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CHAPTER 6

DNA REPLICATION, REPAIR, AND RECOMBINATION


2004 Garland Science Puli!"in#
DNA Re$lica%i&n
6-1 DNA replication is considered semiconservative because
(a) after many rounds of DNA replication, the original DNA double helix is still
intact.
(b) each daughter DNA molecule consists of two new strands copied from the parent
DNA molecule.
(c) each daughter DNA molecule consists of one strand from the parent DNA
molecule and one new strand.
(d) new DNA strands must be copied from a DNA template.
(e) an RNA primer must be used to initiate synthesis of the DNA strand.
6-2 f the genome of the bacterium E. coli re!uires about "# minutes to replicate itself, how
can the genome of the fruit fly Drosophila be replicated in only three minutes$
(a) %he 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) %he nuclear membrane (eeps the Drosophila DNA concentrated in one place in
the cell, which increases the rate of polymeri'ation.
(d) Drosophila DNA contains more origins of replication than E. coli DNA.
(e) &ucaryotes have more than one (ind of DNA polymerase.
6-3 Answer the following !uestions about DNA replication.
A. )n a DNA strand that is being synthesi'ed, which end is growing*the + end, the
, end, or both ends$ &xplain your answer.
-. )n a DNA strand that is being used as a template, where is the copying occurring
relative to the replication origin*+ of the origin, ,, or both$
6-4 f DNA strands were paired in a parallel rather than antiparallel fashion, how would the
replication of the DNA differ from that of normal double.stranded DNA$
(a) Replication would not be semiconservative.
(b) Replication origins would not be re!uired.
(c) %he replication for( would not be asymmetrical.
(d) %he polymerase used would not be self.correcting.
(e) -oth new strands would be synthesi'ed discontinuously.
'(
6-5 )n /igure 01., of a replication bubble2
/igure 01.,
A. ndicate where the origin of replication was located (use )).
-. 3abel the leading.strand template and the lagging.strand template of the right.
hand for( 4R5 as 6 and 7, respectively.
8. ndicate by arrows the direction in which the newly made DNA strands (indicated
by dar( lines) were synthesi'ed.
D. Number the )(a'a(i fragments on each strand 9, ", and + in the order in which
they were synthesi'ed.
&. ndicate where the most recent DNA synthesis has occurred (use :).
/. ndicate the direction of movement of the replication for(s with arrows.
6-6 %he lagging strand is synthesi'ed discontinuously at the replication for( because
(a) the lagging strand template is discontinuous.
(b) DNA polymerase always falls off the template DNA every ten nucleotides or so.
(c) DNA polymerase can polymeri'e nucleotides only in the ,.to.+ direction.
(d) DNA polymerase removes the last few nucleotides synthesi'ed whenever it stops.
(e) None of the above
6-7 s the following statement %R;& or /A3:&$
<hen bidirectional replication for(s from ad=acent origins meet, a leading
strand always runs into a lagging strand.
&xplain your answer with a diagram illustrating se!uential snapshots of the meeting of
two ad=acent replication for(s.
6-8 <hich one of the following statements about the newly synthesi'ed strand of a human
chromosome is correct$
(a) t was synthesi'ed from a single origin solely by continuous DNA synthesis.
(b) t was synthesi'ed from a single origin by a mixture of continuous and
discontinuous DNA synthesis.
(c) t was synthesi'ed from multiple origins solely by discontinuous DNA synthesis.
(d) t was synthesi'ed from multiple origins by a mixture of continuous and
discontinuous DNA synthesis.
(e) t was synthesi'ed from multiple origins by either continuous or discontinuous
DNA synthesis, depending on which specific daughter chromosome is being
examined.
'6
6-9 7ou have discovered an >&xo
?
@ mutant form of DNA polymerase in which the +.to.,
exonuclease function has been destroyed but the ability to =oin nucleotides together is
unchanged. <hich of the following properties do you expect the mutant polymerase to
have$
(a) t will polymeri'e in both the ,.to.+ direction and the +.to., direction.
(b) t will polymeri'e more slowly than the normal &xo
A
polymerase.
(c) %o replicate the same amount of DNA, it will hydroly'e fewer
deoxyribonucleotides than will the normal &xo
A
polymerase.
(d) t will fall off the template more fre!uently than the normal &xo
A
polymerase.
(e) t will introduce fewer mutations into new strands than the normal &xo
A

polymerase.
