MOLECULAR BIOLOGY OF THE CELL, SIXTH EDITION

CHAPTER 5: DNA REPLICATION, REPAIR, AND

RECOMBINATION
© Garland Science 2015

1 Which of the following is correct regarding the mutation rate of genomic DNA in
different organisms?
A. Human cells have a much higher mutation rate compared to bacteria when the rate is
normalized to a single round of replication over the same length of DNA.
B. Mutation rates limit the number of essential genes in an organism’s genome.
C. Mutations in the somatic cells cannot be lethal.
D. Even if the mutation rate was 10 times higher than its current value, germ-cell
stability in humans would not have been affected.
E. All of the above.

2 The mutation rate in bacteria is about 3 nucleotide changes per 10 billion nucleotides per
cell generation. Under laboratory conditions, bacteria such as Escherichia coli can divide and
double in number about every 40 minutes. If a single Escherichia coli cell is allowed to
exponentially divide for 10 hours in this manner, how many mutations would you expect to
observe on average in the genome (4.5 million nucleotide pairs) of each of the resulting bacteria
compared to the original cell? Assume all mutations are neutral; that is, they do not affect the
cell-division time.
A. Less than 0.001
B. About 0.02
C. One or two
D. About 10
E. About 100

3 On average, errors occur in DNA synthesis only once in every ten billion nucleotides
incorporated. Which of the following does NOT contribute to this high fidelity of DNA
synthesis?
A. Complementary base-pairing between the nucleotides
B. “Tightening” of the DNA polymerase enzyme around its active site to ensure correct
pairing before monomer incorporation
 C. Exonucleolytic proofreading by the 3′-to-5′ exonuclease activity of the enzyme to
correct mispairing even after monomer incorporation
D. A strand-directed mismatch repair system that detects and resolves mismatches soon
after DNA replication
E. All of the above mechanisms DO contribute to the fidelity.

4 The nuclear DNA polymerases in human cells …

A. polymerize about 1000 nucleotides per second during DNA replication in vivo.
B. are incapable of 3′-to-5′ exonuclease activity.
C. are capable of 3′-to-5′ DNA polymerase activity.
D. have a single active site that is used for both polymerization and editing.
E. are unable to initiate polymerization de novo (i.e. in the absence of a primer).

5 What is the main source of the free energy for the mechanical work performed by DNA
helicases during DNA replication in our cells?
A. The hydrogen-bonding energy in the DNA double helix
B. Thermal energy in the nucleus
C. ATP hydrolysis by the helicase
D. The energy of SSB binding to single-stranded DNA
E. ATP hydrolysis by DNA topoisomerases

6 During DNA replication in the cell, DNA primase makes short primers that are then
extended by the replicative DNA polymerases. These primers …
A. are made up of DNA.
B. generally have a higher number of mutations compared to their neighboring DNA.
C. are made more frequently in the leading strand than the lagging strand.
D. are joined to the neighboring DNA by DNA ligase.
E. provide a 3′-phosphate group for the DNA polymerases to extend.

7 DNA ligases are used in both DNA replication and repair to seal breaks in the DNA. But
DNA damage can result in single- or double-strand breaks that are not normal ligase substrates.
These need to be processed first before a ligase can act on them. One of the enzymes that is
recruited to some of such breaks is called PNK. It has two separate activities on the DNA, both
of which can help provide a canonical ligase substrate. Which of the following activities would
you expect PNK to have in this context?
A. 5′ kinase (phosphorylation of a free 5′-OH group) and 3′ kinase
 B. 5′ phosphatase (dephosphorylation to create a free 5′-OH group) and 3′ phosphatase
C. 3′ kinase and 3′ phosphatase
D. 5′ phosphatase and 3′ kinase
E. 5′ kinase and 3′ phosphatase

8 Fill in the gap in the following paragraph using what you know about the activities of the
proteins involved in DNA replication.
“Mitochondrial DNA replication requires a set of proteins similar
to those used for the replication of the nuclear genome. However,
mitochondria lack a dedicated DNA ... and use the mitochondrial
RNA polymerase instead.”

9 During DNA replication, the single-strand DNA-binding (SSB) proteins …

A. are generally found more on the leading strand than the lagging strand.
B. bind cooperatively to single-stranded DNA and cover the bases to prevent base-
pairing.
C. prevent the folding of the single-stranded DNA.
D. bind cooperatively to short hairpin helices that readily form in the single-stranded
DNA.
E. All of the above.

10 This protein is present at every replication fork and prevents DNA polymerase from
dissociating, but does not impede the rapid movement of the enzyme. Which of the following is
true regarding this protein?
A. It self-assembles onto DNA at the replication fork.
B. It is assembled on DNA as soon as DNA polymerase runs into a double-strand region
of DNA.
C. Its assembly normally follows the synthesis of a new primer by the DNA primase.
D. It disassembles from DNA as soon as DNA polymerase runs into a double-strand
region.
E. All of the above.

