Deck 28: DNA Replication, repair, and Recombination

Question 1

What type of topoisomerase can introduce supercoils?

A) type I
B) type II
C) type III
D) type IV
E) All topoisomerase can introduce supercoils.

Answer 1

B

Question 2

What name is given to the short sections of DNA found on the lagging strand during DNA synthesis?

A) primer fragments
B) template fragments
C) supercoiled fragments
D) Holliday fragments
E) Okazaki fragments

Answer 2

E

Question 3

UV light causes damage to DNA by forming __________________.

Answer 3

pyrimidine dimers

Question 4

________________ are intermediates in recombination pathways composed of four polynucleotide chains in a cross-like structure.

Question 5

What structure is found at the ends of chromosomes?

A) origin of replication
B) consensus sequence
C) Holliday junction
D) telomere
E) None of the answers is correct.

Question 6

The DNA strand that is replicated continuously is known as the _____________ strand.

Question 7

What proteins use ATP to separate DNA strands at specific sites?

A) topoisomerases
B) single-stranded binding proteins
C) histones
D) gyrases
E) helicases

Question 8

What assay is used to determine mutagenic potential?

A) Kornberg test
B) Okazaki test
C) Ames test
D) Warburg test
E) Ochoa test

Question 9

The primer for DNA synthesis is an RNA molecule formed by the enzyme _______________.

Question 10

The human genetic skin disease caused by a mutation in components of the human nucleotide-excision-repair pathway is called ___________________.

Question 11

Which of the following is a short section of RNA that is extended by DNA polymerase?

A) telomere
B) primer
C) Okazaki fragment
D) Holliday fragment
E) None of the answers is correct.

Question 12

The tertiary structures in DNA are created by the process known as ______________.

Question 13

What must happen to the strands of DNA in order for replication to occur?

A) supercoiling
B) annealing
C) melting
D) unwinding
E) None of the answers is correct.

Question 14

What describes the number of times a DNA strand winds around the helix axis when the axis lies in a plane?

A) linking number
B) writhe number
C) twist number
D) supercoil number
E) None of the answers is correct.

Question 15

During prokaryotic DNA replication,the RNA primer pieces are removed by __________________.

Question 16

What type of topoisomerase does NOT require ATP?

A) type I
B) type II
C) type III
D) type IV
E) All topoisomerases require ATP.

Question 17

Type ________ topoisomerase introduces negative supercoils in DNA while type ________ topoisomerase relaxes supercoil structures.

Question 18

DNA polymerase III is able to correct mistakes in replication due to its _________________ function.

Question 19

One metal ion in the DNA polymerase reaction coordinates the 3'-hydroxyl group of the primer,and the second metal ion interacts with the ______________.

Question 20

DNA serves as the _____ for synthesis of complementary strands of DNA.

A) primer
B) catalyst
C) template
D) primer and template
E) None of the answers is correct.

Question 21

Why is the site of DNA synthesis called the replication fork?

Question 22

The observed error rate in DNA replication is approximately

A) 1 per 10⁶ nucleotides.
B) 1 per 10⁴ nucleotides.
C) 1 per 10¹⁰ nucleotides.
D) 1 per 10¹⁵ nucleotides.
E) None of the answers is correct.

Question 23

The mechanism by which type I topoisomerase relaxes DNA includes which of the following?

A) The OH of Tyr 723 attacks a phosphate group on one DNA strand.
B) When the backbone of one strand is cleaved, the DNA rotates.
C) ATP binds, leading to a conformation change.
D) All the answers are correct.
E) The OH of Tyr 723 attacks a phosphate group on one DNA strand, and when the backbone of one strand is cleaved, the DNA rotates.

Question 24

What is true about DNA polymerases?

A) There are at least five structural classes.
B) All have finger and thumb domains that wrap around the DNA.
C) All catalyze the same reaction, which requires metal cofactors.
D) All the answers are correct.
E) There are five structural classes, and all catalyze the same reaction, which requires metal cofactors.

Question 25

What is a Klenow fragment?

Question 26

What is DNA gyrase?

