Abbreviations in Biochemistry

Methods of Biochemical Analysis to pertinent text sec- Common Abbreviations in Biochemistry These abbre-tions within a chapter. viations can be found at the end of the text. 

Unfortunately, the literature cited here uses the abbreviation Gly, which in biochemistry is generally reserved for the amino acid glycine, for glycerine. 

Abbreviations and symbols for chemical names of special interest in biological chemistry /. Biol Chem. (1966) 241, 527-533 Abbreviations and symbols a compilation Eur. J. Biochem. (1977) 74, 1-6 Trivial names of miscellaneous compounds of importance in biochemistry J. Biol Chem. (1966) 241, 2987-2994 Citation of bibhographic references in biochemical journals... 

The present chapter includes commercially available organic chemicals. Most of the organo- phosphorus, boron, silicon, alkali metal compounds and metal ion salts are in Chapter 4. Naturally occurring commercially available organic compounds of use in biochemistry, molecular biology and biology are included in Chapter 5. Abbreviations of words and some journal names are listed in Chapter 1, pages 1 and 2. 

For our example, let us consider the arduous task of learning common amino acids not only by structure but also by both the three- and one-letter abbreviations. Furthermore, we want students to distinguish between acidic and basic side chains. Such a task is common in biochemistry either in introductory or upper-level course offerings. Frequently, the instructor will make the assignment to memorize the list and leave the students to do it (or not). Based on Herron s principle of minimum effort (Herron 1996), students will need to recognize the value of the learning goal to devote effort toward it. On the one hand,... 

Kinetic equations are commonly expressed in terms of the amount-of-substance concentrations of the chemical species involved. The amount-of-substance concentration is the amount of substance (for which the SI unit is the mole, symbol mol) divided by the volume. As it is the only kind of concentration commonly used in biochemistry it is usually abbreviated to concentration and this shorter form will be used in the remainder of this document without further discussion. The unit almost invariably used for concentration is mol dm", which is alternatively written as mol L, mol 1, or simply KMK (molar). "- ... 

The titration of a weak acid with a strong base puts all our knowledge of acid-base chemistry to work. The example we treat is the titration of 50.00 mL of 0.020 00 M MES with 0.100 0 M NaOH. MES is an abbreviation for 2-(A -morpholino)ethane-sulfonic acid, a weak acid with pK = 6.27. It is widely used in biochemistry as a buffer for the pH 6 region. 

An earlier abbreviation for atomic mass unit (amu) is still in common usage. In biochemistry and molecular biology, the atomic mass unit is often called a dalton (Da) especially in reference to the atomic mass of proteins. 

II-l). In biochemistry this energy-rich, activated component is very often adenosine triphosphate abbreviated as ATP ... 

Units of Amount and Concentration. In chemistry, the customary unit of amount is the mole (1 mole equals the molecular weight expressed in grams) and the unit of concentration is moles per liter. Since in biochemistry we almost always deal with small amounts and low concentrations, we use units which are smaller by the factor of 1000 they are the miUimole (mmol), for amounts, and the millimole per liter (mAf), for concentrations. The unit for coenzymes often is the micromole, umol, being equal to 10 moles. Care should be taken not to use the abbreviation of concentration mM (= millimolar) incorrectly for millimoles, which are amounts. 

Several of these IFNs of mouse and human lymphocytes and fibroblasts are available commercially and have been best prepared in quantity by recombinant DNA procedures because they are produced in very small amounts by the cells. The commercial materials do not generally require further purification for their intended purposes. [Pestkas, Interferons and Interferon standards and general abbreviations. Methods Enzymol, Wiley Sons, 119 1986, ISBN 012182019X Lengyel, Biochemistry of interferons and their actions, Ann Bev Biochem 51 251-282 7982 De Maeyer and De Maeyer-Guignard, Interferons in The Cytokine Handbook, 3rd Edn, Thomson et al. Eds, pp. 491-516 7998 Academic Press, San Diego, ISBN 0126896623.]... 

Abbreviations BSO, D.L-buthionine-. i -sulfoxime L , lipid alkyl radicals LH, lipid LO, Upid alkoxyl radicals LOO, Upid peroxyl radicals L-NAME, yV -nitro-L-arginine-methyl ester MBl, methylene bridge index (mean number of h -aUytic methylene positions per fatty add) NO, nitric oxide NOS, nitric oxide synthase NO, nitrite N02, nitrogen dioxide NO2CI, nitryl chloride O2 , superoxide OH, hydroxyl radical OL, epoxyaUyhc radical OLOO, epoxyperoxyl radical 0=NOO , peroxynitrite SNAP, S-nitroso-iV-acetyl-D.L-penicillamine SOD, superoxide dismutase contd. onp. 98, Subcellular Biochemistry, Volume 36 Phospholipid Metabolism in Apoptosis. 

Biochemists are marvelous at iuveutiug abbreviatious, perhaps because mauy of the molecules of biochemistry are quite complex aud have correspoudiugly complex aud clumsy names. So abbreviation seems like the right way to go. A capable biochemist can speak for quite a while in a way quite unintelligible to those not in the know about the abbreviations. Physicians and lawyers do the same thing but without the abbreviations. 

The importance of X-ray diffraction (discussed in Chapter 3) to biochemistry is obvious, but techniques related to absorption of X-rays and y-rays have also come into widespread use.117 Abbreviations such as XANES and EXAFS are common in the metallopro-tein literature. The names arise from the sharp increase in the absorption coefficient for X-rays as their energy is increased to what is called the K absorption edge. At slightly lower energies absorption of an X-ray by an atom leads to expulsion of an electron or the raising of an electron to an excited state. Absorption of X-rays will expel all except the inner Is electrons. 

The carboxyl group (abbreviated -CO2H or -COOh) is one of the most widely occuring functional groups in chemistry as well as biochemistry. Tlie carboxyl group of a large family of related compounds called Acyl compounds or Carbocylic Acid Derivatives. 

Membranes were incubated with 0.2 nM [3H]NPY ( /Q) for 60 min at 37°C as previously described (Daniels et al., 1995a). Results are presented as the IC50 calculated from non-linear regression analysis of the concentration-dependent displacement data. The abbreviations for the amino acids are in accord with the recommendations of the International Union of Pure and Applied Chemistry/lnternational Union of Biochemistry Joint Commission on Biochemical Nomenclature [(1984) Eur. J. Biochem. 138,9-37]. The symbols represent the L-isomer except where indicated otherwise. 

For documentation purposes, a much-abbreviated reaction scenario for glutaminolysis is shown in Figure 3.3. Glutamine is an amino acid, and glutaminolysis is only part of the more general topic of the metabolism of amino acids, which is covered in the standard texts and references on biochemistry. 

The glycolysis pathway is a prominent reaction sequence featured in texts and treatises on biochemistry and microbiology, according to the previously cited Chapter 3, and an abbreviated version is also sometimes presented, for instance, by Boik (1996). To reiterate, the primary product of glycolysis is pyruvic acid, CH3COCOOH, which may also be represented as the pyruvate ion, or CH3COCOO. The pyravic add or pyruvate further reacts to form carbon dioxide and watCT, or... 

We have chosen not to include abbreviated summaries of the inorganic chemistry, biochemistry, and spectroscopy that students may need as background in order to master the material presented. We instead assume that the instructor using this book will assign reading from relevant sources that is appropriate to the background of the students taking the course. 

Abbreviations used in CSiapters 6 and 7 are described in Biochemical Nomenclature and Related Documents published in 1978 by the International Union of Biochemistry. 

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