CHAPTER 6

DNA REPLICATION, REPAIR, AND RECOMBINATION

 2004 Garland Science Publishing

DNA Replication

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 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 three minutes?
(a) The Drosophila genome is smaller than the E. coli genome.
(b) Eucaryotic DNA polymerase synthesizes DNA at a much faster rate than
procaryotic 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.
(e) Eucaryotes have more than one kind of DNA polymerase.

6-3 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?

6-4 If 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 required.
(c) The replication fork would not be asymmetrical.
(d) The polymerase used would not be self-correcting.
(e) Both new strands would be synthesized discontinuously.

85
6-5 On Figure Q6-5 of a replication bubble:

Figure Q6-5

A. 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 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.

6-6 The lagging strand is synthesized discontinuously at the replication fork 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 polymerize nucleotides only in the 5-to-3 direction.
(d) DNA polymerase removes the last few nucleotides synthesized whenever it stops.
(e) None of the above

6-7 Is the following statement TRUE or FALSE?

When bidirectional replication forks from adjacent origins meet, a leading

strand always runs into a lagging strand.

Explain your answer with a diagram illustrating sequential snapshots of the meeting of
two adjacent replication forks.

6-8 Which one of the following statements about the newly synthesized strand of a human
chromosome is correct?
(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.
(e) It was synthesized from multiple origins by either continuous or discontinuous
DNA synthesis, depending on which specific daughter chromosome is being
examined.

86
6-9 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) To replicate the same amount of DNA, it will hydrolyze fewer
deoxyribonucleotides than will the normal Exo+ polymerase.
(d) It will fall off the template more frequently than the normal Exo+ polymerase.
(e) It will introduce fewer mutations into new strands than the normal Exo+
polymerase.

6-10 Replication of DNA requires 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
3 end.
(c) DNA polymerase can polymerize nucleotides only in the 5-to-3 direction.
(d) DNA polymerase can polymerize DNA only in short fragments.
(e) DNA polymerase has a 3-to-5 exonuclease activity.

6-11 Indicate whether each of the following statements is correct or incorrect. Explain your
answers.
(a) Primase is less accurate than DNA polymerase at copying a DNA template.
(b) The RNA primer remains as a permanent part of the new DNA molecule.
(c) Replication of the leading strand does not require primase.
(d) Longer primers are required to synthesize longer DNA fragments.
(e) Primase can join ribonucleotides to create an RNA strand, using a single-stranded
DNA as a template, without the need for its own primer.

6-12 A. You are studying a strain of bacteria that carries a temperature-sensitive mutation
in one of the genes required for DNA replication. The bacteria grow normally at
the lower temperature, but when the temperature is raised they die. When you
analyze the remains of the bacterial cells grown at the higher temperature you find
evidence of partly replicated DNA. When the strands of this DNA are separated
by heating, numerous single-stranded DNA molecules around 1000 nucleotides
long are found. Which of the proteins listed below are most likely to be impaired
in these mutant bacteria? Explain your answer.
B. Next to the proteins listed below, write the number (1, 2, 3, and so on) that
corresponds to the order in which the proteins function during the synthesis of a
new stretch of DNA.

DNA ligase Primase

DNA polymerase Repair polymerase
Helicase RNA nuclease
Initiator proteins Single-stranded binding protein

87
6-13 Which of the following proteins or protein complexes are most abundant near the
replication fork? Why?
(a) Single-strand binding protein
(b) Sliding clamp
(c) DNA polymerase
(d) Helicase
(e) Primase

6-14 A molecule of bacterial DNA introduced into a yeast cell is imported into the nucleus but
fails to replicate. Where do you think the block to replication arises? Choose the protein
or protein complex below that is most likely responsible for the failure to replicate
bacterial DNA. Give an explanation for your answer.
(a) Primase
(b) Helicase
(c) DNA polymerase
(d) Sliding clamp protein
(e) Initiator proteins

6-15 Indicate whether the following statements about plasmids are TRUE or FALSE.
(a) Replication of plasmid DNA is independent of a replication origin.
(b) Maintenance of plasmid over the course of several cell divisions requires
telomerase activity.
(c) DNA replication in plasmids is bidirectional.
(d) Plasmids are experimentally useful for introducing specific DNA sequences into
yeasts and bacteria.
(e) Plasmids were used to identify the replication origins from human DNA.

