Deck 28: Regulation of Gene Expression

Question 1

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

Answer 1

Both A and C above

Question 2

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.

Answer 2

In some operons (e.g. ,the his operon),attenuation may be the only regulatory mechanism.

Question 3

The operator region normally can be bound by:

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

Answer 3

repressor.

Question 4

"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 5

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 6

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 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 7

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.

Question 8

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.

Question 9

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 10

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 11

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 12

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.

Question 13

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.

Question 14

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 15

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
E)All of the above

Question 16

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

Question 17

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 18

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.

Question 19

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)( $\beta$ -barrel)
B)Helix-turn-helix
C)Homeodomain
D)Leucine zipper
E)Zinc finger

Question 20

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 21

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 22

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

Question 23

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.

Question 24

Define operon and polycistronic mRNA.

Question 25

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

Question 26

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

Question 27

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.

Question 28

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

Question 29

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

Question 30

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 31

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 32

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

Question 33

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

Question 34

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 35

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.
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 36

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.

Question 37

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.

Question 38

Which of the following is a DNA sequence?

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

Question 39

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

Question 40

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.

Question 41

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 42

Define each in one to two sentences:
(a)heterochromatin
(b)euchromatin
(c)chromatin remodeling.

Question 43

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.

Question 44

Explain how synthesis of ribosomal proteins in E.coli is regulated at the level of translation.

Question 46

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.

Question 47

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 48

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 49

Describe briefly the relationship between chromatin structure and transcription in eukaryotes.

Question 50

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 51

Name and contrast the four different types of stem cells found in humans.

Question 52

Describe three different mechanisms by which riboswitches can modulate mRNA.

Question 53

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 54

Describe briefly the process by which steroid hormones affect gene expression.

Question 55

What are three mechanisms of translational repression that are known to exist in eukaryotes?

Question 56

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.

Question 57

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.