Chem 438 - Introductory Biochemistry - Spring 2013
Introduction To Enzymes
Enzymes are the heart of Biochemistry
- protein based catalysts (for us RNA based catalysts are Ribozymes)
- enormously effective catalysts: typically enhance rates by 106 to 1012 fold
- operate under mild conditions: 0 - 100 °C (or perhaps even 130+ °C for some bacteria in deep ocean), 20 -40 °C for most organisms; and low pressures (atmospheric)
- very specific: generally catalyze reaction for a very restricted group of molecules, sometimes for a single naturally occurring molecule of a single chirality.
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.
Six Classes of enzymes
- Oxidoreductases - redox reactions [Rxn 1, p136]
- Transferases - group transfer reactions [Rxn 2, p137]
- Hydrolases - hydrolysis reactions [Rxn 3, p137]
Note that these first three comprize the majority of biologically catalyzed reactions [pie graph, p137]
- Lyases - lysis generating a double bonds (non-oxidative elimination reactions) [Rxn 4, p137]
- Isomerases - isomerization reactions in a single molecule [Rxn 5, p138]
- Ligases - join (ligate) two substrate molecules [Rxn 6, p138]
Look at major aspects of enzyme study:
- Molecular mechanisms of catalysis
- Kinetics, including review
Models for Enzyme Specificity:
- Lock & Key model of Fischer: diagram; Hexokinase example: reaction, methanol and water as ineffective picks.
- Induced-fit model of Koshland: diagram; space-filling models of HK with and without substrate.
Types of specificity:
- Geometric specificity: shape
- Chiral specificity: most chirally specific enzymes are absolutely stereospecific.
- Prochirality, because of their own chiral nature enzymes can often hold substrates in such a way that on one chiral product is made, distinguishing between seemingly identical groups.
- Chemical specificity: functional groups, types of chemical reaction.
CHEMICAL REACTION KINETICS
Gives information on dynamic systems.
Sets the parameters for catalytic mechanisms such as:
- Number of species in rate determining step.
- Which species involved in Transition State.
- Order of steps: Thus for A + B C + D can have many mech.:
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:
- Note: r = -d[S]/dt = d[P]/dt
- Note that for all cases with fixed initial concentrations (except zero order) as [A] decreases r decreases, so need to look at initial rates, that is rate of reaction before a significant amount of reactant is used up.
- Biochem vi = ri
- With enzymes can get very high apparent orders due to allosteric effects.
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].
© R. A. Paselk 2010;
Last modified 20 February 2013