Chapter 28. DNA Replication, Repair, and Recombination

Question 1

perturbations to the base sequence of DNA that cause a mutation. Mutagens are often chemicals but can also be energy sources such as ultraviolet light.

Answer 1

Mutagen

Question 2

The dimeric β subunit of DNA polymerase III that forms a ring that surrounds the DNA duplex.

Answer 2

Sliding clamp

Question 3

Enzymes that catalyze the ATP-driven unwinding of nucleic acids; DNA helicases are important in DNA replication.

Answer 3

Helicase

Question 4

an enzyme that catalyzes the formation of a phosphodiester bond between the 3 inch-OH at the end of one DNA chain and the 5 inch-phosphate at the end of the other chain; it is involved in the synthesis, repair, and splicing of DNA.

Answer 4

DNA ligase

Question 5

a means of repairing DNA in which a stretch of DNA around the site of damage is removed and replaced.

Answer 5

Nucleotide-excision repair

Question 6

an enzyme that digests nucleic acids from the ends of the molecule, rather than at an internal site. Exonucleases can be specific for digestion from the 3 inch or 5 inch ends of the nucleic acid.

Answer 6

Exonuclease

Question 7

small fragments of DNA (approximately 1000 nucleotides) that are formed on the lagging strand at the replication fork of DNA synthesis and later joined.

Answer 7

Okazaki fragment

Question 8

the newly synthesized strand of DNA at the replication fork that is synthesized continuously; see also lagging strand.

Answer 8

Leading strand

Question 9

the newly synthesized strand of DNA at the replication fork that is initially synthesized as Okazaki fragments.

Answer 9

Lagging strand

Question 10

a topological property of circular DNA, which is equal to the number of times a strand of DNA winds around the helix axis.

Answer 10

Linking number

Question 11

the site of DNA synthesis where the parental strands are separated and daughter strands complimentary to each parent are synthesized.

Answer 11

Replication fork

Question 12

a property of an enzyme that enables it to catalyze multiple rounds of elongation or digestion of a polymer while the polymer stays bound to the enzyme.

Answer 12

Processivity

Question 13

enzymes that catalyze the template-directed, primer-dependent addition of deoxynucleotide units, using deoxynucleotide triphosphates as substrates, to the 3 inch end of the DNA chain; chain growth is in the 5 inch to 3 inch-direction; such enzymes replicate and repair DNA.

Answer 13

DNA polymerase

Question 14

In general, the site on a chromosome where replication is initiated. The origin of replication site in E. coli has a length of 245 bp and contains a tandem array of three nearly identical 13-nucleotide sequences and five binding sites for the DnaA protein.

Answer 14

Origin of replication

Question 15

a specialized RNA polymerase that synthesizes the RNA primers for DNA synthesis.

Answer 15

Primase

Question 16

a means of repairing damaged DNA in which the damaged region is corrected in place. For example, pyrimidine dimers are simply cleaved to restore the original nucleotides.

Answer 16

Direct repair

Question 17

DNA repair systems that consist of at least two proteins, one for detecting the mismatch and the other for recruiting an endonuclease that cleaves the newly synthesized DNA strand close to the lesion to facilitate repair.

Answer 17

Mismatch repair

Question 18

A means of repairing DNA in which the damaged base is removed and replaced by a base complementary to the undamaged DNA strand.

Answer 18

Base-excision repair

Question 19

in elongation of polymers, the initial segment of the polymer that is to be extended and on which elongation is dependent.

Answer 19

Primer

Question 20

A complex of DnaA, DnaB and DnaC proteins that bind at the origin of replication on the E. coli chromosome and make single-stranded DNA accessible to other proteins required for replication.

Answer 20

Origin of replication complex (ORC)

Question 21

a reverse transcriptase that contains its own template; a highly processive enzyme that elongates the 3 inch-ending strand of telomeres.

Answer 21

Telomerase

Question 22

A means for repairing double strand breaks in DNA that does not depend on other DNA molecules in the cell.

Answer 22

Nonhomologous end joining (NHEJ)

Question 23

The coordination of DNA replication and cell division in eukaryotes. Mitosis takes place only after DNA synthesis. Two gaps (G1 and G2) in time separate the two processes.

Answer 23

Cell cycle

Question 24

ends of chromosomes; the DNA at the telomere consists of hundreds of repeats of a hexanucleotide sequence characteristic of the organism.

Answer 24

Telomere

Question 25

a simple, rapid means of detecting carcinogens by measuring a chemical&#39s ability to induce mutations in Salmonella bacteria.

Answer 25

Ames test

Question 26

an enzyme that catalyzes the exchange of genetic material that occurs when two DNA molecules recombine.

Answer 26

Recombinase

Question 27

An E. coli protein central to recombination that can initiate recombination by promoting strand invasion.

Answer 27

RecA

Question 28

the initial stage in the recombination process in which four molecules of recombinase and their associated DNA molecules come together.

Answer 28

Recombination synapse

Question 29

a cross-like structure, formed by four polynucleotide chains, that is key intermediate in the recombination process.

Answer 29

Holliday junction

Question 30

Forming a structure of closed, circular DNA in which the DNA is more compact than the relaxed circular DNA; the circular DNA helix twists upon itself to form a superhelix.

Answer 30

supercoiling

Question 31

A model for DNA replication in which the lagging strand loops out of the replication complex with the loop lengthening and shortening, like the slide of a trombone, as replication proceeds.

Answer 31

Trombone model

Question 32

A measure of the helical winding of the DNA strands around each other in a double helix.

Answer 32

Twist

Question 33

a sequence of DNA or RNA which directs the production of a complementary sequence.

Answer 33

Template

Question 34

enzymes that catalyze the interconversion of topoisomers of DNA; topoisomerases can relax supercoiled DNA.

Answer 34

Topoisomerase

Question 35

A measure of the coiling of the axis of the double helix - that is, a measure of supercoiling.

Answer 35

Writhe

Question 36

molecules of DNA that differ from one another only in their linking number.

Answer 36

Topoisomer

Question 37

stretches of DNA in which a trinucleotide sequence is repeated many times. These segments of DNA can expand during DNA replication, causing genetic diseases, such as Huntington disease.

Answer 37

Trinucleotide repeat

Question 38

Genes for DNA-repair proteins that suppress tumor development when at least one copy of the gene is free of a deleterious mutation.

Answer 38

Tumor-suppressor gene