genome organization and evolution
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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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slide2
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
assignment

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
genes
Genes
  • Definition: A gene is a segment of DNA which codes for a protein
    • Caveats:
    • DNA which codes for functional RNA?
    • Control regions?
gene organization
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
the central dogma
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
transmission of information
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
genetic maps
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
identifying genes
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
prokaryote genomes
Prokaryote genomes
  • Example: E. coli
  • 89% coding
  • 4,285 genes
  • 122 structural RNA genes
  • Prophage remains
  • Insertion sequence elements
  • Horizontal transfers
eukaryotic genome
Eukaryotic genome
  • Example: C. elegans
  • 10 chromosomes
  • 19,099 genes
  • Coding region – 27%
  • Average of 5 introns/gene
  • Both long and short duplications
evolution of genomes
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
close relatives
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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