What is a somatic mutation?
- normal body tissue
- may have vast effect on individual
- not passed to offspring
What is a germinal mutation?
- little or not effect on individual
- passed on to all cells of zygote that's formed
Are all mutations harmful? Are they spontaneous or non-spontaneous?
- nature of mutation
- environment Spontaneously occur randomly in genome
What are point mutations? What are the types of point mutations?
Point mutations are a change in one base of a codon
Silent - Change in codon (3 nucleotides) that results in same amino acid -
Missense - Change codon from 1 amino acid to another amino acid
- can cause loss of function
Nonsense - Change codon in AA to a stop codon
- loss of function
What is a frameshift mutation?
Change in reading frame
- changes which bases are read as part of which codons
- changes every codon downstream
- loss of function
If you have a mutation like a missense or nonsense that codes for a different protein would this be dominant or recessive?
Recessive b/c you're coding for something that doesn't work
- as long as you have a copy of the allele that does work then you're fine
- if both copies are messed up then you're fucked
What are the causes of spontaneous mutations?
Deamination of bases
Depurination of bases
All of these lead to errors in DNA replication/repair
DNA has the capability to detect errors but this doesn't always fix the problem. Why?
The enzyme can detect that there is no hydrogen bonding between the Bases so there's a 50% chance it will bring in the correct Base and a 50% chance it'll bring in the wrong base
What is the most common cause of spontaneous mutations?
Tautomeric Shift that can lead to point mutations
- they occur so fast that most of the time nothing happens
- if it occurs during replication than the proofreading enzyme thinks nothing is wrong because there are H-bonds present
How does a tautomeric shift occur?
All 4 bases may exist in 1 of 2 alternate forms
- it's normal ATCG form
- spontaneously switch At Tt Ct Gt which allows it to bind different bases
At binds C
Tt binds G
Ct binds A
Gt binds T
What is deaminination of bases?
Spontaneous mutation that causes point mutation
The bases lose an amino group changing the structure resulting in binding to a different base
- similar to tautomeric shift
WHat is Deuprination of bases?
Purine bases may be sponstaneously released from sugar-phosphate backbone of DNA and replaced with -OH
May be corrected but 3 of 4 bases it's fixed with will be wrong
The nucleotide may also be deleted but causes framshift
How does UV light damage cause mutations?
UV radiation causes pyrimidine problems
- bonds form between 2 adjacent thymines on one strand leads to deletion of 2 bases
- cytosines converted to cytosine hydrate leading to mispairing of bases
Lead to FRAMESHIFTS
What is the paradox of genetic variability?
Genetic variability is necessary in order for populations to adapt to changing environments
This is called evolution. Evolution is a populational phenomenon
- ie. individuals can't change their genes but populations can
What is polymorphism? What is a monomorphic loci?
- presence of more than one allele at a locus
- everyone homozygous for same allele
- no genetic variation at this loci = population is "fixed"
- eg. irish potato famine
What is a gene pool?
all the alleles present in a population
What is a population?
community of individuals of the same type
- mendellian populations have the opportunity to interbreed
How can you determine if 2 individuals belong to same species?
If 2 individuals can breed and produce a viable and fertile offspring
What is allele frequency? How is it measured?
When looking at a gene locus you measure the % (frequency) of each allele in a population
- This is used to measure genetic change in a population
Freq (A) = # A alleles / Total # of alleles
How can you tell how many alleles you're dealing with when analyzing a locus?
It depends on the size of the population you're looking at.
If there are 60 individuals in the population then you have 120 alleles
- Diploid individuals = 2 alleles per individual for a given locus
Calculate the Big T allele frequency (p) for the following population for Beta Thalasseaemia (form of anemia):
- TT (normal) = 400
- Tt (slight anemia) = 75
- tt (anemic) = 25
What is q?
N = 500 ppl = total number of alleles = 1000
freq (T) = p = [2(400) + 1(75)] / [2(400+75+25)] = 875/1000 = 0.875
If p = 0.875 the q = 0.125
What is hardy-weinberg equilibrium? What is an ideal population?
