Unit 5: Enzymes and Carbohydrate Metabolism

1. Enzymes: Introduction

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.

2. Nomenclature and Classification of Enzymes

a) Nomenclature

Enzymes are typically named by adding the suffix "-ase" to the name of their substrate (e.g., Urease, Lactase) or the reaction they catalyze (e.g., DNA Polymerase).

b) Classification (IUBMB)

The International Union of Biochemistry and Molecular Biology (IUBMB) classifies all enzymes into six major classes:

1. (EC 1) Oxidoreductases: Catalyze redox reactions.
2. (EC 2) Transferases: Catalyze the transfer of a functional group.
3. (EC 3) Hydrolases: Catalyze hydrolysis (breaking a bond using water).
4. (EC 4) Lyases: Catalyze bond cleavage by means other than hydrolysis or oxidation.
5. (EC 5) Isomerases: Catalyze rearrangement within a molecule.
6. (EC 6) Ligases: Catalyze the joining of two molecules, using ATP.

3. Activation Energy

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 speed up reaction rates by lowering the activation energy (E_A). They do this by providing an alternative reaction pathway and stabilizing the transition state.

[Image of an energy profile diagram showing a reaction with and without an enzyme]

4. 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 alters the ionization of R-groups in the active site and can lead to denaturation.

[Image of graphs showing enzyme activity vs. temperature and vs. pH]

c) Effect of Substrate Concentration [S]

• As [S] increases, the reaction rate increases...
• ...until the enzyme becomes saturated. At this point, all active sites are occupied, and the reaction reaches its maximum velocity (V_max).

5. Enzyme Inhibition (Reversible and Irreversible)

Inhibitors are molecules that reduce or stop enzyme activity.

a) Reversible Inhibition

The inhibitor binds non-covalently and can be removed.

• Competitive Inhibition: The inhibitor mimics the substrate and binds to the active site. It can be overcome by adding more substrate.
• Non-competitive Inhibition: The inhibitor binds to an allosteric site (a different site), changing the shape of the active site. It cannot be overcome by adding more substrate.

[Image comparing competitive and non-competitive inhibition]

b) Irreversible Inhibition

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

6. 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⁺.
2. Coenzymes: Organic (carbon-based) molecules, often derived from vitamins (e.g., NAD⁺, FAD).

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 (e.g., the heme group).

7. Carbohydrate Metabolism: Introduction

Carbohydrate metabolism is the set of biochemical processes responsible for the synthesis, breakdown, and interconversion of carbohydrates. This unit focuses on the breakdown of glucose to generate ATP.

8. Glycolysis

Glycolysis is a 10-step metabolic pathway that converts one molecule of Glucose (6C) into two molecules of Pyruvate (3C).

• Location: Cytosol of all cells.
• Phases:
  1. Energy Investment Phase: Consumes 2 ATP.
  2. Energy Payoff Phase: Produces 4 ATP and 2 NADH.
• Net Yield (per 1 Glucose):
  • 2 Pyruvate
  • 2 ATP
  • 2 NADH

9. TCA Cycle (Krebs Cycle / Citric Acid Cycle)

Before the cycle, the 2 Pyruvate (3C) from glycolysis are converted to 2 Acetyl-CoA (2C) in the mitochondria. This is the "link reaction."

The TCA Cycle is the final common pathway for the oxidation of fuel molecules. It completely oxidizes Acetyl-CoA to CO₂.

• Location: Mitochondrial Matrix.
• Process: The cycle begins when Acetyl-CoA (2C) combines with Oxaloacetate (4C) to form Citrate (6C). In a series of 8 steps, the cycle regenerates Oxaloacetate and releases energy.

Net Yield (per 1 Glucose, which means 2 turns of the cycle):

• 4 CO₂ (released)
• 6 NADH
• 2 FADH₂
• 2 GTP (or ATP)

10. Electron Transport Chain (ETC)

The ETC (or Oxidative Phosphorylation) is the process that uses the high-energy electrons from NADH and FADH₂ (produced in glycolysis and the TCA cycle) to generate the vast majority of ATP.

• Location: Inner Mitochondrial Membrane.

The Process (Chemiosmosis)

1. Electron Transport: Electrons from NADH and FADH₂ are passed down a series of protein complexes (I, II, III, IV).
2. Proton Pumping: As electrons move, energy is used to pump protons (H⁺) from the matrix into the intermembrane space, creating a strong electrochemical gradient.
3. Final Electron Acceptor: The electrons at the end of the chain are transferred to Oxygen (O₂), which combines with H⁺ to form Water (H₂O).
4. ATP Synthesis: The H⁺ ions flow back into the matrix down their gradient, passing through the ATP Synthase enzyme. This flow drives the "motor" of ATP synthase, which phosphorylates ADP to make ATP.

[Image of the Electron Transport Chain and ATP Synthase on the inner mitochondrial membrane]