Deck 28: Dna Metabolism: Replication, Recombination, and Repair

Question 1

The enzyme that removes the RNA primer from the Okazaki fragment is:

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

Answer 1

A

Question 2

All of the following are characteristic of replication of the E. coli circular chromosome EXCEPT:

A) replication is bi-directional.
B) it initiates at a unique position called oriC.
C) torsional stress introduced in the duplex DNA is relieved by DNA gyrase.
D) the unwinding of the duplex DNA is driven by the translocation of the DNA polymerase.
E) replication forks move in opposite directions.

Answer 2

D

Question 3

DNA polymerases share all of the following characteristics EXCEPT:

A) incoming bases are paired with corresponding bases on the template strand within the polymerase active site
B) polymerization proceeds in a 5'→3' direction
C) polymerization is antiparallel to template strand
D) strong processivity
E) polymerization is dependent upon the presence of an oligonucleotide primer

Answer 3

D

Question 4

Removal of RNA primer and replacement with DNA is carried out by:

A) DNA polymerase I.
B) DNA gyrase.
C) DNA polymerase III.
D) DNA ligase.
E) primerase.

Question 5

SSBs are:

A) substrates for DNA ligases.
B) supercoil stabilizing bodies.
C) single-stranded bodies called Okazaki fragments.
D) single-stranded DNA binding proteins that prevent re-annealing.
E) nucleases that hydrolyze single-stranded RNA primers.

Question 6

The termination of DNA replication in E. coli occurs when ____ protein binds the ____ locus on the DNA and acts as a ____.

A) tag; oriC; helicase
B) ter; tag; polymerase
C) DnaC; DnaG; gyrase
D) Tus; Ter; contrahelicase
E) SSB; primer; RNA polymerase

Question 7

All are characteristics of Okazaki fragments EXCEPT:

A) newly synthesized short lagging strand fragments.
B) synthesis performed in the 5'→3' direction.
C) initiated with an RNA primer.
D) about 20-30 nucleotides in length.
E) binds anti-parallel to the template strand.

Question 8

A pair of β-subunits of DNA polymerase III form a ____ to tether the polymerase to the template thus increasing the ____ of the polymerase.

A) ligase; unwinding
B) sliding clamp; processivity
C) primer binding; primase activity
D) loop of DNA; direction
E) none are true

Question 9

The degree to which the enzyme remains associated with the template through successive cycles of nucleotide addition is referred to as:

A) processivity.
B) turn-over number.
C) progression.
D) semidiscontinuousness
E) dissociativity.

Question 10

E. coli DNA polymerase I has ____ distinct catalytic active site(s) on its single polypeptide chain.

A) 1
B) 2
C) 3
D) 4
E) 5

Question 11

All occur during DNA replication in E. coli EXCEPT:

A) helicase unwinds dsDNA at the replication fork.
B) DNA ligase catalyzes the formation of phosphoester bonds on the lagging strand.
C) DNA polymerase I hydrolyzes RNA from the 5' ends of Okazaki fragments.
D) primase (DnaG) binds to a GC rich region of dsDNA in oriC.
E) all are true.

Question 12

DNA is replicated by a ____ mechanism.

A) dispersive
B) conservative
C) semiconservative
D) liberal
E) none of the above

Question 13

Eukaryotic cells have replication regions called ____ that occur every ____ kbp and the units of replication are called ____.

A) replicons; 2-5; replication forks
B) replication factories; 5-10; replicons
C) replicators; 3-300; replicons
D) replication forks; 5-50; replicators
E) none are true

Question 14

All are properties of DNA polymerase III EXCEPT:

A) It is responsible for incorporating most of the nucleotides in the lagging strand.
B) It synthesizes most of the leading strand prior to aiding in the synthesis of the lagging strand.
C) It contains a 3' to 5' exonuclease activity.
D) It is a large protein complex containing more than five subunits.
E) Much greater processivity than DNA polymerase I.

Question 15

Which of the following is NOT true regarding E. coli replication on the lagging strand?

A) is primarily carried out by DNA polymerase I.
B) synthesized discontinuously.
C) performed in a 5'→3' direction of synthesis
D) initially synthesized as Okazaki fragments
E) requires the enzymes primase and DNA ligase

Question 16

The enzyme that seals nicks in dsDNA where a 3'-OH and 5'-phosphate are juxtapositioned is:

A) DNA polymerase I.
B) DNA gyrase.
C) DNA polymerase III.
D) DNA ligase.
E) primerase.

Question 17

E. coli DNA polymerase I has all of the following characteristics EXCEPT:

A) a 5'→3' exonuclease activity.
B) a 3'→5' exonuclease activity.
C) a 5'→3' DNA polymerase activity.
D) modest processivity (approximately 20 nucleotides).
E) does not require a primer for initiation.

