
binding. These two distinct binding sites are _________________ and
___________________.
Ans: Lactose binding, DNA binding
Difficulty: 2
7. A protein coding gene whose expression in the cell can be quantifiable by sensitive and
reliable techniques of protein detection and therefore used to determine the specific
conditions that induce the expression of any other gene is called a
_________________________.
Ans: reporter gene
Difficulty: 3
8. Cascades of ___________ factors allow for the global regulation of multiple gene sets.
Ans: sigma
Difficulty: 3
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9. The most critical step in the regulation of most bacterial genes is the binding of
_______________________ to the _____________________.
Ans: RNA polymerase, promoter
Difficulty: 2
10. Jacob and Monod found that most of the Lac- mutations they obtained could be mapped
into two genes, ____________and _____________.
Ans: lac Z, lac Y
Difficulty: 1
11. Proteins such as the lac repressor that undergo reversible changes in conformation
(shape) when bound to other molecules are called _____________ proteins.
Ans: allosteric
Difficulty: 3
12. The process by which glucose, even in the presence of lactose, will repress the lac
operon is called _________________ repression.
Ans: catabolite
Difficulty: 2
13. Regulation of the lac operon depends on at least two proteins: ________________, a
negative regulator, and _____________, a positive regulator.
Ans: repressor, CAP
Difficulty: 2
14. The so-called LacI repressor family of proteins has a common DNA binding motif
called a ________________________ motif.
Ans: helix turn helix
Difficulty: 1
15. The presence of _______________ of the enzymes in a catabolic process that breaks
down complex substances into smaller units usually regulates transcription of the genes
for the enzymes.
Ans: substrate
Difficulty: 1
16. The presence of the _______________ usually regulates anabolic pathways that build or
synthesize more complex molecules.
Ans: end product
Difficulty: 1
17. The __________ subunit of RNA polymerase is necessary for initiation of transcription
at a promoter, but is not necessary for elongation.
Ans: sigma
Difficulty: 2
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18. Molecules responsible for stimulating the synthesis of a specific protein, are called
______________.
Ans: inducers
Difficulty: 1
19. The actual site of binding of RNA polymerase in order to initiate transcription is
________________.
Ans: promoter
Difficulty: 1
20. The term that describes the end product of a biosynthetic pathway in its role in
regulation of transcription of the genes is __________________.
Ans: corepressor
Difficulty: 1
Multiple Choice
21.
A)
B)
C)
D)
What would be the phenotype of a mutation that altered lac promoter function?
constitutive
inducible
permanently repressed
none of the above
Ans: A
Difficulty: 2
22.
A)
B)
C)
D)
A common DNA structural feature involved in gene regulatory systems is:
supercoiling of DNA.
looping of the DNA.
unwinding of the double helix.
coiling into Z-DNA.
Ans: B
Difficulty: 1
23. How do negative regulators such as the lac repressor prevent RNA polymerase from
initiating transcription?
A) By blocking passage of the polymerase through the operator.
B) By forming a loop in the operator that restricts the passage of the polymerase.
C) By physically blocking the DNA binding site of RNA polymerase.
D) By binding to the polymerase thus preventing its binding.
Ans: C
Difficulty: 3
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24.
A)
B)
C)
D)
How do positive regulators stimulate initiation of transcription by RNA polymerase?
By allowing passage of the polymerase through the operator.
By binding to the polymerase and increase its ability to initiate transcription.
By causing the helix to unwind in the operator allowing easier initiation.
By making the transcription start site more exposed to the polymerase.
Ans: B
Difficulty: 2
25. Catabolic pathways that break down complex substances into more usable units are
usually regulated by the:
A) end products of the pathway.
B) substrate of an enzyme in the pathway.
C) other metabolites that are limiting.
D) none of the above
Ans: B
Difficulty: 1
26. Anabolic pathways involved in the synthesis of essential molecules are usually
regulated by:
A) end product of the pathway.
B) substrate of the pathway.
C) other metabolites that are limiting.
D) none of the above
Ans: A
Difficulty: 1
27. Which statement is true regarding global gene regulation in bacteria?
A) Sigma factors are not involved in gene regulation, just attachment of the polymerase to
the promoter.
B) Alternative sigma factors recognizing different promoters carry out global gene
regulation.
C) E. coli cells devote more energy to the production of ribosomes during stress so that
global gene regulation can occur.
