What are the 2 categories of mutations and briefly describe?
- Germline: Occurs in cells that produce gametes (e.g. sperm mother cell/ stem cells) & affects offspring (inherited)
- Somatic: Occurs in somatic cells & affect cells/tiss. of individual
What can are the types of mutation that can occur in a gene?
- Frameshift bc of insertion/deletion of 1+ bp (usually introduce premature STOP codon)
- Substitution: 1bp is changed to another bp during replication
- Copy number variation
Differentiate b/w the 2 class of mutations (that occur in the DNA)
- Gene: point mutation- change in 1 bp
- Chromosomal: (gene/)portion in chromosome changes w/in chromosome
Types of base substitution in point mutations & the effects
- Silent mutation: △ in 3rd bp in codon ≠ △ AA
- Missense mutation: △ 1st/2nd bp in codon = △AA (structure & function may/not △)
- Nonsense mutation: △ in bp = STOP codon = premature termination of translation
Differentiate b/w transition & transversion mutations in base substitution
- Transitions: △ bases w/in purines [A&G] (or pyrimidine [T&C])
- Transverse: △ bases from purine to pyrimidine, vice versa (e.g. A -> T or C
Differentiate b/w the 2 types of copy number variation
- Gene amplification: increase no. of genes sequ. in DNA = increase no. of proteins
- Trinucleotide (microsatellite) repeats: 3 bases repeated many times in DNA replication = expand size of OG DNA
What’s the difference b/w forward & reverse mutation when referring to the effects of AA/gene sequence?
- FWD: loss of wild-type (normal) allele
- RVS: Resores the WT allele (or function) e.g. 2 mutations on a same gene = may cause proper function
What are the phenotypic effects of mutation?
- Loss of function: recessive - give total/partial loss
- Gain of function: dominant - create new trait & hyperactivation of protein
What are suppressor mutations & 2 types?
mutation that suppresses the effect of another mutation
- Intragenic suppressor: mutations that occur @ the same gene => can restore codon sequ. = AA sequ.
- Intergenic suppressor: mutations occur in diff. genes, but the interaction of the proteins made are normal
Types of chromosomal mutations & briefly describe
- Deletion: a region of chromo. is lost = genes lost
- Duplication: region is repeated = genes doubled
- Inversion: region broken off & rejoin in reverse order
- Translocation: a region from 1 chromo. break & attaches to another chromo.
What are the spontaneous replication errors?
- Incorporated error: incorrect base added (wobble)
- Strand slippage: new strand form a loop = in next new strand a base(s) is added (insertion). OR template strand loops = base(s) missed when replicated (deletion in new strand)
What are the spontaneous chemical errors & differentiate?
- Depurination: lose purine base bc covalent bond b/w 1’C (sugar) & base breaks => no template for replication (apurinic site) = base randomly added (A)
- Deamination: lose NH2 group from base e.g. C (-NH2) => U so in replication new strand will have A (not G)
Types of chemically induced mutations & causes
- Base analogies: chemicals - have same structure as bases incorporated in DNA & may alter base pairing e.g. 5 bromo-uracil replaces T => pairs w/ A but sometimes G
- Deamination
- Add. -OH groups: hydroxylamine (NH2OH) adds hydroxyl group to C => like T = pair w/ A (not G)
- Alkylating agents: add meth/ethyl to nucleotides e.g. G => like A = pair w/ T
- Oxidation: free-radicals (H2O2) damage DNA e.g. G => 8-oxoguanine => pairs w/ A not G
- Intercalating agents: chemicals inserted b/w “rungs” (bases) = distort 3D structure => insertion/deletion during replication = frameshift
Types of radiation induced mutations & causes
- Ionising radiation: break PO bond => ds breaks in DNA
- Non-ionising radiation: bases absorb UV => form bonds w/ adjacent pyrimidine e.g. 2x T = T dimer = blocks replication
What are transposable elements and causes?
piece of DNA (insertion sequence) that can randomly insert itself in a genome
=> disrupt coding seq.
=> prevent activation of promoter
=> activate genes inappropriately
Describe the process of mismatch repair (in E. coli)
- After replication, A in GATC is methylated on old strand
- mis-match repair complexes brings unmethylated GATC (on new strand) close to mismatched base(s)
- nicks near unmethylated GATC and DNA in b/w mismatch base(s) & GATC is degraded
- DNA pol & DNA ligase fill area w/ correct base
Describe direct repair (in O6-methylguanine & thymine dimers)
- fixes damaged base rather than remove
a) O6-methylguanine (methyltransferase remove CH3) -> guanine
b) photolyase breaks covalent bonds in b/w thymine dimers (photo-reactivation)
Describe the process of base excision repair
- (specific) DNA glycosylase detect modified base (e.g. U from deaminated C) & removes base @ 1’ C of sugar
- AP (apurinic/apyrimidinic) endonuclease cuts @ PO bond
- deoxyribose sugar removed
- DNA pol. puts correct nucleotide & DNA ligase repairs PO bonds
Describe the process of nucleotide excision repair
- (XPC) complex of enzymes scans & encounter damaged DNA (e.g. pyrimidine dimers)
- endonuclease nicks a couple of bases away from damaged DNA
- removal of cut strand by DNA helicase
- resynthesis by DNA pol
- ligation of DNA ligase
*Describe the difference in non-& homologous repair process of ds breaks
- Homologous: uses (near) identical genetic info. from (sister chromatid) => same og DNA
- Non-: not same as og DNA
Describe cisplatins mechanism (as a chemotherapy drug)
cisplatin binds to G&G in dsDNA ≠ transcribed = (mutated) genes -> more mutated ≠ able to produce appropriate proteins for repair in cancer cell ≠ survive
