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Enzyme mechanism - C H A P T E R 7 ENZYME MECHANISM Active...

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80 C H A P T E R 7 ENZYME MECHANISM Active Site Transition State Catalysis Lock and Key Induced Fit Nonproductive Binding Entropy Strain and Distortion Transition-State Stabilization Transition-State Analogs Chemical Catalysis Enzymes do two important things: they recognize very specific sub- strates, and they perform specific chemical reactions on them at fantas- tic speeds. The way they accomplish all this can be described by a number of different models, each one of which accounts for some of the behavior that enzymes exhibit. Most enzymes make use of all these dif- ferent mechanisms of specificity and/or catalysis. In the real world, some or all of these factors go into making a given enzyme work with exqui- site specificity and blinding speed.
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7 Enzyme Mechanism 81 The active site of an enzyme is generally a pocket or cleft that is specialized to recognize specific substrates and catalyze chemical trans- formations. It is formed in the three-dimensional structure by a col- lection of different amino acids (active-site residues) that may or may not be adjacent in the primary sequence. The interactions between the active site and the substrate occur via the same forces that stabilize pro- tein structure: hydrophobic interactions, electrostatic interactions (charge–charge), hydrogen bonding, and van der Waals interactions. Enzyme active sites do not simply bind substrates; they also provide cat- alytic groups to facilitate the chemistry and provide specific interactions that stabilize the formation of the transition state for the chemical reac- tion. During a chemical reaction, the structure of the substrate changes into the structure of the product. Somewhere in between, some bonds are partly broken; others are partly formed. The transition state is the high- est-energy arrangement of atoms that is intermediate in structure between the structure of the reactants and the structure of the products. Figure 7-1 is called a reaction coordinate diagram . It shows the free energy of the reactants, transition state, and product. The free-energy difference between the product and reactant is the free-energy change for the overall reaction and is related to the equilibrium constants [ G RT ln( K eq )]. 1 The free-energy change between the products and reac- tants tells you how favorable the reaction is thermodynamically. It does not tell you anything about how fast it is. Reactions don’t all occur with the same rate. Some energy must be put into the reactants before they can be converted to products. This acti- vation energy provides a barrier to the reaction—the higher the barrier, TRANSITION STATE The transition state is the highest-energy arrangement of atoms dur- ing a chemical reaction.
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