6-16 Most cells in the body of an adult human lack the telomerase enzyme 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. Explain why telomerase might be necessary for the ability of
cancer cells to divide over and over again.

DNA Repair

6-17 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.
(e) The original mouse was defective in DNA repair.

88
6-18 During DNA replication in a bacterium, a C is accidentally incorporated instead of an A
into one newly synthesized DNA strand. Imagine 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?
B. What proportion of its progeny would you expect to contain the mutation after
three more rounds of DNA replication and cell division?

6-19 Mismatch repair of DNA

(a) is carried out solely by the replicating DNA polymerase.
(b) involves cleavage of the DNA backbone to excise a stretch of single-stranded
DNA containing a mispaired base.
(c) preferentially repairs the leading strand to match the lagging strand.
(d) makes replication 100,000 times more accurate.
(e) can occur only on newly replicated DNA.

6-20 Which of the following DNA repair processes accurately restores genetic information
only immediately after the DNA has been replicated? Explain your answer.
(a) Repair of deamination
(b) Repair of depurination
(c) Mismatch repair
(d) Repair of pyrimidine dimers

6-21 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? Possibly, the individuals with the cancer have
(a) inherited a cancer-causing gene that was mutated in an ancestor’s 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.
(e) independently accumulated multiple random mutations over a period of years
leading to cancer.

6-22 If uncorrected, deamination of cytosine in DNA is most likely to lead to

(a) substitution of an AT base pair for a CG base pair.
(b) deletion of the altered CG 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 Which of the following compounds is likely to be the most mutagenic?

(a) One that depurinates DNA.
(b) One that replaces adenine with guanine during DNA replication.
(c) One that nicks the sugar-phosphate backbone.
(d) One that causes thymidine dimers.
(e) One that crosslinks together the two strands of the double helix.

89
6-24 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 Figure Q6-24, where a “yes”
indicates that the mutant is more sensitive than a normal fly and blanks indicate normal
sensitivity.

Figure Q6-24

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?

6-25 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.
(e) DNA repair enzymes preferentially repair the newly replicated strand to match the
original strand.

90
DNA Recombination

6-26 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 in order 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 non-crossover chromosomes will segregate randomly during division.

Figure Q6-26

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 Q6-26 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?

6-27 Identify each statement below as TRUE or FALSE. Explain your answers.
A. Site-specific recombination can repair sites of damaged DNA.
B. Mobile genetic elements comprise nearly half of the human genome.
C. Viruses probably evolved from intracellular mobile genetic elements.
D. Genes that contain instructions for making motor proteins are called mobile
genetic elements.
E. Homologous recombination results in the accumulation of mobile genetic
elements.

91
6-28 Which of the following DNA sequences are commonly carried on mobile genetic
elements? You may choose more than one option.
(a) Transposase gene
(b) Holliday junction
(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 requiring an
RNA intermediate.
(c) include the transposable elements LINE-1, Alu, and Tn10.
(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 likely consequence of introducing high levels of reverse transcriptase into a
human embryo.

6-31 Some retrotransposons and retroviruses integrate preferentially into regions of the
chromosome that are (a) packaged in euchromatin and (b) located outside the coding
regions of genes that contain information for making a protein. Why 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 enzymes needed to replicate themselves.
(d) contain both nucleic acid and protein.
(e) have the same size genomes.

6-33 The enzymes reverse transcriptase and DNA polymerase both synthesize DNA. Which of
the following statements about them are TRUE?
(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 3-to-5 exonuclease
activity.

92
6-34 Once 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 Why do retroviruses need to package reverse transcriptase molecules into their virus
particles even though they carry the gene for reverse transcriptase in their genomes?

93
Answers

6-1 Choice (c) is the answer. Choices (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 Choice (d) is the 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, as eucaryotic polymerases are not faster than procaryotic
polymerases. Choices (c) and (e) are technically correct statements, but are not relevant
to the question.

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

6-4 (c) The antiparallel nature of the strands of normal DNA, combined with the 5-to-3
activity of the DNA polymerase, precludes the continuous synthesis of both
strands and thus requires that the replication fork be asymmetrical. If the strands
were parallel, both new strands could be synthesized continuously.

6-5 See Figure A6-5.

Figure A6-5

6-6 (a) False

(b) False
(c) True
(d) False
(e) False

94
6-7 True. See Figure A6-7 for an illustration of the meeting of two adjacent replication forks.

Figure A6-7

6-8 (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.

