Chapter 8 — An Introduction to Metabolism

8.1 — Metabolism and Energy Transformations

Metabolism encompasses all chemical reactions within an organism, organized into metabolic pathways. These pathways are regulated by enzymes and are essential for maintaining life.

• Metabolic Pathway: A sequence of enzyme-catalyzed reactions transforming a specific molecule through a series of intermediates to a final product.

• Catabolic Pathways: Break down complex molecules into simpler ones, releasing energy (e.g., cellular respiration).

• Anabolic Pathways: Build complex molecules from simpler ones, requiring energy input (e.g., protein synthesis).

• Kinetic Energy: Energy of motion (e.g., moving molecules).

• Potential Energy: Stored energy due to position or structure (e.g., chemical bonds).

• Chemical Energy: A form of potential energy stored in molecular bonds.

• Open Systems: Organisms exchange energy and matter with their environment (e.g., intake of food and oxygen, release of CO2 and heat).

• First Law of Thermodynamics: Energy cannot be created or destroyed, only transformed.

• Second Law of Thermodynamics: Every energy transfer increases the entropy (disorder) of the universe.

Example: Cellular respiration is a catabolic pathway that releases energy by breaking down glucose.

8.2 — Free Energy and Spontaneous Reactions

Free energy determines whether a reaction can occur spontaneously. The change in free energy (ΔG) predicts the direction of chemical reactions.

• Gibbs Free Energy (G): The portion of a system's energy available to do work.

• Equation:

• Exergonic Reactions: Release free energy (ΔG < 0), spontaneous.

• Endergonic Reactions: Require input of free energy (ΔG > 0), nonspontaneous.

• At equilibrium, ΔG = 0 (no net change).

• Spontaneous does not mean fast; high activation energy can slow reactions.

Example: Hydrolysis of ATP is exergonic and powers cellular work.

8.3 — ATP and Cellular Work

ATP (adenosine triphosphate) is the primary energy currency of the cell, coupling energy-releasing and energy-requiring processes.

• Structure: Adenine, ribose, and three phosphate groups.

• ATP Hydrolysis:

• Energy Coupling: ATP hydrolysis drives endergonic reactions by transferring a phosphate group (phosphorylation).

• Types of Cellular Work Powered by ATP:

  • Chemical: Synthesis of macromolecules.

  • Transport: Active transport across membranes.

  • Mechanical: Muscle contraction, movement of motor proteins.

Example: ATP powers the sodium-potassium pump (active transport).

8.4 — Enzymes and Activation Energy

Enzymes are biological catalysts that accelerate chemical reactions by lowering activation energy without being consumed.

• Activation Energy (Ea): The energy required to initiate a reaction.

• Enzyme-Substrate Complex: Temporary association between enzyme and substrate at the active site.

• Induced Fit: The enzyme changes shape to better fit the substrate, facilitating catalysis.

• Factors Affecting Enzyme Activity:

  • Temperature (optimal range; high heat can denature enzymes)

  • pH (optimal for each enzyme)

  • Substrate concentration (saturation point)

  • Cofactors (inorganic or organic; coenzymes are organic cofactors)

• Enzyme Inhibitors:

  • Competitive: Bind active site, compete with substrate.

  • Noncompetitive: Bind elsewhere, change enzyme shape.

Example: Cyanide is a noncompetitive inhibitor of cytochrome c oxidase in the electron transport chain.

8.5 — Regulation of Enzyme Activity

Cells regulate enzyme activity to control metabolic pathways and conserve resources.

• Allosteric Regulation: Regulatory molecules bind to sites other than the active site, stabilizing active or inactive forms.

• Cooperativity: Binding of a substrate to one subunit increases affinity in others (e.g., hemoglobin and oxygen).

• Feedback Inhibition: End product of a pathway inhibits an early enzyme, preventing overproduction.

Example: Feedback inhibition of the amino acid isoleucine synthesis pathway.

Chapter 9 — Cellular Respiration and Fermentation

9.1 — Catabolic Pathways, Redox, and Electron Carriers

Cellular respiration is a catabolic process that extracts energy from organic molecules, primarily glucose, to produce ATP.

• Overall Equation:

• Redox Reactions: Oxidation (loss of electrons), reduction (gain of electrons). "OIL RIG" mnemonic.

• NAD+: Electron carrier; reduced to NADH, which donates electrons to the electron transport chain (ETC).

• ATP Production Mechanisms:

  • Substrate-level phosphorylation: Direct transfer of phosphate to ADP (glycolysis, citric acid cycle).

  • Oxidative phosphorylation: ATP synthesis driven by a proton gradient (ETC, chemiosmosis).

Example: NADH delivers electrons to the ETC, powering ATP synthesis.

9.2 — Glycolysis

Glycolysis is the first stage of cellular respiration, occurring in the cytosol and not requiring oxygen.

• Process: One glucose (6C) → two pyruvate (3C each).

• Phases:

  • Energy investment (uses 2 ATP)

  • Energy payoff (produces 4 ATP, 2 NADH)

Example: Glycolysis supplies ATP and NADH even in the absence of oxygen.

9.3 — Pyruvate Oxidation and the Citric Acid Cycle

Pyruvate is transported into mitochondria and converted to acetyl-CoA, which enters the citric acid cycle (Krebs cycle).

• Pyruvate Oxidation (per pyruvate): 1 acetyl-CoA, 1 NADH, 1 CO2

• Citric Acid Cycle (per turn):

  • 2 CO2

  • 3 NADH

  • 1 FADH2

  • 1 ATP (or GTP)

• Cycle turns twice per glucose.

