Question 1

In the Klenow fragment of many DNA polymerases, the Mg2+ ions that are required for activity are coordinated to which amino acid R-groups?

Accepted Answer

A) histidine and aspartate 
B) two aspartates 
C) aspartate and asparagine 
D) aspartate and glutamate 
E) glutamate and glutamine 
A) histidine and aspartate 
B) two aspartates 
C) aspartate and asparagine 
D) aspartate and glutamate 
E) glutamate and glutamine B

Question 2

Which of the subunits of DNA polymerase III is responsible for the high processivity of the enzyme?

Accepted Answer

A) $\beta$ 
B) $\gamma$ 
C) $\delta$ 
D) $\delta$' 
E) $\varepsilon$ 
A) $\beta$ 
B) $\gamma$ 
C) $\delta$ 
D) $\delta$' 
E) $\varepsilon$ A

Question 3

Type I topoisomerases break _____ strand(s)of DNA; type II topoisomerases break _____strand(s)of DNA. DNA gyrase is a type ___ topoisomerase.

Accepted Answer

A) both; 1; I 
B) both; 1; I. 
C) both; 1; III 
D) 1; both; I 
E) 1; both; II 
A) both; 1; I 
B) both; 1; I. 
C) both; 1; III 
D) 1; both; I 
E) 1; both; II E

Question 4

What is an Okazaki fragment?

Accepted Answer

A) a small section of DNA bound to the leading strand 
B) a small section of DNA bound to the lagging strand 
C) a small section of RNA and DNA bound to the leading strand 
D) a small section of RNA and DNA bound to the lagging strand 
E) none of the above 
A) a small section of DNA bound to the leading strand 
B) a small section of DNA bound to the lagging strand 
C) a small section of RNA and DNA bound to the leading strand 
D) a small section of RNA and DNA bound to the lagging strand 
E) none of the above

Question 5

Which of the following was evidence that DNA polymerase I was not responsible for the bulk of DNA synthesis in vivo?

Accepted Answer

A) the requirement for an RNA primer 
B) the presence of both polymerase and exonuclease activity in the same enzyme 
C) the number of enzyme copies in each cell far exceeded the number of replication forks 
D) the requirement for Mg2+ 
E) none of the above 
A) the requirement for an RNA primer 
B) the presence of both polymerase and exonuclease activity in the same enzyme 
C) the number of enzyme copies in each cell far exceeded the number of replication forks 
D) the requirement for Mg2+ 
E) none of the above

Question 6

Which of the following is required for DNA polymerase I activity?

Accepted Answer

A) 3' hydroxyl group 
B) ATP, GTP, TTP and CTP 
C) Zn2+ 
D) an RNA template 
E) all of the above 
A) 3' hydroxyl group 
B) ATP, GTP, TTP and CTP 
C) Zn2+ 
D) an RNA template 
E) all of the above

Question 7

In eukaryotic replication, which polymerase is analogous to E. coli primase?

Accepted Answer

A) pol $\alpha$ 
B) pol $\beta$ 
C) pol $\gamma$ 
D) pol $\delta$ 
E) pol $\varepsilon$ 
A) pol $\alpha$ 
B) pol $\beta$ 
C) pol $\gamma$ 
D) pol $\delta$ 
E) pol $\varepsilon$

Question 8

A mutation in a gene results in a mutant phenotype. What occurs if the wild-type phenotype is restored by a mutation at another site in the gene?

Accepted Answer

A) reversion 
B) silent mutation 
C) conjugation 
D) silent conjugation 
E) suppression 
A) reversion 
B) silent mutation 
C) conjugation 
D) silent conjugation 
E) suppression

Question 9

What feature of the telomerase enzyme allows it to synthesize DNA without the use of a DNA or RNA primer?

Accepted Answer

A) it synthesizes new DNA in a 3' to 5' direction 
B) it contains an RNA oligonucleotide complementary to the telomeric sequence 
C) since the telomeric sequence is a 15 base repeat, it is synthesized separately from the replication process and merely sealed in place by the ligase action of telomerase 
D) telomeric DNA forms a hairpin that is used to create its own complimentary primer 
E) none of the above 
A) it synthesizes new DNA in a 3' to 5' direction 
B) it contains an RNA oligonucleotide complementary to the telomeric sequence 
C) since the telomeric sequence is a 15 base repeat, it is synthesized separately from the replication process and merely sealed in place by the ligase action of telomerase 
D) telomeric DNA forms a hairpin that is used to create its own complimentary primer 
E) none of the above

Question 10

Which of the following explains the result of type I topoisomerase activity on underwound DNA, considering that no energy (ATP)is used in the reaction?

