genome instability and mutation part 1

Question 1

what is genome instability?

Answer 1

an increased acquisition of genome alterations

Question 2

what is DNA damage?

Answer 2

anything structurally abnormal in DNA

Question 3

exogenous damage + 3 examples

Answer 3

from environment, UV, Xrays, chemicals

Question 4

endogenous damage + 3 examples

Answer 4

from cellular processes, metabolism, DNA rep, fork stalling

Question 5

what does metabolism produce which is harmful to cells

Answer 5

reactive oxygen species (ROS)

Question 6

what are ROS

Answer 6

highly reactive molecular species with unpaired e-

Question 7

how can ROS be induced?

Answer 7

chemicals, radiation, inflammation

Question 8

how is DNA protected from damage?

Answer 8

its in nucleus and packaged around histones

Question 9

pumps as a detoxification mechanism

Answer 9

pumps in cell membrane pump out harmful agents

Question 10

enzymes as a detoxification mechanism

Answer 10

break down harmful agents into safe products

Question 11

proteins as a detoxification mechanism

Answer 11

conjugate chemicals, bind and take out of cell

Question 12

what does loss of base result in?

Answer 12

apurinic/ apyrimidinic site (purine or pyrimidine lost)

Question 13

example of a small adduct

Answer 13

addition of an oxygen or methyl group to DNA

Question 14

what is a bulky adduct

Answer 14

addition of a larger chemical group to the DNA

Question 15

what is a single strand break

Answer 15

1 strand breaks

Question 16

what are cross-links

Answer 16

bases in same or opposite strands pair

Question 17

consequence of unrepaired small adduct

Answer 17

mismatch during DNA rep

Question 18

small adducts: e.g. 8-oxoguanine

Answer 18

when there is oxidative stress on guanine an O is added, changing chemical structure and therefore there is no G-C bond

Question 19

what do bulky adducts do to the helix

Answer 19

distort it

Question 20

consequence of bulky adducts

Answer 20

blocks DNA replication and stall transcription

Question 21

bulky adducts: e.g. benzopyrene

Answer 21

added to guanine causing distortion (change in chemical structure) and so the enzymes in DNA rep cant get past bulky adduct

Question 22

what happens with single strand DNA break

Answer 22

base lost so enzymes cant get past break

Question 23

consequence of single strand break

Answer 23

DNA rep blocked, stalls trascription

Question 24

consequence of double strand DNA break

Answer 24

loss of genetic material

Question 25

consequence of cross links

Answer 25

loss of genetic material

Question 26

intrastrand cross link

Answer 26

bases next to each other bond

Question 27

interstrand cross link

Answer 27

opposite bases bond (not as they are meant to though)

Question 28

what happens to DNA damage in non-dividing cells

Answer 28

accumulates

Question 29

what happens to DNA damage in dividing cells

Answer 29

blocks DNA rep, can be fixed as a mutation (mismatch), mutations passed onto daughter cells

Question 30

what 3 cell types arise from DNA damage which is unrepaired?

Answer 30

senescent cell, apoptotic cell, cancerous cell

Question 31

what is a senescent cell

Answer 31

a cell that goes to sleep and doesn't wake up again

Question 32

what is cell cycle arrest

Answer 32

checkpoints tell cycle to stop or apoptosis

Question 33

what does cell cycle arrest allow for

Answer 33

more time for DNA damage repair, cells can determine if the damage is too great (apoptosis)

Question 34

how are bulky adducts and pyrimidine dimers repaired

Answer 34

nucleotide excision repair

Question 35

how are single strand breaks and abasic sites repaired

Answer 35

Base excision repair

Question 36

how are double stranded breaks and interstand cross links repaired?

Answer 36

Homologous recombination repair/ non-homologous end-joining

Question 37

how is base pair mismatch repaired

Answer 37

mismatch repair pathway

Question 38

how is guanine alkylation repaired

Answer 38

MGMT

Question 39

what is strand slippage

Answer 39

the wrong base is put on the partner strand (insertions/deletions)

Question 40

what is the first line repair

Answer 40

proof reading

Question 41

what is the second line repair

Answer 41

mismatch repair

Question 42

how does mismatch repair work

Answer 42

MutS-alpha recognises mistake on newly synthesised strand, binds to mismatch, recuits MutL-alpha, exonucleases chops away faulty strand, RPA binds to ssDNA to stabilise it, polymerase puts correct DNA back in again and the ligase seals ends

Question 43

how are small insertion or deletion loops corrected

Answer 43

similarly by MutS-beta protiens

Question 44

how is O^6-MeG repaired (direct reversal repair)

Answer 44

methylguanine DNA methyltransferase has a thiol group which binds to methyl group and takes it out of the DNA

Question 45

base excision repair - e.g. 8-oxoguanine

Answer 45

damaged base is recognised and removed by OGG1 (DNA glycosylase), AP site (apurinic or apyrimidinic) is incised by AP endonuclease (APE 1), PARP1 binds to this intermediate (which is a single strand break) and recruits other DNA repair factors, DNA polymerase beta puts correct DNA and then ligase seals for short patch BER

Question 46

what happens in long patch BER

Answer 46

if ends are structurally complex then a different DNA polymerase is recruited, FEN1 excises the additional flap on DNA, ligase seals

Question 47

5 core steps of BER

Answer 47

1. recognition and excision by glycosylase 2. incision of the strand by AP endonuclease 3. end processing 4. repair synthesis, including gap filling 5. ligation

Question 48

important thing with NER

Answer 48

cell knows which strand of DNA is important (strand being transcribed)

Question 49

Transcription coupled NER

Answer 49

recognised by CSA and CSB proteins, chunk of DNA excised by ERCC1 complex, polymerases add new DNA and ligases seal end

Question 50

global genome NER

Answer 50

recognised by XPC, ERCC1 complex excises the DNA, polymerases add correct DNA and ligases seal ends

Question 51

when does non homologous end joining occur

Answer 51

throughout whole cell cycle

Question 52

non homologous end joining

Answer 52

Ku proteins recognise break and bind to ends, Ku recruit DNA PKcs which process the ends (so they can be rejoined) it then pulls the ends together and sticks them with ligase. sometimes there can be additions or deletions but thats okay

Question 53

what is DNA PKcs

Answer 53

DNA protein kinase catalytic subunit

Question 54

when is homologous recombination active

Answer 54

S and G2 phases as a copy of DNA is synthesised

Question 55

homologous recombination

Answer 55

MRN complex recognises the break but is only present in S and G2 phases, 1 stand of DNA is resected by RPA protein, RAD51 binds to the end and invades the sister chromatid and goes along until it finds the matching homologous sequence that you'll have once you synthesise the DNA, it copies the info exactly.