6-10 Replication of DNA re!uires a primer to initiate DNA synthesis because
(a) DNA polymerase can add its first nucleotide only to an RNA chain.
(b) DNA polymerase can add a nucleotide only to a base.paired nucleotide with a free
+ end.
(c) DNA polymerase can polymeri'e nucleotides only in the ,.to.+ direction.
(d) DNA polymerase can polymeri'e DNA only in short fragments.
(e) DNA polymerase has a +.to., exonuclease activity.
6-11 ndicate whether each of the following statements is correct or incorrect. &xplain your
answers.
(a) Brimase is less accurate than DNA polymerase at copying a DNA template.
(b) %he RNA primer remains as a permanent part of the new DNA molecule.
(c) Replication of the leading strand does not re!uire primase.
(d) 3onger primers are re!uired to synthesi'e longer DNA fragments.
(e) Brimase can =oin ribonucleotides to create an RNA strand, using a single.stranded
DNA as a template, without the need for its own primer.
6-12 A. 7ou are studying a strain of bacteria that carries a temperature.sensitive mutation
in one of the genes re!uired for DNA replication. %he bacteria grow normally at
the lower temperature, but when the temperature is raised they die. <hen you
analy'e the remains of the bacterial cells grown at the higher temperature you find
evidence of partly replicated DNA. <hen the strands of this DNA are separated
by heating, numerous single.stranded DNA molecules around 9### nucleotides
long are found. <hich of the proteins listed below are most li(ely to be impaired
in these mutant bacteria$ &xplain your answer.
-. Next to the proteins listed below, write the number (9, ", +, and so on) that
corresponds to the order in which the proteins function during the synthesis of a
new stretch of DNA.
DNA ligase Brimase
DNA polymerase Repair polymerase
Celicase RNA nuclease
nitiator proteins :ingle.stranded binding protein
')
6-13 <hich of the following proteins or protein complexes are most abundant near the
replication for($ <hy$
(a) :ingle.strand binding protein
(b) :liding clamp
(c) DNA polymerase
(d) Celicase
(e) Brimase
6-14 A molecule of bacterial DNA introduced into a yeast cell is imported into the nucleus but
fails to replicate. <here do you thin( the bloc( to replication arises$ 8hoose the protein
or protein complex below that is most li(ely responsible for the failure to replicate
bacterial DNA. Dive an explanation for your answer.
(a) Brimase
(b) Celicase
(c) DNA polymerase
(d) :liding clamp protein
(e) nitiator proteins
6-15 ndicate whether the following statements about plasmids are %R;& or /A3:&.
(a) Replication of plasmid DNA is independent of a replication origin.
(b) Eaintenance of plasmid over the course of several cell divisions re!uires
telomerase activity.
(c) DNA replication in plasmids is bidirectional.
(d) Blasmids are experimentally useful for introducing specific DNA se!uences into
yeasts and bacteria.
(e) Blasmids were used to identify the replication origins from human DNA.
6-16 Eost cells in the body of an adult human lac( the telomerase en'yme because its gene is
turned off and thus 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. &xplain why telomerase might be necessary for the ability of
cancer cells to divide over and over again.
DNA Re$air
6-17 A pregnant mouse is exposed to high levels of a chemical. Eany of the mice in her litter
are deformed, but when they are interbred with each other, all their offspring are normal.
<hich %<) of the following statements could explain these results$
(a) n the deformed mice, somatic cells but not germ cells were mutated.
(b) %he original mouseFs germ cells were mutated.
(c) n the deformed mice, germ cells but not somatic cells were mutated.
(d) %he toxic chemical affects development but is not mutagenic.
(e) %he original mouse was defective in DNA repair.
''
6-18 During DNA replication in a bacterium, a 8 is accidentally incorporated instead of an A
into one newly synthesi'ed DNA strand. magine this error was not corrected and has no
effect on the ability of the progeny to grow and reproduce.
A. After this original bacterium divides once, what proportion of its progeny would
you expect to contain the mutation$
-. <hat proportion of its progeny would you expect to contain the mutation after
three more rounds of DNA replication and cell division$
6-19 Eismatch repair of DNA
(a) is carried out solely by the replicating DNA polymerase.
(b) involves cleavage of the DNA bac(bone to excise a stretch of single.stranded
DNA containing a mispaired base.
(c) preferentially repairs the leading strand to match the lagging strand.
