Deck 10: Transcription in Bacteria

Question 1

A major difference between transcription in bacteria and eukaryotes is that

A) transcription and translation are uncoupled in bacteria.
B) transcription and translation are coupled in bacteria.
C) there is no difference; transcription and translation are coupled in both bacteria andeukaryotes.
D) there are many additional levels of control of gene expression in bacteria.

Answer 1

transcription and translation are coupled in bacteria.

Question 2

Transcription is the process of

A) formation of an RNA transcript complementary to the DNA template strand.
B) formation of an RNA transcript complementary to the DNA non-template strand.
C) formation of RNA transcripts complementary to both strands of DNA.
D) formation of an RNA transcript complementary to the DNA sense (coding) strand.

Answer 2

formation of an RNA transcript complementary to the DNA template strand.

Question 3

Transcription proceeds in the

A) 5' $\rightarrow$ 3' and 3' $\rightarrow$ 5' direction
B) 3' $\rightarrow$ 5' direction only
C) 5' $\rightarrow$ 3' direction only
D) none of the above; 5 ' and 3 'are only important for DNA replication

Answer 3

5' $\rightarrow$ 3' direction only

Question 4

RNA polymerase binds to a specific region on DNA called a(n)

A) origin
B) promoter
C) sigma factor
D) operon

Question 5

Which of the following statements is correct?

A) DNA polymerase requires a primer to get started.
B) RNA polymerase requires a primer to get started.
C) Both DNA and RNA polymerase require primers to get started.
D) Both DNA and RNA polymerase can start synthesis de novo.

Question 6

Promoter strength

A) refers to how rapidly transcript elongation occurs.
B) refers to the relative frequency of transcription initiation.
C) depends on the affinity of RNA polymerase for the promoter region.
D) both B and C

Question 7

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

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 8

Which statement is not true about the bacterial sigma factor?

A) Sigma is a regulatory protein, which is required for the initiation of transcription.
B) Sigma has the ability to join ribonucleotides (NTPs) by phosphodiester bonds using DNA as a template.
C) Sigma properly orients the RNA polymerase complex for transcription at the gene start site.
D) After initiation is complete, sigma does not dissociate completely; some domains are displaced and mRNA synthesis continues.

Question 9

The TATA box (-10 or Pribnow box) has all the following characteristics except:

A) It is both transcribed and translated.
B) It is upstream from most genes.
C) It is part of the binding site for the RNA polymerase.
D) It is part of a consensus (common) sequence of the promoter.

Question 10

Rho-independent terminators have all of the following characteristics except:

A) the consensus sequence is an inverted repeat
B) stem-loop structures can form within the mRNA
C) the repeat sequence is following by 7 to 8 uracil-containing nucleotides
D) sigma factor binding to the terminator triggers transcript release

Question 11

Which statement best describes the role of ATP hydrolysis by the transcriptional terminator Rho?

A) ATP hydrolysis induces a conformational change in the stem-loop structure of the terminator sequence.
B) ATP is used strictly to load Rho onto the mRNA.
C) ATP fuels the travel of Rho along the RNA and dissociation of the RNA-DNA duplex.
D) ATP fuels the travel of Rho in the direction opposite of transcription, resulting in a head-on collision between RNA polymerase and Rho.

Question 12

Which statement regarding bacterial Rho is not true?

A) Rho is a helicase.
B) Rho binds a specific C-rich sequence called a rut site.
C) Rho-dependent transcriptional termination depends on the ability of Rho to access the mRNA.
D) Rho rides along with RNA polymerase until a termination sequence is encountered.

Question 13

RNA polymerase forms a phosphodiester bond between

A) two dNTPs (deoxyribonucleotide triphosphates).
B) two rNTPs (ribonucleotide triphosphates).
C) a phosphodiester bond between a dNTP and an rNTP.
D) B and C

Question 14

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

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

Question 15

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

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

Question 16

"Promoter clearance" refers to a step of transcription initiation in which

A) activators and repressors dissociate from the promoter and sigma factor fully dissociates from RNA polymerase.
B) RNA polymerase unwinds the DNA at the start site of transcription.
C) RNA polymerase pauses before joining the first two nucleotides of the mRNA.
D) a small RNA has been synthesized and some domains of sigma factor dissociate from RNA polymerase.

Question 17

During transcription elongation, RNA polymerase

A) generates positive supercoils (overwinding) ahead of itself.
B) generates positive supercoils (overwinding) behind itself.
C) prevents supercoiling by tracking around the DNA helix.
D) prevents supercoiling by generating nicks in the DNA helix.

Question 18

The Jacob-Monod operon model

A) led to the discovery of mRNA.
B) proposed the existence of a repressor protein.
C) both A and B
D) was later proved to be wrong.

Question 19

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?

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 20

The real inducer of the lac operon is

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

Question 21

CAP is said to be responsible for positive regulation of the lac operon because:

A) CAP binds cAMP.
B) CAP binds the CAP binding site.
C) CAP prevents binding of the repressor to the operator.
D) CAP bound to the CAP binding site increases the frequency of transcription initiation by RNA polymerase.

Question 22

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.

