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 ESSENTIAL CELL BIOLOGY, FOURTH EDITION
CHAPTER 6: DNA REPLICATION, REPAIR, AND
RECOMBINATION
© 2014 GARLAND SCIENCE PUBLISHING

DNA Replication

6-1 The process of DNA replication requires that each of the parental DNA strands be used as a
___________________ to produce a duplicate of the opposing strand.
(a) catalyst
(b) competitor
(c) template
(d) copy

6-2 DNA replication is considered semiconservative because ____________________________.

(a) after many rounds of DNA replication, the original DNA double helix is still intact.
(b) each daughter DNA molecule consists of two new strands copied from the parent
DNA molecule.
(c) each daughter DNA molecule consists of one strand from the parent DNA molecule
and one new strand.
(d) new DNA strands must be copied from a DNA template.

6-3 The classic experiments conducted by Meselson and Stahl demonstrated that DNA
replication is accomplished by employing a ________________ mechanism.
(a) continuous
(b) semiconservative
(c) dispersive
(d) conservative

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6-4 Initiator proteins bind to replication origins and disrupt hydrogen bonds between the two
DNA strands being copied. Which of the factors below does not contribute to the relative
ease of strand separation by initiator proteins?
(a) replication origins are rich in A-T base pairs
(b) the reaction can occur at room temperature
(c) they only separate a few base pairs at a time
(d) once opened, other proteins of the DNA replication machinery bind to the origin

6-5 If the genome of the bacterium E. coli requires about 20 minutes to replicate itself, how can
the genome of the fruit fly Drosophila be replicated in only 3 minutes?
(a) The Drosophila genome is smaller than the E. coli genome.
(b) Eukaryotic DNA polymerase synthesizes DNA at a much faster rate than prokaryotic
DNA polymerase.
(c) The nuclear membrane keeps the Drosophila DNA concentrated in one place in the
cell, which increases the rate of polymerization.
(d) Drosophila DNA contains more origins of replication than E. coli DNA.

6-6 Meselson and Stahl grew cells in media that contained different isotopes of nitrogen (15N
and 14N) so that the DNA molecules produced from these different isotopes could be
distinguished by mass.
A. Explain how “light” DNA was separated from “heavy” DNA in the Meselson and Stahl
experiments.
B. Describe the three existing models for DNA replication when these studies were
begun, and explain how one of them was ruled out definitively by the experiment
you described for part A.
C. What experimental result eliminated the dispersive model of DNA replication?

6-7 Indicate whether the following statements are true or false. If a statement is false, explain
why it is false.
A. When DNA is being replicated inside a cell, local heating occurs, allowing the two
strands to separate.
B. DNA replication origins are typically rich in G-C base pairs.
C. Meselson and Stahl ruled out the dispersive model for DNA replication.

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 D. DNA replication is a bidirectional process that is initiated at multiple locations along
chromosomes in eukaryotic cells.

6-8 How many replication forks are formed when an origin of replication is opened?
(a) 1
(b) 2
(c) 3
(d) 4

6-9 Answer the following questions about DNA replication.

A. On a DNA strand that is being synthesized, which end is growing—the 3′ end, the 5′
end, or both ends? Explain your answer.
B. On a DNA strand that is being used as a template, where is the copying occurring
relative to the replication origin—3′ of the origin, 5′, or both?

6-10 How does the total number of replication origins in bacterial cells compare with the number
of origins in human cells?
(a) 1 versus 100
(b) 5 versus 500
(c) 10 versus 1000
(d) 1 versus 10,000

6-11 Which of the following statements correctly explains what it means for DNA replication to
be bidirectional?
(a) The replication fork can open or close, depending on the conditions.
(b) The DNA replication machinery can move in either direction on the template strand.
(c) Replication-fork movement can switch directions when the fork converges on
another replication fork.
(d) The replication forks formed at the origin move in opposite directions.

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6-12 The chromatin structure in eukaryotic cells is much more complicated than that observed in
prokaryotic cells. This is thought to be the reason that DNA replication occurs much faster
in prokaryotes. How much faster is it?
(a) 2×
(b) 5×
(c) 10×
(d) 100×

6-13 DNA polymerase catalyzes the joining of a nucleotide to a growing DNA strand. What
prevents this enzyme from catalyzing the reverse reaction?
(a) hydrolysis of pyrophosphate (PPi) to inorganic phosphate (Pi) + Pi
(b) release of PPi from the nucleotide
(c) hybridization of the new strand to the template
(d) loss of ATP as an energy source

6-14 Use your knowledge of how a new strand of DNA is synthesized to explain why DNA
replication must occur in the 5′-to-3′ direction. In other words, what would be the
consequences of 3′–to-5′ strand elongation?

6-15 Figure Q6-15 shows a replication bubble.

