Question 1

In homologous genetic recombination,RecA protein is involved in:

Accepted Answer

A) formation of Holliday intermediates and branch migration. 
B) introduction of negative supercoils into the recombination products. 
C) nicking the two duplex DNA molecules to initiate the reaction. 
D) pairing a DNA strand from one duplex DNA molecule with sequences in another duplex,regardless of complementarity. 
E) resolution of the Holliday intermediate. 
A) formation of Holliday intermediates and branch migration. 
B) introduction of negative supercoils into the recombination products. 
C) nicking the two duplex DNA molecules to initiate the reaction. 
D) pairing a DNA strand from one duplex DNA molecule with sequences in another duplex,regardless of complementarity. 
E) resolution of the Holliday intermediate. A

Question 2

Which one of the following statements about enzymes that interact with DNA is true?

Accepted Answer

A) 
E) coli DNA polymerase I is unusual in that it possesses only a 5' $\rightarrow$3' exonucleolytic activity. 
B) Endonucleases degrade circular but not linear DNA molecules. 
C) Exonucleases degrade DNA at a free end. 
D) Many DNA polymerases have a proofreading 5' $\rightarrow$ 3' exonuclease. 
E) Primases synthesize a short stretch of DNA to prime further synthesis. 
A) 
E) coli DNA polymerase I is unusual in that it possesses only a 5' $\rightarrow$3' exonucleolytic activity. 
B) Endonucleases degrade circular but not linear DNA molecules. 
C) Exonucleases degrade DNA at a free end. 
D) Many DNA polymerases have a proofreading 5' $\rightarrow$ 3' exonuclease. 
E) Primases synthesize a short stretch of DNA to prime further synthesis. C

Question 3

List three types of DNA damage that require repair.

Accepted Answer

The defects in DNA that require repair include 
(a)mismatches that occur during replication; 
(b)abnormal bases; 
(c)pyrimidine dimers produced by UV irradiation.Other answers are possible.

Question 4

Briefly describe the biochemical role of the following enzymes in DNA replication in E.coli:
(a)DNA helicase; 
(b)primase; 
(c)the 3' $\rightarrow$ 5' exonuclease activity of DNA polymerase; 
(d)DNA 1igase; 
(e)topoisomerases;
 (f)the 5' $\rightarrow$ 3' exonuclease activity of DNA polymerase I.

Accepted Answer

(a)Helicase unwinds double-stranded DNA

Question 5

The 5'$\rightarrow$3' exonuclease activity of E.coli DNA polymerase I is involved in:

Accepted Answer

A) formation of a nick at the DNA replication origin. 
B) formation of Okazaki fragments. 
C) proofreading of the replication process. 
D) removal of RNA primers by nick translation. 
E) sealing of nicks by ligase action. 
A) formation of a nick at the DNA replication origin. 
B) formation of Okazaki fragments. 
C) proofreading of the replication process. 
D) removal of RNA primers by nick translation. 
E) sealing of nicks by ligase action.

Question 6

DNA synthesis on the lagging strand in E.coli is a complex process known to involve several proteins.Initiation of a new chain is catalyzed by the enzyme (a)_____________,and elongation is catalyzed by the enzyme (b)______________.Synthesis is discontinuous,yielding short segments called (c)_______________,which are eventually joined by the enzyme (d)______________,which requires the cofactor (e)___________.

Accepted Answer

(a)primase; 
(b)DNA

Question 7

Briefly explain the difference between base-excision repair and nucleotide-excision repair.

Accepted Answer

Base excision involves removing only the

Question 8

Match the damage type or repair step at the left with a related enzyme at right.  Only one answer will be the most direct for each.
-excision of a lesion-containing oligonucleotide

Accepted Answer

A) hypoxanthine-N-glycosylase 
B) AP endonuclease 
C) mutH protein 
D) DNA polymerase I 
E) uracil N-glycosylase
F)mutS-mutL complex
G)ABC excinuclease
H)DNA photolyase
I)O6-methylguanine methyltransferase
J)DNA ligase
K)λ integrase
L)RecA protein
M)restriction endonuclease 
A) hypoxanthine-N-glycosylase 
B) AP endonuclease 
C) mutH protein 
D) DNA polymerase I 
E) uracil N-glycosylase
F)mutS-mutL complex
G)ABC excinuclease
H)DNA photolyase
I)O6-methylguanine methyltransferase
J)DNA ligase
K)λ integrase
L)RecA protein
M)restriction endonuclease

Question 9

In a mammalian cell,DNA repair systems:

Accepted Answer

A) are extraordinarily efficient energetically. 
B) are generally absent,except in egg and sperm cells. 
C) can repair deletions,but not mismatches. 
D) can repair most types of lesions except those caused by UV light. 
E) normally repair more than 99% of the DNA lesions that occur. 
A) are extraordinarily efficient energetically. 
B) are generally absent,except in egg and sperm cells. 
C) can repair deletions,but not mismatches. 
D) can repair most types of lesions except those caused by UV light. 
E) normally repair more than 99% of the DNA lesions that occur.

