Deck 4: DNA Replication, Recombination, and Repair

Question 1

Semiconservative replication of DNA means that after two rounds of replication

A) only one of the two parental strands is preserved intact in the progeny molecules of DNA.
B) both parental strands remain intact in one of the progeny molecules of DNA.
C) the two parental strands remain intact in different progeny molecules.
D) one of the parental strands is broken down and dispersed in one of the progeny molecules of DNA, the other parental strand remains intact in one of the progeny molecules.
E) neither of the parental strands appears in the progeny molecules of DNA.

Answer 1

the two parental strands remain intact in different progeny molecules.

Question 2

Which enzyme activity does DNA Pol I not have?

A) 5' to 3' exonuclease
B) 3' to 5' exonuclease
C) 5' to 3' DNA polymerase
D) 3' to 5' DNA polymerase

Answer 2

3' to 5' DNA polymerase

Question 3

Helicase

A) unwinds double stranded DNA by breaking base pairs
B) will decrease the writhing number of negatively supercoiled DNA
C) will increase the linking number of negatively supercoiled DNA
D) nicks one strand of double stranded DNA
E) cuts both strands of double stranded DNA

Answer 3

unwinds double stranded DNA by breaking base pairs

Question 4

A mutation in which an A-T base pair in DNA is replaced by a G-C base pair is referred to as a(an) mutation.

A) Transition
B) Transversion
C) Insertion
D) Inversion
E) Deletion

Question 5

DNA excision repair

A) involves only two distinct steps.
B) requires visible light for activation.
C) replaces both strands of a segment of DNA.
D) is deficient in some human hereditary diseases.
E) is blocked by allopurinol.

Question 6

Listed are four enzymes involved in DNA replication1. DNA polymerase III 2. Primase 3. DNA ligase 4. DNA polymerase I. The correct order of action of these enzymes in lagging strand DNA synthesis is

A) 4,2,1,3
B) 2,1,4,3
C) 4,3,2,1
D) 2,4,1,3
E) 4,1,2,3

Question 7

If the mismatch repair machinery detects a mismatch soon after DNA replication, it can distinguish the parental strand from the newly synthesized strand by

A) methylation
B) the RNA primers
C) the Okazaki fragments
D) single stranded DNA binding protein
E) the degree of supercoiling

Question 8

5'-Methylcytosine residues in DNA are "hot spots" for mutation because they

A) can be deaminated to thymine.
B) can stimulate Z-DNA formation.
C) can easily tautomerize.
D) cannot base pair with guanine.

Question 9

Ionizing radiation is capable of producing genetic mutations by

A) base-changes in the DNA.
B) base-deletions in the DNA.
C) breaking chromosomes.
D) All of the above.
E) Only A and B above.

Question 10

Replication of the DNA in a human chromosome is similar to E. coli DNA replication in all of the following EXCEPT

A) replication is semiconservative.
B) the lagging strand is synthesized discontinuously.
C) multiple DNA polymerases are involved.
D) RNA is used as a primer.
E) only one origin is involved per DNA molecule.

Question 11

Primase is an enzyme in the primosome. It is a

A) DNA ligase.
B) RNA dependent DNA polymerase.
C) DNA dependent RNA polymerase.
D) RNA dependent RNA polymerase.
E) none of the above

Question 12

Which of the following are not required by DNA ligase in order to carry out its enzymatic reaction?

A) a free OH
B) a free 5'-OH
C) a nick in DNA
D) either NAD or ATP
E) a template strand opposite the nick

Question 13

DNA synthesis requires a primer. A primer is

A) an available serine hydroxyl (-OH) group on DNA polymerase III for initiation of DNA synthesis.
B) the complimentary strand of DNA.
C) an available 5'-triphosphate on the nitrogenous bases used in synthesis.
D) a short oligonucleotide with an available hydroxyl group on the ribose or deoxyribose.
E) a short oligonucleotide with an available 2'-hydroxyl group on the ribose or deoxyribose.

