Enzyme catalysis active site

Elucidating Mechanisms for the Inhibition of Enzyme Catalysis An inhibitor interacts with an enzyme in a manner that decreases the enzyme s catalytic efficiency. Examples of inhibitors include some drugs and poisons. Irreversible inhibitors covalently bind to the enzyme s active site, producing a permanent loss in catalytic efficiency even when the inhibitor s concentration is decreased. Reversible inhibitors form noncovalent complexes with the enzyme, thereby causing a temporary de-... 

The transformations described thus far were catalyzed by enzymes in their traditional hydrolytic mode. More recent developments in the area of enzymatic catalysis in nonaqueous media (11,16,33—35) have significantly broadened the repertoire of hydrolytic enzymes. The acyl—enzyme intermediate formed in the first step of the reaction via acylation of the enzyme s active site nucleophile can be deacylated in the absence of water by a number of... 

Transition state theory, 46,208 Transmission factor, 42,44-46,45 Triosephosphate isomerase, 210 Trypsin, 170. See also Trypsin enzyme family active site of, 181 activity of, steric effects on, 210 potential surfaces for, 180 Ser 195-His 57 proton transfer in, 146, 147 specificity of, 171 transition state of, 226 Trypsin enzyme family, catalysis of amide hydrolysis, 170-171. See also Chymotrypsin Elastase Thrombin Trypsin Plasmin Tryptophan, structure of, 110... 

Enzyme specificity is often explained in terms of the geometric configuration of the active site of the enzyme. The active site includes the side chains and peptide bonds that either come into direct contact with the substrate or perform some direct function during catalysis. Each site is polyfunctional in that certain parts of it may hold the substrate in a position where the other parts cause changes in the chemical bonding of... 

In terms of enzyme catalysis, the following factors are likely to influence the magnitude of the rate enhancement in enzymatic processes (a) proximity and orientation effects (b) electrostatic complementarity of the enzyme s active site with respect to the reactant s stabilized transition state configuration (c) enzyme-bound metal ions that serve as template, that alter pK s of catalytic groups, that facilitate nucleophilic attack, and that have... 

Figure 3-2. Reaction mechanism of chymotrypsin as an example of covalent catalysis. Step I involves attack of the enzyme s active site serine on the peptide bond to be cleaved. In step II, a covalent complex is formed between the enzyme and a portion of the substrate (peptide 2) with release of the rest of the substrate (peptide I). Step III involves hydrolysis of the enzyme-substrate complex, which releases peptide 2 and completes the reaction.

Jencks and coworkers9 noted that a likely route for catalysis of carboxylation reactions (replacement of a proton by a carboxyl group) is the generation of low entropy carbon dioxide by a reaction of ATP and bicarbonate adjacent to Nl of biotin. This way of promoting carboxylation produces a situation which is precisely what is created at the stage of the initial formation of products in decarboxylation reactions. Since there is no directional momentum, the proximity of low entropy carbon dioxide and a nucleophile similarly will slow the reaction in the direction of decarboxylation. The same authors suggest that for decarboxylation reactions, nucleophilic addition to carbon dioxide in an enzyme s active site would prevent re-addition and promote the forward reaction if the addition product is itself sufficiently unstable. 

In enzymes, the active site may possess acid and base groups intimately associated with the conjugate base and acid functions, respectively, of the complexed substrate the push-pull mechanism is possible but might not be a driving force. The halogenation of acetone in the presence of aqueous solutions of carboxylic acid buffers exhibits the rate law of Equation 11.2 where the third-order term, although small, has been shown to be significant and due to bifunctional concerted acid-base catalysis (Scheme 11.13) ... 

An inhibitor is any agent that interferes with the activity of an enzyme. Inhibitors may affect the binding of enzyme to substrate, or catalysis (via modification of the enzyme s active site), or both. Researchers use enzyme inhibitors to define metabolic pathways and to understand enzyme reaction mechanisms. Many drugs are designed as inhibitors of target enzymes. Inhibition is also a natural phenomenon. Cells regulate metabolic pathways by specific inhibition of key enzymes. 

The first step in catalysis is the formation of an enzyme-substrate complex. Substrates are bound to enzymes at active-site clefts from which water is largely excluded when the substrate is bound. The specificity of enzyme-substrate interactions arises mainly from hydrogen bonding, which is directional, and the shape of the active site, which rejects molecules that do not have a sufficiently complementary shape. The recognition of substrates by enzymes is accompanied by conformational changes at active sites, and such changes facilitate the formation of the transition state. 

Fats and carbohydrates are metabolized down to carbon dioxide via an acetyl unit, CH3C=0, which is attached to a coenzyme, HSCoA, as a thioester called acetyl CoA. Acetyl CoA enters the citric acid cycle and eventually is converted to two molecules of carbon dioxide. The first step in the citric acid cycle is the aldol of acetyl CoA with oxaloacetate (Fig. 8.6). What is so elegant about this aldol is that the acidic and basic groups within the enzyme s active site provide a route that avoids any strongly acidic or basic intermediates. The enzyme accomplishes an aldol reaction at neutral pH, without an acidic protonated carbonyl or basic enolate intermediate via push-pull catalysis (Section 7.4.3). 

The ready availability of amino acids and their different functionalizations in the side chains allowed for a number of applications in the field of supported catalysis. While the relatively low cost of many amino acids apparently does not seem to justify the preparation of supported catalysts derived from amino acids, other reasons (as mentioned above) may drive towards the immobilization of chiral catalysts, for example to experiment with different solubilities, the easy separation of the product from the catalyst, and the catalyst s recyclability. The immobilization of these compounds on a support can also be seen as an attempt to develop a minimalist version of an enzyme, with the amino acid playing the role of the enzyme s active site and the polymer that of an oversimplified peptide backbone not directly involved in the catalytic activity [34]. It should be mentioned at this point that, in principle, amine-based catalysts offer also the possibility to be recovered by exploiting their solubility profiles in acids. 

The information within an enzyme s active site (its shape and charge distribution) constrains the motions and allowed conformations of the substrate, making it appear more like the transition state. In other words, the information in the structure of the enzyme is used to optimally orient the substrate. As a result of this information transfer, the energy of the enzyme-substrate complex becomes closer to the AG, which means that the energy needed for the reaction to proceed to product is reduced. Consequently there is an increase in the rate of the enzyme-catalyzed reaction. Other factors, such as electrostatic effects, general acid-base catalysis, and covalent catalysis (discussed on pp. 177-180), also contribute to the increased rates of enzyme-catalyzed reactions over non-enzyme catalyzed reactions. 

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