Deck 28: Regulation of Gene Expression

Question 1

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.
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.

Answer 1

B

Question 2

Which statement 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.

Answer 2

A

Question 3

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.

Answer 3

C

Question 4

Which statement 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 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.

Question 5

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.

Question 6

Protein structural motifs often have general functions in common. Which motif is known to be involved in protein dimer formation but not in direct protein-DNA interactions?

A) $\beta$ barrel
B) helix-turn-helix
C) homeodomain
D) leucine zipper
E) zinc finger

Question 7

"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.

Question 8

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.

Question 9

Which base pair has a potential H-bond donor in both the major and minor grooves?

A) A-T
B) G-C
C) T-A
D) C-G
E) All of the answers are correct.

Question 10

Which statement 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.

Question 11

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.

Question 12

Which base pair has 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 answers are correct.

Question 13

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

Question 14

By increasing the spacing between sequence 1 and sequence 2 in the leader peptide of the trp operon of E. coli, attenuation compared with the normal sequence is:

A) unchanged.
B) increased.
C) always decreased.
D) only decreased in the absence of Trp.
E) It cannot be determined from the information given.

Question 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.

Question 16

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.

Question 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.

Question 18

Which base pair 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-T and T-A

Question 19

The operator region normally can be bound by:

A) attenuator.
B) inducer.
C) mRNA.
D) repressor.
E) suppressor tRNA.

Question 20

Which statement 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.

Question 21

Which term BEST describes the process of increasing mRNA production for a gene in response to a stimulus?

A) feedforward activation
B) transcriptional induction
C) feedback inhibition
D) attentuation
E) constitutive gene expression

Question 22

Which class 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

Question 23

Which statement 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.

Question 24

Which effect is NOT expected from changing the sequence in the -10 region of an E. coli promoter for a protein-coding gene?

A) decreased binding of $\sigma$ subunits
B) decreased transcription of the mRNA
C) decreased binding of ribosomes to the mRNA
D) lower concentrations of the protein product in the cell
E) All of these effects would be expected.

Question 25

Formation of the unusual nucleotide pppGpp

Question 26

Which statement 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.

Question 27

Which class 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

Question 28

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

Question 29

Which statement 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.
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.

Question 30

Which statement 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.

Question 31

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?

Question 32

Which factor 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

Question 33

Which type(s) of proteins do(es) NOT interact with mediator?

A) TATA box
B) TATA-binding protein
C) CTD of RNA polymerase
D) TFIIH
E) modification and remodeling enzymes

Question 34

Which method is NOT a way of regulating the concentration of a protein in a cell?

A) transcriptional regulation
B) translational regulation
C) degradation of proteins
D) posttranslational modification of proteins
E) All of these methods are ways of regulating protein concentrations.

Question 35

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.
D) causing self-cleavage of LexA, thus inactivating its binding to operator.
E) competitively binding to LexA operators and serving as an activator.

Question 36

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

Question 37

By mutating selected bases in sequence 3 in the leader peptide of the trp operon of E. coli, attenuation compared with the normal sequence is:

A) unchanged.
B) only increased in the presence of Trp.
C) always increased.
D) decreased.
E) It cannot be determined from the information given.

Question 38

_____ is a DNA sequence.

A) Coactivator
B) Corepressor
C) Enhancer
D) Inducer
E) Transactivator

Question 39

Which factor 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

Question 40

Which type of eukaryotic regulatory proteins interacts with enhancers?

A) basal transcription factors
B) coactivators
C) repressors
D) TATA-binding proteins
E) transactivators

Question 41

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.
D) generally have no introns.
E) are not translated into proteins.

Question 42

If binding of a small molecule to a regulatory protein lowers the K_d of the protein/operator binding interaction, what can reasonably be stated?

A) The small molecule activates transcription by decreasing inhibition by the protein.
B) The small molecule inhibits transcription by increasing inhibition by the protein.
C) The small molecule activates transcription by increasing activation by the protein.
D) The small molecule inhibits transcription by decreasing activation by the protein.
E) None of these statements is reasonable.

Question 43

The leader peptide below is from an E. coli biosynthetic operon. Which amino acid is MOST likely associated with this operon? MKRISTTITTTITITTGNGAG

A) tyrosine
B) threonine
C) glycine
D) tryptophan
E) None of the answers is correct.

Question 44

Allolactose binding to the I gene product in the regulation of the lac operon is an example of what?

A) transcriptional activation by reducing repressor binding
B) transcriptional inhibition by increasing repressor binding
C) transcriptional activation by increasing activator binding
D) transcriptional inhibition by decreasing activator binding
E) architectural regulation

Question 45

If an amino acid is part of a nonspecific DNA:protein interaction, with what parts of DNA is it likely to interact?

