Biochemistry: Molecular Forces, Water Properties & Thermodynamics

Molecular Forces

  • Intramolecular vs. Intermolecular Forces:

    • Intramolecular: Forces within a molecule (e.g., covalent bonds).

    • Intermolecular: Forces between molecules.

  • Electronegativity:

    • Increases across a period, decreases down a group.

    • Difference in electronegativity predicts bond type and polarity.

  • Covalent Bonds:

    • Strongest bonds, formed by electron sharing.

    • Nonpolar Covalent: Small (0.0-$0.4$) electronegativity difference; equal sharing (e.g., N-N, Cl-Br).

    • Polar Covalent: Moderate (0.5-$1.8$) electronegativity difference; unequal sharing, creates a dipole (e.g., O-Cl, O-S).

    • Polarity of Molecules: Can be nonpolar if polar bonds cancel symmetrically (e.g., CO<em>2CO<em>2) or polar if dipoles do not cancel (e.g., H</em>2OH</em>2O).

  • Resonance: Molecules exhibiting multiple covalent structures (e.g., Adenine).

  • Ionic Bonds & Interactions:

    • Occur between fully charged atoms or molecules.

    • Coulomb Energy: E=kq<em>1q</em>2/DrE = kq<em>1q</em>2/Dr (kk = Coulomb's constant, q<em>1,q</em>2q<em>1, q</em>2 = charges, DD = dielectric constant, rr = distance).

    • As rr decreases, EE increases; as DD increases, EE decreases.

  • Hydrogen Bonds (H-bonds):

    • Form between an electronegative atom and a hydrogen covalently bonded to another electronegative atom.

    • Bond energies: 4-20 kJ mol−120 \text{ kJ mol}^{-1} ($1$-5 kcal mol−15 \text{ kcal mol}^{-1}).

    • Strongest when the acceptor atom is in line with the donor atom and H.

  • van der Waals Interactions:

    • Weak attractions and repulsions between transient dipoles (dispersion forces).

    • Bond energies: 2-4 kJ mol−14 \text{ kJ mol}^{-1} ($0.5$-1.0 kcal mol−11.0 \text{ kcal mol}^{-1}).

    • Result in a van der Waals contact distance where attraction balances repulsion.

  • Importance of Weak Interactions: Crucial for macromolecular structure and function, as their cumulative effect provides stability.

Properties of Water

  • Key Properties: Polar molecule, highly cohesive & adhesive, high dielectric constant, higher melting/boiling point, and heat of vaporization compared to most solvents.

  • Hydrogen Bonds: Responsible for water's unusual properties. Each H2OH_2O molecule forms an average of 3.4 H-bonds in liquid and 4 in ice.

  • Solvent Properties:

    • Dissolves salts and charged biomolecules by screening electrostatic interactions.

    • Hydrophilic: Compounds that dissolve easily in H2OH_2O (charged or polar).

    • Hydrophobic: Nonpolar molecules that do not dissolve in H2OH_2O (e.g., lipids).

    • Amphipathic: Contain both polar/charged and nonpolar regions.

  • The Hydrophobic Effect: Nonpolar molecules are driven together in water due to the increase in entropy of water molecules as they are released from ordered cages around nonpolar solutes.

Thermodynamics

  • Vocabulary:

    • System: Matter within a defined space.

    • Surroundings: Matter around the system.

    • Closed System: Isolated from surroundings.

    • Open System: Not completely isolated.

    • Entropy (S): Measure of randomness or disorder.

    • Enthalpy (H): Measure of heat content.

    • Exothermic: Releases heat (reaction).

    • Endothermic: Absorbs heat (reaction).

    • Universe: System + Surroundings.

  • First Law of Thermodynamics: Total energy of a system and its surroundings is constant.

  • Second Law of Thermodynamics: Total entropy of a system plus its surroundings always increases.

    • ΔS<em>surroundings=−ΔH</em>system/T\Delta S<em>{surroundings} = -\Delta H</em>{system} / T

    • ΔS<em>total=ΔS</em>system+ΔSsurroundings\Delta S<em>{total} = \Delta S</em>{system} + \Delta S_{surroundings}

  • Gibbs Free Energy (ΔG\Delta G):

    • ΔG=ΔH−TΔS\Delta G = \Delta H - T\Delta S

    • ΔG\Delta G provides information about reaction spontaneity:

      • −ΔG-\Delta G: Spontaneous reaction (favorable).

      • ΔG=0\Delta G = 0: Equilibrium.

      • +ΔG+\Delta G: Not favorable/not spontaneous.

    • ΔG∘\Delta G^{\circ}: Standard free energy (1.0 M reactants/products, 1 atm, 25∘C25^{\circ}C).

    • \Delta G^{\circ}\' : Standard free energy at pH 7.

    • Calculating ΔG\Delta G for a real reaction: ΔG=ΔG∘+RTln⁡([products][reactants])\Delta G=\Delta G^{\circ} + RT \ln (\frac{[products]}{[reactants]})

  • Thermodynamics and Biological Phenomena:

    • DNA formation: Entropy of system decreases, but heat release increases entropy of surroundings, making ΔStotal\Delta S_{total} positive.

    • Nonpolar gases in water: Decrease entropy by constraining water motion.