Question 1

Describe briefly how equilibrium density gradient centrifugation was used to demonstrate that DNA replication in E. coli is semiconservative.

Accepted Answer

Equilibrium density gradient centrifugat

Question 2

The protein MGMT (O6-methylguanine DNA methyltransferase) is involved in DNA repair. Outline the reaction that is carried out by this protein. Why it is INCORRECT to describe this protein as an enzyme?

Accepted Answer

The protein MGMT is involved in the repa

Question 3

Which compound is NOT a protein that binds to the origin of replication of E. coli (oriC)?

Accepted Answer

A)  DnaA 
B)  DnaB 
C)  integration host factor (IHF) 
D)  histone-like protein (HU) 
E)  Tus 
A)  DnaA 
B)  DnaB 
C)  integration host factor (IHF) 
D)  histone-like protein (HU) 
E)  Tus

Question 4

Name the three possible outcomes or consequences (at the DNA level) of a site-specific recombination event. For each of these, explain concisely (in one sentence) how the relative location and orientation of the recombination sites determines the outcome of the recombination event. Do not describe specific examples of site-specific recombination systems.

Accepted Answer

The three possible outcomes of a site-sp

Question 5

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 answer of A suitable substrate for DNA polymerase is...

Question 6

If DNA replication was conservative, what would be observed after two rounds of the Meselson and Stahl experiment?

Accepted Answer

A)  1:1 high-density to low-density bands. 
B)  1:1 high-density to hybrid-density bands. 
C)  1:2 high-density to low-density bands. 
D)  1:2 high-density to hybrid-density bands. 
E)  1:4 high-density to low-density bands. 
A)  1:1 high-density to low-density bands. 
B)  1:1 high-density to hybrid-density bands. 
C)  1:2 high-density to low-density bands. 
D)  1:2 high-density to hybrid-density bands. 
E)  1:4 high-density to low-density bands.

Question 7

Which statement regarding the regulation of initiation in E. coli is CORRECT?

Accepted Answer

A)  DnaA binds its consensus sequence at oriC only when the sequence is fully acetylated. 
B)  After replication, the DNA at oriC is hemi-acetylated and in this state it cannot bind DnaA. 
C)  After replication the DNA at oriC is hemi-methylated, and in this state it binds DnaA with high affinity. 
D)  The binding affinity of DnaA for its binding sites in oriC is dependent only on methylation of DNA. 
E)  DnaA binds its consensus sequence at oriC only when the sequence is fully methylated. 
A)  DnaA binds its consensus sequence at oriC only when the sequence is fully acetylated. 
B)  After replication, the DNA at oriC is hemi-acetylated and in this state it cannot bind DnaA. 
C)  After replication the DNA at oriC is hemi-methylated, and in this state it binds DnaA with high affinity. 
D)  The binding affinity of DnaA for its binding sites in oriC is dependent only on methylation of DNA. 
E)  DnaA binds its consensus sequence at oriC only when the sequence is fully methylated.

Question 8

What is the role of the chi sequence in recombination DNA repair?

Accepted Answer

A)  It directs RecBCD binding to DNA. 
B)  It acts as a target for an endonuclease activity. 
C)  It acts as a binding site for protein/DNA interactions. 
D)  It triggers the activity of a DNA helicase. 
E)  It acts as a signal for branch migration of double-stranded intermediates. 
A)  It directs RecBCD binding to DNA. 
B)  It acts as a target for an endonuclease activity. 
C)  It acts as a binding site for protein/DNA interactions. 
D)  It triggers the activity of a DNA helicase. 
E)  It acts as a signal for branch migration of double-stranded intermediates.

Question 9

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.

Question 10

Which repair mechanism does NOT require an endonuclease?

Accepted Answer

A)  base-excision repair 
B)  nucleotide-excision repair 
C)  mismatch repair 
D)  photolyase 
E)  All of these require an endonuclease. 
A)  base-excision repair 
B)  nucleotide-excision repair 
C)  mismatch repair 
D)  photolyase 
E)  All of these require an endonuclease.

Question 11

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 mechanism 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 mechanism is used for this type of lesion.

Question 12

Which statement is FALSE regarding DnaA?

Accepted Answer

A)  DnaA is a sequence that is part of oriC in E. coli. 
B)  DnaA is an important component in DNA replication initiation. 
C)  DnaA affects the writhe in oriC in E. coli. 
D)  All of the statements are false. 
E)  None of the statements is false. 
A)  DnaA is a sequence that is part of oriC in E. coli. 
B)  DnaA is an important component in DNA replication initiation. 
C)  DnaA affects the writhe in oriC in E. coli. 
D)  All of the statements are false. 
E)  None of the statements is false.

