DNA Damage and repair Flashcards
What are the types of DNA damage?
Replication errors
base tautomers
covalent modification
non covalent interactions
What is a base tautomer?
alternative isomeric forms present for a small proportion of time. (keto to enol and amino to imino)
What are the changes in base paring in tautomers?
ENOL form of T pairs with G instead of A
IMINO form of A pairs with C instead of T.
What are purines?
bases A and G
what are pyrimidines?
bases C and T
what is a transition in DNA damage?
where the order of purines and pyrimidines are conversed. GC > AT and AT > GC
What is a transversion in DNA damage?
order of purines and pyrimidines is reversed. GC > TA or CG
AT > CG or TA
what causes insertions to occur?
Strand slippage.
what is cytosine deamiation?
hydrolytic deamiation of cytosine to uracil. GC > GU > AU
What is depurination?
the loss of a base via hydrolysis. the glycosidic bond between base and sugar breaks leaving an abasic site (AP site - apurinic/apyrimidinic site)
what is alkylation and what can this do to base pairing?
It is the addition of CH3 groups to DNA bases that can cause the bases to bind to different bases.
What can induce the formation of thymine dimers adjacent to eachother?
UV
What does nitrous acid (HNO2) do to bases?
can cause oxidative deamiation of adenine to hypoxanthine which pairs with C. oxidative damage to guanine produces 8-Oxoguanine that pairs with A instead of C.
What is a frameshift mutation?
a mutation caused by the addition or deletion of a base pair or base pairs in the DNA of a gene resulting in the translation of the genetic code in an unnatural reading frame from the position of the mutation to the end of the gene.
what can cause frameshift mutations
intercalating agents like flat aromatic compounds such as acridine.
How can DNA damage be tested for?
AMES TEST. a short term bacterial test to identify mutagens.
What does Aflotoxin B do and where is it made?
is produced by a mold that grows on peanuts and is activated by liver cytochrome P450 to form a reactive species that modifies guanine leading to mutations. Causes GA to TA transversions.
What are types of DNA repair?
Direct repair which acts directly on the damaged base.
base excision repair that removes the base.
nucleotide excision repair removing the damaged nucleotide
mismatch repair by excision of a long strand containing the mistake
what about DNA makes it possible to repair or replace damaged DNA?
DNA has a double stranded helix structure where information is stored on both strands.
Give an example of direct reversal (demthylation)
the demethylation of methylguanine via mthylguanine-DNA methyl transferase. (MGMT)
it transfers a methyl group from the alkkylated G onto a Cysteine resitude in enzymes active site.
(not really an enzyme as its irreversible)
alkylated form of MGMT is a transcription activator upregulating synthesis of other repair proteins,
How are thymine dimers repaired?
UvrABC excinuclease cut out a section 8 bases on the 5’ side and 4 bases on the 3’ side of the lesion. the gap is then filled with POL I and sealed with ligase.
What is the eynzyme used in nucleotide excision repair? how does it work.
A multienzyme complex which is a hetrotrimer composed of two UvrA and one UvrB which first detect DNA damage. UvrA dimer is then replaced by UvrC where the UvrBC complex does the repair.
8 bases on 5’ side and 4 on 3’ side cut out and filled with POL I and ligase.
What is different in eukaryotes for nucleotide excision repair?
More complex process with 25+ proteins.
XPC (UvrA) recognises legion.
XPA and XPD (UvrB) open and binds the DNA.
RPA (single stranded binding protein) stabalises the open complex.
ERCC1-XPF and XPG (UvrC) create incisions and remove the oligonucleotide.
How is Uracil removed?
AP (apyrimidinic) endonuclease cuts between the posphate backbone.
Uracil–N-glycosylase cuts Uracil bas
gap is filled in by DNA POL I (nick translation) and sealed by ligase.
Uracil-N-glycosylase does not discriminate between U opposite G or U opposite A.
