BIO260 Final Exam Study Sheet.docx

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31 Mar 2012
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BIO260 Final Exam Study Sheet
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Definitions
Promiscuous functions allow gene to act in a wider field of functions
De Novo creation of new functional gene from previous non functional gene
Pleiotropic mutants affect multiple traits
Global suppressor mutations stabilizes proteins so that they can accumulate new mutations and
functions without denaturing
Auxotrophic mutants cannot create their own essential nutrient
Population Genetics
The majority of difference between humans and chimps is in insertions/deletions rather than
single nucleotide polymorphisms
Assumptions
o Diploid
o Sexual reproduction
o Non-overlapping generations
o Random mating
o Equal allele frequencies in sexes
o No migration, mutation or selection
Genotypic frequencies in parental generation
o Mut-Mut = R(ressive)
o Mut-WT = H(half)
o WT WT = D(Dominant)
o R + H + D = 1
Allele frequency in parental generation
o Wildtype: p
o Mutation: q
o p= (H+2D)/2 = H/2 + D
o q= (2R + H)/2 = R + H/2
Genotypic frequencies in offspring generation
o R’ = q2
o D’ = p2
o H’ = 2pq
o P2 + 2pq + q2 = 1
(p+q)2 = 1
(p + q + … + z)n
At HWE
o p' = p
o q’ = q
o etc
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BIO260 Final Exam Study Sheet
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HWE Sex-linked Gene
XA
Xa
Y
XA
XA XA (p2)
XA Xa(pq)
XA Y(p)
Xa
XA Xa(pq)
Xa Xa(q2)
Xa Y(q)
o ~1 of every 3 000 boys affected would mean q= 1/3 000
HWE with Inbreeding
o Common in plants
o Causes a gradual loss in heterozygotes
o Inbreeding coefficient: F = (Ho H)/Ho
Ho is frequency of heteozygote genotypes in absence of inbreeding
H is frequency of hterozygote genotypes with inbreeding
No inbreeding: F=0, Max inbreeding: F=1
HWE with Mutation
o Say mutations occur at rate
o pt= po(1-)t
HWE with Natural Selection
o Fitness (W) is # survivors/# born
o Selection coefficient (S) is 1 W
o Genotypic contribution to the next generation are the old frequencies multiplied by the
fitness
So the number of genotypic frequencies in the next generations before the
selection
o Actual genotypic frequencies in next generation taken by Genotypic contribution
divided by total genotypic contributions
HWE with Migration
o Migration coefficient (m) is a measure of migration between populations
o pt=pav + (p1 pav)(1 m)t
pt is the allele frequency at time t in one population
pav is the average allele frequency of both populations
In diploid population of size N where all individuals are AA except a single Aa, the probability of
fixation by random drift of neutral allele is 1/2N
o Fixation rare in large populations
Evolutionary Genetics
We can revert loss of functions and deletions
o De Novo creation of functional gene
Usually very difficult and takes a long time
o Evolution of activity from pre-existing gene that had another function
Take deletion, mutagenize and select for gain of functions; repeat
Should not take more than 3 generations for more gain of functions to
occur
New promiscuous functions do not impact older functions
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o Wild type (ancestral) functions robust to mutations that expand range of substrate
specificity
However accumulation of mutations in single gene leads to destabilization of
protein and thus denaturing
Technologies can be used to mutate specific genes
o Genetic Engineering cloning, plasmids
o Error Prone PCR is regular PCR but with a bad polymerase
Neutral mutations under selection can expand range of possible activity
o Family of multiple neutral mutants have a boarder mutational space
Mutations are neutral, favourable, or deleterious
Best proxy for pleiotropic effects on fitness is growth rate under multiple conditions
Intragenic effects
o Past stability threshold mutations decrease stability significantly
o Global suppressors act by shifting stability threshold
Intergenic effects
o Redundancy in case of duplicated genes
Mutation in one is ok since there is a functional copy
o System-wide redundancy- parallel pathways
Even if one pathways is blocked, there is still another
o Buffering
Chaperons (Hsp90) buffer effects of mutations
Different organisms have different mutation rates
o Highest mutations rate in RNA dependant polymerases
o We can try to kill viruses either by reducing their mutation rates so they cannot adapt or
increasing their mutations rates so they have too many mutations
Gene duplication
o Southern blotting can be used to see how many copies of genes there are
o Gene amplification can occur by duplications
o Homologs occur in nature
Paralogs in same species are two copies from a duplication event
Orthologs in different species resulted from a speciation event
o Transposition
A transposase gene surrounded by two flanking sequences
Section inside two flanking sequences are transposed
Retrotranscriptase gene can cause copying of the segment inside the flanking
sequences instead of the whole gene moving
Via a RNA intermediate
In gamete cells this can lead to many issues
Unequal cross over leading to too many or not enough copies of a gene
Chromosome rearrangement
Transposition can cause transposon to be inserted in a coding DNA
sequence
Fates of transpositioned genes
Become non-functional pseudo-gene
Sub-function
o Spatially expressed in certain part of body
o Temporally expressed in certain time of development
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