Question 14

All of the following statements are true with regard to DNA replication EXCEPT which one?

A) It involves a transient covalent link between RNA and DNA chains.
B) The over-all process is bidirectional.
C) Chain growth occurs by addition at the end of new strands.
D) The only nucleotides required are deoxynucleoside triphosphates.
E) Chain growth is discontinuous.

Question 15

Eukaryotic chromatin replication:

A) Is facilitated by the presence of a large pool of histones which are synthesized uniformly throughout the cell cycle.
B) Is characterized by conservative segregation of pre_existing H3_H4 tetramers at the replication fork.
C) Requires the presence of a special enzyme, telomerase, which appends short oligonucleotide blocks to the overhanging S' ends of the newly replicated DNA strands.
D) Results in the preferential segregation of the linker histone, H1, to the leading strand.
E) Both B and C.

Question 16

DNA replication

A) is bidirectional proceeding from a single initiation point on each chromosome in eukaryotic cells.
B) is unidirectional in prokaryotic cells.
C) does not require ATP.
D) is initiated on RNA primers.
E) involves the formation, and not the cleavage, of phosphodiester bonds.

Question 17

Indicate which of the following is a correct statement about the process of replication.

A) Only one strand of the DNA duplex is copied.
B) Sigma factor is required for recognition of the point at which replication will be initiated.
C) The DNA of mammalian chromosomes replicates bidirectionally.
D) The only enzyme required for replication is DNA polymerase.
E) replication is conservative.

Question 18

DNA synthesis is called:

A) replication
B) transcription
C) translation
D) transformation
E) polymerization

Question 19

Okazaki fragments are associated with

A) resolution of recombination intermediates.
B) splicing of transcripts.
C) resolution of DNA replication at telomeres.
D) replication of the leading strand.
E) replication of the lagging strand.

Question 20

Which of the following enzymes is involved in extending the ends of linear chromosomal DNA?

A) telomerase
B) ligase
C) primase
D) RNA polymerase
E) DNA polymerase

Question 21

Helicase

A) unwinds double stranded DNA by breaking base pairs.
B) will decrease the writhing number of negatively supercoiled DNA.
C) will increase the linking number of negatively supercoiled DNA.
D) nicks one strand of double stranded DNA.
E) cuts both strands of double stranded DNA.

Question 22

Which of the following is not true of eukaryotic DNA replication?

A) It is semiconservative.
B) It is discontinuous.
C) It proceeds 3' to 5' on the lagging strand.
D) It proceeds 5' to 3' on the leading strand.
E) It requires DNA polymerase activity.

Question 23

Chemicals that bind to DNA by intercalating between the bases

A) can cause frame shift mutations
B) can cause deletion mutations
C) can cause insertion mutations
D) are generally planar hydrophobic molecules
E) all of the above

Question 24

DNA replication involves all the factors listed EXCEPT

A) DNA polymerase.
B) sigma factor.
C) single stranded DNA template and primer.
D) RNA polymerase.
E) deoxyribonucleoside triphosphates.

Question 25

When we say DNA polymerase III has high processivity, we mean

A) that it has 5' to nuclease activity.
B) that it has to 5' nuclease activity.
C) it makes few errors during DNA synthesis.
D) it stays bound to the DNA until the synthesis is finished.
E) it rapidly associates and dissociates with the DNA.

Question 26

Frameshift mutations are possible because of

A) redundant (degenerate) code.
B) intra-allelic suppressor.
C) nonsense codon.
D) universality of the code.
E) non-overlapping code.

Question 27

The protein involved in separating the DNA strands at the initiation of DNA replication is called

A) helicase.
B) DNA polymerase I.
C) DNA polymerase III.
D) primase.
E) DNA gyrase.

