CHAPTER 6

DNA REPLICATION, REPAIR, AND RECOMBINATION

2009 Garland Science Puli!"in#
DNA Re$lica%i&n
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 heli is still
intact
(b) each daughter DNA molecule consists of t!o ne! strands copied from the parent
DNA molecule
(c) each daughter DNA molecule consists of one strand from the parent DNA
molecule and one ne! strand
(d) ne! DNA strands must be copied from a DNA template
6-3 The classic eperiments conducted by "eselson and #tahl demonstrated that DNA
replication is accomplished by employing a ________________ mechanism.
(a) continuous
(b) semiconservative
(c) dispersive
(d) conservative
6-4 $f the genome of the bacterium E. coli requires about %& minutes to replicate itself, ho!
can the genome of the fruit fly Drosophila be replicated in only ' minutes(
(a) The Drosophila genome is smaller than the E. coli genome.
(b) )ucaryotic DNA polymerase synthesi*es DNA at a much faster rate than
procaryotic DNA polymerase.
(c) The nuclear membrane +eeps the Drosophila DNA concentrated in one place in
the cell, !hich increases the rate of polymeri*ation.
(d) Drosophila DNA contains more origins of replication than E. coli DNA.
6-5 "eselson and #tahl gre! cells in media that contained different isotopes of nitrogen (
,-
N
and
,.
N) so that the DNA molecules produced from these different isotopes could be
distinguished by mass.
A. )plain ho! /light0 DNA !as separated from /heavy0 DNA in the "eselson and
#tahl eperiments.
1. Describe the three eisting models for DNA replication !hen these studies !ere
begun, and eplain ho! one of them !as ruled out definitively by the eperiment
you described for part A.
2. 3hat eperimental result eliminated the dispersive model of DNA replication(
6-6 $ndicate !hether the follo!ing statements are true or false. $f a statement is false, eplain
!hy it is false.
A. 3hen DNA is being replicated inside a cell, local heating occurs, allo!ing the
t!o strands to separate.
1. DNA replication orgins are typically rich in 452 base pairs.
2. "eselson and #tahl ruled out the dispersive model for DNA replication.
D. DNA replication is a bidirectional process that is initiated at multiple locations
along chromosomes in eucaryotic cells.
6-7 Ans!er the follo!ing questions about DNA replication.
A. 6n a DNA strand that is being synthesi*ed, !hich end is gro!ing7the '8 end, the
-8 end, or both ends( )plain your ans!er.
1. 6n a DNA strand that is being used as a template, !here is the copying occurring
relative to the replication origin7'8 of the origin, -8, or both(
6-8 9o! does the total number of replication origins in bacterial cells compare !ith the
number of origins in human cells(
(a) , versus ,&&
(b) - versus -&&
(c) ,& versus ,&&&
(d) , versus ,&,&&&
6-9 The chromatin structure in eucaryotic cells is much more complicated than that observed
in procaryotic cells. This is thought to be the reason that DNA replication occurs much
faster in procaryotes. 9o! much faster is it(
(a) %:
(b) -:
(c) ,&:
(d) ,&&:
6-10 DNA polymerase cataly*es the ;oining of a nucleotide to a gro!ing DNA strand. 3hat
prevents this en*yme from cataly*ing the reverse reaction(
(a) hydrolysis of <<i to <i = <i
(b) release of <<i from the nucleotide
(c) hybridi*ation of the ne! strand to the template
(d) loss of AT< as an energy source
6-11 >igure ?@5,, sho!s a replication bubble.
>igure ?@5,,
A. 6n the figure, indicate !here the origin of replication !as located (use 6).
1. Aabel the leading5strand template and the lagging5strand template of the right5
hand for+ BCD as E and F, respectively.
2. $ndicate by arro!s the direction in !hich the ne!ly made DNA strands (indicated
by dar+ lines) !ere synthesi*ed.
D. Number the 6+a*a+i fragments on each strand ,, %, and ' in the order in !hich
they !ere synthesi*ed.