Question 10

In base-excision repair,the first enzyme to act is:

Accepted Answer

A) AP endonuclease. 
B) Dam methylase. 
C) DNA glycosylase. 
D) DNA ligase. 
E) DNA polymerase. 
A) AP endonuclease. 
B) Dam methylase. 
C) DNA glycosylase. 
D) DNA ligase. 
E) DNA polymerase.

Question 11

Which of the following is not a feature of homologous recombination during meiosis?

Accepted Answer

A) A double strand break 
B) Cleavage of two crossover events 
C) Alignment of homologous chromosomes 
D) Formation of a single Holliday intermediate 
E) Exposed 3' ends invade the intact duplex DNA of the homolog 
A) A double strand break 
B) Cleavage of two crossover events 
C) Alignment of homologous chromosomes 
D) Formation of a single Holliday intermediate 
E) Exposed 3' ends invade the intact duplex DNA of the homolog

Question 12

The role of the Dam methylase is to:

Accepted Answer

A) add a methyl group to uracil,converting it to thymine. 
B) modify the template strand for recognition by repair systems. 
C) remove a methyl group from thymine. 
D) remove a mismatched nucleotide from the template strand. 
E) replace a mismatched nucleotide with the correct one. 
A) add a methyl group to uracil,converting it to thymine. 
B) modify the template strand for recognition by repair systems. 
C) remove a methyl group from thymine. 
D) remove a mismatched nucleotide from the template strand. 
E) replace a mismatched nucleotide with the correct one.

Question 13

A suitable substrate for DNA polymerase is shown below.Label the primer and template,and indicate which end of each strand must be 3' or 5'.   To observe DNA synthesis on this substrate in vitro,what additional reaction components must be added?

Accepted Answer

The top strand (the primer)has its 5' en

Question 14

Which of the following is not required for initiation of DNA replication in E.coli?

Accepted Answer

A) DnaB (helicase) 
B) DnaG (primase) 
C) Dam methylase 
D) DNA ligase 
E) DnaA (a AAA+ ATPase) 
A) DnaB (helicase) 
B) DnaG (primase) 
C) Dam methylase 
D) DNA ligase 
E) DnaA (a AAA+ ATPase)

Question 15

Which of the following statements is false? In vitro,the strand-exchange reaction:

Accepted Answer

A) can include formation of a Holliday intermediate. 
B) is accompanied by ATP hydrolysis. 
C) may involve transient formation of a three- or four-stranded DNA complex. 
D) needs RecA protein. 
E) requires DNA polymerase. 
A) can include formation of a Holliday intermediate. 
B) is accompanied by ATP hydrolysis. 
C) may involve transient formation of a three- or four-stranded DNA complex. 
D) needs RecA protein. 
E) requires DNA polymerase.

Question 16

Prokaryotic DNA polymerase III:

Accepted Answer

A) contains a 5' $\rightarrow$  3' proofreading activity to improve the fidelity of replication. 
B) does not require a primer molecule to initiate replication. 
C) has a $\beta$ subunit that acts as a circular clamp to improve the processivity of DNA synthesis. 
D) synthesizes DNA in the 3' $\rightarrow$  5' direction. 
E) synthesizes only the leading strand;DNA polymerase I synthesizes the lagging strand. 
A) contains a 5' $\rightarrow$  3' proofreading activity to improve the fidelity of replication. 
B) does not require a primer molecule to initiate replication. 
C) has a $\beta$ subunit that acts as a circular clamp to improve the processivity of DNA synthesis. 
D) synthesizes DNA in the 3' $\rightarrow$  5' direction. 
E) synthesizes only the leading strand;DNA polymerase I synthesizes the lagging strand.

Question 17

Briefly describe the role of recombination in the generation of antibody (immunoglobin)diversity.

Accepted Answer

The genes for immunoglobin polypeptide c

Question 18

Which mechanism is used to repair a thymidine dimer in DNA?

