Deck 29: Transcription and the Regulation of Gene Expression

Question 1

All are stages in transcription EXCEPT:

A) binding of RNA polymerase holoenzyme at the promoter sites.
B) chain elongation.
C) DNase I activity on RNA polymerase/DNA complex.
D) initiation of polymerization.
E) chain termination.

Answer 1

C

Question 2

Operons are a(n) ____ sequence lying adjacent to the DNA being transcribed and are composed of a promoter located next to a(n) ____ that interacts and is controlled by a(n) ____ protein.

A) initiation; operator; repression
B) operator; repressor; regulatory
C) regulatory; repressor; activator
D) regulatory; operator; regulatory
E) none are true

Answer 2

D

Question 3

The stand of dsDNA that is read by RNA polymerase is termed the ____ strand with RNA polymerase moving ____ along it. The polymerase forms a ____, growing in the ____ direction.

A) template; 5'→3'; transcript; 3'→5'
B) template; 3'→5'; transcript; 5'→3'
C) transcript; 3'→5'; template; 5'→3'
D) nontemplate; 5'→3'; template; 3'→5'
E) nontemplate; 3'→5'; template; 5'→3'

Answer 3

B

Question 4

Both prokaryotes and differentiated eukaryotic cells express ____ of their genes at any given time in the process called ____.

A) a small number; transcription
B) a small number; translation
C) a large number; transcription
D) all; translation
E) all; transcription

Question 5

The ____ strand has the same nucleotide sequence and direction as that of the RNA transcript, with the ____ end of mRNA encoding the N-terminus of the protein.

A) template; 3'
B) template; 5'
C) nontemplate; 3'
D) nontemplate; 5'
E) lagging; 5'

Question 6

Transcription chain elongation is thought to generate ____ supercoils ahead of the transcription bubble and _____ supercoils behind it.

A) positive; negative
B) negative; positive
C) negative; negative
D) positive; positive
E) none of the above

Question 7

Nucleotides in the "plus" direction are said to lie ____ the transcription start site.

A) downstrand of
B) upstream of
C) downstream of
D) upstrand of
E) positive to

Question 8

All are true for the prokaryotic promoter for the rrn gene in E. coli EXCEPT that it:

A) encodes for rRNA.
B) has a −10 region Pribnow box.
C) has a −35 region consensus sequence.
D) has an upstream (UP) element at −55.
E) all are true.

Question 9

In bacteria, single polycistronic mRNA encodes for:

A) a single enzyme although there are many in the metabolic pathway.
B) multiple enzymes of the particular pathway.
C) a single mRNA which is split into multiple mRNAs before translation.
D) a single peptide with multiple catabolic sites.
E) none of the above.

Question 10

The base in DNA that specifies the first base in the RNA transcript is called a(n) ____ and is numbered ____.

A) promoter; −5
B) enhancer; −35
C) transcription start site; 0
D) transcription start site; +1
E) promoter complex; +5

Question 11

The subunit in E. coli RNA polymerase which is required for recognition of the promoter sequence is:

A) ρ (rho).
B) α (alpha).
C) β (beta).
D) β′ (beta prime).
E) σ (sigma).

Question 12

One of the termination mechanisms in bacteria utilizes the ____ factor that is an ATP-dependent helicase.

A) α (alpha)
B) β (beta)
C) γ (gamma)
D) ε (delta)
E) ρ (rho)

Question 13

Treatment of the RNA polymerase/DNA complex with DNase in vitro is a DNA footprinting technique used to:

A) identify the termination sequence for transcription.
B) locate the start site for transcription.
C) locate the promoter site.
D) identify the position of enhancer sequences.
E) none of the above.

Question 14

Intrinsic RNA chain termination is determined by specific sequences in the DNA called ____ sites.

A) termination
B) rho binding
C) template binding
D) supercoil
E) all are true

Question 15

In order for transcription to begin, the DNA-duplex must be "opened" to allow RNA polymerase access to single stranded template. All facilitate "opening" of DNA-duplex EXCEPT:

A) low melting temperature, T_m, in the Pribnow box.
B) A:T rich DNA duplex.
C) negative supercoiling.
D) binding of RNA polymerase σ-subunit.
E) all are true.

Question 16

All are factors or subunits contained within the E. coli RNA polymerase holoenzyme in prokaryotic organisms EXCEPT:

A) ρ (rho).
B) α (alpha).
C) β (beta).
D) β′ (beta prime).
E) σ (sigma).

Question 17

Within the ____ are two consensus sequence elements, the ____ near −10 with a sequence of TATAAT, and the ____ containing the consensus TTGACA.

