6 DNA damage, repair, and mutations Flashcards
what are somatic mutation
mutations in body that only impact you
What are germinal mutations
get transmitted to further generation
what are 2 ways tp get a mutant DNA sequence
DNA damage –> turns into mutant DNA
DNA Repair messes up and created a mutant DNA
what is the origin and frequency of mutation
○ Mostly from replication errors
○ Polymerase makes mistakes
what are some causes of spontaneous mutation rate
○ Genome characteristics
○ Cell age
what are induced mutations
○ Happens in higher frequency
○ From known chemical and physical reagents
○ Base analogs
§ Imposter nucleuotides
○ Hydroxylating, alkylation, deaminating agents
○ UV and ionizing radiation
what are 3 types of mutations
○ SBP (single base pair)
○ SNP (single nucleotide polymorphism)
○ Point mutations (SNP and SBP)
what are 3 types of point mutations
- Transition mutations
- Transversion mutations
- Indels
what is a transition Point mutation
□ Purine –> purine (A=G, G=A)
□ Pyr –> pyr (A=T, T=A)
what is a transversion point mutation
□ Purine <–> pyrimidine
what is an indel point mutation
Deletion or insertion of a base
what are synonymous mutations
○ Silent mutations = nothing happens
what are non-synonymous mutations (sense)
○ Missense mutations = code for a diff AA
○ Nonsense mutations = changes to a stop codon (likely severe)
what is a frameshift mutation
- Frameshift = removal, addition, or substitution
○ Disrupts triplet reading frame
what does a non-coding region mutation do
Affects gene expression
what is slippage
Polymerase accidentally moves on the dna up or down causing insertion or deletion on strand its synthesizing
what are 6 types of nucleotide mispairing
- tautomers
- ionization
- wobble bases
- depurination
- deamination
- oxidative damage
what is a tautomer
Isomeric changes in chemical shape
what is ionization in nucleotide mispairing
Gain or loss of electrons changes binding pattern (ex. T binds to G)
what are wobble bases in nucleotide mispairing
Can sometimes fuck up
what is depurination of nucleotide mispairing
Removal of a purine
Stops replication and transcription
what is deamination
Removal of amine (NH2) grp
Alters base pairing
what is oxidative damage
□ Directly breaks DNA dbl strand
what are induced mutation (what is the inducer)
○ Mutagen: chemical or physical force that increases chance of mutation
§ Replace alter or damage base in dna
what are sometypes of chemical and physical mutations
Chemical
- alkylating agents
- reactive oxygen species
- intercalating agents
- Base analogs
Physical
- UV/Ionizing radiation
what happens when UV light hits a DNA strand
○ Covalently links neighbouring pyrimidines
○ Stops replication
○ Results in transition mutations
what happens when ionizing radiation hit DNA
○ “lightning bolts hitting DNA”
- Likely to cause actual breaks in DNA
what is an alkylating agent in chemical mutagens
addition of alkyl grp to a nucleotide
- disrupts correct base pairing
what is a base analog in chemical mutagens
Chemically similar to ATCG(imposter)
- can be incorrectly incorporated into DNA polymerase
what is a intercalating agent (mutagen)
Inserts between base pairs
- distorts dbl helix
- increases slippage
what is an Abasic site
○ Nucleotide been removed and theres jus a hole in the DNA
what is the non bulky DNA damage and the bulky DNA damage
NON-BULKY
- alkylation
- oxidation
- deamination
- depurination
BULKY
- pyrimidine dimer
- bulky adduct
- base mismatch
- loop
- dbl strand break
what is a revertant
WT that have been mutants and are now WT again
what is the mutagenicity ratio (MR)
total # revertants / # spontaneous revertants
if a compound has no mutagenic effect the MR is
~ 1
if a compound shows signs of being mutagenic the MR is
MR > 1
if a compound kills the cell the MR is
MR < 1
How can we fix the non-bulky damage in DNA
Base excision repair
how can we fix a pyrimidine dimmer and a bulk adduct
Nucleotide excision repair
- (pyrimidine dimmer can also be fixed by direct repair)
what does the mechanism of mismatch repair fix ?
base mismatch and loop
what does non-homologous end joining repair ?
double stranded break
what are the steps taken when DNA has been damaged
- surveillance(detect errors)
- Excision (Find mistake and cut it out)
- polymerization (replace what was cut)
- strand ligation (reconnect bonds in repaired stand)
what is direct repair
○ Some errors can be reverted by using specific enzymes because they happen so often
what is base excision repair
○ One of the simplest way to repair
○ Detection and excision
§ Enzyme removes the whole error
§ Cut strand with endonuclease to allow DNA entry to fix
§ Polymerase replaces error with correct base
§ Can replace 1 base or a whole chunk
what is nucleotide excision repair
For larger damage that affects multiple base pairs
§ Damage detection
□ Global genome surveillance finds
□ Look for stalled RNA polymerase
§ Strand separation
□ Helicase opens DNA
§ excision
□ Endonuclease cuts out whole chunk
§ Polymerization
□ Polymerase fixes
§ Ligation
□ Glued back together by DNA ligase
what is mismatch repair (what does it look for)
○ Uses concept of DNA methylation
○ Detection
§ Template strand has a methyl group and new strand doesn’t so we know which one is right
what are double stranded breaks
○ Most serious of damage
○ Affects both strands so theres no template
what are 2 ways to fix a double stranded break
homologous recombination (HR), non homologous End Joining (NHEJ)
what are traits of homologous recombination (HR)
§ Uses homo chromos as template
§ Active post DNA replication
§ More error proof
what are traits of non homologous End Joining (NHEJ)
§ DNA strands join independent of complementarity
§ Active in dividing and non dividing cells
§ Doesn’t req template strand
§ More prone to errors
§ DNA strands jus glued together
how does NHEJ work
○ Detection
§ Proteins bind to end to supress further damage
○ Strand resection
§ Recruit of kinase and nuclease proteins to make blunt ends
○ Polymerization
§ Polymerase fills end for ligation (sticky ends)
§ Does not add bases (no template)
○ Ligation
§ Ligates the 2 sticky ends together
how does HR repair work
○ Detection
§ Same way NHEJ
○ Strand resection
§ Cuts back from break
§ Creates 3’ overhangs (sticky ends)
○ Strand exchange/invastion
§ Seperates double stranded DNA
§ Forms a Displacement loop (D-Loop)
○ Polymerization
§ Missing DNA copied from template
○ 2 complex pathways from here
§ Synthesis dependant strand annealing pathway (SDSA)
§ Double strand break repair pathway (DSBR)
what is Synthesis dependant strand annealing pathway (SDSA)
- both strands broken
- One broken strand “invades” a matching DNA strand to use as template.
- The broken strand copies the missing DNA using the intact strand as guide.
- The newly made DNA strand separates and sticks back to its original partner strand.
- No Crossing-Over: Unlike other repair methods, SDSA does not swap large sections of DNA between chromosomes, avoiding genetic changes.
what is Double strand break repair pathway (DSBR)
It’s like repairing a torn rope by using a similar rope to guide the fix, but sometimes parts of the ropes get exchanged.
what is the only repair mechanism that doesnt use a polymerase
Direct repair
- uses enzymes
TF NHEJ doesnt use a template strand and HR does
T