11 At the replication fork, the template for the lagging strand is thought to loop around. This
looping would allow the lagging-strand polymerase to move along with the rest of the
replication fork instead of in the opposite direction. The single-strand part of the loop is bound
by the single-strand DNA-binding (SSB) proteins. As each Okazaki fragment is synthesized
toward completion, how does the size of the loop change? What about the size of the SSB-bound
part of the loop?
A. Increases; increases.
B. Increases; decreases.
C. Decreases; increases.
D. Decreases; decreases.
E. Decreases; does not change.

12 The Dam methylase is responsible for methylating the adenine base in GATC sequences
in Escherichia coli. Imagine two E. coli strains, one without any active Dam methylase, and the
other with a hyperactive version of the enzyme that operates faster than the wild-type enzyme.
Which of these strains would you expect to show a “mutator” phenotype?
A. Both of the strains
B. Neither of them
C. Only the first strain
D. Only the second strain

13 In the following schematic drawing, two DNA molecules are shown before and after the
action of a protein that is also involved in the process of DNA replication. What is this protein
called?

A. DNA ligase
B. DNA helicase
C. DNA polymerase I
D. DNA topoisomerase I
E. DNA topoisomerase II
14 What do the enzymes topoisomerase I and topoisomerase II have in common?
A. They both have nuclease activity.
B. They both create double-strand DNA breaks.
C. They both require ATP hydrolysis for their function.
D. They both can create winding (tension) in an initially relaxed DNA molecule.
E. All of the above.

15 In Escherichia coli, replication of DNA can occur throughout the cell cycle while the cell
is also actively transcribing its genes. This means collisions between replication forks and RNA
polymerases are inevitable. Depending on the orientation of the genes, collisions can be rear-end
(when both machines are traveling in the same direction) or head-on (when they are traveling in
opposite directions). In the following paragraph, match each of the letters (A to D) to one
appropriate number below. Do not use a number more than once. Your answer would be a four-
digit number composed of digits 1 to 5 only, e.g. 1253.
“Typically, in a rear-end collision, the (A) of RNA polymerase
collides with the (B) in the replication fork. In contrast, in a head-
on collision, the (C) of RNA polymerase hits the (D) in the fork.”
1. front edge (of RNA polymerase)
2. rear edge (of RNA polymerase)
3. DNA helicase
4. leading-strand DNA polymerase
5. lagging-strand DNA polymerase

16 Which of the following features is common between the replication origins in

Escherichia coli and Saccharomyces cerevisiae?
A. They both normally exist in one copy per genome.
B. Both are specified by DNA sequences of tens of thousands of nucleotide pairs.
C. Both contain sequences that attract initiator proteins, as well as stretches of DNA rich
in A-T base pairs.
D. Both contain GATC repeats that are methylated to prevent the inappropriate “firing”
of the origin.
E. All of the above.

17 You have found a strain of Escherichia coli that has an unusually short doubling time of
only 15 minutes, despite the fact that its complete DNA replication should take almost 35
minutes. You also find that there is only one replication origin on its chromosome from which
two forks originate, just like the normal process described for E. coli. However, you discover
that the origin of replication in this strain has a significantly shorter “refractory period,”
resulting in the reactivation of the origin before the previous round of replication is over. Based
on this model, if you examine the chromosomes of this strain (under conditions of fast growth),
how many replication forks would you expect to observe per chromosome on average?
A. Two, just like the wild-type strain
B. Four
C. Six
D. Eight
E. Ten

18 The telomerase enzyme in human cells …

A. has an RNA component.
B. extends the telomeres by its RNA polymerase activity.
C. polymerizes the telomeric DNA sequences without using any template.
D. removes telomeric DNA from the ends of the chromosomes.
E. creates the “end-replication” problem.

19 If this protein complex does not function normally, the ends of the eukaryotic
chromosomes would activate the cell’s DNA damage response, causing chromosomal fusions
and other genomic anomalies. What is this protein complex called?
A. Telomerase
B. T-loop
C. ORC
D. Shelterin
E. RecA

20 Which of the following schematic drawings better depicts the end of mammalian
chromosomal DNA?

A.
5′
3′
 B.
5′
3′

C.
3′
5′

D.

5′
3′

E.

