El-Khamisy - SSBR Flashcards
Can kinases be targeted?
- yes, v druggable targets
- biggest category of protein targets for inhibitors which have progressed to clinical trials
Is DNA stable?
- must v stable as can find it in ancient bodies
- but only stable if in body
- damage to DNA is mainly hydrolysis of water –> gen reactive species
- approx 7 breaks per cell per min
Are DNA breaks good or bad?
- generally bad, as hallmark of cancer
- but can be good (important that engineering these breaks, ie. they are controlled)
- -> Ig diversity (req engineering of DNA break)
- -> meiosis
- -> induce gene exp if in promoters in neurones of NS
What are the consequences of unrepaired DNA damage?
- cell death (if stop replicating) –> causes degen disease, autoinflam
- cell survival –> causes cancer
How is genome stability achieved?
- genome packing (spatial organisation) –> chroms in certain location in nucleus are more privileged in terms of fixing
- geometry (shape and size)
How does genome instability contrib to cancer?
- enrichment of prot coding mutations in DDR (DNA damage response) genes
- age is most common predisposing factor in cancer –> as much more likely to have accum mutations in prot coding genes by this time
What happens if DNA breaks in non-replicating cells of NS?
- always causes cell death –> causes neurodegenerative disorders
Why are topoisomerases important?
- DNA 2-3m –> packaged and compacted into nucleus
- gens lots of knots/entanglements –> problem as need to unwind
- done by tpms
What are the diff challenges to genomic integrity?
- oxidative and prot linked DNA breaks
- DNA rep
- gene transcrip
- ribose contam
- spont base loss
- endogenous base mods
How are oxidative and prot linked DNA breaks a challenge to genomic integrity?
- DNA topoisomerases sometimes don’t reseal break and left w/ prot attached covalently to DNA, will block transcrip/rep/recomb etc. –> can happen if in prox to ROS
- formaldehyde used to fix cells etc. in lab –> can cross link w/ DNA
How do topoisomerases carry out their role?
- make break in 1/2 strands, allows swivelling of other strand or duplex, then reseal
What is formaldehyde?
- byproduct of demethylation of histones and DNA
How is DNA rep a challenge to genomic integrity
- has to rep every time cell divides
- can make mistakes, leading to DNA damage
How is gene transcrip a challenge to genomic integrity?
- as RNA pol travels across DNA to make RNA, gen +vely wound DNA in front of pol and behind is -vely supercoiled
- this is nascent RNA, so can pair w/ duplex DNA –> gen 3 strand nucleic acid structure = R-loops
- can be bad as expose 1 DNA strand, so can be easily attached (not protected anymore), so considered major source of DNA instability
What are R loops made up of?
- DNA-RNA hybrids
How can R loops be seen in the lab?
- w/ Abs to visualise cells
What seqs can favour R loop formation, and why?
- repetitive regions and GC rich seqs favour R loop formation
- as any event that slows down pol increase chance of formation
Where are repetitive and GC rich seqs often found?
- termination point –> may be good as helps termination signals and causes pol to fall off
What physiological and pathological sources are there of transcrip byproducts?
- physiological = eg. rDNA seqs, CFS
- pathological = eg. nt repeat expansions (in motor neurone disease, Huntington’s etc.)
What are the physiological and pathological consequences of R-loops?
- can be useful to guide termination of transcrip
- can relieve topological constraints and supercoiling
- major source of DNA breaks if left unresolved
How is ribose contam a challenge to genomic integrity?
- RNA much more unstable as ribose, not deoxyribose
- presence of OH makes bond much more unstable (as labile), so contam makes DNA unstable
What is the only diff between ribose and deoxyribose?
- is H/OH on carbon 2
What is the source of ribose contam to DNA?
- take ribose by mistake, instead of deoxyribose, as so abundant (at least 2x order of magnitude)
- DIAG*
How is spont base loss a challenge to genomic integrity and how common is it?
- labile under physiological conditions (hydrolysis)
- v common event