(d) ma(es replication 9##,### times more accurate.
(e) can occur only on newly replicated DNA.
6-20 <hich of the following DNA repair processes accurately restores genetic information
only immediately after the DNA has been replicated$ &xplain your answer.
(a) Repair of deamination
(b) Repair of depurination
(c) Eismatch repair
(d) Repair of pyrimidine dimers
6-21 :everal members of the same family were diagnosed with the same (ind of cancer when
they were unusually young. <hich one of the following is the most li(ely explanation
for this phenomenon$ Bossibly, the individuals with the cancer have
(a) inherited a cancer.causing gene that was mutated in an ancestorFs somatic cells.
(b) inherited a mutation in a gene re!uired for DNA synthesis.
(c) inherited a mutation in a gene re!uired for mismatch repair.
(d) inherited a mutation in a gene re!uired for the synthesis of purine nucleotides.
(e) independently accumulated multiple random mutations over a period of years
leading to cancer.
6-22 f uncorrected, deamination of cytosine in DNA is most li(ely to lead to
(a) substitution of an A% base pair for a 8D base pair.
(b) deletion of the altered 8D base pair from the DNA.
(c) conversion of the DNA into RNA.
(d) generation of a thymine dimer.
(e) None of the above.
6-23 <hich of the following compounds is li(ely to be the most mutagenic$
(a) )ne that depurinates DNA.
(b) )ne that replaces adenine with guanine during DNA replication.
(c) )ne that nic(s the sugar.phosphate bac(bone.
(d) )ne that causes thymidine dimers.
(e) )ne that crosslin(s together the two strands of the double helix.
'*
6-24 7ou have made a collection of mutant fruit flies that are defective in various aspects of
DNA repair. 7ou test each mutant for its hypersensitivity to three DNA.damaging agents2
sunlight, nitrous acid (which causes deamination of cytosine), and formic acid (which
causes depurination). %he results are summari'ed in /igure 01."G, where a >yes@
indicates that the mutant is more sensitive than a normal fly and blan(s indicate normal
sensitivity.
/igure 01."G
A. <hich mutant is most li(ely to be defective in the DNA repair polymerase$
-. <hat aspect of repair is most li(ely to be affected in the other mutants$
6-25 7ou are examining the DNA se!uences that code for the en'yme phosphofructo(inase in
s(in(s and Homodo dragons. 7ou notice that the coding se!uence that actually directs
the se!uence of amino acids in the en'yme is very similar in the two organisms but that
the surrounding se!uences vary !uite a bit. <hat is the most li(ely explanation for this$
(a) 8oding se!uences are repaired more efficiently.
(b) 8oding se!uences are replicated more accurately.
(c) 8oding se!uences are pac(aged more tightly in the chromosomes to protect them
from DNA damage.
(d) Eutations in coding se!uences are more li(ely to be deleterious to the organism
than mutations in noncoding se!uences.
(e) DNA repair en'ymes preferentially repair the newly replicated strand to match the
original strand.
*0
DNA Rec&+ina%i&n
6-26 Comologous recombination is initiated by double.strand brea(s (D:-s) in a
chromosome. D:-s arise from DNA damage caused by harmful chemicals or by
radiation (for example, x.rays). During meiosis, the speciali'ed cell division that
produces gametes (sperm and eggs) for sexual reproduction, the cells intentionally cause
D:-s in order to stimulate crossover homologous recombination. f there is not at least
one occurrence of crossing.over within each pair of homologous chromosomes during
meiosis, those non.crossover chromosomes will segregate randomly during division.
/igure 01."1
A. 8onsider 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$ &xplain.
-. :tarting with the representation in /igure 01."1 of the double stranded maternal
and paternal chromosomes found in your mother, draw two possible
chromosomes you may have received from your mother.
8. <hat does this indicate about your resemblance to your grandfather and
grandmother$
6-27 dentify each statement below as %R;& or /A3:&. &xplain your answers.
A. :ite.specific recombination can repair sites of damaged DNA.
-. Eobile genetic elements comprise nearly half of the human genome.
8. Iiruses probably evolved from intracellular mobile genetic elements.
D. Denes that contain instructions for ma(ing motor proteins are called mobile
genetic elements.
&. Comologous recombination results in the accumulation of mobile genetic
elements.
*,
6-28 <hich of the following DNA se!uences are commonly carried on mobile genetic
elements$ 7ou may choose more than one option.
