Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438

Introductory Biochemistry

Spring 2007

Lecture Notes: 21 February

© R. Paselk 2006


Enzyme Catalysis

Zymogens: define and give examples of trypsin/trypsinogen.

We will look at catalysis in two types of systems:

Mechanisms of Chemical Catalysis

Look at some examples of catalysis in model systems (organic chemistry) and how they might operate in enzymes.

Types of Catalysis:

So how does catalysis work? Recall that the slow step of a reaction is reaching the transition state. Thus if we can find a way to stabilize the transition state (lower Ea) then the reaction rate will be enhanced. Generally we will be looking at three ways to increase rates

  1. stabilize transition states
  2. increase the concentrations of intermediates
  3. use a different reaction pathway.

General acid/general base catalysis: (Recall that a general acid is a proton donor, Bronsted acid definition, such as a buffer, other than the solvent. Specific acid or base is the solvent acid or base species: H+ & OH- for water). What we want is a proton donor (or acceptor) which is present at reasonable concentration at pH 7!

Consider the mutarotation of glucose:

This reaction will be slow because

So the question is, How do we catalyze this process?

Look at specific base and specific acid catalysis first:

reverse to close as other conformer.

reverse to close as other conformer.

Note that both are useful, but only one or the other can be used with specific acid or base catalysts. Would be nice to use both simultaneously.

In organic solvents can use phenol,, and pyridine,, as general acid and base catalysts, respectively. Together they are better than either alone. But better yet is a concerted (both at once) catalyst with both functional groups present, so a three body collision isn't needed:

This is about 7,000 x's faster than the separate species at 0.001M. (Studies in organic media are complicated by fact that charge stabilization catalysis may also be occuring, so not necessarily looking at pure effects.)

It turns out that a general acid or general base catalytic step can each account for about a 100-fold enhancement in explaining an enzyme's rate.

Covalent catalysis: Get formation of a covalent intermediate. Look at formation of methanol from methyl iodide and water. This reaction goes by an SN2 mechanism:

Have a second order nucleophilic attack by hydroxide ion.

With Bromide catalyst get a new mechanism: formation of methyl bromide intermediate which is easier to form and to attack by hydroxide so reaction overall is faster.

Note the new lower activation energies. Only the higher one makes a difference in terms of rate. (Can tell that bromide intermediate is formed since, if we use chiral TDCHI as reactant, catalyzed product does not show inversion of chirality, while uncatalyzed does: must have double inversion.)

To summarize: The catalyst provides a new pathway (a new mechanism) in which all activation energies are lower so the rate determining step has a lower activation energy and thus the rate is faster.

As with general acid/base ctalysis, a covalent catalysis step can account for about a 100-fold enhancement in explaining enzyme rate.

Proximity/orientation: Example: [overhead 7.13, P].


Can get rate enhancements of up to a billion-fold in model systems. So Proximity/orientation can account for a factor of possibly a million to a billion-fold enhancement in explaining enzyme rate.

Pathway Diagrams

C438 Home

Lecture Notes

Last modified 21 February 2007