Question 28

Helicases

A) cut one strand of the double helix.
B) cut both strands of the double helix.
C) require ATP.
D) unwind the double helix.
E) C and D

Question 29

The purpose of the short RNA chains which are synthesized during DNA replication is to:

A) code for genes necessary for replication.
B) provide a primer for DNA synthesis.
C) maintain DNA strands in an open (i.e., not base-paired) from so that polymerases can recognize the template strand.
D) reduce superhelical density.
E) provide a template for ligation of Okazaki fragments.

Question 30

An alteration in the genetic material which eventually gives rise to mutant progeny may originate in which of the following?

A) only the sense strand of the DNA
B) only the anti-sense strand of DNA
C) only both strands simultaneously
D) either strand of DNA
E) mRNA

Question 31

Gyrase (topoisomerase II)

A) unwinds double stranded DNA by breaking base pairs
B) will increase the writhing number of negatively supercoiled DNA
C) will increase the linking number of negatively supercoiled DNA
D) nicks one strand of double stranded DNA
E) cuts both strands of double stranded DNA

Question 32

The rate of DNA replication in eukaryotic cell nuclei is primarily governed by

A) the rate of elongation of DNA chains (i.e., number of nucleotides added per growing chain per second).
B) the number of replication forks per cell.
C) the activity of RNA polymerase III.
D) the number of chromosomes per cell.
E) None of the other answers is correct.

Question 33

Which of the following is NOT an important player in DNA replication?

A) primase
B) DNA polymerase I
C) DNA polymerase II
D) DNA ligase

Question 34

Deamination of 5-methylcytosine in DNA is mutagenic because it

A) produces thymine.
B) produces uracil.
C) changes a base but does not disrupt hydrogen bonding.
D) cannot be repaired.

Question 35

The polynucleotide ligase reaction involves

A) activation of the end of a DNA strand.
B) the formation of a cyclical 2',nucleoside phosphate.
C) the intermediate formation of an anhydride linkage be- tween AMP and the 5'-phosphate of a DNA strand.
D) the intermediate formation of an ester bond between AMP and DNA.
E) the cleavage of GTP.

Question 36

Chemical damage to nuclear DNA from exposure to a mutagenic agent is most dangerous when

A) the resulting mutation is repaired prior to replication of the damaged DNA.
B) the resulting mutation causes a permanent substitution of a single amino acid in an important protein with a chemically similar amino acid
C) the mutagenic agent causes a frameshift mutation near the amino terminus of a protein which promotes spermatogenesis.
D) the chemical change in the DNA results in a silent mutation which is fixed via DNA replication.
E) the resulting mutation is fixed through DNA replication and leads to the activation of a cellular oncogene and malignant transformation in a liver cell.

Question 37

Okazaki fragments are

A) the RNA primer in DNA synthesis.
B) pieces of DNA produced by restriction enzyme digestion.
C) unique to eukaryotes.
D) RNA fragments produced by splicing of primary transcripts.
E) stretches of DNA synthesized on the lagging strand.

Question 38

A frameshift or phase shift mutation

A) can only affect one polypeptide chain made from a polycistronic mRNA.
B) can usually be corrected by a missense mutation.
C) has little effect on most proteins.
D) could not occur in a regulatory gene.
E) None of the other answers is correct.

Question 39

Each of the statements about DNA replication is true EXCEPT which one?

A) DNA replication can be bidirectional.
B) DNA replication can be semiconservative.
C) DNA replication in humans involves RNA.
D) DNA replication requires only one protein, namely, DNA polymerase.

Question 40

Replication of DNA must be discontinuous on at least one strand because

A) nicks are required for the unwinding of supercoils.
B) the to 5' exonuclease continually introduces nicks in the new DNA.
C) the direction of polymerization is always 5' to while the two strands being copied in the replication fork are antiparallel.
D) fork movement is bidirectional.
E) RNA primers are used.

