1-7 DNA Repair

Question 1

What are the different types of DNA damage?

Answer 1

Deamination, Depurination, Alkylation, Pyrimidine Dimer, Mismatch, Inserted Ribonucleotide, Base oxidation, bulky adduct, Single strand break, double strand break,

Question 2

Deamination

Answer 2

cytosine to uracil. after replication will cause an AT pair instead of a CG pair in daughter

Question 3

depurination

Answer 3

removal of purine from dna molecule

Question 4

alkylation.

repaired by?

Answer 4

of guanine, makes it bind to thymine. duaghter strands will become A-T not C-G.

repaired by MGMT (direct reversal)

Question 5

pyrimidine dimer

Answer 5

cross-linking between adjacent thymines by UV. distorts helix and blocks replication.

Question 6

mismatch

Answer 6

incorrectly paired bases

Question 7

inserted ribonucleotide

Answer 7

nucleotide in the sequence is a ribonucleotide instead of deoxyribonucleotide

Question 8

base oxidation

Answer 8

extra hydroxl group bonded to a base

oxidized G pairs with A and causes CG to AT transverse mutation.

Question 9

bulky adduct

Answer 9

large organic molecule is bonded to a nucleotide

Question 10

single strand break

Answer 10

one strand of DNA molecule broken

Question 11

double strand break

Answer 11

both strands broken

Question 12

BER

steps

removes?

strands?

Answer 12

Base excision repair - Important for removing damaged bases that could cause mustations or mispairings or breaks in DNA during replication (repairs deamination, depurination, base oxidation, and single strand breaks.

• Initated by DNA glycoslyases that recognize altered/incorrect bases.
• glycosylase will remove the base, created an abasic (apurinic/apyrimidinic) site.
• AP endonuclease cleaves phosphodiester bond at 5’
• dTTP synthesized.
• Sealed with DNA ligase

endonuclease cleavage at one strand

Question 13

NER

removes? enzymes?

strands?

Answer 13

Nucleotide excision repair - repair pyrimidine dimers and bulky adducts. Involves enzymes XPA through XPG.

Involves endonuclease cleavage a both strands.

Question 14

MGMT

Answer 14

in non placental mammals

-directly repairs alkylation damage by scanning molecule

Question 15

Defective BER is linked to?

Answer 15

cancer, neurological disorders

Question 16

Defective NER leads to?

Answer 16

diseases such as xeroderma pigmentosum - caused by one or more enzymes of excision pathway deficiency.

Question 17

RER

What enzyme used?

Answer 17

used to excise incorrectly placed ribonucleotides in the DNA molecule using RNase H2.

Question 18

Most common type of DNA damage?

Answer 18

transient contamination of DNA with rNTP’s.

Question 19

RER deficiency leads to?

Answer 19

Mutations arising from short deletions.

=Aicardi-Goutieres Syndrome

Question 20

Mismatch Repair

Answer 20

repairs 99% of errors occuring during replication.

• complex of mismatch repair proteins scans newly replicated DNA for mismatches
• removes section of strand containing incorrect base
• resynthesizes missing strand

Question 21

How does the DNA mismatch repair complex know where to look?

Answer 21

newly synthesized DNA contains gaps that have not been sealed yet - guiding the repair apparatus as to where to look for mismatches

Question 22

mutation of any of the 6 genes that code for mismatch repair leads to

Answer 22

predisposition to certain cancers including the most common form of heredity colon cancer (hereditary non-polyposis colon cancer) (HNPCC)

Question 23

Direct reversal

Answer 23

reverses alkylation. involves methyl guanine methyl transferase (MGMT). MGMT covalently transfers the alkyl group to it’s active cysteine cyte.

• inactivates MGMT
• restores guanine to normal

Question 24

double strand break repair (??)

Answer 24

fixes ds breaks via homologous recom and non-homo end joining (NHEJ). Occurs when nick in DNA occurs prior to replication, leading to a long continuous strand ds, and then a blunted strand. ds

Question 25

describe non homologous end joining (?)

