Integrated SequencePhysics Chemistry Organic Biology

Web Resources

The Medical Biochemistry Page - Enzymes, Kinetics and Diagnostic Use
Extremely well designed and written overview of enzymes. Highly recommended.

Kimball's Biology Pages - Enzymes

  click if a link is broken

Special points of emphasis

Work, Energy, and Power


Intermolecular Forces

Chemical Kinetics



In the induced fit model, upon binding its substrate, the active site can be reshaped by interactions with the substrate as the substrate interacts with the enzyme. Upon binding substrates, structural changes are induced on the enzyme, often surrounding the substrate with a nonpolar environment which prevents the stabilization of reactive moeities by water, facilitating the occurrence of the catalyzed mechanism.

Why would water stabilize reagents, hampering enzyme catalysis? Because of its strong polarity, water has a high dielectric constant. Remember the role of a dielectric substance between the plates of a capacitor. When the dipoles of the dielectric substance align themselves parallel to the external electric field produced by the charge on the capacitor plates, the electric fields of their individual dipole moments point in the opposite direction, which has the effect of weakening the net field. This means that the same amount of charge on the capacitor plates can exists at a lower voltage because the field is weaker between the plates.

Within the active site of an enzyme, picture the initial state of reagents in an abstract general way. Picture the electron pair of a nucleophile, for example. Its nucleophilicity depends on there being a certain amount of 'dissatisfaction' in that electron density, in other words, a big voltage difference with some other positive charge density on the nearlby electrophile. If water is interposed, if what the nucleophile sees is the hydrogen ends of water around surrounding it, the nucleophile will already be, in a sense, satisfied. The free energy of the reagents will be lower, and the energy increase to achive the transition state will be greater. This is why enzymes often undergo an induced fit to surround the substrate with a nonpolar environment. Can you name a few amino acids which might be essential to creating the nonpolar environment?

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