Figure Q6-15

A. On the figure, indicate where the origin of replication was located (use O).
B. Label the leading-strand template and the lagging-strand template of the right-hand
fork [R] as X and Y, respectively.
C. Indicate by arrows the direction in which the newly made DNA strands (indicated
by dark lines) were synthesized.
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 D. Number the Okazaki fragments on each strand as 1, 2, and 3 in the order in which
they were synthesized.
E. Indicate where the most recent DNA synthesis has occurred (use S).
F. Indicate the direction of movement of the replication forks with arrows.

Use the following information about a series of in vitro DNA replication experiments to
answer questions 6-16 through 6-22.

You prepare bacterial cell extracts by lysing the cells and removing insoluble debris via
centrifugation. These extracts provide the proteins required for DNA replication. Your DNA
template is a small, double-stranded circular piece of DNA (a plasmid) with a single origin of
replication and a single replication termination site. The termination site is on the opposite side of
the plasmid from the origin.

6-16 In addition to the extracts and the plasmid DNA, are there any additional materials you
should add to this in vitro replication system? Explain your answer.

6-17 Which of the following statements is true with respect to this in vitro replication system?
(a) There will be only one leading strand and one lagging strand produced using this
template.
(b) The leading and lagging strands compose one half of each newly synthesized DNA
strand.
(c) The DNA replication machinery can assemble at multiple places on this plasmid.
(d) One daughter DNA molecule will be slightly shorter than the other.

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You decide to use different bacterial strains (each having one protein of the replication machinery
mutated) in order to examine the role of individual proteins in the normal process of DNA
replication.

6-18 What part of the DNA replication process would be most directly affected if a strain of
bacteria lacking primase were used to make the cell extracts?
(a) initiation of DNA synthesis
(b) Okazaki fragment synthesis
(c) leading-strand elongation
(d) lagging-strand completion

6-19 What part of the DNA replication process would be most directly affected if a strain of
bacteria lacking the exonuclease activity of DNA polymerase were used to make the cell
extracts?
(a) initiation of DNA synthesis
(b) Okazaki fragment synthesis
(c) leading-strand elongation
(d) lagging-strand completion

6-20 What part of the DNA replication process would be most directly affected if a strain of
bacteria lacking helicase were used to make the cell extracts?
(a) initiation of DNA synthesis
(b) Okazaki fragment synthesis
(c) leading-strand elongation
(d) lagging-strand completion

6-21 What part of the DNA replication process would be most directly affected if a strain of
bacteria lacking single-strand binding protein were used to make the cell extracts?
(a) initiation of DNA synthesis
(b) Okazaki fragment synthesis
(c) leading-strand elongation
(d) lagging-strand completion
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6-22 What part of the DNA replication process would be most directly affected if a strain of
bacteria lacking DNA ligase were used to make the cell extracts?
(a) initiation of DNA synthesis
(b) Okazaki fragment synthesis
(c) leading-strand elongation
(d) lagging-strand completion

6-23 Which of the following statements about the newly synthesized strand of a human
chromosome is true?
(a) It was synthesized from a single origin solely by continuous DNA synthesis.
(b) It was synthesized from a single origin by a mixture of continuous and
discontinuous DNA synthesis.
(c) It was synthesized from multiple origins solely by discontinuous DNA synthesis.
(d) It was synthesized from multiple origins by a mixture of continuous and
discontinuous DNA synthesis.

6-24 You have discovered an “Exo–” mutant form of DNA polymerase in which the 3′-to-5′
exonuclease function has been destroyed but the ability to join nucleotides together is
unchanged. Which of the following properties do you expect the mutant polymerase to
have?
(a) It will polymerize in both the 5′-to-3′ direction and the 3′-to-5′ direction.
(b) It will polymerize more slowly than the normal Exo+ polymerase.
(c) It will fall off the template more frequently than the normal Exo+ polymerase.
(d) It will be more likely to generate mismatched base pairs.

6-25 A molecule of bacterial DNA introduced into a yeast cell is imported into the nucleus but
fails to replicate with the yeast DNA. Where do you think the block to replication arises?
Choose the protein or protein complex below that is most probably responsible for the
failure to replicate bacterial DNA. Give an explanation for your answer.
(a) primase
(b) helicase
(c) DNA polymerase

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 (d) initiator proteins

6-26 Most cells in the body of an adult human lack the telomerase enzyme because its gene is
turned off and is therefore not expressed. An important step in the conversion of a normal
cell into a cancer cell, which circumvents normal growth control, is the resumption of
telomerase expression. Explain why telomerase might be necessary for the ability of cancer
cells to divide over and over again.

6-27 Which diagram accurately represents the directionality of DNA strands at one side of a
replication fork?

6-28 Indicate whether the following statements are true or false. If a statement is false, explain
why it is false.
A. Primase is needed to initiate DNA replication on both the leading strand and the
lagging strand.

