From Mendel to Genomics Historically Identify or create mutations, follow inheritance Determine linkage, create maps Now: Genomics Not just a gene, but as many genes as may be involved in a process. www.bastardidentro.com

Genomics: The study of genes and their function Genomics: The study of genes and their function. Genomics aims to understand the structure of the genome, including the mapping genes and sequencing the DNA. Genomics examines the molecular mechanisms and the interplay of genetic and environmental factors in disease. Genomics: Focus: entire genome, not individual genes Uses recombinant DNA methods Methodology in place for sequencing entire genomes

Genomics includes: Functional genomics -- the characterization of genes and their mRNA and protein products. Structural genomics -- the dissection of the architectural features of genes and chromosomes. Comparative genomics -- the evolutionary relationships between the genes and proteins of different species. http://www.medterms.com/script/main/art.asp?articlekey=23242

Bioinformatics Sequencing creates huge amount of information that must be stored and analyzed Bioinformatics is the science of methods for storing and analyzing that information Melding of computer science and molecular biology http://www.swbic.org/products/clipart/images/bioinformatics.jpg

Sequencing the Human Genome Publicly funded consortium Clone-by-clone method Create library of clones of entire genome Order clones using various DNA markers Then sequence each clone Craig Venter and private enterprise Shotgun method Sequence all the clones Use supercomputer to determine order Sequencing done multiple times to get it right.

Clone-by-clone Shotgun approach www.yourgenome.org/ intermediate/all/

Is sequencing a genome the answer? No, only the beginning of the questions. http://www.insectscience.org/2.10/ref/fig5a.gif

Annotation: making sense of the sequence Looking for regulatory regions, RNA genes, repetitive regions, and protein genes. Finding protein genes Look for ORFs (open reading frames) Start codon (ATG), stop codon. Codons must be “in frame”, distance long enough Problems: 3 reading frames x 2 strands, widely spaced genes, introns. Help: new software finds TATA box and other elements; codon bias can help Different codons not used equally in organisms

Where is the reading frame? Could start in one of 3 different places.

Find the start codon. Do all the codons that follow spell out a protein sequence seen before?

Functional Genomics OK you have a sequence. What does the gene do? What is the function of the protein? Search database for similar sequences How does sequence compare to sequences for proteins of known function? Use computer to search for functional motifs. Various proteins that do the same thing have similar structural elements. Example: transcription factors that have lecuine zippers bind to DNA

Fundamental questions Questions can be asked using whole genome information that couldn’t before. How did genomes evolve? What is the minimum number of genes necessary for a free-living organism? Much can be learned about the ecology of an organism by genomics and proteomics. First bacterium sequenced: Mycoplasma genitalium Lives a parasitic existence, evident from genes.

Protein function # of genes Amino acid biosynthesis Purine, pyrimidine, nucleoside and nucleotide metabolism 19 Fatty acid and phospholipid metabolism 8 Biosynthesis of co-factors, prosthetic groups and carriers 4 Central intermediary metabolism 7 Energy metabolism 33 Transport and binding proteins DNA metabolism 29 Transcription 13

Protein synthesis 90 Protein fate 21 Regulatory functions 5 Cell envelope 29 Cellular processes 6 Other categories Unknown 12 Hypothetical Database match 168 No database match Total number 483

Advances in understanding genomes Prokaryotic- eubacterial not all genomes are circular not all genomes are in one piece when is a plasmid not a plasmid but a chromosome? not all genomes are small very little wasted space, very few with introns Significant quantity of genes organized into operons

Understanding-2 Archaeal genomes similar to eubacteria but have histones, sequence similarities to eukaryotes, and introns in tRNA genes Eukaryotic genomes -wide variations low gene density, that is few genes per amount of DNA introns, more in some (humans) than others repetitive sequences

Proteomics Proteome: all the proteins an organism makes Proteomics: the study of those proteins Timing of gene expression Regulation of gene expression Modifications made to proteins Functions of the proteins Subcellular location of proteins http://www.emc.maricopa.edu/faculty/farabee/BIOBK/3_14d.jpg

Proteomics: study of proteins 35,000 genes, 100,000 different proteins must be lots of post translational modifications >100 different ways of modifying proteins addition of groups, crosslinking, inteins many genes code for proteins of unknown function methods of study 2D gel electrophoresis Peptide fragments generated with trypsin, studied by MS

2D gel electrophoresis of proteins Blue and green arrows mark proteins of interest. Proteins of Halobacterium. Left to right: pH Vertical: MW Spots digested w/ trypsin then studied using mass spec. http://www.biochem.mpg.de/en/research/rd/oesterhelt/web_page_list/Proteome_Hasal_cytosolic/absatz_3_bild.gif