Biochemistry Chapter 2: Water and Aqueous Solutions

Introduction

• The document is a set of lecture notes from a biochemistry textbook.
• The notes cover the topic of water and aqueous solutions, specifically focusing on the nature of intermolecular forces, properties of water, and its role in biochemical reactions.

Lecture Connections - Water and Aqueous Solutions

• This section of the course deals with water and the properties it facilitates in biochemical systems.

Chapter 2 - Water and Aqueous Solutions

• It focuses on understanding interactions between molecules.
• Learning goals cover:
  • Interactions between molecules
  • Water as a medium for life
  • Nonpolar moieties aggregation in water
  • How dissolved molecules alter water properties.
  • Weak acids and bases behaviour in water
  • Buffer mechanisms
  • Participation of water in biochemical reactions

Physics of Non-covalent Interactions

• Non-covalent interactions do not involve sharing electrons.
• Different types of interactions:
  • Ionic (Coulombic) Interactions: Electrostatic interactions between charged species or between an ion and a permanent dipole.
  • Dipole Interactions: Electrostatic interactions between uncharged but polar molecules.
  • Van der Waals Interactions: Weak interactions between atoms (regardless of polarity) with attractive (dispersion) and repulsive (steric) components.
  • Hydrophobic Effect: Complex phenomenon of water molecules ordering around nonpolar substances.

Examples of Noncovalent Interactions

• Various examples of non-covalent interactions are implied throughout the lecture notes, yet not explicitly displayed.

Four Types of Noncovalent Interactions

• Interaction types include hydrogen bonding, ionic interactions, hydrophobic interactions, and Van der Waals forces.
• Hydrogen bonding occurs between neutral groups, peptide bonds etc.

Hydrogen Bonds

• Strong dipole-dipole or charge-dipole interactions between acid (proton donor) and base (proton acceptor) molecules.
• Bond strength typically ranges from 4-6 to 6-10 kJ/mol, depending on whether atoms are neutral or charged.
• Frequently involves electronegative atoms like nitrogen and oxygen.
• Strength is maximized when molecules are oriented to maximize electrostatic interaction with ideally the three atoms in a line.

Importance of Hydrogen Bonds

• Crucial for unique water properties, protein structure and function, DNA structure and function, polysaccharide structure and function, binding of substrates to enzymes, hormones to receptors, mRNA and tRNA matching.

Van der Waals Interactions

• Interactions between atoms regardless of polarity, with both attractive (London dispersion) and repulsive (steric) components.
• Attractive forces depend on polarizability, while repulsive forces rely on atomic size.
• Dominates at medium (0.4-0.7 nm)-range distances; repulsion becomes stronger at short distances.

Origin of the London Dispersion Force

• Based on quantum mechanical phenomena.
• Instantaneous polarization due to fluctuating charge distributions.
• Always attractive and stronger in polarizable molecules.
• Significant only at short range.

Biochemical Significance of Van der Waals Interactions

• Weak individual interactions, easily broken and reversible.
• Universal, occurring between any two atoms in close proximity to one another.
• Determines steric complementarity, stabilizes biological macro-molecules, and facilitates binding of polarizable ligands.

Water is the Medium for Life

• Life evolved in water (UV protection).
• Organisms commonly contain 70-90% water.
• Chemical reactions predominantly occur in aqueous milieu.
• Water plays a critical role in protein, nucleic acid, and membrane structure and function.

Structure of the Water Molecule

• The octet rule dictates four electron pairs around oxygen atoms in water, occupying sp³ orbitals.
• Two pairs covalently link the oxygen to two hydrogen atoms while two remaining pairs remain nonbonding (lone pairs).
• The tetrahedral geometry is distorted due to oxygen's high electronegativity.
• Dipole moment due to electronegativity difference between oxygen and hydrogen.

Hydrogen Bonding in Water

• Water molecules can act as both hydrogen bond donors and acceptors.
• Up to four hydrogen bonds per water molecule lead to high boiling/melting point and large surface tension.
• Hydrogen bonding is cooperative within water.

Water as a Solvent

• Good solvent for charged and polar substances (amino-acids, peptides, small alcohols, carbohydrates).
• Poor solvent for nonpolar substances (nonpolar gases, aromatic moieties, aliphatic chains).

Water Dissolves Many Salts

• High dielectric constant diminishes attraction between ions in salt crystals.
• Electrostatic interactions between ions and water reduces energy.
• Entropy of the system increases as the ordered crystal lattice dissolves.

