Enzyme molecules active site

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 action of an enzyme. (A) An enzyme with substrate molecules C and DE. Note that the specific shape of the enzyme s active site matches the shape of the substrate. (B) The enzyme with the substrate molecules bound. (C) The enzyme, unchanged from its original form with the product molecules (CD and E). 

The enzymes are protein molecules having globular structure, as a rule. The molecular masses of the different enzymes have values between ten thousands and hundred thousands. The enzyme s active site, which, as a rule, consists of a nonproteinic organic compound containing metal ions of variable valency (iron, copper, molybdenum, etc.) is linked to the protein globule by covalent or hydrogen bonds. The catalytic action of the enzymes is due to electron transfer from these ions to the substrate. The protein part of the enzyme secures a suitable disposition of the substrate relative to the active site and is responsible for the high selectivity of catalytic action. 

A topologically distinct region on an enzyme that recognizes and binds specific molecules or structures and is far removed from the enzyme s active site. An example is the fibrinogen recognition site on thrombin. This site is spatially distinct from the site for cleavage of the scis-sile bond of fibrinogen. 

The entire iron-porphyrin-protein complex is called a cytochrome and such proteins are important electron-transfer components of cells. Generally, access to the macromolecular region in which the oxidation reactions occur is via a hydrophobic channel through the protein (Mueller et al., 1995). As a result, organic substrates are transferred from aqueous solution into the enzyme s active site primarily due to their hydrophobicity and are limited by their size. This important feature seems very appropriate hydrophobic molecules are selected to associate with this enzyme, and these are precisely the ones that are most difficult for organisms to avoid accumulating from a surrounding aquatic environment. 

Allosteric enzyme. An enzyme the active site of which can be altered by the binding of a small molecule at a nonoverlapping site. 

According to the lock-and-key model, an enzyme is pictured as a large, irregularly shaped molecule with a cleft, or crevice, in its middle. Inside the crevice is an active site, a small region with the shape and chemical composition necessary to bind the substrate and catalyze the appropriate reaction. In other words, the active site acts like a lock into which only a specific key can fit (Figure 24.10). An enzyme s active site is lined by various acidic, basic, and neutral amino acid side chains, all properly positioned for maximum interaction with the substrate. 

FIGURE 24.10 According to the lock-and-key model, an enzyme is a large, three-dimensional molecule containing a crevice with an active site. Only a substrate whose shape and structure are complementary to those of the active site can fit into the enzyme. The active site of the enzyme hex-ose kinase is visible as the cleft on the left in this computergenerated structure, as is the fit of the substrate (yellow) in the active site. 

The study of both heterogeneous catalysts and enzymes is dominated by the concept of the active site. Specifically, in enzymes the active site is known to represent only a small portion of the large protein molecule that is the enzyme [6], The active site may lie at or near the surface, but it may also be buried in an active site groove or crevice that limits access of all but the desired substrate. Clearly, the total surface area of the protein is significantly larger than that of the active site. 

Substrate Molecules acted upon by enzymes. They bind to the enzyme s active site to create an enzyme-substrate complex. 

This effect is also called the propinquity effect and means that the rate of a reaction between two molecules is enhanced if they are abstracted from dilute solution and held in close proximity to each other in the enzyme s active site this raises the effective concentration of the reactants. 

NADH is a coenzyme, an organic molecule that can function only in the presence of an enzyme. The active site of the enzyme binds both the carbonyl substrate and NADH, keeping them in close proximity. NADH then donates H in much the same way as a metal hydride reagent that is, reduction consists of nucleophilic attack followed by protonation. 

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