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Chapter: Chapter 13: DNA Replication and Repair

Multiple Choice

1. TB 13.001. What was probably the first carrier of genetic information in primitive
organisms?
A) DNA that could self-replicate
B) proteins
C) polypeptides
D) RNA that could self-replicate
E) both proteins and polypeptides
Ans: D
Difficulty: Easy
Feedback: 13.Introduction

2. TB 13.002. Who was the first to suggest semiconservative replication?

A) Meselson and Stahl
B) Hershey and Chase
C) Watson and Crick
D) Avery, McCarty and MacLeod
E) Darwin and Wallace
Ans: C
Difficulty: Easy
Feedback: 13.1

3. TB 13.003. Which type of replication results in 2 duplexes made of one parental strand and
one newly synthesized strand?
A) semiconservative replication
B) conservative replication
C) dispersive replication
D) incisive replication
E) reservative replication
Ans: A
Difficulty: Medium
Feedback: 13.1

4. TB 13.004. What type of replication results in the integrity of both parental strands being
disrupted? The new duplex strands are made of both old and new DNA. Neither the parental
strands nor the parental duplex is preserved.
A) semiconservative replication
B) conservative replication
C) dispersive replication
D) incisive replication
E) reservative replication
Ans: C
Difficulty: Medium
Feedback: 13.1

5. TB 13.005. Bacteria are grown in a medium containing 15NH4Cl for a number of generations
so that all of the DNA is made of fully "heavy" DNA. The bacteria are moved to a new medium
and grown in 14NH4Cl so that all new DNA will be light. After one generation time, what does
the DNA look like?
A) All of the DNA is made of 2 "light" strands.
B) All of the DNA is made of 2 "heavy" strands.
C) All of the DNA is made of 1 "heavy" strand and 1 "light" strand.
D) Each strand is made of a mixture of "heavy" and "light" DNA, with each strand being
between 75% and 100% "light".
E) Half of the DNA is made of 2 "light" strands and half of the DNA is made of 2 "heavy"
strands.
Ans: C
Difficulty: Difficult

Feedback: 13.1

6. TB 13.006. Bacteria are grown in a medium containing 15NH4Cl for a number of generations
so that all of the DNA is made of fully "heavy" DNA. The bacteria are moved to a new medium
and grown in 14NH4Cl so that all new DNA will be "light". If replication were conservative, what
would the DNA look like after two generation times.
A) All of the DNA is made of 2 "light" strands.
B) Half of the DNA is made of 2 "light" strands and half of the DNA is made of 1 "light" strand
and 1 "heavy" strand.
C) All of the DNA is made of 1 "heavy" strand and 1 "light" strand.
D) Each strand is made of a mixture of "heavy" and "light" DNA with each strand being
between 75% and 100% "light".
E) 75% of the DNA is made of 2 "light" strands and 25% of the DNA is made of 2 "heavy"
strands.
Ans: E
Difficulty: Difficult
Feedback: 13.1

7. TB 13.007. Bacteria are grown in a medium containing 15NH4Cl for a number of generations
so that all of the DNA is made of fully "heavy" DNA. The bacteria are moved to a new medium
and grown in 14NH4Cl so that all new DNA will be "light". If replication were dispersive, what
would the DNA look like after two generation times.
A) All of the DNA is made of 2 "light" strands.
B) Half of the DNA is made of 2 "light" strands and half of the DNA is made of 1 "light" strand
and 1 "heavy" strand.
C) All of the DNA is made of 1 "heavy" strand and 1 "light" strand.
D) Each strand is made of a mixture of "heavy" and "light" DNA, with each strand being
between 75% and 100% "light".
E) 75% of the DNA is made of 2 "light" strands and 25% of the DNA is made of 2 "heavy"
strands.
Ans: D
Difficulty: Difficult
Feedback: 13.1

8. TB 13.008. Cultured mammalian cells grown in thymidine for many generations were

allowed to undergo replication in the presence of bromodeoxyuridine (BrdU), which replaces

thymidine in DNA. After one round of replication, what does the DNA look like?
A) All chromatids have one strand that contains BrdU and one strand that contains thymidine.
B) All chromatids have two strands that contain BrdU.
C) Half of the chromatids have two strands that contain BrdU and half of the chromatids have 2
strands lacking BrdU.
D) Both of the strands of each chromatid contain mixtures of BrdU and thymidine.
E) All chromatids lack BrdU.
Ans: A
Difficulty: Difficult
Feedback: 13.1

9. TB 13.009. Cultured mammalian cells grown in thymidine for many generations were
allowed to undergo replication in the presence of bromodeoxyuridine (BrdU), which replaces
thymidine in DNA. After two rounds of replication, what does the DNA look like?
A) All chromatids have one strand that contains BrdU and one strand that does not.
B) All chromatids have two strands that contain BrdU.
C) Half of the chromatids have two strands that contain BrdU and half of the chromatids have 2
strands lacking BrdU.
D) Both strands of each chromatid contain mixtures of BrdU and thymidine.
E) Half of the chromatids have two strands that contain BrdU and half of the chromatids have 1
strand lacking BrdU and one strand containing BrdU.
Ans: E
Difficulty: Difficult
Feedback: 13.1

10. TB 13.010. Cultured mammalian cells grown in thymidine for many generations were
allowed to undergo replication in the presence of bromodeoxyuridine (BrdU), which replaces
thymidine in DNA. After two rounds of replication, what would the DNA look like if replication
were conservative?
A) All chromatids have one strand that contains BrdU and one strand that does not.
B) All chromatids have two strands that contain BrdU.
C) Half of the chromatids have two strands that contain BrdU and half of the chromatids have 2
strands lacking BrdU.
D) Both strands of each chromatid contain mixtures of BrdU and thymidine.
E) 75% of the chromatids have two strands that contain BrdU and 25% of the chromatids have 1
strand lacking BrdU and 1 strand containing BrdU.

Ans: E
Difficulty: Difficult
Feedback: 13.1

11. TB 13.011. Cultured mammalian cells grown in thymidine for many generations were
allowed to undergo replication in the presence of bromodeoxyuridine (BrdU), which replaces
thymidine in DNA. After one round of replication, what would the DNA look like if replication
were dispersive?
A) All chromatids have one strand that contains BrdU and one strand that does not.
B) All chromatids have two strands that contain BrdU.
C) Half of the chromatids have two strands that contain BrdU and half of the chromatids have 2
strands lacking BrdU.
D) Both strands of each chromatid contain mixtures of BrdU and thymidine.
E) All chromatids lack BrdU.
Ans: D
Difficulty: Difficult
Feedback: 13.1

12. TB 13.012. The specific site on the bacterial chromosome at which replication begins is
called the ________.
A) beginning
B) origin
C) initiation site
D) initiator
E) replicon
Ans: B
Difficulty: Easy
Feedback: 13.1

13. TB 13.013. Replication moves outward from the origin in ________ direction(s) and is said
to be ________.
A) both, unidirectional
B) both, bidirectional
C) one, bidirectional
D) unique, unidirectional

E) one, unidirectional
Ans: B
Difficulty: Medium
Feedback: 13.1

14. TB 13.014. In replicating bacterial chromosomes, where does replication terminate?

A) at the origin
B) across the circular chromosome from the origin
C) at random locations around the circle
D) one quarter of the way around the DNA circle from the origin
E) near Arnold
Ans: B
Difficulty: Medium
Feedback: 13.1

15. TB 13.015. What happens to DNA (circular DNA or linear DNA that is not free to rotate)
when it becomes overwound?
A) It becomes negatively supercoiled.
B) It breaks into a number of fragments.
C) It becomes positively supercoiled.
D) It stretches.
E) Its mass decreases.
Ans: C
Difficulty: Medium
Feedback: 13.1

16. TB 13.016. The replication fork generates _______ supercoils in the _______ portion of the
DNA molecule.
A) negative, replicated
B) positive, replicated
C) neutral, unreplicated
D) positive, unreplicated
E) negative, unreplicated

Ans: D
Difficulty: Medium
Feedback: 13.1

17. TB 13.017. Where is DNA gyrase normally positioned as it changes positively supercoiled
DNA into negatively supercoiled DNA in the replicating circular, bacterial chromosome?
A) It is permanently located at the origin.
B) It travels along the DNA behind the replication fork.
C) It travels along the DNA ahead of the replication fork.
D) It travels along the DNA at the replication fork as part of the replisome.
E) It is permanently located at the termination site of replication.
Ans: C
Difficulty: Medium
Feedback: 13.1

18. TB 13.018. What supplies the energy that drives the relief of mechanical strain by DNA
gyrase?
A) condensation of ATP
B) condensation of GTP
C) hydrolysis of ATP
D) hydrolysis of GTP
E) a proton gradient
Ans: C
Difficulty: Easy
Feedback: 13.1

19. TB 13.019. Who was the first to purify an enzyme from bacterial extracts that could
incorporate DNA precursors into a polymer?
A) Arthur Kornberg
B) James Watson
C) Francis Crick
D) Jacques Monod
E) Joel B. Piperberg (I wish!)
Ans: A

Difficulty: Easy
Feedback: 13.1

20. TB 13.020. In early experiments with DNA polymerase I, what evidence convinced
investigators that the original unlabeled DNA in the reaction mixture served as the template for
the newly made DNA?
A) The new DNA had the same base composition as the original unlabeled DNA.
B) The new DNA had a variable base composition.
C) The new DNA had a triple helix.
D) The new DNA and the old DNA were made of the same elements.
E) The new DNA was equally stable.
Ans: A
Difficulty: Medium
Feedback: 13.1

21. TB 13.021. Which of the following DNA molecules could serve as an effective template for
DNA synthesis?
1) an intact, linear, double-stranded DNA
2) a single-stranded, circular DNA
3) a partially double-stranded DNA
4) an intact, linear double stranded DNA
A)
B)
C)
D)
E)

1
2
3
4
1 and 4

Ans: C
Difficulty: Medium
Feedback: 13.1

22. TB 13.022. Why is an intact, linear double helix an ineffective template for DNA
polymerase?
A) It has a 3'-hydroxyl group, but lacks a template.
B) It lacks a 3'-hydroxyl group, but has a template.

