Unit 5: Enzymes and Carbohydrate Metabolism

Enzymes

Definition: Enzymes

Enzymes are biological catalysts (usually proteins) that speed up the rate of a chemical reaction without being consumed in the process. They do this by lowering the activation energy.

Nomenclature and Classification

• Nomenclature: Most enzymes are named by adding the suffix "-ase" to the name of their substrate (e.g., Lactase breaks down Lactose) or the reaction they catalyze (e.g., Polymerase makes polymers).
• Classification: The International Union of Biochemistry (IUB) classifies enzymes into 6 major classes based on the reaction type:
  1. Oxidoreductases: Catalyze oxidation-reduction reactions (e.g., Dehydrogenase).
  2. Transferases: Transfer a functional group (e.g., Kinase transfers a phosphate group).
  3. Hydrolases: Break bonds by adding water (e.g., Protease, Lipase).
  4. Lyases: Break bonds without water (e.g., Decarboxylase).
  5. Isomerases: Rearrange atoms within a molecule (e.g., Mutase).
  6. Ligases: Join two molecules together, usually using ATP (e.g., DNA Ligase).
  Mnemonic: Over The Hill Lizards In Love.

Mechanism of Action (Activation Energy)

• Substrate: The reactant molecule that an enzyme binds to.
• Active Site: A specific 3D pocket or groove on the enzyme where the substrate binds.
• Activation Energy (Ea): The energy "hill" that must be overcome for a reaction to start.
• How it works: The enzyme binds the substrate at its active site to form an Enzyme-Substrate (E-S) complex. This binding stresses the substrate's bonds, stabilizing the transition state and lowering the activation energy, thus speeding up the reaction.

Factors Affecting Enzyme Activity

Enzyme activity is highly sensitive to its environment. When an enzyme loses its 3D shape and function, it is denatured.

Temperature

• Effect: As temperature increases, reaction rate increases (molecules move faster).
• Optimum Temperature: The temperature at which the enzyme has its highest activity.
• Denaturation: Above the optimum, the enzyme's 3D structure unfolds (denatures), and the activity drops sharply. (For most human enzymes, this is ~37°C).

pH

• Effect: Each enzyme has an optimum pH at which it functions best.
• Denaturation: Extreme pH (too acidic or too basic) alters the charges on the amino acid R-groups, disrupting ionic bonds and changing the shape of the active site.
  • Example: Pepsin (in the stomach) works best at pH 2, while Trypsin (in the intestine) works best at pH 8.

Substrate Concentration

• Effect: As substrate concentration increases, the reaction rate increases... up to a point.
• Saturation: When all enzyme active sites are occupied ("saturated") with substrate, the reaction reaches its maximum velocity (Vmax). Adding more substrate will not make it go any faster.

Enzyme Inhibition

Inhibitors are molecules that bind to an enzyme and decrease its activity.

Reversible Inhibition

The inhibitor binds non-covalently and can be removed.

• Competitive Inhibition:
  • The inhibitor competes with the substrate for the same active site.
  • It "looks like" the substrate.
  • Can be overcome by adding more substrate.
• Non-competitive Inhibition:
  • The inhibitor binds to a different site on the enzyme (an allosteric site).
  • This binding changes the shape of the active site, so the substrate cannot bind properly.
  • Cannot be overcome by adding more substrate.

Irreversible Inhibition

The inhibitor binds covalently (permanently) to the enzyme, often at the active site, and permanently "kills" it. Many poisons and drugs work this way (e.g., penicillin).

Cofactors and Coenzymes

Many enzymes are inactive on their own and require a non-protein "helper" to function.

• Apoenzyme: The inactive protein part of the enzyme.
• Cofactor: The non-protein helper.
• Holoenzyme: The complete, active enzyme (Apoenzyme + Cofactor).

Types of Cofactors:

• Inorganic Ions: Metal ions like Fe²⁺, Mg²⁺, Zn²⁺.
• Coenzymes: Organic (carbon-based) molecules.
  • Function: They act as carriers, transferring chemical groups (like electrons or atoms) from one reaction to another.
  • Source: Many are derived from vitamins (e.g., NAD+ from Niacin/B3, FAD from Riboflavin/B2).

Prosthetic Groups

• A prosthetic group is a coenzyme or cofactor that is tightly and permanently bound to the apoenzyme.
• Example: The heme group in hemoglobin (which is not an enzyme, but shows the concept) or in catalase.

Carbohydrate Metabolism

This is the central pathway for extracting energy (ATP) from glucose. It occurs in three main stages:

Glycolysis ("Splitting of Sugar")

• Location: Cytosol.
• Process: A 10-step pathway that breaks one Glucose (6-carbon) molecule into two Pyruvate (3-carbon) molecules.
• Reactants: 1 Glucose, 2 ATP (investment), 2 NAD+
• Products (Net): 2 Pyruvate, 2 ATP, 2 NADH
• Anaerobic: This process does not require oxygen.

TCA Cycle (Krebs Cycle / Citric Acid Cycle)

• Location: Mitochondrial Matrix.
• Process: First, Pyruvate is converted to Acetyl-CoA (2-carbon). The Acetyl-CoA then enters the TCA cycle, a "merry-go-round" that breaks it down completely.
• Reactants (per 1 Acetyl-CoA): 1 Acetyl-CoA, 3 NAD+, 1 FAD
• Products (per 1 Acetyl-CoA): 2 CO2 (waste), 1 ATP, 3 NADH, 1 FADH2
• Note: Since 1 Glucose = 2 Pyruvate = 2 Acetyl-CoA, the cycle turns twice per glucose.

Electron Transport Chain (ETC)

• Location: Inner Mitochondrial Membrane.
• Process: The high-energy electron carriers (NADH and FADH2) from Glycolysis and the TCA Cycle "dump" their electrons at the ETC.
• As electrons are passed down a chain of protein complexes, their energy is used to pump H+ protons into the intermembrane space, creating a steep gradient.
• The H+ protons then rush back into the matrix through an enzyme called ATP Synthase. This flow of protons (like water through a dam) powers the synthesis of ~32-34 ATP.
• Final Electron Acceptor: Oxygen (O2) is the final acceptor, which combines with H+ to form water (H2O). This is why we need to breathe oxygen!