genome instability and mutation part 1 Flashcards
what is genome instability?
an increased acquisition of genome alterations
what is DNA damage?
anything structurally abnormal in DNA
exogenous damage + 3 examples
from environment, UV, Xrays, chemicals
endogenous damage + 3 examples
from cellular processes, metabolism, DNA rep, fork stalling
what does metabolism produce which is harmful to cells
reactive oxygen species (ROS)
what are ROS
highly reactive molecular species with unpaired e-
how can ROS be induced?
chemicals, radiation, inflammation
how is DNA protected from damage?
its in nucleus and packaged around histones
pumps as a detoxification mechanism
pumps in cell membrane pump out harmful agents
enzymes as a detoxification mechanism
break down harmful agents into safe products
proteins as a detoxification mechanism
conjugate chemicals, bind and take out of cell
what does loss of base result in?
apurinic/ apyrimidinic site (purine or pyrimidine lost)
example of a small adduct
addition of an oxygen or methyl group to DNA
what is a bulky adduct
addition of a larger chemical group to the DNA
what is a single strand break
1 strand breaks
what are cross-links
bases in same or opposite strands pair
consequence of unrepaired small adduct
mismatch during DNA rep
small adducts: e.g. 8-oxoguanine
when there is oxidative stress on guanine an O is added, changing chemical structure and therefore there is no G-C bond
what do bulky adducts do to the helix
distort it
consequence of bulky adducts
blocks DNA replication and stall transcription
bulky adducts: e.g. benzopyrene
added to guanine causing distortion (change in chemical structure) and so the enzymes in DNA rep cant get past bulky adduct
what happens with single strand DNA break
base lost so enzymes cant get past break
consequence of single strand break
DNA rep blocked, stalls trascription
consequence of double strand DNA break
loss of genetic material
consequence of cross links
loss of genetic material
intrastrand cross link
bases next to each other bond
interstrand cross link
opposite bases bond (not as they are meant to though)
what happens to DNA damage in non-dividing cells
accumulates
what happens to DNA damage in dividing cells
blocks DNA rep, can be fixed as a mutation (mismatch), mutations passed onto daughter cells
what 3 cell types arise from DNA damage which is unrepaired?
senescent cell, apoptotic cell, cancerous cell
what is a senescent cell
a cell that goes to sleep and doesn’t wake up again
what is cell cycle arrest
checkpoints tell cycle to stop or apoptosis
what does cell cycle arrest allow for
more time for DNA damage repair, cells can determine if the damage is too great (apoptosis)
how are bulky adducts and pyrimidine dimers repaired
nucleotide excision repair
how are single strand breaks and abasic sites repaired
Base excision repair
how are double stranded breaks and interstand cross links repaired?
Homologous recombination repair/ non-homologous end-joining
how is base pair mismatch repaired
mismatch repair pathway
how is guanine alkylation repaired
MGMT
what is strand slippage
the wrong base is put on the partner strand (insertions/deletions)
what is the first line repair
proof reading
what is the second line repair
mismatch repair
how does mismatch repair work
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
how are small insertion or deletion loops corrected
similarly by MutS-beta protiens
how is O^6-MeG repaired (direct reversal repair)
methylguanine DNA methyltransferase has a thiol group which binds to methyl group and takes it out of the DNA
base excision repair - e.g. 8-oxoguanine
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
what happens in long patch BER
if ends are structurally complex then a different DNA polymerase is recruited, FEN1 excises the additional flap on DNA, ligase seals
5 core steps of BER
- recognition and excision by glycosylase
- incision of the strand by AP endonuclease
- end processing
- repair synthesis, including gap filling
- ligation
important thing with NER
cell knows which strand of DNA is important (strand being transcribed)
Transcription coupled NER
recognised by CSA and CSB proteins, chunk of DNA excised by ERCC1 complex, polymerases add new DNA and ligases seal end
global genome NER
recognised by XPC, ERCC1 complex excises the DNA, polymerases add correct DNA and ligases seal ends
when does non homologous end joining occur
throughout whole cell cycle
non homologous end joining
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
what is DNA PKcs
DNA protein kinase catalytic subunit
when is homologous recombination active
S and G2 phases as a copy of DNA is synthesised
homologous recombination
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.
