BSCI222 Exam 3 Lecture 9 (Mutation and DNA Repair)

in alternative splicing, how to exons come together?

• splicing factor proteins bind to regulatory sequences in the RNA

• some promote exon inclusion and other promote exon skipping

mutation

a change in the DNA sequence

can mutations have a phenotypic effect

yes. can be both a loss of information and a source of evolutionary innovation

Point Mutation

cause SNPs or INDELs, affect one or a few nucleotides

Chromosomal Mutation

at a greater scale than point mutations. may affect many genes or entire chromosomes

variant

more generic term inclusive of mutations that have recently occurred and those that have been inherited

• “sequence variant”

• many sources use term mutation or mutant to refer to the non-wild type sequence regardless of whether the variant was inherited

in animals, what can early separation of germ line cells cause

can reduce gamete mutations.

• somatic mutations are not passed to offspring

• early gremlin separation can reduce the risk of somatic mutations with more cell division before gamete formation

• most parents carry the variant in the genome

de novo germline mutation

mutation that arises in the germline and is inherited by the offspring

• ex. Hutchison-Gilford Progeria Syndrome

are mutations spontaneous or induced

can be both

what can cause SNPs

substitution - a base is replaced by one of the other three bases

• affects one codon, and may or may not change polypeptide

SNP - transition

base is switched from purine to purine (A-G) or pyrimidine or pyrimidine (C-T)

SNP - transversion

base is switched from pyrimidine to purine (or vice versa)

(A-C, G-T, C-G, A-T)

Insertion

an extra base is inserted → causes frameshift mutation and can change amino acid

Deletion

a base is removed → causes frameshift mutation and can change amino acid

What are the types of mutations

silent, missense, nonsense

silent mutation

alteration of nucleotide does not alter amino acid (“synonymous”)

missense mutation

different amino acid substituted (“non synonymous”)

nonsense mutation

premature stop codon → common in transitions of SER, ARG, GLN, TRP

what are the phenotypic effects of variants

neutral, loss of function, gain of function, lethal, conditional

neutral phenotypic effect

different aa but does not affect activity

• might be conservative substitution (similar aa)

• might be permissive site in protein

loss-of-function phenotypic effect

protein is not as active or is “dead”

gain-of-function phenotypic effect

protein does something new

lethal phenotypic effect

necessary for growth & development

conditional phenotypic effect

shows phenotype only under certain conditions (ex. high temps)

mutation rate equation

total # mutations / total bases in genome

OR

#mutations in a gene / total bases in a gene

spontaneous mutation

errors in DNA replication, recombination, or exposure to a naturally occurring chemical

• mis-incorporation, slippage, unequal crossing over, deprivation, deamination

induced mutation

exposure to a mutagen, any substance or condition that can increase the rate of base change

• chemical, radiation

mutation by mis-incorporation

• source of substitution

• arises during replication

• incorporated errors can be passed on to daughter cells

depurination

spontaneous chemical change

(ex. hydrolysis of a purine base from sugar)

deamination

spontaneous chemical change

(NH2 group converted to =O by weak acids or oxidants)

chemically induced mutation: base analog

mimics nucleotides and is incorporated into DNA

• result: misparis → substitutions

chemically induced mutation: alkylating agent

adds methyl or ethyl group to nucelotides

• result: mispairs → substitutions

chemically induced mutation: delaminating agent

deamination

• result: mispairs → substitutions

chemically induced mutation: oxidative reaction

oxides bases

• result: mispairs → substitutions

chemically induced mutation: intercalating agent

binds to bases, bending helix

• result: insertions and deletions

Radioactively induced mutation

UV light

• induced creation of thymine dimer (extra crosslinks between thymine bases)

DNA repair mechanisms

mismatch, excision, photo reactivation, strand break, translesion synthesis

mismatch repair

repairs soon after DNA replication to catch substitution errors

• good chance that it was newest strand

• recognizes mismatch and identifies old vs new strand to repair new strand using

  • bacteria: chemical modification

  • eukaryotes: presence of nicks

• removed region of strand

base excision repair

works at any time

• specific glycosylase removed the bad base

• AP endonuclease cuts out sugar-phosphate

• polymerase replaces nucleotide

  • pol I in prokaryotes

  • pol B in eukaryotes

• ligase reseals phosphodiester backbones

nucleotide excision repair

scans DNA for bulky damage and removed segment of DNA

• polymerase replaces section

• works for lots of different types of damage

ex. xeroderma pigmentosum: sensitivity to sunlight after exposure

photo reactivation repair

• “direct” repair of thymine dimers

• E.coli - enzyme called photolyase

• doesn’t remove bases, just breaks crosslinks

• works in presence of blue light as source of energy so this is also known as “light repair”

what do placental mammals lack

lack photolyase

• thymine dimers are fixed by nucleotide excision repair only

homologous recombination repair

aka homology directed repair

• strand breaks

• when a copy is available to use as a template

• uses enzymes involved in meiotic recombination

non homologous end joining (NHEJ)

• strand breaks

• when a copy isn’t available

• searches for microhomologies

• repair based on microhomology

• often creates INDELs

• may cause telomere joining

Translesion Synthesis

• uses alternate polymerases to go over a distortion in the strand

• DNA pol II, IV, V in bacteria induced by SOS response

• there are error prone