3′
5′

21 Which of the following spontaneous lesions in DNA occurs most frequently in a

mammalian cell?
A. Depurination
B. Cytosine deamination
C. Guanine oxidation
D. Guanine alkylation
E. Depyrimidination

22 DNA glycosylases constitute an enzyme family found in all three domains of life. They
can …
A. add sugar moieties to DNA.
B. remove sugar moieties from DNA.
C. add a purine or pyrimidine base to DNA.
D. remove a purine or pyrimidine base from DNA.
E. remove a nucleotide from DNA.
23 Upon heavy damage to the cell’s DNA, the normal replicative DNA polymerases may
stall when encountering damaged DNA, triggering the use of backup translesion polymerases.
These backup polymerases …
A. lack 3′-to-5′ exonucleolytic proofreading activity.
B. are replaced by the replicative polymerases after adding only a few nucleotides.
C. can create mutations even on undamaged DNA.
D. may recognize specific DNA damage and add the appropriate nucleotide to restore
the original sequence.
E. All of the above.

24 What are the products of deamination of cytosine and 5-methyl cytosine, respectively?
A. Thymine and uracil
B. Thymine in both cases
C. Uracil and thymine
D. Uracil in both cases
E. Xanthine and hypoxanthine

25 Which of the following repair pathways can accurately repair a double-strand break?
A. Base excision repair
B. Nucleotide excision repair
C. Direct chemical reversal
D. Homologous recombination
E. Nonhomologous end joining

26 This protein folds into a doughnut shape that can encircle DNA. It can load on the DNA
only when the DNA is broken in both strands, so that the DNA can thread through the hole in the
protein. Which of the following proteins do you think matches this description?
A. PCNA, the sliding clamp for DNA polymerases at the replication forks
B. Ku, the protein that recognizes DNA ends and can initiate nonhomologous end
joining
C. MCM, the helicase critical for the initiation and elongation of replication
D. Topoisomerase II, which can create or relax superhelical tension in DNA
E. RecA/Rad51, which carries out strand invasion in homologous recombination

27 In contrast to vertebrates, there is very little DNA methylation in the genomes of

invertebrates such as Drosophila melanogaster and Caenorhabditis elegans. Indicate whether
you expect each of the following statements to be true (T) or false (F) regarding 5′-CG-3′
dinucleotide sequences in the genome. Your answer would be a four-letter string composed of
letters T and F only, e.g. TTTT.
( ) On average, approximately one dinucleotide out of every 16 in the human genome is
a CG dinucleotide.
( ) On average, approximately one dinucleotide out of every 256 in the D. melanogaster
genome is a CG dinucleotide.
( ) The proportion of CG dinucleotides in the human genome is more than that of C.
elegans.
( ) The proportion of CG dinucleotides in the human genome is more than that expected
by chance.

28 In which phases of the eukaryotic cell cycle does homologous recombination often occur
to repair DNA damage?
A. G1 and S phases
B. S and G2 phases
C. G2 and M phases
D. M and G1 phases
E. G1 and G2 phases

29 Which of the following is NOT correct regarding homologous recombination and its
regulation?
A. Loss of heterozygosity can occur if a broken chromosome is repaired using a sister
chromatid instead of its homologous chromosome.
B. Repair of double-strand breaks by homologous recombination is favored during or
soon after DNA replication.
C. Homologous recombination can rescue broken or stalled replication forks in S phase.
D. Excessive use of homologous recombination by human cells can lead to cancer.
E. Low usage of homologous recombination by human cells can lead to cancer.

30 In the following schematic drawing of a Holliday junction that undergoes branch

migration, cutting at which combination of the sites a to d would generate a crossover?
 a
Branch migration
d b

A. a and b
B. a and c
C. a and d
D. b and c
E. b and d

31 In meiosis, a crossover in one position is thought to inhibit crossing-over in the

neighboring regions. This regulatory mechanism …
A. results in a very uneven distribution of crossover points along each chromosome.
B. ensures that even small chromosomes undergo at least one crossover.
C. controls how the Holliday junctions are resolved.
D. All of the above.

32 What group of mobile genetic elements is largely responsible for the resistance of the
modern strains of pathogenic bacteria to common antibiotics?
A. DNA-only transposons
B. Retroviral-like retrotransposons
C. Nonretroviral retrotransposons
D. Site-specific recombinases

33 DNA-only transposons …
A. can be recognized by the presence of short inverted repeats at each end.
B. often encode a transposase that mediates the transposition process.
C. leave double-strand breaks in the donor chromosome.
D. can move by a cut-and-paste mechanism.
 E. All of the above.
34 Which of the following is true regarding retroviral-like retrotransposons?
A. They encode both a reverse transcriptase and an RNA polymerase.
B. They have directly repeated long terminal repeats at their two ends when integrated
into chromosomal DNA.
C. Their genomic RNA can be translated to produce viral coat proteins.
D. They leave double-strand breaks in the original donor DNA.
E. The Alu element in our genome is an example of retroviral-like retrotransposons.

