Deck 12: DNA Replication and Recombination

Question 1

Summarize the similarities and differences in rolling-circle replication, theta replication, and linear eukaryotic replication.

Answer 1

not answered

Question 2

Which of the following typically only have one origin of replication?

A) humans
B) prokaryotes
C) eukaryotes
D) linear model of replication
E) plants

Answer 2

B

Question 3

Which of the following does NOT utilize bidirectional replication?

A) theta model
B) rolling-circle model
C) linear model
D) eukaryotes
E) bacteria

Answer 3

B

Question 4

You are studying a new virus with a DNA genome of 12 Kb. It can synthesize DNA at a rate of 400 nucleotides per second. If the virus uses rolling-circle replication, how long will it take to replicate its genome?

A) 7.5 seconds
B) 15 seconds
C) 30 seconds
D) 1 minute
E) 2 minutes

Question 5

Which statement CORRECTLY describes why the DNA synthesis is discontinuous on one template strand while continuous on the other? (Select all that apply.)

A) It is due to antiparallel nature of the DNA molecule.
B) It is due to the fact that the DNA polymerase is not active enough.
C) It is due to the nature of the DNA polymerase which can only add new nucleotide at the 3ʹ end.
D) It is due to difficulty in unwinding the DNA template for replication.
E) It is due to the semiconservative nature of DNA replication.

Question 6

In the diagram below, which letter indicates the 5'end of the leading strand?

A) A
B) B
C) C
D) D
E) C and D

Question 7

Which of the following enzyme and function pairs is INCORRECTLY matched?

A) DNA gyrase; making and resealing the break to remove the torque as the DNA unwinds
B) DNA ligase; sealing nicks in the sugar-phosphate backbone of newly synthesized DNA
C) DNA helicase; rewinding and reforming the DNA double helix as the replication terminates
D) DNA polymerase III; elongating a new nucleotide strand from the 3'-OH provided by the primers
E) Initiator protein; binding to replication origin and separating DNA to initiate replication

Question 8

Suppose Meselson and Stahl had obtained the following results in their experiment. These results would be consistent with which model of replication?

A) conservative replication only
B) semiconservative and conservative replication
C) semiconservative replication only
D) dispersive replication only
E) semiconservative and dispersive replication

Question 9

Why did the Meselson and Stahl experiment require two rounds of replication?

Question 10

Suppose that some cells are grown in culture in the presence of radioactive nucleotides for many generations so that both strands of every DNA molecule include radioactive nucleotides. The cells are then harvested and placed in new Moderate with nucleotides that are not radioactive so that newly synthesized DNA will not be radioactive. What proportion of DNA molecules will contain radioactivity after two rounds of replication?

A) 0
B) 1/8
C) 1/4
D) 1/3
E) 1/2

Question 11

The diagram shown below is one half of a replication bubble. As the DNA template strands unwind towards the right, new strands of DNA get synthesized. Which of the following represents a lagging strand?

A) A
B) B
C) C
D) D
E) There is no lagging strand in this diagram.

Question 12

Meselson and Stahl showed that DNA is replicated by a:

A) conservative system.
B) semiconservative system.
C) dispersive system.
D) semidispersive system.
E) conservative system in prokaryotes and dispersive system in eukaryotes.

Question 13

During DNA replication, the synthesis of the new strand requires the addition of a new dNTP to the 3ʹ-OH group of the growing nucleotide strand by DNA polymerase. Which of the following provides the energy needed for this step?

A) the template strand
B) the energy of pentose sugar
C) 5ʹ end of the growing DNA
D) cleavage of two phosphate groups from the dNTP
E) The reaction does not require an energy source.

Question 14

Use the following to answer questions
The nuclear genome of a single human cell (i.e., the entire diploid complement) contains about 6.6 billion (6.6 × 10⁹) base pairs of DNA. If synthesis at each replication fork occurs at an average rate of 50 nucleotides per second, all the DNA is replicated in 5 minutes. Assume that replication is initiated simultaneously at all origins.
How many origins of replication exist in a human diploid genome?

A) 220,000
B) 440,000
C) 880,000
D) 2.64 × 10⁷
E) 1.32 × 10⁸

Question 15

Okazaki fragments are found in all of the following EXCEPT in:

A) the leading strand.
B) the lagging strand.
C) eukaryotic DNA.
D) bacterial DNA.
E) linear replication models.

Question 16

What type of synthesis occurs on the leading strand?

