Mod 2 - DNA replication

Question 1

What is DNA replication? (semi-conservative)

Answer 1

when two DNA strands seperate and DNA is copied using the parent strand as a template

Question 2

What did the meselson-stahl experiment set out to do?

Answer 2

to ascertain what type of DNA replication occurs in e.coli bacteria (between semiconservative, conservative, and dispersive)

performed via growing bacteria in a heavy nitrogen (15N) medium, then distinguishing the 14N bacteria from the 15N bacteria via density gradient centrifugation

Question 3

what is the mode of action of type 1 DNA topoisomerase?

Answer 3

makes a single-strand nick to prevent supercoiling

Question 4

what is the mode of action of type 2 DNA topoisomerase?

Answer 4

makes a double strand cut to prevent supercoiling

Question 5

in what direction does DNA replication occur?

Answer 5

5’ -> 3’

Question 6

what is the purpose of DNA helicase?

Answer 6

to break the hydrogen bonds between the base pairs to seperate the DNA strands

Question 7

what is 3’ -> 5’ exonuclease activity?

Answer 7

the mechanism by which polymerase can remove nucleotides that it has just inserted (proofreading)

Question 8

what is 5’ -> 3’ exonuclease activity?

Answer 8

the mechanism by which polymerase can remove DNA that is already attatched to the template

Question 9

what are the 2 bacterial DNA polymerases?

Answer 9

DNA Pol 1 and DNA Pol 3 (III)

Question 10

what are the 2 eukaryotic DNA polymerases?

Answer 10

DNA polymerase alpha (α) and DNA polymerase delta (δ)

Question 11

what are some features of DNA Pol I ? (4)

Answer 11

• 1 subunit
• can do both 3’ ->5’ AND 5’ -> 3’ exonuclease activity
• used for DNA repair and replication
• acts as a DNA-dependent DNA polymerase

Question 12

what are some features of DNA Pol III ? (4)

Answer 12

• at least 10 subunits
• can do 3’ -> 5’
• can’t do 5’ -> 3’
• acts as main replicating enzyme

main replicating enzyme therefore can’t do 5’ -> 3’ exonuclease activity

Question 13

what are some features of DNA Pol alpha ? (3)

Answer 13

• 4 subunits
• can’t do 3’ -> 5’ OR 5’ -> 3’
• used for priming during replication

basically fucking useless. very bad alpha

Question 14

what are some features of DNA Pol delta ? (4)

Answer 14

• 2 or 3 subunits
• can do 3’ -> 5’
• can’t do 5’ -> 3’
• acts as main replicating enzyme

main replicating enzyme therefore can’t do 5’ -> 3’ exonuclease activity

Question 15

what protects the single strands at the replication fork from re-attatching?

Answer 15

single-strand binding proteins (SSB’s)

Question 16

how does the primer work in bacteria?

Answer 16

• made of primase enzyme
• primer is normally 4-15 nucleotides long
• once primer is made, DNA Pol III makes new strand

Question 17

how does the primer work in eukaryotes?

Answer 17

• RNA primer extended by DNA Pol alpha by 20 nucleotides
• DNA Pol delta makes the rest of the new strand

Question 18

where is the primer placed for replication of the lagging strand?

Answer 18

at the replication fork - DNA must locate in a 5’ to 3’ direction

Question 19

how is the lagging strand replicated?

Answer 19

In sections, as when the replication fork moves along the strand, the primer must also move along with it
- forms okazaki fragments when primers are removed

Question 20

how are okazaki fragments joined in bacteria?

Answer 20

• DNA Pol III synthesises DNA until it reaches primer
• DNA Pol I continues synthesis after primer
• DNA ligase joins fragments together

Question 21

how are okazaki fragments joinedi in eukaryotes?

Answer 21

-DNA Pol delta continues to synthesise DNA through the primer -
with the aid of DNA helicase, it pushes the primer to one side, creating a branch point
- FEN1 cuts at the branch point
- DNA ligase joins fragments together

Question 22

what is the end replication problem?

Answer 22

the final okazaki fragment cannot be made as the priming site would be after the end of the parent molecule
- this problem operates on the basis that the primer must attatch to bases.
- would, over time, cause the molecule to become shorter

Question 23

what is the solution to the end replication problem?

Answer 23

telomerase
- extends parental DNA by adding the sequence TTAGGG several times
- adds DNA that can be sacrificed with no adverse affects, as it was not part of the original parent molecule.

Question 24

what kind of cells have telomerase?

Answer 24

stem cells

Question 25

what is senescence?

Answer 25

regular cells dying due to the ends of the chromosome shortening as they do not have telomerase to overcome the end replication problem