Rucete ✏ Lehninger Principles of Biochemistry In a Nutshell
1.3 Physical Foundations
This chapter introduces the physical principles underlying life, focusing on how living cells extract, store, and use energy to maintain order and perform biological work.
Dynamic Steady State vs. Equilibrium
• Living organisms maintain a constant internal composition (dynamic steady state) that is far from equilibrium with their surroundings.
• Cells continuously synthesize and degrade molecules, balancing rates of production and breakdown to keep concentrations steady.
• Maintaining this state requires constant input of energy; when energy is unavailable, cells move toward equilibrium and decay.
Energy and Matter Transformations
• Organisms are open systems, exchanging both energy and matter with their environment.
• Energy is obtained either by taking up and oxidizing chemical fuels (like glucose) or by absorbing sunlight.
• Nearly all living organisms ultimately derive their energy from sunlight, directly or indirectly, through interconnected cycles involving photosynthesis and respiration.
Entropy and Order
• Entropy (disorder) naturally increases in the universe, but life persists by constantly investing energy to maintain and create order.
• The first law of thermodynamics states that energy is conserved, while the second law highlights the tendency toward increasing entropy.
• Information-rich biological molecules (like DNA and proteins) represent highly ordered, low-entropy structures, requiring energy to synthesize and maintain.
Thermodynamics and Free Energy
• The free energy change (ΔG) of a reaction determines whether it can proceed spontaneously (ΔG negative = exergonic; ΔG positive = endergonic).
• Cells couple endergonic (energy-requiring) reactions to exergonic (energy-releasing) reactions to drive biological processes, most commonly using the hydrolysis of ATP.
• Standard free energy change (ΔG°) and equilibrium constant (K_eq) are physical constants that describe a reaction's tendency and can be related mathematically.
ATP and Energy Coupling
• ATP is the universal energy currency of the cell, storing energy in its high-energy phosphate bonds.
• The breakdown (hydrolysis) of ATP to ADP and phosphate is highly exergonic and is coupled to endergonic reactions to make them proceed.
• Cells keep ATP at concentrations far from equilibrium, allowing it to provide a continuous energy supply for cellular processes.
Enzymes and Reaction Pathways
• Most cellular reactions proceed at useful rates only because they are catalyzed by enzymes, which lower activation energy and speed up reactions without being consumed.
• Enzymes stabilize the transition state and often bring reactants together in favorable orientations, increasing reaction rates by many orders of magnitude.
• Enzyme-catalyzed reactions are organized into metabolic pathways—sequences of reactions where the product of one is the reactant for the next.
• Pathways are categorized as catabolic (breaking down molecules to release energy) or anabolic (building complex molecules, requiring energy).
• ATP and electron carriers like NADH and NADPH link catabolism and anabolism, enabling efficient energy transfer.
Regulation of Metabolism
• Metabolism is highly regulated to ensure cellular balance and efficiency, with feedback inhibition and gene regulation adjusting enzyme activity and pathway flux.
• Many metabolites participate in multiple pathways, making cellular metabolism a complex, interconnected web rather than a set of discrete sequences.
• Systems biology approaches are used to analyze and understand this regulatory complexity at a systems level.
In a Nutshell
Living cells are open, energy-dependent systems that maintain a dynamic steady state far from equilibrium. They extract, channel, and store energy to build and regulate complex, ordered structures, constantly opposing entropy. Bioenergetic processes are driven by the coupling of exergonic and endergonic reactions, primarily using ATP as the energy currency. Enzymes catalyze and organize thousands of chemical reactions into metabolic networks, which are tightly regulated to match the cell’s needs and environmental changes.