A) conservative
B) dispersive
C) continuous
D) discontinuous
E) recombinant

Question 17

You are studying a new virus with a DNA genome of 12 Kb. It can synthesize DNA at a rate of 400 nucleotides per second. If the virus uses theta replication, how long will it take to replicate its genome?

A) 7.5 seconds
B) 15 seconds
C) 30 seconds
D) 1 minute
E) 2 minutes

Question 18

You learn that a Mars lander has retrieved a bacterial sample from the polar ice caps. You obtain a sample of these bacteria and perform the same kind of experiment that Meselson and Stahl did to determine how the Mars bacteria replicate their DNA. Based on the following equilibrium density gradient centrifugation results, what type of replication would you propose for these new bacteria?

A) conservative
B) semiconservative
C) dispersive
D) semiconservative or dispersive
E) conservative or dispersive

Question 19

All DNA polymerases synthesize new DNA by adding nucleotides to the _____ of the growing DNA chain.

A) 3' OH
B) 5' OH
C) 3'phosphate
D) 5' phosphate
E) nitrogenous base

Question 20

Use the following to answer questions
The nuclear genome of a single human cell (i.e., the entire diploid complement) contains about 6.6 billion (6.6 × 10⁹) base pairs of DNA. If synthesis at each replication fork occurs at an average rate of 50 nucleotides per second, all the DNA is replicated in 5 minutes. Assume that replication is initiated simultaneously at all origins.
Assuming that the origins are approximately equally distributed across the chromosomes, what is the average number of origins per human chromosome?

A) 4783
B) 19,130
C) 4.6 × 10⁶
D) 1.21 × 10⁹
E) 2.9 × 10¹⁰

Question 21

What is the function of DNA gyrase?

A) connects Okazaki fragments by sealing nicks in the sugar-phosphate backbone
B) unwinds the double helix by breaking the hydrogen bonding between the two strands at the replication fork
C) reduces the torsional strain that builds up ahead of the replication fork as a result of unwinding
D) binds to oriC and causes a short section of DNA to unwind
E) prevents the formation of secondary structures within single-stranded DNA

Question 22

What is the function of DNA ligase?

A) connects Okazaki fragments by sealing nicks in the sugar-phosphate backbone
B) unwinds the double helix by breaking the hydrogen bonding between the two strands at the replication fork
C) reduces the torsional strain that builds up ahead of the replication fork as a result of unwinding
D) binds to oriC and causes a short section of DNA to unwind
E) prevents the formation of secondary structures within single-stranded DNA

Question 23

If a deletion occurs in a gene that encodes DNA polymerase I and no functional DNA polymerase I is produced, what will be the MOST likely consequence of this mutation?

A) The DNA strands would contain pieces of RNA.
B) The DNA would not exist in a supercoiled state.
C) There would be no DNA replication on the leading or lagging strands.
D) There would be no RNA primers laid down.
E) The DNA will not be able to unwind to initiate replication.

Question 24

Which one of the following statements is NOT true for all E. coli DNA polymerases?

A) They require a primer to initiate synthesis.
B) They use dNTPs to synthesize new DNA.
C) They produce newly synthesized strands that are complementary and antiparallel to the template strands.
D) They possess 5' $\rightarrow$ 3'exonuclease activity.
E) They synthesize in the 5' $\rightarrow$ 3'direction by adding nucleotides to a 3'OH group.

Question 25

DNA polymerases require all of the following for DNA replication EXCEPT:

A) a DNA template.
B) a primer.
C) free 3' OH.
D) 3' to 5' polymerase activity.
E) dNTPs.

Question 26

Which of the following enzymes do NOT aid in the unwinding of DNA for replication?

A) helicase
B) single-stranded binding proteins
C) primase
D) gyrase
E) topoisomerase

Question 27

DNA synthesis during replication is initiated from:

A) a free 5' OH.
B) DNA primers.
C) RNA primers.
D) telomerase.
E) DNA polymerase I.

Question 28

If ribonucleotides were depleted from a cell during S phase, how would DNA synthesis be affected? (Ignore energetic considerations.)

A) There would be no effect because ribonucleotides are used in RNA synthesis, not DNA synthesis.
B) DNA synthesis would continue but at a slower rate.
C) There would only be an effect during M phase, not in S phase.
D) DNA synthesis would not be affected because ribonucleotides are only used during the process of transcription.
E) Replication would cease because ribonucleotides are required to initiate DNA synthesis.

Question 29

Which of the following is a protein that facilitates the termination of replication in E. coli?

