Bioinformatics Journal Chasity Watt June 21 -25, 2004

2. DNA-The Molecule of Life

17. Promoters regulate gene expression: which DNA strand will serve as a template�when to start making the mRNA�. Where to start making the mRNA TSP�when to stop making the mRNA and how much to make Bacterial Gene Structure: bacerial prokaryotic genes�one mRNA can contain several coding regions�..can have several cistrons�different genes�coding for differerent proteins related in function Plant and Animal gene structure�Eukaryotic genes�one mRNA contains a single coding region (ORF) DNA with one promotor controlling one gene Introns plant and animal genes often contain Extra DNA: The coding region in some Eukaryotic genes is interrupted by non coding regions that have to be removed before the protein is made. The ORF in the gene are called exons�the extra DNA chunks are called introns The preRNA also contains the sequence information that tell the cell where to trim out the extra DNA (splice junctions) Bioinformatics-LOTS and Lots of information�what do we do with it and how to we organize the information in a useful way. Mining fore useful information in that glut of information is what bioinformatics is about Steps to finding genes 1. Find ORFs..this is the biggest target, easiest to find�look for long stretches of triplet condons that don�t have a stop codon Find the Start Codon-where the protein begins, always an atg Find promoter elements Gene Structure�Codons 61 codons codes for amino acids, but only 20 amino acids. All have carboxyl group and amino group....R groups give chemical properties�makes the molecule hydrophobic Tertiary structure-the protein all folded up nice and neat ORF-Open reading frame A human nucleus has 3 billion base pairs and about 35gs protein coding genes Steven Pechous NCBI NCBI Resources: Sequence Database, Entrez, Genomic Resources, Blast Entrez, The Life Sciences Search Engine: One Key word can access all the databases

18. DNA-Base pairs-G, T, A, C Double helix-base pairs same shape�stack on top of each other and twist around DNA- a script to be passed from cell to cell�the secret to life Watson and Crick discover the double helix Genetic code a story the has evolved over millions of years Examining and interpreting the genetic code: Key to understanding disease and curing disease�heredity How can u read what's inside a molecule? Cytosine, Guanine, 1% of genes active? Revolution- computerization of genetic decoding Human Genome Project-J. Craig Vender-1990 Decoding proteins and genes. Machine that cuts the DNA�labels it and reads it with a laser�is able to read G T A C�codes must be arranged again�AUTOMATION Francis Collns�Human Genome Project�thousand base pairs a second! Out of university labs directly onto the internet�Solara used information�.was a race to get the genome sequenced the fastest. Population from Africa about a hundred thousand years ago�.not much genetic variation�people very similar Proteins�shape defines what it does and how it interacts with other proteins Mutations in proteins can cause very serious consequences�changes in shape make it not able to interact with other proteins�protein in three dimensional shape�.much more complex then linear DNA Human Genes 30,000 Genes make a message but can be spliced in different ways�modifications to proteins can make them function differently. Starting with the same raw ingredients, different arrangements can produce many different complexity Finding Genes. If it has an ORF like a gene�has a promoter like a gene and has a function like a gene Can use restriction enzymes to cut dna into different sizes and run through gel Southern Blots�.radiolabeled probes label DNA�put in a bath with a filter and u can find Used to make maps of chromosomes GMO Genetically Modified organism�transgenic potatoe PCR clones used for complementation DNA Replication-Transcription and Translation Genes distributed throughout genome�hotspots�..gene dense regions�99% stuff�more then half DNA selfish DNA elements�that hitch hike on us and replicate�been there for a billion and a half years