Question 41

Following oxidative deamination with nitrous acid and several rounds of replication, which of the following base pairs would you expect to replace the complementary base pair A-T?

A) T-G
B) G-C
C) C-G
D) T-A
E) G-T

Question 42

DNA gyrase

A) introduces positive super twisting into relaxed double- stranded DNA upon the hydrolysis of ATP.
B) relaxes negatively supercoiled DNA.
C) converts relaxed double-stranded DNA into a negatively supercoiled form upon the hydrolysis ATP.
D) relaxes positively supercoiled DNA upon the hydrolysis of ATP
E) contains only type I topoisomerase activity.

Question 43

DNA polymerase I

A) nicks DNA to initiate DNA replication.
B) has a DNA ligase activity for completing DNA application.
C) synthesizes DNA in a > 5' direction.
D) requires a primer with a free OH.
E) is used only to repair DNA.

Question 44

Which of the following DOES NOT play a role in prokaryotic replication?

A) DNA ligase
B) reverse transcriptase
C) DNA helicase
D) primase
E) DNA polymerase I

Question 45

The ---> 5' exonuclease activity of DNA polymerase I

A) provides primers with free hydroxyl groups for chain extension.
B) is similar to the mode of action of an RNA polymerase.
C) helps remove RNA primers during replication.
D) provides an error-correcting mechanism during replication and repair synthesis.
E) prevents bidirectional replication of the genome.

Question 46

Concerning the polarity of chain elongation during DNA replication

A) one new strand is elongated in the 5' to direction, while the other strand is polymerized in the to 5' direction.
B) both new strands are elongated in the to 5' direction.
C) both new strands are elongated in the 5' to direction.
D) any one new strand can be elongated in either direction.
E) None of the other answers is correct.

Question 47

A template in molecular biology means

A) the sequence of DNA to which the DNA polymerase initially binds.
B) a protein that has a specific binding site for RNA.
C) any macromolecule that provides the pattern for synthesis of another.
D) a polymer that provides the starting point for further growth of the molecule.
E) a temperature sensitive mutant.

Question 48

Which of the following DNA replication enzymes has a major role in lagging strand synthesis, but only a minor role in leading strand synthesis?

A) DNA gyrase
B) DNA polymerase I
C) DNA polymerase delta
D) DNA polymerase III

Question 49

Actinomycin D inhibits the growth of bacteria by

A) specifically inhibiting the initiation of RNA synthesis.
B) blocking the further elongation of polypeptide chain synthesis.
C) intercalating its phenoxazone ring between two G-C base pairs.
D) preventing the binding of aminoacyl-tRNA to the a-site of ribosomes.
E) inhibiting the peptidyl transferase activity of ribosomes.

Question 50

Indicate which of the following is a correct statement about replication.

A) Reverse transcriptase replicates DNA in the to 5' direction.
B) Eukaryotic DNA replication proceeds bidirectionally with multiple initiation sites.
C) replication of the leading strand within a replicon requires multiple initiation.
D) Since there is more DNA in eukaryotes than prokaryotes, the rate of polymerization per growing fork of nucleotides during DNA synthesis in eukaryotes is much greater than in prokaryotes.
E) Initiation of DNA replication in prokaryotes occurs randomly throughout the genome.

Question 51

Which of the following are not required by DNA ligase in order to carry out its enzymatic reaction?

A) a free 3'-OH
B) a free 5'-OH
C) a nick in DNA
D) either NAD or ATP
E) a template strand opposite the nick

Question 52

Why is DNA synthesis started with ribonucleotides rather than deoxyribonucleotides?

A) To mark the newly synthesized strand.
B) RNA polymerase makes fewer errors when priming than DNA polymerase would.
C) DNA polymerases cannot prime.
D) To mark the lagging strand for DNA ligase.

Question 53

Which of the following is specific to prokaryotes?

