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BIO 335 Genetics > Final Exam > Flashcards

Final Exam Flashcards

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1
Q

What is a somatic mutation?

A

Mutation in:

  • normal body tissue
  • may have vast effect on individual
  • not passed to offspring
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2
Q

What is a germinal mutation?

A

Mutation in:

  • gametes
  • little or not effect on individual
  • passed on to all cells of zygote that’s formed
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3
Q

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

A

Not necessarily

Dependent on:

  • nature of mutation
  • environment Spontaneously occur randomly in genome
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4
Q

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

A

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
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5
Q

What is a frameshift mutation?

A

Change in reading frame

  • changes which bases are read as part of which codons
  • changes every codon downstream
  • loss of function
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6
Q

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

A

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
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7
Q

What are the causes of spontaneous mutations?

A

Tautomeric Shifts

Deamination of bases

Depurination of bases

UV radiation

All of these lead to errors in DNA replication/repair

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8
Q

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

A

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

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9
Q

What is the most common cause of spontaneous mutations?

A

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
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10
Q

How does a tautomeric shift occur?

A

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

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11
Q

What is deaminination of bases?

A

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
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12
Q

WHat is Deuprination of bases?

A

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

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13
Q

How does UV light damage cause mutations?

A

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

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14
Q

What is the paradox of genetic variability?

A

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
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15
Q

What is polymorphism? What is a monomorphic loci?

A

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
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16
Q

What is a gene pool?

A

all the alleles present in a population

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17
Q

What is a population?

A

community of individuals of the same type

  • mendellian populations have the opportunity to interbreed
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18
Q

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

A

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

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19
Q

What is allele frequency? How is it measured?

A

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

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20
Q

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

A

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
21
Q

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?

A

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

22
Q

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

A

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)
23
Q

What are the five forces which may change allele frequency?

A
  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)

24
Q

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

A

NO

25
Q

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

A

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
26
Q

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

A

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
27
Q

What is migration?

A

Gene Flow

  • movement of individuals between populations
  • 2-way migration

Makes populations more similar

  • eventually don’t have 2 separate populations
28
Q

What is two way migration?

A

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

29
Q

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?

A

p = (0.9 + 0.3 + 0.6) / 3 = 0.6

q = (0.1 + 0.7 + 0.4) / 3 = 0.4

30
Q

What is random genetic drift?

A

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

31
Q

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
A

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
32
Q

What is the founder principle?

A

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

33
Q

What is non-random mating?

A

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
34
Q

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

A

Inbreeding and positive assortive mating

35
Q

What is mutation?

A

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
36
Q

What is back mutation?

A

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

37
Q

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

A

Δq = µp - νq

µp is the gain in B (rate of fwd mutation)

νq is the loss of B (rate of back mutation)

38
Q

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?

A

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

39
Q

What is selection?

A

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
40
Q

What is fitness?

A

Selection is based on differences in fitness

  • A measure of your ability to produce offspring
41
Q

How do you measure fitness?

A

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
42
Q

How does a difference in fitness impact the next generation?

A

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

43
Q

What is mean population fitness?

A

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)

44
Q

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?

A

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
45
Q

What is fishers fundamental theorem?

A

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
46
Q

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

A

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
47
Q

What is heterosis?

A

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
48
Q

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

A

^ s2

p = ———–

s1 + s2

s is the selection coefficient

BIO 335 Genetics (4 decks)

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