2581 test 2

mutatus is latin for

change

genome sequence variations are

changes in sequence, mutations (small proportion = change in phenotype)

classes of genome sequence variations (four)

substitution, indels (insertions/deletions), inversion, translocation

substitutions effect

SNPs, new allele

two classes of substitutions

transitions: purine fora purine or pyrimidine for a pyrimidine

transversions: purine for a pyrimidine or pyrimidine for a purine

purine

A and G

Pyrimidine

T and C

indels

insertion or deletion of one or many bases (Kb)

large insertions have

breakpoints on either point of insertion/deletion

inversions

inversion of two or more bases, the DNA is flipped 180 degrees (Mb)

large inversions have

break points

translocation

movement of dna between different chromosomes

translocations have

breakpoints where translocations occur

mutation rate

mutations over some measure of time

two mutation rates

gene mutation rate and mutation rate (genome)

gene mutation rate

associated with mutation in a gene, WT allele changes resulting in a change in phenotype

gene mutation rate for bacteria

2-8 x 10^-9 / division

gene mutation rate for drosophila

5-50 x 10^-6 / gamete

gene mutation rate for humans

1-30 x 10^-6 / gamete

variation in rate is due to

variation in the size of genes looked at since some provide a larger target than others

dna sequence mutation rate for bacteria

1-10 x 10^-10 / bp division

dna sequence mutation rate for eukaryotes

1x10^-8 / bp gamete

dna sequence mutation rate for somatic

3x10^-9 / bp mitosis

dna sequence mutation rate for covid

8x10^-4 / bp year (25/year)

consequences of mutation rate

evolutionary change, animal cloning

on average you have how many mutant alleles in you genome not found in parent’s genome

60 novel mutant alleles

change

generation of variation

what is a practical consequence of mutation rate for cloning mammals?

the fibroblast will accumulate mutations; cloned animal is different from the donor

observed ratio of transitions to transversions

2 transitions for every transversion bc of bias

spontaneous replication errors

tautomeric shifts, wobble, strand slippage, unequal crossing over

rare forms of thymine and guanine

proton moves to oxygen

rare forms of cytosine and adenine

proton moves to nitrogen

consequence of tautomeric shifts

cytosine bonds with adenine, thymine bonds with guanine, replication errors due to incorporation of wrong nucleotide

wobble

alternative base pairing chemistry

T-G;C-A

strand slippage

associated with indels, in strands with low sequence complexity, a loop is formed which causes either an insertion or deletion

unequal crossing over

during recombination in meiosis, sequence of low complexity does not align properly causing one strand to have deletion and one insertion

spontaneous chemical changes (two)

deamination and depurination

deamination

instability of amine on cytosine creates uracil which pairs with adenine or methylation of cytosine produces thymine; C to T transition

depurination

rate at which purines leave dna so there is no base, during replication the abasic site is replaced with a

mutagens

base analogs, alkylating agents, deaminating chemicals, hydroxylamine, oxidative radicals, intercalating agents, uv light

base analogs

bromouracil looks like thymine (methyl group substituted with bromine), ionized form of bromouracil recognized as cytosine

alkylating agents

ethyl-methylsulfonate ethylates G and T, base pairs with cytosine and thymine

deaminating chemicals

deamination occurs spontaneously at a constant rate, nitrous acid, higher number of uracil (from cytosine)

hydroxylamine

hydroxyl group on nitrogen of cytosine, pairs with adenine

oxidative radicals

transversions

intercalating agents

flat bending rings that are hydrophobic and slide easily into hydrophobic spaces between stacked base pairs resulting in replication error, associated with insertions

uv light

induces thymine dimers, two thymines have a covalent bond, introduces mutations since replication has trouble repairing this

dna repairs

mismatch repair, direct repair, base excision repair, nucleotide excision repair

how do bacteria recognise newly synthesized vs original strands

methylate dna at specific positions, new strand has no methyl groups

bacteria mismatch repair

go to nearest methyl group, nick strand remove dna and reinstate original sequence

atomic bomb

high rates of radiation increased the somatic mutation rate, higher rate of cancer, germline mutation rate close to spontaneous rate (3.4 x 10^-6)

