1 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.

2 Genomics: The study of genes and their function. Genomics aims to understand the structure of the genome, including 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 and looking at the activity of multiple genes simultaneously

3 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.

4 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

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

Sequencing the Human Genome A Huge job –Human DNA has over 3 trillion has pairs (3 x 10 9 ) –Much of the technology had to be invented and improved to do this particular job 6

7 Clone-by-cloneShotgun approach intermediate/all/

8 Is sequencing a genome the answer? No, only the beginning of the questions. g/2.10/ref/fig5a.gif

9 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

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

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

12 Functional Genomics OK you have a sequence. What does the gene do? What is the function of the protein? –Search the databases for similar sequences –Is the sequence similar 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

About Human Genome The average gene: 3000 bases, but sizes vary greatly –largest known human gene is dystrophin: 2.4 million bases. The total number of genes is estimated at 30,000 Almost all (99.9%) nucleotide bases are exactly the same in all people. The functions are unknown for over 50% of discovered genes. Less than 2% of the genome codes for proteins. Repeated sequences are at least 50% of genome. 13

14 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.

15 Protein function# of genes Amino acid biosynthesis0 Purine, pyrimidine, nucleoside and nucleotide metabolism19 Fatty acid and phospholipid metabolism8 Biosynthesis of co-factors, prosthetic groups and carriers4 Central intermediary metabolism7 Energy metabolism33 Transport and binding proteins33 DNA metabolism29 Transcription13

16 Protein synthesis90 Protein fate21 Regulatory functions5 Cell envelope29 Cellular processes6 Other categories0 Unknown12 Hypothetical Database match168 No database match6 Total number483

17 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

18 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

19 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

20 Proteomics: study of proteins Proteomics –30,000 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

21 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.