Chapter 03 Notes: Energy, Chemical Reactions, and Cellular Respiration (Integrative Approach)

3.1a Classes of Energy

  • Energy is the capacity to do work.

  • Two classes:

    • Potential energy (stored energy, energy of position).

    • Kinetic energy (energy of motion).

  • Both are interconvertible.

3.1a Potential energy and the plasma membrane; Electron shells

  • Potential energy exists in concentration gradients (e.g., across plasma membrane) and electron shells.

  • Conversion to kinetic energy is required for work.

3.1b Forms of Energy

  • Chemical energy: Potential energy stored in molecular bonds (e.g., Triglycerides, Glucose, ATP).

  • Kinetic energy forms:

    • Electrical energy (movement of charged particles).

    • Mechanical energy (moving objects, e.g., muscle contraction).

    • Sound energy (pressure waves).

    • Radiant energy (electromagnetic waves, e.g., visible light).

    • Heat (kinetic energy of molecular movement; often unusable for work).

3.1c Laws of Thermodynamics

  • First law: Energy cannot be created or destroyed; it only changes form.

  • Second law: Energy transformations result in some energy loss as heat; usable energy decreases.

3.2a Chemical Equations

  • Metabolism: all biochemical reactions.

  • Chemical reactions involve bond breaking/forming; expressed as reactants → products.

  • Balanced equations: equal elements on both sides.

3.2b Classification of Chemical Reactions

  • 1) Changes in chemical structure:

    • Decomposition: AB → A + B (e.g., hydrolysis).

    • Synthesis: A + B → AB (e.g., anabolism).

    • Exchange: AB + C → A + BC (groups exchanged).

    • Oxidation–reduction (redox) reactions: electron transfer (oxidized species loses, reduced gains; e.g., NAD+/NADH).

  • 2) Changes in chemical energy:

    • Exergonic: energy released (reactants > products bond energy).

    • Endergonic: energy input required (reactants < products bond energy).

  • 3) Irreversible vs Reversible:

    • Irreversible: net loss of reactants/gain of products.

    • Reversible: reaches equilibrium; no net change (e.g., carbonic acid reaction: ext{CO}_2 + ext{H}_2 ext{O} \rightleftharpoons ext{H}_2 ext{CO}_3 \rightleftharpoons ext{H}^+ + ext{HCO}_3^-).

ATP cycling (Section 3.2b)

  • Continuous formation (from ADP + Pi using exergonic energy) and breakdown (hydrolysis provides energy for endergonic processes).

  • Rapid turnover; sustains cellular work.

3.2c Reaction Rates and Activation Energy

  • Reaction rate: how quickly a reaction occurs.

  • Activation energy (Ea): energy needed to start a reaction.

  • Enzymes: biological catalysts that lower Ea, speeding reactions without changing whether they occur.

3.3a Function of Enzymes

  • Enzymes are catalysts that accelerate specific chemical reactions by lowering activation energy.

3.3b Enzymes: Structure and Location

  • Most are globular proteins with a unique 3D active site that binds specific substrates (induced-fit model).

  • Located intracellularly, in membranes, or secreted.

3.3c Mechanism of Enzyme Action

1) Substrate binds to active site, forming enzyme–substrate complex.
2) Enzyme changes shape (induced fit), straining bonds.
3) Products form and are released.
4) Enzyme is ready to repeat.

  • Cofactors: nonprotein molecules/ions (inorganic or coenzymes) essential for enzyme activity.

3.3d Classification and Naming of Enzymes

  • Six major classes (e.g., Oxidoreductases, Transferases, Hydrolases, Ligases).

  • Named based on substrate/product, subclass, and "-ase" suffix (e.g., Lactase digests lactose).

3.3e Enzymes and Reaction Rates

  • Factors affecting rate:

    • Enzyme concentration (increases rate up to saturation).

    • Substrate concentration (increases rate up to saturation).

    • Temperature (optimal ~40^{\circ} ext{C}; high temps denature).

    • pH (optimal ~6-8; deviations denature).

3.3f Controlling Enzymes

  • Inhibitors: bind to enzymes to reduce activity.

    • Competitive: resemble substrate, bind to active site, compete with substrate.

    • Noncompetitive (Allosteric): bind to an allosteric site, altering active site, not affected by substrate concentration.

3.3g Metabolic Pathways and Multienzyme Complexes

  • Metabolic pathway: series of enzyme-catalyzed reactions.

  • Multienzyme complex: attached enzymes working in sequence; improves efficiency and coordinated regulation (e.g., negative feedback by product).

