QUESTIONS= CHAPTER 6: REPAIR, RECOMBINATION, TRANSPOSONS

Sickle-cell anemia is an example of an inherited disease. Individuals with this disorder have misshapen (sickle shaped) red blood cells caused by a change in the sequence of the β-globin gene. What is the nature of the change?

(a)chromosome loss (b)base-pair change (c)gene duplication (d)base-pair insertion

(b)base-pair change

Even though DNA polymerase has a proofreading function, it still introduces errors in the newly synthesized strand at a rate of 1 per 107 nucleotides. To what degree does the mismatch repair system decrease the error rate arising from DNA replication?

(a)2-fold (b)5-fold (c)10-fold (d)100-fold

(d)100-fold

Beside the distortion in the DNA backbone caused by a mismatched base pair, what additional mark is there on eucaryotic DNA to indicate which strand needs to be repaired?

(a)a nick in the template strand

(b)a chemical modification of the new strand

(c)a nick in the new strand

(d)a sequence gap in the new strand

(c)a nick in the new strand

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 could not affect development but is not mutagenic.

(a)In the deformed mice, somatic cells but not germ cells were mutated.

(d)The toxic chemical could not affect development but is not mutagenic.

The repair of mismatched base pairs or damaged nucleotides in a DNA strand requires a multistep process. Which choice below describes the known sequence of events in this process?

(a)DNA damage is recognized, newly synthesized strand is identified by an existing nick in the backbone, a segment of the new strand is removed by repair proteins, the gap is filled by DNA polymerase, and strand is sealed by DNA ligase.

(b)DNA repair polymerase simultaneously removes bases ahead of it and polymerizes the correct sequence behind it as it moves along the template. DNA ligase seals the nicks in the repaired strand.

(c)DNA damage is recognized, the newly synthesized strand is identified by an existing nick in the backbone, a segment of the new strand is removed by an exonuclease, and the gap is repaired by DNA ligase.

(d)A nick in the DNA is recognized, DNA repair proteins switch out the wrong base and insert the correct base, and DNA ligase seals the nick.

DNA damage is recognized, newly synthesized strand is identified by an existing nick in the backbone, a segment of the new strand is removed by repair proteins, the gap is filled by DNA polymerase, and strand is sealed by DNA ligase

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 in noncoding sequences.

(d)Mutations in coding sequences are more likely to be deleterious to the organism than in noncoding sequences.

If the cytosine in the sequence TCAT is deaminated and not repaired, which of the following is the point mutation you would observe after

this segment has undergone two rounds of DNA replication?

(a)TTAT (b)TUAT (c)TGAT (d)TAAT

(a)TTAT

If the adenosine in the sequence TCAT is depurinated and not repaired, which of the following is the point mutation you would observe after this segment has undergone two rounds of DNA replication?

(a)TCGT (b)TAT (c)TCT (d)TGTT

(c)TCT

Which of the following 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 links between thymidines on opposite DNA strands.

(c)Prolonged exposure to sunlight causes thymidine dimers to form.

(d)Repair proteins recognize thymidine dimers as a distortion in the DNA backbone.

(b)Thymidine dimers are covalent links between thymidines on opposite DNA strands.

Several members of the same family were diagnosed with the same kind of cancer when they were unusually young. Which one of the following is the most likely explanation for this phenomenon? It is possible that the individuals with the cancer have _______________________.

(a)inherited a cancer-causing gene that suffered a mutstion 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

(c)inherited a mutation in a gene required for mismatch repair

1. Ionizing radiation and oxidative damage can cause DNA double-strand breaks.

true

2. After damaged DNA has been repaired, nicks in the phosphate backbone are maintained as a way to identify the strand that was repaired.

false

3. Depurination of DNA is a rare event that is caused by ultraviolet irradiation.

false

4. Nonhomologous end joining is a mechanism that ensures that DNA double-strand breaks are repaired with a high degree of fidelity to the original DNA sequence.

false

5. Nicks generated during DNA replication are for easy identification of the newly synthesized strand but are sealed by DNA ligase shortly after replication is completed.

true

6. Depurination occurs constantly in our cells through spontaneous hydrolysis of the bond linking the DNA base to the deoxyribose sugar.

true

7. . Homologous recombination can repair double-strand breaks without any change in DNA sequence, but nonhomologous end joining always involves a loss of genetic information because the ends are degraded by nucleases before they can be ligated back together.

true

8.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.

true

9. A Holliday junction is not a sequence but a structural intermediate in homologous recombination.

true

During DNA replication in a bacterium, a C is accidentally incorporated instead of an A into one newly synthesized

DNA strand. Imagine that this error was not corrected and that it has no effect on the ability of the progeny to grow and

reproduce.