35 Which of the following is NOT correct regarding long and short interspersed nuclear
elements?
A. Each of them encodes a reverse transcriptase.
B. They rely on the cellular transcription machinery to produce their RNA transcript.
C. They use one of the strands in the target DNA as a primer to synthesize their DNA.
D. Together, they make up about 40% of our genome.
E. They can move into new regions of genome that do not have any homology with their
DNA.

36 Phase variation helps protect the bacterium Salmonella typhimurium against the immune
system of its host by switching the orientation of a certain promoter. This process …
A. is carried out through a DNA transposition mechanism.
B. is irreversible.
C. can often result in the excision of the promoter from the chromosome altogether.
D. is mediated by enzymes that form transient covalent bonds with the DNA.

37 A replication fork is shown schematically below. The strand labeled A is called the …
strand.

3′
5′

B
38 The sliding clamp and the DNA helicase that function at the replication fork both have
three-dimensional structures resembling a ring with a central hole through which DNA is
threaded. Which of these proteins, the clamp (C) or the helicase (H), do you think has a wider
hole in its structure? Write down C or H as your answer.

39 Indicate true (T) and false (F) statements below regarding the initiation of replication in
human cells. Your answer would be a four-letter string composed of letters T and F only, e.g.
TFFF.
( ) Tens of thousands of replication origins are used each time a cell in our body
replicates its DNA.
( ) Different cells in our body use different sets of replication origins.
( ) Both replication forks in a replication bubble are normally active in replication.
( ) Gene expression and chromatin structure can affect the choice of the origins to use as
well as the order in which they are activated.

40 What combination of the following events normally prevents the origins of replication in
the yeast Saccharomyces cerevisiae from “firing” more than once during the cell cycle? Your
answer is a two-letter string composed of letters A to E only, e.g. AB. Order the letters in your
answer alphabetically.
(A) The helicase-loading proteins Cdc6 and Cdt1 are only active in S phase.
(B) The helicase Mcm1 can be delivered to the origin recognition complex (ORC) only in
S phase.
(C) The ORC can only become active (by dephosphorylation) in G1 phase.
(D) The helicase can only become active (by phosphorylation) in S phase.
(E) The ORC can bind to the origin only in S phase.

41 Examples of two general types of DNA damage are shown in the following drawing.
Which type of damage (1 or 2) is more common in our cells?
 1

42 In cells that are exposed to sunlight, ultraviolet (UV) light can result in covalent linkage
between two adjacent DNA bases. If not repaired in time, such dimers can lead to inheritable
mutations. Consider the sequence 5′-GGTATGATCATTATAA-3′ in the chromosome of a cell
that is exposed to intense sunlight. How many possible dimers can form in the region of DNA
double helix corresponding to this sequence?

43 Indicate whether each of the following DNA lesions is typically repaired via the base
excision (B) or nucleotide excision (N) repair pathway? Your answer would be a four-letter
string composed of letters B and N only, e.g. BBBB.
1. Deaminated cytosines
2. Depurinated residues
3. Thymine dimers
4. Bulky guanine adducts

44 Indicate true (T) and false (F) descriptions below regarding the nucleotide excision repair
pathway. Your answer would be a four-letter string composed of letters T and F only, e.g. FFFF.
( ) It involves recognition of distortions in the DNA double helix rather than specific
base changes.
 ( ) It involves endonucleolytic cleavage and helicase-mediated strand removal.
( ) It involves cleavage by the AP endonuclease.
( ) It is coupled to the DNA transcription machinery of the cell.

45 Fill in the blank in the following paragraph. Do NOT use abbreviations.

“In human cells, the predominant pathway to repair double-strand breaks is …, in

which the broken ends are simply rejoined with the concomitant loss of a few
nucleotides. This leaves scars at the breakage sites. This pathway can potentially
create chromosome translocations.”

46 Sort the following steps in the order that they normally happen during the process of
repairing double-strand breaks by homologous recombination. Your answer would be a six-letter
string composed of letters A to F only, e.g. DEFABC.
(A) Ligation
(B) DNA synthesis using undamaged DNA as the template
(C) DNA synthesis using original DNA as the template
(D) Release of the invading strand
(E) Strand invasion
(F) Nuclease digestion (resection)

47 The RecA/Rad51 protein carries out strand exchange during homologous recombination.
Indicate true (T) and false (F) statements about this process below. Your answer would be a
four-letter string composed of letters T and F only, e.g. FFFF.
( ) RecA hydrolyzes ATP upon binding to the invading DNA strand.
( ) RecA forces the invading strand into a conformation that fully mimics the geometry
of a long DNA double helix.
( ) Sampling of the homologous duplex by the invading strand is likely to occur in triplet
nucleotide blocks.
( ) RecA-bound, invading, single-stranded DNA binds and destabilizes the homologous
duplex to allow the sampling of its sequence by base-pairing.