(a) %ransposase gene
(b) Colliday =unction
(c) Recognition site for transposase
(d) Antibiotic resistance gene
(e) Replication origin
6-29 Retrotransposons
(a) are found only in eucaryotes.
(b) can move by either the cut.and.paste mechanism or by a mechanism re!uiring an
RNA intermediate.
(c) include the transposable elements 3N&.9, Alu, and %n9#.
(d) can move only if they encode a reverse transcriptase.
(e) were multiplied to high copy numbers in a common ancestor of all mammals.
6-30 Describe the li(ely conse!uence of introducing high levels of reverse transcriptase into a
human embryo.
6-31 :ome retrotransposons and retroviruses integrate preferentially into regions of the
chromosome that are (a) pac(aged in euchromatin and (b) located outside the coding
regions of genes that contain information for ma(ing a protein. <hy might these mobile
genetic elements have evolved this strategy$
6-32 All viruses
(a) have single.stranded genomes.
(b) lyse the cells they infect.
(c) encode all of the en'ymes needed to replicate themselves.
(d) contain both nucleic acid and protein.
(e) have the same si'e genomes.
6-33 %he en'ymes reverse transcriptase and DNA polymerase both synthesi'e DNA. <hich of
the following statements about them are %R;&$
(a) Reverse transcriptase uses only an RNA template. DNA polymerase uses only a
DNA template.
(b) Reverse transcriptase can use either an RNA or a DNA template. DNA
polymerase uses only a DNA template.
(c) DNA polymerase is used only by cells. Reverse transcriptase is used only by
viruses.
(d) DNA polymerase uses deoxynucleotides. Reverse transcriptase uses
ribonucleotides.
(e) Reverse transcriptase and DNA polymerase both contain a +.to., exonuclease
activity.
*2
6-34 )nce a retrovirus has integrated into the genome of a host cell, why would it not be
possible to eradicate the virus by treating the infected cell with reverse transcriptase
inhibitors$
6-35 <hy do retroviruses need to pac(age reverse transcriptase molecules into their virus
particles even though they carry the gene for reverse transcriptase in their genomes$
*-
An!.er!
6-1 8hoice (c) is the answer. 8hoices (a) and (b) are false. Although choices (d) and (e) are
correct statements, they are not the reasons that DNA replication is called
semiconservative.
6-2 8hoice (d) is the answer. -acteria have one origin of replication and Drosophila has
many. 8hoice (a) is incorrect because the Drosophila genome is bigger than the E. coli
genome. 8hoice (b) is incorrect, as eucaryotic polymerases are not faster than procaryotic
polymerases. 8hoices (c) and (e) are technically correct statements, but are not relevant
to the !uestion.
6-3 A. %he + end. DNA polymerase can add nucleotides only to the +.)C end of a
nucleic acid chain.
-. -oth, due to the bidirectional nature of chromosomal replication.
6-4 (c) %he antiparallel nature of the strands of normal DNA, combined with the ,.to.+
activity of the DNA polymerase, precludes the continuous synthesis of both
strands and thus re!uires that the replication for( be asymmetrical. f the strands
were parallel, both new strands could be synthesi'ed continuously.
6-5 :ee /igure A1.,.
/igure A1.,
6-6 (a) /alse
(b) /alse
(c) %rue
(d) /alse
(e) /alse
*4
6-7 %rue. :ee /igure A1.J for an illustration of the meeting of two ad=acent replication for(s.
/igure A1.J
6-8 (d) &ach newly synthesi'ed strand in a daughter duplex was synthesi'ed by a mixture
of continuous and discontinuous DNA synthesis from multiple origins. 8onsider
a single replication origin2 %he for( moving in one direction synthesi'es a
daughter strand continuously as part of leading.strand synthesisK the for( moving
in the opposite direction synthesi'es a portion of the same daughter strand
discontinuously as part of lagging.strand synthesis.
6-9 8hoice (c) is the answer. An &xo
*
polymerase will be unable to proofread and thus will
hydroly'e fewer nucleotides than one that can proofread, because it cannot remove an
incorrect nucleotide and try again to add the correct nucleotide (thus choice (e) is false).
8hoice (a) is unli(ely because it postulates an entirely new function for the defective
polymerase. 8hoice (b) is incorrect because if the rate of polymeri'ation changes, it
would become faster not slower, as a conse!uence of the &xo
*
polymerase lac(ing a
proofreading function that might cause it to stop fre!uently to chec( its products and
remedy errors. 8hoice (d) is unli(ely, because the ability to stay on the template is due to
the association of polymerase with additional proteins.
