Chem 438 - Introductory Biochemistry - Spring 2013

Lecture Notes:

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:

Specificity
Molecular mechanisms of catalysis
Kinetics, including review

Specificity

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.

http://www.chem.ucsb.edu/~molvisual/ABLE/induced_fit/index.html

FYI

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.

Enzyme Kinetics

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.:

C + X;

B + X

D etc.

Review some Kinetics from General Chemistry:

First Order: r = k[S] for S P; & r =-d[S]/dt = d[P]/dt.
- Example - S_N1 from organic chemistry: A + B C + D as 1st order reaction, as in the hydroxylation of t-alkylchloride:
First order because rate depends only on the formation of the carbocation, which in turn depends only on [R₃CCl]
Second order: r = k[A][B] for A + B P; or can have r = k[A]² ;
- Example - S_N2 from organic chemistry: A + B C + D as 2nd order reaction, as in the hydroxylation of primary alkylchlorides:
Now 2nd order because both RH₂CCl and OH^- (reverse of figure above) are involved in slow step.
Higher order reactions occur, but uncommon.
Zero order: r = k: Only occurs with catalysts, important in enzyme catalysis. 0 order also only occurs above a minimum [A].

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. [Figure 5.1]
Biochem v_i = r_i
With enzymes can get very high apparent orders due to allosteric effects.

FYI

Plots of v_i = 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 v_i vs [S], similar to Mb binding curve. [Figure 5.4a]

M-M plot

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