DNA replication and Repair

Question 1

what are the features of DNA that help the process of replication?

Answer 1

• H bonding B/W base pair allows for accurate replication
• 2 antiparallel strands are templates for each other

Question 2

different models of DNA replication

Answer 2

semi- conservative
conservative
dispersive
DNA helical structure is stable and H bonds must be brocken for strands to unwind
torsional stress in the long, winded molecule needs to be overcome

Question 3

What does semi conservative mean?

Answer 3

newly synthesised DNA Molecules contain one of the old strand and one new strand
one strand is used as template for synthesis of new strand

Question 4

Dispersive replication

Answer 4

DNA is produced in parts from new and old strand as mixture

Question 5

conservative replication

Answer 5

whole new DNA mol produced

Question 6

which experiment proved semi conservative model of replication

Answer 6

Meselson and stahl experiment proved watson and cricks hypothesis

Question 7

describe meselson and Stahls experiment

Answer 7

Bacteria were grown in source of N15(heavier isotope than N14)
N15 was incorporated and taken up by bases of DNA
Cells were collected after each division and DNA was extracted.DNA Centrifuged and density was measured
DNA containing N15 was heavier than N14 if newly synthesised DNA was semiconservative it would have intermediate density as one strand is parental and one new
when they centrifuged they found that DNA sat in middle of test tube

Question 8

phases of DNA replication

Answer 8

1. initiation (different in bacteria and eukaryote)
2. elongation
3. termination

Question 9

explain initiation in bacteria

Answer 9

• in bacteria DNA replication starts on the circular genome on DNA at a point called origin. proteins called initiation complex
• proteins recognise DNA sequence at the origin and bind to it starting to unwind and open the helix
  elongation-
• this forms replication bubble that allows access to proteins that synthesise new strands. they move away from origin as they make new DNA replication fork is produced
• replication happens in both directions- bidirectional

Question 10

replication in eukaryotes

Answer 10

eukaryotes have multiple replication origins
replication origins will start to appear as bubbles which come together

Question 11

explain how new nucleotides are incorporated and DNA is elongated

Answer 11

for DNA mol to increase in length and be replicated a new base must be incorporated at end of DNA molecule
* the base is nucleotide triphosphate which is attacked by OH group of ribose forming phosphodiester bond with the release of 2 phosphate groups called pyrophosphate

Question 12

Role of DNA polymerase

Answer 12

• enzyme joins DNA strands together
• it can only add nucleotides at 3’ end of deoxyribose therefore DNA is made from 5end to 3’ direction
• enzyme responsible for elongation of DNA
• There are several types of DNA polymerase
• DNA polymerase must have a template and can only extend on 3’ end
• they require primer- small pieces of DNA

Question 13

Role of DNA Primase

Answer 13

• Primase is an enzyme that synthesises short RNA sequences called primase. these primase act as starting point for DNA synthesis
• primase functions by synthesising short RNA sequences that are complementary to a single stranded piece of DNA, which serves as its template

Question 14

what enzyme produces RNA Primers?
what are these used for

Answer 14

RNA primer is produced by DNA Primase
* DNA polymerase uses this to continue this primer and create a new DNA

Question 17

role of DNA ligase

Answer 17

ligase enzyme joins Okazaki fragments together making one strand

Question 18

enzymes involved in DNA replication

Answer 18

• DNA plymerase
• DNA helicase
• dna ligase
• topioisomerase
• single stranded DNA binding proteins

Question 19

Role of DNA Helicase

Answer 19

Converts double stranded DNA into single stranded so it can be accessed by polymerase and primase
opens DNA helix and unwinds it

Question 20

single stranded DNA binding proteins

Answer 20

binds to single stranded DNA when double helix is opened up
* protect the single stranded DNA generated during DNA replication preventing it being attacked by nuclease or becoming tangled

Question 21

topioisomerase

Answer 21

when DNA is opened up it generates lots of supercoils and torsion stress ahead of it
proteins that deal with supercoiling of DNA are topoisomerase

Question 22

what is the processivity/ rate of DNA polymerase like
what can be used to improve the processivity

Answer 22

DNA polymerase is a low processivity enzyme this is ability of DNA polymerase to carryout continuous DNA synthesis without frequently dissociating
processivity factor or clamp protein

Question 23

what are clamp proteins

Answer 23

multimeric proteins with a ring shape
When DNA polymerase connects with these its processivity is increased

Question 24

what does fidelity of DNA polymerase means

Answer 24

fidelity refers to DNA polymerases ability to accurately replicate a template

Question 25

what is fidelity of DNA polymerase like

Answer 25

it accurately replicates
error rate= 1 in 10to the power of 10

Question 26

what factors increase accuracy of DNA Polymerase

Answer 26

• Base pairing- correct base pairing at the active site of polymerase enzyme
• proof reading-polymerase enzyme has 3>5 exonuclease activity meaning it checks the base pairing as it goes
  incorrect base pairing activates a second catalytic site which would remove the incorrect base pair

Question 27

uses of DNA polymerase outside the cell

Answer 27

• used in sanger sequencing to sequence long streches of DNA
• used in PCR to amplify pieces of DNA, Diagnostic, forensic and research

Question 28

Drugs that inhibit DNA replication

Answer 28

• antibacterial
• antimicrobial (folate antagonist)
• antiviral(HIV)
  *Herpes simplex(acycloviv)

Question 29

What kind of damages can occur to DNA?

Answer 29

• replication errors(incorrect base inserted), deletion, mutations
• oxidative damage by free radicals
• spontaneous alteration in DNA
• alkylatind agents(product of cellular respiration that binds to DNA)

Question 30

DNA can be damaged by external sources name some damages

Answer 30

• uv light
• pollution
• carcinogens
• radiotherapy(x ray)
• chemotherapy

Question 31

what kind of damages can occur?

Answer 31

• bases can become oxidised, alkylated, deaminated
• bases can become dimerised
• DNA backbone can break- single/ double stranded break
• strands can become crosslinked

Question 32

How does cell deal with errors

Answer 32

direct reversal
nucleotide excision repair
base excision repair
mismatch repair
recombinational repair
non homologous end joining

Question 33

Direct revearsal

Answer 33

for example uv light