Accepted Answer

A) the linking number is decreased by 1 
B) the linking number is increased by 1 
C) the linking number remains the same but the twist decreases by 1 
D) the linking number remains the same but the twist increases by 1 
E) none of the above 
A) the linking number is decreased by 1 
B) the linking number is increased by 1 
C) the linking number remains the same but the twist decreases by 1 
D) the linking number remains the same but the twist increases by 1 
E) none of the above

Question 11

What enzyme that is part of the primosome is responsible for unwinding of the DNA ahead of the replication fork?

Accepted Answer

A) topoisomerase 
B) helicase 
C) primase 
D) clamp loading complex 
E) single-stranded binding protein 
A) topoisomerase 
B) helicase 
C) primase 
D) clamp loading complex 
E) single-stranded binding protein

Question 12

If a segment of a eukaryotic chromosome contained three origins of replication (at the sites indicated with arrows), how would the segment appear when replication was about half completed?

Accepted Answer

The answer of If a segment of a eukaryotic chromosome...

Question 13

Show the reaction (with arrow pushing)for addition of the next nucleotide:

Accepted Answer

The answer of Show the reaction (with arrow pushing)for addition...

Question 14

Which of the following exonuclease activities is present in DNA polymerase I?

Accepted Answer

A) 3' exonuclease that degrades double stranded DNA 
B) 3' exonuclease that degrades hairpin DNA 
C) 5' exonuclease that degrades single stranded DNA 
D) 5' exonuclease that removes RNA from a DNA-RNA duplex 
E) none of the above 
A) 3' exonuclease that degrades double stranded DNA 
B) 3' exonuclease that degrades hairpin DNA 
C) 5' exonuclease that degrades single stranded DNA 
D) 5' exonuclease that removes RNA from a DNA-RNA duplex 
E) none of the above

Question 15

What protein complexes with ATP and cardiolipin to initiate E. coli DNA replication by creating negative superhelical tension in the double stranded DNA?

Accepted Answer

A) DnaA 
B) DnaB 
C) DnaC 
D) DnaJ 
E) DnaK 
A) DnaA 
B) DnaB 
C) DnaC 
D) DnaJ 
E) DnaK

Question 16

In a type I topoisomerase, the active site amino acid _________ is covalently bound to the free _______ end of the cut in the DNA.

Accepted Answer

A) serine; 3' 
B) serine; 5' 
C) tyrosine; 3' 
D) tyrosine; 5' 
E) none of the above 
A) serine; 3' 
B) serine; 5' 
C) tyrosine; 3' 
D) tyrosine; 5' 
E) none of the above

Question 17

Which of the following describes the correct sequence of enzyme activity upon the lagging strand?

Accepted Answer

A) primase, DNA ligase, DNA polymerase I, DNA polymerase III 
B) primase, DNA polymerase I, DNA polymerase III, DNA ligase 
C) DNA polymerase III, primase, DNA polymerase I, DNA ligase 
D) primase, DNA ligase, DNA polymerase III, DNA polymerase I 
E) primase, DNA polymerase III, DNA polymerase I, DNA ligase 
A) primase, DNA ligase, DNA polymerase I, DNA polymerase III 
B) primase, DNA polymerase I, DNA polymerase III, DNA ligase 
C) DNA polymerase III, primase, DNA polymerase I, DNA ligase 
D) primase, DNA ligase, DNA polymerase III, DNA polymerase I 
E) primase, DNA polymerase III, DNA polymerase I, DNA ligase

Question 18

Replication of DNA in E. coli occurs in what type of fashion?

Accepted Answer

A) unidirectional 
B) bidirectional 
C) multidirectional 
D) directionality can change depending upon specific conditions in the cell 
E) none of the above 
A) unidirectional 
B) bidirectional 
C) multidirectional 
D) directionality can change depending upon specific conditions in the cell 
E) none of the above

Question 19

For the following sequence, indicate the RNA primer that would be needed to start synthesis of the Okazaki fragment.
5'-A-A-C-T-A-G-A-C-C-A-G-A-3'

Accepted Answer

3'-U-U-G-A

Question 20

Which of the following DNA polymerases is correctly defined?

