Structural Chemistry And Nomenclature

Naming systems are complex and have to be learned. The naming of lipids often poses problems. When the subject was in its infancy, research workers gave names to substances that they had newly discovered. Often, these substances would turn out to be impure mixtures and as the chemical structures of individual lipids became established, rather more systematic naming systems came into being. Later, these were further formalized under naming conventions laid down by the International Union of Pure and Applied Chemistry (IUPAC) and the International Union of Biochemistry (IUB). Thus, triacylglycerol is now preferred to triglyceride, but the latter is still frequently used especially by nutritionists and clinicians and you will need to learn both (Chapter 3). Likewise, outdated names for phospholipids: 'lecithin' (for phosphatidylcholine, Chapter 6) and 'cephalin' (for an ill-defined mixture of phosphatidylethanolamine and phos-phatidylserine) will be avoided in this book but you should be aware of their existence. Further reference to lipid naming and structures will be given in appropriate chapters.

The very complex naming of the fatty acids is discussed in detail in Chapter 2. Their main structural features are their chain lengths, the presence of unsaturation (double bonds) and of substituent groups. In regard to chain length, it is cumbersome to have to say every time: 'a chain length of ten carbon atoms' and we shall, therefore, refer to a 'IOC fatty acid'. If we wish to refer to a specific carbon atom in a chain, we shall write, for example: 'the substituent at CIO'. The numbering of fatty acid carbon atoms is done from the carboxyl end of the chain with the carboxyl carbon as CI. An old system of identifying carbon atoms was to give them Greek letters. Thus, C2 was the a-carbon, C3 the P-carbon and so on, ending with the rn-carbon as the last in the chain, furthest from the carboxyl carbon. Remnants of this system still survive and can sometimes be discerned in this book. However, we will routinely use the numbering, rather than the Greek lettering system. Hence, we will use 3-hydroxybutyrate, not P-hydroxybutyrate etc.

An important aspect of unsaturated fatty acids is the opportunity for isomerism, which may be either positional or geometric. Positional isomers occur when double bonds are located at different positions in the carbon chain. Thus, for example, a 16C monounsaturated fatty acid may have positional isomeric forms with double bonds at C7 or C9, sometimes written A7 or A9. (The position of unsaturation is numbered with reference to the first of the pair of carbon atoms between which the double bond occurs.) Two positional isomers of an 18C diunsaturated acid are illustrated in Fig. 1.1(c) and (d). Geometric isomerism refers to the possibility that the configuration at the double bond can be cis or trans. (Although the convention Z/E is now preferred by chemists instead of cis/ trans, we shall use the more traditional and more common cis/ trans nomenclature throughout this book.) In the cis form, the two hydrogen substituents are on the same side of the molecule, while in the trans form they are on opposite sides [Fig. 1.1(a) and (b)].

Another important feature of biological molecules is their stereochemistry. In lipids based on glycerol, for example, there is an inherent asymmetry at the central carbon atom of glycerol. Thus, chemical synthesis of phosphoglycerides yields an equal mixture of two stereoisomeric forms, whereas almost all naturally occurring phosphoglycerides have a single stereochemical configuration, much in the same way as most natural amino acids are of the L (or S) series. In the past, naturally occurring compounds were designated L-a- and represented by a Fisher projection (see Fig. 1.2). The glycerol derivative was put into the same category as that glyceraldehyde into which it would be transformed by oxidation, without any alteration or removal of substituents. Phosphatidylcholine was therefore named: L-a-phosphatidylcholine. The IUPAC-IUB

/ \ CH3(CH2)rCH2 CH2(CH2)XCOOH

12 9


(c) cis, cis -9, 12-octadecadienoic acid



(d) cis, cis -6, 9-octadecadienoic acid

Fig. 1.1 Isomerism in unsaturated fatty acids.


7 CD7



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