48 Indicate true (T) and false (F) statements below regarding the use of homologous
recombination in meiosis. Your answer would be a four-letter string composed of letters T and F
only, e.g. FFFF.
 ( ) Meiotic recombination starts with a double-strand break caused by errors in DNA
replication.
( ) Meiotic recombination occurs preferentially between DNA from maternal and
paternal chromosome pairs.
( ) Holliday junctions can form during meiotic recombination, sometimes in pairs.
( ) During meiotic recombination in human cells, the majority of the invading strands
are released, leading to no crossover.

49 Indicate whether each of the following mobile elements in Drosophila is a DNA-only

transposon (D), a retroviral-like retrotransposon (R), or a nonretroviral retrotransposon (N).
Your answer would be a four-letter string composed of letters D, R, and N only, e.g. RRRR.
( ) P elements; these have inverted terminal repeats and move with the help of a
transposase enzyme.
( ) Copia elements; these have directly repeated long terminal repeats and move with the
help of a reverse transcriptase and an integrase.
( ) F elements; these are long interspersed nuclear elements (LINEs).
( ) Mariner elements; these move via a DNA intermediate.

50 Consider three types of mobile genetic elements that are found in our genome: the DNA-
only transposons (D), the retroviral-like retrotransposons (R), and the nonretroviral
retrotransposons (N). Which type appears to still be active and move in our genome, accounting
for a detectable fraction of human mutations? Write down your answer as D, R, or N.

51 As shown in the following drawing, a researcher has engineered three pairs of LoxP sites
(for conservative site-specific recombination) in a region that contains three reporter genes
coding for red, yellow, or cyan fluorescent proteins, respectively. Each type of LoxP sequence
(shown as a black, gray, or white arrowhead) is specific, meaning it does not recombine with the
other types of LoxP sequences. Upon Cre recombinase activation, depending on which
recombination event occurs first (which we assume is random), a number of possible
combinations of reporters can remain in the final DNA. For each of the following combinations,
indicate whether it can (C) or cannot (N) result from this recombination scheme. Do not consider
the re-integration of excised DNA, which happens very rarely. Your answer would be a six-letter
string composed of letters C and N only, e.g. CCCCNN.
 Red Yellow Cyan

( ) Red and yellow

( ) Red only
( ) Yellow only
( ) Cyan only
( ) Yellow and cyan
( ) Red and cyan
Answers:
1. Answer: B
Difficulty: 2
Section: The Maintenance of DNA Sequences
Feedback: The mutation rate per nucleotide pair per replication cycle in humans is
similar to that of Escherichia coli, and both are extremely low, less than one in a billion.
Nevertheless, current mutation rates are thought to limit the number of essential genes in
an organism to about 30,000. The stability of the germ-line genome depends on mutation
rates, as does somatic-cell stability. Cancers typically arise from somatic mutations.
2. Answer: B
Difficulty: 3
Section: The Maintenance of DNA Sequences
Feedback: About 15 cell generations pass in 10 hours of growth. Thus, the expected
average number of mutations is equal to:

(15 generations) × (3 × 10–10 mutations/generation/nucleotide) × (4.5 × 106

nucleotides/genome)
= ~2 × 10–2 mutations per genome.
This is equivalent to about 98% of the bacterial cells having zero mutations and the
remaining 2% having only one mutation each. Please note that the number of mutations in
different cells in a given culture will vary widely around the average calculated above.
3. Answer: E
Difficulty: 2
Section: DNA Replication Mechanisms

Feedback: Base-pairing is the basis of all DNA replication and repair. The other three
mechanisms each increase accuracy by about 100-fold.
4. Answer: E
Difficulty: 1
Section: DNA Replication Mechanisms

