Deck 20: DNA Replication, Repair, and Recombination

Question 1

DNA polymerase does not make mismatched base pairs because

A) there are no hydrogen bonds that line up between the mismatches.
B) the active site does not fit mismatches well.
C) the mismatched pairs make covalent bonds instead of hydrogen bonds.
D) the DNA primer does not allow for mismatched pairs.

Answer 1

the active site does not fit mismatches well.

Question 2

What is the name for the relationship between the original DNA and replicate DNA?

A) father and son
B) parent and children
C) parent and daughter
D) mother and daughter

Answer 2

parent and daughter

Question 3

Which of the following functions does a reverse transcriptase perform?

A) proofreading
B) exonuclease activity
C) convert RNA to DNA
D) convert DNA to RNA

Answer 3

convert RNA to DNA

Question 4

The best definition for DNA replication is when a cell copies its genome and is __________ cell division.

A) entire; a required element of
B) partial; a required element of
C) entire; not required for
D) partial; not required for

Question 5

All DNA is synthesized in which direction?

A) 5 ^' $\rightarrow$ 3 ^'
B) 3 ^' $\rightarrow$ 5 ^'
C) 1 ^' $\rightarrow$ 5 ^'
D) 5 ^' $\rightarrow$ 1 ^'

Question 6

How can DNA strands be synthesized using bidirectional replication?

A) They are not synthesized simultaneously.
B) One strand is synthesized 5 ^' $\rightarrow$ 3 ^' , whereas the other is 3 ^' $\rightarrow$ 5 ^' .
C) They are synthesized through Okazaki fragments.
D) They are synthesized using RNA polymerases.

Question 7

Bidirectional replication is defined as replication

A) with one replication fork.
B) with two replication forks.
C) that unwinds the DNA completely to replicate.
D) that replicates the DNA in a given direction.

Question 8

The complete complex that contains the enzymes and proteins required to replicate DNA is called the

A) primase.
B) polymerase.
C) replisome.
D) DNA gyrase.

Question 9

Which enzyme synthesizes the RNA primer for DNA replication?

A) DNA polymerase
B) DNA primase
C) DNA polymerization
D) DNA Pol III

Question 10

What is the correct order of the following steps to synthesize new DNA? 1. Addition of an RNA primer
2) Extension of the RNA primer
3) Conversion of double-stranded DNA to single-stranded DNA
4) Synthesize new DNA

A) 1; 2; 3; 4
B) 2; 3; 4; 1
C) 3; 1; 2; 4
D) 4; 1; 3; 2

Question 11

HIVRT is closely related to which DNA polymerase?

A) Pol I
B) Pol II
C) Pol III
D) Pol IV

Question 12

If ^{1 5}N DNA replicated using conservative replication in ^{1 4}N media, the outcome would be that new DNA has

A) a single intermediate density.
B) a lower density.
C) only the higher density.
D) one high density and one low density strand.

Question 13

What is a major function of prokaryotic DNA polymerase I besides replication?

A) very slow polymerization rate (1-2 nucleotides) to prevent mistakes
B) DNA translation
C) unlimited processivity
D) checking for exonuclease activity

Question 14

The 3 ^' -hydroxyl group used to initiate DNA synthesis comes from

A) a RNA primer.
B) the magnesium ion.
C) uracils, always.
D) amino acids, always.

Question 15

Semiconservative, as it relates to DNA replication, can be defined as when the original duplex DNA template

A) remains intact to make a new DNA duplex.
B) is broken into fragments.
C) is separated into single strands before replications.
D) can only be replicated once.

Question 16

Why do helicase and gyrase need to work together?

A) Gyrase adds the RNA primer and helicase removes it.
B) Helicase unwinds DNA and gyrase relieves the torsional strain.
C) Helicase synthesizes DNA and gyrase prevents helicase from dissociating.
D) Gyrase synthesizes RNA primers and helicase.

Question 17

Which are the major prokaryotic DNA polymerases?

