Topic 2: Protein polymorphisms and Hardy-Weinberg equilibrium

Question 1

What is genetic variation

Answer 1

• evolution occurs when selection acts on inherited variants that increase an individual’s ability to survive/reproduce
• favourable variants increase in frequency over generations
• amount of genetic variation = ability of population to adapt

Question 2

What are genetic markers

Answer 2

• inherited polymorphism associated with a specific locus on a chromosome
• often gene or noncoding DNA sequence
• proteins or DNA segments

Question 3

What is polymorphism

Answer 3

a character or a gene is polymorphic if more than one state exists in the population

Question 4

What is phenotype a combination of

Answer 4

genetics and environment

Question 5

What are some examples of polymorphisms

Answer 5

• incomplete dominance
• multiple alleles coding for a few traits

Question 6

What are proteins

Answer 6

• polypeptides, chains of amino acids, encoded by DNA
• 20 amino acids, each with a different R group, with a amino group and carboxyl group
• amino acids are joined by peptide bonds, formed by a condensation reaction of the amino group and carboxyl group with removal of water

Question 7

What are the 4 different types of protein structures?

Answer 7

1. Primary - amino acid sequence (length and charge)
2. Secondary - regular substructure: alpha helix, beta sheet
3. Tertiary - 3-dimensional folding
4. Quaternary - aggregation of polypeptides
   - 1 subunit - monomer (leucine amino peptidase)
   - 2 subunits - dimer (malate dehydrogenase)
   - 4 subunits - tetramer (lactate dehydrogenase)

Question 8

Why examine protein variation

Answer 8

advantages over morphology
- variation is genetically determined, very little environmental variation
- show simple Mendelian inheritance
- ubiquitous
- generic - same 20 amino acids in most organism

Question 9

What are the steps of gel electrophoresis

Answer 9

1. Dissect tissues
2. Homogenize
3. Centrifuge, collect supernatant
4. Electrophorese
5. Stain gel slice
6. Score population

Question 10

How can a change in amino acids affect the charge and shape of proteins

Answer 10

• replacement of one amino acid by a different amino acids can effect the shape of the protein or charge
• 4 main amino acids that affect the charge of a protein
• they can be charged or uncharges depending on the pH of the buffer
• negatively charged: aspartic acid, glutamic acid
• positively charged: lysine, arginine

Question 11

How can we identify allozyme alleles in a gel electrophorus score

Answer 11

• alleles at a locus can be named by how fast they run down the gel
• they can be named based on how fast they run down the gel relative to the most common allele
• 1.0 most common allele
• 1.2 runs 1.2x faster than most common allele
• 0.8 runs 20% slower than the most common

Question 12

What are genotype frequencies

Answer 12

f(AA) = nAA/ntotal
f(Aa) = nAa/ntotal
f(aa) = naa/ntotal

Question 13

How do we calculate allele frequencies

Answer 13

p = 2(nAA) + (nAa)/2ntotal
p+q=1
q=1-p

Question 14

What are phenotypic/morphological markers

Answer 14

• few morphological markers are determined by a single gene and inherited in a simple fashion
• most morphological traits are polygenic and continuously distributed

Question 15

How can we truly tell if a population is polymorphic

Answer 15

• a population is not polymorphic if the most common allele has a frequency of 0.9999 and another allele is 0.0001
• proportion of polymorphic loci is more usefully defines as the portion of loci that have the most frequent allele in the population with a allele frequency of less than 0.95

Question 16

What is allelic diversity

Answer 16

• measured as the number of alleles observed in a sample, denoted as k
  can be expressed as an average at a population over loci
• may also be expressed as an average at a locus over populations

Question 17

How do we calculate allele frequencies using more than 2 alleles at a single locus

Answer 17

pi = f(AiAi) + summation(f(AiAj)/2

Question 18

What is the Hardy Weinberg Principle

Answer 18

• single locus genotypic frequencies after one generation can be represented by a binomial or multinomial function of the allele frequencies
• predicts that genotype frequencies will not change over time provided that no factors change the allele frequencies

Question 19

What are assumptions associated with the Hardy Weinberg Principle

Answer 19

• mating is random
• population of infinite size
• no migration
• no mutation
• no selection

Question 20

What would happen if these assumptions were true?

Answer 20

there would be no evolution. much of the study of population genetics and molecular ecology is focused on these major factors that drive evolutionary change

Question 21

What is expected heterozygosity

Answer 21

• the probability that an individual in a population will be a heterozygote at a locus
  1 - summation (pi^2)
• measure can be used to compare levels of genetic variation between loci or populations