A) the major groove only
B) the minor groove only
C) the backbone only
D) both the backbone and the major groove
E) both the backbone and the minor groove

Question 46

Which statement does NOT describe a reason why the major groove is more suited for sequence specificity interactions by DNA binding proteins?

A) The methyl group of T residues is found in the major groove.
B) The major groove is larger, allowing more space for protein side chains.
C) The minor groove is negatively charged because of the crowding by phosphates.
D) Hydrogen bond donor and acceptor patterns are different in the major groove for different base pairs.
E) Two hydrogen bond acceptors exist for all base pairs in the minor groove.

Question 47

Which statement describes the role of the upstream promoter (UP) element in E. coli?

A) It increases transcription by binding to all $\sigma$ subunits.
B) It decreases transcription by binding to all $\sigma$ subunits.
C) It increases transcription by binding to a specific $\sigma$ subunit.
D) It increases transcription by binding to RNA polymerase.
E) It decreases transcription by inhibiting binding by RNA polymerase.

Question 48

What two kinds of regulation exist for the trp operon in E. coli?

A) negative regulation and transcription attenuation
B) negative regulation and positive regulation
C) positive regulation and transcription attenuation
D) negative regulation only
E) transcription attenuation only

Question 49

What two kinds of regulation exist for the lac operon in E. coli?

A) negative regulation and transcription attenuation
B) negative regulation and positive regulation
C) positive regulation and transcription attenuation
D) negative regulation only
E) transcription attenuation only

Question 50

What is the functional complex that leads to proteolysis of LexA?

A) RecA:dsDNA
B) LexA:dsDNA
C) RecA:ssDNA
D) LexA:ssDNA
E) LexA:RecA:ssDNA

Question 51

What is the functional complex that leads to proteolysis of LexA?

A) RecA:dsDNA
B) LexA:dsDNA
C) RecA:ssDNA
D) LexA:ssDNA
E) LexA:RecA:ssDNA

Question 52

What statement is NOT true regarding transcription attenuation of amino acid biosynthetic operons?

A) The leader peptide will contain multiple instances of the amino acid produced by the operon.
B) Transcription attenuation will always be accompanied by other positive or negative regulatory mechanisms.
C) Trancription will be reduced under conditions where concentration of the amino acid produced by the operon is high.
D) Synthesis of the leader peptide depends on the concentration of the aminoacylated tRNA, not the amino acid directly.
E) All of these statements are true.

Question 53

"All secondary structures formed in the trp operon attenuator can act as transcription terminators." Is this statement true or false, and if it is false, why is it false?

A) The statement is true.
B) It is false because domains 3 and 4 will act as an antiterminator.
C) It is false because domains 2 and 3 will act as a terminator.
D) It is false because domains 3 and 4 will act as a terminator.
E) It is false because domains 2 and 3 will act as an antiterminator.

Question 54

Allolactose is an important molecule in regulation of the lac operon. How does allolactose differ from lactose?

A) Lactose contains galactose and glucose, while allolactose contains two glucose units.
B) Lactose is a reducing sugar, while allolactose is not.
C) Lactose contains a $\beta$ -glycosidic bond, while allolactose contains an $\alpha$ -glycosidic bond.
D) Lactose contains a 1 $\rightarrow$ 4 glycosidic bonds, while allolactose contains a 1 $\rightarrow$ 6 glycosidic bond.
E) None of these statements describes differences between lactose and allolactose.

Question 55

Which statement does NOT explain why the lac operon would not be effectively regulated by an attenuation mechanism like the trp operon?

A) Lactose is a substrate for the lac operon protein products.
B) Products of lac operon enzymes are not used in protein synthesis.
C) Transcription and translation do not happen simultaneously for the lac operon.
D) Attenuation is a suitable regulatory mechanism for anabolic amino acid pathways.
E) All of these statements explain why regulation by attenuation would not be effective for the lac operon.

Question 56

Which noncovalent interaction is NOT a possible between cAMP and cAMP receptor protein (CRP)?

A) an ionic interaction between an arginine and the phosphate group
B) a serine donating a hydrogen bond to N7 of adenine
C) a threonine donating a hydrogen bond to the NH₂ substituent at position 6 of adenine
D) a serine donating a hydrogen bond to a phosphate oxygen
E) a backbone NH group donating a hydrogen bond to the 2´ OH

Question 57

Which statement is TRUE regarding the cAMP receptor protein (CRP)?

A) This protein is only involved in activating transcription of the lac operon.
B) A zinc finger structure binds to the DNA.
C) This protein binds as a tetramer to its DNA.
D) This protein distorts the DNA structure when it binds.
E) Binding of cAMP by CRP increases the value of K_d for the protein:DNA interaction.

Question 58

Which outcome will be TRUE when E. coli is grown in the absence of glucose?

