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Unformatted text preview: 8-1Experiment 8Introduction to Internet Proteomics Tools IntroductionBioinformatics is a knowledge-based approach to research and biotechnology: it is the cataloging, storage, and retrieval of information placed in databases on proteins, genes and genomes, regarding their structures, biological functions, cellular localizations, structural modifications, regulations of expression, and mechanisms of action. These databases might be research journals available on-line or a cataloging of information housed by the National Institutes of Health (NIH) and other institutions. They are easily accessed through the Internet and are often cross-referenced. Proteomics is the area of bioinformatics focused on proteins. Biochemical research and biotechnological goals often involves deliberate changes to the primary structure of a protein, by site-directed mutagenesis, to assess structure-function relationships, and these altered proteins must be purified and characterized. Characterizations might include any of the following: primary sequence determination, X-ray crystallography, mass-spectrometry, NMR, kinetic analysis, relative expression levels in cells, etc. Traditionally, the primary structures of purified proteins were obtained by amino acid sequence analysis. Comparisons of amino acid sequences of different proteins provide insight into their function and evolutionary history. Since the 1980s, the cloning of protein encoding genes has permitted the derivation of primary protein structures from sequencing DNA copies of their mRNAs (iecDNAs) for many proteins not purified nor sequenced by traditional methods, such as membrane proteins. Automated amino acid and nucleic acid sequencing methods currently used have made rapid accumulation of primary structural information possible. Indeed, the advent of automated DNA sequencing, and computer-driven information management, permitted entire genomes to have been sequenced, cataloged, and made easily accessible using the Internet. Consequently, purification is not wholly necessary to begin complex molecular, biochemical, and cellular analysis of protein function. With just a fragment of either an amino acid or a DNA sequence, proteins can be identified from a search of genomic databases by sequence similarities with known sequences of related proteins. There are many other cutting-edge techniques being developed, as well as adapting new applications to established techniques, to approach what were once intractable problems. ObjectivesThese out-of-class exercises compliment Experiments 3-7 using the Internet accessed proteomic databases. Be sure to read the Introduction and Theory portions of the Experiments complimentary to these exercises....
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- Fall '10