G2

Question 1

What is the luria and delbruck fluctuation testq

Answer 1

showed that survival of resitant colonies of of E.coli in presence of T1 phage was not because phage was inducing mutations. mutations occured at different times in different plates
phage was environmental selecting agent

Question 2

what is replica plating?

Answer 2

lederberg - exact replica due to stamp on arg+ and arg- identifies arg mutants.

Question 3

What doe mutation hotspots on lacl show?

Answer 3

1. that there is a 5’methylcystosine at each hotspot which can be deaminated to thymine
2. that CTGG is a major indel hot spot, repeated tandemly - addition or loss leads to mutation

Question 4

what is depurination and rate in mammals

Answer 4

loss of pruine base

mammalian cells can lose 1-^4 per 20 hour gen.

Question 5

what is replication slippage

Answer 5

section newly synthesized loops back on itself in ssloop DNAP copies region second time due to loop and in the enxt generation therefore get one with normal one with more repeats.
usually happens at repeats `

Question 6

What are most liable to cross over unequallyy

Answer 6

strs

cross at ares of homology

Question 7

how are photodimers created by UV fixed?

Answer 7

Repaired by CPD photolyase which binds to and split dimers = photoreactivation
(cyclobutane photodimer = CPD)

Question 8

how is O-6 guinanine alkylation repaired?

Answer 8

alkytransferases remove groups

eg. methyltransferase AlkB family of deoxygenases.

Question 9

how do DNA glycosylases work?

Answer 9

hydroylse sugar bonds releasing the altered base leaveing an abasis site

Question 10

how does AP endonuclease work

Answer 10

cleaves damaged strand at 5drp of abasic site

(deoyribosephosphate)

Question 11

how does AP beta lyase work

Answer 11

cleaves DNA at 3’drp of abasic site

Question 12

how does AP beta delta lyase worjk

Answer 12

cleaves at 5’ adn 3’ phosphates around abasic site

Question 13

how are holes left by removed abasic sites fixed

Answer 13

DNAP replaces excised

XRCC1 ligase alpha seals nick

Question 14

Describe long patch BER

Answer 14

initiated by AP endonuclease - eg. APEX1 which cleaves DNA 5’ to abasic site, leaving 3’ hydroxyl group as substrate for DNAP beta
which fills removed base and several bases downstream displacing the strand on the 3’ side of cut.
displaced strand is removed by flap endonuclease and ligated by DNA ligase.

Question 15

what does transcription coupled nt excision repair do?

Answer 15

repairs transcribed DNA regions

Question 16

what does global genomic repair GGR do

Answer 16

correct lesions in any section of genome activated by stalled replication forks

Question 17

describe tc NER

Answer 17

when transcription by RNAP stalled by lesions then CSA and CSB bind to complex
attracting TF11H (10 subunits) which contain helicases XPB and XPD
miscoding region cut out and replaced

Question 18

describe GCR

Answer 18

damage sensor XPC scans for distorted DNA, recognises it and binds to opposite strand
XPC attracts TF11H via XPB ATPase activity.

Question 19

1. what does TF11H do?

Answer 19

opens DNA allowing recuritment of XPA and CDK activating kinases (CAK)

Question 20

2. what does XPA do?

Answer 20

allow release of TF11H and CAK and recruitment of RPA (XPD heicase activity is relased open the DNA further. XPC-CEN2 is released from the complex)

Question 21

3. what does RPA do?

Answer 21

coats the undamaged DNA strands

Question 22

4. what does the release of CAK faciliate?

Answer 22

recruitment of XPF-excision repair complementeing (ERCC1) complex and XPG

Question 23

5. what does XPF excision repair do?

Answer 23

carry out incision 5’ and 3’ in the damged DNA and DNAP fills gap. and XRCC1 ligates

Question 24

Describe the process of DNA mismatch repair

Answer 24

1. reconigtion of damage in enwly replicated DNA by MutS
2. Binding of MutS to distrotions in DNA cuased by mismatches
   - it recognises parent strand and nicks daughter strand
3. attracts MutL, MutH and UVrD
4. MutH cuts the section with the incorrect bases and UVrD DNA helicase activity unwinds DNA.
5. Error containing strand is degraded by ssDNA specific exonucleases (e.g Exo1, ExoV11) and resynthesized by DNAP

Question 25

what non homolgous end joining NHEJ

Answer 25

major pathway for repairing ds breaks DSBR

Question 26

Describe the process of NHEJ

Answer 26

1. initiated by binding of Ku70 and Ku80 to DSBR
2. this recruits DNAPKcs and aligns DNA ends
3. DNAPK recruits endonuclease Artemis which trims the 5’ and 3’ overhangs
4. PNKP is recruited via XRCC4 - LIG4 releases exisiting 5’p and 3’p residues
5. XLF interacts with XRCC4 - LIG4 and DNAP

Question 27

Describe homologous recombination

Answer 27

recognition of double stranded break by MRN complex
MRN associated CtBP which produces 3 ssDNA overhangs and 3ss DNA is stabilised by RPA
RAD52 promotes replacement of RPA with RAD51 to allow fromation of RD51-DNA nuceloprotein filaments
BRAC2 assists the assembly of RAD51 onto RPA ssDNA, RAD51 coated ssDNA enables strand invasion.

Question 28

what is the first step in all BER reactions

Answer 28

removal of abasic site by dna glysoylase

Question 29

what does TFIIH contain

Answer 29

10 subunits including XPB and XPD which are helicases

Question 30

what organisms use BER

Answer 30

pro and euk

Question 31

what are two diseases caused by defects in excision repair systems and how do they differ

Answer 31

xeroderma pigemetosum - has XPG defects

Cockayne syndrome = CSA and CSB defects

Question 32

what does cockayne syndrome cause

Answer 32

dwarfism, deafness and retardation plus premature aging