A) Pol I, Pol III, and Pol $\delta$
B) Pol I, Pol II, and Pol III
C) Pol I, Pol II, and Pol $\delta$
D) Pol I, Pol III, and Pol $\varepsilon$

Question 18

Which prokaryotic polymerase is mainly responsible for DNA proofreading?

A) Pol I
B) Pol II
C) Pol III
D) Pol $\alpha$

Question 19

The role of Mg²⁺ in DNA replication is to the incoming deoxynucleotide.

A) stabilize the positive charges on
B) act as a nucleophile to attack the $\alpha$ -phosphoryl group in
C) stabilize the negative charges on
D) protonate

Question 20

A replication fork is necessary because it allows

A) for DNA replication to start on a single strand.
B) for DNA replication to start on the double strand.
C) DNA to break into half to start replication.
D) DNA to unwind completely to start replication.

Question 21

What would a possible outcome be if all eukaryotic cells had telomerase activity?

A) Cells would die sooner.
B) Cells would have increased synthesis.
C) The rate of synthesis would increase.
D) Cells would live indefinitely.

Question 22

What would a possible outcome be if no primer could be added at the end of a linear chromosome during replication?

A) DNA synthesis would restart on the same strand.
B) DNA synthesis would be enhanced.
C) The chromosome would be shortened every subsequent replication.
D) The chromosome would be elongated every subsequent replication.

Question 23

Tus-Ter terminates DNA synthesis by

A) breaking the single-strand DNA and preventing further synthesis.
B) forcing the primase to dissociate.
C) blocking the opening of helicase.
D) methylating the DNA strand.

Question 24

The most common DNA mutation is the substitution of one base for another. What is the likely outcome from that mutation?

A) increased DNA replication
B) an alteration of the protein's coding sequence
C) prevention of further synthesis
D) cell death

Question 25

When a cytosine is deaminated to form uracil and removed by glycosylase enzymes, a __________ site is generated.

A) nonbasic
B) abasic
C) dibasic
D) deaminated

Question 26

The role of CDK in DNA synthesis is to

A) remove the histones.
B) block further production of pre-RCs while converting pre-RC to RPC.
C) block further production of methylated DNA.
D) terminate synthesis.

Question 27

What is the function of telomerase in termination of DNA synthesis?

A) remove the telomeres
B) reverse transcription of the telomeres
C) bind to single-strand DNA to prevent refolding
D) shorten the DNA strand after each replication

Question 28

What is the specific site on the E. coli genome where DNA replication can initiate?

A) oriC
B) DnaA
C) primase
D) SeqA

Question 29

The function of the $\beta$ -clamp is to

A) keep the torsional strain reduced.
B) add the RNA primer.
C) keep the Pol III complex associated with the DNA.
D) separate the DNA into a single strand.

Question 30

When do somatic mutations occur?

A) G₁ phase
B) S phase
C) G₂ phase
D) after zygote formation

Question 31

What would happen first if a cell was no longer able to produce DnaA?

A) DnaC would not be able to bind to DnaB.
B) DnaB would not bind to primase.
C) The genome would not be unwound.
D) Pol III would not be able to bind to the DNA.

Question 32

Eukaryotic genomes overcome the slow synthesis rate by

A) eliminating the need for unwinding the DNA.
B) providing more replication origins.
C) using multiple primases.
D) only replicating part of the DNA in one cycle.

Question 33

Cytosine can be deaminated because it has a free that can be removed.

A) keto group
B) amine
C) amide group
D) ester group

Question 34

Which of the following is the most common type of DNA damage?

A) deamination of cytosine
B) deamination of uracil
C) methylation of adenine
D) methylation of tyrosine

Question 35

The main function of the primosome is to

A) synthesize primers for leading strand synthesis.
B) synthesize primers for lagging strand synthesis.
C) bind to single-stranded DNA to prevent reannealing.
D) synthesize new DNA on leading and lagging strand.

Question 36

The two key elements of the oriC include

A) three 13-bp repeats and four 9-bp repeats with enriched G-C base pairs.
B) three 13-bp repeats and four 9-bp repeats with enriched A-T pairs.
C) 20 subunits of A-T pairs.
D) the RNA primer.

