BSCI 222 DNA Mutation and Repair

spontaneous mutation

a random internal change in the DNA replication or recombination

abasic site

location in DNA where a nitrogenous base has been removed or lost leaving an empty spot in the sugar phosphate backbone

misincorportation

type of spontaneous mutation where an incorrect nucleotide is incorporated into the DNA during replication, results in a mismatch between the newly synthesized and template strand

slippage

type of spontaneous mutation where, During DNA replication, replication pauses & DNA polymerase disengages, 2 strands fall apart & comeback together, replication resumes.

result of slippage

insertions or deletions in run of same base

or in short tandem repeats

INDEL mutation

a mutation in which one or more nucleotide pairs is added or deleted

in frame mutation

insertion or deletions in multiples of three, but the reading frame remains unchanged

result of in frame mutation

same overall function with longer/shorter proteins

deamination of cytosine

type of spontaneous mutation which removes amine group from cytosine which converts it to uracil

types of spontaneous mutations

misincorporation, slippage, depurination, deamination

deamination of methyl cytosine (5-mC)

type of spontaneous mutation when a methyl group on cytosine is removed leading to conversion of 5-methyl cytosine into thymine

depurination

type of spontaneous mutation where a DNA molecule loses its purine base (hydrolysis of purine from sugar)

induced mutation

a mutation caused by a mutagen from the environment

types of induced mutations

chemical mutagens and radiation

mutagen

any substance or condition that can increase the rate of base change

expanding trinucleotide repeats

specific sequences of 3 nucleotides that are repeated multiple times in a gene

how do expanding trinucleotide repeats/homopolymeric repeats happen

in DNA replication DNA polymerase can misalign during replication, happens when newly synthesized DNA strand detaches from template and re-attaches incorrectly

what happens when trinucleotide repeats expand

it causes an increase in the number of repeats beyond normal range causing genetic disorders

neutral effect

changes amino acid but does not affect activity, might be conservative substitution, might be permissive site in protein

loss-of-function effect

protein is not active or is dead

gain-of-function effect

protein does something new

lethal effect

needed for growth and development

conditional effect

shows phenotype under certain conditons

example of conditional effect

temperature

nonsense mutation

changes a normal codon into a stop codon

missense mutation

A base-pair substitution that results in a codon that codes for a different amino acid.

silent mutation

A mutation that changes a single nucleotide, but does not change the amino acid created.

transversions

a purine and a pyrimidine are interchanged

transitions

purine to purine or pyrimidine to pyrimidine

nonsynonymous mutation

A mutation in a gene that changes the amino acid sequence of the protein that gene encodes.

synonymous mutation

A mutation that does not result in a different amino acid

substitution

A mutation in which a nucleotide or a codon in DNA is replaced with a different nucleotide

types of substitutions

transitions and transversions

insertion

A mutation involving the addition of one or more nucleotide pairs to a gene.

deletion

A change to a chromosome in which a fragment of the chromosome is removed.

somatic mutation

local small effect

germline mutation

entire organism will be affected

heritability depends on

which cell is mutated (somatic or germ line)

mutation

a random error in gene replication that leads to a change

thymine

The base that pairs with Adenine in DNA

base analogs

molecules that resemble the normal bases of DNA, they are structurally similar

what can happen with base analogs

they can be mistakenly incorporated into DNA during replication leading to incorrect base pairing and mutations

UV light effect

induces pyrimidine dimers

pyrimidine dimers

damage in DNA from 2 adjacent pyrimidine bases that covalently bond because of UV light

effect of pyrimidine dimers

distorts DNA structure

thymine dimer

specific pyrimidine dimer that occurs when 2 adjacent thymine bases form a covalent bond because of UV

ionizing radiation effect

leads to strand breakage and base oxidation

example of ionizing radiation

x-rays

transposable elements

DNA sequences that can change their position within the genome

transposable elements nickname

jumping genes

DNA transposons

use cut and paste mechanism where transposable elements are excised from one site and integrated into another

transposase

enzyme that facilitates movement of DNA transposons

purpose of transposable elements

promotes genetic diversity

intercalators

molecules that can insert themselves between base pairs of DNA

intercalation

process that use intercalators which causes DNA helix to unwind and lengthen

effect of intercalation

distorts structure of DNA

common intercolators

ethidium bromide, proflavin, actinomycin D

mismatch repair

repair after DNA replication to catch substitution errors

how mismatch repair works

-mismatch distorts DNA

-recognized by protein/enzymes because old strand has methyl group

-recognize mismatch + nick on newly synthesized strand

-removes newly synthesized strand (containing mismatch)