6-9 Choice (c) is the answer. An Exo— polymerase will be unable to proofread and thus will
hydrolyze 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).
Choice (a) is unlikely because it postulates an entirely new function for the defective
polymerase. Choice (b) is incorrect because if the rate of polymerization changes, it
would become faster not slower, as a consequence of the Exo— polymerase lacking a
proofreading function that might cause it to stop frequently to check its products and
remedy errors. Choice (d) is unlikely, because the ability to stay on the template is due to
the association of polymerase with additional proteins.

6-10 Choice (b) is the answer. Choices (a) and (d) are false statements. Choices (c) and (e) are
true but are not the reason DNA polymerase requires a primer.

95
6-11 (a) Correct. Primase lacks a 3-to-5 exonuclease activity and thus cannot proofread
the nucleotide chain it makes.
(b) Incorrect. A nuclease removes the RNA primer after it provides its 3-OH to
prime the synthesis of DNA. Then enzymes involved in repair synthesis and
ligation join the newly synthesized stretches of DNA to make a continuous strand
containing only DNA.
(c) Incorrect. The leading strand requires primase to initiate DNA synthesis, although
fewer RNA primers will be needed on the leading strand than the lagging strand.
(d) Incorrect. The length of the primer does not correlate with the length of the DNA
strand that is synthesized.
(e) Correct. Like other RNA polymerases, primase does not require a primer to
initiate synthesis of the nucleotide chain.

6-12 A. The 1000-nucleotide fragments that accumulate in the mutant are likely to be
Okazaki fragments. Thus, the mutant is likely to be defective in the function of
RNA nuclease, repair polymerase, or DNA ligase. These proteins are required to
remove the RNA primer, fill in the gap, and stitch together the Okazaki fragments,
respectively. We could test which enzyme was defective by determining if the
fragments contained a short stretch of RNA at the 5 end (nuclease defective) or if
the fragments annealed to the template leaving gaps (repair polymerase
defective).
B. DNA ligase—8
DNA polymerase—5
Helicase—2
Initiator proteins—1
Primase—4
Repair polymerase—7
RNA nuclease—6
Single-stranded binding protein—3

6-13 (a) Single-strand binding protein is required to coat all single-stranded regions of
DNA that form at a replication fork; this requires many molecules of single-strand
binding protein at each fork. Only one or two molecules of each of the other
proteins or protein complexes are required at each replication fork.

6-14 Choice (e) is the answer. DNA from all organisms is chemically identical except for the
sequence of nucleotides. The proteins listed in choices (a) through (d) 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.

96
6-15 (a) False
(b) False
(c) True
(d) True
(e) False

6-16 In the absence of telomerase, the lifespan 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 will disappear. 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.

6-17 Choice (a) or (d) is correct. Choice (b) cannot account for these results since a mutation
in the original mouse’s 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. If 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. 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. A 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, while the other bacteria will
give rise to normal bacteria. The proportion of progeny containing the mutation
will, therefore, remain at 25%.

6-19 Choice (b) is the answer. Choice (a) is incorrect, as mismatch repair requires specialized
repair proteins that act after the DNA is replicated or at other times during the life of a
cell (thus choice (e) is incorrect). Choice (c) is incorrect because mismatch repair repairs
the newly replicated leading strand or the lagging strand to match its template strand.
Choice (d) is incorrect, since mismatch repair makes replication approximately 100 (not
100,000) times more accurate.

97
6-20 (c) Mismatches occur most often as a result of replication errors, in which case the
erroneous base is found only on the newly synthesized strand. In most eucaryotic
cells, the preferential repair of the erroneous base instead of its pairing partner is
thought to require recognition of nicks in the sugar-phosphate backbone of the
newly synthesized DNA strand. These nicks are sealed soon after replication, so
mismatch repair must occur in the short interval between passage of the
replication fork and sealing of the sugar-phosphate backbone in order to
accurately restore the original sequence. When mismatch repair occurs at other
times, it has an equal probability of restoring the original information or setting
the mutation. For the other kinds of DNA damage (U-G mismatch, abasic site,
pyrimidine dimer) it is always evident to determine which strand is damaged and
which strand contains reliable original information.

6-21 Choice (c) is the 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 (choice (a) is incorrect). A defect in
DNA synthesis or nucleotide biosynthesis would likely be lethal (choices (b) and (d) are
incorrect). Choice (e) describes the way that most cancers arise in people late in life, but
it is extremely unlikely that several individuals in the same family spontaneously
acquired similar random mutations leading to the early onset of the same kind of cancer.