A) termination sequence; rho subunit; sigma sub
B) termination sequence; Pribnow box; sigma subunit unit
C) promoter sequence; rho subunit; Pribnow box
D) promoter sequence; Pribnow box; −35 region
E) promoter sequence; rho subunit; −35 region

Question 18

The initiation site binds a ____ nucleotide base pairing with the ____ base exposed within the ____ promoter complex, and then the second base is added to the ____ of the first base.

A) pyrimidine; −1; closed; 3'-O
B) pyrimidine; +1; closed; 5'-O
C) purine; +2; closed; 3'-O
D) purine; −1; open; 5'-O
E) purine; +1; open; 3'-O

Question 19

Nucleotide sequences that identify the location of transcription start sites and regulate the level of transcription are called:

A) sigma factors.
B) Pribnow boxes.
C) TATA boxes.
D) promoters.
E) enhancers.

Question 20

Characteristics of rho (ρ) factor include all EXCEPT that it:

A) recognizes and binds C-rich regions of RNA transcripts.
B) binding regions must be ribosome free.
C) advances in the 5'→3' direction to the transcription bubble.
D) unwinds transcript and template to free nascent RNA.
E) all are true.

Question 21

All are correct about enhancer sequences in eukaryotic cells EXCEPT:

A) they can occur either upstream or downstream of the gene.
B) they can be in either orientation (bi-directional).
C) enhancer function is dependent on recognition by a specific transcription factor.
D) specific transcription factor binding at an enhancer stimulates transcription by interacting with RNA polymerase II.
E) all are correct.

Question 22

The eukaryotic transcription factor that exhibits a sequence specificity for the TATA box is:

A) TFIIB.
B) TFIIC.
C) TFIID/TBP.
D) RNA polymerase II.
E) TFIIH.

Question 23

The DNA-binding proteins that recognize and accurately initiate transcription at specific eukaryotic promoter sequences are called:

A) Enhancers.
B) transcription factors.
C) response elements.
D) chromatin-remodeling complexes.
E) all are true.

Question 24

RNA polymerase II:

A) is located in the nucleolus and transcribes the major ribosomal RNA genes.
B) is located in the nucleoplasm and transcribes the protein-encoding genes through mRNAs.
C) transcribes the 5S RNA genes.
D) transcribes RNA genes associated with tRNA processing.
E) transcribes tRNA genes and protein transport genes.

Question 25

Which of the following is not a component of the araBAD operon?

A) araA, encodes L-arabinose isomerase
B) araK, encodes L-arabinose kinase
C) araD, encodes ribulose-5-phosphate epimerase
D) araC, encodes a regulatory protein that acts as both a repressor and activator
E) araI, the promoter for the operon

Question 26

The heptapeptide repeat in the carboxy terminal domain (CTD) in the RPB1 subunit of RNA polymerase II is phosphorylated to ____.

A) convert to an elongation complex
B) bind to DNA
C) form a holo-RNA polymerase II
D) initiate transcription
E) activate termination

Question 27

Which of the following is true of TATA boxes?

A) they are found within the core sequence of a gene regulatory sequence
B) they are found downstream of the gene being transcribed
C) they represent an area of DNA more easily opened than other areas
D) a and c are true
E) a, b, and c are true

Question 28

Which of the following is true of the lac operon?

A) it is negatively controlled via the lac repressor, a protein that only binds to DNA in the absence of lactose
B) it is positively controlled via CAP, a protein that is activated by binding to ATP
C) lactose represses the lac operon but this repression can be removed by addition of IPTG
D) binding of lactose (or an analog of lactose) increases the affinity of the lac repressor for DNA
E) none of the above

Question 29

All are true for transcription activation EXCEPT:

A) takes place when a transcriptional activator protein bound to DNA makes protein : protein contacts with RNA polymerase.
B) the degree of transcriptional activation is proportional to the strength of the protein : protein interaction.
C) a nucleotide sequence binding site for a DNA-binding protein serves as an activator site if DNA-binding protein can interact with promoter-bound RNA polymerase.
D) if the DNA-bound transcriptional activator makes contact with two different components of RNA polymerase, the transcription is markedly elevated.
E) all are true.

Question 30

Transcription in eukaryotic cells which is resistant to α-amanitin is carried out by RNA polymerase:

A) I only.
B) II only.
C) III only.
D) I and III.
E) I, II and III.

Question 31

All are characteristics of catabolic activator protein (CAP) EXCEPT:

A) ensures that the operons necessary for metabolism for alternate energy sources remains repressed until the supply of glucose is exhausted.
B) overrides the influence of any inducer that might be present.
C) cAMP enhances CAP's affinity for DNA.
D) N-terminal end binds cAMP and C-terminal end binds DNA.
E) all are true.

Question 32

All may be RNA polymerase II promoter constituents EXCEPT:

A) the core element where general transcription factors (GTFs) bind.
B) where enhancers bind transcriptional activators.
C) where silencers bind repressors.
D) a TATA box indicating the transcription start site.
E) all can be constituents.

