Biochem Ch 11

RNA synthesis begins at the base in the DNA sequence designated by the following number: a. +1 (plus one) b. 0 (zero) c. −1 (minus one) d. −10 region (minus ten) e. It varies between genes.

a. +1 (plus one)

What provides the energy for rho-dependent chain termination? a. ATP hydrolysis distinct from any incorporation into the chain. b. Nucleotide hydrolysis associated with incorporation into the chain. c. Torsional stress built into the separating DNA strands. d. There is no energy requirement.

a. ATP hydrolysis distinct from any incorporation into the chain.

How do enhancers differ from promoters? a. Enhancers do not bind RNA polymerase. b. Enhancers include the UP element. c. Enhancers bind the sigma (σ) factor. d. There is no difference; these terms are synonymous.

a. Enhancers do not bind RNA polymerase.

Which of the following is not true about RISC? a. It is only involved in cleaving dsRNA from viruses b. It is involved with processing of miRNA and siRNA c. It uses a protein from the argonaut family d. It unwinds dsRNA and eventually discards the passenger strand

a. It is only involved in cleaving dsRNA from viruses

What is the function of the sigma (σ) subunit of RNA polymerase in E. coli? a. It recognizes promoters where transcription should begin. b. It contains the active site for synthesis of RNA. c. It ensures proper processitvity of the polymerase, so it doesn't stop prematurely. d. It is involved in chain termination. e. It scrunches the DNA

a. It recognizes promoters where transcription should begin.

Which of the following does not influence the timing of expression of an operon? a. Repressors b. Co-repressors c. Presence of substrates of the operon which need to be degraded d. Inducers e. All of these influence the timing of expression

a. Repressors

Which of the following is true concerning the first nucleotide incorporated into an RNA chain? a. The first nucleotide incorporated into the RNA chain retains its 5'-triphosphate b. The first nucleotide is always GMP c. The first nucleotide is always cleaved off post-transcriptionally d. The first nucleotide is always modified after transcription

a. The first nucleotide incorporated into the RNA chain retains its 5'-triphosphate

How do the core enzyme and the holoenzyme of RNA polymerase differ in E. coli? a. The holoenzyme includes the sigma (σ) subunit, the core enzyme does not. b. The core enzyme includes the sigma (σ) subunit, the holoenzyme does not. c. The holoenzyme transcribes from an RNA template, the core enzyme from a DNA template. d. The core enzyme transcribes from an RNA template, the holoenzyme from a DNA template

a. The holoenzyme includes the sigma (σ) subunit, the core enzyme does not.

Which of the following best describes leucine zipper motifs? a. They allow protein-protein interactions via hydrophobic bonds. b. They allow protein-protein interactions via hydrogen bonds. c. They allow protein-protein interactions via electrostatic interactions. d. They allow protein-DNA interactions by fitting into the major groove of DNA

a. They allow protein-protein interactions via hydrophobic bonds.

Which of the following is true about micro RNAs? a. They are a type of non-coding RNA b. They are a type of small interfering RNA c. They have been found only in simple organisms like roundworms d. All of these are true

a. They are a type of non-coding RNA

Alternative splicing of exons is a mechanism to get more than 1 protein from the same gene. a. True b. False

a. True

Attenuation mechanisms rely on alternative secondary structures forming in the mRNA. a. True b. False

a. True

DNA binding domains are distinct from transcription-activation domains. a. True b. False

a. True

Inducers allow for a system in which an enzyme is not made unless it is needed. a. True b. False

a. True

Inducers for operons are often structurally related to the enzyme substrates of that operon. a. True b. False

a. True

Intracellular levels of cyclic AMP can affect the phosphorylation of proteins and enzymes as a secondary messenger. a. True b. False

a. True

The catabolite activator protein can overcome the effect of a repressor binding to the operon. a. True b. False

a. True

The major difference between RNA initiation in eukaryotes and prokaryotes is the number of factors involved in the process. a. True b. False

a. True

The weakness of A−U base pairs at the end of the RNA molecule may help in dissociation of the new RNA product. a. True b. False

a. True

Minor differences in the consensus sequence for RNA Polymerase a. can be exploited to vary the amount of mRNA which is synthesized from that gene. b. dictate the direction that RNA Polymerase proceeds from the promoter. c. dictate whether sigma (σ) factor is required. d. never occur. e. have no effect on transcription

a. can be exploited to vary the amount of mRNA which is synthesized from that gene.