6-22 (a)

6-23 Choice (e) is the answer. Altogether, the DNA repair pathways described in Chapter 6 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. When the two strands are crosslinked
and thus both strands are damaged, entirely different and probably less accurate pathways
of repair are required.

6-24 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 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.

98
6-25 Choice(d) is the answer. Mutations—whether they arise by mistakes in replication or by
damage to the DNA that remains unrepaired—tend to hit the DNA fairly randomly
(choices (a) and (b) are false). However, if a mutation occurs in a protein-coding
sequence rather than in the surrounding DNA, it is more likely to cause a deleterious
change that kills or impairs the organism and thereby decreases the likelihood that the
mutation will be passed on to future generations. Since skinks and Komodo dragons
share a common lizard ancestor, differences in their genomes have arisen during their
divergence from this ancestor. Mutations in noncoding sequences are more likely to have
no effect on the functioning of the organism and thus frequently get passed along to
progeny. Choice (c) is incorrect, as genes that are being expressed tend to be more
loosely packaged than the noncoding DNA. Choice (e) is true, but has no bearing on the
phenomenon described.

6-26 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.
B. See Figure A6-26. The 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.

Figure A6-26

C. Due to extensive crossing over, you resemble both your grandmother and your
grandfather. If there were no crossing over, then you might have a much stronger
resemblance to one than the other.

6-27 A. False. Homologous recombination, not site-specific recombination, is sometimes

used to repair sites of damaged DNA. Site-specific recombination is used mostly
in the mobilization of mobile genetic elements.
B. True. Forty-five percent of the human genome is comprised of mobile genetic elements.
C. True. A good guess for how viruses evolved is that some mobile genetic elements
acquired genes encoding coat proteins and other proteins required for packaging
and cellular escape of the nucleic acids of mobile genetic elements.
D. False. Cellular motor proteins are completely unrelated to mobile genetic elements.
E. False. Site-specific recombination, not homologous recombination, is the primary
mechanism for the accumulation of mobile genetic elements. Homologous
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.

99
6-28 Choices (a), (c), and (d) are correct. A Holliday junction is not a sequence, but a
structural intermediate in homologous recombination (choice (b) is false). Mobile
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 fork that originates elsewhere in the chromosome (choice (e)
is false).

6-29 Choice (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 LINE-1 and Alu sequences (but not the bacterial transposon Tn10, 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). The LINE-1 and Alu retrotransposons that comprise about a
third of the human genome are not identical in sequence or location to the
retrotransposons in other mammals like mice (choice (e) is false).

6-30 The embryo would probably have severe developmental abnormalities or die. The huge
numbers of retrotransposons littering the human genome are largely immobile due to the
accumulation of disabling mutations. However, it is likely 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. High
levels of reverse transcriptase will probably cause many retrotransposition events. The
resultant insertion of retrotransposons is likely to disable genes required for development
or survival.

6-31 The most evolutionarily successful mobile genetic elements are those that are best at
reproducing themselves. In order to increase the number of copies of a particular
element, the element must meet two criteria: (1) it must not kill its host and (2) it must
maximize its ability to continue reproducing. If 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. Thus, elements that devised a way to avoid insertion
into coding regions probably were better able to increase their copy number throughout
the human population. If an element inserts into a heterochromatic region of a
chromosome, its genes may not be expressed and therefore it may become immobile.
Elements that devised a way to direct insertion into euchromatin would be more likely to
maintain mobility and thereby increase their copy number over time.

6-32 Choice (d) is the answer. All viruses contain both protein and nucleic acid. Viruses can
have either double- or single-stranded genomes (choice (a)). Not all viruses lyse the cells
they infect (choice (b)); for example, some bud out of the cell without killing it. Viruses
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)).

100
6-33 Choice (b) is the answer. Reverse transcriptase can use an RNA or DNA template (thus
choice (a) is false). Choice (c) is false because DNA polymerase is often used by DNA
viruses. Choice (d) is false because both enzymes polymerize deoxynucleotides. Choice
(e) is false because reverse transcriptase does not have proofreading exonuclease activity.

6-34 Once the virus has integrated into the genome, it has no further need for reverse
transcriptase. Therefore, an inhibitor of reverse transcriptase may be able to block
infection of other cells by viruses that bud off the infected cell, but it will not be able to
eradicate the integrated virus. If 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.

101