Bio 1B Lecture Outline please print and bring along Fall 2007 B D Mishler Dept of Integrative Biology 2 6810 bmishler berkeley edu Evolution lecture 5 Molecular genetics and molecular evolution Nov 14th 2007 ch 16 296 307 overview ch 17 309 326 overview ch 25 499 508 I Summary of topics to be covered Review the key features of DNA structure and the processes of gene transcription and translation DNA of genes to amino acids of proteins Molecular features of all life forms that support evolution Describe why phylogenetic trees drawn from molecular data should show the same broad patterns as those drawn from fossil data Use the molecular clock principle to estimate divergence times between groups on phylogenetic trees II Molecular genetics DNA deoxyribonucleic acid the genetic material nucleotides adenine A cytosine C guanine G thymine T in the DNA double helix A pairs with T and G pairs with C see Fig 16 7 7th Fig 16 5 6th RNA ribonucleic acid uracil U replaces thymine T mRNA messenger RNA kind of RNA produced by transcription from the DNA and which acts as the message that is decoded to form proteins Fig 17 4 7th Fig 17 3 6th tRNA transfer RNA kind of RNA that brings the amino acids to the ribosomes to make proteins A transfer RNA molecule has an amino acid attached to it and has attached in a different area of the molecule the anti codon corresponding to that amino acid In protein synthesis each codon in the mRNA combines with the appropriate tRNA s anti codon and the amino acids are thus arranged in order and make the protein Figs 17 13 17 16 7th Figs 17 12 17 15 6th amino acids the unit building blocks of proteins a protein is a chain of amino acids in a certain sequence There are 20 amino acids in the proteins of living things genetic code the code relating the nucleotide triplets in the messenger RNA to amino acids in the protein Fig 17 5 7th Fig 17 4 6th codon a triplet of bases nucleotides in RNA coding for one amino acid Conventionally the triplet in the mRNA is the codon and the triplet in the tRNA is the anti codon Evolution 5 pg 1 degenerate more than one codon can code for one amino acid hence some mutations do not result in an amino acid change these are called synonymous mutations as distinct from nonsynonymous mutations which do result in an amino acid change universal the same genetic code is used in all organisms with a few small exceptions Exons vs Introns and alternative splicing Some genes can encode more than one kind of polypeptide depending on which segments are treated as exons during RNA splicing Such variations are called alternative RNA splicing Because of alternative splicing the number of different proteins an organism can produce is much greater than its number of genes mutations a heritable change in DNA Mutations can be deleterious neutral or selected Mutations can involve a change of a nucleotide base change as well as insertions or deletions of genetic material see Fig 25 6 7th III Molecular features that support evolution Common molecular and biochemical features of all life forms Universal use of DNA as the genetic material rules of genetic transmission and genetic code Universal processes of gene expression protein synthesis and protein function The genes and their functions are strikingly similar in different organisms DNA shows evidence of variation diversity the continuity of life and the unitary origin of life The more closely related two species are to each other the more similar their DNA and vice versa humans and chimps are more closely related to each other than either is to gorillas or orangutans Fig 34 38 7th Fig 34 35 6th Evolutionary trees based on DNA are strikingly similar to those based on anatomical developmental and fossil evidence IV Genome sequences The complete DNA genome sequences of more than 300 organisms have been completed mostly prokaryotes but many eukaryotes as well for example yeast fruit fly mustard plant moss rice nematode worm mouse and humans and sequencing of the genomes of thousands of organisms is in progress http www ncbi nlm nih gov Genomes index html Evolution 5 pg 2 Mitochondria and chloroplast have their own genomes in addition to the nuclear genome These are descended from the endosymbiotic bacteria that originally came to live inside the eukaryotic cell A large number of these have been sequenced and provide important phylogentic characters both in their nucleotide sequence and in their gene order Below is an example of the latter from green plants to be explained in lecture V Molecular evolution evolutionary trees from DNA data A series of evolutionary changes involves a progressive accumulation of genetic change in the DNA Even if there were no selection operating i e mutations which arose were selectively neutral because of the finite size of populations and consequent chance events alleles always eventually become lost from a population so there is eventual replacement of allelic types by another This will be covered later in section on genetic drift The more distantly related two species are the more genetic differences amino acid changes or nucleotide changes that will have accumulated between them So the longer the time since the organisms diverged the greater the number of differences in the nucleotide sequence of the gene e g cytochrome c Evolution 5 pg 3 The gene that encodes small subunit ribosomal RNA SSU rRNA was extensivley used for the classification of microorganisms and resulted in recognition of archae and bacteria as two distinct domains within the prokaryotes Evolutionary trees drawn from DNA data agree well with those drawn from the fossil record and can be important where convergent evolution of similar characteristics can cause confusion in drawing evolutionary trees based on the characteristics of organisms and or when the fossil record is poor Almost any type of character for example morphological structures characteristics of cells biochemical pathways genes amino acids or nucleotides can be used for inferring phylogenies provided that they are homologous In addition to direct comparison of specific genes shared by different species complex characters known are rare genomic changes RGCs that have a very low probability of being the result of convergence can also be analyzed As well as gene order such RGCs include intron positions insertions and deletions of genetic material indels retroposon SINE and LINE integrations and gene fusion and fission events substitution times the
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