During which phase do the β'- and σ-subunits of RNA polymerase melt 14 base pairs surrounding the transcription start site, causing the strands to separate? a. chain initiation b. chain elongation c. intrinsic chain termination d. rho-dependent chain termination

a. chain initiation

RNA polymerases from prokaryotes and eukaryotes a. have sequence homology in catalytic subunits b. have identical σ factors c. differ because there is no analogue to the prokaryotic α subunit in eukaryotes d. have the same number and kind of subunits

a. have sequence homology in catalytic subunits

The enzyme principally responsible for RNA synthesis in Escherichia coli a. is a multisubunit enzyme b. consists of a single polypeptide chain c. requires Mn2+ for activity d. requires a DNA primer

a. is a multisubunit enzyme

RNA transcribed from the coding strand instead of the template strand a. is called antisense RNA. b. produces histones. c. is tRNA. d. never occurs

a. is called antisense RNA.

Proteins that recognize DNA with specific base sequences are a. more likely to bind to the major groove. b. more likely to bind to the minor groove. c. equally likely to bind to the major or minor grooves. d. never occur

a. more likely to bind to the major groove.

Capping of eukaryotic mRNA a. occurs at the 5' end. b. occurs at the 3' end. c. occurs at both ends. d. doesn't occur at all.

a. occurs at the 5' end.

The elongation and termination phases of eukaryotic transcription a. require several protein factors b. are better understood than the initiation phase c. are not subject to control mechanisms, only the initiation phase d. proceed at a constant rate and always stop at the same termination sequence

a. require several protein factors

The eukaryotic TATA-binding protein (TBP) functions in a manner similar to a. sigma (σ) factor in E. coli. b. rho (ρ) factor in E. coli. c. lac I in E. coli. d. CAP in E. coli.

a. sigma (σ) factor in E. coli.

A commonly encountered feature of transfer RNA synthesis is a. the precursor of several tRNA molecules is transcribed in one long polynucleotide sequence b. there is little or no base modification after transcription c. modification of the sugar moiety never takes place d. the covalent binding of tRNA to specific proteins

a. the precursor of several tRNA molecules is transcribed in one long polynucleotide sequence

Cyclic AMP affects transcription by a. triggering the action of several protein factors b. phosphorylating a subunit of RNA polymerase c. phosphorylating a transcription factor d. inhibiting DNA looping e. None of these

a. triggering the action of several protein factors

A single operon a. usually contains all the enzymes which are specific for the synthesis of a special biomolecule. b. usually does not contain all the enzymes which are specific for the synthesis of a special biomolecule. c. usually contains only a single structural gene for a critical enzyme. d. usually contains only a gene for a repressor

a. usually contains all the enzymes which are specific for the synthesis of a special biomolecule.

Which of the following offers the best description of a Pribnow box? a. A promoter consensus sequence located at approximately −35. b. A promoter consensus sequence located at approximately −10. c. A sequence forming a hairpin loop signaling the termination of transcription. d. A sequence immediately surrounding the start site of transcription.

b. A promoter consensus sequence located at approximately −10.

Which of the following is not a common modification occurring after polymerization of RNA? a. Methylation of bases. b. Addition of phosphate to the bases. c. Removal of bases from the polymer. d. Addition of bases to the polymer. e. All of these changes are common.

b. Addition of phosphate to the bases.

At what point does the sigma (σ) subunit of RNA polymerase released from the core enzyme? a. Prior to the incorporation of any nucleotides into an RNA strand. b. After transcription begins and about 10 nucleotides have been added to the RNA chain. c. Just prior to chain termination. d. Never; it is an intrinsic part of the core enzyme. e. After RNA polymerase discovers an inverted repeat

b. After transcription begins and about 10 nucleotides have been added to the RNA chain.

