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The first two decades of this century promise to be to biochemistry what the first two decades of the last century were to physical chemistry. With such an explosion of knowledge, the literature becomes quite vast. By far the workhorse Web site for any biochemist who wants to keep abreast of these advances (but can't afford access to the more expensive and more comprehensive databases) is the National Center for Biotechnology Information. From NCBI, numerous databases can be accessed including PubMed. PubMed abstracts about 4,500 journals, including virtually all of the biochemistry and molecular biology journals.
When preparing lectures, I like to spend at least 1-2 hours searching PubMed for the most recent information on topics I am going to cover. It is not at all uncommon to find textbook errors or shortcomings this way, and demonstrate to the students the need to stay abreast of new advances in biochemistry. In conjunction with the PubMed searches I often end up at the College Net search page to locate researchers whose abstracts I plan to cover in class. When Medline abstracts don't include email addresses of authors, individual academic researchers in the U.S. can often be found from their institutional home pages. I estimate that 80% of the researchers I contact with specific questions on their research (based upon what I learned from Medline) will respond, and about half of those within two days. This gives me the time to include their comments in lectures, or even forward their email comments to students. It both surprises and motivates students to realize that top-notch researchers at institutions such as MIT, Harvard, Stanford, or CalTech will take the time to answer questions about topics related to what we are currently discussing in the undergraduate biochemistry course.
From NCBI you can also access many nucleic acid sites and search any of the nearly 15 million gene sequences in the GenBank, or examine any of the over 800 species whose entire genome has been sequenced (including Homo sapiens) from the Entrez genome database. You can also perform BLAST searches from sequence data in either the GenBank or Entrez. Speaking of genomes, did you know that Amoeba dubia has a genome nearly 200 times larger than that of humans? What's up with that? Take a look at the database of genome sizes (DOGS).
Viewing individual protein structures often aids in understanding metabolism at the molecular level. Two sites are invaluable in this regard. At http://www.umass.edu/microbio/rasmol/ the freeware programs Rasmol, Chime, and Protein Explorer can be obtained. These programs are great tools to introduce and explore protein structures on the computer (Fig. 1). At http://www.rcsb.org/pdb/ you can access the protein data bank and obtain the files in PDB format for viewing any of the more than 16,000 entries using the programs above. Maybe you want to know how olestra works. You can use Rasmol to view this molecular octopus, or any other of 1400 small molecules of biochemical interest that can be downloaded in PDB format files. (See Fig. 2.)
Figure 1. The structure of an immunoglobin domain taken from the Rasmol home page. This figure was created using Rasmol software developed by Eric Martz at the University of Massachusetts. |
Figure 2. The structure of Batrachotoxin, a poison from South American frogs, shown in space-filling mode. The Protein Data Bank-formatted file for this molecule was created by Dave Woodcock at Okanagan University College in British Columbia and is displayed using Rasmol software. |
One of the best carbohydrate sites is from the Iowa State University. There are several tutorials there and numerous links. Lipid structures in PDB format that can be used in Rasmol are available at the Membrane Lipid Homepage.
When teaching metabolism, or when generating exams covering metabolic pathways, I spend a good deal of time at the Kyoto Encyclopedia of Genes and Genomes (KEGG) site. Which amino acid side chains of citrate synthase are involved in catalysis? I especially like their metabolism presentation format that allows users to examine selected pathways individually, by species, and to identify enzymes within those pathways whose crystal structures are available in the PDB. For signal transduction pathways, a valuable resource is Science magazine's STKE (you have to be a subscriber for full access).
If you are interested in the plant side of biochemistry, especially anything regarding genetically modified foods, a great resource with many useful links is the Biotechnology Information Resource from the National Agricultural Library.1 What is all the uproar about Starlink® corn? Find out about Bacillus thuringiensis.
PowerPoint users should take the time to register as an instructor and get access to the PowerPoint figures for each chapter of the Lehninger, Cox, and Nelson text. The site is designed for those who have adopted the text, but prospective users can get access. Another useful PowerPoint site is David Bender's at University College London. If your students won't read but will work online, send them to http://www.biology.arizona.edu/biochemistry/biochemistry.html for tutorials and quizzes on many aspects of biochemistry. If they want more challenging evaluations, try the USUHS (Uniformed Services University) Medical School biochemistry exams.
With so many biochemistry sites to choose from, searching the Web for biochemistry topics is like being a "kid in a candy shop." However, to reap the benefits, you must put in a bit of time and have a bit of patience. Good hunting.
Note
- At press time USDA's National Agricultural Library site is no longer being kept up but still contains many links that are superior to those on the replacement site.
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