Unit 4: Enzymes

Enzymes are biological catalysts. They are (mostly) globular proteins that increase the rate of a chemical reaction without being consumed in the process. They are highly specific and highly efficient.

1. Nomenclature and Classification of Enzymes

a) Nomenclature

Enzymes are typically named by adding the suffix "-ase" to the name of their substrate or the reaction they catalyze.

• Substrate: Urease (hydrolyzes Urea), Lactase (hydrolyzes Lactose).
• Reaction: DNA Polymerase (polymerizes DNA), Dehydrogenase (removes hydrogen).

b) Classification (IUBMB)

The International Union of Biochemistry and Molecular Biology (IUBMB) classifies all enzymes into six major classes, each with a unique EC number (Enzyme Commission number).

Mnemonic for the 6 classes: "Over The Hill Lies Invisible Light"

1. (EC 1) Oxidoreductases: Catalyze oxidation-reduction (redox) reactions (e.g., Dehydrogenase, Oxidase).
2. (EC 2) Transferases: Catalyze the transfer of a functional group (e.g., methyl, phosphate) from one molecule to another (e.g., Kinase, Transaminase).
3. (EC 3) Hydrolases: Catalyze hydrolysis reactions (breaking a bond using water) (e.g., Protease, Lipase, Amylase).
4. (EC 4) Lyases: Catalyze the cleavage of C-C, C-O, C-N bonds by means *other* than hydrolysis or oxidation, often forming a double bond (e.g., Decarboxylase, Synthase).
5. (EC 5) Isomerases: Catalyze the rearrangement of atoms within a molecule (e.g., Mutase, Isomerase).
6. (EC 6) Ligases: Catalyze the joining of two molecules, coupled with the hydrolysis of ATP (e.g., DNA Ligase, Synthetase).

2. Enzyme Specificity

This is a hallmark property of enzymes. Specificity refers to the ability of an enzyme to bind and catalyze only one or a small group of substrates.

• Absolute Specificity: Catalyzes only one specific substrate (e.g., Urease only acts on urea).
• Group Specificity: Acts on a group of substrates with a similar structure (e.g., Hexokinase phosphorylates various hexose sugars like glucose, fructose).
• Stereospecificity: Acts on only one stereoisomer (L- or D-) of a substrate.

3. Models of Enzyme Action (Lock-and-Key and Induced-Fit)

a) Active Site

The active site is a specific 3D cleft or pocket on the enzyme's surface where the substrate binds and the chemical reaction occurs.

b) Lock-and-Key Model (Emil Fischer, 1894)

• Concept: The active site has a rigid, pre-formed shape that is perfectly complementary to the substrate, like a lock and its key.
• Limitation: This model is too rigid and does not explain how the enzyme stabilizes the transition state.

c) Induced-Fit Model (Daniel Koshland, 1958)

• Concept: The active site is flexible, not rigid. The binding of the substrate induces a conformational change in the enzyme, causing the active site to "wrap around" the substrate.
• Significance: This is the more accepted model. This "hugging" (induced fit) strains the substrate's bonds and orients the catalytic groups, which helps stabilize the transition state and lower the activation energy.

4. Activation Energy (E_A)

Activation Energy (E_A) is the minimum amount of energy required to start a chemical reaction, or the energy needed to reach the high-energy transition state.

Enzymes do not change the overall free energy (ΔG) of a reaction. Instead, they speed up the reaction rate by lowering the activation energy (E_A). They do this by providing an alternative reaction pathway and stabilizing the transition state.

5. Factors Affecting Enzyme Activity

a) Effect of Temperature

• As temperature increases, the reaction rate increases (more kinetic energy).
• However, above an optimal temperature, the enzyme begins to denature (lose its 3D structure), and the rate drops rapidly.

b) Effect of pH

• Each enzyme has an optimal pH at which its activity is maximal (e.g., Pepsin ≈ pH 2; Trypsin ≈ pH 8).
• Extreme pH (too acidic or basic) alters the ionization state of the amino acid R-groups in the active site and can lead to denaturation.

c) Effect of Substrate Concentration [S]

• At a fixed enzyme concentration, as [S] increases, the reaction rate (velocity, V) increases...
• ...until the enzyme becomes saturated. At this point, all active sites are occupied, and the reaction reaches its maximum velocity (V_max).
• This relationship is described by the Michaelis-Menten equation.

6. Enzyme Inhibition (Reversible and Irreversible)

Inhibitors are molecules that reduce or stop enzyme activity. This is a key mechanism for regulating metabolic pathways and is the basis for many drugs.

a) Reversible Inhibition

The inhibitor binds non-covalently and can be removed, restoring enzyme activity.

b) Irreversible Inhibition

The inhibitor binds covalently to the enzyme, permanently disabling it. Examples include heavy metals (mercury, lead) and some nerve gases.

7. Cofactors and Prosthetic Groups

Many enzymes require a non-protein chemical component to be active.

Apoenzyme (inactive protein part) + Cofactor (non-protein part) = Holoenzyme (active enzyme)

Cofactors can be:

1. Inorganic Ions: Metal ions like Mg²⁺, Zn²⁺, Fe²⁺. They often help in binding the substrate or stabilizing the enzyme structure.
2. Coenzymes: Organic (carbon-based) molecules.
   • They are often derived from vitamins (e.g., NAD⁺ from Niacin/B3; FAD from Riboflavin/B2).
   • They act as transient carriers of specific functional groups.

Prosthetic Groups

A prosthetic group is a coenzyme (or metal ion) that is tightly and covalently (or very strongly) bound to the apoenzyme, forming a permanent part of the active enzyme.

Example: The heme group in enzymes like catalase and cytochrome oxidase is a prosthetic group.