A) The level of cyclic AMP will be low.
B) The CRP (cAMP receptor protein) cannot bind to its target DNA.
C) If lactose is present, synthesis of lac operon mRNA will occur at a high level.
D) A repressor is activated by cyclic AMP and will prevent the binding of RNA polymerase to the lac operon promoter.
E) None of the statements is true.

Question 59

LexA, a protein involved in the SOS response, can be described as both a:

A) negative regulator for transcription and a hydrolase.
B) positive regulator for transcription and a hydrolase.
C) negative regulator for transcription and an isomerase.
D) positive regulator for transcription and an isomerase.
E) None of the answers is correct.

Question 60

Promoters for heat shock proteins in E. coli differ from the general consensus sequence. What is the effect of this difference?

A) These genes are never transcribed at high levels.
B) These genes are always transcribed at high levels.
C) These genes are only expressed in high amounts when an appropriate $\sigma$ subunit is present.
D) These genes recognize multiple different $\sigma$ subunits.
E) These genes are always transcribed at high levels, and they also recognize multiple different $\sigma$ subunits.

Question 61

When tryptophan binds to the Trp repressor, what is the effect on the repressor:operator interaction?

A) The K_d for the repressor:operator complex increases, lowering affinity.
B) The K_d for the repressor:operator complex decreases, increasing affinity.
C) The K_d for the repressor:operator complex increases, increasing affinity.
D) The K_d for the repressor:operator complex decreases, lowering affinity.
E) There is no change in K_d.

Question 62

Which factor is NOT associated with translational regulation?

A) attenuation in the trp operon
B) ribosomal protein/mRNA interactions
C) riboswitches
D) Hfq/OxyS complexes
E) All of these are examples of translational regulation.

Question 63

Match the molecule with its role in the lac operon. Note that a given molecule may have more than one role.

Question 64

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?

Question 65

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?

Question 66

Which statement is FALSE regarding the mediator protein in eukaryotic gene regulation?

A)It contains multiple subunits.
B)It is involved in the formation of complexes with multiple additional proteins.
C)It forms protein:protein interactions with RNA polymerase II.
D)It enhances dephosphorylation of the RNA polymerase carboxy-terminal domain.
E)It is required for transcription of multiple different mRNA species.

Question 67

What is a role of the aptamer in riboswitches?

A) to form tertiary RNA structures in mRNA
B) to bind to small molecules
C) to inhibit the initiation of translation
D) to prevent ribosome binding to the Shine-Dalgarno sequence
E) All of the answers are correct.

Question 68

Which mechanism is NOT a way that galactose metabolism genes are regulated in concert in S. cerevisiae?

A)The promoters contain similar sequences.
B)Many of the mRNA transcripts are polycistronic.
C)Galactose serves as a coactivator for gene expression.
D)Upstream activation sequences are similar for the different genes.
E)All of these mechanisms are used to regulate these genes in concert.

Question 69

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

Question 70

What is the primary conclusion of "domain-swapping" experiments with transcriptional regulatory proteins?

A)Formation of homo- and hetero-dimers provide combinatorial control of gene expression.
B)Multiple protein:protein interactions are required to make transcription occur.
C)Enhancer elements are separate from the promoter site.
D)Zinc fingers are separate domains involved in DNA binding.
E)DNA binding elements and protein:protein interaction regions are often found in separate parts of a protein.

Question 71

What is NOT a common feature found in steroid hormone receptors?

A)a DNA-binding region
B)a transcription activation region
C)a hormone binding region
D)zinc finger motifs
E)
luecine zipper motifs

Question 72

What is the role of FljA in S. typhimurium?

A) It is a protein that is used to synthesize flagellin.
B) It is involved in promoting recombination of flagellin genes.
C) It is a protein that undergoes mutation in order to escape host immune response.
D) It is a transcriptional repressor.
E) None of the answers is correct.

Question 73

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?

Question 74

Describe and contrast positive regulation and negative regulation of gene expression.

Question 75

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?

Question 76

Define operon and polycistronic mRNA.

Question 77

GCN5 is a histone acetyltransferase from S. cerevisiae. Given this, what can reasonably be stated about GCN5?

A) GCN5 functions as a monomer in vivo.
B) GCN5 will convert euchromatin into heterochromatin.
C) GCN5 will reduce the positive charges on histone substrates.
D) GCN5 will have a single histone target.
E) GCN5 could be described as a histone chaperone.

Question 78

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?

Question 79

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 $\beta$ -galactosidase
(d) A mutation that inactivates galactoside permease
(e) A mutation that prevents binding of CRP to its binding site near the lac promoter

Question 80

What statement is FALSE regarding the molecule ppGpp?

A) This molecule is a bacterial second messenger.
B) This molecule is produced in response to low concentrations of amino acids.
C) This molecule acts as an inhibitor of RNA polymerase.
D) This molecule is produced directly from GTP and ATP.
E) This molecule will reduce the synthesis of rRNA.