C) It lacks a 3'-hydroxyl group and a template.

D) It has a 3'-hydroxyl group and has a template.
E) It lacks a 5'-hydroxyl group and has a template.
Ans: A
Difficulty: Medium
Feedback: 13.1

23. TB 13.023. Why is a single-stranded, circular DNA an ineffective template for DNA
polymerase?
A) It has a 3'-hydroxyl group, but lacks a template.
B) It lacks a 3'-hydroxyl group, but has a template.
C) It lacks a 3'-hydroxyl group and a template.
D) It has a 3'-hydroxyl group and has a template.
E) It lacks a 5'-hydroxyl group and has a template.
Ans: B
Difficulty: Medium
Feedback: 13.1

24. TB 13.024. What discovery suggested the presence of other DNA polymerases in bacteria
besides the Kornberg DNA polymerase enzyme?
A) Kornberg DNA polymerase mutants died.
B) Kornberg DNA polymerase mutants grew much more slowly.
C) Mutants with <1% of the normal Kornberg DNA polymerase enzyme activity multiplied at a
normal rate.
D) Mutants with <1% of the normal Kornberg DNA polymerase enzyme activity multiplied at a
low rate.
E) Kornberg DNA polymerase mutants reproduced much faster than normal bacteria.
Ans: C
Difficulty: Medium
Feedback: 13.1

25. TB 13.025. All DNA polymerases lay down nucleotides in a ______ direction and move
along the template in a _______ direction.
A) 3'>5', 5'>3'

B)
C)
D)
E)

N>C. C>N
5'>3', 3'>5'
C>N, N>C
N>C, 5'>3'

Ans: C
Difficulty: Medium
Feedback: 13.1

26. TB 13.026. Which of the following is an accurate description of the polymerization reaction
leading to DNA polymerization?
A) The 3'-hydroxyl group at the end of the primer executes a nucleophilic attack on the 5'-phosphate of the incoming nucleotide triphosphate.
B) The 5'-hydroxyl group at the end of the primer executes a nucleophilic attack on the 5'-phosphate of the incoming nucleotide triphosphate.
C) The 3'-hydroxyl group at the end of the primer executes an electrophilic attack on the 5'-phosphate of the incoming nucleotide triphosphate.
D) The 5'-hydroxyl group at the end of the primer executes an electrophilic attack on the 5'-phosphate of the incoming nucleotide triphosphate.
E) The 3'-hydroxyl group at the end of the primer executes a nucleophilic attack on the 5'-phosphate of the incoming nucleotide triphosphate.
Ans: A
Difficulty: Difficult
Feedback: 13.1

27. TB 13.027. The DNA strand growing toward the replication fork grows ______ in a 5'>3'
direction as the replication fork advances and is called the ________.
A) continuously, leading strand
B) discontinuously, lagging strand
C) continuously, lagging strand
D) discontinuously, leading strand
E) steadfastly, forthright strand
Ans: A
Difficulty: Medium
Feedback: 13.1

28. TB 13.028. The _______ strand fragment grows away from the replication fork toward the
___- end of the previously synthesized fragment to which it is subsequently linked.
A) leading, 5'
B) lagging, 5'
C) leading, 3'
D) lagging, 3'
E) lagging, N-terminal
Ans: B
Difficulty: Medium
Feedback: 13.1

29. TB 13.029. Since one strand of DNA is synthesized continuously during replication and the
other is made discontinuously, replication is said to be ___________.
A) continuous
B) hemicontinuous
C) discontinuous
D) semidiscontinuous
E) semicontinuous
Ans: D
Difficulty: Easy
Feedback: 13.1

30. TB 13.030. When Okazaki incubated bacteria in [3H]-thymidine for ______ and
immediately killed them, the radiolabel was found as part of ________; if the cells were
incubated in labeled DNA precursor for _____, most of the incorporated radioactivity became
part of ________.
A) a few seconds, a large DNA molecule, 1 to 2 minutes, small DNA fragments
B) a few seconds, small DNA fragments, 1 to 2 minutes, small DNA fragments
C) a few seconds, small DNA fragments, 1 to 2 minutes, a large DNA molecule
D) 1 to 2 minutes, small DNA fragments, 2 hours, a large DNA molecule
E) 1 to 2 minutes, a large DNA molecule, a few seconds, a large DNA molecule
Ans: C
Difficulty: Difficult
Feedback: 13.1

31. TB 13.031. During replication, DNA is constructed in small segments called ________ that
are rapidly linked to longer pieces of DNA synthesized earlier.
A) Watson fragments
B) Tokyo fragments
C) Osaka fragments
D) Okazaki fragments
E) Ouabain fragments
Ans: D
Difficulty: Easy
Feedback: 13.1

32. TB 13.032. The enzyme that joins the small fragments of the lagging strand together into a
continuous strand is called _______.
A) DNA gyrase
B) DNA ligase
C) DNA polymerase
D) primase
E) deoxyribonuclease
Ans: B
Difficulty: Easy
Feedback: 13.1

33. TB 13.033. Strand initiation during replication is carried out by an enzyme that makes a
short RNA molecule that is used as a primer; the enzyme is a distinct type of RNA polymerase,
called _______.
A) RNA gyrase
B) RNA ligase
C) ribonuclease
D) primase
E) deoxyribonuclease
Ans: D
Difficulty: Easy
Feedback: 13.1

34. TB 13.034. The RNA primers that initiate replication are subsequently _____ and the
resulting gap in the strand is _______ DNA and then sealed by _______.
A) filled in, removed by, DNA ligase
B) removed, filled in with, DNA ligase
C) removed, filled in with, RNA ligase
D) chemically altered to DNA, excised, DNA ligase
E) chemically altered to DNA, filled in with, DNA ligase
Ans: B
Difficulty: Medium
Feedback: 13.1

35. TB 13.035. Which of the following may be a further advantage of using RNA primers
during initiation of a strand in replication?
A) Using primers may decrease mistakes; such errors as mismatched bases are more likely
during initiation than elongation, and the use of a short, removable RNA segment avoids
inclusion of mismatched bases.
B) Using primers is faster.
C) The RNA of the primers is more stable.
D) The RNA of the primers is more likely to lead to changes in base sequence, which enhances
the rate of mutation and thus evolution.
E) The RNA of the primers allows more efficient packing of the chromosomes after its removal.
Ans: A
Difficulty: Medium
Feedback: 13.1

36. TB 13.036. _________ are DNA unwinding enzymes that unwind the DNA in a reaction
using the energy from ________ to move along one of the DNA strands, breaking the _______
holding the two strands together.
A) DNA helicases, ATP dehydration, disulfide linkages
B) DNA gyrases, ATP hydrolysis, H bonds
C) DNA helicases, ATP hydrolysis, 3'-5'-phosphodiester linkages
D) DNA helicases, ATP hydrolysis, H bonds
E) DNA gyrases, ATP dehydration, H bonds
Ans: D
Difficulty: Medium

Feedback: 13.1

37. TB 13.037. Where is the DnaB helicase first loaded onto the DNA?
A) at the replication terminator site
B) at the replication origin
C) at random locations through the circular chromosome
D) at the operator
E) at the promoter
Ans: B
Difficulty: Easy
Feedback: 13.1

38. TB 13.038. DnaB helicases bind DNA with the help of the _____ protein and move in a
_______ direction along the ________ strand template.
A) DnaC, 5'>3', leading
B) DnaA, 5'>3', leading
C) DnaC, 3'>5', lagging
D) DnaC, 5'>3', lagging
E) DnaA, 5'>3', lagging
Ans: D
Difficulty: Medium
Feedback: 13.1

39. TB 13.039. What proteins bind selectively to single-stranded DNA and are responsible for
keeping it extended and preventing it from being rewound?
A) DNA helicase
B) DNA gyrase
C) single-stranded DNA binding (SSB) proteins
D) ATPase
E) DNA unwindase
Ans: C
Difficulty: Easy
Feedback: 13.1

40. TB 13.040. In bacteria, a _______ is formed when a ________ associates transiently with a
_______.
A) primosome, helicase, DNA polymerase
B) primosome, helicase, primase
C) ribosome, helicase, primase
D) helicosome, primosome, DNA polymerase
E) primosome, helicase, DNA ligase
Ans: B
Difficulty: Medium
Feedback: 13.1

41. TB 13.041. How does DNA polymerase III move from one site on the lagging strand
template to a site closer to replication fork?
A) It hitches a ride with the DNA polymerase that is moving that way along the leading strand
template.
B) It hitches a ride with the DNA polymerase that is moving that way along the lagging strand
template.
C) It moves by itself like a tiny molecular motor.
D) It transports from the earlier Okazaki fragment to the later Okazaki fragment.
E) It is moved toward the replication fork by a complex of proteins called the transportosome.
Ans: A
Difficulty: Medium
Feedback: 13.1

