Mechanisms and effects of mutations Flashcards
Variation
Alterations in the sequence of bases in a specific section of DNA. May lead to altered gene expression, or an altered form of a protein. A genome variant can be classified by size, frequency and clinical effects.
Mutation
An alteration or change in the genetic material that is usually harmful. May arise spontaneously through errors in DNA replication/repair, or from exposure to mutagentic agents eg. UV, chemicals, ionising radiation. Often occur in the coding exons of genes, or the regulatory intronic sequences.
Polymorphisms
An alteration or change in the genetic material that is not harmful. May occur within non-coding segments of the DNA, or within a gene but not altering protein function.
Single nucleotide polymorphisms (SNPs)
Changes in a base at a particular position, occuring in the population at a frequency of >1%.
Examination of the genome
Techniques used to examine the genome include:
- sequencing
- microarray analysis
- fluorescent in-situ hybridisation (FISH)
- light microscopy
Endogenous mechanisms of DNA damage
- depurination; fission of link between purine base (A/G) and sugar
- deamination; cytosine deaminates to uracil, causing substitution G to A
- reactive oxygen; attack purine/pyramidine rings
- methylation of cytosines; leads to spontaneous deamination of C to T
Extracellular agents causing DNA damage
- UV light; causes two adjacent thymine bases to covalently attach, forming a dimer which disrupts 3D structure and can stall replication machinery
- environmental chemicals; interpolate into DNA or cause DNA breaks or chromosome aneuploidy
- ionising radiation; causes breaks in DNA
DNA repair
Most DNA damage is detected at cell cycle checkpoints and repaired. DNA polymerase ‘proof reads’ the bases as it adds them during DNA replication. DNA mismatch repairs correct 99% of residual errors from replication machinery. They can identify and excise errors and chemicals, and repair DNA breaks by homologous recombination or joining broken ends.
Types of mutation
- missense
- nonsense
- frameshift
- duplication
- deletion
- insertion
Single base substitutions
- silent mutation; does not change amino acid sequence due to genetic code degeneracy, not harmful
- missense mutation; changes to a codon for another amino acid, may be harmful
- nonsense mutation; changes to a stop codon, resulting in a truncated protein, harmful
Splice site mutation
Changes in introns and intergenic regions may affect splicing, especially if the variation occurs near the ends. Results in an altered RNA sequence and an altered protein.
Frameshift mutation
Insertion or deletion of base pairs changes the reading frame of the entire amino acid sequence, often producing a premature stop codon. Produces a completely altered or truncated form of a protein (harmful).
Copy number variants
Repeated sequences can mispair or expand, predisposing to large deletions and duplications. Chromosomes misalign at these sequences, causing unequal crossing over which can affect a few or many hundreds of genes.