). $ndicate !here the most recent DNA synthesis has occurred (use #).
>. $ndicate the direction of movement of the replication for+s !ith arro!s.
6-12 3hich of the follo!ing statements about the ne!ly synthesi*ed strand of a human
chromosome is true(
(a) $t !as synthesi*ed from a single origin solely by continuous DNA synthesis.
(b) $t !as synthesi*ed from a single origin by a miture of continuous and
discontinuous DNA synthesis.
(c) $t !as synthesi*ed from multiple origins solely by discontinuous DNA synthesis.
(d) $t !as synthesi*ed from multiple origins by a miture of continuous and
discontinuous DNA synthesis.
6-13 Fou have discovered an /)o
G
0 mutant form of DNA polymerase in !hich the '85to5-8
eonuclease function has been destroyed but the ability to ;oin nucleotides together is
unchanged. 3hich of the follo!ing properties do you epect the mutant polymerase to
have(
(a) $t !ill polymeri*e in both the -85to5'8 direction and the '85to5-8 direction.
(b) $t !ill polymeri*e more slo!ly than the normal )o
=
polymerase.
(c) $t !ill fall off the template more frequently than the normal )o
=
polymerase.
(d) $t !ill be more li+ely to generate mismatched base pairs.
6-14 A molecule of bacterial DNA introduced into a yeast cell is imported into the nucleus but
fails to replicate the yeast DNA. 3here do you thin+ the bloc+ to replication arises(
2hoose the protein or protein comple belo! that is most probably responsible for the
failure to replicate bacterial DNA. 4ive an eplanation for your ans!er.
(a) primase
(b) helicase
(c) DNA polymerase
(d) initiator proteins
6-15 "ost cells in the body of an adult human lac+ the telomerase en*yme because its gene is
turned off and is therefore not epressed. An important step in the conversion of a normal
cell into a cancer cell, !hich circumvents normal gro!th control, is the resumption of
telomerase epression. )plain !hy telomerase might be necessary for the ability of
cancer cells to divide over and over again.
6-16 3hich diagram accurately represents the directionality of DNA strands at one side of a
replication for+(
6-17 $ndicate !hether the follo!ing statements are true or false. $f a statement is false, eplain
!hy it is false.
A. <rimase is needed to initiate DNA replication on both the leading strand and the
lagging strand.
1. The sliding clamp is loaded once on each DNA strand, !here it remains
associated until replication is complete.
2. Telomerase is a DNA polymerase that carries its o!n CNA molecule to use as a
primer at the end of the lagging strand.
D. <rimase requires a proofreading function that ensures there are no errors in the
CNA primers used for DNA replication.
6-18 1ecause all DNA polymerases synthesi*e DNA in the -85to5'8 direction, and the
parental strands are antiparallel, DNA replication is accomplished !ith the use of
t!o mechanismsH continuous and discontinuous replication. $ndicate !hether the
follo!ing items relate to (,) continuous replication, (%) discontinuous replication,
or (') both modes of replication.
______ primase
______ single5strand binding protein
______ sliding clamp
______ CNA primers
______ leading strand
______ lagging strand
______ 6+a*a+i fragments
______ DNA helicase
______ DNA ligase
6-19 The synthesis of DNA in living systems occurs in the -85to5'8 direction. 9o!ever,
scientists synthesi*e short DNA sequences needed for their eperiments on an instrument
dedicated to this tas+.
A. The chemical synthesis of DNA by this instrument proceeds from the '85to5-8
direction. Dra! a diagram to sho! ho! this is possible and eplain the process.
1. Although '85to5-8 synthesis of DNA is chemically possible, it does not occur in
living systems. 3hy not(
6-20 DNA polymerases are processive, !hich means that they remain tightly associated !ith
the template strand !hile moving rapidly and adding nucleotides to the gro!ing daughter
strand. 3hich piece of the replication machinery accounts for this characteristic(
(a) helicase
(b) sliding clamp
(c) single5strand binding protein
(d) primase
6-21 Ise the components in the list belo! to label the diagram of a replication for+ in >igure
?@5%,.