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 B. The sliding clamp is loaded once on each DNA strand, where it remains associated
until replication is complete.
C. Telomerase is a DNA polymerase that carries its own RNA molecule to use as a
primer at the end of the lagging strand.
D. Primase requires a proofreading function that ensures there are no errors in the
RNA primers used for DNA replication.

6-29 Because all DNA polymerases synthesize DNA in the 5′-to-3′ direction, and the parental
strands are antiparallel, DNA replication is accomplished with the use of two mechanisms:
continuous and discontinuous replication. Indicate whether the following items relate to (1)
continuous replication, (2) discontinuous replication, or (3) both modes of replication.

______ primase
______ single-strand binding protein
______ sliding clamp
______ RNA primers
______ leading strand
______ lagging strand
______ Okazaki fragments
______ DNA helicase
______ DNA ligase

6-30 The synthesis of DNA in living systems occurs in the 5′-to-3′ direction. However, scientists
synthesize short DNA sequences needed for their experiments on an instrument dedicated
to this task.
A. The chemical synthesis of DNA by this instrument proceeds in the 3′-to-5′ direction.
Draw a diagram to show how this is possible and explain the process.
B. Although 3′-to-5′ synthesis of DNA is chemically possible, it does not occur in living
systems. Why not?

6-31 DNA polymerases are processive, which means that they remain tightly associated with the
template strand while moving rapidly and adding nucleotides to the growing daughter
strand. Which piece of the replication machinery accounts for this characteristic?
(a) helicase
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 (b) sliding clamp
(c) single-strand binding protein
(d) primase

6-32 Use the components in the list below to label the diagram of a replication fork in Figure Q6-
32.
A. DNA polymerase
B. single-strand binding protein
C. Okazaki fragment
D. primase
E. sliding clamp
F. RNA primer
G. DNA helicase

Figure Q6-32

6-33 Researchers have isolated a mutant strain of E. coli that carries a temperature-sensitive
variant of the enzyme DNA ligase. At the permissive temperature, the mutant cells grow just
as well as the wild-type cells. At the nonpermissive temperature, all of the cells in the
culture tube die within 2 hours. DNA from mutant cells grown at the nonpermissive
temperature for 30 minutes is compared with the DNA isolated from cells grown at the
permissive temperature. The results are shown in Figure Q6-33, where DNA molecules have
been separated by size by means of electrophoresis (P, permissive; NP, nonpermissive).
Explain the appearance of a distinct band with a size of 200 base pairs (bp) in the sample
collected at the nonpermissive temperature.
Page 10 of 31
 Figure Q6-33

6-34 Indicate whether the following statements are true or false. If a statement is false, explain
why it is false.
A. The repair polymerase is the enzyme that proofreads the newly synthesized strands
to ensure the accuracy of DNA replication.
B. There is a single enzyme that degrades the RNA primers and lays down the
corresponding DNA sequence behind it.
C. DNA ligase is required to seal the sugar–phosphate backbone between all the DNA
fragments on the lagging strand.
D. The repair polymerase does not require the aid of the sliding clamp, because it is
only synthesizing DNA over very short stretches.

6-35 Which of the following statements about sequence proofreading during DNA replication is
false?
(a) The exonuclease activity is in a different domain of the DNA polymerase.
(b) The exonuclease activity cleaves DNA in the 5′-to-3′ direction.
(c) The DNA proofreading activity occurs concomitantly with strand elongation.
(d) If an incorrect base is added, it is “unpaired” before removal.

6-36 The sliding clamp complex encircles the DNA template and binds to DNA polymerase. This
helps the polymerase synthesize much longer stretches of DNA without dissociating. While
the loading of the clamp only occurs once on the leading strand, it must happen each time a
new Okazaki fragment is made on the lagging strand. How does the cell expedite this
process?

Page 11 of 31
6-37 The DNA duplex consists of two long covalent polymers wrapped around each other many
times over their entire length. The separation of the DNA strands for replication causes the
strands to be “overwound” in front of the replication fork. How does the cell relieve the
torsional stress created along the DNA duplex during replication?
(a) Nothing needs to be done because the two strands will be separated after
replication is complete.
(b) Topoisomerases break the covalent bonds of the backbone allowing the local
unwinding of DNA ahead of the replication fork.
(c) Helicase unwinds the DNA and rewinds it after replication is complete.
(d) DNA repair enzymes remove torsional stress as they replace incorrectly paired
bases.

6-38 Telomeres serve as caps at the ends of linear chromosomes. Which of the following is not
true regarding the replication of telomeric sequences?
(a) The lagging-strand telomeres are not completely replicated by DNA polymerase.
(b) Telomeres are made of repeating sequences.
(c) Additional repeated sequences are added to the template strand.
(d) The leading strand doubles back on itself to form a primer for the lagging strand.

