6

1. An experiment was designed to obtain nonspecific transcription from both strands of a DNA
molecule. Which of the following strategies would be most effective in achieving this?

A. I nclude the RNA holoenzyme in the reaction.

B. U

se the core enzyme of RNA polymerase.
C. Enrich the preparation with sigma subunit.

D. Use intact DNA .

E. I nclude the RNA holoenzyme in the reaction and use the core enzyme of RNA polymerase are
both effective.

2. Which of the following is not present in the core RNA polymerase?

A. β


B. β

′
C. σ

D. both β and σ

E. n
one of the choices are correct.

3. Which of the following techniques would be most useful in testing the ability of the core RNA
polymerase to bind to the promoter?

A. g

el filtration
B. S

1 mapping
C. immunoblotting

D. DNAse footprinting

E. n
orthern blotting

4. E. coli has seven genes (rrn) that encode rRNAs. Which of the following is a true statement
regarding the rrn promoters?

A. D

skA is required for the regulation of rrn transcription by ppGpp alarmone and iNTP.
B. i NTP directly controls promoter activity.

C. ppGpp directly controls promoter activity .

D. iNTP destabilizes the open promoter complex.

E. D skA destabilizes the open promoter.

5. During a study of the rrn gene in E. coli, A DskA-mutant stain was generated following exposure
to UV light. Predict a possible effect of this mutation.

he lifetime of rrn promoters will be significantly increased.
A. T

B. T

he levels on iNTP will increase.
C. rrn transcription will be insensitive to iNTP and ppGpp.

D. The levels of ppGpp will increase.

E. N
one of the choices are correct.

6. Place the following in the order that they occur during transcription initiation:
1 - formation of open complex; 2 - formation of closed complex;
3 promoter clearance; 4 - synthesis of about 10 nucleotides

A. 1

, 2, 3, 4
B. 2

, 1, 4, 2
C. 2, 1, 2, 4

D. 3, 1, 2, 4

E. 3
, 2, 1, 4

7. Which of the following precursors would be most appropriate to use in an experiment of the first
10 nucleotides in the initiation phase of transcription?

A. [ α-32P]ATP

B. [ 14-C]dATP

C. [β-32P]ATP

D. [γ-32P]ATP

E. [ 14C]CTP

8. Dimethyl sulfate is used to

A. c leave DNA molecules.

B. d

enature or melt DNA promote region.
C. remove methyl groups from RNA.

D. add methyl groups to DNA.

E. p romote the binding of RNA polymerase to DNA.

9. Which of the following statement is false regarding the sigma-factor?

A. I t does not have a DNA-binding domain.

B. I nteraction with the core enzyme unmasks the DNA-binding region.

C. Subregions 2.4 and 4.4 are involved in promoter recognition.

D. It can also bind to the nontemplate strand.

E. I t can bind to the -10 box.

10. Which of the following would most likely occur if an in vitro transcription assay is performed using
a cell extract containing an alpha subunit without the C-terminal domain?

A. P

olymerase would become tightly associated with the promoter.
B. P

olymerase would become more susceptible to proteolysis.
C. Transcription will be accelerated.

D. Polymerase complex would be loosely associated with the promoter.

E. R
ecognition of the UP element would be faster.

11. Which of the following is most involved in elongation of the RNA transcript?

A. s igma factor

B. U

P elements
C. -10 region

D. both sigma factor and UP elements

12. Which of the following does not have a DNA-binding domain?

A. s igma-factor

B. U

P region
C. alpha-factor

D. beta

E. b eta prime


13. Which of the following compounds is effective in inhibiting RNA chain polymerization in an in vitro
transcription assay?

A. t reptomycin

B. a

mpicillin
C. streptolydigin

D. treptomycin and ampicillin

E. a mpicillin and streptolydigin

14. Which of the following are characteristic of intrinsic terminator elements?

A. T

hey contain an inverted repeat.
B. T

hey contain a hairpin loop.
C. They contain several T's in the nontemplate strand of DNA.

D. Only They contain an inverted repeat and they contain a hairpin loop are correct.

E. T
hey contain an inverted repeat, they contain a hairpin loop, and they contain several T's in
the nontemplate strand of DNA are correct.

15. Which of the following is incorrect regarding rho-dependent terminators?

A. T

hey contain several T's in the notemplate strand.
B. T

hey consist of inverted repeats.
C. They form hairpin loops.