6-10 8hoice (b) is the answer. 8hoices (a) and (d) are false statements. 8hoices (c) and (e) are
true but are not the reason DNA polymerase re!uires a primer.
*(
6-11 (a) 8orrect. Brimase lac(s a +.to., exonuclease activity and thus cannot proofread
the nucleotide chain it ma(es.
(b) ncorrect. A nuclease removes the RNA primer after it provides its +.)C to
prime the synthesis of DNA. %hen en'ymes involved in repair synthesis and
ligation =oin the newly synthesi'ed stretches of DNA to ma(e a continuous strand
containing only DNA.
(c) ncorrect. %he leading strand re!uires primase to initiate DNA synthesis, although
fewer RNA primers will be needed on the leading strand than the lagging strand.
(d) ncorrect. %he length of the primer does not correlate with the length of the DNA
strand that is synthesi'ed.
(e) 8orrect. 3i(e other RNA polymerases, primase does not re!uire a primer to
initiate synthesis of the nucleotide chain.
6-12 A. %he 9###.nucleotide fragments that accumulate in the mutant are li(ely to be
)(a'a(i fragments. %hus, the mutant is li(ely to be defective in the function of
RNA nuclease, repair polymerase, or DNA ligase. %hese proteins are re!uired to
remove the RNA primer, fill in the gap, and stitch together the )(a'a(i fragments,
respectively. <e could test which en'yme was defective by determining if the
fragments contained a short stretch of RNA at the , end (nuclease defective) or if
the fragments annealed to the template leaving gaps (repair polymerase
defective).
-. DNA ligase*L
DNA polymerase*,
Celicase*"
nitiator proteins*9
Brimase*G
Repair polymerase*J
RNA nuclease*1
:ingle.stranded binding protein*+
6-13 (a) :ingle.strand binding protein is re!uired to coat all single.stranded regions of
DNA that form at a replication for(K this re!uires many molecules of single.strand
binding protein at each for(. )nly one or two molecules of each of the other
proteins or protein complexes are re!uired at each replication for(.
6-14 8hoice (e) is the answer. DNA from all organisms is chemically identical except for the
se!uence of nucleotides. %he proteins listed in choices (a) through (d) can act on any
DNA regardless of its se!uence. n contrast, the initiator proteins recogni'e specific DNA
se!uences at the origins of replication. %hese se!uences differ between bacteria and
yeast.
*6
6-15 (a) /alse
(b) /alse
(c) %rue
(d) %rue
(e) /alse
6-16 n the absence of telomerase, the lifespan of a cell and its progeny cells is limited. <ith
each round of DNA replication, the length of telomeric DNA will shrin(, until finally all
the telomeric DNA will disappear. <ithout telomeres capping the chromosome ends, the
ends might be treated li(e brea(s arising from DNA damage or crucial genetic
information might be lost. 8ells whose DNA lac(s telomeres will stop dividing or die.
Cowever, 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.
6-17 8hoice (a) or (d) is correct. 8hoice (b) cannot account for these results since a mutation
in the original mouseFs germ cells would have no effect on the fetuses she was already
carrying. Neither can choice (c), as mutations in the germ cells of the fetuses while in
utero would have had no effect on their development, but might have led to mutant mice
among their offspring. f the original mouse were defective in DNA repair (choice (e)),
this would increase the number of mutations caused by the chemical but cannot explain
the observed effects on her offspring and their offspring.
6-18 A. Calf or ,#M. DNA replication in the original bacterium will create two new DNA
molecules, one of which will now carry a mismatched 8.% base pair. :o one
daughter cell of that cell division will carry a completely normal DNA moleculeK
the other cell will have the molecule with the mutation mispaired to a correct
nucleotide.
-. A !uarter or ",M. At the next round of DNA replication and cell division, the
bacterium carrying the mismatched 8.% will produce and pass on one normal
DNA molecule from the undamaged strand containing the % and one mutant DNA
molecule with a fully mutant 8.D base pair. :o at this stage, one out of the four
progeny of the original bacterium is mutant. :ubse!uent cell divisions of these
mutant bacteria will give rise only to mutant bacteria, while the other bacteria will
give rise to normal bacteria. %he proportion of progeny containing the mutation
will, therefore, remain at ",M.