Way of relating allele frequency and genotype frequency
- allows you to see effects of outside forces on the frequencies of a gene
Ideaal population is at equilibrium
- Population is genetically stable (staying the same)
- 1 of 5 forces that act on equilibrium not at play
- effect of mutation on equilibrium miniscule (not at play)
What are the five forces which may change allele frequency?
- small population size
- non-random mating
if none of these forces are acting on a population then the population is stable (not changing)
Does equilibrium mean you have equal numbers of each allele (p = q)?
How do you relate genotype frequency and allele frequency using hardy weinberg? What is the hardy weinberg equilibrium equation?
- Since gametes are haploid the allele frequencies are equal to the frequencies of gametes carrying each allele
- if p = 1 then all population is AA
- if p = 0.1 then q = 0.9 and most of population is BB
- relationship between allele freq and genotype in population
- no other possible genotypes with these two alleles (A & B) so must = 1
How do you figure out if your population is at equilibrium?
Equilibrium means there is no change in allele frequencies
You have to figure out if they're at hardy-weinberg equilibrium (p2+2pq+q2=1)
- step 1 is figuring out allele frequencies (p & q)
- step 2 is plugging in p & q into p2+2pq+q2=1
- step 3 is figuring out expected #'s
- multiply the frequencies by the total number of individuals in population (not alleles)
- step 4 is doing a chi square
- d.f. = total - 1 - 1
- if p < 0.05 then obs doesn't match exp and there is statistically significant difference betwen obs and exp so no equilibrium
- if p>0.05 then it is at equilibrium
What is migration?
- movement of individuals between populations
- 2-way migration
Makes populations more similar
- eventually don't have 2 separate populations
What is two way migration?
Individual can move from one to another and back again
- each population has it's own p and frequency
If there is migration from 1 into 2 as well as from 2 into 1, the populations will eventually become one population.
- more migration that occurs the more the 2 populations become alike (convergence) until they have they reach equilibrium (same p and q)
When the two populations reach equilibrium then the q value (or p) will be the average of the starting q values for both populations
q = (q1 + q2) / 2
You have three populations where migration is occuring.
- p = 0.9
- q = 0.1
- p = 0.3
- q = 0.7
- p = 0.6
- q = 0.4
What will the p and q values be when equilibrium is reached?
p = (0.9 + 0.3 + 0.6) / 3 = 0.6
q = (0.1 + 0.7 + 0.4) / 3 = 0.4
What is random genetic drift?
Due to small population size
- larger population = less likely drift is occuring
- if population < 500 then drift is occuring for sure
If small population then simple mating choice can effect the allele frequencies (p&q)
- Changes are totally random
If a population is small enough, the effects of drift may swamp the other four forces, even selection
You have a small population of 4 individuals with following genotypes:
AA AB AB BB
What are the allele freqencies?
Suppose AA mates with BB; AB with AB, what are the possible offspring?
What force is this?
If both pairs produce the following offspring, what is the new p value?
- AB AB AA AB
If both pairs produce the following offspring, what is the new p value?
AB AB AB BB
p & q both = 0.5
AA x BB = AB
AB x AB = AA, AB, BB
This is genetic drift because the mating choices of the 1st generation change the p & q values of 2nd generation
If both pairs produce AB AB AA AB
- p1 = 5/8 = 0.625
If both pairs produce AB AB AB BB
- p1 = 3/8 = 0.375
What is the founder principle?
The founder principle is a special case of genetic drift
- Founding of a new population by a small number of founder individuals
The allele frequencies (p & q) for all genes in new population begin w/ whatever the founder(s) were carrying
What is non-random mating?
Not all matings are equally likely to occur
Positive Assortative mating
- individuals are more likely to mate w/ others of same genotype
- inbreeding is a type of PAM
If PAM occurs w/ heterozygotes (AB) in a small population you will see:
- net increase of homozygotes
- net decrease of heterozygotes
- p & q allele frequencies will increase and 2pq will decrease
Too few heterozygotes and too many homozygotes is indicative of what?
Inbreeding and positive assortive mating
What is mutation?