D. Rho binds to the growing transcripts.

E. R
ho has helicase activity.

16. Which of the following is true about the holoenzyme in an open complex?

A. T

he DNA is bound mainly to the sigma-subunit.
B. T

here no interaction between the sigma factor and the -10 region.
C. There are two Na+ ions in the core enzyme .

D. Region 2.4 of the sigma-factor binds to the -35 region.

E. T
he DNA is bound mainly to the sigma-subunit and there no interaction between the sigma
factor and the -10 region are both true.


17. A series of E. coli mutants was created by replacing two of the aspartic residues in the b′-subunit.
Which of the following is the most like outcome in these mutants?

A. T

he binding capacity of the subunit for magnesium will be reduced.
B. T

he cells die because such mutations are usually lethal.
C. The subunit will bind more tightly to other subunits in the enzyme complex.

D. The catalytic activity of the enzyme will be increased.

E. T
he binding capacity of the subunit for magnesium will be reduced and the cells die because
such mutations are usually lethal are correct.

18. Which of the following factors is involved in proofreading during transcription?

A. G

reB
B. N

usA
C. sigma-factor

D. rho-factor

E. n
one of the choices are correct.

19. An experiment was conducted to determine the hairpin loop region in termination. Two DNA
templates were prepared and used in an in vitro transcription assay. The samples were analyzed
for release of the RNA polymerase.
Construct 1 - hairpin sequence removed; Construct 2 - two copies of hairpin sequence inserted;
Construct 3 - normal DNA with only one hairpin sequence
Construct Level of truncated Nascent RNA released (arbitrary units)
1 10
2 11
3 10

The data from this experiment suggest that

A. h

airpin loops are not required for termination.
B. t wo hairpin loops rapidly destabilize the polymerase.

C. the data are inconclusive.

D. additional hairpin loops increase the stability of the RNA:DNA hybrid.

E. b oth hairpin loops are not required for termination and two hairpin loops rapidly destabilize the
polymerase are possible explanations.


20. Which of the following techniques is suitable for the study of DNA:RNA hybrid formation during
transcription?

A. D

NA:protein crosslinking
B. D

NAase I footprinting
C. DNA:RNA crosslinking

D. two-dimensional PAGE

E. F
RET analysis

21. The DNA binding sites for RNA polymerases are called ______________.

________________________________________

22. ______________ can be used to block initiation of RNA synthesis.

________________________________________

23. The sigma subunit in RNA polymerase is necessary for the transcription of intermediate genes
and RNA elongation.

True False

24. The core RNA polymerase must bind tightly to the promoter in order to initiate transcription.

True False

25. A closed promoter complex is one in which the holoenzyme is loosely bound and the DNA
remains in double-stranded form.

True False

26. TATAAT is a consensus sequence located at -10 upstream of the transcription start site.

True False

27. The FRET technique allows the study of the movement of two molecules relative to each other.

True False

28. The alpha subunit recognizes the UP promoter element.

True False

29. As transcription proceeds, the strain introduced in DNA is relaxed by DNA topoisomerases.

True False

30. The catalytic centers of some polymerase cores contain magnesium ions.

True False

 6 Key

1. An experiment was designed to obtain nonspecific transcription from both strands of a DNA
molecule. Which of the following strategies would be most effective in achieving this?

A. Include the RNA holoenzyme in the reaction.

B. Use the core enzyme of RNA polymerase.

C. Enrich the preparation with sigma subunit.

D. Use intact DNA .

E. Include the RNA holoenzyme in the reaction and use the core enzyme of RNA polymerase
are both effective.

Blooms Level: 3. Apply

Section: 06.02
Weaver - Chapter 06 #1


2. Which of the following is not present in the core RNA polymerase?

A. β

B. β′

C. σ

D. both β and σ

E. none of the choices are correct.

Blooms Level: 2. Understand

Section: 06.02
Weaver - Chapter 06 #2


3. Which of the following techniques would be most useful in testing the ability of the core RNA
polymerase to bind to the promoter?

A. gel filtration

B. S1 mapping

C. immunoblotting

D. DNAse footprinting

E. northern blotting

Blooms Level: 5. Evaluate

Section: 06.02
Weaver - Chapter 06 #3



4. E. coli has seven genes (rrn) that encode rRNAs. Which of the following is a true statement
regarding the rrn promoters?

A. DskA is required for the regulation of rrn transcription by ppGpp alarmone and iNTP.

B. iNTP directly controls promoter activity.

C. ppGpp directly controls promoter activity .

D. iNTP destabilizes the open promoter complex.

E. DskA destabilizes the open promoter.

Blooms Level: 2. Understand

Section: 06.02
Weaver - Chapter 06 #4


5. During a study of the rrn gene in E. coli, A DskA-mutant stain was generated following
exposure to UV light. Predict a possible effect of this mutation.

