Genome Organization and Evolution

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

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

● Definition: A gene is a segment of DNA which codes for a protein– Caveats:– DNA which codes for functional RNA?– Control regions?

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

● 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

● 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

● 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

● 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

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

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

● 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

● 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