Question 18

Enzymes that catalyze the unwinding of DNA double helix are:

A) topoisomerases.
B) helicases.
C) ligases.
D) gyrases.
E) polymerases.

Question 19

3'-Exonuclease activity of DNA polymerase I of E. coli has all the characteristics EXCEPT:

A) is an "editor" of polymerase activity.
B) is opposite to the polymerase activity.
C) removes nucleotides that do not base pair at the 3'-end of the growing chain.
D) is relatively fast compared to the polymerase activity.
E) all are true.

Question 20

All are correct about DNA gyrase in E. coli EXCEPT:

A) It is a topoisomerase that hydrolyzes ATP during its reaction mechanism.
B) Its mechanism involves the breaking of a single phosphoester bond in one strand of dsDNA.
C) It works to remove positive supercoiling introduced by the DnaB protein (helicase).
D) It works to introduce negative supercoiling in DNA to overcome the torsion stress imposed upon unwinding.
E) All are true.

Question 21

The correct sequence for homologous recombination steps is:
A)ligation.
B)branch migration and strand exchangE.C.nicking.
D)EW or NS cleavage, resolution and re-ligation.
E)strand invasion.

A) B, C, E, A, D
B) C, B, E, D, A
C) D, C, B, A, E
D) C, E, A, B, D
E) C, A, B, E, D

Question 22

All are characteristics of transposons EXCEPT:

A) segments of DNA moved non-enzymatically in the genome.
B) unstable location within genome.
C) range in size from hundreds of bps to 8 kbp.
D) the smallest transposons are called insertion sequences.
E) a major force in evolution.

Question 23

One function of the RecA protein in recombination events is to:

A) produce an endonucleolytic nick on dsDNA.
B) aid in recognition of Chi site by the RecBCD complex.
C) initiate recombination.
D) catalyze the ATP-dependent DNA strand exchange reaction.
E) drive branch migration and process the Holliday junction into recombinant products.

Question 24

Telomeres have all of the characteristics EXCEPT:

A) G-rich nucleotide sequences.
B) structures at the end of eukaryotic chromosomes.
C) eukaryotic counterpart to the prokaryotic γ-complex.
D) short (5-8 bp) tandemly repeated sequences.
E) all are true.

Question 25

Progression through the cell cycle for eukaryotic cells is regulated through a series of ____ that depend on ____, produced at one phase and degraded at another, that bind ____ which regulate specific proteins by phosphorylation.

A) checkpoints; cyclins; cyclin dependent protein kinases (CDKs)
B) cyclins; phosphorylation; protein kinases
C) phosphorylations; cyclins; protein kinases
D) CDKs; cyclins; protein kinases
E) none are true

Question 26

All are characteristics of RNA-directed DNA polymerase EXCEPT:

A) synthesizes polynucleotides in the 5' to 3' direction.
B) often uses a specific tRNA primer.
C) found in retroviruses.
D) also called reverse transcriptase.
E) all are true.

Question 27

The principal DNA polymerase in eukaryotic leading strand DNA replication is:

A) DNA polymerase α (alpha).
B) DNA polymerase β (beta).
C) DNA polymerase γ (gamma).
D) DNA polymerase δ (delta).
E) DNA polymerase ε (epsilon).

Question 28

In general recombination in E. coli, the protein that binds ssDNA forming a nucleoprotein filament capable of strand invasion and homologous pairing is:

A) RecA.
B) RuvB.
C) RuvC.
D) RuvA.
E) RecBCD complex.

Question 29

All are true for the DNA strand-exchange reaction EXCEPT:

A) ATP-dependent.
B) catalyzed by RecA protein.
C) requires DNA polymerase I.
D) complex has 3'-terminal ssDNA affinity for other DNA termini.
E) results in branch migration.

Question 30

All are characteristic of retroviruses EXCEPT:

A) uses viral DNA as a template.
B) reverse transcriptase is required to produce dsDNA for insertion into host genome
C) the viral RNA genome is degraded prior to complete synthesis of dsDNA
D) reverse transcriptase is often error-prone causing viruses to mutate quickly
E) genome can lie dormant for years as a provirus in the host chromosome.

Question 31

In eukaryotic cells, one of the protein kinases that acts on the pre-replication complex (pre-RC) to trigger DNA replication is:

A) ORC.
B) MCM.
C) Cdc6p.
D) RLF.
E) cyclin B-CDK.

Question 32

The protein that moves along dsDNA using ATP-dependent helicase and nuclease activity during general recombination in E. coli is:

A) RecA.
B) RuvB.
C) DNA polymerase I.
D) DNA ligase.
E) RecBCD complex.