Question 37

The function of Dam methylase in DNA synthesis is to methylate the

A) new DNA strand.
B) old DNA strand.
C) RNA primer.
D) primase.

Question 38

Spending time in the sun is a possible cause of DNA damage because UV radiation

A) causes an abasic site to form.
B) produces photoproducts.
C) causes protein misfolding.
D) produces methylated thymidine.

Question 39

Most cancers are caused by which kind of DNA mutation?

A) base substitution
B) abasic site
C) somatic
D) nucleotide deletions

Question 40

Which of the following would cause a genetic mutation?

A) DNA makes too many copies in the cell.
B) DNA synthesis does not occur.
C) DNA damage is not corrected.
D) Death of a cell occurs.

Question 41

Homologous recombination repairs what kind of DNA damage?

A) single-strand break
B) double-strand break
C) mismatched pairs
D) pyrimidine dimers

Question 42

Mutation of the BRCA protein can lead to

A) breast cancer.
B) lymphoma.
C) arthritis.
D) bone tumors.

Question 43

DNA photolyase specifically seeks out what kind of DNA damage?

A) base mismatch
B) abasic sites
C) pyrimidine dimers
D) phosphorylated base

Question 44

What is the mechanism by which replication errors are fixed in E. coli?

A) degrading of the entire DNA strand to start over
B) base excision
C) mismatch repair
D) abasic repair

Question 45

What are the mechanisms for excision nucleotide repairs in eukaryotes?

A) global genomic and mismatch
B) global genomic and base excision
C) transcription-coupled and partial genomic
D) transcription-coupled and global genomic

Question 46

What DNA damage can the MGMT enzyme repair?

A) phosphorylated adenine
B) methylated guanine
C) pyrimidine dimers
D) mismatched bases

Question 47

Methenyltetrahydrofolate (MTHF) absorbs light to form *MTHF. What does the star on MTHF signify?

A) radical
B) excited
C) cation
D) anion

Question 48

Base excision repair removes which kind of bases?

A) mismatched
B) methylated
C) those damaged by ROS
D) uracil

Question 49

If a strand of DNA has a large lesion that distorts the helical nature of the DNA, what would be the mechanism of repair?

A) mismatch repair
B) abasic repair
C) base excision
D) nucleotide excision

Question 50

What is the function of the MutS-MutL-MutH protein complex?

A) base excision
B) mismatch repair
C) DNA adenylation
D) DNA methylation

Question 51

MGMT is called the suicide enzyme because its active site permanently becomes

A) phosphorylated.
B) methylated.
C) protonated.
D) ionized.

Question 52

If a cell has many ROS species, what is the most likely reaction with DNA?

A) Nothing, because ROS do not react with DNA.
B) G-C to T-A replacement
C) O-alkylation of thymine
D) single point excision

Question 53

Which of the following is a specialized direct DNA repair process?

A) DNA photolyase system
B) nucleotide excision repair
C) base excision repair
D) DNA mismatch repair

Question 54

What role does PARP1 have in repairing a single-strand DNA break?

A) recognizes the break
B) removes the methyl group from guanine
C) replaces the mismatched pair
D) absorbs light to become excited

Question 55

What role do BRCA1 and BRCA2 play in DNA repair?

A) find the double-strand break
B) assist with strand invasion
C) repair pyrimidine dimers
D) synthesize new DNA bases

Question 56

Homologous recombination can only be used in late S phase or G2 phase because it

A) requires the presence of an intact sister chromatid as a template.
B) does not require the presence of a homologous template.
C) requires the cell to be in cell division.
D) requires the cell to be in the resting phase.

Question 57

What is a possible outcome when UV light reacts with riboflavin or tryptophan?

A) methylated riboflavin
B) reactive oxygen species
C) spontaneous deglycosylation
D) production of an abasic site

Question 58

The DNA alkylation of guanine is possible because the of guanine is __________ and reacts rapidly with __________ alkylating agents.

