Mutation I Flashcards
describe a substitution gene mutation
one nucleotide replaces another
potential causes of substitutions
1) DNA polymerase errors not fixed by proofreading
2) spontaneous deamination of cytosine to uracil
3) alkylating chemicals change the structure of the N-containing bases
4) UV light can create substitutions indirectly via DNA repair mechanisms
role of alkylating chemicals in genetic model systems?
alkylating chemicals (ENU or EMS) can introduce substitutions in genetic model systems for genetic screens (in fruit flies in the lab)
mechanism by which UV light can create substitutions
1) UVB light creates pyrimidine dimers
2) normal DNA pol cannot replicate through them
3) usually get “undone” by photolyases
4) nucleotide excision repair removed the region around dimers are removed and replaced
5) when they are left there “translesion synthesis” with special DNA pol can occur
6) this is error prone and can cause substitutions
**needs a lot of pyrimidine dimers to get these errors, but we are always getting them
consequences of substitutions depend on..
part of genome/DNA that is substituted
substitutions in non-protein coding sequences (most of the genome) result in?
few consequences (no changes)
substitutions are mostly an issue for ___
protein-coding exons
how might substitutions affect splice donor/acceptor sites
substitutions in splice donor/acceptor sites interferes with splicing and can result in introns being left behind creating a shortened non-functional protein
consequence of substitution in the polyadenylation signal
may prevent poly-A tail formation (mRNA gets degraded quickly)
describe insertions/deletions
one or more nucleotides are added or lost from a DNA sequence (most are small: 1-10 nucleotides, but can also be 1000s of bps or entire arms of chromosomes)
causes of insertions/deletions (indels)
1) replication slippage can add/remove repeats
2) DNA intercalating chemicals stuff themselves into the double helix, disrupting DNA structure during replication, leading to insertions
3) ionizing radiation creates indels via DNA repair mechanisms
example of DNA intercalating chemicals
Ethidium bromide (DNA dye), benzapyrene (BaP, major mutagen of tobacco smoke)
mechanism of how ionizing radiation causes indels
1) causes double stranded breaks in DNA molecules
2) breaks me be uneven (one strand is a bit longer than the other)
3) to be repaired, breaks must be “blunt” (both strands the same length)
4) call may add/remove nucleotides at break point to make it even
5) non-homologous end-joining of free ends can lead to insertions/deletions
consequence for small indels in non-protein coding sequences (most of the genome)
few consequences
consequences of indels in protein-coding exons
can disrupt open reading frames (ORFs) causing frameshift mutations
how many possible reading frames for a single DNA sequence?
three on each strand, six total (-3, -2, -1, +1, +2, +3)
what does a sequence of protein-coding DNA, what is special about the reading frames?
one of the six frames will have an open reading frame (ORF) the encodes a long, functional protein
a random DNA sequence will have stop codons every ____ base pairs on average
64
do open reading frames have the same probability of having a stop codon as a random DNA sequence?
no, ORFs have long stretches (hundreds of base pairs) with no stop codons
do all ORFs start with START codons?
no, because eukaryotic genes have introns so genomic ORFs start with AUG only in the first protein-coding exon of the DNA sequence
do ORFS always end with a STOP codon?
yes, always bound by a stop codons
describe the ORF of a mature mRNA
always begins with AUG and ends with a STOP codon
how do single b.p. indels affect reading frames?
shift all reading frames, including the one with the ORF, leading to STOP codons every 64 bp (on average) in ALL reading frames
consequence of single b.p. indels
typically cause shortened proteins
consequence of micro satellite indels in CREs
may change gene expression levels
