Download Genome Organization and Evolution

Genome Organization and Evolution
Assignment
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
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.
Genes
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Definition: A gene is a segment of DNA which
codes for a protein
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Caveats:
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DNA which codes for functional RNA?
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Control regions?
Gene organization
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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
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Upstream is a binding site
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Location of regulatory region is less predictable
The Central Dogma
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One gene, one protein
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Like most dogmas, not entirely true
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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
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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
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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
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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
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Example: E. coli
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89% coding
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4,285 genes
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122 structural RNA genes
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Prophage remains
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Insertion sequence elements
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Horizontal transfers
Eukaryotic genome
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Example: C. elegans
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10 chromosomes
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19,099 genes
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Coding region – 27%
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Average of 5 introns/gene
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Both long and short duplications
Evolution of genomes
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Adaptation of species is coterminous with
adaptation of genomes
Where do genes come from? (Answer: from other
genes)
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Homologs and paralogs
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Lateral transfer
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Molecular species each have their own family
tree
Genes are widely shared
Close relatives
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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