DNA Repair

6-39 Sickle-cell anemia is an example of an inherited disease. Individuals with this disorder have
misshapen (sickle-shaped) red blood cells caused by a change in the sequence of the β-
globin gene. What is the nature of the change?
(a) chromosome loss
(b) base-pair change
(c) gene duplication
(d) base-pair insertion

6-40 Even though DNA polymerase has a proofreading function, it still introduces errors in the
newly synthesized strand at a rate of 1 per 107 nucleotides. To what degree does the
mismatch repair system decrease the error rate arising from DNA replication?
(a) 2-fold
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 (b) 5-fold
(c) 10-fold
(d) 100-fold

6-41 Which of the choices below represents the correct way to repair the mismatch shown in
Figure Q6-41?

Figure Q6-41

6-42 A mismatched base pair causes a distortion in the DNA backbone. If this were the only
indication of an error in replication, the overall rate of mutation would be much higher.
Explain why.

6-43 Beside the distortion in the DNA backbone caused by a mismatched base pair, what
additional mark is there on eukaryotic DNA to indicate which strand needs to be repaired?
(a) a nick in the template strand
(b) a chemical modification of the new strand
(c) a nick in the new strand
(d) a sequence gap in the new strand

Page 13 of 31
6-44 A pregnant mouse is exposed to high levels of a chemical. Many of the mice in her litter are
deformed, but when they are interbred with each other, all their offspring are normal.
Which two of the following statements could explain these results?
(a) In the deformed mice, somatic cells but not germ cells were mutated.
(b) The original mouse’s germ cells were mutated.
(c) In the deformed mice, germ cells but not somatic cells were mutated.
(d) The toxic chemical affects development but is not mutagenic.

6-45 The repair of mismatched base pairs or damaged nucleotides in a DNA strand requires a
multistep process. Which choice below describes the known sequence of events in this
process?
(a) DNA damage is recognized, the newly synthesized strand is identified by an existing
nick in the backbone, a segment of the new strand is removed by repair proteins, the
gap is filled by DNA polymerase, and the strand is sealed by DNA ligase.
(b) DNA repair polymerase simultaneously removes bases ahead of it and polymerizes
the correct sequence behind it as it moves along the template. DNA ligase seals the
nicks in the repaired strand.
(c) DNA damage is recognized, the newly synthesized strand is identified by an existing
nick in the backbone, a segment of the new strand is removed by an exonuclease,
and the gap is repaired by DNA ligase.
(d) A nick in the DNA is recognized, DNA repair proteins switch out the wrong base and
insert the correct base, and DNA ligase seals the nick.

6-46 Human beings with the inherited disease xeroderma pigmentosum have serious problems
with lesions on their skin and often develop skin cancer with repeated exposure to sunlight.
What type of DNA damage is not being recognized in the cells of these individuals?
(a) chemical damage
(b) X-ray irradiation damage
(c) mismatched bases
(d) ultraviolet irradiation damage

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6-47 You are examining the DNA sequences that code for the enzyme phosphofructokinase in
skinks and Komodo dragons. You notice that the coding sequence that actually directs the
sequence of amino acids in the enzyme is very similar in the two organisms but that the
surrounding sequences vary quite a bit. What is the most likely explanation for this?
(a) Coding sequences are repaired more efficiently.
(b) Coding sequences are replicated more accurately.
(c) Coding sequences are packaged more tightly in the chromosomes to protect them
from DNA damage.
(d) Mutations in coding sequences are more likely to be deleterious to the organism
than mutations in noncoding sequences.

6-48 In somatic cells, if a base is mismatched in one new daughter strand during DNA replication,
and is not repaired, what fraction of the DNA duplexes will have a permanent change in the
DNA sequence after the second round of DNA replication?
(a) 1/2
(b) 1/4
(c) 1/8
(d) 1/16

6-49 Sometimes, chemical damage to DNA can occur just before DNA replication begins, not
giving the repair system enough time to correct the error before the DNA is duplicated. This
gives rise to mutation. If the cytosine in the sequence TCAT is deaminated and not repaired,
which of the following is the point mutation you would observe after this segment has
undergone two rounds of DNA replication?
(a) TTAT
(b) TUAT
(c) TGAT
(d) TAAT

6-50 During DNA replication in a bacterium, a C is accidentally incorporated instead of an A into

one newly synthesized DNA strand. Imagine that this error was not corrected and that it has
no effect on the ability of the progeny to grow and reproduce.
A. After this original bacterium has divided once, what proportion of its progeny would
you expect to contain the mutation?

Page 15 of 31
 B. What proportion of its progeny would you expect to contain the mutation after
three more rounds of DNA replication and cell division?