-DNA repair polymerase fills gap

-DNA ligase seals nick in backbone

NER vs BER

NER is with multiple nucleotides, BER is with just one

when does mismatch repair happen

during S phase of DNA replication

Base Exicision repair

excises purine or pyrimidine first then replaces entire nucleotide

what does base excision repair take out

only the altered base

how does base excision repair work

specific glycosylase removes bad base, AP exonuclease cuts out sugar phosphate, polymerase replaces nucleotide, ligase reseals phosphodiester backbone

which pol is used in eukaryotic BER

pol beta

which pol is used in prokaryotic BER

pol I

AP exonuclease

enzyme in BER which recognizes the abasic site and cleaves the phosphodiester bond creating a nick in the DNA

types of issues that base excision repairs

uracil from deamination, thymine, 8-oxo-G, modified purines

how is uracil from T to U deamination fixed

U is taken out in G-U pair and replaced with C

how is thymine fixed

thymine is taken out in T-G pair and C is put in

how is 8-oxo-G fixed

the 8-oxo-G modification is recognized and cleaved out

8-oxo-G

a product of oxidative damage to DNA in the guanine base where an oxygen atom is added to the 8th position on the guanine purine ring

how are modified purines repaired

the alkylated A or G or hypoxanthine are taken out

hypoxanthine

deamination of adenine

nucleotide excision repair

removes larger defects involving entire stretches of nucleotides at one time

example of something removed by NER

thymine dimers

when does NER occur

anytime, not only right after S-phase

how does NER work

bulky lesion is identified and marked, enzyme binds to marked area and opens DNA to form a bubble, damaged DNA is excised, new DNA is made with DNA polymerization and ligation

recombination repair

method used to fix double stranded breaks in DNA

how does recombination repair work

DNA breaks are recognized with proteins, ends of broken DNA are trimmed, ssDNA overhands and invaded sister chromatid where they pair, DNA synthesis where sister chromatid is template strand, new strands are untangled and ligated

non-homologous recombination

fixes DSBs without a homologous DNA template because 2 broken DNA ends are joined directly

how does non-homologous recombination work

broken ends are trimmed and rejoined with help of proteins

is non-homologous or homologous recombination more accurate

homologous because there is a template

ssDNA

single stranded DNA, overhangs of trimmed DNA

DSB

double stranded breaks, very severe breaks in both strands of DNA helix

translation synthesis

DNA mechanism where cells can replicate DNA even when there are lesions in template strand

how does translation synthesis work

stalls DNA pol and switches to TLS polymerases

photo reactivation repair

direct repair of thymine dimers

what organisms is photo reactivation repair in

bacteria, plants and fungi

what organisms is SOS repair in

primarily bacteria

how does photo reactivation repair work

reverses UV DNA damage by relying on visible light to active photolyase enzyme

photolyase

enzyme activated by sunlight that breaks covalent bonds between thymine bases in dimer, fixing the mutation

SOS repair

last resort DNA repair mechanism used by bacteria to address severe DNA damage that stops replication, allows replication even if there are many complex lesions

how does SOS repair work

recognizes lesions and uses proteins to continue replication

frameshift mutation

mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide

de novo mutation

A new mutation that was not inherited from either parent

direct repair

a repair enzyme recognizes an incorrect structure in the DNA and directly converts it back

mutation frequency

the number of mutant genes divided by the total number of genes within the population

mutation rate

the probability that a gene will mutate when a cell divides

typical mutation rate in organisms

more frequent in prokaryotes