Question 33

Mutations in BACA1 and BACA2 genes causes increased likelihood of ____ because BACA1 protein functions in regulation of the cell cycle in response to ____, and BACA2 protein participates in DNA repair by ____.

A) breast and ovarian cancer; DNA damage control; homologous recombination
B) breast and ovarian cancer; homologous recombination; DNA damage control
C) uterine cancer; transposition; homologous recombination
D) genetic recombination; transposition; homologous recombination
E) none are true

Question 34

AZT (3'-azido-2',3'-dideoxythymidine) is a drug that gets incorporated into growing viral DNA and blocks the activity of:

A) DNA ligase.
B) DNA polymerase β (beta).
C) DNA polymerase α (alpha).
D) reverse transcriptase.
E) none of the above.

Question 35

RuvA, RuvB, and RuvC are involved in all EXCEPT:

A) processing Holliday junctions into recombination products.
B) aiding strand invasions of the 3'-ssDNA into homologous DNA duplexes.
C) Holliday junction-specific helicase complex.
D) dissociates the RecA filament and catalyzes branch migration.
E) all are true.

Question 36

In the initiation of replication in yeast, the pre-replication complex (pre-RC) consists of all EXCEPT:

A) MCM complex.
B) Cdc6p.
C) ORC.
D) CDKs.
E) all are true.

Question 37

All are common forms of DNA damage EXCEPT:

A) replication errors resulting in a missing or incorrect base.
B) bulges due to deletions or insertions.
C) UV-induced base alterations, such as pyrimidine dimers.
D) strand breaks at phosphodiester bonds or within deoxyribose rings.
E) all of the above.

Question 38

An RNA-dependent DNA polymerase that carries the RNA template with it to synthesize repeats at the 3'-ends of chromosomes is called:

A) DNA ligase.
B) telomerase.
C) DNA polymerase γ (gamma).
D) topoisomerase.
E) DNA polymerase β (beta).

Question 39

Compared to their parents, progeny may have new combinations of traits because of:

A) reverse transcriptase.
B) cyclin dependent protein kinase.
C) genetic recombination.
D) processivity.
E) all are true.

Question 40

Reverse transcriptases possess all of the following activities EXCEPT:

A) RNA-directed DNA polymerase activity.
B) RNase H activity.
C) ssDNA-directed DNA polymerase activity.
D) dsDNA-directed DNA polymerase activity.
E) all are true.

Question 41

The exchange of one base for another is called a ____, while insertions and deletions are referred to as ____.

A) frameshift mutation; transition mutations
B) frameshift mutation; point mutations
C) point mutation; transversion mutations
D) point mutation; frameshift mutations
E) transition mutation; transversion mutations

Question 42

All are characteristics of mammalian nucleotide excision repair EXCEPT:

A) sugar-phosphate backbone is cut in two places
B) the region of DNA excised is generally 27-29 bases in length
C) resulting gap is filled in by DNA polymerase β
D) DNA backbone is closed with DNA ligase
E) all are true

Question 43

The region of immunoglobulins that form the structural site complementary to some part of an antigen's structure are:

A) immunoglobulin fold region.
B) hinge region.
C) constant heavy region.
D) hypervariable region.
E) all are true.

Question 44

____ promotes the formation of covalent bonds between ____ thymine residues in a DNA strand creating a ____ ring called a thymidine dimer.

A) Visible light; adjacent; cyclohexyl
B) Visible light; nearby; cyclobutyl
C) UV light; adjacent; cyclobutyl
D) UV light; nearby; cyclohexyl
E) IR light; adjacent; cyclobutyl

Question 45

Mutations in DNA may result from all of the following EXCEPT:

A) spontaneous mutations due to errors in replication.
B) physical insults on the cell, such as UV light.
C) errors in transcription.
D) chemical mutagens.
E) introduction of a base analog into DNA.

Question 46

____ provides a mechanism for generating a variety of protein isoforms of immunoglobulins from a limited number of genes.

A) Genetic recombination
B) Replication licensing
C) DNA polymerase
D) DNA rearrangement
E) All are true

Question 47

Together with ____, ____ provide(s) for genetic variability within species and, ultimately, the evolution of new species.

A) DNA repair; DNA glycosylase
B) DNA glycosylase; recombination
C) recombination; mutations
D) mutations; DNA glycosylase
E) DNA repair; mutations

Question 48

A transversion mutation would be replacing T by:

A) A.
B) C.
C) U.
D) G.
E) either A or G.

Question 49

The repair of cyclobutane pyrimidine dimers involves bacterial ____ and the cofactors ____ and ____.