6-19 8hoice (b) is the answer. 8hoice (a) is incorrect, as mismatch repair re!uires speciali'ed
repair proteins that act after the DNA is replicated or at other times during the life of a
cell (thus choice (e) is incorrect). 8hoice (c) is incorrect because mismatch repair repairs
the newly replicated leading strand or the lagging strand to match its template strand.
8hoice (d) is incorrect, since mismatch repair ma(es replication approximately 9## (not
9##,###) times more accurate.
*)
6-20 (c) Eismatches occur most often as a result of replication errors, in which case the
erroneous base is found only on the newly synthesi'ed strand. n most eucaryotic
cells, the preferential repair of the erroneous base instead of its pairing partner is
thought to re!uire recognition of nic(s in the sugar.phosphate bac(bone of the
newly synthesi'ed DNA strand. %hese nic(s are sealed soon after replication, so
mismatch repair must occur in the short interval between passage of the
replication for( and sealing of the sugar.phosphate bac(bone in order to
accurately restore the original se!uence. <hen mismatch repair occurs at other
times, it has an e!ual probability of restoring the original information or setting
the mutation. /or the other (inds of DNA damage (;.D mismatch, abasic site,
pyrimidine dimer) it is always evident to determine which strand is damaged and
which strand contains reliable original information.
6-21 8hoice (c) is the answer. n fact, affected individuals in some families with a history of
early.onset colon cancer have been found to carry mutations in mismatch repair genes.
Eutations arising in somatic cells are not inherited (choice (a) is incorrect). A defect in
DNA synthesis or nucleotide biosynthesis would li(ely be lethal (choices (b) and (d) are
incorrect). 8hoice (e) describes the way that most cancers arise in people late in life, but
it is extremely unli(ely that several individuals in the same family spontaneously
ac!uired similar random mutations leading to the early onset of the same (ind of cancer.
6-22 (a)
6-23 8hoice (e) is the answer. Altogether, the DNA repair pathways described in 8hapter 1 can
easily repair the DNA damage described in options (a)?(d), these types of damage occur
on one strand of the double helix, and thus can be repaired using the intact genetic
information encoded on the complementary strand. <hen the two strands are crosslin(ed
and thus both strands are damaged, entirely different and probably less accurate pathways
of repair are re!uired.
6-24 A. Er. :elf.Destruct is more li(ely than the other mutants to be defective in the DNA
repair polymerase because Er. :elf.Destruct is defective in repair of all three
(inds of DNA damage. %he repair pathways for all three (inds of damage are
similar in the later steps, including a re!uirement for the DNA repair polymerase.
-. %he other mutants are specific for a particular type of damage. %hus the
mutations are li(ely to be in genes re!uired for the first stage of repair, the
recognition and excision of the damaged bases. Dracula and Eole are li(ely to be
defective in the recognition or excision of thymidine dimersK /aust is li(ely to be
defective in the recognition or excision of ;.D mismatched base pairsK and
Earguerite is li(ely to be defective in the recognition or excision of abasic sites.
*'
6-25 8hoice(d) is the answer. Eutations*whether they arise by mista(es in replication or by
damage to the DNA that remains unrepaired*tend to hit the DNA fairly randomly
(choices (a) and (b) are false). Cowever, if a mutation occurs in a protein.coding
se!uence rather than in the surrounding DNA, it is more li(ely to cause a deleterious
change that (ills or impairs the organism and thereby decreases the li(elihood that the
mutation will be passed on to future generations. :ince s(in(s and Homodo dragons
share a common li'ard ancestor, differences in their genomes have arisen during their
divergence from this ancestor. Eutations in noncoding se!uences are more li(ely to have
no effect on the functioning of the organism and thus fre!uently get passed along to
progeny. 8hoice (c) is incorrect, as genes that are being expressed tend to be more
loosely pac(aged than the noncoding DNA. 8hoice (e) is true, but has no bearing on the
phenomenon described.
6-26 A. Neither. %he copy of chromosome + you received from your mother is a hybrid of
the ones she received from her mother and her father.
-. :ee /igure A1."1. %he right 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.
/igure A1."1
8. Due to extensive crossing over, you resemble both your grandmother and your
grandfather. f there were no crossing over, then you might have a much stronger
resemblance to one than the other.