6-51 Sometimes, chemical damage to DNA can occur just before DNA replication begins, not
giving the repair system enough time to correct the error before the DNA is duplicated. This
gives rise to mutation. If the adenosine in the sequence TCAT is depurinated and not
repaired, which of the following is the point mutation you would observe after this segment
has undergone two rounds of DNA replication?
(a) TCGT
(b) TAT
(c) TCT
(d) TGTT

6-52 Which of the following statements is not an accurate statement about thymine dimers?
(a) Thymine dimers can cause the DNA replication machinery to stall.
(b) Thymine dimers are covalent links between thymidines on opposite DNA strands.
(c) Prolonged exposure to sunlight causes thymine dimers to form.
(d) Repair proteins recognize thymine dimers as a distortion in the DNA backbone.

6-53 Indicate whether the following statements are true or false. If a statement is false, explain
why it is false.
A. Ionizing radiation and oxidative damage can cause DNA double-strand breaks.
B. After damaged DNA has been repaired, nicks in the phosphate backbone are
maintained as a way to identify the strand that was repaired.
C. Depurination of DNA is a rare event that is caused by ultraviolet irradiation.
D. Nonhomologous end joining is a mechanism that ensures that DNA double-strand
breaks are repaired with a high degree of fidelity to the original DNA sequence.

6-54 Several members of the same family were diagnosed with the same kind of cancer when
they were unusually young. Which one of the following is the most likely explanation for
this phenomenon? It is possible that the individuals with the cancer have
_______________________.
(a) inherited a cancer-causing gene that suffered a mutation in an ancestor’s somatic
cells.
Page 16 of 31
 (b) inherited a mutation in a gene required for DNA synthesis.
(c) inherited a mutation in a gene required for mismatch repair.
(d) inherited a mutation in a gene required for the synthesis of purine nucleotides.

6-55 You have made a collection of mutant fruit flies that are defective in various aspects of DNA
repair. You test each mutant for its hypersensitivity to three DNA-damaging agents:
sunlight, nitrous acid (which causes deamination of cytosine), and formic acid (which
causes depurination). The results are summarized in Table Q6-55, where a “yes” indicates
that the mutant is more sensitive than a normal fly, and blanks indicate normal sensitivity.

Table Q6-55

A. Which mutant is most likely to be defective in the DNA repair polymerase?

B. What aspect of repair is most likely to be affected in the other mutants?

6-56 The deamination of cytosine generates a uracil base. This is a naturally occurring nucleic
acid base, and so does not represent a DNA lesion caused by damage due to chemicals or
irradiation. Why is this base recognized as “foreign” and why is it important for cells to have
a mechanism to recognize and remove uracil when it is found in the DNA duplex?

Homologous Recombination

6-57 Select the option that best completes the following statement: Nonhomologous end joining
is a process by which a double-stranded DNA end is joined ___________________.
(a) to a similar stretch of sequence on the complementary chromosome.

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 (b) after repairing any mismatches.
(c) to the nearest available double-stranded DNA end.
(d) after filling in any lost nucleotides, helping to maintain the integrity of the DNA
sequence.

6-58 Nonhomologous end joining can result in all but which of the following?
(a) the recovery of lost nucleotides on a damaged DNA strand
(b) the interruption of gene expression
(c) loss of nucleotides at the site of repair
(d) translocations of DNA fragments to an entirely different chromosome

6-59 Homologous recombination is an important mechanism in which organisms use a “backup”

copy of the DNA as a template to fix double-strand breaks without loss of genetic
information. Which of the following is not necessary for homologous recombination to
occur?
(a) 3′ DNA strand overhangs
(b) 5′ DNA strand overhangs
(c) a long stretch of sequence similarity
(d) nucleases

6-60 In addition to the repair of DNA double-strand breaks, homologous recombination is a

mechanism for generating genetic diversity by swapping segments of parental
chromosomes. During which process does swapping occur?
(a) DNA replication
(b) DNA repair
(c) meiosis
(d) transposition

6-61 Recombination has occurred between the chromosome segments shown in Figure Q6-61.
The genes A and B, and the recessive alleles a and b, are used as markers on the maternal
and paternal chromosomes, respectively. After alignment and homologous recombination,
the specific arrangements of A, B, a, and b have changed.

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 Figure Q6-61

Which of the choices below correctly indicates the gene combination from the replication
products of the maternal chromosome?
(a) AB and aB
(b) ab and Ab
(c) AB and Ab
(d) aB and Ab

6-62 The events listed below are all necessary for homologous recombination to occur properly:
A. Holliday junction cut and ligated
B. strand invasion
C. DNA synthesis
D. DNA ligation
E. double-strand break
F. nucleases create uneven strands

Which of the following is the correct order of events during homologous recombination?
(a) E, B, F, D, C, A
(b) B, E, F, D, C, A
(c) C, E, F, B, D, A
(d) E, F, B, C, D, A

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6-63 Homologous recombination is initiated by double-strand breaks (DSBs) in a chromosome.
DSBs arise from DNA damage caused by harmful chemicals or by radiation (for example, X-
rays). During meiosis, the specialized cell division that produces gametes (sperm and eggs)
for sexual reproduction, the cells intentionally cause DSBs so as to stimulate crossover
homologous recombination. If there is not at least one occurrence of crossing-over within
each pair of homologous chromosomes during meiosis, those noncrossover chromosomes
will not segregate properly.

