DNA mutations/variants

are germline mutations meiotic or mitotic

can be both

name and describe 5 mechanisms of DNA mutation and damage

1. oxidation and hydrolysis - ROS oxidizing bases/strand damage, or spontaneous hydrolysis causing depurination or deamination

2. base modification - mis-pair during replication base damage is temporary only before replication, smoke can add bulky add ons (Benzo-a-pyrene which can block or alter replication)

3. ionizing radiation - Gamma and X rays liberate electrons which breaks bonds (ss or ds break), UV is non ionizing but can still be damaging

4. insertional mutagenesis - transposable elements in a new location disrupting coding or regulatory sequences

5. errors in replication and repair - can cause insertion, deletion, base change, and duplication.

3 types of replication and repair

base excision repair - small base lesion from oxidation or deamination

nucleotide excision repair - bulky lesion/add or UV damage

DS break - homologous recombination (perfect again), template driven, or non-homologous end joining (stick back together, prone to insertion/deletion)

transitions vs transversions

transition is purine to purine (more frequent because mechanisms like deamination make them)

transversion is purine to pyrimidine, more possibilities but less likely

the probability of what increase as father gets older

de novo missense mutations (more cell divisions)

like 6 types of variants

single nucleotide variants, indels, microsatelites, copy number variants, inversions, mobile elements

describe single nucleotide variants

transition/transversions, most have little to no effect because of the wobble position but if its in a regulatory position, or an exon, or splice site it can be bad

what are indels

insertions/deletions, can be small, larger ones are structural variants, everyone has about 100,000 indels, caused by problems in replication or repair

what are microsatelites/STR

short tandem repeats of 2-4 nucleotides because of DNA polymerase slipping, used in forensics to determine family lineage, usually found in ncDNA

what is a structural variant

genomic rearrangements usually over 50 bp, include deletion, insertion, duplication, inversion, translocation

what is a copy number variant

SV that changes DNA copy number usually by deletion or duplication

can be inherited or de novo

effect depends on size, location, and gene dosage

how alike are 2 genomes

99.6% the same

what is allelic heterogeneity

same gene but many different pathogenic alleles

define a missense mutation

bp substitution

synonymous is silent

Difference between conservative and non-conservative in a missense mutation

conservative is within the same class (acidic, polar, etc), non-conservative it not within the same class

how does the cell tell when there is a nonsense mutation

nonsense mediated decay - exon junction complex leaves protein markers where the splice sites are, and as the ribosome passes they get flicked off, so if there are some left after translation, there was an issue

what can splicing defects result in

either skip exons or keep introns

what are synonymous mutations and do they affect anything

when the base changes but the amino acid doesn’t, it can affect splicing

how are STRs used in forensics

amplified by PCR, separated by size (size determines number of repeats), one peak is homozygous, 2 peaks is heterozygous, used to determine paternity

when do we use mtDNA in forensics

when genomic DNA is too damaged to find maternity because there are many copies of this

what are SNPs used in forensics

ancestry and phenotyping

what are the problems of using STR in a crime scene to find the criminal

not reliable, consider chain of custody, contamination, relatives, couldve left sample at a different time, could be chimera (2 different genomes in different cells), de novo affecting the STRs (null allele problem)

what is phenotyping and is it reliable

getting what someone looks like, can get skin, hair, eye colour, but face is multifactorial and polygenic, so unreliable