Metabolic Biochemistry on the Internet

Metabolic biochemistry is a century old field of science where organic chemists studied the reactions of carbon compounds in living cells, mainly using extracts from animal tissues (liver, skeletal muscle, brain) and plants (photosynthesis). The central pathway that links energy needs with biosynthetic pathways, the Krebs Cycle or Citric Acid Cycle, has been described in 1937. All biochemistry textbooks, therefore, contain basic information about the cellular metabolisms of a variety of organisms that can be considered factual. An introductory course like this one is designed to give an overview of these basic elements of intracellular conversions of chemical structures and energy storage. The great variety of textbooks is a living prove to the advanced state of biochemistry. Nevertheless, many details are still under active exploration in laboratories around the world. A plethora of unique chemical pathways in microorganisms, and cell type specific metabolic needs in animals and plants promise many future discoveries. The recent advances in genome sequencing and the concomitant establishment of databases of DNA and amino acid sequences (see NCBI; National Center for Biotechnology Information), protein structures (see PDB; Protein Data Base; Research Collaboratory for Structural Bioinformatics), and higher databases like metabolic pathway maps (see KEGG, EcoCyc, and other (metabolic pathway) databases), provide a gold mine for today's biochemical research. Biochemistry and molecular biology are transforming themselves into Proteomics and Genomics (see ExPasy; WWW server from the  Swiss Institute of Bioinformatics). Knowing the nucleotide sequence of a gene is a major step forward, but the work does and cannot stop there. Metabolism is the coordinated activity of thousands of enzymes that catalyze a similar number of substrates in cyclical and linear stepwise fashion. These pathways are the way of a cell to extract energy from and chemically modify molecular structures for biosynthetic purposes.

For more information check out this book:

Bioinformatics Basics Applications in Biological Science and Medicine, CRC Press
This new book by H.Rashidi and L.Buehler gives you  instructions on using the Internet to retrieve information about metabolic pathways, protein structures, the human genome project, molecular evolution, and hereditary diseases..

KEGG: Kyoto Encyclopedia of Genes and Genomes
This web site is designed to help students use the publicly available resources as an additional resource to their textbooks. The KEGG metabolic database is a supplement, a hopefully useful one, to textbooks, but is not organized like a textbook. Often, one has to find one's way through a lot of information that is not relevant to an introductory biochemistry course. But this should encourage everybody to make use of this tool. As this Web site can be helpful as a supplement to class notes and textbooks, it is, however, not a textbook in its own right.

KEGG is a structured database that allows to search and find information about metabolic pathways in many microorganisms for which the complete genomic sequence is available, but also for the two mammalian species Homo sapiens and Mus musculus. For both species, only a fraction of their respective genome has been sequenced and many genes (and their proteins) remain to be described. The humane genome, however, is projected to be finished in the next two years. In December 1999, the complete sequence of the human chromosome 22 has been published. Complete means somewhere between 90 to 95% of the entire nucleotide sequence. A small portion of chromosomes contains difficult to sequence repeats.

All links termed 'KEGG' used on this class web page refer you to the KEGG table of contents. You can find the table of contents also by clicking on the 'Open KEGG' link on the KEGG home page. Access to the table of content will lead you to all other links necessary to find everything stored in this database.

- Pathway Maps and Ortholog Tables
- Disease Catalogs, Cell Catalogs, and Molecule Catalogs
- Gene Catalogs
- Java Map Browsers
- Computational Tools
To directly search for a compound, enzyme, or gene of interest you can click on the 'Search and compute with KEGG' link on the KEGG home page which will bring you to a page where you will find search features for
- pathway maps
- genome maps
- coloring tools
- prediction tools
- sequence similarity
These links are useful if you know exactly what you are looking for because this search mode requires the exact entry number, e.g. enzyme nomenclature E.C. for hexokinase, or chemical compound number, e.g. C00417 for cis-Aconitate.

For a keyword search or if we only know the name or even partial name of an enzyme, compound, or pathway, we need only be concerned with three links on the table of contents page.

For a more detailed help on how to find a chemical structure, metabolite, enzyme or pathway in KEGG follow the 'Frequently Asked Questions' link here.

H o m e
 Copyright © 2000-2003 Lukas K. Buehler