# A bargain The one minute responses asked for solutions to

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```					A bargain

 The one-minute responses asked for solutions to practice problems

 I'll make a bargain:
{   I'll provide solutions
{   You promise not to skip doing the problem in class!
Monday's practice problem

 HIV-1 virus has a mutation rate up to 0.001 per base per generation

 Assume 100 critical bp in the env gene This makes the chance of a
gene-damaging mutation  = 0:001x100 = 0:1

 As before, a reverse mutation has to hit the same base and restore its
original state Chance of hitting the same base is 0.001. Only 1/3 of
hits will restore the right nucleotide, so  = 0:001 £ 1=3 = 0:0003

 What is   pA (frequency of healthy allele) after 1 generation? It started
at 1.0, but (approximately) 10% mutate, so 0.9. Back mutation does
not matter in this generation as there are no mutant copies available
to back-mutate.

 What is the equilibrium         
pA?  + = 0:003
 What would happen to this gene if it were not under selection? It would
deteriorate fast, losing nearly 10% of copies in the rst generation
Mutation rate issues

 Please note the many possible units:
{   Mutations per base versus per locus (gene)
{   Mutations per year versus per generation

 For most evolutionary purposes we focus on germ line mutation

 In some organisms somatic mutation is equally important evolutionarily
Mutation rates in perspective

 Human genome has 6x109 bp.

 Point mutation rate around 1x10 9 per bp per generation

 Human population around 7 billion

 Every point mutation compatible with life exists somewhere

 Every human has several new point mutations
Mutation rates in perspective

 Most of these mutations are not in genes, and have little to no eect

 Many of the remaining ones are silent

 Most of the coding mutations are harmful, but the majority of those are
recessive (a potential problem for your ospring, not for you)

 New benecial mutations are rare, though very important

 Very dierent from Hollywood image of \mutants"
Outline{Dominance and its implications

1.   Some useful terms

2.   What makes one allele dominant over another?

3.   Allelic series

4.   Codominance and incomplete dominance

5.   Dominance is not superiority!

6.   Overdominance

7.   Underdominance
Some useful terms

 Genotype { the alleles present in an organism

 Phenotype { the traits shown by an organism

 Homozygote { two copies of the same allele

 Heterozygote { copies of two dierent alleles
Denitions

 Dominant{phenotype is seen in the heterozygote

 Recessive{phenotype is NOT seen in the heterozygote

 Incompletely dominant{heterozygote is intermediate (pink vs. red/white)

 Co-dominant{heterozygote expresses both alleles fully (AB blood type)
What makes one allele dominant over another?

 Usually recessive:
{   Deletion or null allele
{   Allele that makes non-functional or poorly functional product
{   Allele that underproduces product
{   Control mutation that disables an ON switch

 Examples:
{   dysfunctional CF alleles
{   temperature-sensitive color of Siamese cats
{   O allele of ABO system
Why are nulls usually recessive?

 Most proteins produced in generous amounts

 Half of normal level generally enough

 This may buer organism against changes in internal or external
environment
General rule for LOF mutations…
Half the amount of wild type gene product is sufficient to
give a wild type phenotype

Example : Tyrosinase                              wild type allele = C
mutant = c

[enzyme
threshold           wild type phenotype
activity]
albino phenotype
Genotype: CC          Cc        cc

 1 wild type copy → enzyme activity above threshold needed for normal
pigmentation, so carriers unaffected (mutant allele → recessive)
What makes one allele dominant over another?

 Usually dominant or incompletely dominant:
{   Allele that overproduces product
{   Control mutation that disables an OFF switch

 Examples:
{   Achondroplastic dwarsm
What makes one allele dominant over another?

 Often dominant or co-dominant:
{   Allele that produces a novel product
{   Control mutation that introduces a new switch

 Examples:
{   Sickle-cell trait (disease is recessive but heterozygote has denite
phenotype)
{   most HLA alleles
{   A and B alleles of ABO
Lac operon
Lac operon

 A null mutation in the inhibitor is recessive
{   If even one copy makes usable inhibitor, LacZ is inhibited

 An inhibitor which no longer recognizes lactose is dominant
{   The super-inhibitor will eventually turn LacZ o even if there is also
regular inhibitor present
Lac operon

 A mutation which destroys the inhibitor binding site is dominant
{   The uninhibited copy will produce LacZ even if the other is inhibited

 A mutation which damages LacZ is recessive
{   The wild-type copy will continue to function
Different alleles with different outcomes… an example

Burmese—cbcb or cbcs or cbc

C?

C gene codes for
tyrosinase… 1st                                                  cc
step in melanin
synthesis
Siamese
cscs or csc
What are these other alleles?
How to explain the unusual phenotypes?                  burnerkitty.com
Dierent ways to the same phenotype

 Alleles, not phenotypes, have dominance

 White color in cats can come from a dominant mutation which kills
melanin-producing cells

 White can also come from a recessive mutation which prevents melanin
synthesis

 One gene can have multiple eects:
{   Dominant-mutation white cats generally deaf
{   Recessive-mutation white cats generally normal
{   Eye color also aected
A single mutation aecting coat and eye color

With thanks to I   Can Has Cheezburger
Codominance and incomplete dominance

 Codominant: shows the full phenotype of both alleles.

 Both alleles produce functional, but dierent, products

 Examples:
{   A and B in the ABO blood group system
{   HLA-DR3 and HLA-DR4

 Incompletely dominant: shows intermediate phenotype.

 Often a dosage eect

 Examples:
{   Pink color in heterozygous
owers
{   Piebald color in cats
Discussion question

 Sickle cell homozygotes have severe disease due to clumping of
hemoglobin which damages (\sickles") red blood cells

 Heterozygotes show some clumping but not severe disease

 Is this codominance or incomplete dominance?
Dominance is not superiority!

It is easy to think of dominant alleles as superior{after all, 'dominant' people
and animals tend to boss others around. However, dominance simply says
which phenotype the heterozygote has. It is not, in itself, an advantage or
Examples:

 Huntington's disease{dominant is worse than recessive

 Cystic brosis{dominant is better than recessive

 Tongue rolling{probably neutral

Dominant alleles can be common or rare.
In the absence of selection, dominant alleles have no particular tendency to
increase over recessive ones.
Overdominance

Watch out! This term sounds as though it's the same kind of thing as
\dominance", but it refers to an advantage or disadvantage, not just to
which allele is expressed.

 Overdominant alleles are alleles with codominance or incomplete
dominance in which the heterozygote is better than either homozygote.

 Sometimes called \hybrid vigor"

 Examples:
{   Many commercially sold grains and vegetables
{   Sickle-cell anemia
Underdominance

Again, watch out! Underdominance is not the same kind of thing as
dominance.

 Underdominant alleles are alleles with codominance or incomplete
dominance in which the heterozygote is worse than either homozygote.

 Examples:
{   Heterozygote of HLA-DR3 and HLA-DR4 has higher diabetes risk than
either homozygote
{   Mimicry in butter
ies
Underdominance

In the African butter
y Pseudacraea eurytus the orange and blue
homozygotes each resemble a local inedible species, but the heterozygote
resembles nothing in particular and is vulnerable to predators.
One-minute responses

 Tear o a half-sheet of paper

 Write one line about the lecture:
{   Was anything unclear?
{   Did anything work particularly well?
{   What could be better?

 Leave at the back on your way out

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