42. TB 13.042. How can the replication of both DNA strands by two tethered polymerases be
accomplished when the template strands run in opposite directions?
A) One of the enzymes polymerizes DNA in the 3'>5' direction.
B) The DNA of the lagging strand loops back on itself so it has same orientation as the leading
strand template.
C) The DNA of the leading strand loops back on itself so it has same orientation as the lagging
strand template.
D) The lagging strand is broken and then rejoined regularly to allow simultaneous synthesis.
E) It just is.
Ans: B

Difficulty: Medium
Feedback: 13.1

43. TB 13.043. As replication proceeds, the lagging strand template of the DNA is looped back
on itself so that it has the same orientation as the leading strand template; the looping DNA
repeatedly grows and shortens during lagging strand replication. This model is often referred to
as the _________.
A) telescope model
B) extension model
C) trombone model
D) French horn model
E) piccolo model
Ans: C
Difficulty: Easy
Feedback: 13.1

44. TB 13.044. Which DNA polymerase in bacteria is mostly involved in DNA repair to correct
damaged DNA sections and removes RNA primers at the 5' ends of Okazaki fragments, replacing
them with DNA?
A) DNA polymerase I
B) DNA polymerase II
C) DNA polymerase III
D) DNA polymerase IV
E) both DNA polymerase I and DNA polymerase III
Ans: A
Difficulty: Easy
Feedback: 13.1

45. TB 13.045. Which DNA polymerase in bacteria synthesizes DNA strands during replication
and forms part of a complex that serves as a large replication machine?
A) DNA polymerase I
B) DNA polymerase II
C) DNA polymerase III
D) DNA polymerase IV
E) both DNA polymerase I and DNA polymerase III

Ans: C
Difficulty: Easy
Feedback: 13.1

46. TB 13.046. What is the name of the noncatalytic component of the DNA polymerase III
holoenzyme that keeps the polymerase associated with the DNA template?
A) -pleated sheet
B) -helix
C) clamp
D) clamp
E) clamp
Ans: C
Difficulty: Easy
Feedback: 13.1

47. TB 13.047. The DNA polymerase on the leading strand template _____________.
1) stays tethered to a single clamp during replication
2) switches from clamp to clamp during replication
3) cycles to a new clamp that has been assembled at an RNA primer-DNA template
junction closer to the replication fork.
4) cycles to a new clamp that has been assembled at an RNA primer-DNA template
junction farther from the replication fork.
A) 1
B) 2
C) 3
D) 4
E) 2 and 3
Ans: A
Difficulty: Easy
Feedback: 13.1

48. TB 13.048. The assembly of the clamp around the DNA requires a multisubunit _______
that is also part of the ________; part of this structure opens the ______ so that it can fit around

the DNA.
A) clamp loader, polymericon, clamp
B) clamp loader, DNA polymerase III holoenzyme, clamp
C) DNA polymerase III holoenzyme, clamp loader, replicon
D) clamp, DNA polymerase III holoenzyme, clamp loader
E) clamp loader, clamp, DNA polymerase III holoenzyme
Ans: B
Difficulty: Medium
Feedback: 13.1

49. TB 13.049. Why did Kornberg initially think that the exonuclease activity he found in his
DNA polymerase preparations was a contaminating enzyme?
A) The action of exonucleases is a lot like endonuclease.
B) The action of exonucleases is so dramatically opposed to the activity of DNA polymerases,
the synthesis of DNA.
C) The action of exonucleases is exactly like the action of DNA polymerase.
D) Purification was so difficult.
E) Enzymes can often run the reverse reactions.
Ans: B
Difficulty: Easy
Feedback: 13.1

50. TB 13.050. Where on the DNA polymerase I molecule do the 5'>3' exonuclease, 3'>5'
exonuclease and DNA polymerase activities reside?
A) all of them on the same domain
B) the two exonucleases on one domain and the polymerase activity on another domain
C) the 5'>3' exonuclease and polymerase activities on 1 domain and the 3'>5' exonuclease
on another
D) the 3'>5' exonuclease and polymerase activities on 1 domain and the 5'>3' exonuclease
on another
E) each enzyme activity on a different domain
Ans: E
Difficulty: Medium
Feedback: 13.1

51. TB 13.051. The 5'>3' exonuclease activity of DNA polymerase I is unusual for what
reason?
A) It works very slowly.
B) It works very quickly.
C) It degrades both RNA and DNA, and exonucleases typically digest one or the other.
D) It is very general and has an extremely high KM.
E) It is very specific and has a very high KM.
Ans: C
Difficulty: Medium
Feedback: 13.1

52. TB 13.052. What is the function of the 5'>3' exonuclease activity of DNA polymerase I?
A) It removes mismatched nucleotides that have been incorporated by mistake.
B) It replaces mismatched nucleotides with the correctly matched nucleotides.
C) It removes the DNA primer laid down by the primase at the 5' end of the Okazaki fragment.
D) It removes the RNA primer laid down by the primase at the 5' end of the Okazaki fragment.
E) It nicks DNA to create a primer in the middle of a DNA chain.
Ans: D
Difficulty: Medium
Feedback: 13.1

53. TB 13.053. What happens simultaneous with the removal of RNA primer by the 5'>3'
exonuclease activity of DNA polymerase I?
1) The DNA double helix is unwound.
2) The gap left by the removal of the RNA primer is filled in with deoxyribonucleotides.
3) The gap left by the removal of the RNA primer is filled in with ribonucleotides.
4) DNA is supercoiled extensively.
A) 1
B) 2
C) 3
D) 4
E) 1 and 2
Ans: B
Difficulty: Medium
Feedback: 13.1

54. TB 13.054. What is responsible for joining the last deoxyribonucleotide added during RNA
primer digestion and the 5' end of the previously synthesized and adjacent DNA fragment?
A) DNA polymerase I
B) DNA polymerase III
C) DNA ligase
D) the holoenzyme
E) DNA gyrase
Ans: C
Difficulty: Easy
Feedback: 13.1

55. TB 13.055. What is the probability that in E. coli an incorrect nucleotide will be
incorporated into DNA during replication and remain there?
A) fewer than 1 in 1 billion nucleotides
B) about 1 in 1000 nucleotides
C) fewer than 1 in about 4 million nucleotides
D) about 1 in 100,000 to 1,000,000 nucleotides
E) about 1 in 10,000 nucleotides
Ans: A
Difficulty: Easy
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56. TB 13.056. How does DNA polymerase discriminate between the insertion of correct and
incorrect base pairs as DNA replication proceeds?
1) Incorrect nucleotides repel each other because of their charges.
2) Distances between atoms and bond angles give incorrect base pairs the same geometry
as correct base pairs.
3) Incorrect base pairs are attracted to tightly to each other and the enzyme.
4) If the new base pair exhibits improper geometry (size and shape), the polymerase active
site cannot adopt the conformation required for catalysis and the incorrect nucleotide is
not incorporated.
A) 1
B) 2
C) 3

D) 4
E) 2 and 3
Ans: D
Difficulty: Medium
Feedback: 13.1

57. TB 13.057. The DNA polymerase can incorporate the wrong nucleotide occasionally. What
is the probability that the wrong nucleotide is incorporated into the growing polynucleotide chain
during replication?
A) fewer than 1 in 1 billion nucleotides
B) about 1 in 1000 nucleotides
C) fewer than 1 in about 4 million nucleotides
D) about 1 in 100,000 to 1,000,000 nucleotides
E) about 1 in 10,000 nucleotides
Ans: D
Difficulty: Medium
Feedback: 13.1

58. TB 13.058. What is the average rate of replication in bacteria like E. coli?
A) about 100 nucleotides/sec
B) about 1,000 nucleotides/min
C) about 1,000 nucleotides/sec
D) about 10,000 nucleotides/sec
E) about 100 nucleotides/min
Ans: C
Difficulty: Easy
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59. TB 13.059. In in vitro replication systems using cellular extracts, how can specific proteins
be removed from the preparation for the purpose of analyzing how their absence adversely
affects the replication process?
A) targeted denaturation by altered pH
B) targeted denaturation by altering the temperature
C) precipitation of the protein that is to be deleted with specific antibodies to remove it from

solution
D) precipitation of the protein that is to be deleted with ammonium sulfate to remove it from
solution
E) precipitation of the protein that is to be deleted with RNA to remove them from solution
Ans: C
Difficulty: Medium
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60. TB 13.060. The small portions in which eukaryotic cells replicate their genomes are called
_______.
A) replicants
B) replicons
C) repliants
D) replicosomes
E) tracts
Ans: B
Difficulty: Easy
Feedback: 13.1

61. TB 13.061. What technique was used in the discovery of the existence in eukaryotic cells of
replicons, a discovery in which single DNA molecules were shown to be replicated
simultaneously at several sites along their length?
A) scanning electron microscopy
B) confocal laser scanning microscopy
C) autoradiography
D) polyacrylamide gel electrophoresis
E) isoelectric focusing
Ans: C
Difficulty: Medium
Feedback: 13.1

62. TB 13.062. What evidence below suggested that the sequence of DNA was unimportant in
the timing of replication?
A) The inactive, heterochromatized X chromosome in female mammals replicates late in S

phase, while the active euchromatic X chromosome replicates at an earlier stage.

