Question 1

Define the term "riboswitch." Regulation of gene expression by riboswitches is common in bacteria but not in eukaryotes. Offer reasons why this is the case.

Accepted Answer

A riboswitch is a regulatory segment of

Question 2

How does a regulatory protein with a helix-turn-helix motif recognize a specific DNA sequence?

Accepted Answer

A)  The regulatory protein opens up the two strands of DNA and detects functional groups on the bases on one of the strands. 
B)  The regulatory protein opens up the two strands of DNA and detects functional groups on the bases on both strands. 
C)  The regulatory protein detects functional groups on the base pairs that project into the major grooves of double-stranded DNA. 
D)  The regulatory protein detects specific sequences in the sugar-phosphate backbone of the DNA double helix. 
A)  The regulatory protein opens up the two strands of DNA and detects functional groups on the bases on one of the strands. 
B)  The regulatory protein opens up the two strands of DNA and detects functional groups on the bases on both strands. 
C)  The regulatory protein detects functional groups on the base pairs that project into the major grooves of double-stranded DNA. 
D)  The regulatory protein detects specific sequences in the sugar-phosphate backbone of the DNA double helix.

Question 3

Draw a rough sketch of a helix-turn-helix motif and show the site of interaction with the DNA double helix.

Accepted Answer

A helix-turn-helix motif is a common DNA

Question 4

Diagram the three-step transcription initiation process in E. coli.

Accepted Answer

The three-step transcription initiation

Question 5

What different catalytic activity does RNA polymerase have while "elongating" versus "backtracking?"

Accepted Answer

RNA polymerase is an enzyme responsible

Question 6

Regulation of the tryptophan operon occurs through

Accepted Answer

A)  a tryptophan-activated repressor that binds to operator sites 
B)  transcriptional attenuation by differential folding of RNA 
C)  a ribozyme riboswitch 
D)  both A and B 
A)  a tryptophan-activated repressor that binds to operator sites 
B)  transcriptional attenuation by differential folding of RNA 
C)  a ribozyme riboswitch 
D)  both A and B

Question 7

RNA polymerase has a _______ error rate because it has _______________ mechanism.

Accepted Answer

A)  high, no proofreading 
B)  low, proofreading 
C)  high, proofreading 
D)  low, no proofreading 
A)  high, no proofreading 
B)  low, proofreading 
C)  high, proofreading 
D)  low, no proofreading

Question 8

The real inducer of the lac operon is

Accepted Answer

A)  lactose 
B)  allolactose 
C)  IPTG 
D)  galactose 
A)  lactose 
B)  allolactose 
C)  IPTG 
D)  galactose

Question 9

Describe an experiment that showed that RNA polymerase can rotate DNA. Did the results of this experiment determine whether RNA polymerase rotates around DNA or vice versa in vivo?

Accepted Answer

One experiment that showed that RNA poly

Question 10

"When glucose is abundant, bacteria use it exclusively as their food source, even when other sugars are present." Discuss this statement in the context of how the presence of glucose effects induction of the lac operon.

Accepted Answer

The statement that bacteria use glucose

Question 11

Are transcription and translation "coupled" or "uncoupled" in bacteria? Explain your answer.

Accepted Answer

Transcription and translation are "coupl

Question 12

Which of the following is almost always associated with high levels of transcription?

Accepted Answer

A)  use of an alternative sigma factor 
B)  the presence of an UP element in a promoter 
C)  the presence of a Rho-independent terminator 
D)  the linkage of genes in an operon 
A)  use of an alternative sigma factor 
B)  the presence of an UP element in a promoter 
C)  the presence of a Rho-independent terminator 
D)  the linkage of genes in an operon

Question 13

In which transcriptional complex(es) is the DNA duplex intact (not unwound)?

Accepted Answer

A)  the closed complex 
B)  the open complex 
C)  the elongating complex 
D)  A and B 
A)  the closed complex 
B)  the open complex 
C)  the elongating complex 
D)  A and B

Question 14

A compound known as X-gal is widely used in molecular biology research. When wild-type E. coli is grown on an agar plate containing X-gal, the bacterial colonies turn blue. In contrast, when lacZ mutants are grown on an agar plate containing X-gal, the bacterial colonies remain their normal white color. What is X-gal likely to be?

Accepted Answer

A)  a compound chemically similar to glucose 
B)  a compound chemically similar to galactose 
C)  a compound chemically similar to lactose 
D)  a compound that cannot be transported into lacZ mutants 
A)  a compound chemically similar to glucose 
B)  a compound chemically similar to galactose 
C)  a compound chemically similar to lactose 
D)  a compound that cannot be transported into lacZ mutants

Question 15

You have discovered a bacterial operon involved in the synthesis of vitamin E. This operon is regulated by a repressor protein that binds to an operator sequence. Vitamin E is the allosteric effector of the repressor; i.e., the molecule that binds to the repressor to regulate its activity. Predict how vitamin E will influence repressor activity.

