Lecture 5- DNA damage and mutation Flashcards
Mutation
An alteration to the genetic material (DNA or RNA) that produces a heritable change in the nucleotide sequence
Wild type
The standard form of a gene or an organism
Mutant
The altered gene or organism produced by mutation
Forward mutation
A process that converts a wild type to a mutant
Reversion
A process that converts a mutation to a wild type
Phenotype
A description of what an organism looks like
Genotype
A description of the genes of an organism
Mutagen
A chemical or physical agent that causes mutation
Spontaneous mutation
Genetic changes that arise naturally during the life of an organism
Induced mutation
Genetic changes caused by a specific mutagen
What are the 3 different types of mutation?
Global change
Localised change
Base pair substitution
Global change mutation
Large scale genomic changes
Chromosomal aberrations: deletions, insertions, duplications and inversions
Genome re-arrangement: redistribution if genetic material between chromosomes (translocation) that often arise from chromosome breakage
Change in chromosome number: trisomy of chromosome 21 (Down’s syndrome) which usually arises from mistakes in chromosome segragation at cell division
Localised change
Affects a small number of nucleotides
Base substitution: point mutation (single base, frame shifts)
Delection, insertion
Duplication: sequence is repeated
Inversion: sequence inverted
Translocation or transposition: movement of a piece of DNA from one location to another
Base pair substitutions
Point mutation: a mutation that results in the substitution of one base pair for a different base pair
These can be 2 types:
Transition mutation: change a purine for a purine or change a pyrimidine for a pyrimidine
Transversion mutation: change a purine for a pyrimidine or change a pyrimidine for a puring
What are the 5 possible outcomes of mutations?
Silent/samesense: no effect
Missense: amino acid substitution
Nonsense: amino acid changed to stop codon
Readthrough: stop codon changed to amino acid
Frame shift: base pair deletions or insertions in a gene induce a shift in the reading frame
What are the 4 different effects of point mutation?
No effect: silent
Missense: protein polymorphism
Change of function
Loss of function
Why are adduct and lesion interchangeable?
They both mean DNA damage
What are the 2 main categories of damage?
Affecting a single strand of DNA
Affecting both strands of DNA
DNA damage that affects a single strand of DNA
Easier to fix as there is still an undamaged strand that can acts as a template
Adduct/lesion: 1 or 2 nucleotides altered e.g. methylated base
Nick
Mismatch
DNA damage that affects both strands of DNA
Replicated adduct: a gap opposite the adduct as DNA polymerase skips the damaged region
Chromosomal break/interstrand crosslink
What is a spontaneous mutation?
Damage from spontaneous degradation of DNA (endogenous factors)
Loss of bases
Loss of amine groups from bases
Mutations from damage by metabolic products (reactive oxygen species)
Fixation of mismatches and other mistakes by DNA polymerases
What are the 3 different types of spontaneous mutation?
Depurination
Deamination
Tautomeric shift
Depurination (spontaneous mutation)
The glycosidic bond between the base and sugar is cleaved by hydrolysis resulting in an apurinic or apyrimindic site/abasic site as a base has dropped out. Loss of adenine or guanine are the most common. A human cell loses several thousand purines each day.
Deamination (spontaneous mutation)
Amine groups on the rings of bases are susceptible to spontaneous oxidation to aldehyde groups- deamination. This alters the pairing properties of the bases e.g. cytosine deaminates to uracil which can base pair with adenine when replication occurs
Tautomeric shifts (spontaneous mutation)
Bases in DNA can occur in several forms, tautomers, which differ in the positions of their atoms and in the bonds between the atoms. The keto form of each base is normally present in DNA, whereas the imino and enol forms of bases are rare. DNA bases can isomerise with the different isomers having different base pairing properties. These changes are a significant source of spontaneous mutation.
Tautomeric shift of guanine
Guanine will undergo a tautomeric shift to its rare enol form G* prior to replication. In its enol form it will pair with thymine and post replication is reverts back to its normal keto form.
Describe tautomeric shifts, step by step
Hydrogen atoms move to form bases with altered hydrogen bonding properties creating a tautomeric shift.
When a tautomeric shift occurs in adenine, adenine can bind to cytosine.
A tautomeric shift in guanine allows it to bind to thymine.
This error is passed on through replication and onto mRNA which can lead to a different amino acid being incorporated into a protein.
What is an induced mutation?
damdage from external (Exogenous) sources. Mis-repair of damage caused by: Radiation Alkylation of bases Crosslinking agents Intercalated molecules
What are the 3 main causes of induced mutations?
Exogenous oxidative damage
Radiation
Chemical mutations
Endogenous oxidative damage - example
The products of oxidative processes that form the basis of aerobic life.
E.g. thymine glycol formed by hydroxyl radical attach of thymine, thymine glycol blocks DNA replication
Damage limitation of endogenous oxidative damage
Oxidation of FADH2 on flavoproteins leads to production of hydrogen peroxide and superoxide. Catalases (Kats), peroxidases (e.g. alkyl hydroperoxide reductase, Ahp) and superoxide dismutases (SODs) minimise the accumulation of these two oxidants. Glutathione is a tripeptide used as a cellular antioxidant to mop up ROS (reactive oxygen species)
What are the indirect effects of radiation induced mutations?
Particle interacts with other molecules which then interact with the DNA
e.g. radiolysis of water to give hydroxyl radicals which damage bases
What are the direct effects of radiation induced mutations?
Particle imparts its energy directly to the DNA molecule. Breakage of the bonds that hold the sugar phosphate backbone together.
Ultraviolet light has a direct effect on DNA.
What are the main products of UV irradiation- radiation induced mutations
Cyclobutane pyrimidine dimers and 6-4 photoproducts
Formed at adjacent pyrimidines resulting in covalently fused dimers.
Lesions interfere with normal base pairing and can cause base substitutions.
Double helix is distorted- this damage is bulky lesion.
What is the order of lesions that are formed preferentially - radiation induced mutations
TT
TC
CT
CC
6-4 photoproduct - radiation induced mutation
The C6 carbon of one pyrimidine covalently links with the C4 carbpn of an adjacent pyrimidine.
The backbone becomes distorted resulting in a bulky leasion
Chemical mutagens, alkylating agents - induced mutation
Natural and artificial agents
Alkylating agents: add methyl or ethyl groups to bases. This can alter the pairing properties and are called miscoding lesions. Some block replication.
Chemical mutagens, Benz(o)pyrene - induced mutation
Carcinogenic ingredient of hydrocarbons in chimney soot, cigarette smoke and car exhausts if metabolised to an epoxide that acts on the N2 group of guanine.
Chemical mutagens, Mutagens produced by metabolic activation - induced mutation
Many mutagens are not active and require bioactivation to electrophiles that bind covalently to DNA.
Acetylaminofluorene is an aromatic amine originally used as an insecticide that is converted to an alkylating agent by esterification.
Chemical mutagens, DNA crosslinking - induced mutation
Certain chemicals covalently join two bases in complementary strands to form an interstrand crosslink. DNA crosslinks prevent separation of two strands so block transcription and DNA replication.
Interstrand crosslinks are typically produced by bifunctional agents
Chemical mutagens, DNA intercalating agents - induced mutation
DNA double helix is partly held together by stacking interactions. Some chemicals are capable of intercalating the stacked DNA bases. Intercalation can cause single nucleotide insertions and deletions blocking replication/transcription.