B) The inactive, heterochromatized X chromosome in female mammals replicates early in S
phase, while the active euchromatic X chromosome replicates at a later stage.
C) The inactive, heterochromatized X chromosome in female mammals replicates late in M
phase, while the active euchromatic X chromosome replicates at an earlier stage.
D) Incorporation of radioactive DNA precursors in replicating cells begins over heterochromatic
regions in the nucleus.
E) Incorporation of radioactive DNA precursors in replicating cells ends over heterochromatic
regions in the nucleus.
Ans: A
Difficulty: Medium
Feedback: 13.1

63. TB 13.063. DNA sequences comprising the yeast origin of replication can be removed from
yeast cells and inserted into bacterial DNA molecules. What ability does this confer upon the
bacterial DNA molecules?
1) It confers on them the ability to replicate within a yeast cell.
2) It confers on them the ability to denature.
3) It confers on them the ability to replicate in cellular extracts containing the required
eukaryotic replication proteins.
4) It confers on them the ability to form very tight supercoils.
A) 1
B) 2
C) 3
D) 1 and 3
E) 4
Ans: D
Difficulty: Medium
Feedback: 13.1

64. TB 13.064. DNA sequences comprising the yeast origin of replication can be removed from
yeast cells and inserted into bacterial DNA molecules. Because these sequences promote
replication of the DNA in which they are contained, they are referred to as __________.
A) polygamous replicating sequences
B) autonomous replicating sequences
C) analogous replicating sequences
D) both autonomous replicating sequences and ARSs
E) ARSs

Ans: D
Difficulty: Medium
Feedback: 13.1

65. TB 13.065. Autonomous replicating sequences that have been isolated and analyzed share
several distinct elements. Which distinct elements below are shared by autonomous replicating
sequences?
1) the core element
2) a conserved sequence of 11 base pairs, which functions as a specific binding site for the
origin recognition complex
3) a conserved sequence of 11 base pairs, which functions as the origin recognition complex
A) 1
B) 2
C) 3
D) 1 and 3
E) 1 and 2
Ans: E
Difficulty: Medium
Feedback: 13.1

66. TB 13.066. What binds to the ORC to assemble the prereplication complex (pre-RC) that is
competent to initiate replication?
A) the ORC factors
B) licensing factors
C) competence factors
D) initiation factors
E) enlisting factors
Ans: B
Difficulty: Easy
Feedback: 13.1

67. TB 13.067. At what stage of the cell cycle do the key protein kinases, like cyclin-dependent
kinase become activated?
A) right after mitosis

B)
C)
D)
E)

right before mitosis

just before the start of S phase
in the middle of the G2 phase
in the G0 phase

Ans: C
Difficulty: Easy
Feedback: 13.1

68. TB 13.068. Cyclin-dependent kinase activity stays high through mitosis after rising prior to
DNA synthesis. Which of the following results from its elevated activity?
A) Chromosomes decondense.
B) It suppresses the formation of new prereplication complexes.
C) It enhances the formation of new prereplication complexes.
D) It enlarges the histones by removing their phosphate groups.
E) It shrinks the histones by binding amino groups to them.
Ans: B
Difficulty: Medium
Feedback: 13.1

69. TB 13.069. Why does it appear that each origin can only be activated once per cell cycle?
A) Mcm proteins are displaced from the DNA after replication and cannot reassociate with a
replication origin that has already fired.
B) The ORC is denatured after replication and cannot return to the DNA.
C) The DNA becomes naked until the next round of cell division.
D) Mcm proteins reassociate with DNA immediately and prevent further replication from that
DNA.
E) Mcm proteins bind to other proteins in the cytoplasm; together they actively inhibit further
replication.
Ans: A
Difficulty: Medium
Feedback: 13.1

70. TB 13.070. The collection of proteins in eukaryotes that forms the replicative complex is
known as the __________.

A)
B)
C)
D)
E)

replicand
replicon
replisome
replimere
polymerizer

Ans: C
Difficulty: Easy
Feedback: 13.1

71. TB 13.071. Which eukaryotic DNA polymerase replicates mitochondrial DNA and does not
appear to be involved in nuclear DNA replication?
A) polymerase
B) polymerase
C) polymerase
D) polymerase
E) polymerase
Ans: A
Difficulty: Easy
Feedback: 13.1

72. TB 13.072. Which eukaryotic DNA polymerase functions in DNA repair, but does not
appear to be involved in nuclear DNA replication?
A) polymerase
B) polymerase
C) polymerase
D) polymerase
E) polymerase
Ans: D
Difficulty: Easy
Feedback: 13.1

73. TB 13.073. Which eukaryotic DNA polymerase is both a DNA polymerase and an RNA
primase, with the two catalytic activities present on different subunits? Its RNA primase and

DNA polymerase activities are responsible for initiating the synthesis of each Okazaki fragment.
The RNA primase subunit lays down a short RNA primer and then the DNA polymerase subunit
extends it with about 20 deoxyribonucleotides.
A) polymerase
B) polymerase
C) polymerase
D) polymerase
E) polymerase
Ans: E
Difficulty: Easy
Feedback: 13.1

74. TB 13.074. Which eukaryotic DNA polymerase is thought to be the primary DNAsynthesizing enzyme during replication of the lagging strand?
A) polymerase
B) polymerase
C) polymerase
D) polymerase
E) polymerase
Ans: B
Difficulty: Easy
Feedback: 13.1

75. TB 13.075. Which eukaryotic DNA polymerase is thought to be the primary DNAsynthesizing enzyme during replication of the leading strand?
A) polymerase
B) polymerase
C) polymerase
D) polymerase
E) polymerase
Ans: B
Difficulty: Easy
Feedback: 13.1

76. TB 13.076. Which prokaryotic DNA polymerase resembles the eukaryotic DNA
polymerases and , and which similar structural feature do the three polymerases have in
common?
A) DNA polymerase I, a sliding clamp (PCNA) that is similar to the clamp
B) DNA polymerase II, a sliding clamp (PCNA) that is similar to the clamp
C) DNA polymerase III, a sliding clamp (PCNA) that is similar to the clamp
D) DNA polymerase III, a rolling active site (PCNA)
E) DNA polymerase II, a rolling active site (PCNA)
Ans: C
Difficulty: Medium
Feedback: 13.1

77. TB 13.077. The PCNA sliding clamp used in eukaryotic replication was first discovered as
an antigen that reacted with the autoantibodies of patients suffering from what disease?
A) lupus erythematosus
B) diabetes
C) rheumatoid arthritis
D) myasthenia gravis
E) multiple sclerosis
Ans: A
Difficulty: Easy
Feedback: 13.1

78. TB 13.078. The clamp loader that loads PCNA onto DNA is called _______ and is
analogous to the E. coli DNA polymerase III clamp loader complex.
A) RFC
B) KFC
C) NBC
D) TLC
E) SEC
Ans: A
Difficulty: Easy
Feedback: 13.1

79. TB 13.079. What is responsible for removing the RNA primer and short DNA segment
added by eukaryotic DNA polymerase ?
A) FEN-1
B) DNA polymerase
C) DNase H
D) both FEN-1 and DNase H
E) DNA ligase
Ans: A
Difficulty: Easy
Feedback: 13.1

80. TB 13.080. What is responsible for filling the gap left by the nucleases that digest the
primer and the short DNA segment added to it by polymerase ?
A) DNA polymerase
B) DNA polymerase
C) DNA polymerase
D) both DNA polymerase and DNA polymerase
E) RNase H1
Ans: B
Difficulty: Easy
Feedback: 13.1

81. TB 13.081. What is responsible for joining eukaryotic Okazaki fragments together?
A) DNA ligase
B) DNA polymerase
C) DNA polymerase
D) DNA polymerase
E) RNase H1
Ans: A
Difficulty: Easy
Feedback: 13.1

82. TB 13.082. Which eukaryotic DNA polymerase appears to be the primary DNAsynthesizing enzyme during replication of the lagging strand?
A) polymerase
B) polymerase
C) polymerase
D) polymerase
E) polymerase
Ans: B
Difficulty: Easy
Feedback: 13.1

83. TB 13.083. Which eukaryotic DNA polymerase appears to be the primary DNAsynthesizing enzyme during replication of the leading strand?
A) polymerase
B) polymerase
C) polymerase
D) polymerase
E) polymerase
Ans: C
Difficulty: Easy
Feedback: 13.1

84. TB 13.084. If cells are given a very short exposure (pulses) to radioactive DNA nucleotide
precursors, where is most of the radiolabel located?
A) in the cytoplasm
B) associated with the nuclear matrix
C) in the mitochondria
D) in the DNA loops surrounding the nuclear matrix
E) in the mesosome
Ans: B
Difficulty: Easy
Feedback: 13.1

85. TB 13.085. If cells are given a very short exposure to radioactive DNA nucleotide
precursors followed by unlabeled DNA precursors for an hour or so before fixation, where is
most of the radiolabel located?
A) in the cytoplasm
B) associated with the nuclear matrix
C) in the mitochondria
D) in the DNA loops surrounding the nuclear matrix
E) in the mesosome
Ans: D
Difficulty: Easy
Feedback: 13.1

86. TB 13.086. What evidence suggests that the assembly of DNA into nucleosomes is a very
rapid event?
A) Radiolabel is incorporated in a very short time.
B) Nucleosomes have a very unusual shape.
C) Electron micrographs of replicating DNA show nucleosomes forming on both daughter
duplexes very near the replication fork.
D) Electron micrographs of replicating DNA show nucleosomes forming on both daughter
duplexes at a large distance from the replication fork.
E) Nucleosomes are twice as big near the replication fork.
Ans: C
Difficulty: Medium
Feedback: 13.1