Question 13

The ABC excinuclease is essential in:

Accepted Answer

A)  base-excision repair. 
B)  methyl-directed repair. 
C)  mismatch repair. 
D)  nucleotide-excision repair. 
E)  SOS repair. 
A)  base-excision repair. 
B)  methyl-directed repair. 
C)  mismatch repair. 
D)  nucleotide-excision repair. 
E)  SOS repair.

Question 14

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 15

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

DNA synthesis on the lagging strand in E

Question 16

Which factor does NOT consume energy by breaking phosphoanhydride bonds?

Accepted Answer

A)  the action of DnaB 
B)  the action of DnaG 
C)  DNA gyrase 
D)  TUS/Ter binding 
E)  DNA ligase 
A)  the action of DnaB 
B)  the action of DnaG 
C)  DNA gyrase 
D)  TUS/Ter binding 
E)  DNA ligase

Question 17

Which mechanism is used to repair a chemically modified base in DNA?

Accepted Answer

A)  mismatch repair 
B)  base-excision repair 
C)  nucleotide-excision repair 
D)  direct repair 
E)  More than one mechanism 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 mechanism is used for this type of lesion.

Question 18

Which statement is FALSE regarding the repair of 1-methyladenine in DNA to adenine?

Accepted Answer

A)  This is an example of direct repair. 
B)  This repair process requires iron atoms as cofactors. 
C)  $\alpha$-Ketoglutarate and oxygen are also substrates in this reaction. 
D)  The protein responsible for carrying out this reaction can also repair 3-methylcytosine. 
E)  The process involves carboxylation followed by hydrolysis. 
A)  This is an example of direct repair. 
B)  This repair process requires iron atoms as cofactors. 
C)  $\alpha$-Ketoglutarate and oxygen are also substrates in this reaction. 
D)  The protein responsible for carrying out this reaction can also repair 3-methylcytosine. 
E)  The process involves carboxylation followed by hydrolysis.

Question 19

Describe the process of nucleotide-excision repair of lesions like pyrimidine dimers in E. coli.

Accepted Answer

Nucleotide excision repair (NER) is a DN

Question 20

The proofreading function of DNA polymerase does NOT involve:

Accepted Answer

A)  a 3' $\rightarrow$ 5' exonuclease. 
B)  base pairing. 
C)  detection of mismatched base pairs. 
D)  phosphodiester bond hydrolysis. 
E)  reversal of the polymerization reaction. 
A)  a 3' $\rightarrow$ 5' exonuclease. 
B)  base pairing. 
C)  detection of mismatched base pairs. 
D)  phosphodiester bond hydrolysis. 
E)  reversal of the polymerization reaction.

Exam 25: DNA Metabolism

Describe briefly how equilibrium density gradient centrifugation was used to demonstrate that DNA replication in E. coli is semiconservative.

The protein MGMT (O6-methylguanine DNA methyltransferase) is involved in DNA repair. Outline the reaction that is carried out by this protein. Why it is INCORRECT to describe this protein as an enzyme?

Which compound is NOT a protein that binds to the origin of replication of E. coli (oriC)?

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?

If DNA replication was conservative, what would be observed after two rounds of the Meselson and Stahl experiment?

Which statement regarding the regulation of initiation in E. coli is CORRECT?

What is the role of the chi sequence in recombination DNA repair?

In homologous genetic recombination, RecA protein is involved in:

Which repair mechanism does NOT require an endonuclease?

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

Which statement is FALSE regarding DnaA?

The ABC excinuclease is essential in:

Prokaryotic DNA polymerase III:

Which factor does NOT consume energy by breaking phosphoanhydride bonds?

Which mechanism is used to repair a chemically modified base in DNA?

Which statement is FALSE regarding the repair of 1-methyladenine in DNA to adenine?

Describe the process of nucleotide-excision repair of lesions like pyrimidine dimers in E. coli.

The proofreading function of DNA polymerase does NOT involve:

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

DNA-Based Information Technologies

Lipids

Biological Membranes and Transport

Biosignaling

Bioenergetics and Biochemical Reaction Types

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

Hormonal Regulation and Integration of Mammalian Metabolism

Genes and Chromosomes

RNA Metabolism

Protein Metabolism

Regulation of Gene Expression

Filters

The protein MGMT (O⁶-methylguanine DNA methyltransferase) is involved in DNA repair. Outline the reaction that is carried out by this protein. Why it is INCORRECT to describe this protein as an enzyme?