CH 15 Genetics

Salvador Luria and Max Delbruck

variation between different cultures is significant supporting the hypothesis of random mutation

Somatic mutation

any cell but germ

Germ-line mutation

in gametes and are inherited

Autosomal mutation

within genes on autosomes

X and Y linked mutations

occur on X or Y chromosomes

Point mutations

base substitutions in which one base is altered

Frameshift mutations

result from insertions or deletions of a base pair

Missense mutations

change codon resulting in an altered AA within protein coding portion

Nonsense

changes codon into stop codon

Silent mutation

alters codon but does not result in change in aa, or occurs in non coding portion

Transition

pyrimidine replaced with pyrimidine or purine replaced with purine

Transversion

purine replaced with pyrimidine and vise versa

Purine

2 ringed base of nucleotide, A and G

Pyrimidine

single ringed base of nucleotide, C, T, and U

Do transitions or transversions occur more often?

transitions

Bonding patterns of bases

A with T, C with G, U replaces T

Phenotypic effects of mutation

loss of function, gain of function, morphological, nutritional (biochemical), behavioral, regulatory, lethal, conditional, neutral

Mechanism of DNA errors

tautomeric shifts, slippage, depurination, deamination, oxidative damage, transposons, base analogs, alkylating agents

Tautomeric shifts

transition, alternate forms by single proton shift, Normal: keto T binds to amino A, amino C binds to keto G, Shift: enol T binds to keto G, imino C binds to amino A

Slippage

DNA pol slips or stutters during replication, typically in repetitive sequences, can lead to insertions and deletions

depurination

loss of base

deamination

conversion of amino to a keto group, common to cytosine to change to uracil

keto

T and G, shift to enol

amino

A and C, shift to imine

oxidative damage

superoxide O2., hydroxyl radical OH., hydrogen peroxide H2O2

transposons

integrated into new genomic locations can act as mutagens; jumping genes

Base analogs

substitute for purines/pyrimidines during replication, effect tautomeric equilibriums, 5-BU can be substituted

alkylating agents

donate alkyl group to amino or keto group in nucleotides to later base pairing affinity, EMS

acridine dyes

cause frameshift mutations by intercalating in between the bases

UV radiation

creates pyrimidine dimers (T usually) that distort DNA conformation in way that causes errors in DNA replication

ionizing radiation

X ray, gamma, cosmic - mutagenic

Ames Test

combine chemical being tested with liver enzymes before testing to make sure processed version of chemical is also not mutagenic, uses strains of Salmonella that are sensitive to mutagens

DNA error repair systems

proofreading, mismatch repair, post replication repair, SOS system, photoreactivation repair, Bas and nucleotide excision repair, DNA double strand break repair

Proofreading

exonuclease activity increases fidelity

Mismatch repair

fixes some mistakes that escapes proofreading

How does repair system know which is correct strand?

Methylation

Post replication repair

requires recombination mediated by RecA protein

SOS system

activated by presence of large number of mismatches and gaps, mutagenic but saves cells from death

Photoreactivation repair

nonhuman, removes thmine dimers caused by UV light, dependent on photoreactivation enzyme

Base and Nucleotide excision repair steps

remove mutation with nuclease, gaps filled with DNA Pol, ligation

Base excision repair

recognition of erroneous base by DNA cutting of the DNA backbone by AP endonuclease , cytosine deamination fixing

Nucleotide excision repair

repairs bulky lesions and involves uvr genes, human alt to photoreactivation repair

DNA double strand break repair types

homologous recombination repair and non homologous end joining

Homologous recombination repair

fixes double strand break by digesting back the 5’ end of broken helix, this lets undamaged 3’ end of sister chromatid to overhang and allow DNA pol to copy sequence onto damaged strand

Non homologous end joining

activated in G1, error prone, 3 proteins bind to ends, trim ends, and ligate them

Transposable elements

mobile genetic element

insertion sequences (IS)

move from one location to another, can cause mutations

bacterial transposons

larger than IS, can introduce multiple drug resistance to bacterial plasmids, move from plasmids to bacteria chromosomes

autonomous

can move independently

nonautonomous

can only move in presence of autonomous element

Retrotransposons

copy paste, RNA intermediate, can be aut or nonaut

Copia

copy and paste example

Human transposable elements

SINES and LINES

SINES

nonautonomous, short, cut and paste

LINES

autonomous, long, cut and paste

Cut and paste

DNA

Copy and paste

RNA intermediate, retrotransposon