Which of following statements describes a difference between replication of DNA and transcription of RNA? a. Nucleoside triphosphates are the precursors for replication, but nucleoside diphosphates are used for transcription. b. Both strands of DNA are copied in replication, but usually only one is copied in transcription. c. Base pairing is used to copy the sequence in replication, but not in transcription. d. The chain grows from the 5' to the 3' end in replication, but 3' to 5' in transcription. e. None of these

b. Both strands of DNA are copied in replication, but usually only one is copied in transcription.

Which of these terms does not describe the DNA strand used to direct RNA synthesis? a. Template strand b. Coding strand c. Antisense strand d. Negative or "−" strand e. All these terms describe the DNA strand used to direct RNA synthesis

b. Coding strand

Which of the following correctly describes a difference between RNA & DNA polymerases? a. RNA polymerases usually do not need a template, while DNA polymerases do. b. DNA polymerases usually require a primer (i.e., they can only continue a strand, not start one), while most RNA polymerases do not. c. RNA polymerases usually synthesize introns, while DNA polymerases synthesize cistrons. d. RNA polymerases polymerize 5' → 3', while DNA polymerases polymerize 3' → 5'. e. None of these

b. DNA polymerases usually require a primer (i.e., they can only continue a strand, not start one), while most RNA polymerases do not.

Which of the following statements about eukaryotic and prokaryotic RNA polymerases, is false? a. There are 3 different RNA polymerases in eukaryotes, instead of just one. b. Eukaryotic polymerases have the same number of subunits as prokaryotic ones. c. Only prokaryotic polymerases use sigma factor. d. The enzymatic mechanism is the same for both types of organisms.

b. Eukaryotic polymerases have the same number of subunits as prokaryotic ones.

Post-transcription processing of mRNA in prokaryotes is required. a. True b. False

b. False

The end of the new mRNA molecule in E. coli. usually terminates in a string of A's a. True b. False

b. False

The leucine zipper is different from other DNA binding domains, since it requires the DNA-binding protein to form a dimer. a. True b. False

b. False

There is only one sigma subunit, since the same RNA Polymerase must bind to all genes in E. coli. a. True b. False

b. False

Which of following statements concerning RNA transcription is false? a. The DNA strands become separated during synthesis. b. Synthesis of RNA is as accurate as synthesis of DNA c. The template strand is read in the 3' → 5' direction. d. All 4 ribonucleotides are required. e. A primer is required for RNA synthesis

b. Synthesis of RNA is as accurate as synthesis of DNA

What is the need for a primer in transcription? a. It ensures the fidelity of the newly synthesized RNA strand. b. There is none. c. RNA polymerases requires a preexisting strand with a nucleotide having a 3'−OH. d. RNA polymerase requires a preexisting strand with a nucleotide having a 5'−OH.

b. There is none.

Response elements a. are similar to operons in that they are controlled by a single promoter b. are enhancers of transcription activated by metabolic factors c. are not affected by steroids d. are silencers of transcription triggered by the presence of metal ions

b. are enhancers of transcription activated by metabolic factors

Operons a. control the expression of constitutive genes. b. are subject to positive or to negative control. c. are not affected by mutations in the genes for repressors or inducers. d. occur in both prokaryotes and eukaryotes.

b. are subject to positive or to negative control.

Which of the following best describes the order of events at the promoter? a. open complex → closed complex → transcription initiation b. closed complex → open complex → transcription initiation c. open complex → transcription initiation → closed complex d. transcription initiation → open complex → closed complex

b. closed complex → open complex → transcription initiation

Phosphorylation of the CTD of RNA polymerase II occurs during which phase of transcription? a. initial binding to the promoter b. conversion from the closed complex to the open complex c. termination of transcription d. None of these

b. conversion from the closed complex to the open complex

Initiation of RNA biosynthesis involves a. recognition of the promoter region by the α subunit of RNA polymerase b. conversion of the closed-promoter complex to the open-promoter complex c. binding of one of the α subunits of RNA polymerase to each strand of DNA d. incorporation of four pyrimidine nucleotides in succession

b. conversion of the closed-promoter complex to the open-promoter complex

Polyadenylation of eukaryotic mRNA a. occurs at the 5' end. b. occurs at the 3' end. c. occurs at both ends. d. doesn't occur at all.

b. occurs at the 3' end.