D) All promoters are recognized by all sigma factors.
Ans: B
Difficulty: 3
28. In the genotype presented below, what will the expression phenotype for galactosidase be (I+p+ocZ-Y-A+/I+p+o+Z-Y+A-)?
A) inductive
B) consitiutive
C) absent
D) lethal
Ans: B
Difficulty: 2
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29. In the genotype presented below, what will the expression phenotype for -galactoside
permease be (I+p+ocZ-Y-A+/I+p+o+Z-Y+A-)?
A) constitutive
B) inductive
C) absent
D) lethal
Ans: B
Difficulty: 2
30. In the genotype presented below, what will the expression phenotype for thiogalactoside
transacetylase be (I+p+ocZ-Y-A+/I+p+o+Z-Y+A-)?
A) constitutive
B) inductive
C) absent
D) lethal
Ans: A
Difficulty: 2
31. Why is glucose involved in the catabolite repression of the lactose operon?
A) It has nothing to do with regulation of the lactose operon.
B) It is produced by the enzymatic breakdown of lactose, its presence thereby signifying
the presence of lactose in the cell.
C) It is also a substrate for -galactosidase.
D) Its presence in the cell increases the amount of lac represor in the cell.
Ans: B
Difficulty: 4
32. A common amino acid motif found in many of the polypeptides that function as
repressors is:
A) Leucine zipper motif.
B) Zinc finger motif.
C) Helix turn helix motif.
D) Helix loop helix motif.
Ans: C
Difficulty: 1
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33. How does tryptophan, the end product of the trp operon, function in the regulation of
the operon?
A) It binds to the repressor preventing it from binding to DNA thus allowing transcription
of the operon.
B) It binds to the repressor and only then can the repressor bind to DNA allowing
transcription of the operon.
C) It binds directly to DNA and inhibits transcription of the operon.
D) It binds to the repressor and only then can this complex bind to DNA preventing
transcription of the operon.
Ans: D
Difficulty: 2
34. What term describes a second level of regulation of the trp operon that occurs in TrpRmutants suggesting that it is repressor independent?
A) modulation
B) derepression
C) attenuation
D) amplification
Ans: C
Difficulty: 2
35. In E. coli, the heat shock response, switching off the synthesis of some proteins and
switching on of different proteins, is mediated by:
A) inactivation of certain repressor proteins by elevated temperature.
B) denaturing of DNA in the promoters in the genes of heat sensitive proteins.
C) synthesis of alternative sigma factors at high temperatures, which then regulate
transcription of heat shock genes.
D) increasing the promoter affinity of already existing polymerase sigma factors at high
temperatures.
Ans: C
Difficulty: 2
36. How are complex processes such as sporulation, synthesis of flagella, and nitrogen
fixation that require the transcription of multiple sets of genes regulated in bacteria?
A) Multiple operons are simultaneously induced.
B) Cascades of sigma factors synthesized in a temporal order, allow the turning on of
successive sets of genes.
C) The end product of one operon is used as an inducer of the next operon in sequence.
D) There are single operons consisting of many genes for each of these processes.
Ans: B
Difficulty: 3
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37. How does phage T7 differentially control the transcription of its “early” and “late”
genes?
A) It has two RNA polymerases, each specific for either early or late genes.
B) The early and late genes have promoters that specify their timing of transcription.
C) The phage uses the E. coli polymerase to transcribe the early genes, and its own
polymerase to transcribe the late genes.
D) Products of the early genes are actually the inducers of the late genes.
Ans: C
Difficulty: 2
38.
A)
B)
C)
D)
As a general principle of gene regulation through operons regulatory genes encode:
trans-acting proteins that interact with cis-acting DNA elements.
cis-acting proteins that interact with cis-acting DNA elements.
cis-acting proteins that interact with trans-acting DNA elements.
trans-acting proteins that interact with trans-acting DNA elements.
Ans: A
Difficulty: 2
39. In the trp operon, attenuation occurs through the recognition of two Trp codons in the
leader sequence. What would happen if these two codons were mutated to stop codons?
A) This operon will be insensitive to attenuation by tryptophan.
B) The structural genes will be transcribed in the presence or absence of tryptophan.
C) The tryptophan biosynthetic enzymes will be synthesized.
D) None of these results will take place.
E) All of these results will take place.
Ans: E
Difficulty: 4
40. Which partial diploid strain will produce -galactosidase constitutively, and maintain
normal induction of the permease and transacetylase?