who discovered transposable elements

barbara mcclintock

alt names for transposons

selfish dna, jumping genes, transposable element

consequence of transposition

increase in genome sizes, disruption of genes, altered expression, genome rearrangement

how much of the genome is transposable elements

45%

consequence of transposition: increase in genome sizes

selfish nature of transposons has co-evolved with mechanisms that suppress transposition

mechanism that suppresses transposition in drosophila

piwi RNAs

consequence of transposition: disruption of genes

transposon moves into gene disrupting this to disrupt the process the gene participates in

consequence of transposition: altered expression

introduced to regulatory sequences to alter gene regulation, can decrease expression in genes

consequence of transposition: genome rearrangement

because of transposon length they can pair with one another if homologous, can undergo recombination

consequence of transposition: genome rearrangement direct orientation on the same chromosome

deletion of product, misaligned - deletions and duplications

consequence of transposition: genome rearrangement inverted orientation on the same chromosome

inversion

consequence of transposition: genome rearrangement direct orientation on different chromosomes

translocations

mechanisms of transposition

duplication of target sequence, type 2 transposons (replicative or cut and paste), type 1 retrotransposition

duplication of target sequence

when inserted into a new site, transposase induces a ds staggered break, single stranded regions are filled with flanking direct repeats

flanking direct repeats

direct repeat of 5 bases

signature of presence of transposable elements

4-8 bp flanking repeat sequence left behind

type 2 transposons

transpose with dna intermediates, have short inverted repeats at the end (terminal inverted repeats)

type 2 transposons: replicative

transposon replicated into its new site, original is maintained

type 2 transposons: cut and paste

transposon is cut out and reinserted at a different point

type 1 retrotransposition

transposes using an rna intermediate, have long terminal direct repeats, eukaryote specific

type 1 retrotransposition mechanism

transposon transcribed into mRNA, mRNA copied into DNA using reverse transcriptase, DNA copy inserted into new site in genome

how do we know type 1 retrotransposition mechanism

LTR look similar to insertion of retrovirus into genome

retrotransposition

rna template to make dna copy, ds copy inserted into genome of host using transposon like mechanism, direct flanking repeats

retrotransposition experiment

transposon carries intron, if it uses a dna intermediate, intron would remain, if mRNA it is spliced out

SNPs are

genetic markers (alleles)

linkage disequilibrium

SNPs are close to one another so the chance of recombination event separates them is low

how to find if mutational change is cause of phenotypic change

allele is concentrated in only one group and not in the unaffected group

if haplotypes show up with affected individuals…

SNPs caused this or there is a change nearby associated due to linkage disequilibrium

manhattan plot axis

y axis shows probability the association is not random

x axis shows the chromosomal position of SNPs

more SNPs

more distantly related

less SNPs

more closely related

how many horses established thoroughbreds

three

what makes throroughbreds fast?

fast horses have a transposon in the promoter region that lowers levels of myostatin and more muscle, slower horses have high levels of myostatin

myostatin

protein that suppresses muscle development

traditional breeding

dilution, only half of genes going to progeny

GWAS

looks for major genes with major effects for direct identification of potential winners

how can one determine phylogeny

looking at SNPs and grouping them

What is used to characterise individual phenotypes

genome wide association studies

human evolution

homo erectus, homo heidelbergensis, neanderthal and denisovans and homo sapiens

homo erectus and homo heidelbergenesis is from

africa

neanderthals were from

europe

denisovans were from

asia

why do i need to classify alleles

system of organization, organization with respect to the effect of dna sequence changes, simplification

allele nomenclature

gene name and superscript

what is a functional allele

a gene that will be able to express that active gene product

allele classification based on transmission (inheritance)

complete dominance (haplosufficeint), recessive, incomplete dominance (partial dominance, haploinsufficeint)

complete dominance; haplosufficeint

homozygous or heterozygous for phenotype (big letter), when heterozygous one allele is sufficient

recessive

homozygous for small letter

what do i look at to see dominance

heterozygote, which phenotype is seen