Answer 25

in NHEJ, the two broken ends of DNA are joined via DNA ligase - more error prone pathway but necessary when no template available - favored by higher eukaryotes (humans)

Question 26

Describe homologous recombination (?)

Answer 26

HR more accurate - uses a homo sequence (identical) as template to repair double strand breaks. Often used with dsb are created during replication

Question 27

what is the DNA Damage Response? major regulators?

Answer 27

DDR - pathway that involves signals, sensors, transducers, and effectors to accomplish cell cycle transitions, dna rep, dna repair, apoptosis. -major regulators are the PI3K related Kinases (PIKKs) including ATM and ATR.

Question 28

ATM

Answer 28

functions in response to rare DSBs.

Question 29

ATR

Answer 29

activated during every S phase to - regulate rep origin firing - repair damaged forks - prevent premature mitosis onset

Question 30

Xeroderma Pigmentosum

Answer 30

defective NER (specifically because of XPA through XPG)

Question 31

Hereditary Non-Polyposis Colon Cancer (HNPCC)

Answer 31

Due to mutations in any of the mismatch repair(MMR) genes. Develops the mutator phenotype (mutations accumulate in cells more frequently).

Question 32

Aicardi–Goutières Syndrome (AGS) -

Answer 32

Mutations in the RNase H2 subunits, hindering RER. Due to short deletions. Rare neuroinflammatory disorder

Question 33

Ataxia Telangiectasia

Answer 33

Due to homozygously inheriting mutations in the ataxia telangiectasia mutated (ATM) gene. Predisposes the individual to cancers and neurodegenerative diseases.

Question 34

exo vs endo nucleases

Answer 34

endo - cut like scissors within DNA exo - chew from outside. 5'-'3 exo start at 5' 3-5' exo start at 3' end

Question 35

what is a mutation?

Answer 35

permanent, heritable alterations in the base sequences of DNA

Question 36

in BER, the lesion is removed by

Answer 36

dna glycosylase

Question 37

distamycin

Answer 37

DNA groove binder. interacts with A-T in minor groove. Terminal end of molecule attracts the drug

Question 38

Actinomycin

Answer 38

DNA intercalators - blocks chain elongation

Question 39

cisplatin

Answer 39

dna crosslinking agent. anti-cancer for testicular and ovarian. crosslinks cause helix unwinding which prevent additional transcription/replication. eventual cell death

Question 40

in NER, endonuclease makes nicks on either side of the lesion, which is then removed to make a gap which is filled by ____ to make the final phosphodiester bond.

Answer 40

DNA polymerase

Question 41

What happens if the cell cycle checkpoint is reached, and DNA damage is not repaired.

Answer 41

DNA damage response (DDR) pathway is initiated. ATM is recruited to activate p53, which leads the cell to senescence or apoptosis.

Question 42

Xeroderma pigmentosum patients lack one or more enzymes required for:

Answer 42

excision repair

Question 43

The proofreading activity of DNA polymerase involves:

Answer 43

A. 3'-->5' exonuclease function

Question 44

Ultraviolet light produces thymine dimers in DNA strands. Excision repair requires all of the enzymes listed EXCEPT: A. primase B. DNA polymerase C. DNA ligase D. nuclease

Answer 44

A. Primase

Question 45

HNPCC? caused by?

Answer 45

hereditary non-polypsis colon cancer - caused by mutation in any of the 6 mismatch repair genes ussually only one allele inherited, doesnt appear until second allele mutates autosomal dominant?

Question 46

NER vs BER endonuclease activity

Answer 46

NER - both strands | BER - one strand

Question 47

xeroderma pigmentosum

Answer 47

family of diseases caused mutations/deficiencies in one or more of the excision pathway enzymes XPC, RPA, TFIIH, XPG, ERCC1-XPF autosomal recessive sensitive to UV light. damage not reversed

Question 48

ataxia telangiectasia

Answer 48

caused by defect in DNA repair gene ATM autosomal recessive