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. 2.7.1.1 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
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