Accepted Answer

A)  When vitamin E binds to the repressor, the repressor binds to the operator. 
B)  When vitamin E binds to the repressor, the repressor cannot bind to the operator. 
C)  When vitamin E binds to the repressor, the repressor can bind to RNA polymerase. 
D)  When vitamin E binds to the repressor, the repressor cannot bind to RNA polymerase. 
A)  When vitamin E binds to the repressor, the repressor binds to the operator. 
B)  When vitamin E binds to the repressor, the repressor cannot bind to the operator. 
C)  When vitamin E binds to the repressor, the repressor can bind to RNA polymerase. 
D)  When vitamin E binds to the repressor, the repressor cannot bind to RNA polymerase.

Question 16

Show how you could use DNase I footprinting to demonstrate that a sigma ($\sigma$) factor is required for specific binding of RNA polymerase to a bacterial gene promoter.

Accepted Answer

See Fig. 9.13c, p. 254. End-label a DNA

Define the term "riboswitch." Regulation of gene expression by riboswitches is common in bacteria but not in eukaryotes. Offer reasons why this is the case.

How does a regulatory protein with a helix-turn-helix motif recognize a specific DNA sequence?

Draw a rough sketch of a helix-turn-helix motif and show the site of interaction with the DNA double helix.

Diagram the three-step transcription initiation process in E. coli.

What different catalytic activity does RNA polymerase have while "elongating" versus "backtracking?"

Regulation of the tryptophan operon occurs through

RNA polymerase has a _ error rate because it has _________ mechanism.

The real inducer of the lac operon is

Describe an experiment that showed that RNA polymerase can rotate DNA. Did the results of this experiment determine whether RNA polymerase rotates around DNA or vice versa in vivo?

"When glucose is abundant, bacteria use it exclusively as their food source, even when other sugars are present." Discuss this statement in the context of how the presence of glucose effects induction of the lac operon.

Are transcription and translation "coupled" or "uncoupled" in bacteria? Explain your answer.

Which of the following is almost always associated with high levels of transcription?

In which transcriptional complex(es) is the DNA duplex intact (not unwound)?

Show how you could use DNase I footprinting to demonstrate that a sigma ( $\sigma$ ) factor is required for specific binding of RNA polymerase to a bacterial gene promoter.

The Beginnings of Molecular Biology

The Structure of DNA

The Versatility of RNA

Protein Structure and Folding

Genome Organization and Evolution

DNA Replication and Telomere Maintenance

DNA Repair Pathways

Recombinant Dna Technology and Molecular Cloning

Tools for Analyzing Gene Expression

Transcription in Eukaryotes

Epigenetic Mechanisms of Gene Regulation

RNA Processing and Post-Transcriptional Gene Regulation

The Mechanism of Translation

Genetically Modified Organisms: Use in Basic and Applied Research

Genome Analysis: DNA Typing, Genomics, and Beyond

Medical Molecular Biology

Filters

Exam 10: Transcription in Bacteria

Define the term "riboswitch." Regulation of gene expression by riboswitches is common in bacteria but not in eukaryotes. Offer reasons why this is the case.

How does a regulatory protein with a helix-turn-helix motif recognize a specific DNA sequence?

Draw a rough sketch of a helix-turn-helix motif and show the site of interaction with the DNA double helix.

Diagram the three-step transcription initiation process in E. coli.

What different catalytic activity does RNA polymerase have while "elongating" versus "backtracking?"

Regulation of the tryptophan operon occurs through

RNA polymerase has a _______ error rate because it has _______________ mechanism.

The real inducer of the lac operon is

Describe an experiment that showed that RNA polymerase can rotate DNA. Did the results of this experiment determine whether RNA polymerase rotates around DNA or vice versa in vivo?

"When glucose is abundant, bacteria use it exclusively as their food source, even when other sugars are present." Discuss this statement in the context of how the presence of glucose effects induction of the lac operon.

Are transcription and translation "coupled" or "uncoupled" in bacteria? Explain your answer.

Which of the following is almost always associated with high levels of transcription?

In which transcriptional complex(es) is the DNA duplex intact (not unwound)?

Show how you could use DNase I footprinting to demonstrate that a sigma ( σ\sigmaσ ) factor is required for specific binding of RNA polymerase to a bacterial gene promoter.

The Beginnings of Molecular Biology

The Structure of DNA

The Versatility of RNA

Protein Structure and Folding

Genome Organization and Evolution

DNA Replication and Telomere Maintenance

DNA Repair Pathways

Recombinant Dna Technology and Molecular Cloning

Tools for Analyzing Gene Expression

Transcription in Eukaryotes

Epigenetic Mechanisms of Gene Regulation

RNA Processing and Post-Transcriptional Gene Regulation

The Mechanism of Translation

Genetically Modified Organisms: Use in Basic and Applied Research

Genome Analysis: DNA Typing, Genomics, and Beyond

Medical Molecular Biology

Filters

RNA polymerase has a _ error rate because it has _________ mechanism.

Show how you could use DNase I footprinting to demonstrate that a sigma ( $\sigma$ ) factor is required for specific binding of RNA polymerase to a bacterial gene promoter.