BSC1010: Intro to Biology I K. Maltz Chapter 21

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

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

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

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

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

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

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

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

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

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

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

Proteomes

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

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...

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

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