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Genome Organization and Evolution
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Assignment
For 2/24/04
Read: Lesk, Chapter 2Exercises 2.1, 2.5, 2.7, p 110
Problem 2.2, p 112Weblems 2.4, 2.7, pp 112-113
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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.
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Genes
● Definition: A gene is a segment of DNA which codes for a protein– Caveats:– DNA which codes for functional RNA?– Control regions?
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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
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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
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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
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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
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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
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Prokaryote genomes
● Example: E. coli● 89% coding● 4,285 genes● 122 structural RNA genes● Prophage remains● Insertion sequence elements● Horizontal transfers
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Eukaryotic genome
● Example: C. elegans● 10 chromosomes● 19,099 genes● Coding region – 27%● Average of 5 introns/gene● Both long and short duplications
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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
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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