BIO 3102 Lecture Notes - Lecture 4: Nonsynonymous Substitution, Synonymous Substitution, Conserved Sequence

• School: University of Ottawa
• Department: Biology
• Course: BIO 3102
• Professor: Linda Bonen

Document Summary

Rates = # substitutions per site per unit time (year or generation) 1. r = rate: k = #sub between 2 homologous sequences, t = time of divergence, then, r = k/2t, length of evolutionary time separating. #1 and #2: once have two parameters can find the 3rd one, within coding sequences, can separate the rates into, ka = amino acid-altering substitution rate, # non-synonymous sub. Site /year: ks = synonymous substitution rate, # synonymous sub. Rates of nt substitution in different parts of genes (and sequences near genes) Nondegenerate substitutions are non-synonymous, functional constraint against changes in the amino acids: 1. Non-degenerate sites under greatest functional constraint: any change will alter protein, 2. Sequences that are selectively neutral will evolve rapidly: pseudogenes, 4-fold degenerate, introns, can be useful in molecular clock studies, 3. Flanking (5") & untranslated regions somewhat constrained: because contain gene regulatory signals. Ka nonsynonymous rate and ks synonymous rate.