Chapter 34 DNA Replication
Matching Questions
Use the following to answer questions 1–10:
Choose the correct answer from the list below. Not all of the answers will be used.
a) helicases
b) Type I
c) Type II
d) G-rich strand
e) telomeres
f) topoisomerases
g) DNA polymerase
h) A-DNA
i) trombone-slide model
j) template
k) Holliday
l) Okazaki
1.
_______________ catalyzes the addition of deoxyribonucleotides to DNA.
2.
The _______________ describes the lengthening of the loop formed by the lagging strand
during replication.
Ans: i
Section: 34.2
3.
The strands of DNA must be relaxed or unwound for replication by _______________.
Ans: f
Section: 34.1
4.
The type of topoisomerase that does not require ATP is _______________.
Ans: b
Section: 34.1
5.
The type of topoisomerase that can introduce supercoils is _______________.
Ans: c
Section: 34.1
6.
DNA can serve as a(n) _______________ to direct synthesis of the complementary strand of
DNA or RNA.
Ans: j
Section: 34.1
7.
The small DNA synthesized on the lagging strand are called _______________ fragments.
Ans: l
Section: 34.2
Ans: g
Section: 34.1
Chapter 34 DNA Replication
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8.
Proteins that use ATP hydrolysis to separate the DNA during replication are called
_______________.
9.
The ends of chromosomes are called _______________.
Ans: e
Section: 34.2
10.
A(n) _______________ is critical in the formation of a telomere.
Ans: d
Section: 34.2
Fill–in-the-Blank Questions
11.
Elongation of the DNA strand proceeds in the _____ direction.
Ans: 5 → 3 Section: 34.1
12.
The dimeric 2 subunit of DNA polymerase III acts as a(n) ____.
Ans: sliding clamp Section: 34.2
13.
Type _____ topoisomerase introduces negative supercoils in DNA, while type
_____topoisomerase relaxes supercoil structures.
Ans: II; I Section: 34.2
14.
The primer for DNA synthesis is an RNA molecule formed by the enzyme _____.
Ans: primase Section: 34.1
15.
The DNA strand that is replicated continuously is known as the _____ strand.
Ans: leading Section: 34.2
16.
Proofreading by DNA polymerase increases accuracy by a factor of _____ times.
Ans: 1000 Section: 34.1
17.
During DNA replication, the RNA primer pieces are removed by _____.
Ans: DNA polymerase I Section: 34.1
18.
The accuracy for DNA polymerase depends on the proper formation of a _____.
Ans: Watson–Crick base pair Section: 34.1
19.
In eukaryotes, each origin of replication represents a replication unit, or _____.
Ans: replicon Section: 34.2
20.
In E. coli, dnaA protein binds to the _____.
Ans: origin of replication Section: 34.2
Ans: a
Section: 34.1
Chapter 34 DNA Replication
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Multiple-Choice Questions
21.
The observed error rate in DNA replication is
A)
1 per 106 nucleotides.
B)
1 per 104 nucleotides.
C)
1 per 108 nucleotides.
D)
1 per 1015 nucleotides.
E)
None of the above.
22.
What do DNA polymerases require for replication to begin?
A)
supercoiled DNA
B)
single-stranded template DNA
C)
a primer strand to elongate
D)
All of the above.
E)
None of the above.
Ans: C Section: 34.1
23.
Polymerase I has which of the following?
A)
a 3 → 5 exonuclease site
B)
a 5 → 3 exonuclease site
C)
C locus binding site
D)
A and B.
E)
A, B, and C.
Ans: D Section: 34.1
24.
The Klenow fragment
A)
has primase activity.
B)
is an E. coli DNA polymerase fragment.
C)
has exonuclease activity.
D)
A and B
E)
B and C
Ans: E Section: 34.1
25.
What is DNA gyrase?
A)
a bacterial topoisomerase II
B)
a bacterial topoisomerase I
C)
a bacterial helicase
D)
All of the above.
