CH13. Enzymes http://www.youtube.com/ watch? v=AcXXkcZ2jWM&feature=rel ated
Jan 02, 2016
Outline• What characteristic features define enzymes?• Can the rate of an enzyme-catalyzed reaction be defined in a
mathematical way?• What equations define the kinetics of enzyme-catalyzed
reactions?• What can be learned from the inhibition of enzyme activity?• What is the kinetic behavior of enzymes catalyzing bimolecular
reactions?• How can enzymes be so specific? • Are all enzymes proteins?• Is it possible to design an enzyme to catalyze any desired
reaction?
Virtually All Reactions in Cells Are Mediated by Enzymes
• Enzymes catalyze thermodynamically favorable reactions, causing them to proceed at extraordinarily rapid rates (see Figure 13.1)
• Enzymes provide cells with the ability to exert kinetic control over thermodynamic potentiality
• Living systems use enzymes to accelerate and control the rates of vitally important biochemical reactions
• Enzymes are the agents of metabolic function
Virtually All Reactions in Cells Are Mediated by Enzymes
Figure 13.1 Reaction profile showing the large free energy of activation for glucose oxidation. Enzymes lower ΔG‡, thereby accelerating rate.
13.1 What Characteristic Features Define Enzymes?
• Enzymes can accelerate reactions as much as 1016 over uncatalyzed rates
• Urease is a good example: – Catalyzed rate: 3x104/sec – Uncatalyzed rate: 3x10 -10/sec – Ratio is 1x1014
Specificity
• Enzymes selectively recognize proper substrates over other molecules
• Enzymes produce products in very high yields - often much greater than 95%
• Specificity is controlled by structure - the unique fit of substrate with enzyme controls the selectivity for substrate and the product yield
Enzymes are the Agents of Metabolic Function
Figure 13.2 The breakdown of glucose by glycolysis provides a prime example of a metabolic pathway.
13.2 Can the Rate of an Enzyme-Catalyzed Reaction Be Defined in a Mathematical Way?
• Kinetics is the branch of science concerned with the rates of reactions
• Enzyme kinetics seeks to determine the maximum reaction velocity that enzymes can attain and binding affinities for substrates and inhibitors
• Analysis of enzyme rates yields insights into enzyme mechanisms and metabolic pathways
• This information can be exploited to control and manipulate the course of metabolic events
Several kinetics terms to understand
• rate or velocity • rate constant • rate law • order of a reaction • molecularity of a reaction
Chemical Kinetics Provides a Foundation for Exploring Enzyme Kinetics
• Consider a reaction of overall stoichiometry as shown:
• The rate is proportional to the concentration of A
[ ] [ ]
[ ][ ]
A P
d P d Av
dt dtA
v k Adt
Catalysts Lower the Free Energy of Activation for a Reaction
• A typical enzyme-catalyzed reaction must pass through a transition state
• The transition state sits at the apex of the energy profile in the energy diagram
• The reaction rate is proportional to the concentration of reactant molecules with the transition-state energy
• This energy barrier is known as the free energy of activation
• Decreasing ΔG‡ increases the reaction rate• The activation energy is related to the rate constant
by: /G RTk Ae
Catalysts Lower the Free Energy of Activation for a Reaction
Figure 13.5 Energy diagram for a chemical reaction (A→P) and the effects of (a) raising the temperature from T1 to T2, or (b) adding a catalyst.
The Transition State
Understand the difference between G and G‡
• The overall free energy change for a reaction is related to the equilibrium constant
• The free energy of activation for a reaction is related to the rate constant
• It is extremely important to appreciate this distinction
The Michaelis-Menten Equation is the Fundamental Equation of Enzyme Kinetics
• Louis Michaelis and Maud Menten's theory • It assumes the formation of an enzyme-substrate
complex • It assumes that the ES complex is in rapid
equilibrium with free enzyme • Breakdown of ES to form products is assumed to
be slower than 1) formation of ES and 2) breakdown of ES to re-form E and S
[ES] Remains Constant Through Much of the Enzyme Reaction Time Course in Michaelis-Menten Kinetics
Figure 13.8 Time course for a typical enzyme-catalyzed reaction obeying the Michaelis-Menten, Briggs-Haldane models for enzyme kinetics. The early state of the time course is shown in greater magnification in the bottom graph.
[ET]=[E]+[ES]
Product formation rate=k1([ET]-[ES])[S]
[ES] dissociation=k2[ES]+k-1[ES]
d[ES]=0, steady state assumption
k1([ET]-[ES])[S] = k2[ES]+k-1[ES]
(k2+k-1)/k1 = ([ET]-[ES])[S]/[ES]
v = d[P]/dtv = k2[ES]v = k2[ET][S]/Km+[S]
Understanding Km
The "kinetic activator constant" • Km is a constant • Km is a constant derived from rate constants • Km is, under true Michaelis-Menten conditions, an
estimate of the dissociation constant of E from S • Small Km means tight binding; high Km means weak
binding
Km = (k-1+k2)/k1
Km = [S]([Et]-[ES])/[ES]
Understanding Vmax
The theoretical maximal velocity • Vmax is a constant • Vmax is the theoretical maximal rate of the reaction -
but it is NEVER achieved in reality • To reach Vmax would require that ALL enzyme
molecules are tightly bound with substrate • Vmax is asymptotically approached as substrate is
increased
The Turnover Number Defines the Activity of One Enzyme Molecule
A measure of catalytic activity • kcat, the turnover number, is the number of
substrate molecules converted to product per enzyme molecule per unit of time, when E is saturated with substrate.
• If the M-M model fits, k2 = kcat = Vmax/Et
• Values of kcat range from less than 1/sec to many millions per sec
The Ratio kcat/Km Defines the Catalytic Efficiency of an Enzyme
The catalytic efficiency: kcat/KmAn estimate of "how perfect" the enzyme is
• kcat/Km is an apparent second-order rate constant • It measures how the enzyme performs when S is low • The upper limit for kcat/Km is the diffusion limit - the
rate at which E and S diffuse together