A) I+ocZ+Y-A-/I+o+Z-Y+A+
B) I+o+Z+Y+A+/I+o+Z-Y+A+
C) I+ocZ-Y+A+/I+ocZ-Y+A+
D) I+ocZ+Y+A+/I+ocZ-Y+A+
Ans: A
Difficulty: 4
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41. Initiation of transcription by RNA polymerase involved the binding of which of the
following subunits to the core enzyme?
A) delta
B) sigma
C) gamma
D) alpha
E) zeta
Ans: B
Difficulty: 2
42.
A)
B)
C)
D)
E)
The transition from transcriptional initiation to elongation involves:
binding of sigma factor
release of sigma factor
release of RNA polymerase from DNA
binding of RNA polymerase to DNA
binding of rho factor
Ans: B
Difficulty: 2
43. Proteins that undergo reversible changes in conformation when bound to another
molecule are called:
A) reversible peptides
B) allosteric proteins
C) inducer proteins
D) repressor proteins
E) allostatic proteins
Ans: B
Difficulty: 3
44. A single DNA unit that enables the simultaneous regulation of more than one gene in
response to environmental changes is called:
A) promoter
B) operator
C) regulator
D) inducer
E) operon
Ans: E
Difficulty: 2
45.
A)
B)
C)
DNA sites can act:
only in cis
only in trans
either in trans or in cis
Ans: A
Difficulty: 2
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46.
A)
B)
C)
D)
E)
The scientists who proposed the operon theory were:
Monod and Jacob
Watson and Crick
Hardy and Weinberg
Darwin and Mendel
Hershey and Chase
Ans: A
Difficulty: 1
47. A philosophic rule that states, “The simplest, most economical explanation is preferable
to a more complex one.” is:
A) Monod and Jacob's rule
B) Watson and Crick's rule
C) Occam's razor
D) operon theory
Ans: C
Difficulty: 3
48.
A)
B)
C)
D)
E)
A reporter gene is:
a protein encoding gene whose expression is easily quantifiable.
often fused to another protein to access its activity.
often fused to another genes' regulatory region to determine control.
all of the above.
none of the above.
Ans: B
Difficulty: 2
49.
A)
B)
C)
D)
E)
The sigma factor that mediates a global heat shock response in E. coli is:
sigma 70
sigma 32
sigma 34
sigma 72
sigma 36
Ans: B
Difficulty: 1
50.
A)
B)
C)
D)
E)
In the regulation of the trp operon, tryptophan acts as a:
repressor
attenuator
activator
corepressor
operator
Ans: D
Difficulty: 3
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Matching
Match the following terms with the best definition
a) inducer
b) repressor
c) in trans
d) in cis
e) 70
f) 24
g) 32
h) microarray
i) rho factor
j) promoter
51. ______ the action of a DNA region that affects the activity of genes on the same
chromosome.
Ans: d
Difficulty: 2
52. ______ an effector molecule that causes the cell to produce larger amounts of the
enzymes involved in its metabolism.
Ans: a
Difficulty: 1
53. ______ normal housekeeping sigma factor.
Ans: e
Difficulty: 1
54. ______ the action of a DNA element that encodes a diffusible product that can influence
the activity of other genes.
Ans: c
Difficulty: 2
55. ______ an alternative sigma factor that mediates the global response to heat shock.
Ans: g
Difficulty: 2
56. ______ a region on a DNA molecule to which RNA polymerase binds and initiates
transcription.
Ans: j
Difficulty: 1
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57. ______ an oligomeric protein that attaches to certain DNA sites in order to assist in
termination of transcription.
Ans: i
Difficulty: 3
58. ______ a protein that binds to an operator locus and blocks transcription of that operon.
Ans: b
Difficulty: 1
59. ______ a technique that can measure relative changes in transcription between two
samples.
Ans: h
Difficulty: 2
60. ______ an alternative sigma factor always present.
Ans: f
Difficulty: 2
True or False
61. Because there is no nuclear membrane in prokaryotes, transcription and translation from
a single gene can be taking place at the same.
Ans: True
Difficulty: 1
62. Negative regulation of gene expression usually takes place through enhancement of
RNA polymerase activity.
Ans: False
Difficulty: 1
63. Positive regulators actually physically bind to RNA polymerase and enhance the
enzyme's ability to initiate transcription.