A) telomerase
B) DNA gyrase
C) Tus
D) primase
E) topoisomerase

Question 30

DNA polymerase I and DNA polymerase III both have _____ activity but only DNA polymerase I has _____ activity.

A) 5' $\rightarrow$ 3'exonuclease; 3' $\rightarrow$ 5' exonuclease
B) 5' $\rightarrow$ 3' polymerase; 3' $\rightarrow$ 5' polymerase
C) 3' $\rightarrow$ 5' polymerase; 5' $\rightarrow$ 3' polymerase
D) 3' $\rightarrow$ 5' exonuclease; 5' $\rightarrow$ 3 ' exonuclease
E) 5' $\rightarrow$ 3' polymerase; 3' $\rightarrow$ 5' exonuclease

Question 31

The proofreading function of DNA polymerases involves _____ activity.

A) 5' $\rightarrow$ 3' exonuclease
B) 3' $\rightarrow$ 5'exonuclease
C) 5' $\rightarrow$ 3' telomerase
D) 3' $\rightarrow$ 5' telomerase
E) 5' $\rightarrow$ 3' gyrase

Question 32

Are Okazaki fragments formed on the leading strand during DNA replication? Explain your answer.

Question 33

Which different DNA polymerases are found in eukaryotic cells? What are their functions?

Question 34

What type of bonds does DNA ligase create between adjacent nucleotides?

A) hydrogen
B) phosphodiester
C) ionic
D) metallic
E) ribonucleotide

Question 35

DNA primase requires a _____ template and _____ nucleotides to initiate primer synthesis.

A) DNA; DNA
B) RNA; RNA
C) DNA; RNA
D) RNA; DNA
E) leading strand; DNA

Question 36

Why do eukaryotic chromosomes have multiple origins of replication, whereas prokaryotic chromosomes typically have only one origin?

Question 37

What is the function of single-strand-binding proteins?

A) connect Okazaki fragments by sealing nicks in the sugar-phosphate backbone
B) unwind the double helix by breaking the hydrogen bonding between the two strands at the replication fork
C) reduce the torsional strain that builds up ahead of the replication fork as a result of unwinding
D) bind to oriC and cause a short section of DNA to unwind
E) prevent the formation of secondary structures within single-stranded DNA

Question 38

What does "proofreading" refer to with regard to DNA replication?

Question 39

Which of the following eukaryotic DNA polymerases and their role is INCORRECTLY paired?

A) $\delta$ (delta); lagging strand synthesis of nuclear DNA
B) $\varepsilon$ (epsilon); translesion DNA synthesis
C) $\eta$ (eta); translesion DNA synthesis
D) $\gamma$ (gamma); replication and repair of mitochondrial DNA
E) $\theta$ (theta); DNA repair

Question 40

Draw a replication fork and indicate all key components and orientations, including lagging and leading strands, DNA helicase, RNA primer, and DNA gyrase.

Question 41

Explain the effect on DNA replication of mutations that destroy each of the following activities in DNA polymerase. Also, for each kind of mutation, how might you detect the effect in an in vitro replication reaction?
a. 5'to 3' polymerase
b. 5'to 3' exonuclease
c. 3' to 5' exonuclease

Question 42

Which of the following statements explaining the mechanism of action of telomerase is correct? (Select all that apply.)

A) The extension of telomeres via telomerase occurs at the 3ʹ overhang with a G-rich sequence.
B) Telomerase carries a short single-stranded DNA component that is used as a template to extend the telomere.
C) The extension of telomeres via telomerase occurs at the 5ʹ end, where DNA polymerase cannot add a new deoxynucldotide after the removal of the very last RNA primer.
D) The extension at the 3ʹ overhang is followed by the extension of 5ʹ complementary strand via a currently unknown mechanism.
E) Telomerase finishes complementary base pairing of the 5ʹ complementary strand.

Question 43

Discuss the main differences in the initiation of recombination proposed by the Holliday model and the double-stranded-break model.

Question 44

List and describe the key events of DNA replication in their relative order for E. coli.

Question 45

Which of the following statements BEST describes heteroduplex DNA?

A) A single-stranded DNA molecule of one chromosome pairs with a single-stranded DNA molecule of another chromosome.
B) A single-stranded DNA molecule of one chromosome pairs with a single-stranded RNA molecule of another chromosome.
C) Heteroduplex DNA consists of sequences from two different species that are brought together through homologous recombination.
D) Heteroduplex DNA consists of an RNA primer and newly synthesized DNA on the lagging strand.
E) In heteroduplex DNA newly synthesized DNA has yet to be reassembled into nucleosomes.

