DNA repair: DNA damage and mutation

mutation

• any alteration to the genetic material that produces a heritable change in the nucleotide sequence

somatic mutations

• arise in somatic tissues

• mutation passed onto daughter cells by mitosis

• the earlier in development the mutation takes place, the larger the number of clone cells containing the mutation

germ-line mutation

• arise in cells that will produce gametes

• passed onto future generations so that all their somatic and germ-line cells carry the mutation

forward mutation

• process that converts a wild-type to a mutant

reversion

• process that converts a mutant to a wild-type

types of mutation: global change

• global change - big chunks of DNA rearranged/lost

• chromosomal aberrations (deletions, insertions, duplications, inversions)

• genome rearrangements (translocation between chromosomes)

• changes in chromosome number (polyploidy)

types of mutation: localised changes

• localised changes - affect a small number of bases

• base substitutions - point mutations:

single base changes

frame shifts

• deletion/insertion

• duplication

• inversion

• translocation

base pair substitutions

• transition mutation - swapping like for like (purine for purine or pyrimidine for pyrimidine)

• transversion mutation - swap purine for pyrimidine or vice versa, number of possible transversions twice then number of possible transitions

• transitions arise more frequently as they are easier to carry out

base pair substitutions - point mutations

• samesense/silent - changes one codon for another which codes for same amino acid (DNA polymorphism)

• missense - base substitution that results in a different amino acid in the protein 

• missense (protein polymorphism) - base substitution that results in a different amino acid in the protein but the substituted protein has a similar chemical structure so has little effect on the function of the protein (neutral mutation)

• nonsense - changes a codon that codes for an amino acid into a stop codon so the protein is truncated

• frameshift - change in reading frame of the gene, alter all amino acids encoded for by the nucleotides following the mutation - big effect on phenotype

point mutations - frame shift

• frameshift - change in reading frame of the gene, alter all amino acids encoded for by the nucleotides following the mutation - big effect on phenotype

• deletion of one of the bases - frameshift to the right

• insertion of a base - frameshift to the left

• can introduce premature stop codons

• 3 bases added - put sequence back into frame but you add an amino acid

• in-frame insertion/deletion - insertions or deletions that do not affect the reading frame so no frame shift takes place

spontaneous mutation

genetic changes that arise naturally during the life of an organism

induced mutation

genetic changes that are caused by a specific mutagen

factors affecting mutation rates

• frequency with which changes in DNA take place

• probability of alteration being repaired

• probability that the mutation will be detected

spontaneous DNA damage and breakdown: depurination

• glycosidic bond between the base and sugar is cleaved by hydrolysis so purine/pyrimidine removed

• results in an apurinic/apyrimidinic site

• loss of purines most common

• no complementary base present so during replication an incorrect nucleotide is incorporated into the newly synthesised strand opposite the abasic site

• this leads to an incorporated error which is transformed into a replicated error

spontaneous DNA damage and breakdown: deamination

• amine groups undergo spontaneous oxidation to aldehyde groups

• alters pairing properties of bases - leads to base pairing mismatch and can give rise to transition mutations if unrepaired

spontaneous DNA damage and breakdown: tautomeric shifts

• hydrogen atoms move to form a bond with other atoms so that bases can bond with other bases they wouldn’t normally form H bonds with

• keto (G/T) or amino (A/C) form of the base normally present in DNA, enol and imino forms of base are rare

• can result in different amino acids being incorporated into the protein

• mispairing of bases through wobble - other forms of bases able to pair due to flexibility in the DNA helical structure

incorporated error

• when a base substitution causes a mispaired base to be incorporated into a newly sythesised nucleotide chain

• leads to replicated error so that the mutation is permanent - all base pairings correct so no way for repair systems to detect the error

induced mutations: base analogs

• chemicals with similar structures to any of the 4 nitrogenous bases in DNA

• chemicals cannot be distinguished from the DNA bases so are incorporated into newly synthesised DNA molecules which can lead to base mispairing

induced mutations: alkylation of bases

• donate alkyl groups to nucleotide bases

• alter pairing properties so often called miscoding lesions

• mispairing of bases takes place

induced mutations: intercalated molecules

• intercalate between adjacent bases in DNA so that the 3D structure of the helix is distorted

• this leads to single nucleotide insertions/deletions which leads to a frame shift mutation

• can also block replication and transcription

• generate insertion and deletion mutations so can reverse changes produced

reactive oxygen species induced DNA damage

• oxygen radicals bring about chemical changes to DNA which can lead to base mispairing

• e.g superoxide anions, hydroxyl radicals - unpaired electrons highly reactive (most damaging)

• hydroxyl attack on thymine forms thymine glycol which cannot pair with any other nucleotide

• formamidopyrimidine formed by hydroxyl attack on guanine

• hydroxylamine adds hydroxyl group to cytosine so that hydroxylaminocytosine formed - increases frequency of tautomer that pairs with adenine instead of guanine

damage limitation

• catalases, peroxidases and superoxide dismutases convert mutagens into less toxic intermediates

• this removes mutagens from the environment so that they don’t cause damage

• avoiding damage is better than having a good DNA repair system

radiation

• ionising radiation can dislodge electrons from atoms so that free radicals and reactive ions produced

• hydroxyl radicals generate damaged bases

• clustered lesions can lead to chain breaks

• direct effects - particle imparts its energy directly to the DNA molecule so that phosphodiester bonds that hold the sugar phosphate backbone together broken

UV radiation

• sunburn - DNA damage going on in cells

• pyrimidine bases absorb UV light - chemical bonds form between adjacent pyrimidine molecules on the same strand of DNA to create cyclobutane pyrimidine dimers (CPD) and 6-4 photoproducts

• this creates bulky lesions that distort the configuration of DNA and block replication so cell division is inhibited and the cell dies

DNA crosslinking

• certain chemicals capable of covalently joining 2 bases in complementary strands to form an interstrand crosslink

• this prevents separation of the 2 strands so blocks transcription and DNA replication

• typically produced by bifunctional agents