DNA Structure and Replication

Question 1

DNA Polymerase

Answer 1

-Synthesizes new DNA in a 5’ to 3’ direction.
-Synthesizes new DNA antiparallel to the template DNA.
-Requires a nucleic acid primer (3’ OH) to initiate synthesis.
-Most can proofread.

Question 2

What is the source of energy for DNA synthesis reaction?

Answer 2

New nucleotides constantly being added to the 3’ end. The free nucleotide provides energy for the reaction.The potential energy is raised by dNTPs, the formation of three phosphate groups together before two are cleaved.

Question 3

Origins of replication: Eukaryotic vs Prokaryotic

Answer 3

Eukaryotic have multiple origins, prokaryotic has a single origin.

Question 4

What binds at the origin to unwind dsDNA?

Answer 4

Initiator Proteins

Question 5

Leading Strand

Answer 5

continuous synthesis and synthesis
directly follows the opening of the fork.

Question 6

What do DNA Polymerases require that RNA Polymerases do not?

Answer 6

a 3’ OH. So – primase lays down an RNA primer which provides the 3’ OH for DNA polymerase.

Question 7

Nucleotide

Answer 7

organic molecules consisting of a nucleoside and a phosphate.

Question 8

Purines vs Pyrimidines

Answer 8

The purines in DNA are adenine and guanine, the same as in RNA. The pyrimidines in DNA are cytosine and thymine; in RNA, they are cytosine and uracil. Purines are larger than pyrimidines because they have a two-ring structure while pyrimidines only have a single ring.

Question 9

Nitrogenous base

Answer 9

nitrogen-containing biological compounds that form nucleosides

Question 10

Base Pairing Rules

Answer 10

In DNA/RNA base pairing, adenine (A) pairs with uracil (U), and cytosine (C) pairs with guanine (G).

Question 11

Which bases are pyrimidines and which bases are purines?

Answer 11

he purines in DNA are adenine and guanine, the same as in RNA. The pyrimidines in DNA are cytosine and thymine; in RNA, they are cytosine and uracil.

Question 12

What chemical group is associated with the 3’ and 5’ ends of DNA?

Answer 12

phosphate groups

Question 13

Okazaki fragments

Answer 13

short sequences of DNA nucleotides which are synthesized discontinuously and later linked together by the enzyme DNA ligase to create the lagging strand during DNA replication.

Question 14

Ligase

Answer 14

The DNA ligase is responsible for sealing any breaks in the sugar-phosphate backbone of the strand

Question 15

Telomerase

Answer 15

Extends the un replicated end to preserve the length of telomeres

Question 16

How are DNA Polymerase mistakes minimized?

Answer 16

1. Proofreading - done in DNA synthesis
2. Mismatch repair- done immediately after synthesis.

Question 17

Prokaryotic Polymerases

Answer 17

I – Primer removal and replacement
II – Repair
III – Main synthesis enzyme

Question 18

Prokaryotic Polymerase Duties

Answer 18

5’-3’ Synthesis activity(Pol I, II and III)
3’-5’ Exonuclease activity – proofreading(Pol I, II and III)
5’-3’ Exonuclease activity – removal of primers(Pol I only)

Question 19

How do DNA Polymerases proofread?

Answer 19

a 3’→5’
exonuclease.

Question 20

What phase of the cell cycle does DNA replication take place?

Answer 20

S phase

Question 21

Primer Removal

Answer 21

5’-3’ exonuclease

Question 22

Which DNA pol removes and replaces primers?

Answer 22

DNA Polymerase I

Question 23

Why is DNA synthesis “discontinuous” on the lagging strand?

Answer 23

new RNA primers must be added as opening of the replication fork continues to expose new template. This produces a series of disconnected Okazaki fragments.

Question 24

DNA Pol function

Answer 24

polymerizes deoxyribonucleotide monomers into DNA.

Question 25

Topoisomerase

Answer 25

enzyme that cuts DNA, allows it to unwind, and rejoins it. Works ahead of the twist and helicase.

Question 26

RNA Primer

Answer 26

must be added to DNA Template strand to supply 3’ end for DNA polymerase.

Question 27

How is primer added?

Answer 27

Primase (type of RNA pol)

Question 28

What keeps the DNA polymerase from falling off the DNA during synthesis?

Answer 28

A ring, the sliding camp.

Question 29

Synthesis of leading strand(bacteria)

Answer 29

1. RNA primer added
2. DNA polymerase reads, adding deoxyribonucleotides.

Question 30

Synthesis of lagging strand (bacteria)

Answer 30

-synthesized moving away from the fork.
1. primer added
2. first okazaki fragment synthesized
3. second okazaki fragment synthesized
4. primer replaced
5. nick closed

Question 31

How are okazaki fragments synthesized?

Answer 31

In bacteria, DNA pol 3 dissociates from the 3’ end of an okazaki fragment when the polymerase encounters primer for next segment. Pol 1 attaches to 3’ end and moves in a 5’-3’ direction removing RNA primer and replacing the ribonucloetides it with deoxyribonucleotides.

Question 32

Lagging strand synthesis: differences in organisms.

Answer 32

1. Eukaryote okazaki fragments are shorter than bacteria.
2. Eukaryote lagging strand synthesis has a specific DNA pol.
3. Removal of primers is different.

Question 33

DNA Polymerase III

Answer 33

In bacteria DNA synthesis, extends the leading strand, or extends okazaki fragments.

Question 34

Replisome

Answer 34

macromolecular DNA synthesizing machine

Question 35

Telomere

Answer 35

end of a eukaryotic chromosome, generally a problem at the end of lagging strands. Excess DNA is degraded, which is a problem.

Question 36

Nucleotide excision repair

Answer 36

system that works on DNA damage caused by UV light or other chemicals. Removes thymine dimers.

Question 37

Phosphodiester bond

Answer 37

3’ OH group of one nucleotide and the 5’ phosphate of the next.

Question 38

DNA Pol I

Answer 38

5’-3’ synthesis
3’-5’ proofreading
5’-3’ primer removal

Question 39

DNA Pol II

Answer 39

5’-3’synthesis
3’-5’ proofreading

Question 40

DNA Pol III

Answer 40

3’-5’ proofreading
5’-3’ synthesis