lecture 13. Sept. 4 - 11-1 The Effect of Homoplasy on...

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11-1The Effect of Homoplasy on Protein DivergenceLike the rate of DNA sequence divergence, the rate of protein sequence divergence also becomesnon-linear with time.Eventuallythe amount of divergence between two proteins reaches a limit ofabout 15% identity, the value that would be found by chance if one were to compare two unrelatedproteins of the same length.This limit is not a great deal lower than the nucleotide limit of about 25%.This may seem surprising, because there are only 3 possible nucleotide substitutions but 19 possibleamino acid substitutions at each site.The reason that the protein divergence limit is so high is that a fewamino acids tend to be common.If a common amino acid is found at the same site in two homologousproteins, this is often the result of homoplasy and not of common ancestry.Some amino acid substitutions are more likely to take place than others. Amino acids such astryptophan,tyrosine,phenylalanine, prolineandcysteineoften play important roles in the structure ofproteins.Cysteines in different parts of a protein, for example, often react with each other to formsulfur-sulfur bonds that stabilize the protein’stertiarystructure (Figure below).
11-2The importance of sulfur-sulfur bonds in stabilizing the tertiary structure of the enzymeribonuclease.If one or more of these bonds is broken, either chemically or when one of the cysteineshas been substituted by another amino acid, the enzyme loses its catalytic activity.Because these amino acids cannot be substitutedby others without large changes in the protein’sproperties, they tend to have low substitution rates (Figure below).Thus, if two proteins with lowpercent identity are compared and are found to have tryptophans, tyrosines, phenylalanines, prolines orcysteines in the same positions, this is a strong clue that in spite of their many other differences they arein fact homologous and have diverged from a common ancestor.Note, however, that these amino acidsare sometimes equivalent to each other.For example, phenylalanines, tryptophans and tyrosines canoften substitute for each other.
11-3The relative mutabilities of amino acids, represented as circles of different sizes.Amino acidswith large effect on protein tertiary structure are shown in red.The Relative Roles of Natural Selection and Random Drift inEvolutionary DivergenceWe can now see how divergence takes place in genes at the molecular level, but we have not yetaddressed the processes that bring about this divergence.We saw earlier that 21 allele substitutionshave occurred in different primate lineages during the divergence of the A and B alleles of the ABO

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Term
Spring
Professor
French
Tags
Bacteria, DNA, Proteins, Evolution, Radioactive Dating, fossil record, Cambrian

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