A. DNA polymerase
1. single5strand binding protein
2. 6+a*a+i fragment
D. primase
). sliding clamp
>. CNA primer
4. DNA helicase
>igure ?@5%,
6-22 Cesearchers have isolated a mutant strain of E. coli that carries a temperature5sensitive
variant of the en*yme DNA ligase. At the permissive temperature, the mutant cells gro!
;ust as !ell as the !ild5type cells. At the nonpermissive temperature, all of the cells in the
culture tube die !ithin % hours. DNA from mutant cells gro!n at the nonpermissive
temperature for '& minutes is compared !ith the DNA isolated from cells gro!n at the
permissive temperature. The results are sho!n in >igure ?@5%%, !here DNA molecules
have been separated by si*e by means of electrophoresis (<, permissiveJ N<,
nonpermissive). )plain the appearance of a distinct band !ith a si*e of %&& base pairs
(bp) in the sample collected at the nonpermissive temperature.
>igure ?@5%%
6-23 Telomeres serve as caps at the ends of linear chromosomes. 3hich of the follo!ing 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 bac+ on itself to form a primer for the lagging strand.
DNA Re$air
6-24 #ic+le5cell anemia is an eample of an inherited disease. $ndividuals !ith this disorder
have misshapen (sic+le5shaped) red blood cells caused by a change in the sequence of the
K5globin gene. 3hat is the nature of the change(
(a) chromosome loss
(b) base5pair change
(c) gene duplication
(d) base5pair insertion
6-25 )ven though DNA polymerase has a proofreading function, it still introduces errors in the
ne!ly synthesi*ed strand at a rate of , per ,&
L
nucleotides. To !hat degree does the
mismatch repair system decrease the error rate arising from DNA replication(
(a) %5fold
(b) -5fold
(c) ,&5fold
(d) ,&&5fold
6-26 3hich of the choices belo! represents the correct !ay to repair the mismatch sho!n in
>igure ?@5%@(
>igure ?@5%@
6-27 A mismatched base pair causes a distortion in the DNA bac+bone. $f this !ere the only
indication of an error in replication, the overall rate of mutation !ould be much higher.
)plain !hy.
6-28 1eside the distortion in the DNA bac+bone caused by a mismatched base pair, !hat
additional mar+ is there on eucaryotic DNA to indicate !hich strand needs to be
repaired(
(a) a nic+ in the template strand
(b) a chemical modification of the ne! strand
(c) a nic+ in the ne! strand
(d) a sequence gap in the ne! strand
6-29 A pregnant mouse is eposed to high levels of a chemical. "any of the mice in her litter
are deformed, but !hen they are interbred !ith each other, all their offspring are normal.
3hich two of the follo!ing statements could eplain these results(
(a) $n the deformed mice, somatic cells but not germ cells !ere mutated.
(b) The original mouseMs germ cells !ere mutated.
(c) $n the deformed mice, germ cells but not somatic cells !ere mutated.
(d) The toic chemical affects development but is not mutagenic.
6-30 The repair of mismatched base pairs or damaged nucleotides in a DNA strand requires a
multistep process. 3hich choice belo! describes the +no!n sequence of events in this
process(
(a) DNA damage is recogni*ed, the ne!ly synthesi*ed strand is identified by an
eisting nic+ in the bac+bone, a segment of the ne! 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
polymeri*es the correct sequence behind it as it moves along the template. DNA
ligase seals the nic+s in the repaired strand.
(c) DNA damage is recogni*ed, the ne!ly synthesi*ed strand is identified by an
eisting nic+ in the bac+bone, a segment of the ne! strand is removed by an
eonuclease, and the gap is repaired by DNA ligase.
(d) A nic+ in the DNA is recogni*ed, DNA repair proteins s!itch out the !rong base
and insert the correct base, and DNA ligase seals the nic+.