A) DNA replication is tied to the cell cycle.
B) The replication template is chromatin.
C) Each chromosome has multiple origins of replication.
D) Chromosomal DNA is linear.
E) DNA replication uses DNA polymerase III.

Question 54

After deamination of a cytidine residue in DNA, the new residue will complement with which of the following?

A) Adenosine
B) Inosine
C) Thymidine
D) Guanosine
E) Uridine

Question 55

Xeroderma pigmentosa is a genetically inherited disorder in which the cells of patients are:

A) unable to excise thymine dimers.
B) unable to ligate Okazaki fragments.
C) unable to remove RNA primers.
D) unable to fill gaps in DNA.
E) unable to relax supercoiling.

Question 56

DNA polymerase catalyzes elongation of DNA chains

A) in the 5' to direction through the addition of a deoxyribonucleotide complementary to the primer.
B) in the to 5' direction through the addition of a deoxyribonucleotide to the OH of the primer strand.
C) in the 5' to direction through the addition of a ribonucleotide to the OH of the primer strand selecting a purine or pyrimidine base complementary to the template strand.
D) in the to 5' direction through the addition of a deoxyribonucleotide to the OH of the primer strand selecting a purine or pyrimidine base complementary to the template strand.
E) in the 5' to direction through the addition of a deoxyribonucleotide to the OH of the primer strand selecting a purine or pyrimidine base complementary to the template strand.

Question 57

Short chains of nucleic acid can be isolated from cells in which DNA is undergoing replication. These segments, known as Okazaki fragments, have which of the following properties?

A) They are double_stranded.
B) They are removed by nuclease activity.
C) They are DNA_RNA hybrids.
D) They arise from the nicking of the sugar_phosphate backbone of the parental DNA chain.
E) They contain covalently linked RNA and DNA.

Question 58

Uracil is occasionally incorporated into DNA during replication. Why is it subsequently removed?

A) The presence of uracil would interfere with parental strand recognition.
B) Uracil is unstable and would cause mutations if left in the DNA.
C) Uracil makes the same hydrogen bonds as thymine so it might be confused with thymine.
D) Cytosine is unstable and occasionally converts to uracil.

Question 59

Which of the following is NOT an important player in DNA replication?

A) primase
B) DNA polymerase I
C) DNA polymerase II
D) DNA ligase

Question 60

With respect to mutations

A) transitions arise from the replacement of one purine to another purine or one pyrimidine to another pyrimidine.
B) transversions arise from the replacement of one pyrimidine to another pyrimidine.
C) transitions arise through deletions of a nucleotide in the DNA sequence.
D) transversions arise through the insertion of a nucleotide in the DNA sequence.
E) both transitions and transversions cause frameshift mutations.

Question 61

Which of the following enzymes is the most sensitive to inhibition by alpha-amanitin?

A) prokaryotic DNA polymerase I
B) prokaryotic DNA polymerase III
C) eukaryotic DNA polymerase alpha
D) eukaryotic RNA polymerase I
E) eukaryotic RNA polymerase II

Question 62

Okazaki fragments are

A) products of leading strand synthesis.
B) short single_stranded RNA molecules.
C) synthesized by DNA polymerase III.
D) excised by DNA polymerase I.

Question 63

Which of the following is a target for base excision repair?

A) deaminated adenine in RNA
B) methylated cytosine in DNA
C) methylated adenine in RNA
D) deaminated cytosine in DNA

Question 64

DNA polymerase I is extremely accurate in its ability to make a complementary copy of the template. The key activity that allows the polymerase to be so accurate is the

A) polymerase activity.
B) 5' => exonuclease activity.
C) => 5' exonuclease activity.
D) reverse transcriptase activity.
E) pyrophosphatase activity.

Question 65

The formation of tautomers of the DNA bases can be mutagenic because they can cause

A) depurination.
B) strand breakage.
C) abnormal base pairing.
D) cross-linking.

Question 66

Which of the following are not required for the enzymatic synthesis of DNA by DNA polymerase I?