The sequences in eukaryotic DNA known as introns are a. those included in the final sequence of messenger RNA b. the intervening sequences not expressed in the final sequence of messenger RNA c. the binding sites for DNA polymerase d. the binding sites for RNA polymerase

b. the intervening sequences not expressed in the final sequence of messenger RNA

Which of the following is not a key step in the activation of mRNA synthesis in eukaryotes? a. Binding of TBP to the DNA. b. Binding of other transcription factors. c. Binding of RNA Pol I. d. Phosphorylation of the RNA Pol. e. All of these are necessary to initiate RNA synthesis in eukaryotes.

c. Binding of RNA Pol I.

Which ends of eukaryotic mRNA are protected from degradation? a. 5' end only b. 3' end only c. Both ends d. Neither end e. The RNA is circular and has no ends.

c. Both ends

Identify the part of the RNA polymerase that constitutes the operator and the promoter and modulates the production of proteins whose amino acid sequence is specified by the structural genes under their control. a. Transcription start site b. Termination site c. Control site d. Restriction site

c. Control site

How do eukaryotic and prokaryotic RNA polymerases compare? a. Since eukaryotic RNA polymerases are more complex, little homology has been found between the actual protein sequences in the catalytic subunits. b. Since eukaryotic transcription is less complex than in prokaryotes, monomeric RNA polymerases are used. c. Despite their added complexity, eukaryotic and prokaryotic RNA polymerases are generally homologous. d. Eukaryotic and prokaryotic RNA polymerases are virtually identical.

c. Despite their added complexity, eukaryotic and prokaryotic RNA polymerases are generally homologous.

Which of the conditions would result in the least amount of transcription of the lac operon?

c. III (high glucose, low lactose)

Which of the following is not true? a. The mechanism of activation of eukaryotic genes involves addition and removal of phosphate residues from some of the transcription factors. b. In plants, there are 5 RNA polymerases. c. RNA Pol IV is the primary RNA synthesizer in plants d. Of the RNA Polymerases in eukaryotes, Pol II is the most extensively studied.

c. RNA Pol IV is the primary RNA synthesizer in plants

Which enzyme transcribes genes encoding tRNA in eukaryotes? a. RNA polymerase I b. RNA polymerase II c. RNA polymerase III d. Different tRNAs are transcribed by different RNA polymerases.

c. RNA polymerase III

Which of the following transcription factors is involved in the elongation phase of eukaryotic transcription? a. TFIIA b. TFIID c. TFIIF d. There are no transcription factors associated with elongation.

c. TFIIF

The combination of events revolving around chromatin remodeling that controls transcription is known as: a. The genetic code b. The second genetic code c. The histone code d. Histone deacetylase code e. None of these

c. The histone code

All of the following apply to attenuation mechanisms, except: a. They are used most often for operons for amino acid synthesis. b. They involve the synthesis of proteins in the regulation of RNA synthesis. c. The rate of RNA synthesis is regulated by the conformation of the protein being synthesized. d. They require the presence of partially completed mRNA molecules. e. All of these apply to attenuation mechanisms

c. The rate of RNA synthesis is regulated by the conformation of the protein being synthesized.

What provides the energy for the conversion from the open complex to chain elongation? a. ATP hydrolysis distinct from any incorporation into the chain. b. Nucleotide hydrolysis associated with incorporation into the chain. c. Torsional stress built into the separating DNA strands. d. Binding of rho (ρ) factor to the holoenzyme. e. None of these

c. Torsional stress built into the separating DNA strands.

Identify the component of the prokaryotic promoter that is 40 to 60 bases subsequent to the transcription start site and that enhances the binding of RNA polymerase. a. Core promoter b. −35 element c. UP element d. Pribnow box

c. UP element

General transcription activation in eukaryotes requires a. a specific enhancer common to all genes b. a specific silencer common to all genes c. a protein called Mediator d. a CREB binding protein e. none of these

c. a protein called Mediator

A transcription factor is a. a subunit of RNA polymerase II that does not have a prokaryotic analogue. b. the part of the promoter sequence closest to the start of transcription. c. a protein other than RNA polymerase that is involved in transcription. d. a sequence that determines whether an upstream element will be an enhancer or silencer.

c. a protein other than RNA polymerase that is involved in transcription.

