Chapter 8 — 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 chemical reactions, each catalyzed by a specific enzyme.

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

• Anabolic Pathways: Build larger molecules from smaller 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 matter and energy with their environment (e.g., intake of food and oxygen, release of CO2 and heat).

Laws of Thermodynamics:

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

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

Additional info: Entropy is a measure of energy dispersal and the number of possible arrangements of matter.

8.2 — Free Energy and Spontaneous Reactions

Gibbs free energy (G) determines the capacity of a system to do work. The change in free energy predicts whether a reaction is spontaneous.

• Gibbs Free Energy Equation:

• Exergonic Reactions: Release free energy ( is negative); spontaneous.

• Endergonic Reactions: Require input of free energy ( is positive); nonspontaneous.

• At equilibrium, ; no net change occurs.

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

8.3 — ATP and Cellular Work

ATP (adenosine triphosphate) is the primary energy currency of the cell, transferring energy to drive cellular processes.

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

• ATP Hydrolysis:

• Energy Coupling: ATP hydrolysis is exergonic and is coupled to endergonic cellular processes.

• Phosphorylation: Transfer of a phosphate group to another molecule, increasing its reactivity or altering protein shape.

Remember: ATP transfers, but does not create, energy.

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.

• Active Site: Region on enzyme where substrate binds.

• Induced Fit: Active site changes shape to facilitate catalysis upon substrate binding.

Factors Affecting Enzyme Activity:

• Temperature (optimal range; excessive heat denatures enzymes)

• pH (each enzyme has an optimal pH)

• Substrate concentration (rate increases until enzyme saturation)

• Cofactors (nonprotein helpers; organic cofactors are coenzymes)

Enzyme Inhibitors:

8.5 — Regulation of Enzyme Activity

Cells regulate enzyme activity to control metabolism and conserve resources.

• Allosteric Regulation: Regulatory molecule binds away from active site, stabilizing active or inactive enzyme forms.

• Allosteric Activator: Increases enzyme activity.

• Allosteric Inhibitor: Decreases enzyme activity.

• Cooperativity: Binding of a substrate to one subunit affects binding at other subunits (e.g., hemoglobin and oxygen).

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

Remember: Feedback inhibition prevents wasteful overproduction of pathway products.

Chapter 9 — Cellular Respiration and Fermentation

9.1 — Catabolic Pathways, Redox, and Electron Carriers

Cellular respiration is a catabolic process that breaks down organic molecules to produce ATP, primarily through redox reactions.

• Overall Equation:

• Oxidation: Loss of electrons.

• Reduction: Gain of electrons.

• NAD+: Electron carrier; reduced to NADH during catabolism.

• Substrate-level Phosphorylation: Direct transfer of phosphate to ADP to form ATP (in glycolysis and citric acid cycle).

• Oxidative Phosphorylation: ATP production driven by a proton gradient established by the electron transport chain (ETC).

9.2 — Glycolysis

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

• Breaks one glucose (6C) into two pyruvate (3C each).

• Two phases: Energy investment (uses 2 ATP), energy payoff (produces 4 ATP and 2 NADH).

ATP is produced by substrate-level phosphorylation.

9.3 — Pyruvate Oxidation and the Citric Acid Cycle

Pyruvate is transported into the mitochondrial matrix 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):

• Cycle turns twice per glucose molecule.

• Major function: Generate NADH and FADH2 for the ETC.

9.4 — Oxidative Phosphorylation and Chemiosmosis

Most ATP is produced during oxidative phosphorylation, which involves the electron transport chain and chemiosmosis.

• ETC Location: Inner mitochondrial membrane.

• NADH and FADH2 donate electrons, which move through protein complexes, releasing energy to pump H+ into the intermembrane space.

• Oxygen is the final electron acceptor, forming water.

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

Note: Efficiency is about 34%; the rest of the energy is lost as heat.

9.5 — Fermentation and Anaerobic Respiration

When oxygen is unavailable, cells regenerate NAD+ through fermentation, allowing glycolysis to continue.

• Fermentation: No additional ATP beyond glycolysis (2 ATP per glucose).

• Both regenerate NAD+ by oxidizing NADH.

Note: Anaerobic respiration uses an ETC with a final electron acceptor other than oxygen.

9.6 — Other Fuels and Regulation of Respiration

Cells can metabolize carbohydrates, fats, and proteins for energy. Respiration is regulated to match cellular energy needs.

• Carbohydrates: Enter glycolysis as sugars.

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

• Proteins: Amino acids enter after deamination.

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

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.

10.2 — Chloroplasts and the Overall Process

Photosynthesis occurs in chloroplasts, primarily in leaf mesophyll cells. It is an endergonic redox process driven by light energy.

• Key Structures: Stomata (gas exchange), stroma (Calvin cycle), thylakoids (light reactions), grana (thylakoid stacks).

• Overall Equation:

• O2 released comes from water, not CO2.

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

Light reactions convert solar energy into chemical energy (ATP and NADPH) using photosynthetic pigments and electron transport chains.

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

• Pigments: Chlorophyll a (main pigment), chlorophyll b and carotenoids (accessory pigments).

• Photosystems: Complexes that absorb light and transfer excited electrons.

• Linear Electron Flow: H2O → PSII → ETC → PSI → NADP+ → NADPH; produces ATP, NADPH, and O2.

• Cyclic Electron Flow: Uses PSI only; produces additional ATP but no NADPH or O2.

• Chemiosmosis: H+ gradient in thylakoid space drives ATP synthase (photophosphorylation).

10.4 — The Calvin Cycle

The Calvin cycle uses ATP and NADPH to fix CO2 into organic molecules (G3P) in the stroma. It is an anabolic pathway with three phases:

• Phase 1 — Carbon Fixation: CO2 combines with RuBP (catalyzed by rubisco) to form 3-phosphoglycerate (3-PGA).

• Phase 2 — Reduction: ATP and NADPH convert 3-PGA into G3P.

• Phase 3 — Regeneration: Most G3P is used to regenerate RuBP, enabling the cycle to continue.

Carbon Accounting (per 3 CO2):

• 6 G3P produced; 1 net G3P output, 5 used to regenerate RuBP

• Consumes 9 ATP and 6 NADPH

Note: Two net G3P are needed to form one glucose molecule. The Calvin cycle depends on ATP and NADPH from the light reactions.

Connecting Chapters 8–10

• Metabolism: Energy transformations, ATP, and enzyme regulation (Chapter 8)

• Cellular Respiration: Harvesting energy from organic molecules to produce ATP (Chapter 9)

• Photosynthesis: Using light energy to build organic molecules (Chapter 10)

• Redox Carriers: NADH (respiration), NADPH (photosynthesis)

• ATP: Powers cellular work, produced in both respiration and photosynthesis

Essential Concepts to Remember

1. Energy cannot be created or destroyed, only transformed.

2. Catabolic pathways break down molecules; anabolic pathways build molecules.

3. Exergonic reactions: negative; endergonic: $\Delta G$ positive.

4. Enzymes lower activation energy, not .

5. ATP couples energy-releasing and energy-requiring processes.

6. Oxidation = loss of electrons; reduction = gain of electrons.

7. Glycolysis: 2 pyruvate, 2 net ATP, 2 NADH per glucose.

8. Oxygen is the final electron acceptor in aerobic respiration.

9. Most ATP is made via oxidative phosphorylation.

10. Fermentation regenerates NAD+ for glycolysis.

11. Light reactions: produce ATP, NADPH, O2.

12. Calvin cycle: uses CO2, ATP, NADPH to make G3P.

13. Photosynthesis and respiration both involve electron transfer and energy transformations.

Study Tip

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