DNA Replication

Question 1

What are the common features to all DNA polymerases?

Answer 1

• Template Dependent
• Primer dependent
• Catalyze addition of dNTP to 3’ endof growing chain
• Highly Accurate (misincorporate at ~10^-6)

Question 2

What is the mechanism of addition of a nucleotide to a DNA chain?

Question 3

What is an exonuclease?

Answer 3

An enzyme that can remove a nucleotide from the end of a DNA chain (can be eithe 3’ or ‘5)

Question 4

What is an endonuclease?

Answer 4

An enzyme that can cleave a nucleotide from within the chain (not just at 5’ or 3’end)

Question 5

In which direction does DNA replication proceed?

Answer 5

It is bidirectional and both replication forks are synthesized simltaneously.

Question 6

What are Okazaki Fragments?

Answer 6

Segments that are synthesized discontinuously on the lagging strand during DNA replication.

Question 7

How are RNA primers removed from the end of newly synthesized DNA?

Answer 7

5’ Exonuclease.

Question 8

How is the gap left by removal of RNA polymerase filled?

Answer 8

DNA polymerase

Question 9

What seals/joins ends of Okazaki fragments?

Answer 9

DNA Ligase - reforms phosphodiester linkage between free 5’ phosphate group and free 3’ OH group

Question 10

What are the names, functions, and exonuclase activity of the DNA ploymerases in E. coli?

Question 11

What is the meant by the processivity of a DNA polymerase enzyme?

Answer 11

How many nucleotides can be added to the strand befor the enzyme falls off.

Question 12

What is the function of a helicase?

Answer 12

To unwind the 2 strands of DNA in replication

Question 13

How does a helicase unwind the double strande DNA molecule?

Answer 13

By hydrolysis of ATP

Question 14

What is the purpose of single stranded binding proteins (SSB)?

Answer 14

To prevet the DNA strands from reannealing before it is replicated

Question 15

What is the purpose of topoisomerases?

Answer 15

Allow unwinding to occur by relieving tension on the DNA strands by nicking and rejoining them as replication proceeds

Question 16

During what phase of the cell cycle does DNA replication occur?

Answer 16

During S phase

Question 17

What is 3’ overhang and what causes it? Why could it be a problem?

Answer 17

3’ overhang is the extra bases at the 3’ end of replicated DNA caused by removal of RNA primers at the 5’ end.

It can cause progressive shortening of replicated DNA, and potential loss of genetic information

Question 18

What is the solution for 3’ overhang?

How does it work?

Answer 18

Telomeres . Synthesized by telomerase.

It is a tandemly repeated sequence on the end of chromosomes (AGGGTT in humans)

Question 19

What is the problem caused by depurination?

Answer 19

Mutations occur (10,000 purines lost per day in mamalian genome)

Question 20

What is a spontaneous mutation that can occur with cytosine?

Answer 20

Deamination to uracil. Approximately 100 times per day in mamalian genome

Question 21

What mutation can be caused by UV light

Answer 21

Pyrimidine Dimer Formation

Question 22

What is mismatch repair?

Answer 22

Repairs mistake in daughter strand - DNA segment replaced

Question 23

What occurs in base excision repair?

Answer 23

Glycosylases recognizes Uracil, Oxidised Bases, Alkylated base, or pyrimidine dimers.

-AP endonuclease cleaves glycoside bond —->DNA polymerase repairs strand —-> DNA ligase rejoins backbone

Question 24

Nucleotide Excision Repair

Answer 24

Recognize DNA damage e.g. Helix distortion

Damage modification

Damage removal

Replacement

Question 25

What is a transposon

Answer 25

Segment of DNA that can move from its original positionin the genome to a new location