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Genome Organization and Evolution

Genome Organization and Evolution. For 2/24/04 Read: Lesk, Chapter 2 Exercises 2.1, 2.5, 2.7, p 110 Problem 2.2, p 112 Weblems 2.4, 2.7, pp 112-113. Assignment. For 3/02/04

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Genome Organization and Evolution

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  1. Genome Organization and Evolution

  2. For 2/24/04 Read: Lesk, Chapter 2 Exercises 2.1, 2.5, 2.7, p 110 Problem 2.2, p 112Weblems 2.4, 2.7, pp 112-113 Assignment

  3. For 3/02/04 Pick any two bioinformatics projects or resources, such as those in the previous lecture. For each, write a brief survey (~1000 words), giving such information as: the history of the project; the participants; the funding; its purpose and scope. Sources: web site, mailing lists, faqs, published papers. Assignment

  4. Genes • Definition: A gene is a segment of DNA which codes for a protein • Caveats: • DNA which codes for functional RNA? • Control regions?

  5. Gene organization • A gene may occur on either strand of DNA • Genes are continuous stretches (almost always) in prokaryotes • Genes are (often) discontinuous stretches (exons) in eukaryotes. The intervening regions are called introns • Upstream is a binding site • Location of regulatory region is less predictable

  6. The Central Dogma • One gene, one protein • Like most dogmas, not entirely true • Alternative splicing permits the manufacture of many products from a single gene • The protein products are sometimes called the proteome • With current technology, more gene information is available than protein information

  7. Transmission of information • The continuity of life is a reflection of the (nearly) faithful transmission of genetic information • The adaptation of life (evolution) is a result of imperfect transmission of information, and natural selection

  8. Genetic maps • Variable number tandem repeats (VNTRs – minisatellites), 10-100 bp, are a sort of genetic fingerprint • Short tandem repeat polymorphisms (STRPs – microsatellites), 2-5 bp, are another kind of marker • A sequence tagged site (STS), 200-600 bp, is a known unique location in the genome

  9. Identifying genes • A long ORF is probably a gene (but what about eukaryotes? AG and GT splice signals) • A gene promoter site has identifiable characteristics (TATA box) • If it looks like a known gene, it's a gene

  10. Prokaryote genomes • Example: E. coli • 89% coding • 4,285 genes • 122 structural RNA genes • Prophage remains • Insertion sequence elements • Horizontal transfers

  11. Eukaryotic genome • Example: C. elegans • 10 chromosomes • 19,099 genes • Coding region – 27% • Average of 5 introns/gene • Both long and short duplications

  12. Evolution of genomes • Adaptation of species is coterminous with adaptation of genomes • Where do genes come from? (Answer: from other genes) • Homologs and paralogs • Lateral transfer • Molecular species each have their own family tree • Genes are widely shared

  13. Close relatives • Yeast, fly, worm and human share at least 1308 groups of proteins • Unique to vertebrates: immune proteins (for example) • Unique molecules are adapted from ancient molecules of different purpose but similar design • Most new proteins come from domain rearrangement • Most new species come from control region variation

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