87. TB 13.087. Why has the PCNA sliding clamp been referred to as a molecular toolbelt?
1) FEN-1 is thought to be recruited to the replication fork through an interaction with the
PCNA sliding clamp.
2) DNA ligase is thought to be recruited to the replication fork through an interaction with
the PCNA sliding clamp.
3) The PCNA sliding clamp has an ability to bind to a diverse array of proteins.
4) The PCNA sliding clamp has an ability to denature nearby and associated proteins.
A) 1
B) 2
C) 3
D) 4
E) 1, 2 and 3

Ans: E
Difficulty: Medium
Feedback: 13.1

88. TB 13.088. During which process is PCNA thought to play a major role in orchestrating
events?
1) DNA replication
2) DNA repair
3) DNA hydrolysis
4) DNA recombination
A) 1
B) 2
C) 3
D) 4
E) 1, 2 and 4
Ans: E
Difficulty: Medium
Feedback: 13.1

89. TB 13.089. Collectively, the nucleosomes that form during the replication process are
comprised of _________.
1) histone molecules that are inherited from parental chromosomes
2) a roughly equivalent mixture of acidic proteins from the parental chromosomes and newly
synthesized histones.
3) histone molecules that have been newly synthesized
A) 1
B) 2
C) 1 and 3
D) 4
E) 1, 2 and 3
Ans: C
Difficulty: Medium
Feedback: 13.1

90. TB 13.090. Which of the following describes elements of a model for the distribution of
parental nucleosomes and their histones during replication?
A) (H3H4)2 tetramers present prior to replication remain intact and are distributed randomly
between the two daughter duplexes.
B) Old and new (H3H4)2 tetramers are thought to be intermixed on each daughter DNA
molecule.
C) The two H2A/H2B dimers of each parental nucleosome fail to remain together as the
replication fork moves through the chromatin.
D) The H2A/H2B dimers of a nucleosome separate from one another and bind randomly to the
new and old (H3H4)2 tetramers already present on the daughter duplexes.
E) All of these are correct.
Ans: E
Difficulty: Difficult
Feedback: 13.1

91. TB 13.091. Which of the following describes elements of a model for the distribution of
parental nucleosomes and their histones during replication?
1) The (H3-H4)2 tetramer from parental nucleosomes can be split into two H3-H4 dimers,
each of which may combine with a newly synthesized H3-H4 dimer to form a mixed (H3-H4)2
tetramer.
2) A mixed tetramer (H3-H4)2 assembles with H2A-H2B dimers.
3) A mixed octamer (H3-H4)2 assembles with H2A-H2B dimers.
4) A mixed hexamer (H3-H4)2 assembles with H2A-H2B dimers.
A) 1
B) 2
C) 3
D) 4
E) 1, and 2
Ans: E
Difficulty: Difficult
Feedback: 13.1

92. TB 13.092. The stepwise assembly of nucleosomes and their orderly spacing along the
DNA is facilitated by what?
A) a network of accessory proteins
B) a number of histone chaperones that are able to accept newly synthesized histones and
transfer them to daughter strands

C) a number of histone chaperones that are able to accept parental histones and transfer them to
daughter strands
D) CAF-1, which is able to accept either parental histones or newly synthesized histones and
transfer them to daughter strands
E) All of these are correct.
Ans: E
Difficulty: Difficult
Feedback: 13.1

93. TB 13.093. What recruits CAF-1 to the advancing replication fork?

1) an interaction with another CAF-1
2) an interaction with the sliding clamp
3) an interaction with PCNA
4) an interaction with the nitrogenous bases of the DNA
A) 1
B) 2
C) 3
D) 2 and 3
E) 4
Ans: D
Difficulty: Medium
Feedback: 13.1

94. TB 13.094. What is the most common mechanism for repairing damage to DNA?
A) direct repair of the damage
B) selective excision of the damaged section and use of the complementary strand to replace the
excised portion
C) simple removal of damaged portion without replacement
D) simplistic repair of the damage
E) altruistic repair of the damage
Ans: B
Difficulty: Medium
Feedback: 13.2

95. TB 13.095. Which type of DNA repair removes via a cut-and-patch mechanism a variety of
bulky lesions, like pyrimidine dimers and nucleotides to which various chemical groups have
been attached?
A) nucleotide excision repair
B) base excision repair
C) mismatch repair
D) double-strand breakage repair
E) All of these are correct.
Ans: A
Difficulty: Easy
Feedback: 13.2

96. TB 13.096. In the transcription-coupled repair pathway, how is the presence of a lesion
thought to be detected?
A) There are special enzymes that scan the DNA for such lesions.
B) The lesion may be signaled by a stalled RNA polymerase.
C) The lesion may be signaled by a stalled DNA polymerase.
D) The lesion may be signaled by a stalled peptidyl transferase.
E) The lesion may be detected single-stranded binding proteins.
Ans: B
Difficulty: Medium
Feedback: 13.2

97. TB 13.097. What is the advantage of transcription-coupled repair?

A) It allows the cell to do two things at once.
B) It ensures that the genes of least importance to the cell receive the highest priority on the
repair list.
C) It ensures that the genes of greatest importance to the cell receive the highest priority on the
repair list.
D) It is repairs noncoding sequences preferentially.
E) It is the most accurate method of repair.
Ans: C
Difficulty: Medium
Feedback: 13.2

98. TB 13.098. Which method of repair can be slower, less efficient and responsible for
correcting DNA strands in the parts of the genome that are not being currently transcribed?
1) transcription-coupled pathway of NER
2) global genomic pathway of NER
3) base excision repair
4) replicative repair
A) 1
B) 2
C) 3
D) 4
E) 1 and 2
Ans: B
Difficulty: Easy
Feedback: 13.2

99. TB 13.099. What is the proper order of the steps involved in nucleotide excision repair?
1) Release of the damaged DNA segment between the incisions
2) Sealing of strand by DNA ligase
3) Lesion recognition
4) Separation of the duplex's two strands in the region of the lesion in preparation for its
removal.
5) Filling of gap by DNA polymerase
6) Binding of the XPB and XPD subunits of TFIIH to DNA in the region of the lesion
7) Cutting of the damaged strand on both sides of lesion by endonucleases
A) 6 3 4 7 1 5 2
B) 3 6 4 7 1 2 5
C) 3 6 7 4 1 5 2
D) 3 6 4 7 1 5 2
E) 6 3 7 4 2 1 5
Ans: D
Difficulty: Difficult
Feedback: 13.2

100. TB 13.100. After cuts are made on the two sides of the lesion in nucleotide excision repair,
what holds the damaged part of the strand in position for a while before its final removal?

A)
B)
C)
D)
E)

ionic bonds
van der Waals forces
H bonds
3'-5' phosphodiester linkages
disulfide linkages

Ans: C
Difficulty: Medium
Feedback: 13.2

101. TB 13.101. What established a previously unsuspected link between DNA repair and
transcription?
1) RNA synthesis was found to be instrumental in DNA repair.
2) A small subset of RNAs was found to be required for DNA repair.
3) Two subunits of the transcription factor TFIIH were found to be helicases that
were responsible for unwinding DNA during DNA repair.
4) RNases were essential for the process.
A)
B)
C)
D)
E)

1
2
3
4
1 and 3

Ans: C
Difficulty: Medium
Feedback: 13.2

102. TB 13.102. Which DNA repair mechanism removes altered nucleotides generated by
reactive chemicals present in the diet or produced by metabolism?
A) nucleotide excision repair
B) base excision repair
C) mismatch repair
D) double-strand breakage repair
E) the global genomic pathway
Ans: B
Difficulty: Easy
Feedback: 13.2

103. TB 13.103. Place the steps in base excision repair in the correct order.
1) Damaged base is removed by cleavage of glycosidic linkage attaching it to
deoxyribose of backbone.
2) Baseless deoxyribose phosphate remaining in the site is excised by a specialized
(AP) endonuclease and a DNA polymerase.
3) DNA glycosylase recognizes the alteration in DNA.
4) The strand is sealed by DNA ligase III.
5) Gap is filled by DNA polymerase ; it inserts a nucleotide complementary to the
undamaged strand.
A)
B)
C)
D)
E)

1-3
31
13
32
31

254
24-5
245
154
254

Ans: E
Difficulty: Difficult
Feedback: 13.2

104. TB 13.104. What enzyme cleaves the DNA backbone to remove the beheaded deoxyribose
phosphate during base excision repair?
A) an AP endonuclease
B) phosphodiesterase activity of polymerase
C) 5'>3' exonuclease
D) 3'>5' exonuclease
E) DNA glycosylase
Ans: A
Difficulty: Medium
Feedback: 13.2

105. TB 13.105. What enzyme is responsible for recognizing a chemical alteration in the DNA
and removing the base by cleavage of the bond holding the base to the deoxyribose sugar
moiety?
A) an AP endonuclease
B) phosphodiesterase activity of polymerase

C) 5'>3' exonuclease
D) 3'>5' exonuclease
E) DNA glycosylase
Ans: E
Difficulty: Easy
Feedback: 13.2

106. TB 13.106. Why did natural selection favor the use of thymine as a base in DNA instead of
uracil even though uracil was presumably present in RNA, when it served as the genetic material
during the early evolution of life?
A) Thymine was more stable.
B) Thymine paired better with adenine than did uracil.
C) Retention of uracil as a DNA base would make it hard to tell whether a uracil was supposed
to be at a particular site or whether it resulted from damage to cytosine.
D) Thymine is resistant to all chemical treatments.
E) Retention of uracil as a DNA base would make it hard to tell whether a uracil was supposed
to be at a particular site or whether it resulted from damage to guanine.
Ans: C
Difficulty: Medium
Feedback: 13.2

107. TB 13.107. Which DNA repair mechanism recognizes a distortion in double helix
geometry caused by DNA polymerase's insertion of an incorrect nucleotide during replication,
one that escaped the enzyme's proofreading exonuclease?
A) nucleotide excision repair
B) base excision repair
C) mismatch repair
D) double-strand breakage repair
E) transcription-coupled pathway
Ans: C
Difficulty: Easy
Feedback: 13.2

108. TB 13.108. What must the mismatch repair system be able to distinguish in order to tell

which nucleotide of a mismatched pair to replace?