A) N-7; nucleophilic; electrophilic
B) N-5; nucleophilic; electrophilic
C) N-7; electrophilic; nucleophilic
D) N-5; electrophilic; nucleophilic

Question 59

Which of the following best describes base excision?

A) removal and replacement of individual bases that have been damaged by various chemical reactions
B) repair of large lesions that distort DNA
C) removal of individual bases that have been phosphorylated
D) repair of small lesions that distort DNA

Question 60

What is NOT a likely repair system used if a strand of DNA has a pyrimidine dimer?

A) mismatch repair
B) direct repair pathway
C) base excision
D) nucleotide excision

Question 61

Describe the differences among Pol I, Pol II, and Pol III in prokaryotic organisms.

Question 62

An HIV infection begins with what first step?

A) fusion of the cell membrane and viral envelope
B) release of viral DNA and synthesis of cDNA
C) protein synthesis and processing
D) budding of infectious virus

Question 63

The definition of a retrotransposon is a segment of

A) DNA that goes through an RNA intermediate to be moved.
B) RNA that goes through a DNA intermediate to be moved.
C) DNA that needs to be excised.
D) DNA that is folded incorrectly.

Question 64

The definition of a transposon is a segment of

A) DNA that can move from one region to another.
B) RNA that can move from one region to another.
C) DNA that is easily transcribed.
D) DNA that is in need of repair.

Question 65

Lysogeny by bacteriophages causes what result to the host DNA?

A) integration of virus DNA into host DNA
B) production of new bacteriophage particles
C) cell death
D) formation of Holliday junctions

Question 66

If a bacteriophage activates the lytic cycle, what is the result to the host DNA?

A) integration of virus DNA into host DNA
B) production of new bacteriophage particles
C) cell death
D) formation of Holliday junctions

Question 67

Describe the differences between Pol $\alpha$ 0, Pol $\delta$ , and Pol $\varepsilon$ in eukaryotic organisms.

Question 68

Describe the Meselson-Stahl experiment and how it provided biochemical evidence that DNA replication is semiconservative.

Question 69

Individuals with mutations of BRCA have increased incidence of cancer because of their

A) increased ability to form pyrimidine dimers.
B) decreased ability to repair single-strand DNA breaks.
C) decreased ability to repair double-strand DNA breaks.
D) increased ability to form methylated guanine.

Question 70

An advantage of viral DNA using LTR to produce a four-nucleotide overhang on the 3'end is to

A) start replication.
B) help with alignment of the viral DNA to the host DNA.
C) start a base mismatch repair sequence.
D) help with cell meiosis.

Question 71

A Holliday junction can best be defined as a region of

A) quadruplex DNA.
B) duplex DNA.
C) DNA damage.
D) DNA pyrimidine duplexes.

Question 72

Lynch syndrome is a genetic deficiency in repairs.

A) DNA excision
B) single-strand
C) double-strand
D) mismatch

Question 73

Describe the experiment that demonstrated that complete unwinding of the chromosome does not occur.

Question 74

DNA crossover is important during meiosis because it allows

A) the organization of genes on the chromosome to change.
B) DNA repair to occur.
C) exchange of genetic information.
D) base excision to occur.

Question 75

Using the figure below, identify conservative replication, dispersive replication, and semiconservative replication.

Question 76

AZT is such a good HIV drug because it

A) prevents new DNA from being replicated.
B) prevents HIV from binding to the cell.
C) allows DNA to repair itself after viral DNA is added.
D) allows DNA to be replicated at a slower rate.

Question 77

Describe how Okazaki fragments allow for simultaneous synthesis of double-stranded DNA.

Question 78

In what stage of the cell cycle does homologous recombination largely occur?

A) G1
B) S
C) G2
D) meiosis

Question 79

The importance of V(D)J recombination is that it gives rise to new

A) viruses being formed.
B) DNA combinations.
C) antibodies.
D) RNA combinations.

Question 80

If one parent has Lynch syndrome but the other does not, what is the likelihood that the child will also have Lynch syndrome?

A) 10%
B) 25%
C) 50%
D) 100%