6-31 Fou are eamining the DNA sequences that code for the en*yme phosphofructo+inase in
s+in+s and Nomodo dragons. Fou notice that the coding sequence that actually directs the
sequence of amino acids in the en*yme is very similar in the t!o organisms but that the
surrounding sequences vary quite a bit. 3hat is the most li+ely eplanation for this(
(a) 2oding sequences are repaired more efficiently.
(b) 2oding sequences are replicated more accurately.
(c) 2oding sequences are pac+aged more tightly in the chromosomes to protect them
from DNA damage.
(d) "utations in coding sequences are more li+ely to be deleterious to the organism
than mutations in noncoding sequences.
6-32 #ometimes chemical damage to DNA can occur ;ust 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. $f the cytosine in the sequence T2AT is deaminated and not
repaired, !hich of the follo!ing is the point mutation you !ould observe after this
segment has undergone t!o rounds of DNA replication(
(a) TTAT
(b) TIAT
(c) T4AT
(d) TAAT
6-33 During DNA replication in a bacterium, a 2 is accidentally incorporated instead of an A
into one ne!ly synthesi*ed DNA strand. $magine that this error !as not corrected and
that it has no effect on the ability of the progeny to gro! and reproduce.
A. After this original bacterium has divided once, !hat proportion of its progeny
!ould you epect to contain the mutation(
1. 3hat proportion of its progeny !ould you epect to contain the mutation after
three more rounds of DNA replication and cell division(
6-34 #ometimes chemical damage to DNA can occur ;ust 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. $f the adenosine in the sequence T2AT is depurinated and not
repaired, !hich of the follo!ing is the point mutation you !ould observe after this
segment has undergone t!o rounds of DNA replication(
(a) T24T
(b) TAT
(c) T2T
(d) T4TT
6-35 3hich of the follo!ing statements is not an accurate statement about thymidine dimers(
(a) Thymidine dimers can cause the DNA replication machinery to stall.
(b) Thymidine dimers are covalent lin+s bet!een thymidines on opposite DNA
strands.
(c) <rolonged eposure to sunlight causes thymidine dimers to form.
(d) Cepair proteins recogni*e thymidine dimers as a distortion in the DNA bac+bone.
6-36 $ndicate !hether the follo!ing statements are true or false. $f a statement is false, eplain
!hy it is false.
A. $oni*ing radiation and oidative damage can cause DNA double5strand brea+s.
1. After damaged DNA has been repaired, nic+s in the phosphate bac+bone are
maintained as a !ay to identify the strand that !as repaired.
2. Depurination of DNA is a rare event that is caused by ultraviolet irradiation.
D. Nonhomologous end ;oining is a mechanism that ensures that DNA double5strand
brea+s are repaired !ith a high degree of fidelity to the original DNA sequence.
6-37 #everal members of the same family !ere diagnosed !ith the same +ind of cancer !hen
they !ere unusually young. 3hich one of the follo!ing is the most li+ely eplanation for
this phenomenon( $t is possible that the individuals !ith the cancer have
_______________________.
(a) inherited a cancer5causing gene that suffered a mutstion in an ancestorMs somatic
cells
(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
6-38 Fou have made a collection of mutant fruit flies that are defective in various aspects of
DNA repair. Fou test each mutant for its hypersensitivity to three DNA5damaging agentsH
sunlight, nitrous acid (!hich causes deamination of cytosine), and formic acid (!hich
causes depurination). The results are summari*ed in Table ?@5'O, !here a /yes0 indicates
that the mutant is more sensitive than a normal fly, and blan+s indicate normal sensitivity.
Table ?@5'O
A. 3hich mutant is most li+ely to be defective in the DNA repair polymerase(
1. 3hat aspect of repair is most li+ely to be affected in the other mutants(
H&'&l&#&u! Rec&'ina%i&n and M&ile Gene%ic Ele'en%! and (iru!e!