A. The lifetime of rrn promoters will be significantly increased.

B. The levels on iNTP will increase.

C. rrn transcription will be insensitive to iNTP and ppGpp.

D. The levels of ppGpp will increase.

E. None of the choices are correct.

Blooms Level: 5. Evaluate

Section: 06.02
Weaver - Chapter 06 #5


6. Place the following in the order that they occur during transcription initiation:
1 - formation of open complex; 2 - formation of closed complex;
3 promoter clearance; 4 - synthesis of about 10 nucleotides

A. 1, 2, 3, 4

B. 2, 1, 4, 2

C. 2, 1, 2, 4

D. 3, 1, 2, 4

E. 3, 2, 1, 4

Blooms Level: 4. Analyze

Section: 06.03
Weaver - Chapter 06 #6



7. Which of the following precursors would be most appropriate to use in an experiment of the
first 10 nucleotides in the initiation phase of transcription?

A. [α-32P]ATP

B. [14-C]dATP

C. [β-32P]ATP

D. [γ-32P]ATP

E. [14C]CTP

Blooms Level: 5. Evaluate

Section: 06.03
Weaver - Chapter 06 #7


8. Dimethyl sulfate is used to

A. cleave DNA molecules.

B. denature or melt DNA promote region.

C. remove methyl groups from RNA.

D. add methyl groups to DNA.

E. promote the binding of RNA polymerase to DNA.

Blooms Level: 1. Remember

Section: 06.03
Weaver - Chapter 06 #8


9. Which of the following statement is false regarding the sigma-factor?

A. It does not have a DNA-binding domain.

B. Interaction with the core enzyme unmasks the DNA-binding region.

C. Subregions 2.4 and 4.4 are involved in promoter recognition.

D. It can also bind to the nontemplate strand.

E. It can bind to the -10 box.

Blooms Level: 2. Understand

Section: 06.01
Weaver - Chapter 06 #9



10. Which of the following would most likely occur if an in vitro transcription assay is performed
using a cell extract containing an alpha subunit without the C-terminal domain?

A. Polymerase would become tightly associated with the promoter.

B. Polymerase would become more susceptible to proteolysis.

C. Transcription will be accelerated.

D. Polymerase complex would be loosely associated with the promoter.

E. Recognition of the UP element would be faster.

Blooms Level: 4. Analyze

Section: 06.03
Weaver - Chapter 06 #10


11. Which of the following is most involved in elongation of the RNA transcript?

A. sigma factor

B. UP elements

C. -10 region

D. both sigma factor and UP elements

Blooms Level: 2. Understand

Section: 06.04
Weaver - Chapter 06 #11


12. Which of the following does not have a DNA-binding domain?

A. sigma-factor

B. UP region

C. alpha-factor

D. beta

E. beta prime

Blooms Level: 2. Understand

Section: 06.02
Weaver - Chapter 06 #12



13. Which of the following compounds is effective in inhibiting RNA chain polymerization in an in
vitro transcription assay?

A. treptomycin

B. ampicillin

C. streptolydigin

D. treptomycin and ampicillin

E. ampicillin and streptolydigin

Blooms Level: 2. Understand

Section: 06.04
Weaver - Chapter 06 #13


14. Which of the following are characteristic of intrinsic terminator elements?

A. They contain an inverted repeat.

B. They contain a hairpin loop.

C. They contain several T's in the nontemplate strand of DNA.

D. Only They contain an inverted repeat and they contain a hairpin loop are correct.

E. They contain an inverted repeat, they contain a hairpin loop, and they contain several T's in
the nontemplate strand of DNA are correct.

Blooms Level: 2. Understand

Section: 06.05
Weaver - Chapter 06 #14


15. Which of the following is incorrect regarding rho-dependent terminators?

A. They contain several T's in the notemplate strand.

B. They consist of inverted repeats.

C. They form hairpin loops.

D. Rho binds to the growing transcripts.

E. Rho has helicase activity.

Blooms Level: 2. Understand

Section: 06.05
Weaver - Chapter 06 #15



16. Which of the following is true about the holoenzyme in an open complex?

A. The DNA is bound mainly to the sigma-subunit.

B. There no interaction between the sigma factor and the -10 region.

C. There are two Na+ ions in the core enzyme .

D. Region 2.4 of the sigma-factor binds to the -35 region.

E. The DNA is bound mainly to the sigma-subunit and there no interaction between the sigma
factor and the -10 region are both true.

