Practical Abbreviations in Applied Biochemistry

149 Village on my way through London's Heathrow airport. Cargo Village is literally miles away from the passenger terminals on the other side of the airport, and I nearly missed my connection for the Sudan. To my knowledge, that was the only crisis (or near crisis) associated with the production of the book. Relaxing on the terrace of the Grand Hotel, overlooking the Blue Nile, just a short walk from the palace where Gordon of Khartoum was murdered by the followers of the Mahdi, I tried to ignore my exotic surroundings and bring some degree of objectivity to bear on the correction of the proofs. Subsequently, as a source of information for final-year lecture and MSc seminars, and for answering queries from students, the Concise Encyclopedia (in the form of a complete set of page proofs) proved remarkably effective. Since it places equal emphasis on all areas of Biochemistry, we hope this book will be just as useful to clinical, microbiological and plant biochemists, in both teaching and research. Already we have started collecting, classifying and revising for the second edition. Criticisms of the first edition and suggestions for new entries will be gratefully received. All new material will be thoroughly researched, edited to the style of the Concise Encyclopedia, and, with any luck read in proof on the banks of the great grey-green, greasy Limpopo river.

Note added in proof: By analogy with humans and elephants, it is to be expected that the gestation period of an article in

Biochemical Education will be somewhat shorter than that of an encyclopedia, albeit a concise one. Barely six months have elapsed between submission and typesetting of the present manuscript. During this period the Concise Encyclopedia has been published and there has even been time for a preliminary assessment of its success. Several biochemists have already written to express enthusiasm for the project (eg "I have dipped into it very frequently since my volume arrived here, and I have been very delighted by the type of information that you have put into the book"), and valuable suggestions for future entries have started to arrive. Sales in the USA have been brisk, and a second printing has been ordered by the publishers; this has given us the opportunity to correct some minor printing errors. Thgmas A Scott

This is w h a t F r a n k Vella t h o u g h t o f the Concise Encyclopedia: This is a useful and handy reference work on biochemistry. For me, it will replace the scurrying through the index pages of several textbooks (often to no avail) when I need to find out something about an unfamiliar biochemical compound or process. There are over four thousand entries. They vary in length from one line to an eleven-page essay (with fourteen figures and a table) on vitamins, and are extensively crossreferenced. Some entries contain references to the literature. Microbiological, animal, and plant areas are well represented. The writing is clear, concise and complemented by structural formulae, metabolic pathways, figures and tables. If updated periodically, this book could quickly become an important source book of value to teachers, graduate students, and many others in all areas of biological science.

B i o c h e m i c a l E d u c a t i o n 11(4) 1983

Practical A b b r e v i a t i o n s in A p p l i e d B i o c h e m i s t r y J M MACARULLA and A MARINO

Department of Biochemistry University of Pais Vasco Bilbao, Spain Introduction Abbreviated forms of representing the name and/or structure of biomolecules are often found in biochemical literature. Tentative or definite rules are periodically established by IUPAC-IUB1,2,3 in order to consolidate efforts of rationalizing the biochemical nomenclature. One of the main objectives of these rules is to avoid any ambiguity or imprecision. With these ideas in mind, we would like to propose a series of minimal abbreviations that, in the same way as longer and more widely accepted ones, could designate monomers as well as more complex substances, unambiguously. Many of the abbreviations proposed here consist of a single letter. However, their meaning is made clear by the context. Indeed, this is what happens with some of the initials currently in use. For instance, the letter G can symbolize, according to the context, guanine, guanosine, glycine, Gibbs free energy, a class of immunoglobulins, glycerate, etc. In the same way, it could mean glucose. 4 Aim of this paper Our suggested abbreviations do not intend to modify the rules established by IUPAC-IUB, but rather to help biochemistry teachers to express the formulae and structures of biomolecules in a clear and concise way. Our abbreviations could be used in textbooks and research papers as long as IUPAC-IUB does not define more universal ones. According to the context, a capital A following the abbreviated name of an aldose indicates the corresponding aldonic acid, while a U means the uronic acid. In this case we prefer U over A because the acid, under physiological conditions, ie at neutral pH, will be in the salt form (A: aldonate, U: uronate), and the letter U is more specific. Generally speaking, if the structure of the molecule under consideration is very complex, shorter abbreviations may be used for each of its components, since the danger of ambiguity is obviated by the context.

Rules (1) Abbreviated names are based on the English name of the substance, and should be used in the same form even in other languages. (2) The most common substances are designated by a single letter and the less frequent ones by more than one letter. (3) The same abbreviation may have different meanings if ambiguities are avoided by the context. If not, the use of abbreviations is precluded. (4) Speaking of carbohydrates, a lower case 'u' means a ketose, eg R = ribose, Ru = ribulose. (5) Similarly, an T indicates a polyol: R1 = ribitol, Inl = inositol. (6) Ac stands for acetyl and Ac for acyl. N indicates the location of these radicals: NAc = N-acetyl, NAc = N-acyl.

