topics covered thus far include:

Definition: detailed sequence of atom and/or electron transfers catalyzed by the enzyme in the process of converted S to P

What's involved in this catalysis?

1. Transition state effects

a. proximity effects (multisubstrate reactions): in the above diagram, the enzyme E is able to bring together the two substrates, S₁ and S₂. Increasing their effective concentrations serves to decrease the free energy of activation (symbolized here by G') relative to the non-enzymatic reaction where the free energy of activation is G.

b. transition state stabilization: non-covalent interactions (H-bonding, etc.) that stabilize the transition state and thereby reduce the activation energy barrier.

2. chemical effects

acid-base catalysis (E, S exchange H⁺)

covalent catalysis (E forms covalent bond to S)

but first…a few words on chemical mechanisms

note 1: a double-headed arrow symbolizes the movement of an electron pair as shown in the following examples

examples illustrating acid-base reactions

examples illustrating oxidation-reduction reactions

note 2: most reactions can be conveniently described as the interaction of a nucleophile (electron rich species typically with a negative charge or unshared electron pair) or an electrophile (electron deficient species)

What conclusions might we draw from this? Polar amino acids involved in catalytic centers:

example: acetylcholinesterase

Amino acid side chains in different microenvironments can display different pK_a values from those seen in pure amino acids. That is, for the equilibrium shown below, ZH predominates if pH<pK_a and Z- predominates if pH>pK_a.

Now, back to point 2 under "chemical effects". Although both acid-base catalysis and covalent catalysis (listed under this heading of chemical effects) are important, we will focus on just the former.

How are polar amino acids in the catalytic site involved in the following hydrolysis reaction? How does the enzyme, ribonuclease, orchestrate the insertion of a molecule of water (shown in a circle) in RNA?

We will represent this process as a series of "steps". The catalytic site is shown in the following cartoon. The two key residues are H12 (pK_a 5.8; shown on the right) and H119 (pK_a 6.2; shown on the left)

Step 1

Step 2

Step 3

Step 4

Finally, we can get some idea of the pH range where this enzyme operates from considering the pK_a values of the two histidine residues and the predominant species which is needed for catalytic activity.