Single enzymatic reactions

Radiolabeled RNA can be generated either by incorporation of a (a32p) nucleoside triphosphate during an in vitro transcription reaction or by the transfer of (y P)-ATP to the 5 terminus of a dephosphorylated RNA molecule (41). The authors prefer the first mentioned method, as it needs only a single enzymatic reaction. 

The product of a NHase/amidase cascade reaction is an acid, which is the same as the single enzymatic reaction performed by a nitrilase. However, the NHases usually have different substrate specificities than nitrilases, making them more suitable for the production of certain compounds. Although most organisms have both NHase and amidase activity (see earlier text), it is sometimes preferable, in a synthetic application, to combine enzymes from different organisms. The reasons for this are the enantioselectivity of the amidase or specific activity or substrate specificity of either of the enzymes. In this way, products with different enantiomeric purity can be obtained. Recently, a coupling of a NHase with two different amidases with opposite enantiopreference together with an -amino-a-caprolactam racemase that allows the formation of small aliphatic almost enantiopure (R)- or (S)-amino acids via dynamic kinetic resolution processes has been described [52]. 

Indeed, asymmetric acetylahon of ( )-38 with vinyl acetate and lipase PS-C gave (R)-acetate 39 and the recovered (S)-alcohol 38 of sahsfactory enantiomeric purihes after a single enzymatic reaction. It must be noted that the trimethylsilylethynyl group of 38 was recognized by lipase PS-C as a group bulkier than the n-decyl group. 

Tokunaga M, Kitamura K, Saito K, Iwane A H and Yanagida T 1997 Single molecule imaging of fluorophores and enzymatic reactions achieved by objective-type total internal reflection fluorescence microscopy Biochem. Biophys. Res. Commun. 235 47-53... 

Km for an enzymatic reaction are of significant interest in the study of cellular chemistry. From equation 13.19 we see that Vmax provides a means for determining the rate constant 2- For enzymes that follow the mechanism shown in reaction 13.15, 2 is equivalent to the enzyme s turnover number, kcat- The turnover number is the maximum number of substrate molecules converted to product by a single active site on the enzyme, per unit time. Thus, the turnover number provides a direct indication of the catalytic efficiency of an enzyme s active site. The Michaelis constant, Km, is significant because it provides an estimate of the substrate s intracellular concentration. 

The simplest type of enzymatic reaction involves only a single reactant or substrate. The substrate forms an unstable complex with the enzyme that decomposes to give the product species or, alternatively, to generate the substrate. 

The response characteristics of enzyme electrodes depend on many variables, and an understanding of the theoretical basis of their function would help to improve their performance. Enzymatic reactions involving a single substrate can be formulated in a general way as... 

Typical single-substrate enzymatic reactions can be described by the kinetic scheme (see Refs. 1 and 2 for more extensive discussions). 

Let us consider an enzymatic reaction in which two substrates are utilized to from two products (in the nomenclature of enzyme reaction mechanisms this situation is referred to as a bi-bi mechanism). A reaction in which one substrate yields two products is referred to as a uni-bi mechanism, and one in which two substrates combine to form a single product is referred to as a bi-uni mechanism (see Copeland, 2000, for further details). For the purposes of illustration let us use the example of a group transfer reaction, in which a chemical species, X, is transferred from one substrate to the other in forming the products of the reaction ... 

Figure 6.2 Effect of preincubation time with inhibitor on the steady state velocity of an enzymatic reaction for a very slow binding inhibitor. (A) Preincubation time dependence of velocity in the presence of a slow binding inhibitor that conforms to the single-step binding mechanism of scheme B of Figure 6.3. (B) Preincubation time dependence of velocity in the presence of a slow binding inhibitor that conforms to the two-step binding mechanism of scheme C of Figure 6.3. Note that in panel B both the initial velocity (y-intercept values) and steady state velocity are affected by the presence of inhibitor in a concentration-dependent fashion.

FIA has also found wide application in pharmaceutical analysis.214,215 Direct UV detection of active ingredients is the most popular pharmaceutical analysis application of FIA. For single component analysis of samples with little matrix interference such as dissolution and content uniformity of conventional dosage forms, many pharmaceutical chemists simply replace a column with suitable tubing between the injector and the detector to run FIA on standard HPLC instrumentation. When direct UV detection offers inadequate selectivity, simple online reaction schemes with more specific reagents including chemical, photochemical, and enzymatic reactions of derivatization are applied for flow injection determination of pharmaceuticals.216... 

For the quantitative description of the metabolic state of a cell, and likewise which is of particular interest within this review as input for metabolic models, experimental information about the level of metabolites is pivotal. Over the last decades, a variety of experimental methods for metabolite quantification have been developed, each with specific scopes and limits. While some methods aim at an exact quantification of single metabolites, other methods aim to capture relative levels of as many metabolites as possible. However, before providing an overview about the different methods for metabolite measurements, it is essential to recall that the time scales of metabolism are very fast Accordingly, for invasive methods samples have to be taken quickly and metabolism has to be stopped, usually by quick-freezing, for example, in liquid nitrogen. Subsequently, all further processing has to be performed in a way that prevents enzymatic reactions to proceed, either by separating enzymes and metabolites or by suspension in a nonpolar solvent. 

Interpretation of KIEs on enzymatic processes (see Chapter 11) has been frequently based on the assumption that the intrinsic value of the kinetic isotope effect is known. Chemical reactions have long been used as models for catalytic events occurring in enzyme active sites and in some cases this analogy has worked quite well. One example is the decarboxylation of 4-pyridylacetic acid presented in Fig. 10.9. Depending on the solvent, either the zwitterionic or the neutral form dominates in the solution. Since the reaction rates in D20/H20 solvent mixtures are the same (see Section 11.4 for a discussion of aqueous D/H solvent isotope effects), as are the carbon KIEs for the carboxylic carbon, it is safe to assume that this is a single step reaction. The isotope effects on pKa are expected to be close to the value of 1.0014 determined for benzoic acid. This in mind, changes in the isotope effects have been attributed to changes in solvation. 

Thus far only reactions involving a single substrate have been considered. Most enzymatic reactions have two substrates. Unlike chemical processes, the sequence in which the substrates bind to the enzyme may be important. If two substrates, A and B, bind in a specific order (e.g., A binds first) as illustrated in Equation 11.37 the mechanism is called ordered sequential. 

Fig. 5.4 Monitoring of the enzymatic reaction and cathepsin B inhibition by ESI-MS. MS instrument Shimadzu LCMS-2010 single-stage quadrupole mass spectrometer, (a) The ESI-MS spectrum obtained after analysis of the enzyme reaction, containing the cleavage products AMC (m/z 175.9) and Z-FR (m/z 456.1) m/z 244.9 and m/z 329.9 belong to...

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