Control of transcription in prokaryotes does not involve a. enhancers. b. silencers. c. leucine zipper proteins. d. alternative σ factors.

c. leucine zipper proteins.

A mutation in the lac A gene would result in a. continuous production of the proteins encoded by the three structural genes b. continuous production of the lac repressor c. normal operation of the lac operon, but with an alteration in the proteins encoded by the lac A gene d. no transcription from the lac operon

c. normal operation of the lac operon, but with an alteration in the proteins encoded by the lac A gene

Consensus sequences are a. sequences that are invariant throughout the DNA. b. sequences required for transcription to occur c. sequences that have many bases in common d. sequences that lie far upstream of the core promoter.

c. sequences that have many bases in common

Which of the following RNAs is noted for having a "cloverleaf" structure? a. mRNA b. rRNA c. tRNA d. All of these

c. tRNA

Where is the TATA box located? a. At the transcription start site (+1). b. −10 region. c. −25 region. d. −40 region

c. −25 region.

Which is not associated with bacterial promoters? a. the transcription start site b. the Pribnow box c. the −35 element d. 3' antiterminator

d. 3' antiterminator

Which of the following is the best description of an operon? a. An enhancer that positively regulates gene expression. b. An silencer that negatively regulates gene expression. c. A binding element for the sigma (σ) factor. d. A group of genes under the control of a common promoter.

d. A group of genes under the control of a common promoter.

As in prokaryotes, the regulatory regions for eukaryotic genes: a. may be close to the genes they control b. may be upstream of the genes they control c. may be downstream of the genes they control d. All of these are true

d. All of these are true

Chain termination occurs, in vivo, when: a. RNA Polymerase gets to the end of the DNA. b. The factor called rho (ρ) binds to the DNA. c. A hairpin loop forms in the template. d. Either a hairpin loop forms or rho (ρ) catches up with transcription stalled by a hairpin loop e. None of these

d. Either a hairpin loop forms or rho (ρ) catches up with transcription stalled by a hairpin loop

Which of the following statements about the various RNA Polymerases in eukaryotes is false? a. Permanent RNAs, such as tRNA and rRNA use different RNA Polymerases. b. The different RNA Polymerases share some subunits. c. The RNA Polymerase for mRNA is designated RNA Pol II. d. Eukaryotic RNA polymerases are generally monomeric.

d. Eukaryotic RNA polymerases are generally monomeric.

Which of the conditions would result in the greatest amount of transcription of the lac operon?

d. IV (low glucose, high lactose)

Which of the following is not a property of the sigma (σ) subunit? a. It tells the RNA Polymerase where to sit down. b. It helps point the RNA Polymerase in the proper direction. c. It causes the RNA Polymerase to bind tightly to the DNA. d. It stays with the RNA Polymerase throughout synthesis.

d. It stays with the RNA Polymerase throughout synthesis.

CREB contains the following structural motif: a. Helix-turn-helix b. β−barrel c. Zinc finger d. Leucine zipper

d. Leucine zipper

Which of the following is more often associated with transcription being switched off? a. Presence of histone remodeling complexes SWI/SNF b. Active Histone Acetyltransferase c. Unmethylated cytosines d. Methylated cytosines e. None of these

d. Methylated cytosines

Which ends of prokaryotic mRNA are protected from degradation? a. 5' end only b. 3' end only c. Both ends d. Neither end e. The RNA is circular and has no ends.

d. Neither end

Which of following statements concerning RNA transcription is false? a. The release of pyrophosphate from a nucleoside triphosphate drives the reaction. b. RNA is synthesized from the 5' end to the 3' end. c. DNA to RNA base pairing includes A to U and G to C. d. Transcription requires the use of a primer. e. None of these

d. Transcription requires the use of a primer.

Non-coding RNAs are known to: a. bind to mRNA targeting them for destruction b. bind to mRNA preventing their translation c. promote RNA silencing d. all of these

d. all of these

TATA-binding protein (TBP) is normally required for transcription by a. Pol I. b. Pol II. c. Pol III. d. all of these polymerases. e. none of these polymerases

d. all of these polymerases.