1) It must be able to distinguish the newly-made strand from the parental strand.
2) It must be able to distinguish which chain possesses the newest phosphate groups.
3) It must be able to distinguish which chain contains the ribose sugars.
4) It must be able to distinguish which chain contains the oldest phosphate groups.
A) 1
B) 2
C) 3
D) 4
E) 1 and 2
Ans: A
Difficulty: Medium
Feedback: 13.2

109. TB 13.109. In mammalian cells, a complex of proteins binds to the broken ends of the
DNA duplex and catalyzes a series of reactions that rejoin the broken strands. This is an
example of what kind of repair?
A) nucleotide excision repair
B) base excision repair
C) mismatch repair
D) double-strand breakage repair
E) nonhomologous end joining
Ans: E
Difficulty: Easy
Feedback: 13.2

110. TB 13.110. A double-stranded breakage repair pathway that requires the presence of a
second chromosome carrying the same sequence of genes as the damaged chromosome is called
_________.
A) nonhomologous end joining repair
B) homologous recombination
C) NHEJ
D) DNA methylation repair
E) nonhomologous recombination
Ans: B
Difficulty: Easy
Feedback: 13.2

111. TB 13.111. Patients with the classical form of xeroderma pigmentosum have a defect in
one of the genes involved in ______________.
A) nucleotide excision repair
B) replication
C) base excision repair
D) transcription
E) base excitation repair
Ans: A
Difficulty: Easy
Feedback: 13.3

112. TB 13.112. What happens once damage caused by lesions in the genome, like a thymidine
dimer, is bypassed during replication and replication must continue?
A) The bypass DNA polymerase continues replication.
B) The replicative DNA polymerase continues replication.
C) The bypass DNA polymerase continues replication.
D) The normal replicative DNA polymerase continues replication.
E) The bypass DNA polymerase continues replication.
Ans: D
Difficulty: Medium
Feedback: 13.3

113. TB 13.113. The DNA polymerases in a relatively large family of polymerases in which
each member is specialized for incorporating nucleotides opposite particular types of DNA
lesions in the template strand engage in a type of DNA synthesis called __________. They have
an unusually spacious active site that ____________.
A) translesion synthesis, unwinds DNA double helices
B) translesion synthesis; is able to physically accommodate altered nucleotides that would not fit
in the active site of a replicative polymerase
C) transdimensional synthesis; incorporates the nucleotide that would have paired with the
undamaged version of the template base
D) transdimensional synthesis; unwinds DNA synthesis
E) transliteral synthesis; is able to physically accommodate altered nucleotides that would not fit
in the active site of a replicative polymerase

Ans: B
Difficulty: Difficult
Feedback: 13.3

114. Human Perspectives Question 13.001

What causes xeroderma pigmentosum (XP)?
A) XP patients possess a deficient translation system.
B) XP patients possess an overly efficient DNA repair system.
C) XP patients possess a deficient DNA repair system.
D) XP patients possess a deficient transcription mechanism.
E) XP patients cannot metabolize the amino acid phenylalanine.
Ans: C
Difficulty: Easy
Feedback: Human Perspectives

115. Human Perspectives Question 13.002

An inherited disorder characterized by acute sensitivity to light, neurological dysfunction due to
neuron demyelination and dwarfism without an evident rise in skin cancer frequency is called
________.
A) xeroderma pigmentosum
B) Cockayne syndrome
C) Cockayde syndrome
D) trichothiodystrophy
E) colon cancer
Ans: B
Difficulty: Easy
Feedback: Human Perspectives

116. Human Perspectives Question 13.003

Which DNA repair mechanism is deficient in cells from a Cockayne syndrome patient?
A) base excision repair
B) transcription-coupled pathway of nucleotide excision repair
C) global pathway of nucleotide excision repair
D) mismatch repair

E) double strand breakage repair

Ans: B
Difficulty: Medium
Feedback: Human Perspectives

117. Human Perspectives Question 13.004

Cockayne syndrome patients have normal skin cancer rates. This suggests that which DNA
repair mechanism is operating normally?
A) base excision repair
B) transcription-coupled pathway of nucleotide excision repair
C) global pathway of nucleotide excision repair
D) mismatch repair
E) double strand breakage repair
Ans: C
Difficulty: Medium
Feedback: Human Perspectives

118. Human Perspectives Question 13.005

Some XP patients in rare cases also have Cockayne syndrome symptoms. This happens in
people who have specific mutations in a particular gene. What gene is affected when this
happens?
A) XPA gene
B) XPB gene
C) XPD gene
D) XPX gene
E) CSA gene
Ans: C
Difficulty: Easy
Feedback: Human Perspectives

119. Human Perspectives Question 13.006

Which disease is characterized by both DNA repair and transcription deficiencies, including
sensitivity to the sun without elevated risks of cancer and a number of additional symptoms like
brittle hair and scaly skin?

A)
B)
C)
D)
E)

xeroderma pigmentosum
Cockayne syndrome
XP-V syndrome
trichothiodystrophy
colon cancer

Ans: D
Difficulty: Easy
Feedback: Human Perspectives

120. Human Perspectives Question 13.007

The two most common forms of skin cancer are ____________.
A) basal cell carcinoma and squamous cell carcinoma
B) malignant melanoma and squamous cell carcinoma
C) basal cell carcinoma and malignant melanoma
D) basal cell carcinoma and keratoma
E) keratoma and squamous cell carcinoma
Ans: A
Difficulty: Easy
Feedback: Human Perspectives

121. Human Perspectives Question 13.008

From what kinds of cells does malignant melanoma arise?
A) connective tissue cells
B) epithelial cells
C) glial cells
D) skin pigment cells
E) concentric cells
Ans: D
Difficulty: Easy
Feedback: Human Perspectives

122. Human Perspectives Question 13.009

What is one of the greatest risk factors for developing malignant melanoma as an adult?
A) saturated fats in the diet

B)
C)
D)
E)

unsaturated fats in the diet

a severe, blistering sunburn as a child or adolescent
application of too much hand cream
excessive abrasion of the skin

Ans: C
Difficulty: Easy
Feedback: Human Perspectives

123. Human Perspectives Question 13.010

What is estimated to be responsible for up to 15% of colon cancers?
A) mutations in genes that encode the proteins required for a normal cytoskeleton
B) mutations in genes that encode the proteins required for mismatch repair
C) mutations in genes that encode the proteins required for base excision repair
D) mutations in genes that encode the proteins required for nucleotide excision repair
E) mutations in genes that control production of colon mucous
Ans: B
Difficulty: Easy
Feedback: Human Perspectives

124. Human Perspectives Question 13.011

Why do mutations that cripple the mismatch repair system inevitably lead to a higher mutation
rate in other genes?
A) Mutations that cripple mismatch repair accelerate production of new mutants in other genes.
B) Mutations that cripple mismatch repair prevent mutations in other genes from being created.
C) Mutations that cripple mismatch repair prevent mistakes made during transcription of other
genes from being corrected.
D) Mutations that cripple mismatch repair prevent mistakes made during replication in other
genes from being corrected.
E) Mutations that cripple mismatch repair prevent mistakes made during translation of other
genes from being corrected.
Ans: D
Difficulty: Medium
Feedback: Human Perspectives

125. Human Perspectives Question 13.012

Radon (222Rn) forms during the radioactive disintegration of what material?
A) water
B) uranium
C) radium
D) plutonium
E) lead
Ans: B
Difficulty: Easy
Feedback: Human Perspectives

126. Human Perspectives Question 13.013

Exposure to radon causes cancer in what way?
A) When ingested, it causes double strand DNA breaks raising the risk of colon cancer.
B) When breathed into the lungs, it can lead to double strand DNA breaks that raise the lung
cancer risks.
C) When touching the skin, it can lead to double strand DNA breaks that raise skin cancer risks.
D) When ingested, it can lead to mismatches that raise the colon cancer risks.
E) When breathed into the lungs, it can lead to mismatches that raise the lung cancer risks.
Ans: B
Difficulty: Medium
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127. Human Perspectives Question 13.014

What individuals are at greatest risk for developing malignant melanoma?
A) Caucasians with moderately dark skin
B) Caucasians with extremely light skin
C) African Americans
D) Eskimos
E) Native Americans
Ans: B
Difficulty: Medium
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128. Human Perspectives Question 13.015

Why are many Caucasians with extremely light skin so susceptible to malignant melanoma?
1) They have melanocytes that lack a functioning receptor for a hormone that is
secreted by nearby skin epithelial cells in response to ultraviolet radiation.
2) They have pigment cells that lack a functioning receptor for a hormone that is
secreted by nearby skin epithelial cells in response to ultraviolet radiation.
3) These individuals are less able to respond to the presence of UV-light by
making melanin.
4) These individuals are better able to respond to the presence of UV-light by
making melanin.
A)
B)
C)
D)
E)

1
2
3
1, 2 and 3
4

Ans: D
Difficulty: Medium
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129. Human Perspectives Question 13.015

Which of the circumstances below can lead to premature (or accelerated) aging in humans or
animal models?
A) increased free radicals
B) increased mitochondrial DNA mutations
C) mutations in a protein of the nuclear envelope
D) unrepaired covalent crosslinks between two strands of a DNA duplex that lead to increased
apoptosis
E) All of these are correct.
Ans: D
Difficulty: Difficult
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130. Human Perspectives Question 13.016

What does the product of the XPF gene do?
A) It unwinds DNA.
B) It makes one of the cuts in the base excision repair pathway.