Figure Q6-43

A. Consider the copy of Chromosome 3 that you received from your mother. Is it
identical to the Chromosome 3 that she received from her mother (her maternal
chromosome) or identical to the Chromosome 3 she received from her father (her
paternal chromosome), or neither? Explain.
B. Starting with the representation in Figure Q6-43 of the double-stranded maternal
and paternal chromosomes found in your mother, draw two possible chromosomes
you may have received from your mother.
C. What does this indicate about your resemblance to your grandfather and
grandmother?

6-64 Indicate whether the following statements are true or false. If a statement is false, explain
why it is false.
A. Homologous recombination cannot occur in prokaryotic cells, because they are
haploid, and therefore have no extra copy of the chromosome to use as a template
for repair.
B. The first step in repair requires a nuclease to remove a stretch of base pairs from
the 5′ end of each strand at the site of the break.
C. The 3′ overhang “invades” the homologous DNA duplex, which can be used as a
primer for the repair DNA polymerase.

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D. The DNA template used to repair the broken strand is the homologous chromosome
inherited from the other parent.

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 ANSWERS

6-1 (c)

6-2 Choice (c) is the correct answer. Choices (a) and (b) are false. Although choice (d) is a
correct statement, it is not the reason that DNA replication is called semiconservative.

6-3 (b)

6-4 (b)

6-5 Choice (d) is the correct answer. Bacteria have one origin of replication, and Drosophila has
many. Choice (a) is incorrect because the Drosophila genome is bigger than the E. coli
genome. Choice (b) is incorrect, because eukaryotic polymerases are not faster than
prokaryotic polymerases.

6-6 A. The DNA samples collected were placed into centrifuge tubes containing cesium
chloride. After high-speed centrifugation for 2 days, the heavy and light DNA
products were separated by density.
B. The three models were conservative, semiconservative, and dispersive. The
conservative model suggested a mechanism by which the original parental strands
stayed together after replication and the daughter duplex was made entirely of
newly synthesized DNA. The semiconservative model proposed that the two DNA
duplexes produced during replication were hybrid molecules, each having one of the
parental strands and one of the newly synthesized strands. The dispersive model
predicted that the new DNA duplexes each contained segments of parental and
daughter strands all along the molecule. The conservative model was ruled out by
the density-gradient experiments.
C. The dispersive model was ruled out by using heat to denature the DNA duplexes and
then comparing the densities of the single-stranded DNA. If the dispersive model
had been correct, individual strands should have had an intermediate density.
However, this was not the case; only heavy strands and light strands were observed,
which convincingly supported the semiconservative model for DNA replication.

6-7 A. False. The two strands do need to separate for replication to occur, but this is
accomplished by the binding of initiator proteins at the origin of replication.
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 B. False. DNA replication origins are typically rich in A-T base pairs, which are held
together by only two hydrogen bonds (instead of three for C-G base pairs), making it
easier to separate the strands at these sites.
C. True.
D. True.

6-8 (b)

6-9 A. The 3′ end. DNA polymerase can add nucleotides only to the 3′-OH end of a nucleic
acid chain.
B. Both, as a result of the bidirectional nature of chromosomal replication.

6-10 (d)

6-11 (d)

6-12 (c)

6-13 (a)

6-14 There would be several detrimental consequences to 3′–to-5′ strand elongation. One of
those most directly linked to the processes of DNA replication involves synthesis of the
lagging strand. After the RNA primers are degraded, the DNA segments remaining will have
5′ ends with a single phosphate group. The incoming nucleotide will have a 3′-OH group.
Without the energy provided by the release of PPi from the 5′ end, the process of elongation
would no longer be energetically favorable.

6-15 See Figure A6-15.

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 Figure A6-15

6-16 You will probably add exogenous nucleoside triphosphates to serve as the building blocks
needed to make new strands of DNA. Although these monomers will be present in the
extracts, they will be present at lower concentrations than are normally found inside the
cell. They may also be subject to hydrolysis, and the nucleoside diphosphates that are the
products of this hydrolysis are not usable substrates for DNA replication. For both of these
reasons, it is important to add excess nucleotides to the reaction mixture for efficient DNA
replication to occur.

