Question 1

In contrast to vertebrates, there is very little DNA methylation in the genomes of invertebrates such as Drosophila melanogaster and Caenorhabditis elegans. Indicate whether you expect each of the following statements to be true (T) or false (F) regarding 5?-CG-3? dinucleotide sequences in the genome. Your answer would be a four-letter string composed of letters T and F only, e.g. TTTT.
(  )	On average, approximately one dinucleotide out of every 16 in the human genome is a CG dinucleotide.
(  )	On average, approximately one dinucleotide out of every 256 in the D. melanogaster genome is a CG dinucleotide.
(  )	The proportion of CG dinucleotides in the human genome is more than that of C. elegans.
(  )	The proportion of CG dinucleotides in the human genome is more than that expected by chance.

Accepted Answer

In a random DNA sequence, one out of e...

Question 2

You have found a strain of Escherichia coli that has an unusually short doubling time of only 15 minutes, despite the fact that its complete DNA replication should take almost 35 minutes. You also find that there is only one replication origin on its chromosome from which two forks originate, just like the normal process described for E. coli. However, you discover that the origin of replication in this strain has a significantly shorter "refractory period," resulting in the reactivation of the origin before the previous round of replication is over. Based on this model, if you examine the chromosomes of this strain (under conditions of fast growth) , how many replication forks would you expect to observe per chromosome on average?

Accepted Answer

A)   Two, just like the wild-type strain
B)   Four
C)   Six
D)   Eight
E)   TenF) B) and E)
G) B) and C)

Question 3

Consider three types of mobile genetic elements that are found in our genome: the DNA-only transposons (D), the retroviral-like retrotransposons (R), and the nonretroviral retrotransposons (N). Which type appears to still be active and move in our genome, accounting for a detectable fraction of human mutations? Write down your answer as D, R, or N.

Accepted Answer

Some nonretroviral retrotransposons (su...

Question 4

The RecA/Rad51 protein carries out strand exchange during homologous recombination. Indicate true (T) and false (F) statements about this process below. Your answer would be a four-letter string composed of letters T and F only, e.g. FFFF.
( )	RecA hydrolyzes ATP upon binding to the invading DNA strand.
( )	RecA forces the invading strand into a conformation that fully mimics the geometry of a long DNA double helix.
( )	Sampling of the homologous duplex by the invading strand is likely to occur in triplet nucleotide blocks.
( )	RecA-bound, invading, single-stranded DNA binds and destabilizes the homologous duplex to allow the sampling of its sequence by base-pairing.

Accepted Answer

RecA binds cooperatively to the invadi...

Question 5

The nuclear DNA polymerases in human cells …

Accepted Answer

A)   polymerize about 1000 nucleotides per second during DNA replication in vivo.
B)   are incapable of 3′-to-5′ exonuclease activity.
C)   are capable of 3′-to-5′ DNA polymerase activity.
D)   have a single active site that is used for both polymerization and editing.
E)   are unable to initiate polymerization de novo (i.e. in the absence of a primer) .F) A) and E)
G) None of the above

Question 6

What are the products of deamination of cytosine and 5-methyl cytosine, respectively?

Accepted Answer

A)   Thymine and uracil
B)   Thymine in both cases
C)   Uracil and thymine
D)   Uracil in both cases
E)   Xanthine and hypoxanthineF) A) and E)
G) A) and D)

Question 7

If this protein complex does not function normally, the ends of the eukaryotic chromosomes would activate the cell's DNA damage response, causing chromosomal fusions and other genomic anomalies. What is this protein complex called?

Accepted Answer

A)   Telomerase
B)   T-loop
C)   ORC
D)   Shelterin
E)   RecAF) A) and B)
G) None of the above

Question 8

DNA glycosylases constitute an enzyme family found in all three domains of life. They can …

Accepted Answer

A)   add sugar moieties to DNA.
B)   remove sugar moieties from DNA.
C)   add a purine or pyrimidine base to DNA.
D)   remove a purine or pyrimidine base from DNA.
E)   remove a nucleotide from DNA.F) A) and D)
G) A) and E)

Question 9

DNA ligases are used in both DNA replication and repair to seal breaks in the DNA. But DNA damage can result in single- or double-strand breaks that are not normal ligase substrates. These need to be processed first before a ligase can act on them. One of the enzymes that is recruited to some of such breaks is called PNK. It has two separate activities on the DNA, both of which can help provide a canonical ligase substrate. Which of the following activities would you expect PNK to have in this context?

