Enzymes: Biochemistry

Enzymes

• Enzymes are proteins that act as catalysts to speed up biochemical reactions.
• Enzymes lower the activation energy of a reaction, making it easier to occur.

Enzyme-Catalyzed Reaction Diagram

• With an enzyme, the free energy diagram would show a lower activation energy peak compared to the uncatalyzed reaction.

Enzyme Active Sites

• Active site: Where the substrate binds and the reaction occurs.
• Allosteric site: Where molecules can bind to regulate enzyme activity (noncompetitive inhibitors or activators).

Factors Affecting Enzyme Function

• Temperature: Enzymes have an optimal temperature range; high temperatures can denature the enzyme
• pH: Enzymes have an optimal pH range; deviations can disrupt enzyme structure and function.
• Substrate Concentration: Increasing substrate concentration increases reaction rate until saturation.
• Inhibitors and Activators: These molecules can decrease or increase enzyme activity, respectively.

Induced Fit

• "Induced fit" refers to the conformational change an enzyme undergoes upon substrate binding, which results in tighter binding of the substrate to the active site and enhances the reaction.

Enzyme Inhibition

• Competitive inhibition: An inhibitor binds to the active site, blocking substrate binding.
• Noncompetitive/Allosteric inhibition: An inhibitor binds to an allosteric site, changing the enzyme's shape and reducing its activity.

Enzyme Regulation

• Activators bind to an enzyme and stabilize the active form, increasing its activity.
• Inhibitors bind to an enzyme and stabilize the inactive form, decreasing its activity.

Allosteric Regulation

• Allosteric regulation is when a regulatory molecule binds to an enzyme at one site (allosteric site) and affects the function of the enzyme at a different site (active site).

Catabolic Pathways

• Three pathways: Fermentation, Anaerobic respiration, and Aerobic/Cellular respiration.
• Fermentation: Partial degradation of sugars that occurs without oxygen.
• Anaerobic respiration: Similar to aerobic respiration but uses other substances than oxygen to accept electrons.
• Aerobic/Cellular respiration: Complete breakdown of organic molecules with oxygen, yielding more ATP.

Cellular Respiration

• Reactants: Glucose (C6H12O6) and Oxygen (O2).
• Products: Carbon Dioxide (CO2), Water (H2O), and ATP.
• Glucose is oxidized to CO2.
• Oxygen is reduced to Water.

Cellular Respiration Fuel

• Can be fueled by carbohydrates, fats, and proteins.

Redox Reactions

• Redox reaction: A chemical reaction involving the transfer of electrons between two species.
• Oxidation: The loss of electrons from a substance.
• Reduction: The gain of electrons to a substance.

Oxidizing and Reducing Agents

• Oxidizing agent: The substance that accepts electrons (is reduced).
• Reducing agent: The substance that donates electrons (is oxidized).

Electron Acceptors

• Aerobic/Cellular respiration: Oxygen (O2)
• Anaerobic respiration: Sulfate, nitrate and sulfur

Stages of Aerobic/Cellular Respiration

• Glycolysis
• Pyruvate Oxidation and Citric Acid Cycle (Krebs Cycle)
• Oxidative Phosphorylation (Electron Transport Chain and Chemiosmosis)

Glycolysis

• Input: Glucose, 2 ATP
• Output: 2 Pyruvate, 2 NADH, 4 ATP (net gain of 2 ATP)
• Products/Net Yield: 2 ATP (net), 2 NADH, 2 Pyruvate
• Location: Cytosol.
• ATP Production: Substrate-level phosphorylation.

Pyruvate Oxidation

• Input: 2 Pyruvate
• Output: 2 Acetyl CoA, 2 CO2, 2 NADH
• Products/Net Yield: 2 Acetyl CoA, 2 NADH, 2 CO2
• Location: Mitochondrial matrix.
• ATP Production: None directly.

Citric Acid Cycle (Krebs Cycle)

• Input: 2 Acetyl CoA
• Output: 4 CO2, 6 NADH, 2 FADH2, 2 ATP
• Products/Net Yield (per 1 Acetyl CoA): 1 ATP, 3 NADH, 1 FADH2, 2 CO2
• Products/Net Yield (per 2 Acetyl CoA): 2 ATP, 6 NADH, 2 FADH2, 4 CO2
• Location: Mitochondrial matrix.
• ATP Production: Substrate-level phosphorylation.

Oxidative Phosphorylation

• Consists of the Electron Transport Chain and Chemiosmosis.

Electron Transport Chain (ETC)

• Structure: A series of protein complexes embedded in the inner mitochondrial membrane.
• Function: Accepts electrons from NADH and FADH2, passes them down the chain, and uses the energy to pump protons (H+) across the inner mitochondrial membrane.
• Purpose: Creates a proton gradient that drives ATP synthesis via chemiosmosis.

Chemiosmosis

• Mechanism: H+ ions flow down their concentration gradient through ATP synthase, a protein complex in the inner mitochondrial membrane.
• Enzyme Involved: ATP synthase.
• End Result: The energy from the H+ gradient is used to phosphorylate ADP, producing ATP.

Energy Flow in Cellular Respiration

• Glucose → NADH/FADH2 → Electron Transport Chain → Proton-Motive Force → ATP

Anaerobic Respiration

• Differs from aerobic respiration by using a final electron acceptor other than oxygen (e.g., sulfate, nitrate).

Fermentation

• Similar to anaerobic respiration in that it doesn't use oxygen.
• Different from anaerobic respiration because it does not involve an electron transport chain.

Fermentation

• Consists of glycolysis plus reactions that regenerate NAD+, which can then be reused by glycolysis.

Types of Fermentation

• Alcohol Fermentation:
  • Final electron acceptor: Acetaldehyde.
  • Product: Ethanol and CO2.
• Lactic Acid Fermentation:
  • Final electron acceptor: Pyruvate.
  • Product: Lactate.

Regulation of Catabolism

• Cells regulate catabolism through feedback inhibition, where the end product of a metabolic pathway inhibits an enzyme early in the pathway.