5: Molecular Interactions, Thermodynamics & Reaction Coupling
- Page ID
- 3885
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)While the diversity of organisms and the unique properties of each individual organism are the products of evolutionary processes, initiated billions of years ago, it is equally important to recognize that all biological systems and processes, from growth and cell division to thoughts and feelings, obey the rules of chemistry and physics, and in particular the laws of thermodynamics.
- 5.0: Introduction
- This page emphasizes the significance of physicochemical properties in biology, detailing how molecular interactions affect the characteristics of substances and systems. It underscores the need to understand these interactions for a comprehensive view of biology, while acknowledging contributions from various authors and editorial support.
- 5.1: A very little thermodynamics
- This page explores the differences between biological and simple physicochemical systems, noting that living organisms remain in a non-equilibrium state crucial for life, in contrast to systems that achieve thermodynamic equilibrium. It uses the analogy of a gold bar in a closed room to illustrate energy transfer and equilibrium.
- 5.2: Reactions: favorable, unfavorable, and their dynamics
- This page explains the complexity of biological systems in relation to thermodynamics. It describes how favorable and unfavorable reactions drive processes like molecule synthesis. The first law of thermodynamics highlights energy conservation and its transformation into less useful forms, such as heat from friction. Entropy is introduced as a key concept, addressing energy distribution and usability within systems.
- 5.3: Thinking entropically (and thermodynamically)
- This page revisits essential concepts in thermodynamics and chemical reactions, focusing on the first law of thermodynamics and energy conservation in closed systems. It introduces the Gibbs free energy equation (ΔG = ΔH - TΔS) within biological contexts and explains the equilibrium constant (Keq), highlighting its role in the balance of reactants and products. It underscores that molecular activity persists at equilibrium, ensuring a dynamic balance in reactions.
- 5.4: Reaction rates
- This page explains the difference between thermodynamic favorability and reaction kinetics, emphasizing that while thermodynamics helps determine a reaction's potential via its equilibrium constant, it doesn't guarantee a significant reaction rate. Kinetics must be examined to assess how fast a reaction occurs. An example of cellulose in wood reacting with oxygen illustrates the relevance of kinetics in understanding actual reaction rates.
- 5.5: Coupling Reactions
- This page explores the balance of catabolic and anabolic reactions in cellular metabolism, explaining how unfavorable reactions can occur when coupled with favorable ones. It illustrates Le Chatelier's principle, emphasizing the impact of concentration changes on reaction equilibrium and the dynamic nature of these processes.
- 5.6: Molecules, London Dispersion Forces, and van der Waals interactions
- This page defines matter by exploring atomic organization and the interactions between atoms and molecules. It highlights that atoms consist of a positively charged nucleus and negatively charged electrons, which interact through van der Waals forces, specifically London Dispersion Forces.
- 5.7: Covalent bonds
- This page explains covalent bonds, formed by the sharing of electron pairs, leading to unique molecular properties and stronger interactions than van der Waals forces. It highlights the complexity of larger molecular structures and how their geometry influences properties. The page also discusses the dynamic aspects of molecular interactions, like bond rotation and resonance structures, which complicate the prediction of three-dimensional configurations in larger molecules.
- 5.8: Bond Stability and Thermal Motion (a non-biological moment)
- This page discusses the interactions of molecules in aqueous solutions, emphasizing the influence of temperature on molecular movement and equilibrium. It highlights that biological processes predominantly occur in liquid environments where stochastic interactions, driven by thermal motion, result in variability that affects gene expression and cellular functions. This understanding is essential for studying biological systems and their dynamics.
- 5.9: Bond polarity, inter- and intramolecular interactions
- This page explores covalent bonds, emphasizing variations in electron sharing caused by differing electronegativities. It details how unequal electronegativity leads to polar bonds, resulting in charge separation and dipoles that enable electrostatic interactions, such as hydrogen bonds, which are stronger than van der Waals forces but weaker than covalent bonds. The page contrasts polar bonds (e.g., O and N with H and C) with non-polar bonds (e.g.
- 5.10: The implications of bond polarity
- This page outlines the physical properties of small molecules, emphasizing melting and boiling points as key phase transition indicators. It explains how temperature changes affect molecular interactions, with polar bonds playing a crucial role. Water is highlighted for its unique hydrogen bonding, resulting in higher melting and boiling points. Additionally, the page introduces hydrophobic and hydrophilic interactions, along with the concept of amphipathic molecules.
- 5.11: Interacting with Water
- This page explains the solubility of molecules in water, distinguishing between hydrophilic, hydrophobic, and amphipathic types. It discusses how hydrophilic substances dissolve due to hydrogen bonds, whereas hydrophobic substances do not dissolve, increasing system energy and decreasing water's disorder, leading to unfavorable thermodynamic conditions. The page also introduces concepts such as colloids and van der Waals interactions, highlighting their significance in the dynamics of solubility.
Contributors and Attributions
Michael W. Klymkowsky (University of Colorado Boulder) and Melanie M. Cooper (Michigan State University) with significant contributions by Emina Begovic & some editorial assistance of Rebecca Klymkowsky.