Ans: True
Difficulty: 1
64. The concept that proteins bind to DNA and regulate transcription holds true for both
positive as well as negative regulation of gene expression.
Ans: True
Difficulty: 1
65. Attenuation of gene expression is unique to prokaryotes, because it requires translation
of a leader sequence at the same time transcription is taking place.
Ans: True
Difficulty: 1
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66. A chaperone protein is used to aid in the transport of other proteins across cellular
membranes.
Ans: False
Difficulty: 2
67. Bacteriophage T7 promotors are recognized by both E. coli RNA polymerase as well as
T7- specific RNA polymerase.
Ans: True
Difficulty: 3
68. An underlying principle of prokaryotic gene regulation is that it occurs through the
binding of regulatory proteins to specific DNA sequences.
Ans: True
Difficulty: 1
69. There is only one site on the operator to which the lac repressor binds.
Ans: False
Difficulty: 2
70. In the trp operon, the protein repressor alone cannot bind to the operator to be a negative
regulator.
Ans: True
Difficulty: 1
71. The mechanisms of gene regulation discovered in E. coli are not found in most other
prokaryotes.
Ans: False
Difficulty: 2
72. In prokaryotes, the primary point of gene regulation occurs by either blocking or
enhancing transcription.
Ans: True
Difficulty: 1
73. The occurrence of constitutive mutations of all three of the lactose utilizing enzymes
indicates that their synthesis is regulated together, probably by another gene.
Ans: True
Difficulty: 1
74. Many of the DNA sequences to which negative or positive regulatory proteins bind have
the same sequence on both strands of DNA reading in the 5'-3' direction.
Ans: False
Difficulty: 2
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75. In the operon model of gene regulation, transcription is shut off by the binding of the
repressor to the promoter.
Ans: False
Difficulty: 1
76. Both inducers and corepressors lead to allostearic alterations in the repressor molecule.
Ans: True
Difficulty: 2
77. The presence of a diffusable gene product (protein) is a requirement for genes to act in
trans.
Ans: True
Difficulty: 3
78. A distinguishing feature of control of gene expression in prokaryotes is that
transcription and translation occur completely independently of each other.
Ans: False
Difficulty: 2
79. Attenuation of the trp operon requires the presence of tryptophanyl-tRNAtrp.
Ans: True
Difficulty: 3
80. In a repressible operon, the repressor alone can bind to the operator and shut down
transcription.
Ans: False
Difficulty: 2
Short Answer
81. Describe the conditions for maximum induction of the lactose operon.
Ans: This would be in a medium containing lactose, but lacking glucose. Under these
conditions, the repressor binds inducer and becomes unable to bind to the
operator, while CAP complexed with cAMP binds to a site near the promoter to
assist RNA polymerase in the initiation of transcription.
Difficulty: 3
82. Describe the two binding domains on the lac repressor protein.
Ans: The repressor has two distinct binding domains, one for the operator and one for
the inducer.
Difficulty: 2
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83. Why is the lactose operon not induced in the presence of both lactose and glucose?
Ans: Glucose acts in catabolite repression of the operon, even in the presence of
lactose.
Difficulty: 3
84. Describe the molecular subunit structure of the lac repressor, and explain what enables
it to bind to the operator.
Ans: The lac repressor protein is a tetramer of four LacI-encoded subunits, with each
subunit containing an inducer-binding domain as well as a domain that recognizes
and binds to DNA at the operator. Binding of the repressor to two sites in the
operator simultaneously, causes a loop in the DNA of the operator to form, thus
restricting binding of polymerase to the operator.
Difficulty: 4
85. What is the unique feature about the base sequence of the lac operator to which the lac
repressor binds?
Ans: The lac repressor binds to a region of the operator with rotational symmetry, that
is a similarity of sequence on the two strands when read in the 5'-3' directions,
similar to a palindrome but not a perfect palindrome.
Difficulty: 3
86. In the example of the lac operon, and most operons, what is the significance of a
polycistronic message?
Ans: This allows the coordinate expression of several functionally related genes.
Difficulty: 2
87. Briefly describe the three classes of genes which must be sequentially induced in
Rhizobium in order to bring about a functioning nitrogen-fixing nodule in a leguminous
plant.
Ans: nod genes that elicit the early steps of nodule formation, fix genes that contribute
to the development and metabolism of bacteroids, and are essential to nitrogen
fixation, and nif genes that encode the polypeptide subunits of the nitrogenase
complex.
