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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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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