A) a bacterial type II topoisomerase
B) a bacterial type I topoisomerase
C) a bacterial helicase
D) a eukaryotic helicase
E) None of the answers is correct.

Question 27

How can the leading and lagging strands be synthesized in a coordinated fashion?

A) Specific enzymes control the size of the DNA opening.
B) Lagging-strand binding proteins inhibit leading-strand replication if the strands become disproportionate in size.
C) DNA polymerase III is a dimeric holoenzyme, and the looped lagging strand allows the enzyme to proceed in the same direction with each strand.
D) Leading and lagging strand syntheses are catalyzed by two distinct and noninteracting replisomes, but the rate is controlled by helicase.
E) None of the answers is correct.

Question 28

Which of the following best describes the directionality of DNA replication?

A) 5' → 3' direction on both strands
B) 3' → 5' direction on both strands
C) 5' → 3' direction on the leading strand, 3' → 5' on the lagging strand
D) 3' → 5' direction on the leading strand, 5' → 3' on the lagging strand
E) None of the answers is correct.

Question 29

Which of the following is (are)true?

A) Naturally occurring DNA usually has negative supercoiling.
B) Forms with the same linking number can be interconverted without cleavage.
C) The twist value rarely changes in naturally occurring DNA.
D) All the answers are correct.
E) Naturally occurring DNA usually has negative supercoiling, and forms with the same linking number can be interconverted without cleavage.

Question 30

Why is shape complementarity so important in DNA replication?

Question 31

Aflatoxin B₁ is a compound that is converted to a reactive epoxide by a cytochrome P450 enzyme and causes

A) a G-C to T-A transversion.
B) an intrastrand cross-link.
C) deamination of adenine.
D) deamination of cytosine.
E) None of the answers is correct.

Question 32

How is replication specificity dictated?

A) Proper base-pairing is dictated more by shape than by hydrogen bonding capacity.
B) Enzyme interactions with the DNA act as a "ruler" to determine if the properly spaced base pair has been formed.
C) The bond is broken and reformed to ensure its accurate placement at each base pair.
D) All the answers are correct.
E) A and B are both correct.

Question 33

Photolyase functions to

A) repair pyrimidine dimers.
B) remove damaged bases.
C) ligate single-strand breaks.
D) remove 6-4 photoproducts.
E) None of the answers is correct.

Question 34

What is the formula for the linking number?

A) Lk = Wr − Tw
B) Lk = Wr + Tw
C) Tw = Wr + Lk
D) Lk = Tw/Wr
E) None of the answers is correct.

Question 35

Common types of mutations that arise in DNA replication include

A) the mismatch of bases in the DNA.
B) the deletion of one or more bases in the DNA.
C) the insertion of one or more bases in the DNA.
D) All the answers are correct.
E) the deletion of one or more bases in the DNA and the insertion of one or more bases in the DNA.

Question 36

Huntington's disease is caused by

A) pyrimidine dimers.
B) trinucleotide expansion.
C) improper DNA methylation.
D) suppressor mutants.
E) None of the answers is correct.

Question 37

Describe the general three-step process that is catalyzed by a type I topoisomerase.

Question 38

How are DNA strand breaks sealed?

Question 39

Topoisomerases are enzymes that introduce or eliminate supercoils in DNA during replication.What is the difference in mechanism and energy requirements for topoisomerase types I and II?

Question 40

One function of the two metal cations that are required by DNA polymerases is

A) to stabilize the negative charge of the transition state.
B) to bind ATP.
C) to complex with a Tyr residue in the active site.
D) to cleave improperly matched bases
E) None of the answers is correct.

Question 41

What role does the protein RecA play in recombination?

Question 42

What does the phrase "recombination of genetic material" refer to?

Question 43

How are single-stranded regions of DNA maintained during polymerization?

Question 44

What has been learned about ATP binding and hydrolysis in the helicase mechanism through the use of the non-hydrolyzable ATP analog,AMP-PNP?

Question 45

Describe the consequences of incorrect DNA replication or DNA damage.

Question 46

How is the processivity of DNA polymerase III accomplished?

Question 47

Why is thymine instead of uracil used in DNA?

Question 48

What is a processive polymerase enzyme versus a distributive enzyme?