Question 33

All are lac repressor properties EXCEPT:

A) tetrameric protein expressed constitutively.
B) binding site for DNA.
C) binding site for mRNA.
D) binding site for inducer.
E) blocks elongation so initiation is aborted.

Question 34

Heat shock element (HSE) is a(n) ____ found in the ____ region of genes whose transcription is activated in response to ____.

A) silencer; enhancer; cold
B) response element; promoter; elevated temperature
C) promoter; enhancer; elevated temperature
D) enhancer; response element; elevated temperature
E) silencer; promoter; cold

Question 35

When the cellular level of tryptophan decreases in E. coli:

A) tryptophan-bound Trp repressor associates with trp operator.
B) Trp aporepressor has lowered affinity for trp promoter allowing RNA. polymerase binding and transcription of the trp operon.
C) tryptophan binds trp inducer to promote positive control of trp promoter.
D) trp repressor has a greater affinity for trp operator.
E) none of the above.

Question 36

In prokaryotes, gene expression is often responsive to small molecules where increasing synthesis of enzymes for metabolism of a certain substrate is termed ____ and the substrate is called ____. Likewise metabolic products that decrease synthesis of enzymes for their production are called ____ and carry out ____.

A) autoregulation; regulatory; co-repressors; initiation
B) co-induction; induction; co-repressors; initiation
C) induction; co-inducer; co-repressors; repression
D) induction; co-inducer; repressor; co-repression
E) all are true

Question 37

All of the following are control mechanisms that regulate transcription in prokaryotes EXCEPT:

A) protein : protein interactions
B) DNA : protein interactions
C) RNA : protein interactions
D) a and b
E) a, b, and c

Question 38

Expression of genes independently of regulation is termed:

A) negative regulation.
B) constitutive expression.
C) transcription expression.
D) repressible regulation.
E) autoregulation.

Question 39

The metallothionein gene promoter consists of all EXCEPT:

A) TATA box.
B) GC box.
C) glucocorticoids response element (GRE).
D) heat shock element (HSE).
E) all are true.

Question 40

All are components of the lac operon EXCEPT:

A) the structural genes for lacZ, lacY and lacA.
B) the operator and promoter sequences.
C) lacI gene.
D) promoter for the lacI gene.
E) all are correct.

Question 41

During RNA chain elongation, ____ proceeds ahead of the transcription bubble introducing _____ supercoils

A) gyrase; negative
B) gyrase; positive
C) topoisomerase; negative
D) topoisomerase; positive
E) none of the above

Question 42

The recurring structural feature in DNA-binding proteins is the presence of ____ segments that fit into the ____ grove of B-DNA.

A) α-helix; major
B) β-sheet; major
C) β-turn; minor
D) β-barrel; minor
E) all are true

Question 43

Huge multi-subunit entities that mediate ATP-dependent conformational changes that peel 50bp of DNA from the edge of nucleosome core particles and create a "bulge" in the DNA:core nucleosomes association are called:

A) histone deacetylase complexes (HDACs).
B) DNA-bound transcriptional activators.
C) chromatin-remodeling complexes .
D) general transcriptional factors (GTFs).
E) all are true.

Question 44

Which of the following is required for RNA splicing to occur?

A) a free 5´ hydroxyl created by hydrolysis of the phosphate ester bond
B) a cyclic phospodiester at the 3´ end of the RNA molecule
C) a 2´ hydroxyl group
D) the enzyme splicase
E) none of the above

Question 45

Transcription of a typical gene encoding a polypeptide in eukaryotes involves all of the following EXCEPT:

A) the splicing together of a number of exons in the DNA prior to transcription.
B) synthesis by RNA polymerase II.
C) transcription of DNA corresponding to both introns and exons.
D) transcription of the DNA which encodes the N-terminal of the polypeptide prior to DNA encoding to the C-terminal.
E) addition of the poly(A)⁺ tail.

Question 46

The structural motif found in a number of transcriptional factors which is not a DNA-binding domain, but rather is associated with protein-protein interactions is:

A) a leucine zipper.
B) a zinc finger.
C) a helix-turn-helix.
D) an enhancer element.
E) all of the above.

Question 47

Most eukaryotic RNA consists of coding regions, called ____, and noncoding regions, called ____.

A) introns; exons
B) exons; introns
C) spliceons; codons
D) codons; spliceons
E) introns; codons

Question 48

Enzymes that acetylate the ε-amino group of lysine in the histidine tails are called ____ and are involved in ____.

