Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438 - Introductory Biochemistry - Spring 2013

Lecture Notes:

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Enzyme Catalysis

Mechanisms of Chemical Catalysis, cont.

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. [Figure 6.1, 6.2] 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 (Slide)

(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:

mutarotation reaction for 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:

base-catalyzed reaction steps for glucose mutarotation

reverse to close as other conformer.

acid-catalyzed reaction steps for glucose mutarotation

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,phenol structure, and pyridine,pyridine structure, 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:

concerted catalysis of glucose mutarotation by 1-hydroxypyridine

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 (Slide)

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

SN2 mechanism for the reaction of hydroxide ion with methyl iodide to give iodide ion and methanol

reaction coordinate diagram for the reaction of hydroxide and methyl iodide

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.

SN2 mechanism for the reaction of hydroxide ion with methyl iodide to give iodide ion and methanol catalyzed by bromide ion

reaction coordinate diagram for the reaction of hydroxide and methyl iodide catalyzed by bromide ion

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: [Figure 6.14]

 

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.

Stabilization of Transition State Conformation: (Strain/distortion; Charge neutralization)

Strain/distortion example: Alkyl phosphate hydrolysis:

structural diagram illustrating strain in alkyl phosphate hydrolysis

The base-catalyzed hydrolysis of A takes place more than one-hundred-million times faster than that of B, apparently due to the strain in the five membered ring in A.

Metal ion catalysis:

metal ions can act as electrophilic catalysts in covalent type catalytic mechanisms and also as counter ions in charge stabilization in TS catalytic mechanisms.

Enzyme Examples of Catalysis

Now want to put it all together and look at example enzymes to try to explain their activities.

Lysozyme

Have looked at model of Lysozyme - globular with cleft to accommodate substrate (model) [Figure 6.30]. Functions as an antibiotic, hydrolyzing polysaccharide strand in cell walls of bacteria. For Lysozyme the substrate is a carbohydrate polymer, as shown below. [Figure 6.29]

Evidence:

So now let's look at the enzyme itself:

Chymotrypsin

(digestive enzyme).

Zymogens

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© R. A. Paselk 2010;

Last modified 27 February 2013