Ice — Water in a Solid State

• Water presents multiple crystal forms; hexagonal ice is common.
• Hexagonal ice forms a regular lattice, which results in low entropy.
• Hexagonal ice possesses lower density than liquid water, causing ice to float.

The Hydrophobic Effect

• Responsible for nonpolar molecules association or folding in aqueous solutions.
• Crucial factor behind protein folding, protein-protein interactions, lipid micelle formation, steroid hormone-receptor binding.

Low Solubility of Hydrophobic Solutes can be Explained by Entropy

• Bulk water is highly disordered with high entropy.
• Water near a hydrophobic solute becomes highly ordered, leading to low entropy.
• Low entropy is thermodynamically unfavorable, resulting in low solubility for hydrophobic solutes.

Origin of the Hydrophobic Effect(1) (2)

• Amphipathic lipids disperse in water, with nonpolar tails surrounded by highly ordered water molecules.
• Entropy of the system decreases.

Micelles

• Hydrophobic groups sequester from water.
• Ordered shell of water molecules minimizes to increase entropy.

Hydrophobic Effect Favors Ligand Binding

• Hydrophobic sites on enzymes and receptors bind hydrophobic substrates/ligands like steroid hormones.
• Many drugs exploit the hydrophobic effect for interaction.

Colligative Properties

• Solution properties (boiling point, melting point, osmolarity) are independent of the dissolved substance's nature.
• Other properties (viscosity, surface tension, taste, color) depend on the solute's chemical nature.
• Cell cytoplasm contains highly concentrated solutions, resulting in high osmotic pressure.

Effect of Extracellular Osmolarity

• Differences in extracellular osmolarity lead to water movement in or out of cells causing possible cell shrinkage (hypertonic) or swelling (hypotonic)

Ionization of Water

• Water molecules can dissociate heterolytically into a proton and a hydroxide ion.
• Dissociation is rapid and reversible.
• Pure water has low electrical conductivity due to minimal ionization.

Proton Hydration

• Protons exist in solution as hydronium (oxonium) ions.
• Hydronium ions are solvated by water molecules.
• Covalent and hydrogen bonds are interchangeable, allowing fast proton mobility via proton hopping.

Proton Hopping

• Proton movement between hydronium ions occurs through hopping, a sequential process of proton transfer.

Ionization of Water: Quantitative Treatment

• Ionization of water follows an equilibrium process.
• Equilibrium constant (K_eq) and the ionic product of water (K_w) are key parameters describing water's ionization.

What is pH?

• pH is a measure of hydrogen ion concentration in solution (pH = -log[H+]).
• pH and pOH add up to 14.

pH Scale:

• The pH scale quantifies acidity or alkalinity of a solution.

Dissociation of Weak Electrolytes: Principle (Example)

• Weak electrolytes partially dissociate in solutions.
• The extent of dissociation depends on the acid dissociation constant (K_a).
• The pH can be calculated from K_a, if known, but some algebra is required.

Dissociation of Weak Electrolytes:Simplification.

• The given equation can simplify if the amount of dissociated species in a solution is much less compared to the amount of the undissociated acid.

pk_a Measures Acidity

• pK_a is a measure of acid strength and depends on the value of K_a

Buffers - mixtures of weak acids and their anions

• Buffers resist changes in pH, maintaining homeostasis.
• Buffers are most effective at their pKa value.

Henderson-Hasselbalch Equation: Derivation

• Describes the relationship between pH, pK_a, and concentrations of acid and conjugate base.

Biological Buffer Systems

• Biological fluids employ buffer systems (phosphate, bicarbonate, histidine) to maintain appropriate pH.
• Often buffer systems in vitro are based on sulfonic acids of cyclic amines (HEPES, PIPES, CHES).

Water as a Reactant in Biochemistry

• Water participates in various biochemical reactions, through hydrolysis or condensation reactions.

Bound Water in Proteins

• Water is present in proteins.

Chapter 2 Summary

• Intermolecular forces, water properties and structure, weak acid/base behavior in water, water's role in biochemical reactions.

Explore the critical role of water in biochemical systems in this quiz based on Chapter 2. Understand intermolecular forces, the properties of water, and how they facilitate life processes. Test your knowledge on topics such as buffer mechanisms and the interaction of nonpolar molecules in water.