Feedback: Eukaryotic DNA polymerases are not as fast as their bacterial counterparts,
presumably due to the difficulty in replicating through nucleosomes. All known DNA
polymerases polymerize DNA from 5′ to 3′ and require a free 3′ end provided by a
primer. The self-correcting polymerases have an additional 3′-to-5′ exonuclease activity
that takes place at a distinct site in the enzyme.
5. Answer: C
Difficulty: 1
Section: DNA Replication Mechanisms
 Feedback: The helicase at the replication fork binds and hydrolyses ATP to move on the
DNA in a stepwise fashion.
6. Answer: B
Difficulty: 1
Section: DNA Replication Mechanisms
Feedback: The DNA primase enzyme syntheses RNA primers (with free 3′-OH groups)
that are extended and later replaced by DNA that is more accurately synthesized. This
happens more frequently in the lagging strand.
7. Answer: E
Difficulty: 3
Section: DNA Replication Mechanisms
Feedback: The DNA ligase reaction normally requires a free 3′-OH group and a 5′-
phosphate group on the two DNA ends to proceed. If a break has created 3′-phosphate
and 5′-OH ends instead, for example, an enzyme such as PNK can dephosphorylate the 3′
end in the upstream molecule, and phosphorylate the 5′ end in the downstream molecule,
to create the canonical ends.
8. Answer: primase
Difficulty: 3
Section: DNA Replication Mechanisms
Feedback: Like the RNA polymerases involved in transcription, primases do not require
priming and can synthesize RNA molecules that can be used as primers for DNA
synthesis by the replicative DNA polymerases. RNA polymerase is used to create RNA
primers for mitochondrial DNA replication.
9. Answer: C
Difficulty: 2
Section: DNA Replication Mechanisms
Feedback: The SSB proteins bind cooperatively to the regions of exposed single-stranded
DNA (which are routinely found in the lagging strand) and prevent the formation of
hairpin helices without blocking the base-pairing potential.
10. Answer: C
Difficulty: 2
Section: DNA Replication Mechanisms
Feedback: The sliding clamp is normally loaded (more frequently on the lagging strand)
on the primer–template duplex by the clamp loader, a process that requires ATP
hydrolysis by the loader. As soon as the polymerase runs into a double-strand region
downstream, the clamp releases the polymerase but is not itself immediately
disassembled from DNA.
11. Answer: A
Difficulty: 3
Section: DNA Replication Mechanisms
 Feedback: The double-strand region of the loop represents the growing Okazaki fragment
and gradually increases in size. Additionally, as each Okazaki fragment is growing, the
fork is also traveling, exposing more single-stranded DNA in the loop. The loop size
resets to zero upon initiating the synthesis of the next Okazaki fragment.
12. Answer: A
Difficulty: 3
Section: DNA Replication Mechanisms
Feedback: An inactive or hyperactive Dam methylase can interfere with strand-directed
mismatch repair, as both make it harder to distinguish between the newly replicated and
old DNA strands. Both situations are expected to increase the overall mutation rate,
giving rise to a mutator phenotype.
13. Answer: E
Difficulty: 2
Section: DNA Replication Mechanisms
Feedback: This untangling of intertwined DNA is mediated by the enzyme topoisomerase
II. This type of reaction helps solve the winding problem during replication.
14. Answer: A
Difficulty: 3
Section: DNA Replication Mechanisms
Feedback: Unlike topoisomerase I, which can only relieve the tension in DNA through
introducing a nick (single-strand break) in one of the DNA strands, topoisomerase II can
actively introduce or relieve tension by creating double-strand breaks (that remain tightly
associated with the enzyme) using energy from ATP hydrolysis.
15. Answer: 2413
Difficulty: 3
Section: DNA Replication Mechanisms
Feedback: The replication fork in E. coli can progress almost 20 times faster than the
RNA polymerase, meaning that rear-end collisions are typically between the rear edge of
the RNA polymerase and the front edge of the leading-strand DNA polymerase that is
traveling (faster) in the same direction on the same template strand. In a head-on
collision, however, the front edge of RNA polymerase hits the DNA helicase that is
traveling on the same (lagging) strand in the opposite direction. Note that the
polymerases translocate with respect to their template in the 3′-to-5′ direction, while the
helicase in the fork translocates in the 5′-to-3′ direction.
16. Answer: C
Difficulty: 1
Section: The Initiation and Completion of DNA Replication in Chromosomes
Feedback: The yeast origins of replication are similar to the bacterial origins in that they
are A-T-rich and have particular sequences that attract replication initiator proteins. In
higher eukaryotes, in contrast, the determinants of the replication origins are probably
 less sequence-specific. E. coli and S. cerevisiae both have relatively short origins
compared to higher organisms.
17. Answer: C
Difficulty: 3
Section: The Initiation and Completion of DNA Replication in Chromosomes

