Module 8: V5 - V8

Question 1

How does DNA synthesis work?

Answer 1

by adding nucleotides at the 3’ end of the new strand resulting in the formation of a phosphodiester bond

Question 2

In which direction does DNA synthesis occur?

Answer 2

5’ to 3’

Question 3

Which end of a primer is the polymerization reaction going to start during DNA synthesis?

Answer 3

at the 3’ end

Question 4

In which direction does DNA synthesis occur on the leading strand?

Answer 4

towards the replication fork (continuous)

Question 5

In which direction does DNA synthesis occur on the lagging strand? What are the implications of this?

Answer 5

away from the replication fork
polymerase starts and stops DNA synthesis resulting in the formation of short fragments which must be joined together (discontinuous)

Question 6

What is the role of helicase?

Answer 6

opens the replication fork

Question 7

How is the lagging strand prevented from binding to the leading strand?

Answer 7

the presence of single stranded binding proteins on the lagging strand

Question 8

What is the name of short fragments produced on the lagging strand during DNA synthesis?

Answer 8

Okazaki fragments

Question 9

What is primase involved in?

Answer 9

the formation of RNA primers on the lagging strand

Question 10

What is DNA polymerase III involved in?

Answer 10

synthesis of the lagging and leading strand

Question 11

What is DNA polymerase I involved in?

Answer 11

removes the primer and fills in the section with DNA

Question 12

What is DNA ligase involved in?

Answer 12

forms a bond between the newest DNA and the DNA of fragment 1 as DNA polymerase 1 is unable to do this

Question 13

How are enzymes on the lagging strand able to move in the direction of the replication fork?

Answer 13

DNA becomes looped around so that they can all travel together

Question 14

What is the role of a beta-sliding clamp?

Answer 14

assists DNA polymerase on the leading strand so that it can travel for a long time

Question 15

What is the role of the clamp loader?

Answer 15

joins to DNA polymerase enzymes

Question 16

What happens when the primase comes in and produces the next primer?

Answer 16

the clamp-loader has a clamp ready to go and bends around to where the primer has been added and adds that beta-clamp onto the DNA with the primer

Question 17

What happens when a beta-clamp is released and the polymerase has come off after completing the Okazaki fragment?

Answer 17

a new DNA polymerase binds to the next beta-clamp to produce the next Okazaki fragment

Question 18

What is the role of a centromere found in a chromosome?

Answer 18

important for moving the chromosomes within the cell during mitosis or meiosis

Question 19

What are the roles of telomeres found in a chromosome?

Answer 19

important for protecting the ends of the chromosomes

Question 20

Why is replication of the end of a DNA molecule a problem for eukaryotes?

Answer 20

all the way along the lagging strand RNA primers are replaced by DNA until the end of the molecule where the primer can be removed but cannot be replaced with DNA because no 3’ end is available

Question 21

How is the issue associated with replication of the end of a DNA molecule fixed?

Answer 21

telomeres prevent chromosomes getting shorter and shorter during DNA synthesis

Question 22

Which enzyme add telomeres onto chromosomes?

Answer 22

telomerase

Question 23

What does telomerase synthesise?

Answer 23

a very unusual DNA structure at the end of eukaryotic chromosomes

Question 24

How accurate are DNA polymerases?

Answer 24

extraordinarily accurate, one mistake every 10^9 - 10^10 nucleotides (in E. coli, one error every 1,000-10,000 replications)

Question 25

How is DNA polymerase so accurate?

Answer 25

utilises two mechanisms which are binding of the nucleotides in the active site and proofreading

Question 26

What happens if DNA polymerase mechanisms fail?

Answer 26

DNA repair may be able to fix errors in the DNA sequence later

Question 27

Which enzyme is involved in proofreading?

Answer 27

3’ -> 5’ exonuclease which removes nucleotides

Question 28

How does 3’ -> 5’ exonuclease remove incorrect base pair matchups?

Answer 28

mismatched C=T blocks polymerase active site (AS) -> polymerase shifts around so C=T pair is moved into the exonuclease AS which removes the mispaired dC allowing the polymerase to shift back with a free AS ready for addition of the correct nucleotide

Question 29

Which DNA polymerases have 3’ -> 5’ exonuclease activity?

Answer 29

both polymerase I and III

Question 30

What is the unique exonuclease activity of DNA polymerase I?

Answer 30

5’ -> 3’ exonuclease which allows polymerase to move forwards removing nucleotides while also adding nucleotides