C) It makes one of the cuts in the nucleotide excision repair pathway.

D) It replicates mitochondrial DNA.
E) It changes adenine to uracil.
Ans: C
Difficulty: Medium
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131. Human Perspectives Question 13.016

Defects in DNA repair systems that result primarily in an increased mutation rate in the body's
cells are associated with _________.
A) accelerated aging
B) accelerated heart rate
C) an increased susceptibility to cancer
D) an increased susceptibility to pneumonia
E) a decreased susceptibility to cancer
Ans: C
Difficulty: Medium
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132. Human Perspectives Question 13.017

Defects in DNA repair systems that result primarily in cell death are associated with _________.
A) accelerated aging
B) accelerated heart rate
C) an increased susceptibility to cancer
D) an increased susceptibility to pneumonia
E) a decreased susceptibility to cancer
Ans: A
Difficulty: Medium
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Essay

133. Human Perspectives Question 13.018.

What is the deficit that seems to explain the fact that some individuals can suffer from the
combined symptoms of xeroderma pigmentosum (XP) and Cockayne syndrome (CS)?
Ans: Individuals who suffer from symptoms of XP and CS have mutations in the XPD gene.
This gene encodes a subunit of the transcription factor TFIIH, which plays a role in both
transcription and DNA repair. The TFIIH of such an individual has defects that render it unable
to carry out either transcription or DNA repair in a normal fashion.
Difficulty: Difficult
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134. Human Perspectives Question 13.019.

What is the cause of CS and the widespread abnormalities associated with it in most CS
sufferers?
Ans: Most cases of CS can be traced to a mutation in either the CSA or CSB gene, which are
thought to be involved in the coupling of transcription to DNA repair. Such genes may also
affect the transcription of certain genes, which may explain the more widespread abnormalities
of CS patients.
Difficulty: Difficult
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135. Human Perspectives Question 13.020.

Which kinds of skin cancer arise from epithelial cells?
Ans: Basal cell and squamous cell carcinomas.
Difficulty: Difficult
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136. Human Perspectives Question 13.021.

How could two different diseases be caused by a deficiency in the same protein?
Ans: The mutation in each case could be localized to different domains of the protein in
question. These different domains are responsible for different activities. A deficiency in one
activity may lead to one set of symptoms; a deficiency in the other activity may lead to a
completely different set of symptoms, like growth retardation and abnormal development of the
nervous system.

Difficulty: Difficult
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137. Human Perspectives Question 13.022.

Why is malignant melanoma so much more dangerous than basal cell or squamous cell
carcinomas?
Ans: Malignant melanoma metastasizes more easily than the other two types of cancer and can
consequently spread to other parts of the body where it can establish secondary tumors if it is not
detected soon enough.
Difficulty: Difficult
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138. Human Perspectives Question 13.023.

What type of cell is affected in malignant melanoma?
Ans: Pigment cells (melanocytes) in the skin.
Difficulty: Difficult
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139. Human Perspectives Question 13.024.

Why does a mutation in one of the genes that codes for a protein needed for mismatch repair lead
to elevated mutation rates in other genes?
Ans: Such a mutation leads to mutations in other genes, since the repair system is disabled. It
will fail to detect all of the mutations induced during the normal course of cell activities before
the next cell division and the mutations will thus be passed on to the next generation. Normally,
the majority of such mismatches are detected and repaired prior to the next cell division.
Difficulty: Difficult
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140. Human Perspectives Question 13.025.

What is one of the consequences of double-strand DNA breaks that have either gone unrepaired

or been repaired incorrectly? What kinds of environmental agents to which we are commonly
exposed can cause breaks in DNA? What is the most serious environmental hazard that can
cause double-stranded breaks in DNA that may go unrepaired or be repaired incorrectly thus
leading to cancer? How does radon cause cancer?
Ans: Cancer. X-rays, gamma rays and radioactive emissions like radon. Radon (222R) is a
radioactive isotope formed during the disintegration of uranium. Some areas of the planet
contain relatively high levels of uranium in the soil; houses built in these regions can contain
dangerous levels of radon gas. About 1% of houses in the United States have radon levels that
produce more than 10 picocuries per liter of radiation. When radon gas is breathed into the lungs,
it can lead to double-stranded DNA breaks that increase the risk of lung cancer. A significant
fraction of lung-cancer deaths in nonsmokers is probably due to radon exposure.
Difficulty: Difficult
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141. Human Perspectives Question 13.026.

Studies on a human and mice with a corresponding mutation have suggested that the unrepaired
crosslinks caused by the mutation lead to increased cell death. What is another name for
increased cell death? What do increased rates of apoptosis cause? Defects in DNA repair
systems that result primarily in an increased mutation rate in the body's cells are associated with
what? Defects in DNA repair systems that result primarily in cell death are associated with
what?
Ans: Apoptosis. Increased apoptosis rates directly or indirectly promotes premature aging. An
increased susceptibility to cancer. Accelerated aging.
Difficulty: Difficult
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142. Critical Thinking Question 13.001.

Cultured mammalian cells are placed in culture in the presence of BrdU. At the end of one
generation time (the first replication), what do the chromosomes look like?
Ans: Each chromosome will consist of two chromatids. One strand of each chromatid will
contain thymidine along with the other nucleotides. The other strand will contain adenosine,
cytosine and guanosine, but the thymidine will be replaced by BrdU.
Difficulty: Difficult
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143. Critical Thinking Question 13.002.

You are studying replication in a particular bacterial strain. At 37C, the bacteria appear
perfectly normal. If the temperature is raised to 43C, however, they stop growing and are
unable to replicate their DNA. If some of them are placed back at 37C, they begin to replicate
their DNA and are again perfectly normal. What is wrong?
Ans: The bacteria probably carry a temperature-sensitive mutant of one of the genes whose
product is essential for replication.
Difficulty: Difficult
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144. Critical Thinking Question 13.004.

If a DNA polymerase were discovered that was able to synthesize DNA without the requirement
of a free 3'-hydroxyl group, which feature of DNA replication would be least likely to be
needed?
Ans: There would be no need to make RNA primers with RNA primase.
Difficulty: Difficult
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145. Critical Thinking Question 13.005.

What kind of enzyme would be needed to eliminate the necessity for bidirectional replication at
the replication fork?
Ans: The DNA polymerase would have to be able to synthesize DNA in both 5'>3' and 3'
>5' directions.
Difficulty: Difficult
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146. Critical Thinking Question 13.006.

Why was it important that Okazaki used a very short pulse of radioactive precursor and then
sacrificed the cells immediately in his initial experiment?
Ans: If the labeling period had been too long, the presence of radiolabeled fragments would
have been swamped and difficult to detect against a higher background of label incorporated into
large DNA molecules. If the cells had not been killed immediately after the pulse, the label in
the fragments would have become part of the larger DNA molecule in a very short time.

Difficulty: Difficult
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147. Critical Thinking Question 13.007.

Would the presence of an RNA synthesis inhibitor be likely to interfere with replication in
bacteria?
Ans: An RNA synthesis inhibitor might be expected to interfere with replication, since the
synthesis of DNA requires the synthesis of RNA primers produced by a special RNA polymerase
called primase.
Difficulty: Difficult
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148. Critical Thinking Question 13.008.

Despite the numerous checkpoints present in the cell to prevent the placement of the wrong
nucleotide in a replicating DNA, a few mistakes can be made. Why is this a positive
development?
Ans: Mistakes, such as these, lead to mutations and mutations are the stuff of evolution. If
replication were perfect, the incidence of mutation would be substantially lower and evolution
would have proceeded more slowly, if at all.
Difficulty: Difficult
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149. Critical Thinking Question 13.009.

What is the major reason for the multiple initiation sites for eukaryotic replication?
Ans: There are two major reasons for the multiple initiation sites. First, eukaryotic genomes are
bigger than prokaryotic genomes and tend to be linear instead of circular as prokaryotic genomes
often are. Second, eukaryotic DNA polymerases are slower than those of bacteria and thus more
initiation sites would help to speed up replication of the longer eukaryotic genomes.
Difficulty: Difficult
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150. Critical Thinking Question 13.010.

Which chromosomal DNA - centromeres or active genes - would be most likely to replicate first?
Ans: The DNA encoding active genes would be likely to replicate first, since it is euchromatin
and relatively decondensed. Since centromeres are heterochromatin and relatively condensed,
they will most likely be replicated later, since it takes time to unwind the DNA enough to
replicate it.
Difficulty: Difficult
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151. Critical Thinking Question 13.011.

