Question 1

The deamination of cytosine generates a uracil base.This is a naturally occurring nucleic acid base, and so does not represent a DNA lesion caused by damage due to chemicals or irradiation.Why is this base recognized as "foreign" and why is it important for cells to have a mechanism to recognize and remove uracil when it is found in the DNA duplex?

Accepted Answer

The answer of The deamination of cytosine generates a uracil...

Question 2

The DNA duplex consists of two long covalent polymers wrapped around each other many times over their entire length.The separation of the DNA strands for replication causes the strands to be "overwound" in front of the replication fork.How does the cell relieve the torsional stress created along the DNA duplex during replication?

Accepted Answer

A) Nothing needs to be done because the two strands will be separated after replication is complete. 
B) Topoisomerases break the covalent bonds of the backbone, allowing the local unwinding of DNA ahead of the replication fork. 
C) Helicase unwinds the DNA and rewinds it after replication is complete. 
D) DNA repair enzymes remove torsional stress as they replace incorrectly paired bases.

Question 3

DNA polymerase catalyzes the joining of a nucleotide to a growing DNA strand.What prevents this enzyme from catalyzing the reverse reaction?

Accepted Answer

A) hydrolysis of pyrophosphate (PPi) to inorganic phosphate (Pi) + Pi 
B) release of PPi from the nucleotide 
C) hybridization of the new strand to the template 
D) loss of ATP as an energy source

Question 4

Figure 6-63 shows a replication bubble.  
Figure 6-63
A.On the figure, indicate where the origin of replication was located (use O).
B.Label the leading-strand template and the lagging-strand template of the right-hand fork [R] as X and Y, respectively.
C.Indicate by arrows the direction in which the newly made DNA strands (indicated by dark lines) were synthesized.
D.Number the Okazaki fragments on each strand as 1, 2, and 3 in the order in which they were synthesized.
E.Indicate where the most recent DNA synthesis has occurred (use S).
F.Indicate the direction of movement of the replication forks with arrows.

Accepted Answer

The answer of Figure 6-63 shows a replication bubble. ...

Question 5

Homologous recombination is an important mechanism in which organisms use a "backup" copy of the DNA as a template to fix double-strand breaks without loss of genetic information.Which of the following is NOT necessary for homologous recombination to occur?

Accepted Answer

A) 3′ DNA strand overhangs 
B) 5′ DNA strand overhangs 
C) a long stretch of sequence similarity 
D) nucleases

Question 6

Sickle-cell anemia is an example of an inherited disease.Individuals with this disorder have misshapen (sickle-shaped) red blood cells caused by a change in the sequence of the β-globin gene.What is the nature of the change?

Accepted Answer

A) chromosome loss 
B) base-pair change 
C) gene duplication 
D) base-pair insertion

Question 7

The chromatin structure in eukaryotic cells is much more complicated than that observed in prokaryotic cells.This is thought to be the reason why DNA replication occurs much faster in prokaryotes.How much faster is it?

Accepted Answer

A) 2× 
B) 5× 
C) 10× 
D) 100×

Question 8

The classic experiments conducted by Meselson and Stahl used isotopes of which element to distinguish newly synthesized DNA from parental DNA?

Accepted Answer

A) carbon 
B) nitrogen 
C) oxygen 
D) hydrogen

Question 9

Match between columns Premises: Meselson and Stahl ruled out the dispersive model for DNA replication.
DNA replication origins are typically rich in G-C base pairs.
DNA replication is a bidirectional process that is initiated at multiple locations along chromosomes in eukaryotic cells.
When DNA is being replicated inside a cell, local heating occurs, allowing the two strands to separate.

Accepted Answer

The Answer of False and True is...

Question 10

The sliding clamp complex must be reloaded for the synthesis of each Okazaki fragment on the lagging strand, while on the leading strand the clamp complex remains assembled over much longer stretches of DNA.Considering this information, explain how the cell is able to replicate the leading and lagging strands at the same rate.

Accepted Answer

The answer of The sliding clamp complex must be reloaded...

Question 11

The events listed below are all necessary for homologous recombination to occur properly:
A.Holliday junction cut and ligated
B.strand invasion
C.DNA synthesis
D.DNA ligation
E.double-strand break
F.nucleases create uneven strands
Which of the following is the correct order of events during homologous recombination?

