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Chapter 3: Energy, Catalysis, and Biosynthesis

CHAPTER 6

DNA REPLICATION, REPAIR, AND RECOMBINATION

( 2004 Garland Science Publishing

DNA Replication

6-1DNA 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.

6-2If 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.

6-3Answer the following questions about DNA replication.

A.On a DNA strand that is being synthesized, which end is growingthe 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 origin3( of the origin, 5(, or both?

6-4If 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.

6-5On 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.

6-6The 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

6-7Is 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.

6-8Which 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.

6-9You 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.

6-10Replication 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.

6-11Indicate 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.

6-12A.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 ligasePrimaseDNA polymeraseRepair polymeraseHelicaseRNA nucleaseInitiator proteinsSingle-stranded binding protein6-13Which 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

6-14A 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

6-15Indicate 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.

6-16Most 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

6-17A 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 mouses 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.

6-18During 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?

6-19Mismatch 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.