Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 438

Introductory Biochemistry

Spring 2007

Lecture Notes: 15 February

© R. Paselk 2006



Enzymes are the heart of Biochemistry

Enzymes generally have a cleft for active site, generally <5%of surface: look like pac man. Need large structure to maintain shape etc. with many weak bonds.

Look at major aspects of enzyme study:


Models for Enzyme Specificity:


Enzyme Kinetics


Gives information on dynamic systems.

Sets the parameters for catalytic mechanisms such as:

A C + X;

B + X D etc.

Review some Kinetics from General Chemistry:

We have now reviewed kinetics as tools. Before we go to enzymes a few comments:


Plots of vi = d[P]/dt vs. [S] for 0 - 3rd order

Look at simple, one-substrate enzymes:

For simple enzyme, S P get rectangular hyperbola type plot for vi vs [S], similar to Mb binding curve.

Let's look at a mathematical model and attempt to generate curve. This was first done by Michaelis and Menten for an equilibrium model. Better is the steady state model of Haldane and Briggs (more general), which we will derive.

For S P assume

And for initial reaction conditions [P] = 0 & therefore k4 = 0, so have

Now vi = d[P]/dt = k3[ES] (Note that kcat is often used instead of k3);

Assume steady state (steady state assumption: d[ES]/dt= 0):

d[ES]/dt= 0; Thus: 0 = d[ES]/dt= k1[E][S] - k2[ES] - k3[ES].

Continuing we can now substitute for E (free enzyme), because hard to find, and gather constants:

[E] = [Et] - [ES]; then

d[ES]/dt= k1([Et] [S] - [ES][S]) - k2[ES] - k3[ES],

gathering constants: ,

Now define

Then , where KM is the Michaelis-Menten constant.

{Note that if k2 >> k3 (that is the equil. of E+S with ES is rapid compared to breakdown of ES to P), then M-M const = 1/(affinity)= the dissociation constant, but only in these special conditions.}

Now a couple of tricks: Solve for [ES]:

and recall that k3[Et] = Vmax and therefore vi = k3[ES], and dividing both sides by k3, vi/k3 = [ES]

Substituting: and ,

But maximum possible velocity must = k3[Et] = Vmax

So, Which is known as the Michaelis-Menten Equation.

Pathway Diagrams

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Last modified 15 February 2006