Feedback: Even though each round of replication takes 35 minutes, the “firing” interval
can be adjusted independently, and even go out of control. In this strain, possibly due to
mutations in the methylation pathway, the origins can become activated every 15
minutes, resulting in an average of six forks (three bubbles) per chromosome, the newest
of which have started about 30 minutes after the oldest ones.
18. Answer: A
Difficulty: 1
Section: The Initiation and Completion of DNA Replication in Chromosomes
Feedback: Telomerase uses its RNA component as a template to polymerize DNA
sequences at the chromosome ends to solve the “end-replication” problem.
19. Answer: D
Difficulty: 1
Section: The Initiation and Completion of DNA Replication in Chromosomes
Feedback: With the help of the t-loop structure, shelterin “hides” the telomere ends from
the cell’s double-strand break detector and repair systems.
20. Answer: D
Difficulty: 3
Section: The Initiation and Completion of DNA Replication in Chromosomes
Feedback: The telomeres have 3′ overhangs and are folded in structures called t-loops,
which help protect the chromosome ends.
21. Answer: A
Difficulty: 1
Section: DNA Repair
Feedback: Depurination (that is, the hydrolytic removal of purine bases from DNA) is by
far the most common endogenous DNA lesion in our cells. Please refer to Table 5–3 for
details.
22. Answer: D
Difficulty: 1
Section: DNA Repair
Feedback: These enzymes can recognize altered bases in DNA and catalyze their removal
by hydrolyzing the glycosidic bond between the base and the deoxyribose sugar.
23. Answer: E
Difficulty: 1
 Section: DNA Repair
Feedback: The translesion polymerases come in different flavors and some of them are
very efficient in repairing specific damage, but they generally have a low fidelity as they
cannot proofread. The cell thus limits their usage to very few polymerization steps.
24. Answer: C
Difficulty: 2
Section: DNA Repair
Feedback: The use of thymine instead of uracil by DNA has the advantage that
deamination of cytosine (to uracil) can be readily detected as an abnormal base in DNA.
However, deamination of 5-methyl cytosine (a modification that is found in vertebrate
DNA) can produce thymine and lead to mutations at a higher rate.
25. Answer: D
Difficulty: 1
Section: DNA Repair
Feedback: Compared to the faithful homologous recombination pathway to repair
double-strand breaks, nonhomologous end joining is a “quick and dirty” solution that
often results in mutations at the site of repair.
26. Answer: B
Difficulty: 3
Section: DNA Repair
Feedback: The Ku dimer forms a hole that accommodates a DNA double helix. In
addition, its structure reflects the fact that it should only bind to free DNA ends (for
example, from double-strand breaks) in a fashion similar to threading a needle.
27. Answer: FFFF
Difficulty: 3
Section: DNA Repair
Feedback: In a random DNA sequence, one out of every 16 dinucleotides is a CG.
However, these dinucleotides are found at a much lower frequency in the human
genome, which is probably related to the fact that cytosine methylation at these sites
(which has a role in transcription regulation) can be followed by deamination to cause a
C-to-T substitution. Consistent with this notion, the CG frequency in D. melanogaster
and C. elegans is close to the expected value.
28. Answer: B
Difficulty: 2
Section: Homologous Recombination
Feedback: Homologous recombination is used to repair DNA damage during and shortly
after the S phase of the cell cycle, when a sister chromatid is available for faithful
repairs.
29. Answer: A
Difficulty: 2
 Section: Homologous Recombination
Feedback: If a homologous chromosome is used (instead of a sister chromatid) to repair a
double-strand break, one of the parental alleles of the affected gene can be replaced by
the other allele, leading to loss of heterozygosity.
30. Answer: E
Difficulty: 3
Section: Homologous Recombination
Feedback: Cutting at b and d would result in a crossover. Cutting at a and c would only
lead to a heteroduplex (no crossover). The other combinations are not normally chosen.
31. Answer: B
Difficulty: 2
Section: Homologous Recombination
Feedback: The poorly understood regulatory mechanism of crossover control ensures a
roughly even distribution of crossover points along chromosomes. It also ensures that
each chromosome undergoes at least one crossover every meiosis. For many organisms,
roughly two crossovers per chromosome occur, one on each arm.
32. Answer: A
Difficulty: 1
Section: Transposition and Conservative Site-Specific Recombination
Feedback: DNA-only transposons that carry genes encoding antibiotic-inactivating
enzymes are largely responsible for the spread of antibiotic resistance in bacterial strains.
33. Answer: E
Difficulty: 1
Section: Transposition and Conservative Site-Specific Recombination
Feedback: DNA-only transposons often encode a transposase to move by a cut-and-paste
mechanism that results in a broken donor chromosome. Short inverted repeats of DNA
sequence are found at the ends of these transposons.
34. Answer: B
Difficulty: 1
Section: Transposition and Conservative Site-Specific Recombination
Feedback: Retroviral-like retrotransposons resemble retroviruses in their replication, but
lack the ability to produce a protein coat. They have directly repeated long terminal
repeats at each end and are transcribed by cellular RNA polymerases. The transcript is
then used as a template by a reverse transcriptase (encoded by the element) to make a
double-stranded DNA copy that is then integrated into a new site on the chromosome