A) histone deacetylases; restoring chromatin to a repressed state
B) histone acetyltransferases (HATs); initial events in transcriptional activation
C) histone activases; formation of the de-repression complex
D) Schiff base formation; promoting the formation of closed complexes
E) none of the above

Question 49

The production of multiple transcripts from a single gene includes all EXCEPT:

A) constitutive splicing.
B) use of different promoters.
C) selection of different polyadenylation sites.
D) alternative splicing of the primary transcript.
E) all are true.

Question 50

Lac repressor is an example of the DNA-binding motif common to many prokaryotic regulatory proteins and is:

A) a homeobox.
B) a zinc finger.
C) a basic region-leucine finger.
D) a helix-turn-helix.
E) none of the above.

Question 51

The initial event in the conversion of an hnRNA to the mature RNA which leaves the nucleus is:

A) formation of ribonucleoprotein particles (RNPs).
B) capping the 5'-end of the transcript with a guanylyl group by guanylyl transferase.
C) addition of a poly(A) tail to the 3'-end of the transcript by poly(A) polymerase.
D) splicing together of the exons.
E) transesterification reactions in lariat formation.

Question 52

Which is/are true of protein isoforms?

A) they are related polypeptides
B) they have identical structure and function
C) they are the result of different transcripts of a single gene
D) a and c
E) a, b, and c

Question 53

The leucine zipper is a protein motif held together by:

A) H-bonds.
B) hydrophobic interactions.
C) ionic interactions.
D) metal ion binding.
E) protein:DNA interactions.

Question 54

All are components of the basic rule of macromolecular recognition EXCEPT:

A) protein recognizes nucleotide sequences by atomic contacts with bases and sugar-phosphate backbone usually in the major groove.
B) protein contacts involve H-bonds and salt bridges with electronegative oxygens of the phosphodiester linkages.
C) proteins present a three-dimensional shape or contour structurally and chemically complementary to the surface of the DNA sequence.
D) numerous atomic interactions underlie recognition and binding.
E) all are components.

Question 55

During RNA chain elongation, ____ follows behind the transcription bubble removing _____ supercoils

A) gyrase; negative
B) gyrase; positive
C) topoisomerase; negative
D) topoisomerase; positive
E) none of the above

Question 56

All are true for homeobox domains EXCEPT:

A) typically comprise about 90% of the protein mass.
B) found in virtually every eukaryote.
C) act as sequence-specific transcriptional factors.
D) contain helix-turn-helix motifs.
E) all are true.

Question 57

Spliceosomes include all of the following EXCEPT:

A) snRNPs.
B) RNA-annealing proteins.
C) ATP-dependent RNA-unwinding proteins.
D) enzymes catalyzing transesterification of phosphoesters.
E) all are components.

Question 58

All are true for translation in eukaryotic cells EXCEPT:

A) transcription and translation are spatially separated.
B) mRNAs are monocistronic.
C) transcription occurs in the nucleus.
D) primary transcripts undergo processing to mature mRNAs.
E) all are true.

Question 59

The base-pair edges in the ____ groove act as a(n) ____ identifiable through ____ with specific proteins.

A) minor; enhancer; H-bonding
B) minor; recognition matrix; H-bonding
C) major; recognition matrix; H-bonding
D) major; repressor; ionic binding
E) major; transcriptional silencer; ionic bonding

Question 60

Characteristics of the Zn-finger motif include all EXCEPT:

A) repeated motif in DNA-binding proteins.
B) 2 Cys and 2 Met coordinate the Zn.
C) binds the major groove of DNA.
D) interacts with about five nucleotides/ Zn-finger.
E) all are true.

Question 61

The araBAD operon allows for the use of what metabolite by E. coli?

A) arachidonic acid
B) arabinose
C) allose
D) altrose
E) none of the above

Question 62

Which of the following is true regarding the araBAD operon?

A) binding of arabinose causes dimerization of AraC allowing it to bind to araO₂ and araI₁
B) when bound to arabinose, the AraC dimer must also bind to a CAP-cAMP dimer for translation to occur
C) expression of araC occurs in concert with the expression of araB, araA and araD
D) AraC bound to arabinose can bind to CAP regardless of whether or not cAMP is present
E) none of the above

Question 63

Explain the transcription termination mechanism that is dependent on the rho termination factor.​

Question 64

During RNA chain elongation gyrase proceeds ahead of the transcription bubble in order to _____.

A) remove negative supercoils by introducing positive supercoils
B) remove positive supercoils by introducing negative supercoils
C) remove negative supercoils by creating relaxed DNA
D) remove positive supercoils by creating relaxed DNA
E) none of the above

Question 65

Explain the functions of the transcription factors that are a part of the eukaryotic preinitiation complex (PIC).​

Question 66

How does catabolite activator protein (CAP) activate transcription of the lac operon?​

Question 67

Describe the structure of an exosome.​

Question 68

Discuss the capping and methylation of eukaryotic heterogeneous nuclear RNA (hnRNA).​