1. BSC1010: Intro to Biology I
K. Maltz
Chapter 21

2. Genome and Proteome Again
Genome- the GENETIC composition of a cell or species
Stores information in the form of GENES
Is copied and passed from generation to generation
The accumulation of changes/mutations over many generations IS THE DRIVING FORCE FOR EVOLUTIONARY CHANGE
Proteome- the proteins a cell or organism can make
Allows researchers to understand aspects of biology including
Organism complexity
Interaction between organisms and their environment

3. Prokaryotic Genome
We’re interested in the genomes of bacteria because they cause disease, we can often apply that information on a larger scale, to understand evolution, and to use the information as a tool for research and biotechnology
Most prokaryotes have a single circular chromosome, although more than one copy may be present in an individual cell
Some have more than 1 chromosome, others have a linear chromosome, and some have 1 circular and 1 linear chromosome!
Vibrio cholerae circular but 2 different chromosomes circular
Borrelia burgdorferi- (lyme disease) linear
Agrobacterium tumefaciens (crown gall disease in plants) linear and circular

4. Eukaryotic Genome Protists, Fungi, Animals, Plants included
Contain short sequences of “repetitive DNA”
Sets of linear chromosomes
Includes: Nuclear genomes, mitochondrial genomes, chloroplast genomes

5. Nuclear Genome Why do we sequence them?
Availability of sequences for model organisms
Identify and treat human diseases
Improved traits of livestock and plants
Establish evolutionary relationships
Large number of genes and large number of base pairs

6. Repetitive Sequences Two categories:
Moderately Repetitive- few hundred-several thousand copies
Highly Repetitive- 10,000+ copies

7. Transposition
TEs (transposable elements) are short segments that can move to a new spot on the genome
AKA “jumping genes” discovered by Barbara McClintock
DNA transposons move via a DNA molecule and have elements that are similar but run in both directions (may be palindromic sequences) and a region that encodes for transposase enzyme
Retroelements code for reverse transcriptase and integrase

8. DNA Transposons First transposase recognized repeats
Then it cleaves at both ends of the TE
The transposase moves it, cleaves the dna at the new site, and re inserts it in its new place

9. Retroelements Rna polymerase turns it into rna
Reverse transcriptase turns dna into doube stranded rna
Integrase rinserts it into chromosome so it has 2 copies

10. Homologous Genes 2 genes that derive from the same ancestral gene
Mutations that accumulate over time make them slightly different
Two or more homologs within a species are called paralogs
Two or more paralogs that perform similar functions in different species are called gene families
There are several theories that explain how they copy

11. Homologous Gene Theories
Misaligned crossover causes duplication
Over time they accumulate mutations that make them a little different from each other

12. Human Genome Project 10/1/1990-4/14/2003 Many countries collaborated
Goals included to ID all human genes, to sequence the entire genome, to form a database to manage the info, to analyze the genomes of model organisms, and to develop programs to understand and address the ethical issues that arise from the information

13. Proteomes

14. Bioinformatics
Use of computers, mathematical tools, and statistical techniques to record, store, and analyze biological information
Computational molecular biology- computers characterize the molecular components of living things
Sequences must be stored first and then the sequences can be analyzed to see if they contain a gene, might cause disease, if they are regulated in any way, if we can get the primary structure of the protein it codes for, and to look for evolutionary relationships between genes

15. Genome Databases
"The systematic study of the absolute nuclear DNA content across numerous animal species will, without doubt, provide many interesting suggestions concerning the question of evolution."
- Vendrely and Vendrely, 1950
diArk | index
Genome Projects Home
NCBI Genome Project Home
Animal Genome Size Database:: Home
Just in case you were wondering...

16. What Else Can We Do?
Data mining- extract useful information from the databases
Identify orthologs (homologous genes in different species)
BLAST- (basic local information search tool) starts with a genetic sequence and then finds homologous sequences within a large database

17. BLAST
Phenylalanine hydroxylase- turns phenylalanine into tyrosine if deficient you have phenylketonuria