DNA damage and repair

Question 1

spontaneous deamination of DNA

Answer 1

at 37 degC, spontaneous deamination of C, A and G bases in DNA

C deaminates to form U
A to hypoxanthine
G to xanthine

Question 2

What does C deaminate to?

Answer 2

U

Question 3

What does A deaminate to?

Answer 3

hypoxanthaine

Question 4

What does G deaminate to?

Answer 4

xanthine

Question 5

What happens during spontaneous depurination?

Answer 5

cleavage of the glycosol bond connecting purines to the backbone

leaves the backbone of DNA intact

Question 6

What are depurinated sites called?

Answer 6

abasic (lacking a base)

or

AP sites

Question 7

What are APsites?

Answer 7

depurinated sites

Question 8

What forms from hydroxyl radical and G?

Answer 8

8-oxoguanine

Question 9

What does 8-oxoguanine do?

Answer 9

mutagenic

it pairs with A not C in DNA replication

Question 10

What can replication stress give rise to?

Answer 10

DNA singlestrand breaks SSB

Question 11

What can SSBs give rise to?

Answer 11

souble strand breaks DSB

Question 12

2 types of mutations

Answer 12

1. point mutations - single AA change
2. frameshift mutation - insertion/deletion of bases

Question 13

types of point mutations

Answer 13

1. silent - has no effect on AA sequence
2. missense - new AA substitution
3. nonsense - stop codon for an AA

Question 14

types of frameshift mutations

Answer 14

deletion - change in AA dequence

insertion - change in AA sequence

-> frameshift - multiple changes in AA

-> non-frameshift - insertion of single AA

Question 15

what does gene amplification produce

Answer 15

multiple copies of the gene

Question 16

what does gene deletion result in

Answer 16

reduced/loss of protein function

hemizygous - loss of 1 copy

homozygous - loss of both copies

Question 17

example of gene amplification

Answer 17

HER2 amplificaiton in breast cancer

Question 18

example of gene deletion

Answer 18

PTEN in prostate cancer

Question 19

What can DNA damage be?

Answer 19

• misincorporation of a single base
• chemical modification of bases
• chemical cross-links between the 2 strands of the double helix
• breaks in 1/both of the phosphodiester backbonoes

Question 20

What thing can correct DNA mismatches during replication?

Answer 20

DNA polymerase

Question 21

what can happen at exonuclease

Answer 21

the polynucleotide chain can leave polymerase site, go to active site of exonuclease

here, nucleotides can be removed, removing any incorrect bases

Question 22

5 DNA repair mechanisms

Answer 22

1. BER: base excision repair
2. NER: nucleotide excision repair
3. MMR: mis-match repair
4. NHEJ: non-homologous end joining
5. HR: homologous recombination

Question 23

How does BER work?

Answer 23

BER used to correct damaged DNA bases or single strand DNA breaks

DNA glycolase excises faulty base

2nd strand used as a template

DNA polymerase fills in DNA gaps

DNA ligase seals the DNA

no defects to BER are inherited

Question 24

important protein in BER

Answer 24

PARP

Question 25

NER

Answer 25

acts on variety of helix-distorting DNA lesions important in the response to adduct forming chemo agents (Pt based) removal of damage such as pyrimidine dimers - UV light

Question 26

important protein in NER

Answer 26

XPA XPC

Question 27

inherited disorders from NER

Answer 27

XP - xeroderma pigmentosum autosomal recessive inherited condition mutations in XP genes - XPA, XPC sensitivity to sunlight - inc skin cancers neurological impairment

Question 28

problems with xeroderma pigmentosum

Answer 28

sensitivity to sunlight neurological impairment

Question 29

similarities in BER and NER

Answer 29

DNA polymerase fills gap DNA ligase seals nick

Question 30

MMR - mismatch repair

Answer 30

catches damage not repaired by BER/NER removes mis-paired nucleotides that result from replication errors consist of at least 2 proteins - 1 to detect the mismatch - other for recruiting endonuclease that cleaves the newly synthesised DNA repair of DNA adducts from Pt chemo agents

Question 31

important protein in MMR

Answer 31

MLH1

Question 32

NHEJ - non homologous end joining

Answer 32

double strand breaks critical - cell must repair asap ATM halts cell cycle - checkpoint rapid repair mechanism repairs 85% of DNA damage from ionising radiation operates at ALL stages of cell cycle BUT IS ERROR PRONE

Question 33

important protein in NHEJ

Answer 33

ATM

Question 34

inherited condition with NHEJ

Answer 34

ATM - ataxia telangiectasia mutated gene autosomal recessive inherited condition neurological condition ataxia = lack of order, poor coordination telangiectasia - dilated/spider blood vessels (eye) mutations in ATM severe sensitivity to ionising radiation 20% incidence in developing cancers immunodeficiency - higher levels of infection mean age of death = 25yrs (1/3 cancer, 1/3 chronic lung disease)

Question 35

HRR - homologous recombination repair

Answer 35

ERROR FREE only works in S and G2 phases of cell cycle needs sister chromstids present ATM BRCA1, BRCA2

Question 36

What inheritence are BRCA mutations?

Answer 36

autosomal dominant inherited condition

Question 37

synthetic lethality

Answer 37

- normal cells can rely on BRCA2 and PARP for DNA repair - BRCA BC are addicted to PARP (BER) - BRCA BC are sensitive to PARP inhibition -> give PARP inhibitors for BC