protecting the genome Flashcards
what are free radicals?
byproduct of normal metabolism in human cells that sometime react with DNA and cause chemical changes
what are the most common free radicals? how is t formed?
reactive oxygen species generated most often by the incomplete reduction of oxygen during mitochondrial oxidative phosphorylation
at what wavelength does DNA absorb UV light most efficiently? shorter wavelengths=? are shorter wavelength highly damageable to DNA? which UV light is most damaging to our DNA?
260nm
higher energy
yes
UVB
what are other types of radiation?
X-rays and radioactive elements
what are ionising radiation (IR)? how do they affect DNA?
penetrating radiation that causes DNA damage
damages DNA either directly or by generating ROS from water
what are exogenous chemicals that cause DNA damage?
environmental pollutants
natural toxins
dietary chemicals
anti-cancer drugs
how does mechanical damage arise?
mechanical damage are endogenous physical damage that arise from errors in chromosome replication or segregation causing chromosome to be torn apart by the mitotic spindle apparatus
what are mechanical DNA damage?
failure of controlled replication origin firing may cause re-replication in the centromeric region resulting in one sister chromatid with 2 centromeres. depending on how the spindles attach, the outcome may be chromosome mis-segregation or physical breakage of the chromosomal DNA
what are types of biological damage?
viruses –> insert their genomes into the genome of their host cells
DNA replication errors that result from nucleotide disincorporation or replication slippage
chromosome segregation failure (=2 sister chromatid will move to a single pole)
much of endogenous genome damage are unpreventable and must e repaired by cellular mechanisms. what are these mechanisms?
3 mechanisms:
- neutralising reactive oxygen species (ROS)
- avoiding DNA replication errors
- avoiding chromosome segregation errors
how do cells avoid DNA replication errors?
DNA polymerase of replisome, during elongation sense nucleotide mis-incorporation and use their 3’- to 5’- exonuclease activity to remove the offending nucleotide before resuming synthesis
what is the spindle assembly checkpoint?
mechanism that prevents aberrant chromosome segregation at anaphase and any resulting aneuploid or chromosome breaks
it uses specialised proteins in the kinetochore to sense the spindle tension
what is depurination?
removal of a purine base (A or G) from DNA by hydrolysis, leaving an basic site (=no base)
it blocks replication and transcription and needs repairing by base excision repair
what is deamination?
removal of an amino group
if happens to cytosine, cytosine becomes uracil and uracil in DNA is thought to block DNA rep and must be repaired by base excision repair
if happens to 5-methyl-cytosine, it becomes thymine which unless removed becomes a fixed mutation in the DNA sequence
what is mismatch repair?
if DNA polymerase missed a few mistakes a 2nd set of proteins correct the errors
it involves recognition of the affected region, followed by removal and re-synthesis of one DNA strand, using the parental strand as template
it must distinguish between the newly synthesised strand with the error from the parental strand
how does mismatch repair work?
MutSa and MutLa (repair enzymes) recognise base mismatches
they then diffuse away from the mismatch to reach nicks in the newly synthesised strand bound by either PCNA or RFC
exonuclease (EXO1) is then recruited to degrade the newly synthesis strand towards and through the mismatching region
PCNA then recruits a DNA polymerase to re-synthesise the gaped region, leaving nicks to be sealed by DNA ligase
what is base excision repair?
repair mechanism that repairs the DNA with damages or missing bases or with a single strand breaks
how does base excision repair work?
DNA glycosylase identifies and removes the damaged base by cleaving the glycosyl bond between the base and DNA backbone
endonuclease then cuts the sugar-phosphate backbone
the baseless sugar-phosphate is removed
and DNA polymerase fills the gap using the undamaged strand as a template and DNA ligase seals it
what is nucleotide excision repair?
removes DNA damage that distorts the DNA double helix
on what depends the way the damage is recognised?
depends on wether it is in a region transcribed by RNApIII (transcription coupled NER) or elsewhere in the genome (global NER)
what are the steps of NER?
XPC recognises damaged DNA to initiate the global repair pathway
DNA is unwound around the damage region by helicases
endonuclease make an incision several nucleotides upstream and downstream of the damaged region
25-30 nucleotides are excised around the damage region. DNA is re-synthesised and sealed by DNA polymerase and DNA ligase
what is the Cockayne’s syndrome (CS)?
disease associated with defective NER and is characterised by short stature and neurological dysfunction and mild skin sensitivity
it is an autosomal recessive disorder caused by mutations in the genes for CSA or CSB proteins which have roles in transcription coupled repair which is required for post-translational modification of RNApolII
what are the 2 most common pathways for repairing double strand breaks?
homologous recombination and non-homologous end-joining
what does homologous recombination do?
uses undamaged section of similar DNA as template
enzymes interlace the damage and undamaged strands to get them to exchange sequences of nucleotides and finally fit in the missing gaps to end up with 2 complete double stranded segments