Accepted Answer

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

Question 12

During DNA replication in a bacterium, a C is accidentally incorporated instead of an A into one newly synthesized DNA strand.Imagine that this error was not corrected and that it has no effect on the ability of the progeny to grow and reproduce.
A.After this original bacterium has divided once, what proportion of its progeny would you expect to contain the mutation?
B.What proportion of its progeny would you expect to contain the mutation after three more rounds of DNA replication and cell division?

Accepted Answer

The answer of During DNA replication in a bacterium, a...

Question 13

Which of the following statements is NOT an accurate statement about thymine dimers?

Accepted Answer

A) Thymine dimers can cause the DNA replication machinery to stall. 
B) Thymine dimers are covalent links between thymidines on opposite DNA strands. 
C) Prolonged exposure to sunlight causes thymine dimers to form. 
D) Repair proteins recognize thymine dimers as a distortion in the DNA backbone.

Question 14

Nonhomologous end joining can result in all but which of the following?

Accepted Answer

A) the recovery of lost nucleotides on a damaged DNA strand 
B) the interruption of gene expression 
C) loss of nucleotides at the site of repair 
D) translocations of DNA fragments to an entirely different chromosome

Question 15

Match between columns Premises: After damaged DNA has been repaired, nicks in the phosphate backbone are maintained as a way to identify the strand that was repaired.
Nonhomologous end joining is a mechanism that ensures that DNA double-strand breaks are repaired with a high degree of fidelity to the original DNA sequence.
Depurination of DNA is a rare event that is caused by ultraviolet irradiation.
Ionizing radiation and oxidative damage can cause DNA double-strand breaks.

Accepted Answer

The Answer of True and False is...

Question 16

You prepare bacterial cell extracts by lysing the cells and removing insoluble debris via centrifugation.These extracts provide the proteins required for DNA replication.Your DNA template is a small, double-stranded circular piece of DNA (a plasmid) with a single origin of replication and a single replication termination site.The termination site is on the opposite side of the plasmid from the origin.  Figure 6-11
Which of the following statements is TRUE with respect to this in vitro replication system?

Accepted Answer

A) There will be only one leading strand and one lagging strand produced using this template. 
B) The leading and lagging strands compose one half of each newly synthesized DNA strand. 
C) The DNA replication machinery can assemble at multiple places on this plasmid. 
D) One daughter DNA molecule will be slightly shorter than the other.

Question 17

If the genome of the bacterium E.coli requires about 20 minutes to replicate itself, how can the genome of the fruit fly Drosophila be replicated in only 3 minutes?

Accepted Answer

A) The Drosophila genome is smaller than the E.coli genome. 
B) Eukaryotic DNA polymerase synthesizes DNA at a much faster rate than prokaryotic DNA polymerase. 
C) The nuclear membrane keeps the Drosophila DNA concentrated in one place in the cell, which increases the rate of polymerization. 
D) Drosophila DNA contains more origins of replication than E.coli DNA.

Question 18

Initiator proteins bind to replication origins and disrupt hydrogen bonds between the two DNA strands being copied.Which of the factors below does not contribute to the relative ease of strand separation by initiator proteins?

Accepted Answer

A) replication origins are rich in A-T base pairs 
B) the reaction can occur at room temperature 
C) they only separate a few base pairs at a time 
D) once opened, other proteins of the DNA replication machinery bind to the origin

Question 19

You prepare bacterial cell extracts by lysing the cells and removing insoluble debris via centrifugation.These extracts provide the proteins required for DNA replication.Your DNA template is a small, double-stranded circular piece of DNA (a plasmid) with a single origin of replication and a single replication termination site.The termination site is on the opposite side of the plasmid from the origin.  
Figure 6-11A
In addition to the extracts and the plasmid DNA, are there any additional materials you should add to this in vitro replication system? Explain your answer.

Accepted Answer

The answer of You prepare bacterial cell extracts by lysing...

Question 20

You are examining the DNA sequences that code for the enzyme phosphofructokinase in skinks and Komodo dragons.You notice that the coding sequence that actually directs the sequence of amino acids in the enzyme is very similar in the two organisms but that the surrounding sequences vary quite a bit.What is the most likely explanation for this?

Accepted Answer

A) Coding sequences are repaired more efficiently. 
B) Coding sequences are replicated more accurately. 
C) Coding sequences are packaged more tightly in the chromosomes to protect them from DNA damage. 
D) Mutations in coding sequences are more likely to be deleterious to the organism than mutations in noncoding sequences.

Exam 6: DNA Replication and Repair