Transcription in eukaryotes differs from RNA synthesis in prokaryotes a. by requiring a primer. b. by simplifying the process with multifunctional enzymes. c. in using more complex σ factors. d. by having multiple RNA polymerases rather than one.

d. by having multiple RNA polymerases rather than one.

In the template DNA strand formed during transcription, the area from the end of the Upstream Promoter (UP) element to the transcription start site (TSS) is called the _____. a. proximal promoter b. core promoter c. distal promoter d. extended promoter

d. extended promoter

Initiation of transcription in eukaryotes is primarily controlled a. by two transcription factors b. by keeping the TATA-binding protein physically separated from other transcription factors c. by the order of binding of TFIIA and TFIIB d. in the formation of the preinitiation complex

d. in the formation of the preinitiation complex

In prokaryotic RNA synthesis a. the rate of incorporation of nucleotides is constant throughout the elongation process b. the ρ (rho) protein is always required for termination c. a unique series of three bases leads to termination d. inverted-repeat sequences in the DNA being transcribed can lead to termination

d. inverted-repeat sequences in the DNA being transcribed can lead to termination

Which of the following is not part of the core promoter? a. the transcription start site b. the Pribnow box (−10 region) c. the −35 region d. the UP element

d. the UP element

Which of the following is not a characteristic of catabolite activator protein (CAP)? a. it is a positive regulator of the lac operon b. when the cell has sufficient glucose and lactose, CAP will not be bound to the CAP binding site c. CAP binding near the promoter site depends on CAP complexation with cAMP d. the binding of CAP to DNA requires ATP hydrolysis

d. the binding of CAP to DNA requires ATP hydrolysis

The promoter site is a. the start site for transcription in DNA b. the binding site for regulatory proteins that stimulate transcription c. the general region of DNA downstream from the start site d. the site on DNA at which RNA polymerase binds to initiate transcription e. None of these

d. the site on DNA at which RNA polymerase binds to initiate transcription

Which of the following is not a structural motif encountered in DNA-binding proteins? a. helix-turn-helix b. leucine zipper c. zinc finger d. β−barrel

d. β−barrel

Which of the following is involved in regulation of eukaryotic transcription? a. Histone acetyltransferase b. Histone deacetylase c. Chromatin remodeling complexes d. Octamer sliding e. All of the choices

e. All of the choices

Which of the following is true about riboswitches: a. They have a molecule sensing domain called an aptamer b. There are known pathogens that use riboswitches as part of their mechanism c. They respond to specific molecules and control translation in a way that is often similar to transcription attenuation d. They contain a sensing domain and a decision making domain e. All of these

e. All of these

Which of the following is true? a. Mediator is a giant complex with a mass over 1 million Daltons b. Mediator contains many subunits called Med proteins c. Mediator bridges the RNA Polymerase at the promoter region with enhancers d. Mediator is the ultimate regulator of eukaryotic transcription e. All of these

e. All of these

Splicing reactions for exons involve the following mechanisms, except: a. Small nuclear RNAs b. Ribozymes c. Lariat mechanisms d. Participation of special G residues e. All of these are involved in splicing reactions

e. All of these are involved in splicing reactions

Alternative removal of exons from mRNA is important in which of the following? a. Troponins and other contractile proteins. b. Different types of collagen. c. The disease lupus. d. Alzheimer's disease. e. All of these.

e. All of these.

Which of the following influence the amount of expression of an operon? a. Availability of the specific sigma factor for that operon. b. How well the Pribnow box conforms to the consensus sequence. c. Attenuation mechanisms. d. Presence of 3' 5' cyclic AMP. e. All of these.

e. All of these.

In eukaryotes, which of the following types of RNA undergo some base modification after polymerization of the monomers? a. mRNA b. tRNA c. rRNA d. mRNA and tRNA e. mRNA and rRNA f. all of these

f. all of these

Explain the significance of a structural gene in the synthesis of proteins

A structural gene is a gene that directs the synthesis of a protein under the control of some regulatory gene. β-Galactosidase is coded for by a structural gene (lacZ). Also, structural genes encode the gene products that are involved in the biochemical pathway of the operon. Two structural genes—lacY and lacA—form a part of the operon. lacY encodes the enzyme lactose permease, whereas lacA encodes an enzyme called transacetylase.