Contents

1. THE PRINCIPLES OF THERMODYNAMICS. Thermodynamic systems. Concept of heat and temperature. Equivalence between heat and work. Joule's experiment. First principle of Thermodynamics. Reversible and irreversible processes. Entropy and the second principle of thermodynamics. Mechanical interpretation of heat and entropy. Quantum interpretation of heat and entropy. Equivalence of the principles of maximum entropy and minimum energy. The concept of free energy. Enthalpy, Helmhotz Free Energy and Gibbs Free Energy.

2. STATISTICAL MECHANICS AND MICROSCOPIC SYSTEMS. Thermodynamics and microscopic models. Statistical mechanics: entropy and the atomic model. Boltzmann's distribution and the partition function. Applications to proteins and nucleic acids.

3. ENERGY PRODUCTION IN PHOTOSYNTHESIS. Dark phase and luminous phase. Chloroplast structure. Chromophors. Absorption and transport of solar radiation energy. Marcus theory of electronic transfer. The quantum tunnel effect and estimation of the tuneling distance. Photoreceptors, antenna model, antenna energy transport mechanism in the photochemical center. Net electronic transfer rate. The photochemical center: reactions of charge transfer, structure and operation of photochemical centers. Photosynthetic transport chain in bacteria. Photosynthetic transport chain in plants: Emerson's cooperative effect and the two photosynthetics. Fixation of CO₂ in the Calvin cycle. The capacity to fix CO₂ and the climate change.

4. ENERGY PRODUCTION IN FERMENTATIONS AND RESPIRATION. Production of ATP in fermentations: phosphorylation at substrate level. ATP production linked to respiration: oxidative phosphorylation and the mitochondria. The mitochondrial electronic transport chain: transporters and their arrangement, location of transporters in the internal mitochondrial membrane. Particles: ATP synthases. The coupling problem between electronic transport and oxidative phosphorylation: chemical coupling hypothesis, conformational coupling hypothesis, chemosmotic coupling hypothesis. The ATPase F1-Fo complex: properties, structure, ATP synthesis mechanism.

5. TRANSPORT WORK. Definition of transport work. Simple diffusion. Fick's first law. Fick's second law. Simple diffusion model through the cell membrane. Membrane permeability. Facilitated diffusion. Facilitated iffusion models. The glucose transporter. Ionic channels. Channels operated by voltage. Ionic equilibrium and the Nernst equation. Simple models of ion channels operated by voltage. Channels operated by ligand binding. The Monod-Wyman-Changeaux model. Entropic force in exit channels. Active transport. Active transport of glucose. Glucose flow in the gut.

6. MECHANICAL WORK. Molecular motors. Cytoskeleton. Structure of microtubules and actin filaments. Polymerization, nucleation and elongation. Simple polymerization model. Polar polymerization model. Polymerization model with ATP hydrolysis. Polymerization disasters. Translational motors: myosin, kinesin and dinein. Muscle contraction. Translation models: the random path model. Relationship between polymerization speed and ATP consumption. Rotational motors and the Brownian ratchet. Polymerization motors and centriole location. Translocation motors and secretion systems.

7. BIOSYNTHESIS WORK. Differences between anabolism and catabolism. Relationship between ΔG values and metabolic pathway regulation points. Energetic aspects of metabolic pathways and control strategies: common intermediaries, compartmentalization and enzymatic control. Some energetic aspects of enzymatic catalysis: thermodynamics and time, chemical kinetics, energy interpretations of the catalytic action of enzymes. Examples of biosynthesis work: gluconeogenesis compared to glycolysis.

8. ENERGY AND THE BIOSPHERE. Phototrophic and chemotrophic living systems. Cycle of matter and flow of energy in the biosphere. Energy efficiency and conversion. Transport and storage of energy.

9. THE THERMODYNAMICS OF IRREVERSIBLE PROCESSES AND BIOLOGY. Thermodynamics of open systems. Systems not far from balance: internal entropy production speed, Onsager equations, stationary state, principle of minimal entropy production. Systems far removed from balance: Bénard instability, Zhabotinski reaction. Dissipative structures: possible applications to the study of living systems.

10. FORMATION OF BIOLOGICAL PATTERNS. Cell differentiation and embryogenesis. Morphogenic gradients. The model of the French flag. Formation of heterocycists in photosynthetic organisms. Turing patterns with and without diffusion. Generation of temporary patterns: the growth of microorganisms on the surface. Effect of biological noise on patterns. Advantages of biological noise. The ComK system of competition in B. subitilis and the bacterial mechanisms of persistence.

11. A THERMODYNAMIC VISION OF THE ORIGIN OF LIFE AND EVOLUTION. Definition of life. Current theories about the origin of life. Thermodynamic definition of life: self-replication. Spontaneous self-replication. Life understood as a phase transition: the concept of life on the edge of chaos. Concept of self-organized criticality. Darwinism and evolution: the concept of morphogenic space. The role of genes in evolution.