Question 46

What would be a likely result of expressing telomerase in somatic cells?

A) premature aging
B) cancer
C) lower rates of replication
D) immortality of gametes
E) early termination of replication

Question 47

In the diagram below, the arrow indicates the direction of movement of a replication fork. a. Which strand, top or bottom, is the leading strand? Explain.
b. On which strand, top or bottom, would you expect to find Okazaki fragments? Explain.

Question 48

Explain the need for and mechanism of licensing of DNA replication.

Question 49

You have discovered a special dye that reveals the position of recombination sites on meiotic chromosomes. You use this dye to count the number of recombination sites and then compare this to the number of genetic exchanges that you can detect by looking at the segregation of markers across the genome. You find many more recombination sites as compared to genetic exchanges. Explain this result.

Question 50

For which of the following is the "end-replication problem" relevant?

A) circular DNA
B) linear chromosomes
C) the centromere region of a chromosome
D) rolling-circle model of replication
E) theta model of replication

Question 51

(a) Explain the significance of telomerase in cells of the germ line. (b) Explain the significance of telomerase in cancer cells.

Question 52

The radioactive labeling experiment similar to Meselson and Stahl's experiment was performed to determine what happens to histone proteins in eukaryotic DNA replication. Preexisting and newly synthesized histone proteins were labeled with radioactive isotopes of different atomic mass. Select the statement(s) that are consistent with the diagram shown. (Select all that apply.)

A) The newly synthesized histone and preexisting histones exist separately and associate with a different pool of DNA.
B) The newly synthesized histone and preexisting histones mix and form smeared bands, representing heterogeneous mixture.
C) The newly synthesized histone only associates with newly synthesized DNA while the preexisting histone associates with the old DNA.
D) The newly synthesized histone and preexisting histones tend to mix together and reassociate with DNA after each round of the replication.
E) The preexisting histones tend to associate with newly synthesized DNA while the newly synthesized histone associates exclusively with the old DNA.

Question 53

Which of the following statements is TRUE regarding nucleosome formation during DNA replication?

A) Nucleosomes are only reassembled on the lagging strand.
B) Nucleosome assembly consists entirely of newly synthesized histones.
C) Nucleosome assembly occurs at a faster rate in prokaryotes than in eukaryotes.
D) The addition of newly synthesized histones is a part of nucleosome assembly.
E) Nucleosome assembly does not occur during semiconservative replication.

Question 54

Telomerase uses _____ to synthesize new DNA.

A) exonuclease activity
B) a licensing factor
C) strand invasion
D) a DNA template
E) an RNA template

Question 55

_____ are tandemly repeated DNA sequences located at the ends of eukaryotic chromosomes.

A) Replication bubbles
B) Telomeres
C) Nucleosomes
D) Licensing factors
E) Holliday junctions

Question 56

You discover a drug that specifically inhibits DNA synthesis. You apply the drug to yeast cells after S phase but before prophase of meiosis. You find a drastic reduction in recombination in the meiotic products. How can you explain this?

Question 57

Telomerase activity is MOST likely to be found in which cells in humans?

A) red blood cells
B) muscle cells
C) neurons
D) germ line
E) any type of somatic cell

Question 58

Which of the following is a necessary step in the Holliday model of recombination?

A) DNA primase generates an RNA primer.
B) The RNA template of telomerase binds to the telomere.
C) Topoisomerases aid in supercoiling.
D) DNA polymerase $\alpha$ initiates DNA synthesis.
E) A single-strand break occurs in the DNA molecule.

Question 59

Which of the following statements is TRUE of DNA polymerases of eukaryotic cells?

A) The same DNA polymerase replicates mitochondrial, chloroplast, and nuclear DNA.
B) There are only two different DNA polymerases that function in the process of replication.
C) Some DNA polymerases have the ability to function in DNA repair mechanisms.
D) All eukaryotic DNA polymerases have 3' $\rightarrow$ 5' exonuclease activity.
E) Leading strand synthesis and lagging strand synthesis are performed by the same type of DNA polymerase.

Question 60

The Holliday model describes which of the following processes?

A) semiconservative replication
B) homologous recombination
C) end replication
D) RNA primer synthesis
E) rolling-circle replication

Question 61

What does the term "noncrossover recombinant" mean with respect to homologous recombination?