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Biochemistry dictionary

Version 0.95 (Spring 2005)

Biochemistry is a vast subject that occurs at the intersection of a number of disciplines, from chemistry and physics to medicine and psychology. One of the daunting tasks facing the prospective student of biochemistry is to acquire the vocabulary with which biochemical concepts are described and discussed. The difficulty of this task has become especially acute with the explosion of knowedge occurring in this field, driven largely by the steady and rapid accumulation of genomic information, and the need to understand its meaning. Another challenge is to keep sight of the interrelationships among the vast collection of information and observations, and to make new connections that enrich understanding. This project began as my attempt to organize some biochemical inforamation in a form useful and pleasing to myself, with a distant hope that others might find it helpful as well. As the project evolved (and I became more involved with teaching), I made inclusion of most of the basic concepts an explicit goal, with the beginning student in mind. Given the enormity of the subject, there will inevitably be gaps and the information here will be limited and selective for the immediate, foreseeable future. Please also see the notes below on organization of the dictionary, and on browsers and formatting. Comments and questions are welcome.

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General References for the entries herein:

Stryer L.  Biochemistry (W.H. Freeman, 3rd ed. 1988; 4th ed. 1995)
Creighton TE.  Proteins: Structures and Molecular Properties (W.H. Freeman, 2nd ed. 1993)
Fersht A. Enzyme Structure and Mechanism (W.H. Freeman, 2nd ed. 1985)
Fraústo da Silva JJR, Williams RJP. The Biological Chemistry of the Elements: The Inorganic Chemistry of Life. (Oxford, 1991)
Koolman J & Rohm K-H. Color Atlas of Biochemistry (Thieme, 1996)
Kyte J. Mechanism in Protein Chemistry (Garland Publishing, 1995)
Schulz GE, Schirmer RH. Principles of Protein Structure (Springer-Verlag, 1979)
Staunton J. Primary metabolism: a mechanistic approach (Oxford University Press, 1978)
Voet D, Voet JG, Pratt CW. Fundamentals of Biochemistry (2nd ed., John Wiley & Sons, 1999)
Zubay GL. Biochemistry (McGraw-Hill, 4th ed. 1998)

Additional references from the literature are included with individual entries in some cases.

Notes on scope and organization

In developing this dictionary, I have attempted to not assume any prior knowledge of biochemistry. However, knowledge of chemistry, especially basic organic chemistry, is for the most part presumed. In some cases, familiarity with elementary cell biology would be helpful.

The organization is as follows. There are two webpages for each letter with entries corresponding to terms beginning with that letter, the "list" page and the "definitions" page. One can always select a letter from the header at the top of the page. Selecting a letter results in display of a page with a simple list of terms, i.e. the list page. The "List terms" link also will display the list page for the current letter. In many cases, there are individual term entries. A term in the list page of a given letter is a link to an individual entry if the following # symbol is a also a link. If the following # symbol is not a link, then the term links to within the "Show all definitions", or definitions page. The definitions page contains the definitions for all terms beginning with that letter. This webpage is lengthy for some letters. The individual term entries are linked here via definition headings. Links within the definitions themselves may not always be consistent, but generally if you are within the definitions pages, you will tend to stay there. The individual entries are typically more detailed than those on the definitions page. There are also external links. In particular, enzyme entries in the ExPASy ENZYME database are linked to in a separate window via the EC (Enzyme Commission of the IUBMB) number links. There are at present a few other external links to public databases, such as the Protein Data Bank (PDB) and websites of interest.

Notes on browsers and formatting:

Browser behaviors: There are a number of places in the site that make use of javascript "behaviors" that will not work properly with many older browsers, particularly Netscape. I recommend that you use the latest version of Microsoft Internet Explorer. (I am using IE 6.0 on a PC running Windows 2000.) Most behavior is compatible with versions 4.0 or greater with Netscape or Internet Explorer.

Greek letters: Another important note is that some browsers fail to show the "symbol" font. There are many terms in biochemistry (and science in general) that include Greek letters. For example, when the term a-helix is encountered, you may see it as "a-helix". I have tried to use bold font to also mark places where symbol font is used. (If you see a single character in bold, that should be a tip-off.) The best bet is to use IE 6 if you can get it. If you are experiencing problems, feel free to let me know what's happening.

Margins and printing: A left margin is set in the formatting of these web pages. If you are printing from your browser and the right hand side is cut off in your printouts, set the left margin to zero. (For IE 6, go to Page Setup in the File menu. There you will find the margin settings.) You may exprience difficulty if you attempt to export these web pages to Microsot Word, due to their complex table structure.

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© 2012 Jeff D Cronk, Gonzaga University