Topic 2: Protein polymorphisms and Hardy-Weinberg equilibrium Flashcards
What is genetic variation
- 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
What are genetic markers
- inherited polymorphism associated with a specific locus on a chromosome
- often gene or noncoding DNA sequence
- proteins or DNA segments
What is polymorphism
a character or a gene is polymorphic if more than one state exists in the population
What is phenotype a combination of
genetics and environment
What are some examples of polymorphisms
- incomplete dominance
- multiple alleles coding for a few traits
What are proteins
- 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
What are the 4 different types of protein structures?
- Primary - amino acid sequence (length and charge)
- Secondary - regular substructure: alpha helix, beta sheet
- Tertiary - 3-dimensional folding
- Quaternary - aggregation of polypeptides
- 1 subunit - monomer (leucine amino peptidase)
- 2 subunits - dimer (malate dehydrogenase)
- 4 subunits - tetramer (lactate dehydrogenase)
Why examine protein variation
advantages over morphology
- variation is genetically determined, very little environmental variation
- show simple Mendelian inheritance
- ubiquitous
- generic - same 20 amino acids in most organism
What are the steps of gel electrophoresis
- Dissect tissues
- Homogenize
- Centrifuge, collect supernatant
- Electrophorese
- Stain gel slice
- Score population
How can a change in amino acids affect the charge and shape of proteins
- 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
How can we identify allozyme alleles in a gel electrophorus score
- 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
What are genotype frequencies
f(AA) = nAA/ntotal
f(Aa) = nAa/ntotal
f(aa) = naa/ntotal
How do we calculate allele frequencies
p = 2(nAA) + (nAa)/2ntotal
p+q=1
q=1-p
What are phenotypic/morphological markers
- few morphological markers are determined by a single gene and inherited in a simple fashion
- most morphological traits are polygenic and continuously distributed
How can we truly tell if a population is polymorphic
- 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
What is allelic diversity
- 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
How do we calculate allele frequencies using more than 2 alleles at a single locus
pi = f(AiAi) + summation(f(AiAj)/2
What is the Hardy Weinberg Principle
- 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
What are assumptions associated with the Hardy Weinberg Principle
- mating is random
- population of infinite size
- no migration
- no mutation
- no selection
What would happen if these assumptions were true?
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
What is expected heterozygosity
- 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
