Chapter 3 Notes: Energy, Reactions, Enzymes, and Cellular Respiration

3.1 Energy

  • Energy: capacity to do work; has no mass or volume; invisible but effects are observable.
  • Classes of energy: potential energy (stored) and kinetic energy (motion); can convert between them.
  • Examples of energy conversion: water behind a dam (potential → kinetic as it falls); bow and arrow (potential from tension → kinetic when released).
  • Energy in cells: concentration gradients (e.g., Na+ across the plasma membrane) store potential energy; movement of ions (or electrons) provides kinetic energy to do work.
  • Forms of energy (kinetic): electrical, mechanical, sound, radiant, heat; chemical energy (a form of potential energy) stored in bonds.
  • Chemical energy: stored in chemical bonds; released when bonds are broken during reactions; major energy storage molecules include triglycerides, glucose, and ATP. Proteins also store energy but are primarily structural/functional.
  • Thermal energy (heat): a byproduct of energy transformations; not usable to do work; heat production explains energy “cost” of transformations.
  • Law overview:
    • First law (conservation): energy cannot be created or destroyed, only transformed.
    • Second law: some energy is always released as heat during transformations; no 100% efficient conversion.
  • Key equation (glucose oxidation example, in context): not included here; see 3.4 for full pathway details.

3.2 Chemical Reactions

  • Metabolism: all biochemical reactions in the body.

  • Chemical reactions: bonds are broken and new bonds formed; represented by chemical equations with reactants and products.

  • Reactants vs. products: left side are reactants; right side are products; arrow indicates reaction direction.

  • Example balanced equation: ext{Ca}^{2+} + 2 ext{Cl}^{-}
    ightarrow ext{CaCl}_{2}

  • Classification by changes in chemical structure:

    • Decomposition: AB → A + B (catabolic; energy-rich bonds broken).
    • Synthesis: A + B → AB (anabolic; bonds formed).
    • Exchange: AB + C → A + BC (mixture of decomposition/synthesis; common in biology).

  • Classification by chemical energy change:

    • Exergonic: reactants have more energy than products; energy released (e.g., glucose + O₂ → CO₂ + H₂O).
    • Endergonic: products have more energy than reactants; energy input required (e.g., amino acids → dipeptide).

  • ATP cycling: ATP formed from ADP + Pi (endergonic) and ATP hydrolysis to ADP + Pi (exergonic); ATP acts as energy intermediary.

  • Reversible vs irreversible:

    • Irreversible: net conversion in one direction (e.g., A + B → AB).
    • Reversible: can proceed in both directions; reaches equilibrium; carbonic acid system: ext{CO}2 + ext{H}2 ext{O}
      ightleftharpoons ext{H}2 ext{CO}3
      ightleftharpoons ext{H}^+ + ext{HCO}_3^-

  • Activation energy (Ea) and reaction rate: rate depends on Ea; higher Ea slows reaction; lowering Ea (via catalysts) speeds up the reaction.

  • NAD+/NADH role: redox chemistry transfers energy; NADH carries energy/electrons to the electron transport system.

  • Net direction of reaction: tied to energy changes and equilibrium state.

3.3 Enzymes

  • Function: enzymes accelerate physiological reactions by lowering Ea.
  • Structure: globular proteins with an active site; substrate binds to active site forming enzyme–substrate complex.
  • Mechanism (induced-fit): substrate binding induces slight enzyme shape change to better fit substrate; lowers Ea; products released; enzyme is free to catalyze again.
  • Cofactors and coenzymes: cofactors are nonprotein helpers (inorganic: e.g., zinc); organic cofactors (coenzymes) include vitamins/NAD+ that assist enzyme activity.
  • Classification and naming: six major enzyme classes (oxidoreductase, transferase, hydrolase, isomerase, ligase, lyase); names often reflect substrate/product and end with -ase.
  • Enzyme kinetics: reaction rate depends on enzyme and substrate concentrations; saturation occurs when all enzyme molecules are engaged; temperature and pH affect structure and rate; optimal ranges exist (e.g., human enzymes operate best near 37°C; optimal pH often 6–8; exceptions like pepsin in stomach pH 2–4).
  • Inhibition and control:
    • Competitive inhibition: inhibitor resembles substrate and competes for active site; elevated substrate can overcome inhibition.
    • Noncompetitive (allosteric) inhibition: inhibitor binds to a site other than active site; changes enzyme shape; not overcome by substrate increase.
  • Metabolic organization:
    • Metabolic pathways: sequences of enzyme-catalyzed steps; products of one step are substrates for the next.
    • Multienzyme complexes: enzymes physically linked to channel intermediates and allow coordinated regulation.
    • Negative feedback: product acts as allosteric inhibitor to down-regulate early steps; phosphorylation/dephosphorylation as additional regulation.
  • Practical note: lactase, lactase in membranes; pancreatic amylase in lumen; some enzymes (ribozymes) are RNA-based.

3.4 Cellular Respiration

  • Overview: a multistep pathway that oxidizes organic molecules to release energy for ATP synthesis; O2 is typically required for maximum ATP production.
  • Overall glucose oxidation: ext{C}6 ext{H}{12} ext{O}6 + 6 ext{O}2
    ightarrow 6 ext{CO}2 + 6 ext{H}2 ext{O}
  • Location and stages: glycolysis in cytosol (no O2 required); intermediate stage, citric acid cycle, and electron transport system in mitochondria (aerobic).
  • Four stages of glucose oxidation (and locations):
    • Glycolysis (cytosol; no O2 required) → substrate: glucose; products: 2 pyruvate, 2 ATP (net), 2 NADH.
    • Intermediate stage (mitochondria; requires O2) → pyruvate + CoA → acetyl-CoA + CO2; 2 NADH total per glucose.
    • Citric acid cycle (mitochondria; aerobic) → acetyl-CoA → CO2; per acetyl-CoA: 1 ATP, 3 NADH, 1 FADH2; 2 turns per glucose (from 2 acetyl-CoA): 2 ATP, 6 NADH, 2 FADH2.
    • Electron transport system (inner mitochondrial membrane) → NADH/FADH2 donate electrons to chain; O2 final electron acceptor forms H2O; proton gradient drives ATP synthase to make ATP (oxidative phosphorylation).
  • ATP production summary:
    • Substrate-level phosphorylation: glycolysis (2 ATP), citric acid cycle (2 ATP) → 4 ATP total.
    • Oxidative phosphorylation: NADH contributes ~3 ATP each; FADH2 ~2 ATP each (via ETC).
    • Theoretical total: up to 38 ATP per glucose; actual net yield is ~30 ATP due to transport and shuttle costs.
  • Fate of pyruvate with insufficient oxygen: pyruvate is reduced to lactate by lactate dehydrogenase to regenerate NAD+; glycolysis can continue but net yield per glucose is only 2 ATP.
  • Other fuel molecules: fatty acids enter as acetyl-CoA via β-oxidation (aerobic); amino acids feed into glycolysis, intermediate stage, or citric acid cycle; ammonia from deamination is excreted as urea.
  • Quick recap of energy accounting (from glucose):
    • Glycolysis: 2 ATP (net) + 2 NADH
    • Intermediate stage: 2 NADH
    • Citric acid cycle: 2 ATP + 6 NADH + 2 FADH2 (per glucose)
    • ETC: NADH → ~3 ATP each; FADH2 → ~2 ATP each
    • Net theoretical ATP: 38; actual net ATP: ~30
  • Additional notes:
    • Oxygen is the final electron acceptor in the ETC; without O2, oxidative phosphorylation slows or stops.
    • Cori cycle: lactate can be transported to liver to be converted back to glucose.
  • Practical relations:
    • Energy yield depends on cell type and shuttle systems; fever and temperature affect enzyme activity and reaction rates.

3.4a Overview of Glucose Oxidation

  • Net reaction: ext{C}6 ext{H}{12} ext{O}6 + 6 ext{O}2
    ightarrow 6 ext{CO}2 + 6 ext{H}2 ext{O}
  • ATP produced via substrate-level and oxidative phosphorylation; location spans cytosol and mitochondria.

3.4b Glycolysis

  • Location: cytosol; oxygen independent.
  • Substrate and products: glucose → 2 pyruvate; net ATP = 2; net NADH = 2.
  • Fate of pyruvate depends on O2 availability (aerobic vs anaerobic, lactate production).

3.4c Intermediate Stage

  • Location: mitochondria; requires oxygen.
  • Pyruvate dehydrogenase converts pyruvate to acetyl-CoA; CO2 released; NADH formed.
  • Occurs twice per glucose (one per pyruvate).

3.4d Citric Acid Cycle

  • Location: mitochondrial matrix; aerobic.
  • Acetyl-CoA → CO2; ATP, NADH, FADH2 generated per turn; two turns per glucose.

3.4e The Electron Transport System

  • Location: inner mitochondrial membrane (cristae).
  • NADH/FADH2 donate electrons; O2 is final electron acceptor to form H2O.
  • Proton pumping creates a gradient; ATP synthase uses gradient to form ATP (oxidative phosphorylation).

3.4f ATP Production

  • NADH yields ~3 ATP; FADH2 yields ~2 ATP in ETC.
  • Summary: glycolysis 2 ATP (substrate-level); intermediate stage 2 NADH → ~6 ATP; citric acid cycle 2 ATP + 6 NADH → ~18 ATP + 2 FADH2 → ~4 ATP; total ~38 theoretical; actual ~30 ATP due to transport costs.

3.4g The Fate of Pyruvate with Insufficient Oxygen

  • Pyruvate → lactate via lactate dehydrogenase to regenerate NAD+; glycolysis can continue; net ATP per glucose ~2.
  • Lactate can be shuttled to liver (Cori cycle) for reconversion to glucose.

3.4h Other Fuel Molecules That Are Oxidized in Cellular Respiration

  • Fatty acids: β-oxidation to acetyl-CoA; enter CAC; requires oxygen.
  • Amino acids: feed into glycolysis, intermediate stage, or CAC depending on type; amino group converted to urea.