E)
None of the above.
Ans: A Section: 34.1
26.
Replication moves from the
A)
5 → 3 direction.
B)
3 → 5 direction.
C)
5 → 5 direction.
D)
3 → 3 direction.
E)
None of the above.
Ans: A Section: 34.1
Ans: C Section: Introduction
Chapter 34 DNA Replication
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27.
What is true about E. coli DNA polymerases?
A)
There are five structural classes.
B)
All have finger and thumb domains that wrap around the DNA.
C)
All catalyze the same reaction, which requires metal cofactors.
D)
B and C
E)
A, B, and C
28.
How is replication specificity dictated?
A)
Watson-Crick hydrogen bonding must occur.
B)
Enzyme interactions with the DNA act as a “ruler” to determine whether the properly
spaced base pair has been formed.
C)
The bond is broken and reformed to ensure its accurate placement at each base pair.
D)
A and B
E)
A, B, and C
Ans: D Section: 34.2
29.
What function does helicase perform during replication?
A)
It stabilizes the negative charge of the transition state.
B)
It utilizes ATP to power strand separation.
C)
It adds negative supercoils to DNA.
D)
A and C
E)
None of the above.
Ans: B Section: 34.2
30.
How can the leading and lagging strands be synthesized in a coordinated fashion?
A)
Specific enzymes control the size of the DNA opening.
B)
Lagging-strand binding proteins inhibit leading-strand replication if the strands become
disproportionate in size.
C)
Polymerase III is a dimeric holoenzyme, and the looped lagging strand allows the enzyme
to proceed in the same direction with each strand.
D)
All of the above.
E)
None of the above.
Ans: C Section: 34.2
31.
The free end of the eukaryotic chromosome is thought to form a unique DNA structure that
allows for complete replication. This structure involves a G-rich repeating sequence and forms a
A)
replication fork.
B)
large duplex loop.
C)
supercoiled loop.
D)
displacement loop
E)
None of the above.
Ans: B Section: 34.2
32.
The term processivity
A)
indicates the error rate for a polymerase.
B)
is the deletion of one or more bases in the DNA.
C)
is specifically the speed of replication.
D)
is the ability to catalyze many reactions without releasing substrate.
E)
A, B, and C
Ans: D Section: 34.2
Ans: E Section: 34.1
Chapter 34 DNA Replication
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33.
The ends of the eukaryotic chromosomes are called
A)
pyrimidine caps.
B)
telomeres.
C)
G-rich ends.
D)
replicon ends.
E)
None of the above.
34.
DNA clamps
A)
are composed of β2 subunits.
B)
form a ring around the front of the fork of DNA.
C)
allow the polymerase to move along the DNA molecule without falling off.
D)
All of the above.
E)
None of the above.
Ans: D Section: 34.2
35.
Replication of telomers involves
A)
an RNA-dependent DNA polymerase.
B)
GC capping.
C)
looping of the DNA ends.
D)
helicase-dependent ATP melting of the strands.
E)
None of the above.
Ans: A Section: 34.2
36.
How would a mutation that reduced uracil formation affect DNA replication?
A)
The effect would be negligible because uracil is found in RNA not DNA.
B)
The effect would be minimal because UTP is formed from the emanation of CTP.
C)
Uracil could be synthesized by a salvage pathway and so the effect would be minimal.
D)
DNA synthesis depends on dCTP formed by nucleotide reductase of dUTP.
E)
DNA synthesis depends on the synthesis of a short strand of RNA primer, thus DNA
synthesis would be negatively impacted.
Ans: E Section: 34.2
37.
What is it about the structure of nucleotides that requires 5 to 3 elongation of DNA?
A)
Okazaki fragments use the hydrolysis of the pyrophosphate bonds to drive 5’ to 3’ DNA
synthesis.
B)
Okazaki fragments are not sterically hindered by a 2-OH found in ribonucleotides,
making 5 to 3 synthesis possible on both strands.
