BIOL 425 Lecture Notes - Lecture 5: Hydrogen Bond, Hydrolysis, Pyruvate Dehydrogenase
Document Summary
This increases the rate of the reaction as enzyme-substrate interactions align reactive chemical groups and hold them close together. The binding of the reagents to the enzyme gives the reaction intramolecular character, which gives a massive rate increase. However, the situation might be more complex, since modern computational studies have established that traditional examples of proximity effects cannot be related directly to enzyme entropic effects. Also, the original entropic proposa has been found to largely overestimate the contribution of orientation entropy to catalysis. Proton donors and acceptors, i. e. acids and bases, may donate and accept protons in order to stabilize developing charges in the transition state. This typically has the effect of activating nucleophile and electrophile groups, or stabilizing leaving groups. Histidine is often the residue involved in these acid/base reactions, since it has a pka close to neutral ph and can therefore both accept and donate protons. many reaction mechanisms involving acid/base catalysis assume a substantially altered pka.