Difficulty: 2
88. Distinguish between positive and negative regulation of transcription.
Ans: Negative regulation involves the inhibition of RNA polymerase activity by
physically blocking the DNA binding site of RNA polymerase, and positive
regulation involves the enhancement of RNA polymerase activity by establishing
a contact with RNA polymerase that enhances the enzyme's ability to initiate
transcription.
Difficulty: 2
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89. Explain how three enzymes appear simultaneously when lactose is introduced into a
bacterial culture medium as the sole carbon source.
Ans: These three enzymes are translated from a continuous polycistrontic message
transcribed from all three genes.
Difficulty: 2
90. How does the operator function in the regulation of an operon?
Ans: Binding of the repressor to the operator site, blocks the promoter. Specifically,
binding of the repressor to the operator keeps RNA polymerase from recognizing
the promoter.
Difficulty: 2
91. Explain how the CAP protein functions as a positive regulator of the lac operon.
Ans: A small nucleotide known as cAMP binds to a protein called cAMP activator
protein or CAP. The binding of cAMP to CAP enables CAP to bind to DNA in
the regulatory region of the lac operator, and this DNA binding of CAP increass
the ability of RNA polymerase to transcribe lac genes.
Difficulty: 3
92. What are the two roles glucose plays in lac gene transcription?
Ans: Glucose functions to reduce the level of cAMP, and also inhibits the cellular
uptake of lactose.
Difficulty: 2
93. What is the role of the  subunit of RNA polymerase in transcription?
Ans: The sigma subunit binds to RNA polymerase allowing it to bind to specific DNA
sequences at the promoter.
Difficulty: 2
94. What are the three enzymes in the lactose operon and what is their enzymatic function?
Ans: -galactosidase splits lactose into glucose and galactose, -galactoside permease
transports lactose in the medium into the E. coli cell and transacetylase that adds
an acetyl group to lactose and other  galactosides.
Difficulty: 1
95. Explain the terms, trans acting, and cis acting elements.
Ans: Elements that act in trans can diffuse through the cytoplasm and act at target DNA
sites on any DNA molecule in the cell. Elements that act in cis can only influence
the expression of adjacent genes on the same DNA molecule.
Difficulty: 2
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Experimental Design and Interpretation of Data
96. Will the production of normal -galactosidase be constitutive, inductive, or absent for
each of the following genotypes: (A) I+p+o+Z +Y +A +, (B) I-p+o+Z +Y+A +, (C) I+p+ocZY+A +, (D) I+p+o+Z -Y +A+.
Ans: (A) inductive, (B) constitutive, (C) absent, (D) absent.
Difficulty: 2
97. Explain how the presence or absence of the amino acid tryptophan attenuates the
transcription of the genes in the trp operon.
Ans: This addresses attenuation or control of gene expression by premature termination
of transcription. There are about 140 bases upstream from the first trp gene. This
is called a leader sequence. There is a short open reading frame in the leader
containing 14 codons, two of which code for trp. When tryptophan is present, the
ribosome moves quickly past the trp codons and proceeds to the end of the
leader's codons, allowing formation of the stem-loop 3-4 structure which causes
the termination of transcription and thereby attenuation of trp-gene expression. In
the absence of tryptophan, the ribosome stalls at the two trp codons in the RNA
leader and a 2-3 stem-loop forms which prevents the formation of the 3-4 stemloop allowing transcription to proceed through the leader into the structural genes.
Difficulty: 4
98. What would be the phenotype of a mutation in the CAP protein gene and why?
Ans: A mutation in the CAP protein would probably be a low-level inducible
phenotype, due to the fact that the CAP-cAMP complex would not function as a
positive regulator assisting the Polymerase in initiation of transcription.
Difficulty: 3
99. More than 20 different DNA-binding proteins in bacteria are similar to the LacI
repressor, creating the LacI repressor family of proteins. Why do they all not bind at the
lac operator, and repress the lac operon?
Ans: Each of the LacI repressor proteins recognizes a slightly different operator DNA
sequence, thus allowing them to only act on specific genes.
Difficulty: 2
100. What was the advantage to Jacob and Monod by selecting lactose utilization in E. coli in
order to discover the operon concept in gene regulation?
Ans: The advantage of this lactose utilization system in E. coli allows the ability to
grow very large populations of bacteria in order to isolate rare mutants.
Difficulty: 2
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