BIOL 310 - Ch 18 Lecture Notes

Mutations

• a change to the genetic code

• categories — somatic vs germ-line

• types

  • base substitutions

  • insertions & deletions

  • expanding repeats

Somatic vs Germ-line

• somatic

  • every cell that is not a gamete

  • a portion of the cells are mutant

• germ-line

  • all cells carry the mutation or none of the cells carries mutations

Mutations Types

• base substitutions

  • transitions — purine to purine or pyrimidine to pyrimidine

  • transversions — purine to pyrimidine (vise versa)

    

  • missense mutation - new amino acid replaces

  • nonsense mutation - stop codon generated

  • silent mutation - new codon still generates original amino acid

• insertions & deletions

  • loss or gain of codon into genetic code which throws the three base pairs off

• expanding nucleotide repeats

  • DNA polymerase can fall off & the repeats have a tendency to form hairpin loops

  • when another nuclease attaches onto the hairpin section to elongate — extra five repeats in the loop

    • next time the strand serves as a template will have thirteen repeats from an original eight

    • the offspring will also have thirteen repeats

phenotypic effects of mutations

• neutral mutation — no effect

• loss of function — forward mutation (wild type to mutant state)

• gain of function — reverse mutation (mutant to wild type state)

• intergenic suppressor

  • second mutation on second gene reverts phenotype

• intragenic suppressor

  • second mutation within the original gene reverts phenotype

mutation rates

• mutations per unit (cell division, gamete, genome replicated)

• the rate can be “affected” by

  • probability of a mutation: induced or spontaneous

  • likelihood of repair

  • likelihood of detection

• generalizations

  • spontaneous mutations rate is low — 1 to 100 per 10 billion bacterial cells & 1 to 10 per million gametes in eukaryotes

• varies by gene & organism

  • adaptive mutation — some areas of the genome sustain mutation; genetic diversity at that locus can be beneficial (improve at population level)

    • areas of the genome differ between high or low mutation rate; some areas might be significant to conserve

causes of mutations

• what is happening - Bromouracil

• spontaneous

  • mispairing

  • replication errors

  • deletions & insertions — strand slippage

  • unequal crossover

  • depurination

  • deamination

• induced

  • chemically induced

    • base analogs — bases that look similar to the wild-type bases but have different hydrogen bonding properties

    • alkylation

      • altered bases such as CG → TA

    • deamination

      • altered bases such as CG → TA

    • oxidation

    • hydroxylation

      • altered bases such as CG → TA

    

    • intercalation

      • dyes that attach themselves to the DNA & act as bases, can pair with wild-type bases

      • shoved between nitrogenous bases

      • a type of insertion mutation - frame shift

    

  • radiation

    • ionizing radiation (x-rays)

      • breaks chromosomes and can cause deletions, duplications, inversions, and translocations

        

      • homologous recombination: two copies of chromosome I if one has a break the cell can use the chromosome that is complete to fill in the other with gaps

      • non-homologous end joining: multiple chromosomes present and both sustain breaks; the cell shoves them together (last ditch effort)

    • UV — hydrolysis of cytosine: mispairing during replication

      • thymine dimers block replication & transcription

      • polymerases stall at the dimers and fall off

radiation & mutation

• cumulative effect

  • large dose all at once = accumulated dose over time

  • radiation measured in Roentgen units

determining mutagenicity

• the ames test

  • histidine auxotrophs — bacteria that cannot produce their own supply of histidine due to a frameshift in a gene of Histidine operon

  • putative mutagen

  • media with histidine traces for DNA replication by the bacteria culture

  • treatment plate with more colonies suggest that the chemical added is more mutagenic than the control

radiation & humans

• lethal levels are highly damaging

• sub-lethal levels

  • increased somatic mutations

  • effectively no germline mutations

transposable elements

• ~45% of human genome is transposons

• mutation effects

  • deletions, inversions, duplications

  • during replication recombination event between different regions of the same chromosome with the same transposon yields deletion product

  

  • transposons in inverse orientation (facing towards each other) yields an inversion product

  

  • two colinear transposons & two homologous chromosomes have a recombination event to yield one chromosome with a deletion and one with a duplication

  

DNA repair mechanisms in E. coli

• DNA replication error is 1 error per 10,000 nucleotides

• after proofreading it becomes 1 per billion nucleotides

• mismatch repair — enzymes that can key in problems to errors not caught by proofreading; recruit enzymes to fix any bumps in the DNA

  • recruit mismatch repair complex to problem region; fill gap by ligase and polymerase

excision repair

• base excision pair — removing abnormal or chemically modified bases

• nucleotide excision repair — remove larger defects such as thymine dimers

• DNA repair endonuclease — binds to & excises the damaged base(s)

  • DNA polymerase fills in the gap

  • DNA ligase seals the nick left by DNA polymerase

nucleotide excision repair

• proteins recognize damaged bases

• nicks are produced and the ‘damaged’ section is removed

• gaps are filled in by polymerase & ligase seals any remaining nicks

faulty repair and genetic disease

• failure to repair

  • increase standing mutation load

  • increase likelihood of disease phenotype

  • associated with increase cancer incidence