Acid-base catalysis, enzymic

As implied above, there is nothing dramatically special about photocatalysis. It is simply another type of catalysis alongside, as it were, redox catalysis, acid-base catalysis, enzyme catalysis, thermal catalysis and others. Consequently, it is worth reemphasising that any description of photocatalysis must correspond to the general definition of catalysis. This said, it could be argued that the broad label photocatalysis simply describes catalysis of a photochemical reaction. 

A catalyst is defined as a substance that influences the rate or the direction of a chemical reaction without being consumed. Homogeneous catalytic processes are where the catalyst is dissolved in a liquid reaction medium. The varieties of chemical species that may act as homogeneous catalysts include anions, cations, neutral species, enzymes, and association complexes. In acid-base catalysis, one step in the reaction mechanism consists of a proton transfer between the catalyst and the substrate. The protonated reactant species or intermediate further reacts with either another species in the solution or by a decomposition process. Table 1-1 shows typical reactions of an acid-base catalysis. An example of an acid-base catalysis in solution is hydrolysis of esters by acids. 

Catalytic mechanisms employed by enzymes include the introduction of strain, approximation of reactants, acid-base catalysis, and covalent catalysis. 

The structural and chemical mechanisms used by enzymes to achieve transition state stabilization have been reviewed in detail elsewhere (e.g., see Jencks, 1969, Warshel, 1998, Cannon and Benkovic, 1998, Copeland, 2000, Copeland and Anderson, 2002 and Kraut et al., 2003). Four of the most common strategies used by enzymes for transition state stabilization—approximation, covalent catalysis, acid/base catalysis, and conformational distortion—are discussed below. 

This chapter discusses the aspects of the kinetic behavior of reactions in liquid solutions that are most germane to the education of a chemical engineer. Particular emphasis is placed on catalysis by acids, bases, and enzymes and a useful technique for correlating kinetic data. 

Homogeneous catalytic processes are those in which the catalyst is dissolved in a liquid reaction medium. There are a variety of chemical species that may act as homogeneous catalysts (e.g., anions, cations, neutral species, association complexes, and enzymes). All such reactions appear to involve a chemical interaction between the catalyst and the substrate (the substance undergoing reaction). The bulk of the material in this section will focus on acid-base and enzyme catalysis. Students interested in learning more about these subjects and other aspects of homogeneous catalysis should consult appropriate texts (11-12, 16-29) or the original literature. 

Enzymes are often considered to function by general acid-base catalysis or by covalent catalysis, but these considerations alone cannot account for the high efficiency of enzymes. Proximity and orientation effects may be partially responsible for the discrepancy, but even the inclusion of these effects does not resolve the disparity between observed and theoretically predicted rates. These and other aspects of the theories of enzyme catalysis are treated in the monographs by Jencks (33) and Bender (34). 

Generally, HNLs utilize an acid-base catalysis mechanism. The amino acid residues at active sites of these enzymes differ significantly, but share the common motif for cyanogenesis. 

Now let s look at what we can do with the water. Because it has more negative charge (a higher electron density), OH is more reactive than HOH. By providing an appropriately placed base to at least partially remove one of the protons from the attacking water molecule, we can increase the reactivity of this water and make the reaction go faster. This is known as acid-base catalysis and is widely used by enzymes to help facilitate the transfer of protons during chemical reactions. 

No large conformational changes occur in the enzyme during catalysis, but many small movements take place. The structural basis for the catalytic power of ribonuclease thus resides in several different features tight, specihc binding of a strained conformation of the substrate, general acid-base catalysis by His-12 and His-119, and preferential stabilization of the transition state by ionic interactions with Lys-41. 

Proton transfers are particularly common. This acid-base catalysis by enzymes is much more effective than the exchange of protons between acids and bases in solution. In many cases, chemical groups are temporarily bound covalently to the amino acid residues of the enzyme or to coenzymes during the catalytic cycle. This effect is referred to as covalent catalysis (see the transaminases, for example p. 178). The principles of enzyme catalysis sketched out here are discussed in greater detail on p. 100 using the example of lactate dehydrogenase. 

Inhibition of Dehydroquinase Type II Dehydroquinase type II is an important enzyme in the shikimic and quinic routes. It ensures the reversible conversion of 3-dehydroquinate (DHQ) into 3-dehydroshrkimate (DHS). Ehmination of the hydroxyl is assisted by an acid/base catalysis that is associated with a residue of the active site. 

In a reaction that establishes the flavonoid heterocyclic C-ring, chalcone isomerase (CHI) catalyzes the stereospecific isomerization of chalcones to their corresponding (2S)-flavanones, via an acid base catalysis mechanism. Almost 40 years ago, the first flavonoid enzyme to be described was CHI (in the adopted hometown of the authors of this chapter). Since then CHI has been analyzed in great detail, and surprisingly, it shows little similarity to other known protein sequences, although CHI-like sequences have recently been reported from plants and other organisms. ... 

The pH-rate profile for the action of the enzyme shows a typical pH maximum, with sharply lower rates at either higher or lower pH than the optimum these facts suggest that both an acidic and a basic group are required for activity (Herries, 1960). The two essential histidine residues could serve as these groups if, in the active site, one were protonated and the other present in its basic form. The simultaneous acid-base catalysis would parallel that of the model system (discussed below) of Swain and J. F. Brown. The essential lysine, which binds phosphate, presumably serves to bind a phosphate residue of the ribonucleic acid. These facts led Mathias and coworkers to propose the mechanism for the action of ribonuclease that is shown in (13) (Findlay et al., 1961). 

Acid-base catalysis appears to be an important factor in virtually all enzymatic reactions. The rates of proton transfer reactions have been well studied in model systems,30 but not during the course of enzyme catalysis. The protonation and deprotonation of acids and bases can be represented as... 

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