150 (7) A means aldonic acid or aldonate: GA = gluconic acid (gluconate), GaA = galactonic acid (galactonate). (8) U means uronic acid or uronate: GU = glucuronic acid (glucuronate), GaU = galacturonic acid (galacturonate). (9) Unless otherwise stated, all sugars belong to the D series, all aminoacids to the L series. Stereospecific numbering is always used for glycerol. Thus: G = D-glucose, Ala = L-alanine, Gro-3-P = sn-Glycerol 3-phosphate. (10) Unless otherwise stated, glucose, xylose, hexosamines, glucuronic acid, neuraminic acid, when integrated in polymers, are in the pyranose p form. (11) Unless otherwise stated, ribose, deoxyribose and fructose, when integrated in polymers, adopt the furanose f form. (12) In carbohydrates, glycolipids or glycoproteins, the a or /3 anomeric form should be expressed together with the number of the carbon involved in the glycoside linkage: G ( l a 4)G = maltose, G(1/~ ~ 4)G = ceUobiose. (13) If both monosaccharides have their anomeric carbons involved in the glucosidic bond, this should be indicated by a double-headed arrow: G ( l a "~, 2~)F = sucrose, G ( l a ~ 2 a ) G trehalose. (14) A polymer can be expressed in similar way: [G(la ~ 4)] n = amylose [X(1/3 ~ 4)] n = hemiceUulose [NAG(l/3 ~ 4)] n = chitin The last monomer can usually be left unrepresented in these abbreviated formulae. (15) When a given monomer is involved in various glycosidic bonds, this can be expressed writing the abbreviated formula on more than one line.

Table 1 Some abbreviated forms for the designation of usual carbohydrates Compound or group Acetyl N-acetylgalactosamine N-acetylglucosamine N-acetylneuraminic acid Acyl Arabinose Choline Erythrose Erythrulose Fructose Galactose Galacturonic acid Glyceric acid Glycerol Glucose Glucuronic acid Idose Mannose Xylose Xylulose

IUPAC-IUB Symbol Ac GalNAc GlcNAc NeuAc Acyl Ara Cho Ery Eru Fru Gal GalA Gri Gro Glc GlcA Ido Man Xyl

Biochemical Education 11(4) 1983

Minimal Abbreviation mc NAGa NAG NAN

Ac Ar C E Eu F Ga GaU GA G1 G GU I M X Xu

G ( l a ~ 4) G(la~6)

] G n =glycogen

[GU(1/~ -+ 3)NAGa(lfl 4 ~ 4)] 1" S

= chondrointin sulphate A n

WAGa(I/~ ~ 4) Ga(1/3 ~ 4) G(1/3 ~ 1) Cer = GM2 ganglioside 3 2a NAN The above rules can be further exemplified, as shown in Tables 1 and 2, for simple and complex compounds respectively.

Table 2 Some abbreviated forms for the designation of more complex biomolecules Compound

IUPAC-IUB Symbol

Ceramide Phosphatidylcholine Triacylglycerol Phosphatidylethanolamine Phosphatidylserine Sphyngomyelin Ribose 5-phosphate Glucose 6-Phosphate Glycerol 3-phosphate

Minimal Abbreviation

Cer PtdCho TriacylGro PtdEtn PtdSer CerPtdCho Rib-5-P Glc-6-P Gro-3-P

Cer PC TG PE PS SP R5P G6P G 13P

Discussion Tables 1 and 2 show both the IUPAC-IUB and our abbreviations for a series of compound that appear frequently in biochemistry courses. Thus, N-Acetylneuraminic Acid, NeuAc, may be substituted by NAN. References 1 Biochemical Nomenclature and Related Documents. IUB, (1978) 2 Abbreviated Terminology for Oligosaccharide Chains. J Biol Chem 257, 3347-3351 (1982) 3 The nomenclature of Lipids. Biochem J 171, 21-35 (1978) 4 j M Macarulla and F M Gofii (1981). Biomol~culas 2nd edn Revert~ SA Spain C a l m o d u l i n a n d I n t r a c e l l u l a r Ca ++ R e c e p t o r s Edited by S Kakiuchi, H Hidaka and A R Means. pp 476. Plenum Press, New York and London. 1982. $49.50. ISBN 0 - 3 0 6 - 4 1 1 0 9 - 1 This volume contains the proceedings of a sateUite symposium to the Eighth International Congress of Pharmacology held in Japan in July 1981. The collection together of a wide range of articles on this exciting area will undoubtedly prove to be a useful reference work for both researchers and students. However for students new to this area, what was really lacking is a general introductory chapter or overview. There are 28 papers and the book is divided into three main sections: "Molecular Basis of Calmodulin Function", "Ca 2+ and Protein Phosphorylation", and "Ca 2+ Regulation of Microfilament System". G Thorold