Download DNA damage and repair

DNA damage and repair
•Types of damage
•Direct reversal of damage
•Excision repair in prokaryotes and eukaryotes
base excision
nucleotide excision
•Nonhomologous end-joining in eukaryotes
•Mismatch repair
•Recombination repair, error-prone bypass and
error-free bypass
DNA damage vs. mutation
•DNA damage refers to a chemical alteration
of the DNA (e.g. G-C bp to methyl-G-C is DNA
damage)
•Mutation refers to a change in a base-pair
(e.g. G-C bp to A-T bp is a mutation)
•There are long term (inhertided) implications
when DNA damage is converted to mutation
Most inherited syndromes in humans
are due to mutations
•Whether a syndrome occurs or not depends
on where the mutation occurs and how a
protein altered by the mutation is affected
•Mutation may cause a protein:
-to be non-functional
-to have an altered function
-to act less efficiently
-to function as the wild type
Causes of gene mutations
•Spontaneous
-errors by DNA Polymerases during replication
can lead to base changes
-slipped strand mispairing can occur at
homopolymeric runs (mono, di, or trinucleotide
repeats)
-chemical modification of bases followed by
mispairing
•Exposure to mutagens
-ionizing radiation
-UV radiation
Slipped Strand Mispairing
Normal replication
Backwards slippage
causes insertion
Forwards slippage
causes deletion
Spontaneous deamination of C gives rise to U,
and spontaneous deamination of 5-methylC gives
rise to T.
Spontaneous deamination of A gives rise to
hypoxanthine which can base-pair with C (but with
2 H-bonds instead of 3).
Cytosine
Hypoxanthine
deamination
Electron rich centers in DNA susceptible to
electrophilic attack
Alkyation highly
mutagenic (forms a
“noncoding base”)
Alkyation “harmless”
Alklyation of guanine by EMS leads to base-pairing
with thymine
Pyrimidine dimers
Model for
Photoreactivation
Mechanism of O6-methylguanine methyl
transferase activity
O6-methylguanine methyl transferase is a “suicide enzyme.”
It is irreversibly inactivated after activity.
Base excision repair in E. coli
See also Fig.
10-13
The human BER pathway
DNA pol b
APE1
DNA pol b
APE1
APE1=apurinic/apyrimidinic endonuclease
Nucleotide excision repair in E. coli
Human global genome NER
Xeroderma pigementosum
Model for nonhomologous end-joining
DNA-PKcs
Ku heterodimer
(Ku70 and
Ku80)
Mismatch Repair in Prokaryotes
•Occurs when DNA Polymerase puts in the wrong
nucleotide during replication and the proofreading
activity does not correct it.
•Repair would ideally occur on the correct strand, the
newly synthesized strand.
•E. coli methylates A of GATC sequence.
•There is a time lapse before newly synthesized
strand is methylated.
•Repair occurs on unmethylated (newly synthesized)
strand during this window of time.
Mismatch repair in E. coli
Fig. 10-3
Mismatch Repair in Eukaryotes
•Eukaryotes are also capable of mismatch repair.
•Less well understood than prokaryotes.
•Homologues of mutS and mutL genes exist so enzymes
involved in eukaryotic mismatch repair likely to be similar to
prokaryotic enzymes.
•BUT, no homologue of MutH (the protein that recognizes
the unmethylated newly synthesized strand), so recognition
of newly synthesized strand does not appear to occur via a
methylation signal.
•Failure of mismatch repair in humans can lead to hereditary
nonpolyposis colon cancer (HNPCC)
Recombination repair in E. coli
Error prone SOS bypass in E. coli
Also known as
trans-lesion
synthesis
Reversion of ochre his- mutation in E. coli
umuC- + muc+
umuC+
umuC-
Error-prone and error-free bypass in humans
•Error-prone repair: DNA Pol z (zeta) inserts bases at random
to get by pyrimidine dimers
•Relatively error-free bypass: DNA Pol h (eta) inserts two
dAMPs across from pyrimidine dimers which are often (but not
always) T-T dimers
•The two A’s cannot base pair though because the two T’s are
still joined together
•DNA Pol h cannot synthesize more DNA after adding the two
dAMPs
•Another polymerase continues….
Activities of DNA polymerases alpha and eta
on damaged and undamaged bases