A) Mg++
B) a template strand
C) ATP
D) dTTP
E) a primer with a free 3'-OH

Question 67

During the SOS response to DNA damage (as by UV light) which of the following is not true?

A) RecA protein synthesis is increased.
B) The LexA protein is destroyed.
C) Synthesis of the LexA protein is increased.
D) The LexA repressor protein shuts down the house keeping genes.
E) The synthesis of SSB and the uvrABC complex proteins are increased.

Question 68

Okazaki fragments

A) are found on the leading strand of newly synthesized DNA
B) are the short regions of RNA added by the primosome
C) do not contain RNA
D) is another name for restriction fragments
E) prime DNA Pol I directed DNA synthesis

Question 69

High fidelity DNA replication and repair

A) are due to the combined proofreading functions found on DNA polymerase I and III.
B) are due to the action of recBCD protein complex.
C) are monitored by lexA protein and the SOS response.
D) involve the formation of chi form intermediates.
E) are solely due to nucleic acid structure.

Question 70

Some frameshift mutations may be corrected by a

A) transition.
B) transversion.
C) double deletion.
D) missense mutation.

Question 71

What is the function of the to 5' exonuclease activity of bacterial DNA polymerases?

A) removes mismatched bases during replication
B) removes pyrimidine dimers
C) removes the RNA primers of Okazaki fragments
D) initiates mRNA synthesis
E) processes precursors of ribosomal RNA

Question 72

Topoisomerase I

A) unwinds double stranded DNA by breaking base pairs.
B) will decrease the writhing number of negatively supercoiled DNA.
C) will decrease the linking number of negatively supercoiled DNA.
D) nicks one strand of double stranded DNA.
E) cuts both strands of double stranded DNA.

Question 73

Synthesis of the leading strand at the replication fork is carried out by

A) DNA polymerase I.
B) DNA polymerase III.
C) DNA polymerase II.
D) RNA polymerase holoenzyme.
E) primase.

Question 74

An enzyme which can seal a nick in a DNA duplex is called a

A) sigma factor.
B) lipase.
C) ligase.
D) reverse transcriptase.
E) nuclease.

Question 75

In eukaryotes, which DNA polymerase is responsible for the replication of mitochondrial DNA?

A) alpha
B) beta
C) gamma
D) delta
E) epsilon

Question 76

All of the following statements are TRUE EXCEPT

A) excision repair requires a special ribonuclease.
B) DNA synthesis in bacteria requires RNA synthesis.
C) DNA polymerase I probably functions in excision repair.
D) RNA polymerase requires a template.
E) DNA synthesis in eukaryotes initiates at multiple sites.

Question 77

Which is the complementary strand of this sequence: 3' AGTCAGACCAGAC 5'?

A) 5' AGTCAGACCAGAC 3'
B) 3' GTCTGGTCTGACT 5'
C) 5' GTCTGGTCTGACT 3'
D) 5' CAGACCAGACTGA 3'

Question 78

Which of the following enzymes is involved in extending the ends of linear chromosomal DNA?

A) telomerase
B) ligase
C) primase
D) RNA polymerase
E) DNA polymerase a

Question 79

On the lagging strand, the primer on an Okazaki fragment is removed by the '--->exonuclease activity of DNA polymerase I. What enzyme replaces the degraded primer with deoxyribonucleotides?

A) DNA polymerase III
B) DNA ligase + NAD
C) terminal transferase
D) DNA polymerase I
E) DNA gyrase

Question 80

DNA polymerase I catalyzes the reaction of a

A) deoxynucleoside diphosphate with the OH end of a DNA chain.
B) deoxynucleoside diphosphate with the 5'-OH end of a DNA chain.
C) deoxynucleoside triphosphate with the OH end of a DNA chain.
D) deoxynucleoside triphosphate with the 5'-OH end of a DNA chain.
E) none of these.