A. After this original bacterium has divided once, what proportion of its progeny would you expect to contain the

mutation?

½.

B.What proportion of its progeny would you expect to contain the mutation after three more rounds of DNA

replication and cell division?

¼.

A mismatched base pair causes a distortion in the DNA backbone. If this were the only indication of an error in

replication, the overall rate of mutation would be much higher. Explain why.

Distortion in DNA backbone is insufficient information for mismatch repair system to identify which base is incorrect

and which was originally part of the chromosome when replication began>> corrected only 50% of the time by random

chance>> mutation rate would be=

- less than in a system that lacked the mismatch repair enzymes (1 mistake/107 bp),

- BUT greater than error rate in system that accurately identifies the newly synthesized strand (1 mistake/ 109 bp)

Homologous recombination is an important mechanism in which organisms use a "back-up" copy of the DNA as a template to fix double-strand breaks without loss of genetic information. Which of the following is not necessary for homologous recombination to occur?

(a)3′ DNA strand overhangs

(b)5′ DNA strand overhangs

(c)a long stretch of sequence similarity

(d)nucleases

(b)5′ DNA strand overhangs

In addition to the repair of DNA double-strand breaks, homologous recombination is a mechanism for generating genetic diversity by swapping segments of parental chromosomes. During which process does swapping occur?

(a)DNA replication

(b)DNA repair

(c)meiosis

(d)transposition

(c)meiosis

Which of the following mobile genetic elements carry both a transposase gene and a reverse transcriptase gene?

(a)L1

(b)B1

(c)Alu

(d)Tn3

(a)L1

Which of the following is true of a retrovirus but not of the Alu retrotransposon?

(a)It requires cellular enzymes to make copies. (b)It can be inserted into the genome.

(c)It can be excised and moved to a new location in the genome.

(d)It encodes its own reverse transcriptase.

(d)It encodes its own reverse transcriptase.

Which of the following DNA sequences is not 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

(b)Holliday junction

Which of the following proteins is not encoded in the HIV genome?

(a)reverse transcriptase (b)envelope protein (c)RNA polymerase (d)capsid protein

(c)RNA polymerase

The events listed below are all necessary for homologous recombination to occur properly:

A.Holliday junction cut and ligated

B.strand invasion

C.DNA synthesis

D.DNA ligation

E.double-strand break

F.nucleases create uneven strands

Which of the following is the correct order of events during homologous recombination?

(a)E, B, F, D, C, A (b)B, E, F, D, C, A (c)C, E, F, B, D, A (d)E, F, B, C, D, A

(d)E, F, B, C, D, A

Some retrotransposons and retroviruses integrate preferentially into regions of the chromosome that are packaged

in euchromatin and are also located outside the coding regions of genes that contain information for making a protein.

Why might these mobile genetic elements have evolved this strategy?

Successful=the best at reproducing themselves>> element must meet two criteria:

(1) not kill its host,

(2) maximize its ability to continue reproducing.

--If element inserts into coding region>> might disable the gene>> selective disadvantage in reproduction or survival

Host>> elements that devised a way to avoid insertion into coding regions

--If element inserts into heterochromatic>>its genes may not be expressed and become immobile>>>>

--Elements devised a way to direct insertion into euchromatin to maintain mobility AND increase their copy number over time.

Which of the choices below correctly indicates the gene combination from the replication products of the maternal chromosome?

(a)AB and Ab

(b)ab and Ab

(c)AB and Ab

(d)aB and Ab

(d)aB and Ab