• Oxaloacetate is regenerated each cycle.

Example: The citric acid cycle generates electron carriers for the ETC.

9.4 — Oxidative Phosphorylation and Chemiosmosis

Oxidative phosphorylation is the main source of ATP in aerobic respiration, involving the electron transport chain and chemiosmosis.

• Electron Transport Chain (ETC): Located in the inner mitochondrial membrane; electrons from NADH and FADH2 pass through protein complexes, releasing energy to pump H+ ions.

• Oxygen: Final electron acceptor, forming water.

• Chemiosmosis: H+ flows back into the matrix through ATP synthase, driving ATP production.

Example: ATP synthase produces ATP as protons flow down their gradient.

9.5 — Fermentation and Anaerobic Respiration

Fermentation allows glycolysis to continue in the absence of oxygen by regenerating NAD+.

• Alcohol Fermentation: Pyruvate → ethanol + CO2 (e.g., yeast).

• Lactic Acid Fermentation: Pyruvate → lactate (e.g., muscle cells, some bacteria).

• Anaerobic Respiration: Uses an ETC with a final electron acceptor other than oxygen.

Example: Yeast perform alcohol fermentation under anaerobic conditions.

9.6 — Other Fuels and Regulation of Respiration

Cells can metabolize carbohydrates, fats, and proteins for energy, and regulate respiration based on energy needs.

• Carbohydrates: Enter glycolysis as sugars.

• Fats: Glycerol enters glycolysis; fatty acids undergo beta oxidation to acetyl-CoA.

• Proteins: Amino acids enter after deamination.

• Regulation: Phosphofructokinase (PFK) is a key regulatory enzyme; high ATP inhibits glycolysis via feedback inhibition.

Example: During fasting, fats are broken down for ATP production.

Chapter 10 — Photosynthesis

10.1 — Photosynthesis Feeds the Biosphere

Photosynthesis is the process by which autotrophs convert light energy into chemical energy, sustaining most ecosystems.

• Autotrophs: Produce organic molecules from inorganic sources (e.g., plants, algae).

• Heterotrophs: Obtain organic molecules by consuming other organisms (e.g., animals, fungi).

• Photoautotrophs: Use sunlight as an energy source.

Example: Plants are photoautotrophs that support food webs.

10.2 — Chloroplasts and the Overall Process

Photosynthesis occurs in chloroplasts, primarily in leaf mesophyll cells, and consists of light reactions and the Calvin cycle.

• Key Structures:

  • Stomata: Gas exchange openings

  • Stroma: Fluid interior, Calvin cycle site

  • Thylakoids: Membrane sacs with chlorophyll

  • Grana: Stacks of thylakoids

• Overall Equation:

• Photosynthesis is an endergonic redox process; water is oxidized, CO2 is reduced.

• O2 released comes from water.

• Stages:

  • Light reactions (thylakoid membranes): Produce ATP, NADPH, O2

  • Calvin cycle (stroma): Uses ATP and NADPH to fix CO2 into G3P

Example: Chloroplasts in leaf cells carry out photosynthesis.

10.3 — Light Reactions: Light, Pigments, and ATP Production

Light reactions capture solar energy, producing ATP and NADPH while releasing O2.

• Light: Electromagnetic energy; visible light (380–740 nm) is used in photosynthesis.

• Pigments:

  • Chlorophyll a: Main pigment

  • Chlorophyll b, carotenoids: Accessory pigments

• Photosystems:

  • Photosystem II (P680): Functions first, splits water

  • Photosystem I (P700): Functions second, produces NADPH

• Linear Electron Flow: H2O → PSII → ETC → PSI → NADP+ → NADPH

• Cyclic Electron Flow: Uses PSI only, produces extra ATP but no NADPH or O2

• Chemiosmosis: H+ gradient across thylakoid membrane drives ATP synthase (photophosphorylation).

Example: Light reactions in chloroplasts generate ATP and NADPH for the Calvin cycle.

10.4 — The Calvin Cycle

The Calvin cycle uses ATP and NADPH to fix CO2 into organic molecules (G3P) in the stroma of chloroplasts.

• Phases:

  • Carbon fixation: CO2 + RuBP (via rubisco) → 3-PGA

  • Reduction: ATP and NADPH convert 3-PGA to G3P

  • Regeneration: Most G3P regenerates RuBP

• For every 3 CO2: 6 G3P formed, 1 net G3P output, 5 G3P used to regenerate RuBP, 9 ATP and 6 NADPH consumed.

• The Calvin cycle depends on products of the light reactions and does not directly require light.

Example: The Calvin cycle produces G3P, which can be used to synthesize glucose and other carbohydrates.

Connecting All Three Chapters

• Energy Transformations: Energy cannot be created or destroyed; it changes forms in metabolism, respiration, and photosynthesis.

• Catabolic vs. Anabolic: Respiration is catabolic (breakdown, energy release); photosynthesis is anabolic (building, energy input).

• Electron Carriers: NADH (respiration), NADPH (photosynthesis) shuttle electrons for energy transformations.

• ATP: Central molecule for energy transfer in cells; produced by both respiration and photosynthesis.

• Enzyme Regulation: Controls metabolic pathways, prevents waste.

Study Tip: For each pathway, ask: Where does it happen? What enters? What leaves? Why does the cell need it?