Only source of new types of alleles
- Changes in allele frequencies due to mutation alone are extremely slow
- all populations undergoing mutation but change so small/slow it doesn't really affect hardy-weinberg equilibrium
What is back mutation?
if an allele can mutate then it can mutate back to original
- A→B and B→A
- FWD mutation rate is µ
- BACK mutation rate is ν
µ typically larger than v b/c B can mutate to something else instead of back to A
What is the change in p & q due to mutation for A→B and B→A?
Δq = µp - νq
µp is the gain in B (rate of fwd mutation)
νq is the loss of B (rate of back mutation)
What is the q1 after one round of mutation if :
µ = 10-5
ν = 10-6
p0 = 0.9
q0 = 0.1
What is p1 after one round of mutation?
Remember this is forward mutation
Δq = µp - νq
Δq = (10-5)(0.9) - (10-6)(0.1) = 0.0000089
q1 = q0 + Δq = 0.1 + 0.0000089 = 0.1000089
p1 = p0 - q1 = 0.9 - 0.1000089 = 0.7999911
What is selection?
- individuals best able to survive and reproduce will do so more than others
if differences in ability are genetic
- genes conferring the higher ability will increase in frequency
What is fitness?
Selection is based on differences in fitness
- A measure of your ability to produce offspring
How do you measure fitness?
- average number of offspring left by a genotype
- AA = 10, AB = 8, BB = 4
A allele is conferring some kind of advantage (more fit)
Relative Fitness (w)
- calculates fitness in relation to the most fit genotype
- most fit genotype is set to "1" and the rest are measure against that
- Darwininan Fitness: AA = 10, AB = 8, BB = 4
- Relative Fitness: AA = 10/10 = 1, AB = 8/10 = 0.8, BB = 4/10 = 0.4
Selection Coefficient (s)
- the amount of selection against a genotype
- s = 1 - w
- s (AA) = 1-1 =0, s (AB) = 1- 0.8 = 0.2, s (BB) = 1 - 0.4 = 0.6
How does a difference in fitness impact the next generation?
With a difference in fitness, each genotype no longer has an equal likelihood of contributing to the gene pool of the next generation.
The contribution to the next generation is a result of frequency x fitness.
If w: AA = 1, AB = 0.8, BB = 0.4 then every generation should see an increase in AA and a decrease in BB
What is mean population fitness?
How fit a population is as a whole
W = p2 (wAA) + 2pq (wAB) + q2 (wBB)
- As selection proceeds the mean pop fitness should increase
pn2 (wAA) + pq (wAB)
pn+1 = --------------------------------------------
p2 (wAA) + 2pq (wAB) + q2 (wBB)
You calculated mean population fitness when going from p0 generation to p1.
p0 = 0.5 and p1 = 0.58.
q0 = 0.5 and q0 = 0.42
What does this mean? What kind of force is this?
The % of p alleles (frequency) jumped from 50% to 58% and the % of q alleles dropped from 50% to 42%
the p allele is more fit and selection is occuring
- the more fit allele is increasing and the less fit allele is decreasing
- the overall mean population fitness is increasing too
What is fishers fundamental theorem?
The rate of change of allele frequencies from one generation to the next is directly proportional to the amount of genetic variability.
- when p=q then you can see the biggest change occur due to selection
- but as the frequency of less fit allele decreases it gets much harder for
When p & q are close to eachother then you can see big change
as difference between 2 gets bigger it gets harder to make substantial change
- Why its really hard to wipe out a harmful recessive allele
How does selection impact a recessive lethal allele? How does selection affect a dominant lethal allele?
Recessive lethal allele
- once it's frequency is brought down to low % then it's very hard to get rid of
Dominant lethal allele
- it is gone after one generation
What is heterosis?
BOTH alleles selected for
Heterozygote more fit than either homozygote
Keeps “harmful” allele at a fairly high frequency
eg. sickle cell anemia
SS = no anemia but susceptible to malaria
Ss = no anemia and not susceptible to malaria
ss = anemia but not susceptible to malaria
What equation can you use to figure out p0 (p at equilibrium) when faced with a heterosis situation?
p = -----------
s1 + s2
s is the selection coefficient