6-17 (b) Leading and lagging strands are synthesized bidirectionally from the replication origin,
and are joined together by DNA ligase where the two replication forks meet at the
termination site. Choice (a) is not correct, because this answer implies that the replication
fork is not bidirectional and that replication continues around the plasmid until the process
makes it back to the origin of replication. Choice (c) is incorrect because the origin is a
specialized sequence where initiator proteins bind and open the DNA so that the DNA
replication machinery can assemble. Choice (d) is incorrect because the daughter DNA
molecules will be same size as the original plasmid (and each other).

6-18 Choice (a) is the best answer because DNA synthesis cannot begin without the initial
primers. Choice (b) is a good answer because lagging-strand synthesis requires continual
use of RNA primers for discontinuous replication to occur.

6-19 (d)

6-20 (a) Because helicase unwinds the two DNA template strands, replication of both strands
depends upon the activity of helicase at the time of initiation.

6-21 (b)

6-22 (d)
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6-23 (d) Each newly synthesized strand in a daughter duplex was synthesized by a mixture of
continuous and discontinuous DNA synthesis from multiple origins. Consider a single
replication origin. The fork moving in one direction synthesizes a daughter strand
continuously as part of leading-strand synthesis; the fork moving in the opposite direction
synthesizes a portion of the same daughter strand discontinuously as part of lagging-strand
synthesis.

6-24 (d)

6-25 Choice (d) is the correct answer. DNA from all organisms is chemically identical except for
the sequence of nucleotides. The proteins listed in choices (a) to (c) can act on any DNA
regardless of its sequence. In contrast, the initiator proteins recognize specific DNA
sequences at the origins of replication. These sequences differ between bacteria and yeast.

6-26 In the absence of telomerase, the life-span of a cell and its progeny cells is limited. With each
round of DNA replication, the length of telomeric DNA will shrink, until finally all the
telomeric DNA has disappeared. Without telomeres capping the chromosome ends, the ends
might be treated like breaks arising from DNA damage, or crucial genetic information might
be lost. Cells whose DNA lacks telomeres will stop dividing or die. However, if telomerase is
provided to cells, they may be able to divide indefinitely because their telomeres will
remain a constant length despite repeated rounds of DNA replication.

6-27 (d)

6-28 A. True.
B. False. Although the sliding clamp is only loaded once on the leading strand, the
lagging strand needs to unload the clamp once the polymerase reaches the RNA
primer from the previous segment and then reload it where a new primer has been
synthesized.
C. True.
D. False. Primase does not have a proofreading function, nor does it need one because
the RNA primers are not a permanent part of the DNA. The primers are removed,
and a DNA polymerase that does have a proofreading function fills in the remaining
gaps.

6-29 ___3___ primase

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 ___2___ single-strand binding protein
___3___ sliding clamp
___3___ RNA primers
___1___ leading strand
___2___ lagging strand
___2___ Okazaki fragments
___3___ DNA helicase
___2___ DNA ligase

6-30 A. The actual chemical reaction in DNA synthesis is the same regardless of whether
going in the 5′-to-3′ or in the 3′-to-5′ direction. The most important distinction
between these two options is that if DNA is synthesized in the 3′-to-5′ direction, the
5′ end of the elongating strand, rather than the 3′ end, will have a nucleoside
triphosphate.

B. DNA synthesis from 3′ to 5′ does not allow proofreading. If the last nucleotide added
is mispaired and is removed, the last nucleotide on the growing strand is a
nucleoside monophosphate and the nucleotide coming in only has a hydroxyl group
on the 3′ end. Thus, there is no favorable hydrolysis reaction to drive the addition of
new nucleotides.

6-31 (b)

6-32 See Figure A6-32.

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 Figure A6-32

6-33 DNA ligase has an important role in DNA replication. After Okazaki fragments are
synthesized, they must be ligated (covalently connected) to each other so that they finally
form one continuous strand. At the nonpermissive temperature this does not happen, and
although there may be a range of fragments, the notable band at 200 base pairs is the
typical size of an individual Okazaki fragment.

6-34 A. False. The repair polymerase is used to fill in the spaces left vacant after the RNA
primers are degraded.
B. False. This is a two-step process that requires two different enzymes. First, a
nuclease removes the RNA primers. Then, the repair polymerase fills in the
complementary DNA sequence.
C. True.
D. True.

6-35 (b)

6-36 The cell employs an additional protein in order to make the constant reloading of the sliding
clamp on the lagging strand much more efficient. The protein, called the clamp loader,
harnesses energy from ATP hydrolysis to lock a sliding clamp complex around the DNA for
every successive round of DNA synthesis.

6-37 (b)

6-38 (d)
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6-39 (b)

6-40 (d)

6-41 (a)

6-42 The distortion in the DNA backbone is insufficient information for the mismatch repair
system to identify which base is incorrect and which was originally part of the chromosome
when replication began. Without additional marks that identify the difference between the
newly synthesized strand and the template strand, the repair would be corrected only 50%
of the time by random chance. The error rate (and therefore the mutation rate) would still
be less than in a system that lacked the mismatch repair enzymes (1 mistake per 107 base
pairs), but greater than the error rate in a system that accurately identifies the newly
synthesized strand (1 mistake per 109 base pairs).