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 23

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

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 24

In the absence of arabinose, the regulatory protein AraC

A) forms a dimer, binds to two regulatory sequences near the promoter, and activatestranscription of the arabinose operon structural genes.
B) forms a dimer, binds to two distant sites, and forms a DNA loop that blocks access of RNApolymerase to the arabinose operon promoter.
C) binds to the arabinose operator and represses transcription of the arabinose operonstructural genes
D) binds to the arabinose operator and represses transcription of the arabinose operonstructural genes.

Question 25

Regulation of the tryptophan operon occurs through

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 26

A riboswitch regulates gene expression

A) by influencing transcriptional initiation.
B) by influencing whether transcription continues to the end of a gene or operon.
C) by influencing whether a mRNA is translated.
D) B or C

Question 27

Which part of a riboswitch-regulated mRNA binds to a regulatory metabolite molecule?

A) the -35 element
B) the aptamer
C) the expression platform
D) the terminator sequence

Question 28

A riboswitch is a domain within certain mRNAs that has all of the following characteristics, except:

A) Riboswitches act as switchable "on-off" elements that selectively bind metabolites and control gene expression.
B) All riboswitches are ribozymes.
C) Riboswitches have two structural domains: an aptamer and an expression platform.
D) Riboswitches have the potential to form alternative anti-terminator and terminator hairpins.

Question 29

Alternative sigma factors

A) induce specific groups of functionally related genes.
B) replace the "standard" sigma factor $\sigma$ ⁷⁰ when cells are actively growing in optimal conditions.
C) bind to riboswitches.
D) are secreted by cells for quorum sensing.

Question 30

Quorum sensing is a mechanism by which

A) bacteria "count" the numbers of mRNA molecules that are made for a specific gene.
B) bacteria adjust the stability of an mRNA based on the presence of a metabolite.
C) bacteria change their transcriptional output in a manner that depends on their population density.
D) bacteria adjust total transcription levels in proportion to glucose levels.

Question 31

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

Question 32

Diagram a typical bacterial promoter. Exact sequences are not necessary.

Question 33

Draw a rough sketch of the structure of the bacterial RNA polymerase holoenzyme based on X-ray crystallography. Point out the position of the active site.

Question 34

Design an experiment to demonstrate that the RNA polymerase holoenzyme binds DNA more tightly compared with the core polymerase. Show sample positive results.

Question 35

Which DNA strand is part of the DNA-RNA hybrid in the RNA polymerase "open complex," the template or nontemplate strand? Explain your answer.

Question 36

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

Question 37

Diagram the key features of the bacterial elongation complex. Include a rough sketch showing the direction of RNA synthesis and where a new phosphodiester bond forms.

Question 38

Compare and contrast Rho-dependent and Rho-independent termination.

Question 39

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

Question 40

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?

Question 41

Transcription has a significant local effect on DNA structure (i.e., whether underwound or overwound). Discuss these structural changes and the enzymes that are required to resolve the situation.

Question 42

Diagram Jacob and Monod's operon model. Discuss some of the testable hypotheses put forth by this model.

Question 43

Draw diagrams of the lac operon that illustrate repressed transcription, basal transcription, and activated transcription.

Question 44

"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.

Question 45

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

Question 46

For bacterial operon induction, describe a specific example of the following: "The repressor and activators are DNA binding proteins that undergo allosteric modification."

Question 47

For bacterial operon induction, describe a specific example of the following: "DNA looping is a mechanism used in gene regulation."

Question 48

Present a model to explain attenuation in the trp operon in E. coli. Is attenuation the main regulatory mechanism? Explain your answer.

Question 49

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.

Question 50

You have discovered a novel riboswitch that you think acts as a metabolite-responsive ribozyme. Design an experiment to demonstrate self-cleaving activity and metabolite specificity. Show sample positive results.

Question 51

A particular sequence containing six base pairs is located in ten different organisms. The observed sequences are: 5′-ACGCAC-3′, ATACAC, GTGCAC, ACGCAC, ATACAC, ATGTAT, ATGCGC, ACGCAT, GTGCAT, and ATGCGC. What is the consensus sequence?

Question 52

Draw a diagram of a prokaryotic gene being transcribed and translated. Show the nascent mRNA with ribosomes attached. With an arrow, indicate the direction of transcription.

Question 53

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.

Question 54

Consider E. coli cells, each having one of the following mutations:(a) A mutant lac operator sequence that cannot bind lac repressor(b) A mutant lac repressor that cannot bind to the lac operator(c) A mutant lac repressor that cannot bind to allolactose(d) A mutant lac promoter that cannot bind CAP plus cAMPWhat effect would each mutation have on the function of the lac operon (assuming no glucose is present)?

Question 55

You are studying a new operon in bacteria involved in tyrosine biosynthesis.
(a) You sequence the operon and discover that it contains a short open reading frame at the 5′ end of the operon that contains two codons for tyrosine. What prediction would you make about this leader sequence, the RNA transcript, and the peptide that it encodes?
(b) How would you predict this operon is regulated; i.e., is it inducible or repressible by tyrosine? Why?
(c) Would this kind of regulation work in a eukaryotic cell? Why or why not?

Question 56

You are studying a repressor protein that you suspect forms a DNA loop between two operator sites, one located very near the promoter and the other located at a distance site upstream. Describe an experiment to test your hypothesis.