Accepted Answer

A) polymerase I: DNA repair 
B) polymerase I: RNA primer excision 
C) polymerase II: DNA repair 
D) polymerase III: nucleotide incorporation during replication 
E) all of the above 
A) polymerase I: DNA repair 
B) polymerase I: RNA primer excision 
C) polymerase II: DNA repair 
D) polymerase III: nucleotide incorporation during replication 
E) all of the above

Exam 25: DNA Replication

In the Klenow fragment of many DNA polymerases, the Mg2+ ions that are required for activity are coordinated to which amino acid R-groups?

Which of the subunits of DNA polymerase III is responsible for the high processivity of the enzyme?

Type I topoisomerases break _____ strand(s)of DNA; type II topoisomerases break _____strand(s)of DNA. DNA gyrase is a type ___ topoisomerase.

What is an Okazaki fragment?

Which of the following was evidence that DNA polymerase I was not responsible for the bulk of DNA synthesis in vivo?

Which of the following is required for DNA polymerase I activity?

In eukaryotic replication, which polymerase is analogous to E. coli primase?

A mutation in a gene results in a mutant phenotype. What occurs if the wild-type phenotype is restored by a mutation at another site in the gene?

What feature of the telomerase enzyme allows it to synthesize DNA without the use of a DNA or RNA primer?

Which of the following explains the result of type I topoisomerase activity on underwound DNA, considering that no energy (ATP)is used in the reaction?

What enzyme that is part of the primosome is responsible for unwinding of the DNA ahead of the replication fork?

If a segment of a eukaryotic chromosome contained three origins of replication (at the sites indicated with arrows), how would the segment appear when replication was about half completed?

Show the reaction (with arrow pushing)for addition of the next nucleotide:

Which of the following exonuclease activities is present in DNA polymerase I?

What protein complexes with ATP and cardiolipin to initiate E. coli DNA replication by creating negative superhelical tension in the double stranded DNA?

In a type I topoisomerase, the active site amino acid _________ is covalently bound to the free _______ end of the cut in the DNA.

Which of the following describes the correct sequence of enzyme activity upon the lagging strand?

Replication of DNA in E. coli occurs in what type of fashion?

For the following sequence, indicate the RNA primer that would be needed to start synthesis of the Okazaki fragment. 5'-A-A-C-T-A-G-A-C-C-A-G-A-3'

Which of the following DNA polymerases is correctly defined?

The Scope of Biochemistry

The Matrix of Life: Weak Interactions in an Aqueous Environment

The Energetics of Life

Nucleic Acids

Introduction to Proteins: the Primary Level of Protein Structure

The Three-Dimensional Structure of Proteins

Protein Function and Evolution

Contractile Proteins and Molecular Motors

Carbohydrates: Sugars, Saccharides, Glycans

Lipids, Membranes and Cellular Transport

Enzymes: Biological Catalysts

Chemical Logic of Metabolism

Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

Citric Acid Cycle and Glyoxylate Cycle

Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism

Photosynthesis

Lipid Metabolism I: Fatty Acids, Triacylglycerols, and Lipoproteins

Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates

Lipid Metabolism Ii: Membrane Lipids, Steroids, Isoprenoids, and Eicosanoids

Metabolism of Nitrogenous Compounds I: Principles of Biosynthesis, Utilization, and Turnover

Metabolism of Nitogenous Compounds II: Amino Acids, Porphyrins, and Neurotransmitters

Nucleotide Metabolism

Mechanisms of Signal Transduction

Genes, Genomes and Chromosomes

DNA Restructuring: Repair, Recombination, Rearrangement, Amplification

Information Readout: Transcription and Post-Transcriptional Processing

Information Decoding: Translation and Post-Translational Protein Processing

Regulation of Gene Expression

Filters

In the Klenow fragment of many DNA polymerases, the Mg²⁺ ions that are required for activity are coordinated to which amino acid R-groups?

Type I topoisomerases break ___ strand(s)of DNA; type II topoisomerases break _strand(s)of DNA. DNA gyrase is a type _ topoisomerase.

In a type I topoisomerase, the active site amino acid ___ is covalently bound to the free _ end of the cut in the DNA.