enzymes

Chapter 23: Enzymes

Chem 104 K. Dunlap

EnzymesRibbon diagram of cytochrome c oxidase, the enzyme that directly uses oxygen during respiration.

Enzyme CatalysisEnzyme: A biological catalyst.– With the exception of some RNAs that catalyze their own

self-cleavage, all enzymes are proteins.– Enzymes can increase the rate of a reaction by a factor of 109 to 1020 over

an uncatalyzed reaction.– Some catalyze the reaction of only one compound.

– Others are stereoselective; for example, enzymes that catalyze the reactions of only L-amino acids.

– Others catalyze reactions of specific types of compounds or bonds; for example, trypsin catalyzes hydrolysis of peptide bonds formed by the carboxyl groups of Lys and Arg.

Enzyme CatalysisTrypsin catalyzes the hydrolysis of peptide bonds formed by the carboxyl group of lysine and arginine.

Classification of EnzymesEnzymes are commonly named after the reaction or reactions they catalyze.– Example: lactate dehydrogenase, acid phosphatase.

Enzymes are classified into six major groups according to the type of reaction catalyzed:– Oxidoreductases: Oxidation-reduction reactions.– Transferases: Group transfer reactions.– Hydrolases: Hydrolysis reactions.– Lyases: Addition of two groups to a double bond, or removal of

two groups to create a double bond.– Isomerases: Isomerization reactions.– Ligases: The joining to two molecules.

Classification of Enzymes1. Oxidoreductase:

2. Transferase:

3. Hydrolase:

Classification of Enzymes

4. Lyase:

5. Isomerase:

6. Ligase:

Enzyme Terminology

Apoenzyme: The protein part of an enzyme.Cofactor: A nonprotein portion of an enzyme that is necessary for catalytic function; examples are metallic ions such as Zn2+ and Mg2+.Coenzyme: A nonprotein organic molecule, frequently a B vitamin, that acts as a cofactor.Substrate: The compound or compounds whose reaction an enzyme catalyzes.Active site: The specific portion of the enzyme to which a substrate binds during reaction.

Schematic of an Active Site

Schematic diagram of the active site of an enzyme and the participating components.

Terms in Enzyme Chemistry

Activation: Any process that initiates or increases the activity of an enzyme.

Inhibition: Any process that makes an active enzyme less active or inactive.

Competitive inhibitor: A substance that binds to the active site of an enzyme thereby preventing binding of substrate.

Noncompetitive inhibitor: Any substance that binds to a portion of the enzyme other than the active site and thereby inhibits the activity of the enzyme.

Enzyme Activity

Enzyme activity: A measure of how much a reaction rate is increased.We examine how the rate of an enzyme-catalyzed reaction is affected by:– Enzyme concentration.– Substrate concentration. – Temperature.– pH.

The effect of enzyme concentration on the rate

Substrate concentration, temperature, and pH are constant.

The effect of substrate concentration on the rate

Enzyme concentration, temperature, and pH are constant.

The effect of temperature on the rate

Substrate and enzyme concentrations and pH are constant.

The effect of pH on the rate Substrate and enzyme concentrations and temperature are

constant.

Lock-and-key model- The enzyme is a rigid three-dimensional body.– The enzyme surface contains the active site.

Induced FitThe active site becomes modified to accommodate the

substrate.

Competitive InhibitionWhen a competitive inhibitor enters the active site, the substrate

cannot enter.

Noncompetitive InhibitionThe inhibitor binds itself to a site other than the active site (allosterism), thereby changing the conformation of the active site. The substrate still binds but there is no catalysis.

Enzyme kinetics in the presence and the absence of inhibitors.

Mechanism of Action

– Both the lock-and-key model and the induced-fit model emphasize the shape of the active site.

– However, the chemistry of the active site is the most important.

– Just five amino acids participate in the active site in more than 65% of the enzymes studied to date.

– These five are His > Cys > Asp > Arg > Glu.– Four of these amino acids have either acidic or basic

side chains; the fifth has a sulfhydryl group (-SH).

Catalytic Power• Enzymes provide an alternative pathway for reaction. (a) The

activation energy profile for a typical reaction. (b) A comparison of the activation energy profiles for a catalyzed and uncatalyzed reactions.

Enzyme RegulationFeedback control: An enzyme-regulation process where the product of a series of enzyme-catalyzed reactions inhibits an earlier reaction in the sequence.

– The inhibition may be competitive or noncompetitive.

Enzyme Regulation

• Proenzyme (zymogen): An inactive form of an enzyme that must have part of its polypeptide chain hydrolyzed and removed before it becomes active.– An example is trypsin, a digestive enzyme.– It is synthesized and stored as trypsinogen, which has no

enzyme activity.– It becomes active only after a six-amino acid fragment is

hydrolyzed and removed from the N-terminal end of its chain.

– Removal of this small fragment changes not only the primary structure but also the tertiary structure, allowing the molecule to achieve its active form.

Enzyme Regulation

Allosterism: Enzyme regulation based on an event occurring at a place other than the active site but that creates a change in the active site.– An enzyme regulated by this mechanism is called an

allosteric enzyme.– Allosteric enzymes often have multiple polypeptide

chains.– Negative modulation: Inhibition of an allosteric enzyme.– Positive modulation: Stimulation of an allosteric enzyme. – Regulator: A substance that binds to an allosteric

enzyme.

Enzyme Regulation

• The allosteric effect. Binding of the regulator to a site other than the active site changes the shape of the active site.

Enzyme RegulationEffects of binding activators and inhibitors to allosteric

enzymes. The enzyme has an equilibrium between the T form and the R form.

Enzyme RegulationProtein modification: The process of affecting enzyme activity by covalently modifying it.– The best known examples of protein modification involve

phosphorylation/dephosphorylation.– Example: Pyruvate kinase (PK) is the active form of the

enzyme; it is inactivated by phosphorylation to pyruvate kinase phosphate (PKP).

Enzyme Regulation

Isoenzyme (Isozymes): An enzyme that occurs in multiple forms; each catalyzes the same reaction.– Example: lactate dehydrogenase (LDH) catalyzes the oxidation

of lactate to pyruvate.– The enzyme is a tetramer of H and M chains.– H4 is present predominately in heart muscle.

– M4 is present predominantly in the liver and in skeletal muscle.

– H3M, H2M2, and HM3 also exist.

– H4 is allosterically inhibited by high levels of pyruvate while M4 is not.

– H4 in serum correlates with the severity of heart attack.

Enzyme RegulationThe isozymes of lactate dehydrogenase (LDH). The electrophoresis gel depicts the relative isozyme types found in different tissues.

Enzymes Used in Medicine

Insert Table 23.2, page 648

Transition-State Analogs

• Transition state analog: A molecule whose shape mimics the transition state of a substrate.

• Figure 23.17 The proline racemase reaction. Pyrrole-2-carboxylate mimics the planar transition state of the reaction (next screen).

Transition-State Analog

Transition-State Analogs• Abzyme: An antibody that has catalytic activity

because it was created using a transition state analog as an immunogen. (a) The molecule below is a transition analog for the reaction of an amino acid with pyridoxal-5’-phosphate. (b) The abzyme is then used to catalyze the reaction on the next screen.

Transition-State Analogs