Final Exam

Question 1

What is a somatic mutation?

Answer 1

Mutation in:

• normal body tissue
• may have vast effect on individual
• not passed to offspring

Question 2

What is a germinal mutation?

Answer 2

Mutation in:

• gametes
• little or not effect on individual
• passed on to all cells of zygote that’s formed

Question 3

Are all mutations harmful? Are they spontaneous or non-spontaneous?

Answer 3

Not necessarily

Dependent on:

• nature of mutation
• environment Spontaneously occur randomly in genome

Question 4

What are point mutations? What are the types of point mutations?

Answer 4

Point mutations are a change in one base of a codon

Silent - Change in codon (3 nucleotides) that results in same amino acid -

no change

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

Question 5

What is a frameshift mutation?

Answer 5

Change in reading frame

• changes which bases are read as part of which codons
• changes every codon downstream
• loss of function

Question 6

If you have a mutation like a missense or nonsense that codes for a different protein would this be dominant or recessive?

Answer 6

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

Question 7

What are the causes of spontaneous mutations?

Answer 7

Tautomeric Shifts

Deamination of bases

Depurination of bases

UV radiation

All of these lead to errors in DNA replication/repair

Question 8

DNA has the capability to detect errors but this doesn’t always fix the problem. Why?

Answer 8

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

Question 9

What is the most common cause of spontaneous mutations?

Answer 9

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

Question 10

How does a tautomeric shift occur?

Answer 10

All 4 bases may exist in 1 of 2 alternate forms

• it’s normal ATCG form
• spontaneously switch A^t T^t C^t G^t which allows it to bind different bases

A^t binds C

T^t binds G

C^t binds A

G^t binds T

Question 11

What is deaminination of bases?

Answer 11

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

Question 12

WHat is Deuprination of bases?

Answer 12

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

Question 13

How does UV light damage cause mutations?

Answer 13

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

Question 14

What is the paradox of genetic variability?

Answer 14

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

Question 15

What is polymorphism? What is a monomorphic loci?

Answer 15

Polymorphism

• presence of more than one allele at a locus

Monomorphic loci

• everyone homozygous for same allele
• no genetic variation at this loci = population is “fixed”
• eg. irish potato famine

Question 16

What is a gene pool?

Answer 16

all the alleles present in a population

Question 17

What is a population?

Answer 17

community of individuals of the same type

• mendellian populations have the opportunity to interbreed

Question 18

How can you determine if 2 individuals belong to same species?

Answer 18

If 2 individuals can breed and produce a viable and fertile offspring

Question 19

What is allele frequency? How is it measured?

Answer 19

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

Question 20

How can you tell how many alleles you’re dealing with when analyzing a locus?

Answer 20

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

Question 21

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?

Answer 21

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

Question 22

What is hardy-weinberg equilibrium? What is an ideal population?

Answer 22

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)

Question 23

What are the five forces which may change allele frequency?

Answer 23

1. mutation
2. migration
3. small population size
4. non-random mating
5. selection

if none of these forces are acting on a population then the population is stable (not changing)

Question 24

Does equilibrium mean you have equal numbers of each allele (p = q)?

Answer 24

NO

Question 25

How do you relate genotype frequency and allele frequency using hardy weinberg? What is the hardy weinberg equilibrium equation?

Answer 25

A (p) B (q) A (p) AA p2 AB pq B (q) AB pq BB q2 * 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 If a population is at hardy weinberg equilibrium (no forces acting on it) then you have p² + 2pq + q² = 1 * no other possible genotypes with these two alleles (A & B) so must = 1

Question 26

How do you figure out if your population is at equilibrium?

Answer 26

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

Question 27

What is migration?

Answer 27

Gene Flow * movement of individuals between populations * 2-way migration Makes populations more similar * eventually don't have 2 separate populations

Question 28

What is two way migration?

Answer 28

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

Question 29

You have three populations where migration is occuring. Pop. 1: * p = 0.9 * q = 0.1 Pop. 2 * p = 0.3 * q = 0.7 Pop. 3 * p = 0.6 * q = 0.4 What will the p and q values be when equilibrium is reached?

Answer 29

^ p = (0.9 + 0.3 + 0.6) / 3 = 0.6 ^ q = (0.1 + 0.7 + 0.4) / 3 = 0.4

Question 30

What is random genetic drift?

Answer 30

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

Question 31

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

Answer 31

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

Question 32

What is the founder principle?

Answer 32

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

Question 33

What is non-random mating?

Answer 33

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 * 1:2:1 * p & q allele frequencies will increase and 2pq will decrease

Question 34

Too few heterozygotes and too many homozygotes is indicative of what?

Answer 34

Inbreeding and positive assortive mating

Question 35

What is mutation?

Answer 35

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

Question 36

What is back mutation?

Answer 36

if an allele can mutate then it can mutate back to original * A→B and B→A A→B * FWD mutation rate is µ B→A * BACK mutation rate is ν µ typically larger than v b/c B can mutate to something else instead of back to A

Question 37

What is the change in p & q due to mutation for A→B and B→A?

Answer 37

Δq = µp - νq ## Footnote µp is the gain in B (rate of fwd mutation) νq is the loss of B (rate of back mutation)

Question 38

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?

Answer 38

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

Question 39

What is selection?

Answer 39

Differential reproduction * 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

Question 40

What is fitness?

Answer 40

Selection is based on differences in fitness * A measure of your ability to produce offspring

Question 41

How do you measure fitness?

Answer 41

Darwinian Fitness * average number of offspring left by a genotype * eg. * 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

Question 42

How does a difference in fitness impact the next generation?

Answer 42

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

Question 43

What is mean population fitness?

Answer 43

How fit a population is as a whole \_ W = p² (w_AA) + 2pq (w_AB) + q² (w_BB) * As selection proceeds the mean pop fitness should increase p_n² (w_AA) + pq (w_AB) p_n+1 = -------------------------------------------- p² (w_AA) + 2pq (w_AB) + q2 (w_BB)

Question 44

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?

Answer 44

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

Question 45

What is fishers fundamental theorem?

Answer 45

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

Question 46

How does selection impact a recessive lethal allele? How does selection affect a dominant lethal allele?

Answer 46

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

Question 47

What is heterosis?

Answer 47

Heterozygote advantage * 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

Question 48

What equation can you use to figure out p₀ (p at equilibrium) when faced with a heterosis situation?

Answer 48

^ s2 p = ----------- s1 + s2 s is the selection coefficient