Enzyme terminology

Enzymes often are known by common names obtained by adding the suffix -ase to the name of the substrate or to the reaction that they catalyze. Thus, glucose oxidase is an enzyme that catalyzes the oxidation of glucose glucose-6-phosphatase catalyzes the hydrolysis of phosphate from glu-cose-6-phosphate and urease catalyzes the hydrolysis of urea. Common names also are used for some groups of enzymes. For example, an enzyme that transfers a phosphate group from ATP to another molecule is usually called a kinase, instead of the more formal phosphotransferase.  

Many enzymes require additional small molecules called cofactors for their activity. Cofactors can be simple inorganic ions such as Mg2+ or complex organic molecules known as coenzymes. The cofactor usually binds tightly to a 

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Enzyme kinetics is studied for two reasons (1) it is a practical concern to determine the activity of the enzyme under different conditions (2) frequently the analysis of enzyme kinetics gives information about the mechanism of enzyme action. Chapter 7, Enzyme Kinetics, begins with an introductory section on the discovery of enzymes, basic enzyme terminology and a description of the six main classes of enzymes and the reactions they catalyze. The remainder of the chapter deals with basic aspects of chemical kinetics, enzyme-catalyzed reactions and various factors that affect the kinetics. 

In 1946, Evans et al. [236] observed that 2-methylpropene polymerization with BF3 only starts in the presence of a small amount of water. By analogy to enzyme-co-enzyme terminology, they called water the cocatalyst. The term... 

Much of the confusion in pectic enzyme terminology was clarified by Demain and PhaflF in 1957 12) and Deuel and Stutz in 1958 11). Their classification of depolymerases was based on the substrate attacked (pectin m. non-esterified polygalacturonic acid), the mode of attack (random or endo attack vs. terminal or exo attack), and the optimal pH for enzyme activity. However it was assumed that hydrolysis was the... 

Imagine that this reaction is catalyzed by substance E. In general the substrate concentration will greatly exceed that of the catalyst. If E is an enzyme, for example, concentrations such as [S]o = 10-3 M and [E]o = 10-9 M are not atypical. The development will continue to be expressed in the terminology used by enzymologists even though the material presented applies to catalytic reactions in general. 

A different concept of chiral recognition was used by Lehn et al. (1978) for the differentiation between pairs of enantiomeric anions. Following the terminology used for metallo-enzymes, the chiral crown ether [309] acts as an apo-receptor, complexing a metal cation and thus becoming a chiral metal receptor that may discriminate between enantiomeric anions (cascade-type complexation). Extraction experiments with racemic mandelic acid dissolved in... 

As we saw earlier in this chapter, substrates are the molecules which undergo chemical change as a result of enzyme activity. Many enzymes will only operate when in the presence of essential co-factors or coenzymes. The term coenzyme is not entirely appropriate as it implies that, like enzymes themselves, these compounds do not undergo chemical change. This is not true and more accurate terminology would be co-substrate. Coenzymes are always much smaller than the enzymes with which they operate and are not heat sensitive as are the proteins. 

The NC-IUBMB has introduced a number of changes in the terminology following the proposals made by Barrett, Rawlings and co-workers [7] [8]. The term peptidase should now be used as a synonym for peptide hydrolase and includes all enzymes that hydrolyze peptide bonds. Previously the term peptidases was restricted to exopeptidases . The terms peptidase and protease are now synonymous. For consistency with this nomenclature, the term proteinases has been replaced by endopeptidases . To complete this note on terminology, we remind the reader that the terms cysteine endopeptidases and aspartic endopeptidases were previously called thiol proteinases and acid or carboxyl proteinases , respectively [9],... 

These enzymes often also catalyse the reverse reaction, oxidation of an alcohol to an aldehyde or ketone (see Box 11.2). In such reactions, the cofactor NAD+ abstracts hydride from the alcohol, and may thus be regarded as an oxidizing agent hence the dehydrogenase terminology for some enzymes, even when they are carrying out a reduction. 

The terminology vitamin Bg covers a number of structurally related compounds, including pyridoxal and pyridoxamine and their 5 -phosphates. Pyridoxal 5 -phosphate (PLP), in particular, acts as a coenzyme for a large number of important enzymic reactions, especially those involved in amino acid metabolism. We shall meet some of these in more detail later, e.g. transamination (see Section 15.6) and amino acid decarboxylation (see Section 15.7), but it is worth noting at this point that the biological role of PLP is absolutely dependent upon imine formation and hydrolysis. Vitamin Bg deficiency may lead to anaemia, weakness, eye, mouth, and nose lesions, and neurological changes. 

A similar aldol reaction is encountered in the Krebs cycle in the reaction of acetyl-CoA and oxaloacetic acid (see Section 15.3). This yields citric acid, and is catalysed by the enzyme citrate synthase. This intermediate provides the alternative terminology for the Krebs cycle, namely the citric acid cycle. The aldol reaction is easily rationalized, with acetyl-CoA providing an enolate anion nucleophile that adds to the carbonyl of oxaloacetic acid. We shall see later that esters and thioesters can also be converted into enolate anions (see Section 10.7). 

The obvious product of the aldol reaction would be the thioester citryl-CoA. However, the enzyme citrate synthase also carries out hydrolysis of the thioester linkage, so that the product is citric acid hence the terminology. The hydrolysis of the thioester is actually responsible for disturbing the equilibrium and driving the reaction to completion. 

This level of ionization is particularly relevant in some enzymic reactions where histidine residues play an important role (see Section 13.4.1). This means that the imidazole ring of a histidine residue can act as a base, assisting in the removal of protons, or, alternatively, that the imidazolium cation can act as an acid, donating protons as required. The terminology used for such donors and acceptors of protons is general acid catalyst and general base catalyst respectively. 

Enzyme Nomenclature. Recommendations (1992) Academic Press, New York Nomenclature of multiple forms of enzymes J. Biol Chem. (1977) 252, 5939-5941 Catalytic activity Units of enzyme activity Eur. J. Biochem. (1979) 97, 319-320 Symbolism and terminology in enzyme kinetics Eur. J. Biochem. (1982) 128, 281-291... 

A term usually synonymous to rate of reaction in the field of enzyme kinetics. Rate is the preferred terminology. See Rate of Reaction Rate of Conversion... 

STEREOCHEMICAL TERMINOLOGY, lUPAC RECOMMENDATIONS RESTRICTION ENZYMES DEOXYRIBONUCLEASES Retinoids,... 

The manifold intermediates in homogeneous transition-metal catalysis are certainly metal complexes and therefore show a behaviour like ordinary coordination compounds associations of phosphorus donors open up multifarious additional controls. Both, substrates and P ligands are Lewis bases that we have to consider and that compete at the coordination centers of the metal, leading to competitive, non-competitive or uncompetitive activation or inhibition processes in analogy to the terminology of enzyme chemistry... 

With the increased use of enzymes in polymer chemistry, the enzymology terminology to describe the reaction kinetics and the enantioselectivity of a reaction has become more and more common in polymer literature. The parameter of choice to describe the enantioselectivity of an enzyme-catalyzed kinetic resolution is the enantiomeric ratio E. The enantiomeric ratio is defined as the ratio of the specificity constants for the two enantiomers, R) and S) (1) ... 

Since a similar reaction with two stereoisomers leads to different results (one enantiomer reacts, the other does not) kinetic resolution should be called enantiospecific. However, this does not seem to have become common terminology, so it may be better to characterise the reaction by the enantiomeric ratio E. The enantiomeric ratio is the ratio of the specificity constants of the enzyme for the two enantiomers... 

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