More Complicated Enzyme Reactions

If the overall reaction rate is controlled by step three (k3) (i.e. if that is the rate limiting step), then the observed isotope effect is close to the intrinsic value. On the other hand, if the rate of chemical conversion (step three) is about the same or faster than processes described by ks and k2, partitioning factors will be large, and the observed isotope effects will be smaller or much smaller than the intrinsic isotope effect. The usual goal of isotope studies on enzymatic reactions is to unravel the kinetic scheme and deduce the intrinsic kinetic isotope effect in order to elucidate the nature of the transition state corresponding to the chemical conversion at the active site of an enzyme. Methods of achieving this goal will be discussed later in this chapter. 

In the remaining part of our presentation of the formal kinetics of enzyme isotope effects a few more complicated examples will be discussed. The methods developed here should be also useful for unraveling other complicated enzyme reactions, and in reading and understanding the modern literature on isotope effects on enzymatic processes. 

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The enzyme catalyzed reactions that lead to geraniol and farnesol (as their pyrophosphate esters) are mechanistically related to the acid catalyzed dimerization of alkenes discussed m Section 6 21 The reaction of an allylic pyrophosphate or a carbo cation with a source of rr electrons is a recurring theme m terpene biosynthesis and is invoked to explain the origin of more complicated structural types Consider for exam pie the formation of cyclic monoterpenes Neryl pyrophosphate formed by an enzyme catalyzed isomerization of the E double bond m geranyl pyrophosphate has the proper geometry to form a six membered ring via intramolecular attack of the double bond on the allylic pyrophosphate unit... 

Hundreds of metabohc reac tions take place simultaneously in cells. There are branched and parallel pathways, and a single biochemical may participate in sever distinct reactions. Through mass action, concentration changes caused by one reac tion may effect the kinetics and equilibrium concentrations of another. In order to prevent accumulation of too much of a biochemical, the product or an intermediate in the pathway may slow the production of an enzyme or may inhibit the ac tivation of enzymes regulating the pathway. This is termed feedback control and is shown in Fig. 24-1. More complicated examples are known where two biochemicals ac t in concert to inhibit an enzyme. As accumulation of excessive amounts of a certain biochemical may be the key to economic success, creating mutant cultures with defective metabolic controls has great value to the produc tion of a given produc t. 

Determining balanced conditions for a single substrate enzyme reaction is usually straightforward one simply performs a substrate titration of reaction velocity, as described in Chapter 2, and sets the substrate concentration at the thus determined Ku value. For bisubstrate and more complex reaction mechanism, however, the determination of balanced conditions can be more complicated. 

What about reactions of the type A + B — C This is a second-order reaction, and the second-order rate constant has units of M min-1. The enzyme-catalyzed reaction is even more complicated than the very simple one shown earlier. We obviously want to use a second-order rate constant for the comparison, but which one There are several options, and all types of comparisons are often made (or avoided). For enzyme-catalyzed reactions with two substrates, there are two Km values, one for each substrate. That means that there are two kcJKm values, one for each substrate. The kcJKA5 in this case describes the second-order rate constant for the reaction of substrate A with whatever form of the enzyme exists at a saturating level B. Cryptic enough The form of the enzyme that is present at a saturating level of B depends on whether or not B can bind to the enzyme in the absence of A.6 If B can bind to E in the absence of A, then kcJKA will describe the second-order reaction of A with the EB complex. This would be a reasonably valid comparison to show the effect of the enzyme on the reaction. But if B can t bind to the enzyme in the absence of A, kcat/KA will describe the second-order reaction of A with the enzyme (not the EB complex). This might not be quite so good a comparison. 

The mechanism for bacterial synthesis of PHA is not the simple dehydration reaction between alcohol and carboxyl groups. It is more complicated and involves the coenzyme A thioester derivative of the hydroxyalkanoic acid monomer (produced from the organic feedstock available to the bacteria) [Kamachi et al., 2001], Growth involves an acyl transfer reaction catalyzed by the enzyme PHA synthase (also called a polymerase) [Blei and Odian,... 

For the analogous side-chain removal reaction required for semi-synthetic cephalosporin manufacture more complicated processes have been developed. The side-chain of cephalosporin C can be split off enzymatically, but only after its amino group has been removed by a combined enzymatic and spontaneous reaction sequence (Matsumoto, 1993). Amongst other companies, Hoechst has replaced their chemical process by a two-enzyme process, thus reducing the amount of waste from 31 ton to 0.3 ton per ton of 7-... 

In Chapter 8, we addressed proton transfer reactions, which we have assumed to occur at much higher rates as compared to all other processes. So in this case we always considered equilibrium to be established instantaneously. For the reactions discussed in the following chapters, however, this assumption does not generally hold, since we are dealing with reactions that occur at much slower rates. Hence, our major focus will not be on thermodynamic, but rather on kinetic aspects of transformation reactions of organic chemicals. In Section 12.3 we will therefore discuss the mathematical framework that we need to describe zero-, first- and second-order reactions. We will also show how to solve somewhat more complicated problems such as enzyme kinetics. 

For a single substrate-single product reaction with one path (assume path A is insignificant), the pH dependence of ka/Ka reflects the ionization of groups on the free enzyme (Ka, Kb) and free substrate and is not affected by any of the intermediates. The pH dependencies of ka and Kb separately are more complicated and, as well as Kb and Kb, involve KJ and Kb which depend on the number of intermediates and steady state rate constants. Using the terminology of del Rosario and Hammes (499). 

It should be noted that this solution procedure requires the knowledge of elementary rate constants, klt k2, and k3. The elementary rate constants can be measured by the experimental techniques such as pre-steady-state kinetics and relaxation methods (Bailey and Ollis, pp. 111 -113, 1986), which are much more complicated compared to the methods to determine KM and rmax. Furthermore, the initial molar concentration of an enzyme should be known, which is also difficult to measure as explained earlier. However, a numerical solution with the elementary rate constants can provide a more precise picture of what is occurring during the enzyme reaction, as illustrated in the following example problem. 

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