DNA damage and repair Flashcards
What effects do abasic site have on DNA strand?
i) Loss of coding info (lack base)
ii) no site for polymerase (aldehyde chain is not a substrate for DNA pol)
iii) cause DNA backbone cleavage (once converted to aldehyde form)
Types of DNA damage
i) spontaneous (naturally)
–> ROS, free radicals (interaction between DNA and chemical agents during mechanism)
ii) Environmental (e.g. UV, X-rays)
–> alkylating agents
Major form of nucleotides with abasic sites
hemiacetal
What happens if nucleotide with abasic site is converted to minor form?
from hemiacetal to aldehyde
–> susceptible to beta elimination
–> form 5’ phosphate and 3’ aldehyde chain (not substrate for DNA pol)
How does depurination or depyrimindation occur?
With help of water, base is removed form nucleotide through hydrolysis
–> form abasic sites (highly mutagenic)
Difference between DNA damage and mutation
Damage: alteration in DNA structure
Mutation: the change in DNA can be replicated and inherited
How is ROS formed?
From oxidative phosphorylation –> e- leaking
–> superoxide (O2-)
—> H2O2 through SOD
——> hydroxyl radicals (reduction)
What pairs with 8-oxo-G?
anti –> still pair C (steric clash is found)
syn –> pair with A (new H bond donor at N7)
Why would 8-oxo-G possibily cause DNA mutation?
can change from 8-oxo-G:C to 8-oxo-G:A
–> later become heritable
Types of spontaneous DNA damage
i)Depurination/depyrimidination
ii)Deamination
iii)Oxidative damage (ROS)
What is one common oxidative leision in DNA?
8-oxo-G, carbonyl grp added C8’ of guanine
What happens during deamination of C?
C to U as amino grp removed on C
–> H atom on NH2 replaced with O (H bond acceptor)
–>C:G –> U:G (damage)
Where does UV damage usually occur within DNA?
2 pyrimindine bases close tgt
100,000 per cell per day
UV damage everyday per cell
Two products formed from UV damage on DNA
Cyclobutane pyrimidine dimer (CPD)
–> can be between two thymine as well
6,4 photoproduct
–> bond formed between C4’ and C6’ of two pyrimidine bases
structural feature for cyclobutane pyrimidine
Formation of 4 carbon ring
–> pyrimidine bases brought close tgt
What does O6MeG base pairs with?
C and T (50% for each)
What happens after O6 methylated in guanine?
Before: O6 as acceptor, H in N7 as donor
After: CH3 has no effect, N7 becomes acceptor
Structural feature of 6,4 photoproduct
bond formed between C4’ of one and C6’ of another
500 per cell per day
Frequency of lesions per cell from depyrimidination everyday
What types of CPD can cause mutagenesis?
CT and CC
–> as AA would also be inserted on the opposite side
–> change their sequence
10,000 per cell per day
Depurination
Example of alkylation damage
O6 in guanine methylated
Types of environmental DNA damage
i) UV damage (CPD, 6,4 photoproduct)
ii) Alkylation damage (O6MeG)
Frequency of lesions per cell from alkylation everyday
5000 per cell per day
Why does thymine dimer not cause mutagenesis?
TLS pol for UV prefer to add AA to opposite side
–> no sequence change
What type of enzyme is MGMT?
suicide enzyme
–> can only be used once as methyl group attached will inactivate the enzyme
Residues in MGMT important for function
arginine bind to minor groove
–> base flips out into active site of MGMT
Function of DNA glycosylase in base excision repair (BER)
recognize damaged base
cleave N-glycosidic bond
Frequency of lesions per cell from depyrimidination everyday
500 per cell per day
5000 per cell per day
Frequency of lesions per cell from alkylation everyday
Frequency of lesions per cell from deamination everyday
100 per cell per day
Frequency of lesions per cell from depurination everyday
10,000 per cell per day
Frequency of lesions per cell from UV everyday
100,000 per cell per day
What system can repair O6MeG?
Direct repair by MGMT
characteristics of DNA glycosylase for BER
each can only recongize one type of damaged base