C)
The hydrolysis of the triphosphate on the 5-OH drives elongation, dictating a 5 to 3
direction for DNA synthesis.
D)
The triphosphate on the 5-OH undergoes a nucleophilic attack by the Mg2+ in DNA
polymerase.
E)
The direction of polymerization is determined by primase, not the nucleotide structure.
Ans: C Section: 34.2
Ans: B Section: 34.2
Chapter 34 DNA Replication
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38.
If it could be targeted directly to cancer cells, would dideoxy-ATP (ddATP) make a good
cancer drug?
A)
No, because ddATP would promote the unwinding of supercoiled DNA and promote
DNA synthesis.
B)
No, because ddATP would promote Okazaki fragment formation due to loss of steric
hindrance.
C)
Yes, because ddATP has a lower Km for DNA polymerase and acts as a competitive
inhibitor for dATP.
D)
Yes, because ddATP has no 3OH and so synthesis stops when it is incorporated into
DNA.
E)
Yes, because ddATP acts as an analog of dGTP and causes mismatch and mutations.
39.
If you were to subject E. coli circular DNA to gel electrophoresis in the absence (lane 1) and
presence (lane 2) of topoisomerase I, what would you expect to find?
A)
Both lanes would look the same because the DNA is still the same size, with only a small
portion uncoiled.
B)
Lane 1 would run farther than lane 2 due to a smaller charge/density ratio of the DNA in
lane 1.
C)
Lane 1 would run farther than lane 2 due to relaxed and therefore slower moving DNA in
lane 2.
D)
Lane 2 would run farther than lane 1 due to a smaller charge/density ratio of the DNA in
lane 1.
E)
Lane 2 would run farther than lane 1 due to relaxed and therefore slower moving DNA in
lane 1.
Ans: C Section: 34.2
40.
The mode of DNA replication termed the trombone model describes a mechanism whereby the loop
lengthens and shortens like the slide on a trombone. Specifically, what loop is being described?
A)
The loop refers to the clamp of the DNA polymerase.
B)
The loop is the strand of RNA synthesized by the primase.
C)
The loop refers to the unwinding of the DNA by topoisomerase I.
D)
The loop is made by the leading strand as it completes replication.
E)
The loop is formed by the 3 to 5 lagging strand on the DNA template.
Ans: E Section: 34.2
Short-Answer Questions
41.
Why are enzymes, other than DNA polymerase, required for replication?
Several additional enzymes are necessary to separate the two strands of DNA prior to
replication.
Section: Introduction
Ans: C Section: 34.2
Chapter 34 DNA Replication
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42.
What is the difference between Type I and Type II topoisomerase with respect to the
thermodynamics of the reactions catalyzed?
43.
How are breaks sealed in discontinuous DNA formed during replication?
energy provided by hydrolysis of ATP to AMP and PPi.
Section: 34.2
44.
What are the minimal requirements for DNA replication?
ion; and DNA polymerase.
Section: 34.1
45.
What is a processive polymerase enzyme versus a distributive polymerase enzyme?
In contrast, a distributive enzyme releases the polymer between successive steps.
Section: 34.2
46.
How is the processivity of DNA polymerase III accomplished?
DNA clamp.
Section: 34.2
47.
How are single-stranded regions of DNA maintained?
Ans:
Single-stranded binding proteins (SSB) bind to the single-stranded regions of DNA.
Section: 34.2
48.
How does the trombone-slide mechanism work to coordinate replication?
lagging strand. See Figure 34.19.
Section: 34.2
49.
Write the chemical reaction for the addition of the dNTP to a DNA strand at the 3 end.
incoming dNTP with the displacement of pyrophosphate. See Figure 34.20.
Section: 34.2
hydrolysis of ATP.
Section: 34.1
Chapter 34 DNA Replication
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50.
Why is DNA gyrase the target for several different antibiotics?