Transcript Slide 1
BIO 3102 MOLECULAR EVOLUTION • Study of evolution of macromolecules - nature of changes (in DNA, protein) & their impact Evolutionary change involves genetic change D Genotype D Phenotype M.C. Escher “Sky & water” • Use of molecular data to help reconstruct evolutionary history - phylogenetic trees modern species extinct lineages cenancestor - most recent primordial life form common ancestor of extant organisms Brown Fig.16.1 Closely-related organisms have more similar protein sequences than distant organisms MOLECULAR CLOCKS www.csmt.ewu.edu/.../ chem163/163LT1.html “Web-of-life” “Taking an axe to the Tree of Life...” Ford Doolittle “... far more complex scenario than Darwin could have imagined... Many [microbes] swap genes back and forth, or engage in gene duplication, recombination, gene loss or gene transfers...” www.whoi.edu/cms/images/oceanus/2005/4/v43n2-teske_edwards1en_8591.gif Dalhousie University News July 11, 2007 A B 1. Which tree is more accurate? 2. Is the frog more closely related to the fish or to the human, based on this tree? “The tree-thinking challenge” Science 310:979, 2005 Extant Fossil Fossil Schopf PNAS 91:6735, 1994 Volpe & Rosenbaum Fig.14.3 Mass extinctions, as well as radiations leading to taxonomic diversity App1.Fig.2 “Loss and recovery of wings in stick insects” Nature 421: 264, 2003 Male Female Winged Partially winged Wingless Morphological data Phylogeny based on molecular data EVOLUTIONARY INFORMATION FROM DNA SEQUENCES? GENE - sequence of DNA (or RNA) that is essential for a specific function 1. Protein-coding genes U.S. Dept of Energy Human Genome Program, http://www.ornl.gov/hgmis 2. RNA-specifying genes 3. Functional DNA elements - regulatory - structural Do not use term in text (p.9): “Untranscribed genes” for #3 “SILENT” GENE - untranscribed, but potentially functional at DNA level PSEUDOGENE - non-functional DNA with high degree of similarity to a functional gene How can pseudogenes arise during evolution? Orthologous genes - descendants of an ancestral gene that was present in the last common ancestor of two or more species Paralogous genes - arose by gene duplication within a lineage “TYPICAL” EUKARYOTIC PROTEIN-CODING GENE Where is the promoter? 5’ UTR ? 3’ UTR ? What regions will be present in the mRNA? Is there an error in this figure? Fig.1.4 “TYPICAL” BACTERIAL GENE ORGANIZATION How many promoters in this region? How many proteins encoded? Operon = cluster of co-transcribed genes Evolutionary advantages of operon organization? Fig.1.6 PROTEIN-CODING GENES DNA 5’ …. ATG GGA TTG CCC GCC …. 3’ “coding strand” 3’ .… TAC CCT AAC GGG CGG …. 5’ “template strand” mRNA 5’ …. AUG GGA UUG CCC GCC …. 3’ - DNA usually shown as single-stranded with coding strand in 5’ to 3’ orientation … so genetic code table can be used directly Codon families have 1 – 6 members 5’ …. AUG GGA UUG CCC CAC …. 3’ For the 61 sense codons, how many substitution mutations are possible? Genetic code is not “universal” Some mitochondria, a few bacteria, a few protists use a non-standard code Table 1.4 Vertebrate mitochondrial code UGA = Trp (instead of stop codon) AUA, AUG = Met AGA, AGG = stop codons Possible implications of different codes in nature? AMINO ACIDS – Venn diagram showing properties Fig. 1.9 Amino acid substitution matrices Amino acid substitutions: Conservative Ile Radical Cys Table 4.7 BLOSUM62 matrix - based on observed frequencies of amino acids replacing other amino acids during protein evolution, particularly within conserved regions BLOSUM = BLOcks Substitution Matrix www.doc.ic.ac.uk/