  • Regulation: phosphorylation (kinases add P, dephosphorylation (phosphatases remove P) can activate/inactivate enzymes.

3.4 Cellular Respiration (Overview)

  • Exergonic pathway oxidizing organic molecules to synthesize ATP (endergonic).

  • Requires oxygen for maximum ATP.

3.4a Overview of Glucose Oxidation

  • Stepwise breakdown of glucose: ext{C}_6 ext{H}_{12} ext{O}_6 + 6 ext{O}_2 \rightarrow 6 ext{CO}_2 + 6 ext{H}_2 ext{O}.

  • ATP production:

    • Substrate-level phosphorylation (direct transfer).

    • Oxidative phosphorylation (via electron transport system).

  • Occurs in cytosol (glycolysis) and mitochondria (intermediate stage, citric acid cycle, ETC).

3.4a Four stages and location

1) Glycolysis: cytosol; anaerobic.
2) Intermediate stage: mitochondria; links glycolysis to citric acid cycle; twice per glucose.
3) Citric acid cycle (Krebs): mitochondrial matrix; aerobic.
4) Electron transport system (oxidative phosphorylation): inner mitochondrial membrane; aerobic.

3.4b Glycolysis

  • Cytosol; anaerobic.

  • Net products per glucose: 2 ext{ ATP}, 2 ext{ NADH}, 2 ext{ pyruvate}.

  • Regulation: inhibited by ATP (negative feedback).

  • Pyruvate fate:

    • Sufficient O2: enters mitochondria.

    • Insufficient O2: converted to lactate to regenerate NAD+ for continued glycolysis (anaerobic fermentation, 2 ext{ ATP} total).

3.4c Intermediate Stage (Pyruvate Processing)

  • Mitochondrial matrix; twice per glucose.

  • Pyruvate + CoA + NAD+ → Acetyl CoA + CO2 + NADH (catalyzed by pyruvate dehydrogenase).

3.4d Citric Acid Cycle (Krebs)

  • Mitochondrial matrix.

  • Acetyl CoA combines with oxaloacetate.

  • Per cycle outputs: 1 ext{ ATP} (substrate-level), 3 ext{ NADH}, 1 ext{ FADH}_2, 2 ext{ CO}_2.

  • Two turns per glucose: 2 ext{ ATP}, 6 ext{ NADH}, 2 ext{ FADH}_2, 4 ext{ CO}_2.

3.4e The Electron Transport System (ETC) and Oxidative Phosphorylation

  • Function: transfers electrons from NADH/FADH2 to O2, forming water; energy used to pump H+ across inner mitochondrial membrane.

  • H+ gradient drives ATP synthase to produce ATP (chemiosmosis).

  • Oxygen is final electron acceptor.

3.4f ATP Production

  • NADH yields ~3 ext{ ATP}; FADH2 yields ~2 ext{ ATP} via oxidative phosphorylation.

  • Total ATP per glucose: ~30-32 ext{ ATP} (including 2 ext{ ATP} from glycolysis, 2 ext{ ATP} from citric acid cycle, and ~26-28 ext{ ATP} from oxidative phosphorylation).

3.4g Other Fuel Molecules Oxidized in Cellular Respiration

  • Fatty acids: beta-oxidation converts to acetyl CoA; requires oxygen; high energy yield.

  • Amino acids: enter at various points; amine groups excreted as urea.

Quick reference: Key formulas and concepts

  • Overall glucose oxidation: ext{C}_6 ext{H}_{12} ext{O}_6 + 6 ext{O}_2 \rightarrow 6 ext{CO}_2 + 6 ext{H}_2 ext{O}

  • Glycolysis net: ext{Glucose} \rightarrow 2 ext{Pyruvate} + 2 ext{NADH} + 2 ext{ATP} (net)

  • NADH/FADH2 as energy carriers: per NADH ~3 ATP; per FADH2 ~2 ATP.

  • Pyruvate fate under low O2: Pyruvate → Lactate + NAD+ regeneration; 2 net ATP per glucose.

  • Carbonic acid buffering: ext{CO}_2 + ext{H}_2 ext{O} \rightleftharpoons ext{H}_2 ext{CO}_3 \rightleftharpoons ext{H}^+ + ext{HCO}_3^-

  • ATP cycling: ADP + Pi \rightleftharpoons ATP.

Connections to broader topics

  • Energy forms underpin physiology (muscle contraction, ion transport).

  • Thermodynamics explains metabolic pathway design and regulation.

  • Enzymes optimize reaction rates and maintain homeostasis.

  • Clinical scenarios (cyanide poisoning, enzyme inhibitors) illustrate metabolic impacts on health.