6-27 A. /alse. Comologous recombination, not site.specific recombination, is sometimes
used to repair sites of damaged DNA. :ite.specific recombination is used mostly
in the mobili'ation of mobile genetic elements.
-. %rue. /orty.five percent of the human genome is comprised of mobile genetic elements.
8. %rue. A good guess for how viruses evolved is that some mobile genetic elements
ac!uired genes encoding coat proteins and other proteins re!uired for pac(aging
and cellular escape of the nucleic acids of mobile genetic elements.
D. /alse. 8ellular motor proteins are completely unrelated to mobile genetic elements.
&. /alse. :ite.specific recombination, not homologous recombination, is the primary
mechanism for the accumulation of mobile genetic elements. Comologous
recombination does sometimes aid in the repair of DNA damage caused by the
excision of a mobile genetic element from the chromosome, but it does not aid in
the insertion of the element into a new location.
**
6-28 8hoices (a), (c), and (d) are correct. A Colliday =unction is not a se!uence, but a
structural intermediate in homologous recombination (choice (b) is false). Eobile
genetic elements often have no replication origin, since their movement and proliferation
occurs by a type of repair DNA synthesis and their replication during cell division occurs
by passage of a replication for( that originates elsewhere in the chromosome (choice (e)
is false).
6-29 8hoice (a) is the answer. Retrotransposons are found only in eucaryotes.
Retrotransposons (by definition) move only through an RNA intermediate (choice (b) is
false), and include 3N&.9 and Alu se!uences (but not the bacterial transposon %n9#, so
choice (c) is false). Retrotransposons do not necessarily need to provide their own
reverse transcriptase so long as there is an alternative source of reverse transcriptase in
the cell (choice (d) is false). %he 3N&.9 and Alu retrotransposons that comprise about a
third of the human genome are not identical in se!uence or location to the
retrotransposons in other mammals li(e mice (choice (e) is false).
6-30 %he embryo would probably have severe developmental abnormalities or die. %he huge
numbers of retrotransposons littering the human genome are largely immobile due to the
accumulation of disabling mutations. Cowever, it is li(ely that at least a few of the
millions of copies of the transposons still contain the sites necessary for
retrotransposition, although they do not encode a functional reverse transcriptase. Cigh
levels of reverse transcriptase will probably cause many retrotransposition events. %he
resultant insertion of retrotransposons is li(ely to disable genes re!uired for development
or survival.
6-31 %he most evolutionarily successful mobile genetic elements are those that are best at
reproducing themselves. n order to increase the number of copies of a particular
element, the element must meet two criteria2 (9) it must not (ill its host and (") it must
maximi'e its ability to continue reproducing. f an element inserts into the coding region
of a gene, it might disable the gene and thereby confer a selective disadvantage in the
reproduction or survival of its host. %hus, elements that devised a way to avoid insertion
into coding regions probably were better able to increase their copy number throughout
the human population. f an element inserts into a heterochromatic region of a
chromosome, its genes may not be expressed and therefore it may become immobile.
&lements that devised a way to direct insertion into euchromatin would be more li(ely to
maintain mobility and thereby increase their copy number over time.
6-32 8hoice (d) is the answer. All viruses contain both protein and nucleic acid. Iiruses can
have either double. or single.stranded genomes (choice (a)). Not all viruses lyse the cells
they infect (choice (b))K for example, some bud out of the cell without (illing it. Iiruses
can have as few as three genes or more than a hundred (choice (e)). No virus is able to
replicate in the absence of a host cell (choice (c)).
,00
6-33 8hoice (b) is the answer. Reverse transcriptase can use an RNA or DNA template (thus
choice (a) is false). 8hoice (c) is false because DNA polymerase is often used by DNA
viruses. 8hoice (d) is false because both en'ymes polymeri'e deoxynucleotides. 8hoice
(e) is false because reverse transcriptase does not have proofreading exonuclease activity.
6-34 )nce the virus has integrated into the genome, it has no further need for reverse
transcriptase. %herefore, an inhibitor of reverse transcriptase may be able to bloc(
infection of other cells by viruses that bud off the infected cell, but it will not be able to
eradicate the integrated virus. f the virus integrates into the genome of a cell with the
potential to divide, it will be faithfully propagated along with all the genomic DNA to all
progeny of that cell.
6-35 Retroviruses carry their own reverse transcriptase with them, as they must produce a
double.stranded DNA copy of their genome before their genes can be transcribed and
expressed.
,0,