6-39 9omologous recombination is an important mechanism in !hich organisms use a /bac+5
up0 copy of the DNA as a template to fi double5strand brea+s !ithout loss of genetic
information. 3hich of the follo!ing is not necessary for homologous recombination to
occur(
(a) '8 DNA strand overhangs
(b) -8 DNA strand overhangs
(c) a long stretch of sequence similarity
(d) nucleases
6-40 $n addition to the repair of DNA double5strand brea+s, homologous recombination is a
mechanism for generating genetic diversity by s!apping segments of parental
chromosomes. During !hich process does s!apping occur(
(a) DNA replication
(b) DNA repair
(c) meiosis
(d) transposition
6-41 Cecombination has occurred bet!een the chromosome segments sho!n in >igure ?@5.,.
The genes A and B, and the recessive alleles a and b, are used as mar+ers on the maternal
and paternal chromosomes, respectively. After alignment and homologous recombination,
the specific arrangements of A, B, a, and b have changed.
>igure ?@5.,
3hich of the choices belo! 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
6-42 The events listed belo! are all necessary for homologous recombination to occur
properlyH
A. 9olliday ;unction cut and ligated
1. strand invasion
2. DNA synthesis
D. DNA ligation
). double5strand brea+
>. nucleases create uneven strands
3hich of the follo!ing is the correct order of events during homologous recombination(
(a) ), 1, >, D, 2, A
(b) 1, ), >, D, 2, A
(c) 2, ), >, 1, D, A
(d) ), >, 1, 2, D, A
6-43 9omologous recombination is initiated by double5strand brea+s (D#1s) in a
chromosome. D#1s arise from DNA damage caused by harmful chemicals or by
radiation (for eample 5rays). During meiosis, the speciali*ed cell division that produces
gametes (sperm and eggs) for seual reproduction, the cells intentionally cause D#1s so
as to stimulate crossover homologous recombination. $f there is not at least one
occurrence of crossing5over !ithin each pair of homologous chromosomes during
meiosis, those noncrossover chromosomes !ill not segregate properly.
>igure ?@5.'
A. 2onsider the copy of chromosome ' that you received from your mother. $s it
identical to the chromosome ' that she received from her mother (her maternal
chromosome) or identical to the chromosome ' she received from her father (her
paternal chromosome), or neither( )plain.
1. #tarting !ith the representation in >igure ?@5.' of the double5stranded maternal
and paternal chromosomes found in your mother, dra! t!o possible
chromosomes you may have received from your mother.
2. 3hat does this indicate about your resemblance to your grandfather and
grandmother(
6-44 "obile genetic elements are sometimes called /;umping genes,0 because they move from
place to place throughout the genome. The eact mechanism by !hich they achieve this
mobility depends on the genes contained !ithin the mobile element. 3hich of the
follo!ing mobile genetic elements carry both a transposase gene and a reverse
transcriptase gene(
(a) L1
(b) B1
(c) Alu
(d) Tn3
6-45 3hich of the follo!ing is true of a retrovirus but not of the Alu retrotransposon(
(a) $t requires cellular en*ymes to ma+e copies.
(b) $t can be inserted into the genome.
(c) $t can be ecised and moved to a ne! location in the genome.
(d) $t encodes its o!n reverse transcriptase.
6-46 3hich of the follo!ing DNA sequences is not commonly carried on mobile genetic
elements( Fou may choose more than one option.
(a) transposase gene
(b) 9olliday ;unction
(c) recognition site for transposase
(d) antibiotic resistance gene
6-47 9$P is a human retrovirus that integrates into the host cellMs genome and !ill eventually
replicate, produce viral proteins, and ultimately escape the host cell. 3hich of the
follo!ing proteins is not encoded in the 9$P genome(
(a) reverse transcriptase
(b) envelope protein
(c) CNA polymerase
(d) capsid protein
6-48 #ome retrotransposons and retroviruses integrate preferentially into regions of the
chromosome that are pac+aged in euchromatin and are also located outside the coding
regions of genes that contain information for ma+ing a protein. 3hy might these mobile
genetic elements have evolved this strategy(