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Proximity and Orientation
If the reactants and chemical R groups are aligned properly with the active site, the reaction will proceed faster. Entropy loss will also be reduced because of the reduction of random tumbling and substrate stretching.
Covalent Catalysis
The transient covalent bond of the substrate with an amino R group in the active site can reduce the energy of the later transition states. The serine hydroxyl group can form the relatively stable acyl-enzyme intermediate in proteases like chymotrypsin. the SH group is always in the right place, so it again speeds up the reaction.
Acid-base catalysis
Enzyme provides acid-base catalysis because it can act as either a proton donor or acceptor. The histidine imidazole group is usually involved because it can be either an acid or a base at neutral pH.
Electrostatic Destabilization
Enzyme provides electrostatic destabilization because of the repulsive charges between enzyme and substrate. When these are relieved, the reaction occurs more rapidly.
Transition state bonds
Tightest binding of the enzyme is with the transition state which lowers activation energy and speeds up the reaction.
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