using an integrase (also encoded by the element). This mechanism keeps the original
copy unchanged. Alu elements are nonretroviral retrotransposons.
35. Answer: A
Difficulty: 2
Section: Transposition and Conservative Site-Specific Recombination
 Feedback: Most short interspersed nuclear elements (SINEs) do not encode any proteins
and spread by pirating enzymes encoded by other transposons, such as long interspersed
nuclear elements (LINEs).
36. Answer: D
Difficulty: 2
Section: Transposition and Conservative Site-Specific Recombination
Feedback: Phase variation in Salmonella is brought about by a conservative site-specific
recombinase encoded by the bacterium. The recombinases that catalyze conservative site-
specific recombination form transient, high-energy covalent bonds with the DNA and use
this energy to complete the DNA rearrangements, an action reminiscent of
topoisomerases.
37. Answer: lagging
Difficulty: 2
Section: DNA Replication Mechanisms
Feedback: Strand A is extended 5′-to-3′ (from right to left) whereas the fork moves in the
opposite direction; therefore, the strand should be polymerized discontinuously.
38. Answer: C
Difficulty: 3
Section: DNA Replication Mechanisms
Feedback: The central hole in the clamp can accommodate a double-stranded DNA
molecule with extra room for smooth sliding. However, the helicase only allows a single
strand of DNA to pass through its central hole.
39. Answer: TTTT
Difficulty: 2
Section: The Initiation and Completion of DNA Replication in Chromosomes
Feedback: Human cells have probably hundreds of thousands of potential origins, out of
which about 40,000 are used each time a cell divides. Depending on gene expression and
chromatin state, different sets of origins can be used in different cells of the body. Once
an origin is activated, the resulting replication bubble expands on both sides of the origin.
40. Answer: CD
Difficulty: 3
Section: The Initiation and Completion of DNA Replication in Chromosomes
Feedback: The helicase is delivered to the ORC by active Cdc6 and Cdt1 proteins in G1
phase, but is activated by phosphorylation only in S phase. At the same time,
phosphorylation of ORC prevents its reactivation in S phase. ORC can be reactivated
again later in G1.
41. Answer: 2
Difficulty: 1
Section: DNA Repair
 Feedback: Depurination (2) and deamination (1) are both common, although
depurination is by far the most common endogenous DNA lesion in our cells.
42. Answer: 5
Difficulty: 3
Section: DNA Repair
Feedback: UV irradiation can cause two adjacent pyrimidine bases (T or C) to form these
covalent dimers. Please note that the complementary strand should also be taken into
account. The possible sites of damage are TC and TT doublets in the strand shown, and
TT, TC, and CC doublets in the complementary strand.
43. Answer: BBNN
Difficulty: 2
Section: DNA Repair
Feedback: Please note that depurinated residues are repaired through only part of the base
excision repair pathway.
44. Answer: TTFT
Difficulty: 1
Section: DNA Repair
Feedback: In nucleotide excision repair, a multienzyme complex recognizes DNA
double-helix distortions caused by damage. This pathway involves cutting the strand
containing the damage at two positions flanking the damage. A helicase is also recruited
and catalyzes strand removal. This pathway is also linked to the transcription machinery.
45. Answer: nonhomologous end joining
Difficulty: 1 Section: DNA Repair
Feedback: In nonhomologous end joining, the broken ends are simply brought together
and rejoined by DNA ligation, often concomitant with the loss of nucleotides at the site
of joining.
46. Answer: FEBDCA
Difficulty: 2
Section: Homologous Recombination
Feedback: This order of events results in the accurate repair of double-strand breaks.
47. Answer: FFTT
Difficulty: 2
Section: Homologous Recombination
Feedback: RecA binds cooperatively to the invading strand, forcing blocks of three
nucleotides into a conformation mimicking that of three nucleotides in a double helix
(although, between adjacent triplets, the DNA backbone is untwisted and stretched out).
This complex then binds and destabilizes the target homologous duplex, allowing the
sampling to take place by base-pairing interactions. RecA hydrolyzes its bound ATP after
the strand exchange is completed.
48. Answer: FTTT
 Difficulty: 2
Section: Homologous Recombination
Feedback: Meiotic recombination requires an initial double-strand break. In contrast to
the breaks resulting from DNA damage, this one is provided in a controlled manner by a
specialized meiotic protein.
49. Answer: DRND
Difficulty: 2
Section: Homologous Recombination
Feedback: P elements and mariner elements are DNA-only transposons in different
Drosophila species, copia is an abundant retroviral-like retrotransposon, and F elements
are nonretroviral retrotransposons.
50. Answer: N
Difficulty: 1
Section: Transposition and Conservative Site-Specific Recombination
Feedback: Some nonretroviral retrotransposons (such as Alu elements) are still moving in
our genome, accounting for perhaps two mutations out of every thousand new human
mutations. Although our genome is also littered with relics of retroviral-like
retrotransposons, none appear to be active today.
51. Answer: CNNCNC
Difficulty: 3
Section: Transposition and Conservative Site-Specific Recombination
Feedback: The arrangement of LoxP sites matters. For example, here, it does not allow
the final combination (yellow + cyan) because deleting the red reporter requires the use
of the white sequence, which also deletes the yellow reporter.