PCB 3063 Lecture Notes - Lecture 7: Dna Gyrase, Dna Ligase, Dna Replication

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18 Jun 2018

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single strand binding proteins (SSB)

protein that binds to single stranded DNA during replication to prevent it from annealing with a

complementary strand

DNA gyrase

E. coli topoisomerase enzyme that relieves the torsional strain that builds up ahead of the replication

fork

primase

- enzyme that synthesizes a short stretch of RNA on a DNA template

- functions to provide a 3'OH group for the attachment of a DNA nucleotide

primer

- short stretch of RNA on a DNA template

- provides a 3'OH group for the attachment of a DNA nucleotide at the initiation of replication

DNA polymerase III

- bacterial DNA polymerase that adds new nucleotides to the 3' end of a growing DNA strand

- has 3'-5' exonuclease activity (proofreading)

DNA polymerase I

- bacterial DNA polymerase that removes and replaces RNA primers with DNA nucleotides

- has both 3'-5' and 5'-3' exonuclease activity

- two fragments: "Klenow" and "small"

- lots of copies in cell

DNA ligase

enzyme that catalyzes the formation of a phosphodiester bond between adjacent 3'OH and 5'PO4

groups

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Document Summary

Single strand binding proteins (ssb) protein that binds to single stranded dna during replication to prevent it from annealing with a complementary strand. Dna gyrase: coli topoisomerase enzyme that relieves the torsional strain that builds up ahead of the replication fork primase. Enzyme that synthesizes a short stretch of rna on a dna template. Functions to provide a 3"oh group for the attachment of a dna nucleotide primer. Short stretch of rna on a dna template. Provides a 3"oh group for the attachment of a dna nucleotide at the initiation of replication. Bacterial dna polymerase that adds new nucleotides to the 3" end of a growing dna strand. Bacterial dna polymerase that removes and replaces rna primers with dna nucleotides. Has both 3"-5" and 5"-3" exonuclease activity. Dna ligase enzyme that catalyzes the formation of a phosphodiester bond between adjacent 3"oh and 5"po4 groups proofreading. Dna polymerases remove and replace incorrectly paired nucleotides during replication mismatch repair.

Related Questions

1.When a protein binds to DNA at a site defined by a particular nucleotide sequence, with which parts of the DNA does the protein primarily interact?

A. the phosphate and deoxyribose groups in the DNA backbone

B. the phosphate and deoxyribose groups in the DNA backbone, and hydrophobic interactions with the nucleotide bases

C. nucleotide bases within the major grooves of the DNA

D. nucleotide bases within the major and minor grooves of the DNA

E. none of the above

2. Which of the following proteins binds to DNA with sequence specificity?

A. POI Ill holoenzyme

B. DnaA

C. DnaB

D. Dam methylase

E. Both B and D

3. Which of the following is NOT a functional parallel among all known cellular systems of DNA replication?

A. Replication is initiated at specific sites

B. Replication is continuous on the leading strand and discontinuous on the lagging strand

C. DNA replication is semiconservative

D. Replication forks move away from the origin in one direction

E. Nucleases, polymerases and ligases replace RNA primers with DNA and seal the remaining nick

4. A DNA polymerase cannot synthesize a DNA strand de novo (from the beginning) from a mixture of dNTPs. Which of the following explains the role of the primer in the reaction promoted by this enzyme?

A. The primer is an initiation protein with attached nucleotides that binds to the template and to which new nucleotides are added to the 3 ' end.

B. The primer is an initiation protein with attached nucleotides that binds to the template and to which new nucleotides are added to the 5' end.

C. The primer is a preexisting strand of RNA or DNA to which new nucleotides are added to the 3' end.

D. The primer is a preexisting strand of RNA or DNA to which new nucleotides are added to the 5' end.

E. The primer is a preexisting strand of DNA synthesized by DNA pol I, prior to replicative DNA synthesis by DNA pol Ill.

5. Universal features of DNA polymerases include:

A. 5'-3' exonuclease function.

B. Formation of an 'closed' conformation of the polymerase when the template-nucleotide base pair is correct.

C. Use of a single magnesium ion to orient reacting molecules and assist in dissipation of the negative charge that develops during nucleotidyl transfer.

D. Alignment of conserved residues in the active site for attack of the DNA primer by the 3 'OH on the incoming nucleotide.

E. Continuous unbinding and rebinding of the polymerase to the DNA template as each nucleotide is added.

byzantiumscorpion425

Which of the following are required for DNA replication by DNA polymerase?

A. Template strand

B. Short, complementary primer strand

C. 5'-dXTPs

D. 3'-dXTPs

E. Answers (A) and (C)

F. Answers (A) and (D)

G. Answers (A), (B), and (C)

H. Answers (A), (B), and (D)

Which of the following are reasons why DNA replication must be discontinuous?

A. The complementary strands have opposite polarity

B. Only 5'-dXTPs are available in cells

C. DNA polymerase only adds 5-'dXTPs to 3'-OH ends

D. All the above

E. Answers (A) and (C)

F. Answers (B) and (C)

G. Answers (A) and (B)

Which of the following are roles of RNA polymerases in DNA replication?

A. RNA polymerase (primase) initiates replication at the origin

B. RNA polymerase synthesizes the primers for Okazaki fragments

C. Both (A) and (B)

D. Neither (A), nor (B)

Which of the following statements describes the activity of DNA polymerase?

A. DNA polymerase adds 3â-dXTPs to the 5â-OH terminus of the primer
B. DNA polymerase adds 5'-dXTPs to the 3â-OH terminus of the primer
C. DNA polymerase adds 5â-dXTPs to the 3â-phosphate terminus of the primer
D. DNA polymerase adds 3â-dXTPs to the 5â-phosphate terminus of the primer

oliveraccoon574

1. During DNA replication, proteins unwind the DNA duplex, and separate the DNA strands. Those proteins include:

a.) DNA polymerase and ligase

b.) Single-stranded DNA binding and protein primase

c.) Helicase and DNA polymerase

d.) Helicase and single-stranded DNA binding protein

2. What determines the nucleotide sequence of the newly synthesized strand during DNA replication?

a.) The particular DNA polymerase catalyzing the reaction

b.) The relative amounts of the four nucleotide triphosphates (ATP, GTP, CTP, and TTP) in the cell

c.) The nucleotide sequence of the template strand

d.) The primase used in the reaction

e.) Both A and D

3. The leading and the lagging strands differ in that

a.) The leading strand is synthesized in the same direction as the movement of the replication fork, and the lagging strand is synthesized in the opposite direction.

b.) The leading strand is synthesized by adding nucleotides to the 3â hydroxyl (OH) end of the growing strand, and the lagging strand is synthesized by adding nucleotides to the 5â phosphate (PO4) end.

c.) The leading strand is synthesized continuously, whereas the lagging strand is synthesized in short fragments that are ultimately stitched together.

d.) Both A and B

e.) Both A and C

PCB 3063 Lecture Notes - Lecture 7: Dna Gyrase, Dna Ligase, Dna Replication

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