6-43 (c)

6-44 Choices (a) or (d) are correct. Choice (b) cannot account for these results because a
mutation in the original mouse’s germ cells would have no effect on the fetuses she was
already carrying. Neither can choice (c), because mutations in the germ cells of the fetuses
while in utero would have had no effect on their development, but they might have led to
mutant mice among their offspring.

6-45 (a)

6-46 (d)

6-47 (d)

6-48 (b)

6-49 (a)

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6-50 A. One-half, or 50%. DNA replication in the original bacterium will create two new
DNA molecules, one of which will now carry a mismatched C-T base pair. So one
daughter cell of that cell division will carry a completely normal DNA molecule; the
other cell will have the molecule with the mutation mispaired to a correct
nucleotide.
B. One-quarter, or 25%. At the next round of DNA replication and cell division, the
bacterium carrying the mismatched C-T will produce and pass on one normal DNA
molecule from the undamaged strand containing the T and one mutant DNA
molecule with a fully mutant C-G base pair. So at this stage, one out of the four
progeny of the original bacterium is mutant. Subsequent cell divisions of these
mutant bacteria will give rise only to mutant bacteria, whereas the other bacteria
will give rise to normal bacteria. The proportion of progeny containing the mutation
will therefore remain at 25%.

6-51 (c)

6-52 (b)

6-53 A. True.
B. False. It is believed that the nicks are generated during DNA replication as a means
of easy identification of the newly synthesized strand but are sealed by DNA ligase
shortly after replication is completed.
C. False. Depurination occurs constantly in our cells through spontaneous hydrolysis
of the bond linking the DNA base to the deoxyribose sugar.
D. False. Homologous recombination can repair double-strand breaks without any
change in DNA sequence, but nonhomologous end joining always involves a loss of
genetic information because the ends are degraded by nucleases before they can be
ligated back together.

6-54 Choice (c) is the correct answer. In fact, affected individuals in some families with a history
of early-onset colon cancer have been found to carry mutations in mismatch repair genes.
Mutations arising in somatic cells are not inherited, so choice (a) is incorrect. A defect in
DNA synthesis or nucleotide biosynthesis would probably be lethal, so choices (b) and (d)
are incorrect.

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6-55 A. Mr Self-destruct is more likely than the other mutants to be defective in the DNA
repair polymerase because Mr Self-destruct is defective in the repair of all three
kinds of DNA damage. The repair pathways for all three kinds of damage are similar
in the later steps, including a requirement for the DNA repair polymerase.
B. The other mutants are specific for a particular type of damage. Thus, the mutations
are likely to be in genes required for the first stage of repair—the recognition and
excision of the damaged bases. Dracula and Mole are likely to be defective in the
recognition or excision of thymidine dimers; Faust is likely to be defective in the
recognition or excision of U-G mismatched base pairs; and Marguerite is likely to be
defective in the recognition or excision of abasic sites.

6-56 Uracil is an RNA base and it is recognized as a mutational lesion because, as it is formed
from the deamination of cytosine, it will be paired with a guanine in the context of the DNA
duplex. Uracil pairs by forming two hydrogen bonds, similar to thymine, and is thus a poor
partner for guanine, which forms three hydrogen bonds with cytosine. The mismatch causes
a distortion of the DNA backbone, allowing the repair machinery to recognize the uracil as a
lesion. Because uracil pairs preferably with adenine (its partner in double-stranded RNA),
the deamination of cytosine to uracil is highly mutagenic. If unrepaired, it can result in the
transition of a C-G base pair to a T-A base pair.

6-57 (c)

6-58 (a)

6-59 (b)

6-60 (c)

6-61 (d)

6-62 (d)

6-63 A. Neither. The copy of Chromosome 3 you received from your mother is a hybrid of
the ones she received from her mother and her father.

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Essential Cell Biology, 4e Test Bank

B. See Figure A6-43. The correct answers include any chromosome in which a portion
matches the information from the paternal chromosome and the remainder matches
the information from the maternal chromosome.

Figure A6-43

C. As a result of extensive crossing-over, you resemble both your grandmother and

your grandfather. If there were no crossing-over, you might have a much stronger
resemblance to one than the other.

6-64 A. False. Homologous recombination also occurs in prokaryotic cells, and typically
occurs very shortly after DNA replication, when the newly replicated duplexes are in
close proximity.
B. True.
C. True.
D. False. Although it is called homologous recombination, this is not a process that
depends on the proximity of parental homologs. When used as a mechanism for
DNA repair, homologous recombination uses the sister chromatids in an
undamaged, newly replicated (homologous) DNA helix as a template.

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