The DNA sequences flanking the ORC-binding site exhibit lowered duplex stability. What can
you guess about the nucleotide sequence in this area?
Ans: The sequence of this region of the ARS is A-T-rich. Since A-T base pairs bond with only
two H bonds, sections of DNA containing these base pairs are held together less tightly than
areas of DNA, which have predominantly G-C base pairs (which contain three H bonds per base
pair).
Difficulty: Difficult
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152. Critical Thinking Question 13.012

After exonucleases have excised the damaged portion of DNA, how can DNA polymerase fill in
the gap? Is there a primer?
Ans: The free 3'-hydroxyl group at one end of the gap serves as the primer, allowing DNA
polymerase to fill it in using the opposing strand as a complementary template.
Difficulty: Difficult
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153. Critical Thinking Question 13.013

What enzyme activity are the Mcm proteins (Mcm2 Mcm7) thought to exhibit once they have
been loaded onto the replication origin and associated into a ring-shaped complex? What role
does this enzyme activity play in replication and to what protein in E. coli is it analogous?
Ans: Helicase activity. The helicase activity is responsible for unwinding DNA at the
replication fork. It is analogous to DnaB in E. coli.

Difficulty: Difficult
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154. Critical Thinking Question 13.014

You are the enzyme responsible for carrying out mismatch repair. You notice a mismatched pair
in the DNA strand and you know it is your job to remove one of the bases in the mismatched
pair. How would you decide which nucleotide to remove?
Ans: You would look at the DNA strands and identify the strand with the methylated adenosines.
You would then remove the base from the nonmethylated (new) strand. The old strand would be
assumed to be correct. The new strand is assumed to be where the mistake was made.
Difficulty: Difficult
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155. Critical Thinking Question 13.015.

You are synthesizing DNA in vitro and add DNA ligase from an old container to the mix by
mistake. If the DNA ligase is still active, the reaction will work fine and you will obtain normal
results. What would you expect to happen if the DNA ligase preparation is no longer active?
Ans: Since DNA ligase connects the Okazaki fragments together, the lagging strand will not be
formed and the Okazaki fragments will remain fragments.
Difficulty: Difficult
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156. Critical Thinking Question 13.016.

If you use an inactive DNA ligase by mistake in an in vitro DNA repair system, what would have
been the result?
Ans: The faulty bases in the DNA needing repair would be excised and the new DNA sequence
would be laid into the appropriate place, but DNA ligase would be unable to covalently link the
"patch" to the old strand. Thus, the repair could and would not be completed.
Difficulty: Difficult
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157. Critical Thinking Question 13.017.

What would be the likely result if single-stranded binding proteins were not working properly
during replication?
Ans: The separated strands of DNA would tend to renature more than usual perhaps before the
replication machinery had done its job. This could be a major deficit and could lead to the death
of the organism. At the very least, it would be likely to slow down replication.
Difficulty: Difficult
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158. Critical Thinking Question 13.018.

What is thought to displace nucleosomes during replication? The core histone octamer of a
nucleosome consists of an (H3H4)2 tetramer together with a pair of H2A/H2B dimers. What are
two contrasting models that describe how parental nucleosomes are distributed during
replication?
Ans: The movement of the replication machinery along the DNA. One model suggests that the
(H3H4)2 tetramers present prior to replication remain intact and are distributed randomly
between the two daughter duplexes. Thus, old and new (H3H4)2 tetramers are thought to be
intermixed on each daughter DNA molecule. According to this model, the two H2A/H2B dimers
of each parental nucleosome fail to remain together as the replication fork moves through the
chromatin. Instead, the H2A/H2B dimers of a nucleosome separate from one another and bind
randomly to the new and old (H3H4)2 tetramers already present on the daughter duplexes.
Another viewpoint suggests that the (H3H4)2 tetramer from parental nucleosomes can be split
into two H3H4 dimers, each of which may combine with a newly synthesized H3H4 dimer to
form a mixed (H3H4)2 tetramer, which then assembles with H2A/H2B dimers.
Difficulty: Difficult
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159. Art Question 13.001.

In the figure below, how many of the second-generation progeny in the dispersive model are
composed of two full parental DNA strands? How many of the second-generation progeny in the
conservative model are composed of two full parental DNA strands?

Ans: None, each progeny strand is a combination of new and old material. One.
Difficulty: Medium
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160. Art Question 13.002.

In the figure below, what would the results for semiconservative replication look like at 0.5
generation times? What would the conservative model look like at 0.5 generation times?

Ans: Half the DNA would be at the heavy position and half at the hybrid position. Twice as
much DNA would be at the heavy position as at the light position.
Difficulty: Medium
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161. Art Question 13.003.

In the figure below, most of the chromosomes stain uniformly dark in one chromatid and
uniformly light in another. A few chromosomes, however, seem to have exchanged homologous
dark and light portions. What has happened?

Ans: The exchange of homologous portions of the chromatids is the result of sister chromatid
exchange, which is a common occurrence during mitosis.
Difficulty: Medium
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162. Art Question 13.004.

In the figure below, what Greek letter resembles the appearance of the replicating circular
bacterial chromosome when it is about halfway through the replication process?

Ans: The Greek letter theta ().

Difficulty: Medium
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163. Art Question 13.005.

In the figure below, why don't the structures depicted serve as appropriate templates?

Ans: All three structures in this figure have a template strand but no primer with a 3'-hydroxyl
free end.
Difficulty: Medium
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164. Art Question 13.006.

In the figure below, how long does it take for the bulk of radiolabeled precursor to move from
smaller pieces of DNA to larger DNA fragments?

Ans: By 60 seconds, most of the precursor has been incorporated into larger pieces of DNA. By
120 sec, the vast majority of radiolabeled precursor has been incorporated into larger DNA
fragments.
Difficulty: Medium
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165. Art Question 13.007.

In the mechanism depicted in the figure below, what provides the energy for the unwinding of
DNA and what enzyme catalyzes the process? What prevents the DNA from reforming the
duplex from reforming as DNA is unwound during replication?

Ans: Helicase catalyzes the reaction, which is driven by ATP hydrolysis. Single-stranded DNAbinding proteins (SSBs).
Difficulty: Medium
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166. Art Question 13.008

Look at the figure below. How do the two DNA polymerase III molecules move together, even
though they are moving toward opposite ends of their respective templates?

Ans: This is accomplished by causing the lagging-strand template to form a loop.

Difficulty: Medium
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167. Art Question 13.009.

In the figure below, what holds the DNA polymerase on the DNA? Where do the -clamps
assemble on the replicating DNA strands? After completion of an Okazaki fragment, the DNA
polymerase disengages from the -clamp and cycles to a recently assembled -clamp waiting on
an upstream RNA primer-DNA template junction. What happens to the -clamp that was left
behind on the finished Okazaki fragment?

Ans: The -sliding clamp holds the DNA polymerase on the DNA as it moves along the
template strand and synthesizes the complementary strand. They assemble at the end of each
RNA primer-DNA template junction. The -clamp is left behind on the finished Okazaki
fragment for a period of time, but it is eventually disassembled and reutilized.
Difficulty: Medium
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168. Art Question 13.010.

Which exonuclease activity of DNA polymerase I depicted in the figure below removes the RNA
primer? What does the 3' > 5' exonuclease activity of DNA polymerase I do and for what
property of DNA replication is it responsible?

Ans: The 5' > 3' exonuclease activity. The 3' > 5' exonuclease activity of DNA polymerase
I removes mispaired nucleotides from the 3' end of the growing DNA strand. It is largely
responsible for maintaining the accuracy of DNA synthesis (proofreading).
Difficulty: Medium
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169. Art Question 13.011.

As shown in the figure below, how many H bonds are made in A-C base pairs? How many H
bonds are there in G-T base pairs?

Ans: 2 H bonds. 2 H bonds.

Difficulty: Medium
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170. Art Question 13.012.

According to the figure below, what is responsible for the formation of the pyrimidine dimer
within the DNA duplex that is pictured there?

Ans: UV irradiation.
Difficulty: Medium
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171. Art Question 13.013

According to the figure below, what is responsible for damage recognition in the transcriptioncoupled pathway of nucleotide excision repair? What is responsible for damage recognition in
the global genomic pathway of nucleotide excision repair? What is responsible for DNA repair
synthesis in nucleotide excision repair? What is responsible for sealing the new DNA into the
DNA duplex?

Ans: A stalled RNA polymerase in conjunction with a CSB protein. It is mediated by an XPCcontaining protein complex. DNA polymerase and/or . DNA ligase I.
Difficulty: Medium
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172. Art Question 13.014.

In the figure below, what does phosphodiesterase do in the base excision repair process in
combination with the other enzymes involved?

Ans: After uracil-DNA glycosylase has removed the uracil base mistakenly found in DNA from
its phosphate-sugar backbone, the phosphodiesterase enzyme activity of DNA polymerase in
combination with an AP endonuclease (which cleaves the phosphate-sugar backbone) removes
the sugar and phosphate group to which the uracil had been attached. After this has been done,
DNA polymerase fills in the correct nucleotide, attaching it to the free 3'-hydroxyl end
resulting from the excision and leaving behind a nick in the chain. The nick is sealed by DNA
ligase III.
Difficulty: Medium
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173. Art Question 13.015.

According to the figure below, what is responsible for detecting the lesion in double-strand break
repair? What joins the broken ends of the DNA together in double-strand break repair?

Ans: The lesion is detected by a heterodimeric, ring-shaped protein called Ku that binds to the
broken ends of the DNA. The DNA-bound Ku recruits another protein, called DNA-PKCS, which
is the catalytic subunit of a DNA-dependent protein kinase, the substrates of which have not as
yet been identified. DNA ligase IV.
Difficulty: Medium
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