Water, Acids, Bases, Buffers, and pH in Biological Systems

Water and Its Unique Properties

Structure and Polarity of Water

Water (H2O) is a fundamental molecule in biological systems, characterized by its polar covalent bonds and bent molecular geometry. These features give rise to many of water's unique physical and chemical properties essential for life.

• Polar Covalent Bonds: The oxygen atom in water is more electronegative than hydrogen, resulting in unequal sharing of electrons and partial charges (δ− on oxygen, δ+ on hydrogen).

• Electronegativity: Oxygen's Pauling electronegativity is 3.5, while hydrogen's is 2.1, creating a strong dipole moment.

• Molecular Geometry: Water has a bent shape (approximately 104.5° bond angle), further contributing to its polarity.

• Example: Water's polarity allows it to dissolve many ionic and polar substances, making it an excellent solvent.

Hydrogen Bonding in Water

The polarity of water molecules enables them to form hydrogen bonds with each other and with other polar molecules. Hydrogen bonds are weak interactions but collectively have significant effects on water's behavior.

• Hydrogen Bond: An attraction between the partial positive charge of hydrogen in one water molecule and the partial negative charge of oxygen in another.

• Properties: Hydrogen bonds hold water molecules together, but allow them to move relative to each other, giving water fluidity and cohesion.

• Example: Ice forms a crystalline structure due to stable hydrogen bonding, making it less dense than liquid water.

Properties of Water Relevant to Biology

Cohesion and Surface Tension

Cohesion refers to the tendency of water molecules to stick together due to hydrogen bonding, which also leads to surface tension at the air-water interface.

• Cohesion: Responsible for water droplets and the transport of water in plants.

• Surface Tension: The surface of water resists external force, allowing small objects or insects to rest on it.

• Example: Water droplets on leaves and capillary action in plant xylem.

Adhesion

Adhesion is the ability of water molecules to stick to other substances, which is also due to hydrogen bonding.

• Adhesion: Important for processes like water transport in plants and wetting surfaces.

• Example: Water climbing up a paper towel or plant stem.

Density and States of Water

Unlike most substances, water is less dense as a solid (ice) than as a liquid, due to the arrangement of hydrogen bonds in ice.

• Ice Floats: Hydrogen bonds stabilize the structure, creating open spaces between molecules.

• Biological Importance: Aquatic life survives under ice in winter.

Water as a Solvent

Hydrophilic and Hydrophobic Molecules

Water's polarity allows it to interact differently with various substances.

• Hydrophilic: "Water-loving" molecules, typically polar or ionic, dissolve readily in water (e.g., salts, sugars).

• Hydrophobic: "Water-fearing" molecules, typically non-polar, do not dissolve in water (e.g., oils, fats).

• Example: Acetic acid (hydrophilic) vs. Squalene (hydrophobic).

Solutions, Solvents, and Solutes

A solution consists of a solvent (the dissolving medium, often water) and solute (the dissolved substance).

• Solvent: The component present in the greatest amount (usually water in biological systems).

• Solute: The substance dissolved in the solvent.

• Example: Saltwater: water is the solvent, salt is the solute.

Acids, Bases, and pH

Dissociation of Water

Water molecules can dissociate into ions, a process that is rare but crucial for biological chemistry.

• Dissociation Reaction: $2H_2O \rightleftharpoons H_3O^+ + OH^-$

• Hydronium Ion (H3O+): Formed when a water molecule gains a proton.

• Hydroxide Ion (OH-): Formed when a water molecule loses a proton.

• Concentration: In pure water, $[H^+] = [OH^-] = 1 \times 10^{-7}$ M.

pH Scale

The pH scale measures the concentration of hydrogen ions in a solution, indicating its acidity or basicity.

• Definition: $pH = -\log[H^+]$

• Neutral pH: At $[H^+] = 1 \times 10^{-7}$ M, pH = 7.

• Acidic Solution: pH < 7 (higher $[H^+]$)

• Basic Solution: pH > 7 (lower $[H^+]$)

• Example: Lemon juice (pH ~2), blood (pH ~7.4).

Acids and Bases

Acids and bases alter the pH of aqueous solutions by donating or accepting protons.

• Acid: Substance that increases $[H^+]$ (e.g., HCl dissociates to H+ and Cl-).

• Base: Substance that decreases $[H^+]$ or increases $[OH^-]$ (e.g., NaOH dissociates to Na+ and OH-).

• Weak Acids/Bases: Partially dissociate and establish equilibrium in solution.

• Example: Carbonic acid (H2CO3) is a weak acid important in blood buffering.

Buffers in Biological Systems

Role and Mechanism of Buffers

Buffers are substances that minimize changes in pH by accepting or donating protons. They are crucial for maintaining stable pH in biological fluids.

• Buffer System: Typically consists of a weak acid and its conjugate base.

• Example: Carbonic acid-bicarbonate buffer in blood:

$H_2CO_3 \rightleftharpoons H^+ + HCO_3^-$

• Function: When excess acid or base is added, the buffer system counteracts the disturbance to maintain equilibrium.

Table: Comparison of Hydrophilic and Hydrophobic Molecules

Property	Hydrophilic Molecules	Hydrophobic Molecules
Polarity	Polar or ionic	Non-polar
Solubility in Water	High	Low
Examples	Acetic acid, salts, sugars	Squalene, oils, fats
Biological Role	Transport, metabolism	Membrane structure, energy storage

Additional info:

• Column chromatography and fractionation of cobra venom are mentioned as techniques and data of the week, relevant for biochemistry lab skills but not covered in detail here.

• Students are encouraged to review molecular mass, mole, molarity, scientific notation, and logarithms for quantitative understanding of solutions and pH.