Week 5 L4: ds DNA repair

Question 1

What are the 3 mechanisms for ds repair?

Answer 1

non-homologous end-joining
Single-strand annealing
Homologous recombination

Question 2

What is the best pathway for repair?

Answer 2

homologous recombination

Question 3

What are the flaws with non-homologous recombination and single-stranded annealing?

Answer 3

Can result with deletion in that region.

local change sin DNA.

Question 4

What are the oncogenic markers in homologous recombination?

Answer 4

BRACA-1 BRACA-2

Question 5

What is a feature of BRACA-1?

Answer 5

Has an affinity for various branch DNA species.

Question 6

Why are the changes to DNA not too important?

Answer 6

happens in somatic cells not germline cells.

Question 7

What is the key protein in NHEJ?

Answer 7

Ku protein

Question 8

What are the features of Ku?

Answer 8

heterodimer of 2 subunits
70/80 kD
Mediates the interaction between the 2 broken ends, acts like a splint.

Question 9

What is the enzyme that carries out the ligation in NHEJ?

Answer 9

DNA ligase IV with XRCC4

Question 10

Does Ku dimer make specific contacts to DNA?

Answer 10

NO

Question 11

How does Ku bind to DNA?

Answer 11

non-specific contacts to DNA. acts like a basket to hold DNA. DNA held in splint to align broken ends

Question 12

How can a mismatch occur in DNA bases?

Answer 12

• Errors in DNA repair
• From homologous recombination (2 seq being recombined are not 100% identical) in heteroduplex location there will be non-watson crick pairs.

Question 13

What is confusing about mismatch pairs?

Answer 13

How do we know what base is the original???

Question 14

How do we tell parental vs newly-replicated DNA?

Answer 14

The dam methyltransferase methylate’s Bases.
when the DNA is replicated, the new bases transiently are not subject to Dam methylation. transiently a hemi-methylatd site

Question 15

What enzyme methylates DNA?

Answer 15

dam methyltransferase

Question 16

What can you call the newly synthesised stand?

Answer 16

hemi-methylated site

Question 17

What do we call the mismatch correction mechanism and what strand does it act upon?

Answer 17

methyl-directed mismatch correction.

on unmethylated strand

Question 18

Where are the dam sites located?

Answer 18

usually up to a kbp away from the mismatch.

Question 19

What are the first 3 proteins involved in methyl-directed mismatch correction?

Answer 19

MutS, MutH, MutL

Question 20

What is the function of MutS?

Answer 20

mismatch recognition acts as a MUTS2 dimer

Question 21

What is the function of MutH?

Answer 21

latent endonuclease, binds at dam site

Question 22

What is the function of MutL?

Answer 22

latent ATPase

mediates MutS-MutL interaction

Question 23

What activates the endonuclease activity of MutH?

Answer 23

the communication of S+L to H at the dam site

Question 24

What does H do when activated?

Answer 24

cleaves the unmethylated strand

Question 25

What is the role of the exonuclease?

Answer 25

removes DNA to allow DNA synthesis of strand to allow Pol III an ligase to repair DNA

Question 26

What are the protein's which bind to Mismatch in DNA? | HUMANS

Answer 26

recognition: complex of MSH2 and GTPB (MSH6 in yeast) Followed by of MLH1-PMS2 (PMS1 in yeast)

Question 27

What do mutations in the mismatch recognition site lead to?

Answer 27

HUMAN CANCER HPNCC syndrome germline mutations in hMSG2 and hMLH1

Question 28

What is the key protein (regulator) for upregulation of genes for DNA repair?

Answer 28

LexA

Question 29

What happens to LexA in the presence of RecA?

Answer 29

LexA cuts itself so it is no longer a repressor but a non-repressor and the repair genes are no longer repressed. upregulated

Question 30

What is the coordinated response to DNA damage called?

Answer 30

SOS response of E.coli

Question 31

What is indicative that DNA damage has occurred?

Answer 31

RecA filament

Question 32

What genes does LexA repress? (regulate)

Answer 32

umuC, UvrA, UvrB, ruvA, runB

Question 33

What are the whole cell responses to DNA damage in EUK?

Answer 33

activate repair transcriptional regulation cell cycle control apoptosis or senescene

Question 34

What is the key tumour suppressor protein which coordinates the response to DNA damage?

Answer 34

p53 | coordinated within cell cycle

Question 35

What is the last resort of p53?

Answer 35

APOPTOSIS