Deck 6: DNA Replication and Repair

Question 1

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.

Answer 1

D

Question 2

Which diagram accurately represents the directionality of DNA strands at one side of a replication fork? (a)


(b)


(c)


(d)

Figure 6-19

A)Diagram A
B)Diagram B
C)Diagram C
D)Diagram D

Answer 2

Diagram D

Question 3

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

Answer 3

C

Question 4

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.

Question 5

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 (PP_i) to inorganic phosphate (P_i) + P_i
B)release of PP_i from the nucleotide
C)hybridization of the new strand to the template
D)loss of ATP as an energy source

Question 6

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.

Question 7

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. Figure 6-11
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

Question 8

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. Figure 6-11
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

Question 9

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.

Question 10

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

Question 11

How does the total number of replication origins in bacterial cells compare to the number of origins in human cells?

A)1 versus 100
B)5 versus 500
C)10 versus 1000
D)1 versus 10,000

Question 12

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. Figure 6-11
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

Question 13

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. Figure 6-11
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.

Question 14

The classic experiments conducted by Meselson and Stahl used isotopes of which element to distinguish newly synthesized DNA from parental DNA?

A)carbon
B)nitrogen
C)oxygen
D)hydrogen

Question 15

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.

Question 16

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.

Question 17

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
B)sliding clamp
C)single-strand binding protein
D)primase

Question 18

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. Figure 6-11
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

Question 19

The chromatin structure in eukaryotic cells is much more complicated than that observed in prokaryotic cells.This is thought to be the reason why DNA replication occurs much faster in prokaryotes.How much faster is it?

A)2×
B)5×
C)10×
D)100×

Question 20

How many replication forks are formed when an origin of replication is opened?

A)1
B)2
C)3
D)4

Question 21

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 inherited

A)a cancer-causing gene that suffered a mutation in an ancestor's somatic cells.
B)a mutation in a gene required for DNA synthesis.
C)a mutation in a gene required for mismatch repair.
D)a mutation in a gene required for the synthesis of purine nucleotides.

Question 22

Recombination has occurred between the chromosome segments shown in Figure 6-40.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. Figure 6-40
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

Question 23

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

Question 24

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
B)5-fold
C)10-fold
D)100-fold

Question 25

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

Question 26

Which of the choices below represents the correct way to repair the mismatch shown in Figure 6-25?


(a)


(b)


(c)


(d)

Figure 6-25

A)Choice A
B)Choice B
C)Choice C
D)Choice D

Question 27

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

Question 28

Telomeres serve as caps protecting the ends of linear chromosomes.Which of the following is FALSE 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.

Question 29

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.

Question 30

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.
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.

Question 31

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 that you would observe after this segment has undergone two rounds of DNA replication?

A)TCGT
B)TAT
C)TCT
D)TGTT

Question 32

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

Question 33

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.

Question 34

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

Question 35

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

Question 36

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.

Question 37

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

Question 38

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

Question 39

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

Question 40

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.

Question 41

Which scientists first proposed a general strategy for DNA replication.How did they imagine it would work and what was their reasoning?

Question 43

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

Question 44

How were Meselson and Stahl able to separate "light" DNA from "heavy" DNA.Explain how this experimental approach was used to rule out two of the three models for DNA replication.

Question 45

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.
Figure 6-11A
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.

Question 46

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.

Question 47

DNA helicase has an essential role in DNA replication, but its unwinding activity also creates problems ahead of the replication fork, requiring the function of another class of enzymes.Describe the problem caused by DNA helicase, name the enzymes that resolve the problem, and explain the mechanism of resolution.

Question 49

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 6-61, where a "yes" indicates that the mutant is more sensitive than a normal fly, and blanks indicate normal sensitivity.
Table 6-61
A.Which mutant is most likely to be defective in the DNA repair polymerase? Why?
B.What aspect of repair is most likely to be affected in the other mutants?

Question 50

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 6-59, 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.
Figure 6-59

Question 51

A bacterial chromosome introduced into a yeast cell will not be duplicated along with yeast DNA chromosomes during cell division.Explain this observation.

Question 52

The sliding clamp complex must be reloaded for the synthesis of each Okazaki fragment on the lagging strand, while on the leading strand the clamp complex remains assembled over much longer stretches of DNA.Considering this information, explain how the cell is able to replicate the leading and lagging strands at the same rate.

Question 54

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.

Question 55

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?

Question 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?

Question 57

In terms of its function, is telomerase more like DNA polymerase or Primase? Explain your reasoning.

Question 59

Figure 6-63 shows a replication bubble.
Figure 6-63
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.
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.

Question 61

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?