Accepted Answer

A) Mismatch repair 
B) Base-excision repair 
C) Nucleotide-excision repair 
D) Direct repair 
E) More than one is used for this type of lesion 
A) Mismatch repair 
B) Base-excision repair 
C) Nucleotide-excision repair 
D) Direct repair 
E) More than one is used for this type of lesion

Question 19

The high fidelity of DNA replication is due primarily to immediate error correction by the 3' -> 5' exonuclease (proofreading)activity of the DNA polymerase.Some incorrectly paired bases escape this proofreading,and further errors can arise from challenges to the chemical integrity of the DNA.List the four classes of repair mechanisms that the cell can use to help correct such errors.

Accepted Answer

The four classes are listed in

Question 20

An Okazaki fragment is a:

Accepted Answer

A) fragment of DNA resulting from endonuclease action. 
B) fragment of RNA that is a subunit of the 30S ribosome. 
C) piece of DNA that is synthesized in the 3' $\rightarrow$5' direction. 
D) segment of DNA that is an intermediate in the synthesis of the lagging strand. 
E) segment of mRNA synthesized by RNA polymerase. 
A) fragment of DNA resulting from endonuclease action. 
B) fragment of RNA that is a subunit of the 30S ribosome. 
C) piece of DNA that is synthesized in the 3' $\rightarrow$5' direction. 
D) segment of DNA that is an intermediate in the synthesis of the lagging strand. 
E) segment of mRNA synthesized by RNA polymerase.

Exam 25: Dna Metabolism

In homologous genetic recombination,RecA protein is involved in:

Which one of the following statements about enzymes that interact with DNA is true?

List three types of DNA damage that require repair.

Briefly describe the biochemical role of the following enzymes in DNA replication in E.coli: (a)DNA helicase; (b)primase; (c)the 3' →\rightarrow→ 5' exonuclease activity of DNA polymerase; (d)DNA 1igase; (e)topoisomerases; (f)the 5' →\rightarrow→ 3' exonuclease activity of DNA polymerase I.

The 5' →\rightarrow→ 3' exonuclease activity of E.coli DNA polymerase I is involved in:

Briefly explain the difference between base-excision repair and nucleotide-excision repair.

Match the damage type or repair step at the left with a related enzyme at right. Only one answer will be the most direct for each. -excision of a lesion-containing oligonucleotide

In a mammalian cell,DNA repair systems:

In base-excision repair,the first enzyme to act is:

Which of the following is not a feature of homologous recombination during meiosis?

The role of the Dam methylase is to:

A suitable substrate for DNA polymerase is shown below.Label the primer and template,and indicate which end of each strand must be 3' or 5'. To observe DNA synthesis on this substrate in vitro,what additional reaction components must be added?

Which of the following is not required for initiation of DNA replication in E.coli?

Which of the following statements is false? In vitro,the strand-exchange reaction:

Prokaryotic DNA polymerase III:

Briefly describe the role of recombination in the generation of antibody (immunoglobin)diversity.

Which mechanism is used to repair a thymidine dimer in DNA?

An Okazaki fragment is a:

The Foundations of Biochemistry

Water

Amino Acids, peptides, and Proteins

The Three-Dimensional Structure of Proteins

Protein Function

Enzymes

Carbohydrates and Glycobiology

Nucleotides and Nucleic Acids

Recombinant Dna Technology

Lipids

Biological Membranes and Transport

Biosignaling

Principles of Bioenergetics

Glycolysis, gluconeogenesis, and the Pentose Phosphate Pathway

Principles of Metabolic Regulation

The Citric Acid Cycle

Fatty Acid Catabolism

Amino Acid Oxidation and the Production of Urea

Oxidative Phosphorylation and Photophosphorylation

Carbohydrate Biosynthesis in Plants and Bacteria

Lipid Biosynthesis

Biosynthesis of Amino Acids, nucleotides, and Related Molecules

Integration and Hormonal Regulation of Mammalian Metabolism

Genes and Chromosomes

Rna Metabolism

Protein Metabolism

Regulation of Gene Expression

Filters

Briefly describe the biochemical role of the following enzymes in DNA replication in E.coli: (a)DNA helicase; (b)primase; (c)the 3' $\rightarrow$ 5' exonuclease activity of DNA polymerase; (d)DNA 1igase; (e)topoisomerases; (f)the 5' $\rightarrow$ 3' exonuclease activity of DNA polymerase I.

The 5' $\rightarrow$ 3' exonuclease activity of E.coli DNA polymerase I is involved in: