Chapter 3 Study Notes – Chemical Reactions, Enzymes & Cellular Respiration

Chemical Equations & Metabolism

• Metabolism

  • Sum of all biochemical reactions in a living organism.

• Chemical Reactions

  • Break existing bonds & form new ones.

  • Represented by a chemical equation.

  • Reactants: written on the left; present before reaction starts.

  • Products: written on the right; substances formed.

  • Example (balanced): $\text{A} + \text{B} \to \text{C}$ (arrow shows direction). Balanced = equal number of each element on both sides.

Classification of Chemical Reactions

• Three criteria: structural change, energy change, reversibility.

By Structural Change

• Decomposition (Catabolic)

  • Large → small; $\text{AB} \to \text{A} + \text{B}$.

  • Example: Hydrolysis of sucrose → glucose + fructose.

• Synthesis (Anabolic)

  • Small → large; $\text{A} + \text{B} \to \text{AB}$.

  • Example: Dehydration synthesis of a dipeptide.

• Exchange

  • Parts swapped; $\text{AB} + \text{C} \to \text{A} + \text{BC}$.

  • Example: Creatine phosphate + ADP → creatine + ATP (also used for ATP production in muscle).

• Oxidation–Reduction (Redox)

  • Electron transfer reactions.

  • Oxidized = loses e⁻.

  • Reduced = gains e⁻.

  • Occur simultaneously; electrons may move alone or with H⁺.

  • Example: NAD⁺ + 2e⁻ + H⁺ → NADH (NAD⁺ reduced, glucose oxidized).

By Energy Change

• Exergonic: Reactants have more potential energy than products; energy released (e.g., decomposition).

• Endergonic: Reactants have less potential energy than products; energy absorbed (e.g., synthesis).

By Reversibility

• Irreversible: Net loss of reactants, gain of products; e.g., $\text{A} + \text{B} \to \text{AB}$.

• Reversible: Reaches equilibrium; reaction direction shifts with changes in [reactants]/[products].

  • Carbonic acid example: $\text{CO}<em>2 + \text{H}</em>2\text{O} \leftrightarrows \text{H}<em>2\text{CO}</em>3 \leftrightarrows \text{HCO}_3^- + \text{H}^+$.

Reaction Rates & Activation Energy

• Reaction rate: Speed of product formation.

• Activation energy (E_a): Minimum energy to break bonds.

  • In labs: heat can supply E_a.

  • In cells: temperature rise would denature proteins → cells use enzymes as catalysts to lower E_a.

Enzymes – Function

• Biological catalysts; increase reaction rate; do not change net energy, equilibrium, or direction.

• Lower $E_a$ → allow reactions to occur at body temperature.

Enzyme Structure & Location

• Mostly globular proteins (≈60–2500 aa).

• Active site: 3-D pocket; highly specific → usually binds one substrate → forms transient enzyme–substrate complex.

• Distribution:

  • Intracellular (e.g., DNA polymerase).

  • Membrane-bound (e.g., intestinal lactase).

  • Secreted (e.g., pancreatic amylase).

Mechanism of Enzyme Action (Induced-Fit)

1. Substrate enters active site → complex forms.

2. Enzyme conformational change → tighter fit, strains bonds.

3. Bonds broken/formed → products.

4. Products released; enzyme reused.

• Cofactors: Non-protein helpers required for function.

  • Inorganic (e.g., Zn²⁺ for carbonic anhydrase).

  • Organic (coenzymes; vitamins, modified nucleotides).

Enzyme Kinetics

• Concentration effects

  • ↑[enzyme] or ↑[substrate] → ↑ rate until saturation (all active sites occupied).

• Temperature

  • Optimal ≈ $40^{\circ} \text{C}$ (104 °F) for human enzymes.

  • Moderate fever ↑enzyme activity.

  • > optimal → denaturation; disrupts weak intramolecular bonds.

• pH

  • Optimal pH ≈ 6–8 (varies: stomach enzymes lower).

  • Deviations alter electrostatic interactions → denaturation.

Enzyme Regulation via Inhibition

• Competitive inhibitors

  • Resemble substrate; bind active site.

  • Effect depends on substrate:[inhibitor] ratio.

• Noncompetitive (Allosteric) inhibitors

  • Bind other site; conformational change closes active site.

  • Not overcome by ↑[substrate].

• Negative feedback: Product often allosterically inhibits first enzyme of pathway.

Cellular Respiration – Overall Concepts

• Multistep exergonic oxidation of organic molecules → ATP (endergonic).

• Net equation for glucose:
  $\text{C}<em>6\text{H}</em>{12}\text{O}<em>6 + 6\,\text{O}</em>2 \to 6\,\text{CO}<em>2 + 6\,\text{H}</em>2\text{O} + \text{Energy (≈30 ATP)}$

• Four stages:

  1. Glycolysis (cytosol, anaerobic)

  2. Intermediate Stage (mitochondrial matrix)

  3. Citric Acid Cycle (CAC) (matrix)

  4. Electron Transport System (ETS) (inner membrane/cristae)

  • Stages 2–4 require O₂ (aerobic).

Glycolysis

• 10 enzymes in cytosol; O₂ not required.

• Glucose (6C) → 2 pyruvate (3C) + $2\,\text{ATP}_{\text{net}} + 2\,\text{NADH}$.

• Steps 1 & 3 invest ATP; steps 7 & 10 generate ATP via substrate-level phosphorylation.

• Regulation: ATP allosterically inhibits phosphofructokinase (PFK) (negative feedback).

• Pyruvate fate

  • Adequate O₂ → enters mitochondrion.

  • Low O₂ → reduced to lactate (regenerates NAD⁺, allows glycolysis to continue; yields only 2 ATP/glucose).

Intermediate Stage (Pyruvate Oxidation)

• Occurs twice per glucose in mitochondrial matrix.

• Catalyzed by pyruvate dehydrogenase.
  $\text{Pyruvate} + \text{CoA} + \text{NAD}^+ \to \text{Acetyl CoA} + \text{CO}_2 + \text{NADH}$

• Produces: 2 CO₂ (per glucose) & 2 NADH.

Citric Acid Cycle (Krebs)

• 9 enzymes in matrix; aerobic.

• Per turn (per acetyl CoA):

  • 1 ATP (substrate-level)

  • 3 NADH, 1 FADH₂

  • 2 CO₂; CoA released.

• Two turns per glucose → 2 ATP, 6 NADH, 2 FADH₂.

• Regulation at citrate synthase (first step):

  • High NADH/ATP → slows cycle; low → speeds up.

Electron Transport System & Oxidative Phosphorylation

• Located on inner mitochondrial membrane (cristae).

• Components: sequential electron carriers + H⁺ pumps + ATP synthase.

• Steps:

  1. Electrons from NADH/FADH₂ transferred down chain to O₂ (final acceptor) → H₂O.

  2. Energy drives H⁺ pumps → gradient (outer compartment high [H⁺]).

  3. H⁺ flows back via ATP synthase → drives $\text{ADP} + P_i \to \text{ATP}$.

• Oxidative phosphorylation: indirect ATP formation using redox energy (vs. substrate-level).

ATP Yield per Glucose

• Some ATP consumed during transport → Net ≈ 30 ATP.

• NADH donates at first pump (≈3 ATP each); FADH₂ at second (≈2 ATP each).

Anaerobic Conditions: Lactate Pathway

• ETS slows → NADH accumulates → limited NAD⁺.

• Lactate dehydrogenase: $\text{Pyruvate} + \text{NADH} \to \text{Lactate} + \text{NAD}^+$.

• Allows glycolysis to persist (2 ATP only).

• Relevant in hypoxia, CV/respiratory disease.

Alternative Fuel Molecules

• Fatty acids

  • β-oxidation: remove 2 C → acetyl CoA; enters CAC. Requires O₂ (cannot occur anaerobically).

• Amino acids

  • Deaminated; carbon skeleton enters various points (pyruvate, acetyl CoA, CAC intermediates).

  • Amine group → urea → excreted by kidneys.

Review & Conceptual Connections

• Reactant vs. Product: position in equation; energy content often differs.

• Synthesis reaction = anabolic, endergonic.

• Energy currency produced: ATP.

• Le Châtelier’s Principle in reversible reactions: shift toward side with decreased concentration.

• Fever: mild ↑T boosts enzymatic rate; high fever risks protein denaturation → loss of function.

• Enzyme & Ea: inverse relationship; enzymes lower Ea.

• Active site: substrate-binding pocket; specificity enforced by shape & chemistry.

• Cofactors: enable proper binding or catalysis.

• Substrate conc./Temp./pH: change rate until optimum; extreme values denature.

• Competitive vs. Noncompetitive inhibition: active-site occupancy vs. allosteric binding.

• Four stages of respiration: glycolysis (cytosol) → intermediate stage, CAC, ETS (mitochondria).

• Importance of NADH/FADH₂: carry high-energy electrons to ETS.

• ETS key steps: electron transfer to O₂, proton pumping, ATP synthesis.

• ATP tally: 2 (gly) + 2 (CAC) + 26–28 (ETS) minus shuttling costs ≈ 30.

• Insufficient O₂: pyruvate → lactate to regenerate NAD⁺.

• O₂ required for β-oxidation: final electron acceptor in ETS, necessary for continual NAD⁺/FAD recycling.