Accepted Answer

A)   5′ kinase (phosphorylation of a free 5′-OH group)  and 3′ kinase
B)   5′ phosphatase (dephosphorylation to create a free 5′-OH group)  and 3′ phosphatase
C)   3′ kinase and 3′ phosphatase
D)   5′ phosphatase and 3′ kinase
E)   5′ kinase and 3′ phosphataseF) B) and C)
G) All of the above

Question 10

What do the enzymes topoisomerase I and topoisomerase II have in common?

Accepted Answer

A)   They both have nuclease activity.
B)   They both create double-strand DNA breaks.
C)   They both require ATP hydrolysis for their function.
D)   They both can create winding (tension)  in an initially relaxed DNA molecule.
E)   All of the above.F) C) and D)
G) D) and E)

Question 11

The Dam methylase is responsible for methylating the adenine base in GATC sequences in Escherichia coli. Imagine two

Accepted Answer

A)   Both of the strains
B)   Neither of them
C)   Only the first strain
D)   Only the second strain
E)   coli strains, one without any active Dam methylase, and the other with a hyperactive version of the enzyme that operates faster than the wild-type enzyme. Which of these strains would you expect to show a "mutator" phenotype?F) None of the above
G) A) and B)

Exam 5: DNA Replication, Repair, and Recombination

Correct Answer
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RecA binds cooperatively to the invadi...
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Correct Answer
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In a random DNA sequence, one out of e...
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Correct Answer
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Some nonretroviral retrotransposons (su...
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What do the enzymes topoisomerase I and topoisomerase II have in common?

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The nuclear DNA polymerases in human cells …

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Correct Answer
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DNA glycosylases constitute an enzyme family found in all three domains of life. They can …

Correct Answer
verified

The Dam methylase is responsible for methylating the adenine base in GATC sequences in Escherichia coli. Imagine two

Correct Answer
verified

What are the products of deamination of cytosine and 5-methyl cytosine, respectively?

Correct Answer
verified

If this protein complex does not function normally, the ends of the eukaryotic chromosomes would activate the cell's DNA damage response, causing chromosomal fusions and other genomic anomalies. What is this protein complex called?

Correct Answer
verified

Correct Answer
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Exam 5: DNA Replication, Repair, and Recombination

Correct Answerverified RecA binds cooperatively to the invadi...View AnswerShow Answer

Correct Answerverified In a random DNA sequence, one out of e...View AnswerShow Answer

Correct Answerverified Some nonretroviral retrotransposons (su...View AnswerShow Answer

What do the enzymes topoisomerase I and topoisomerase II have in common?

Correct AnswerverifiedShow Answer

The nuclear DNA polymerases in human cells …

Correct AnswerverifiedShow Answer

Correct AnswerverifiedShow Answer

DNA glycosylases constitute an enzyme family found in all three domains of life. They can …

Correct AnswerverifiedShow Answer

The Dam methylase is responsible for methylating the adenine base in GATC sequences in Escherichia coli. Imagine two

Correct AnswerverifiedShow Answer

What are the products of deamination of cytosine and 5-methyl cytosine, respectively?

Correct AnswerverifiedShow Answer

If this protein complex does not function normally, the ends of the eukaryotic chromosomes would activate the cell's DNA damage response, causing chromosomal fusions and other genomic anomalies. What is this protein complex called?

Correct AnswerverifiedShow Answer

Correct AnswerverifiedShow Answer

Correct Answer
verified

RecA binds cooperatively to the invadi...
View Answer

Correct Answer
verified

In a random DNA sequence, one out of e...
View Answer

Correct Answer
verified
Some nonretroviral retrotransposons (su...
View Answer

Correct Answer
verified

Correct Answer
verified

Correct Answer
verified

Correct Answer
verified

Correct Answer
verified

Correct Answer
verified

Correct Answer
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Correct Answer
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