Unit 2: Enzymes

Table of Contents

Enzyme Classification and Structure

Enzymes are biological catalysts (usually proteins) that speed up biochemical reactions without being consumed. The molecule an enzyme acts upon is called the substrate.

Classification and Nomenclature

Enzymes are classified into six major classes by the International Union of Biochemistry and Molecular Biology (IUBMB) based on the type of reaction they catalyze. They often have the suffix "-ase".

  1. Oxidoreductases: Catalyze oxidation-reduction reactions (e.g., *dehydrogenase*, *oxidase*).
  2. Transferases: Transfer a functional group (e.g., methyl, phosphate) from one molecule to another (e.g., *kinase*, *transaminase*).
  3. Hydrolases: Break bonds by adding water (hydrolysis) (e.g., *lipase*, *amylase*, *peptidase*).
  4. Lyases: Break bonds by means other than hydrolysis or oxidation, often forming a double bond (e.g., *decarboxylase*).
  5. Isomerases: Catalyze the rearrangement of atoms within a molecule (isomerization) (e.g., *isomerase*, *mutase*).
  6. Ligases: Join two molecules together, usually coupled with the hydrolysis of ATP (e.g., *DNA ligase*, *synthetase*).

Prosthetic Groups, Cofactors of Enzyme

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

  • Apoenzyme: The inactive protein part of the enzyme.
  • Cofactor: The non-protein part. This is a broad term.
    • Inorganic Ions: Metal ions that act as cofactors (e.g., Mg2+, Zn2+, Fe2+).
    • Coenzyme: An organic (non-protein) molecule that acts as a cofactor. Many vitamins are precursors to coenzymes.
  • Prosthetic Group: A coenzyme or metal ion that is tightly and covalently bound to the apoenzyme. (e.g., the heme group in hemoglobin).
  • Holoenzyme: The complete, active enzyme, consisting of the apoenzyme plus its cofactor/coenzyme.
    Formula: Apoenzyme + Cofactor = Holoenzyme

Properties of Enzymes as Catalysts

  1. High Catalytic Efficiency: They are extremely efficient, speeding up reactions by factors of 106 to 1012.
  2. High Specificity: Enzymes are highly specific for their substrate and the reaction they catalyze (e.G., *urease* only hydrolyzes *urea*).
  3. Mild Conditions: They operate under mild conditions of temperature (e.g., 37°C) and pH (e.g., 7.4) found in living organisms.
  4. Regulation: Their activity can be controlled (activated or inhibited) by other molecules, allowing for metabolic regulation.

Specific Activity

Definition: A measure of enzyme purity. It is defined as the number of units of enzyme activity per milligram of total protein.

As an enzyme is purified, its specific activity increases (because the "units of activity" stay the same, but the "mg of protein" decreases as non-enzyme proteins are removed).

Turn Over Number (TON)

Definition: The maximum number of substrate molecules converted to product per enzyme molecule per unit time (usually per second).

It represents the catalytic efficiency of a single enzyme molecule when it is fully saturated with substrate. (Also known as kcat).

Mechanism of Enzyme Action

Enzymes work by lowering the activation energy (Ea) of a reaction, thus making it proceed faster. They do this by providing an alternative reaction pathway via an enzyme-substrate complex (ES).

Reaction: E (Enzyme) + S (Substrate) leftharpoons ES (Complex) → E (Enzyme) + P (Product)

Lock and Key Model

  • Proposed by Emil Fischer in 1894.
  • Concept: The active site of the enzyme has a specific 3D shape that is perfectly complementary to the shape of the substrate.
  • The substrate (the "key") fits perfectly into the rigid active site (the "lock").
  • Limitation: This model is too rigid. It doesn't explain how enzymes can be flexible or how the transition state is stabilized.
Modern Context (Beyond Syllabus): The Induced Fit Model (by Daniel Koshland) is a more accepted model. It proposes that the active site is flexible. The binding of the substrate *induces* a change in the shape of the active site, leading to a perfect fit *after* binding, which helps to stabilize the transition state.

Factors Affecting Enzyme Activity

The rate of an enzyme-catalyzed reaction is influenced by several factors.

Effect of pH

  • Every enzyme has an optimum pH at which its activity is maximum (e.g., pepsin in the stomach, pH ~2; trypsin in the intestine, pH ~8).
  • At pH values above or below the optimum: The enzyme's activity decreases rapidly.
  • Reason: Extreme pH (highly acidic or basic) alters the ionization state of the amino acid residues in the active site and throughout the protein. This disrupts the enzyme's 3D structure (denaturation) and its ability to bind the substrate.

Effect of Temperature

  • Low Temperature: Reaction rate is low because molecules have low kinetic energy.
  • Increasing Temperature: As temperature rises, the reaction rate increases (more kinetic energy, more collisions), up to a certain point.
  • Optimum Temperature: The temperature at which the enzyme shows maximum activity (for most human enzymes, ~37-40°C).
  • High Temperature: Above the optimum, the rate drops sharply.
  • Reason: High temperatures provide too much thermal energy, which breaks the weak bonds (H-bonds, hydrophobic interactions) that maintain the enzyme's 3D structure. The enzyme unfolds and loses its active site shape. This is an irreversible process called denaturation.