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

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