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Biocatalysis and Biodegradation
Spring Semester, 2010
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Course Outline
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- Microbial Environmental Biochemistry.
Organic compounds, scope and sources. The role of microbes in recycling organic matter. Enzymology and genetics of environmentally relevant microbial reactions. Gene designation nomenclature and GenBank designations, nucleic acid databases. Integrated protein and nucleic acid databases (Entrez). Molecular evolution of novel biochemical pathways in bacteria commonly found in soil and water.
- Biocatalysis and Biodegradation.
What are biocatalysis, biodegradation and bioremediation? Finding information on bioremediation on the Internet. Using search engines. Comparing different Internet search engines. Doing multiple parallel searches at once. Browsing. Checking links. Finding lists to browse. Microbial catabolic enzymes - the Biocatalysts. Enzyme Commission nomenclature - the "mechanisms." Enzyme databases. Enzyme Commission (EC) codes and their relevance to enzyme mechanistic classes. Assigning EC codes. Entry of unique pathways into intermediary metabolism. Systematic organization of biocatalysis/biodegradation information. Bioremediation: A case study.
- Introduction to the University of Minnesota Biocatalysis/Biodegradation Database and HTML.
What is the UM-BBD? Why was it created: its goals and users. UM-BBD information resources such as ChemFinder, EXTOXNET, Kyoto LIGAND enzyme database, GenBank, PubMed, the DSM and ATCC microorganism databases. Ways to verify or validate information. Searching and browsing the UM-BBD. Elements of HTML. UM-BBD File Name conventions. A minimum Web page. Viewing source. Consistency, standards. Using templates. Cutting and pasting. Viewing local files. Linking, adding links. Transferring files to a personal webspace and viewing them there.
- Compiling and Validating Metabolic Pathway Information.
Intermediary Metabolism and its Databases. Why and how a biodegradation pathway connects to intermediary metabolism. How to measure the validity of biochemical information. Using the Entrez PubMed Browser. Creating a bibliography on an assigned microbial metabolic pathway, both in written form and as Entrez citation and search URLs. Finding or assigning EC codes to the enzymes in your pathway. Describing the significance of your assigned pathway.
- Pathway and Compound Information in the UM-BBD.
The UM-BBD directory structure. Creating that structure on your own computer, and on your personal webspace. Creating a "pathway map in progress" for your pathway. Using the ChemSketch chemical drawing program. Drawing compound structures as gif files. Making your pathway HTML and compound structure information available on the World Wide Web in your personal webspace.
- Enzyme Substrates.
Physico-chemical properties of organic molecules: how to get the information and how to use it. Systematic chemical nomenclature systems: IUPAC and CAS Registry. Searching selected chemical databases. Discovering other sources of chemical information. Finding CAS number and other information. Authoring HTML UM-BBD compound pages. Adding compound links to your "pathway map in progress".
- Enzyme Reactions.
Drawing reaction graphics as gif files. Adding highlighting to reaction graphics. Finding enzyme information in GenBank and PubMed. Authoring HTML UM-BBD reaction pages. Adding reaction links to your "pathway map in progress".
- The Finishing Touch.
Authoring graphical pathway maps. Creating clickable graphic pathway maps. Creating PubMed link records. Verifying all links and checking the format of your own pathway. Doing the same for a pathway of another class member. Reflecting on what you have learned in this course. Conclusions.
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