Blooms Level: 2. Understand

Section: 06.03
Weaver - Chapter 06 #16


17. A series of E. coli mutants was created by replacing two of the aspartic residues in the b′-
subunit. Which of the following is the most like outcome in these mutants?

A. The binding capacity of the subunit for magnesium will be reduced.

B. The cells die because such mutations are usually lethal.

C. The subunit will bind more tightly to other subunits in the enzyme complex.

D. The catalytic activity of the enzyme will be increased.

E. The binding capacity of the subunit for magnesium will be reduced and the cells die
because such mutations are usually lethal are correct.

Blooms Level: 5. Evaluate

Section: 06.03
Weaver - Chapter 06 #17


18. Which of the following factors is involved in proofreading during transcription?

A. GreB

B. NusA

C. sigma-factor

D. rho-factor

E. none of the choices are correct.

Blooms Level: 2. Understand

Section: 06.03
Weaver - Chapter 06 #18



19. An experiment was conducted to determine the hairpin loop region in termination. Two DNA
templates were prepared and used in an in vitro transcription assay. The samples were
analyzed for release of the RNA polymerase.
Construct 1 - hairpin sequence removed; Construct 2 - two copies of hairpin sequence
inserted; Construct 3 - normal DNA with only one hairpin sequence
Construct Level of truncated Nascent RNA released (arbitrary units)
1 10
2 11
3 10

The data from this experiment suggest that

A. hairpin loops are not required for termination.

B. two hairpin loops rapidly destabilize the polymerase.

C. the data are inconclusive.

D. additional hairpin loops increase the stability of the RNA:DNA hybrid.

E. both hairpin loops are not required for termination and two hairpin loops rapidly destabilize
the polymerase are possible explanations.

Blooms Level: 5. Evaluate

Section: 06.05
Weaver - Chapter 06 #19


20. Which of the following techniques is suitable for the study of DNA:RNA hybrid formation during
transcription?

A. DNA:protein crosslinking

B. DNAase I footprinting

C. DNA:RNA crosslinking

D. two-dimensional PAGE

E. FRET analysis

Blooms Level: 5. Evaluate

Section: 06.03
Weaver - Chapter 06 #20


21. The DNA binding sites for RNA polymerases are called ______________.

promoters

Blooms Level: 1. Remember
Section: 06.02
Weaver - Chapter 06 #21



22. ______________ can be used to block initiation of RNA synthesis.

Rifampicin

Blooms Level: 2. Understand
Section: 06.03
Weaver - Chapter 06 #22


23. The sigma subunit in RNA polymerase is necessary for the transcription of intermediate genes
and RNA elongation.

FALSE

Blooms Level: 2. Understand
Section: 06.01
Weaver - Chapter 06 #23


24. The core RNA polymerase must bind tightly to the promoter in order to initiate transcription.

FALSE

Blooms Level: 2. Understand
Section: 06.03
Weaver - Chapter 06 #24


25. A closed promoter complex is one in which the holoenzyme is loosely bound and the DNA
remains in double-stranded form.

TRUE

Blooms Level: 2. Understand
Section: 06.02
Weaver - Chapter 06 #25


26. TATAAT is a consensus sequence located at -10 upstream of the transcription start site.

TRUE

Blooms Level: 1. Remember
Section: 06.02
Weaver - Chapter 06 #26


27. The FRET technique allows the study of the movement of two molecules relative to each
other.

TRUE

Blooms Level: 2. Understand
Section: 06.05
Weaver - Chapter 06 #27



28. The alpha subunit recognizes the UP promoter element.

TRUE

Blooms Level: 1. Remember
Section: 06.02
Weaver - Chapter 06 #28


29. As transcription proceeds, the strain introduced in DNA is relaxed by DNA topoisomerases.

TRUE

Blooms Level: 2. Understand
Section: 06.04
Weaver - Chapter 06 #29


30. The catalytic centers of some polymerase cores contain magnesium ions.

TRUE

Blooms Level: 1. Remember
Section: 06.02
Weaver - Chapter 06 #30

 6 Summary

Category # of Questions
Blooms Level: 1. Remember 5
Blooms Level: 2. Understand 16
Blooms Level: 3. Apply 1
Blooms Level: 4. Analyze 2
Blooms Level: 5. Evaluate 6
Section: 06.01 2
Section: 06.02 11
Section: 06.03 10
Section: 06.04 3
Section: 06.05 4
Weaver - Chapter 06 30