Opening the book…
- 5.0: Introduction
- This page explains the connection between evolutionary biology and the physical and chemical principles that govern biological behavior. It stresses that living organisms maintain a non-equilibrium state, distinguishing them from simpler systems. The text highlights that biological systems at equilibrium are non-viable, while those in a state of non-equilibrium sustain life, reflecting the historical continuity of life over billions of years.
- 5.1: Approaching Thermodynamics
- This page explores the relationship between macroscopic and molecular worlds via Brownian motion, illustrating the existence of atoms and energy transfer. It explains thermodynamics laws for both closed and open systems, highlighting that living organisms need energy and matter exchange. Additionally, it introduces cryptobiosis, showcasing how some organisms like tardigrades can survive in suspended states while still maintaining non-equilibrium.
- 5.2: Coupling thermodynamically favorable and unfavorable reactions
- This page explores the complexity of biological systems, particularly how macromolecules like DNA and proteins emerge from thermodynamically unfavorable reactions, which become stable when coupled with favorable ones. It introduces Gibbs free energy (ΔG) to differentiate between energy-releasing (negative ΔG) and energy-requiring (positive ΔG) reactions.
- 5.3: Reaction rates
- This page covers the equilibrium constant (Keq) and its significance in biological reaction dynamics, indicating thermodynamic favorability and the influence of activation energy (Ea) on reaction speed. Enzymes can lower Ea to speed up reactions. It also explains that a closed system is essential for maintaining equilibrium, as escaping reactants or products can disrupt this balance.
- 5.4: Coupling Reactions
- This page discusses the continuous chemical reactions in cells, driven by thermodynamic principles. Favorable reactions (catabolism) break down molecules, while unfavorable reactions (anabolism) synthesize them, often linked through shared intermediates. Le Chatelier's principle illustrates how concentration changes affect reaction equilibrium, aiding molecule production. Catalysts enhance reaction efficiency, vital for life.
- 5.5: Inter- and intra-molecular interactions
- This page explores the fundamental nature of matter, stating that atoms, made up of a positively charged nucleus and negatively charged electrons, are the building blocks. It introduces London Dispersion Forces (LDFs), which arise from electron cloud distortions and vary in strength based on distance and molecular shape. Additionally, it compares different molecular representations and their significance in understanding molecular organization.
- 5.6: Covalent bonds
- This page examines covalent bonds, emphasizing that the sharing of electron pairs creates stable entities with properties different from individual atoms. It highlights the strength of covalent bonds compared to van der Waals interactions and introduces macromolecules, noting their dynamic structures and the effects of changes in shape, temperature, and bonds.
- 5.7: Bond Stability and Thermal Motion (a non-biological moment)
- This page discusses the role of the environment, particularly water, in molecular behavior and the significance of temperature, which reflects the average kinetic energy of molecules. It explains how temperature affects the phase of substances—higher temperatures enable gas formation, while lower temperatures foster liquids and solids. The thermal motion impacts molecular interactions and stability, influencing binding processes essential in biology.
- 5.8: Bond polarity, inter- and intramolecular interactions
- This page explains electronegativity, the tendency of atoms to attract electrons. It distinguishes between non-polar covalent bonds, where equal sharing occurs due to similar electronegativities, and polar bonds, characterized by unequal sharing and partial charges. Specific examples include polarized bonds between oxygen or nitrogen with carbon or hydrogen, and non-polar C-H bonds.
- 5.9: The implications of bond polarity
- This page discusses the importance of melting and boiling points as physical properties of small molecules, highlighting phase transitions and the influence of molecular size. It contrasts the behaviors of small and large molecules, emphasizing water's high melting and boiling points due to its polar structure and hydrogen bonds, which lead to stronger intermolecular interactions. These properties, including surface tension, significantly affect organisms' interactions with water.
- 5.10: Interacting with Water
- This page discusses the solubility of molecules in water, categorizing them as hydrophilic, hydrophobic, or amphipathic. Hydrophilic molecules, like sugars and amino acids, easily dissolve due to hydrogen bond formation with water, while hydrophobic molecules, such as fats, do not dissolve well and increase free energy. The role of entropy is highlighted, explaining how hydrophobic interactions disrupt water's hydrogen bonding, thus increasing order and decreasing entropy.
This page titled 5: Molecular Interactions, Thermodynamics and Reaction Coupling was last modified on Thu, 08 Jan 2026 22:57:27 GMT and is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by Michael W. Klymkowsky and Melanie M. Cooper.
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