A) DNA methylase; S-adenosyl methionine; ATP
B) DNA carboxylase; CoA; CoQ
C) DNA polymerase I; flavin; TPP
D) photolyase; flavin; NADH
E) photolyase; flavin; pterin

Question 50

The vast diversity of immunoglobulin sequences is explained by:

A) DNA rearrangement
B) large sections of DNA devoted to immunoglobulin formation
C) susceptibility of the immunoglobulin genes to mutation
D) sensitivity of formed immunoglobulin proteins to environmental factors
E) all of the above

Question 51

When the methyl-directed repair system detects a mismatch in dsDNA it:

A) corrects the DNA strand that is methylated by removal of a single base and replacing with the correct one
B) corrects the DNA strand that is methylated by removal of a sting of nucleotides and replacing with correctly matched nucleotides
C) corrects the DNA strand that is not methylated by removal of a single base and replacing with the correct one
D) corrects the DNA strand that is not methylated by removal of a sting of nucleotides and replacing with correctly matched nucleotides
E) none of the above.

Question 52

Which of the following statements explains why the adenine analog, 2-aminopurine (2-AP), can cause mutations in DNA when it is inserted in place of a site normally occupied by A?

A) 2-AP forms 2 hydrogen bonds with thymine
B) 2-AP undergoes oxidative deaminiation to hypoxanthine which basepairs with C
C) 2-AP can form a single hydrogen bond with C
D) 2-AP is often found as a schiff base that crosslinks with T
E) none of the above

Question 53

B-cells, T-cells, and macrophages are cell types capable of ____ as a mechanism of producing ____ essential to the immune response.

A) replication rearrangement; antibodies
B) complimentarity modification; antigens
C) DNA replication; genes
D) DNA rearrangement; antibodies
E) All are true

Question 54

A transition mutation would be replacing A by:

A) T.
B) C.
C) U.
D) G.
E) either T or C

Question 55

Misincorporation of all subsequent amino acids results from ____ mutations.

A) chemical
B) base shift
C) frameshift
D) transition
E) all are true

Question 56

What type of mutation most likely results from the alkylation of the oxygen on position 6 of guanine base producing O⁶-methylguanine?

A) deletion
B) insertion
C) transition
D) transversion
E) frameshift

Question 57

When the thymine analog, 5-bromouracil, incorporates into DNA normally occupied by thymine, what type of mutation can occur?

A) T-A to A-T, only.
B) T-A to C-G, only.
C) C-G to T-A, only.
D) both b and c are correct.
E) a, b, and c are correct.

Question 58

Nitrous acid causes the oxidative deamination of cytosine producing uracil. What point mutation is the logical result?

A) C-G to A-T, only
B) C-G to T-A, only
C) C-G to G-C, only
D) both a and b are correct
E) a, b and c are correct

Question 59

In base-excision repair, the first enzyme in the sequence is ____ creating a(n) ____ site.

A) DNA polymerase III; ligase binding
B) DNA glycosylase; apurinic or apyrimidinic
C) DNA polymerase I; apurinic or apyrimidinic
D) DNA ligase; polymerase III binding
E) AP endonuclease; ligase binding

Question 60

Which of the following statements explains why the thymine analog, 5-bromouracil (5-BU), can cause mutations in DNA when it is inserted in place of a site normally occupied by T?

A) the bromine of 5-BU is similar in size to the methyl group of T and thus pairs with A
B) 5-BU is often found as the enol tautomer that hydrogens more effectively with G than with A
C) the bromine is subject to nucleophilic attack by a methyl transferase resulting in newly synthesized DNA being recognized as the methylated parent strand
D) the 5-BU is subject to removal resulting in a frame-shift mutation
E) none of the above

Question 61

Discuss pyrimidine dimers in DNA. How are they repaired?​

Question 62

Which of the following activities is NOT associated with the DNA polymerase III holoenzyme?

A) 3'-exonuclease
B) 5'-exonuclease
C) sliding clamp
D) removal of single stranded binding proteins
E) all are activities of the holoenzyme

Question 63

Which of the following would most likely cause a frameshift mutation?

A) an alkylating agent such as methyl iodide
B) a base analog such as 5-bromouracil
C) a chemical mutagen such as nitrous acid
D) an intercalation agent such as acridine orange
E) none of the above

Question 64

Which of the following DNA repair mechanisms is correctly defined?

A) mismatch repair system: corrects errors created from chemical modification of DNA
B) photolyase: repairs cyclobutane dimers formed between adjacent cytosine residues
C) base excision repair: uses DNA glycosylase to remove a damaged base by cleaving the glycosidic bond
D) nucleotide excision repair: removes a single nucleotide by cutting the phosphodiester backbone
E) none of the above

Question 65

Discuss the directionality of DNA replication in E. coli.​

Question 66

Describe the enzymatic apparatus that assembles at the replication fork during DNA replication.​

Question 67

Define the types of recombination. What are the enzymes of general recombination in E.coli?​

Question 68

Discuss insertions and deletions in DNA.​