Bioinformatics Student host Chris Johnston Speaker Dr Kate McCain

Molecular Biology and Biological Chemistry Genetic Material Genetic Material DNA organize inanimate molecules into functioning living cells DNA organize inanimate molecules into functioning living cells Nucleotides Four bases in DNA molecule GATC Genes are many thousand nucleotides long

Central Dogma Transcription Translation Transcription Translation DNA RNA Protein DNA RNA Protein RNA polymerase Ribosome RNA polymerase Ribosome Proteins do all the work Catalysts called Enzymes

Gene Structure and Information content DNA has been the same for billions of years DNA has been the same for billions of years Use of Energy is important Promoter Sequence Positive regulation Allow transcription Negative regulation Prevent transcription

The Genetic Code Nucleotides information storage and transfer (DNA RNA) Nucleotides information storage and transfer (DNA RNA) Amino Acids Make proteins that do work Amino Acids Make proteins that do work Degeneracy genetic code robust hard for nucleotide to change function of protein it encodes Degeneracy genetic code robust hard for nucleotide to change function of protein it encodes

Protein Structure and Function 20 amino acids 20 amino acids Protein Chain Protein Chain Starts at Amino group – amino terminus Starts at Amino group – amino terminus Ends at Carboxylic acid group – carboxy terminus Ends at Carboxylic acid group – carboxy terminus Native Structure – complex globular structure Native Structure – complex globular structure Amino acids determine shape Amino acids determine shape Shape helps perform role Shape helps perform role

Molecular Biology Tools Restriction Enzyme Digest Restriction Enzyme Digest Enzymes that break double strands used like scissors later pasted to DNA to isolate given nucleotides Restriction mapping Cloning insert DNA into vectors and replicate to get large numbers

Molecular Biology Tools Gel electrophoresis Gel electrophoresis Uses electrodes to separate molecules by size. Blotting and Hybridization Looking for one or more fragments Probes used to find unique piece

Genomics and Impact Genome – Organisms complete set of DNA Genome – Organisms complete set of DNA Chromosomes Chromosomes Genes made up of 50 to 250 million base pairs Genes made up of 50 to 250 million base pairs Proteins perform the work Proteins perform the work 20 amino acids 20 amino acids 3D structure defines function in cell 3D structure defines function in cell

Human Genome Project DNA sequence consists of 3 billion base pairs DNA sequence consists of 3 billion base pairs Will guide research and discovery for years Will guide research and discovery for years Find out how cells-genes-proteins work to create living organisms Find out how cells-genes-proteins work to create living organisms

Medicine and the New Genetics Genetic Testing Genetic Testing Confirm or predict risk of disease Confirm or predict risk of disease Prognosticate disease path Prognosticate disease path Detecting mutations Detecting mutations Pharmacogenomics Drugs for a genotype Minimal side effects Work faster Cheaper cost to develop Faster to develop

Other Benefits Molecular Medicine Molecular Medicine Microbial Genomics Microbial Genomics Risk assessment Risk assessment Bioarchaeology, Anthropology, Evolution, and Human migration Bioarchaeology, Anthropology, Evolution, and Human migration DNA identification DNA identification Agriculture, Livestock breeding, and Bioprocessing Agriculture, Livestock breeding, and Bioprocessing

Resources form the NCBI National Center for Biotechnology Information National Center for Biotechnology Information Infrastructure for Molecular Biology research Infrastructure for Molecular Biology research Diverse Data a challenge Diverse Data a challenge Sequence Data needs to be used for analysis and retrieval Sequence Data needs to be used for analysis and retrieval

GenBank DNA sequence Database DNA sequence Database 133,000 sequences form species other than human 133,000 sequences form species other than human Protein sequence Protein sequence

GenBank Building GenBank Building GenBank DNA sequence given unique corresponding Accession number DNA sequence given unique corresponding Accession number When sequence changed “gi” number given to new sequence When sequence changed “gi” number given to new sequence BLAST algorithms screen for contaminated unwanted erroneous sequence data BLAST algorithms screen for contaminated unwanted erroneous sequence data

GenBank BankIt and Sequin BankIt and Sequin Submission tools to build GenBank Submission tools to build GenBank

RefSeq Reference Sequence Reference Sequence Aims to nonredundant source of sequence data Aims to nonredundant source of sequence data Gene characterization Gene characterization Mutation analysis Mutation analysis Expression studies Expression studies Polymorphism discovery Polymorphism discovery Submitted data gets organized Submitted data gets organized

Entrez Integrated access and retrieval system Integrated access and retrieval system Links many resources to help Scientists find what they need Links many resources to help Scientists find what they need Significant innovation for Bioinformatics Significant innovation for Bioinformatics

BLAST Family of sequence comparisons algorithms Family of sequence comparisons algorithms Nucleotides and protein sequences understood by comparison to one another Nucleotides and protein sequences understood by comparison to one another Type in sequence and BLAST finds similar in the Entrez system Type in sequence and BLAST finds similar in the Entrez system