Module 2: Water, Weak Interactions, and Buffers – Biochemistry Study Notes

Water: Structure, Function, and Biological Importance

General Properties of Water

Water is the most abundant molecule in living organisms and plays both passive and active roles in biochemistry.

• Passive Role: The structure and function of biomolecules are influenced by their interactions with water. For example, protein folding is driven by the tendency to bury hydrophobic residues away from water.

• Active Role: Water participates directly in many biochemical reactions, such as the release of a water molecule during peptide bond formation.

Example: Peptide bond formation between amino acids releases a water molecule.

Water as the Matrix of Life

Water is essential for life as we know it, shaping the search for extraterrestrial life and the study of alternative solvents (e.g., ammonia, formamide).

• Life on Earth is fundamentally linked to water.

• Alternative liquids are considered for life in other environments, but water's unique properties make it especially suitable.

Structure/Function Relationship of Water

The simplicity of water's structure makes it an ideal model for understanding structure-function relationships in biochemistry.

• Electronegativity: Oxygen is more electronegative than hydrogen, resulting in a permanent dipole.

• Partial Charges: Oxygen carries a partial negative charge; hydrogens carry partial positive charges.

• Dipole Effects: Enables water to form electrostatic interactions and hydrogen bonds.

Hydrogen Bonds

General Features

Hydrogen bonds are electrostatic interactions between an electronegative atom (acceptor) and a hydrogen atom covalently linked to another electronegative atom (donor).

• Oxygen and nitrogen are common hydrogen bond donors and acceptors in biomolecules.

• Hydrogen bonds are critical for physiological processes and molecular recognition.

Strength and Geometry

• Hydrogen bonds are relatively weak (~5% strength of a covalent bond).

• They are longer than covalent bonds (about double the length).

• Strength depends on geometry; anti-parallel beta sheets are more stable than parallel ones due to optimal hydrogen bonding geometry.

Unusual Properties of Water

Hydrogen Bonding Capacity

• Each water molecule can form four hydrogen bonds (two as donor, two as acceptor).

• In liquid water, each molecule participates in an average of 3.4 hydrogen bonds in dynamic clusters.

• Hydrogen bonds confer internal cohesion, affecting water's physical properties.

Thermal Properties

• Heat of Vaporization: Amount of heat required to vaporize a liquid at its boiling point.

• Specific Heat Capacity: Amount of heat required to raise the temperature of a substance by one degree.

Comparison of Water with Other Solvents

Solvent	Melting Point (°C)	Boiling Point (°C)	Heat of Vaporization (J/g)
Water	0	100	2,260
Methanol	-97	65	1,100
Ethanol	-117	78	857
Propanol	-127	97	697
Butanol	-89	117	590
Acetone	-95	56	524
Hexane	-95	69	333
Benzene	6	80	394
Chloroform	-63	61	247

Biological Implications

• Water's high specific heat and heat of vaporization help organisms maintain constant body temperature.

• Ice floats on water due to its lower density, resulting from an ordered hydrogen-bonded structure.

Polywater: A Case Study in Scientific Skepticism

Polywater Properties

• Polywater was claimed to have higher boiling point, lower freezing point, and higher viscosity than regular water.

• Later found to be a result of impurities, not a new form of water.

Property	Polywater
Freezing Temp	-40°C
Boiling Temp	150°C
Density	1.4 g/cm³
Viscosity	15x greater than regular water

Water as a Solvent

Electrostatic Interactions

• Water dissolves charged solutes by forming hydration layers.

• Its small size and permanent dipole allow interaction with both positive and negative ions.

Hydrogen Bonds in Solvation

• Biomolecules with functional groups capable of hydrogen bonding dissolve well in water.

• Water can act as both donor and acceptor in hydrogen bonds.

Solubility of Dissolved Molecules

• Hydrophilic: Polar molecules, high solubility.

• Hydrophobic: Non-polar molecules, low solubility.

• Amphipathic: Molecules with both hydrophilic and hydrophobic regions (e.g., fatty acids).

Solubility of Gases

• Non-polar gases (CO₂, O₂) have limited solubility in water, requiring specialized transport mechanisms.

Gas	Structure	Polarity	Solubility (mg/L at 18°C)
Oxygen	O₂	Non-polar	9.0
Carbon dioxide	CO₂	Non-polar	900
Ammonia	NH₃	Polar	1,000
Hydrogen sulfide	H₂S	Polar	1,860

Behavior of Amphipathic Substances

• Amphipathic molecules (e.g., phospholipids) form micelles or bilayers in water, with hydrophilic regions facing water and hydrophobic regions sequestered away.

• Hydrophobic interactions drive the formation and stabilization of biomolecular structures.

Weak Interactions in Biomolecules

Importance to Structure and Function

Non-covalent interactions are crucial for the three-dimensional structure and dynamic behavior of biomolecules.

• Enable transient, dynamic interactions and flexibility.

• Influence molecular recognition, enzyme binding, and stabilization of structures.

Types of Non-Covalent Interactions

• Hydrogen Bonds

• Ionic (Electrostatic) Interactions

• Hydrophobic Interactions

• van der Waals Interactions

Hydrogen Bonds

• Functional groups in biomolecules can form hydrogen bonds with water, within the same molecule (intramolecular), or with other molecules (intermolecular).

• Critical for specificity of interactions, but less so for formation of higher-order structures.

Ionic (Electrostatic) Interactions

• Can be attractive (opposite charges) or repulsive (like charges).

• Strength is reduced by water's shielding effect.

• Depends on distance and medium between charged groups.

van der Waals Forces

• Short-range interactions between permanent and induced dipoles.

• Maximal when atoms are separated by the sum of their van der Waals radii.

• Abundant in the core of folded proteins.

Hydrophobic Effect

• Polar groups interact with water; non-polar regions are shielded away.

• Protein folding involves clustering of non-polar side chains in the interior and polar side chains on the surface.

• Folding creates a more ordered state, seemingly contradicting the Second Law of Thermodynamics.

Thermodynamics of the Hydrophobic Effect

• Water molecules around hydrophobic regions are more ordered, decreasing entropy.

• Association of non-polar regions releases ordered water, increasing entropy.

• Folding of polypeptides decreases their entropy but increases the entropy of associated water.

Ionization of Water and pH

Ionization of Water

• Water can ionize to form hydrogen ions (H⁺) and hydroxide ions (OH⁻).

$H_2O \leftrightarrow H^+ + OH^-$ $K_{eq} = \frac{[H^+][OH^-]}{[H_2O]} = 1.8 \times 10^{-16}~M$ $[H_2O] = 55.5~M$ $K_w = [H^+][OH^-] = 1.0 \times 10^{-14}~M^2$

The pH Scale

• pH is a logarithmic scale expressing hydrogen ion concentration.

$pH = -\log [H^+] = \log \frac{1}{[H^+]}$ Example: $[H^+] = 1 \times 10^{-5}~M$ gives $pH = 5$ $[H^+] = 1 \times 10^{-6}~M$ gives $pH = 6$ A difference of 1 pH unit equals a 10-fold difference in $[H^+]$.

Weak Acids and Bases: Dissociation Constants

• Strong acids/bases dissociate completely; weak acids/bases do not.

• The extent of dissociation is quantified by the acid dissociation constant ($K_a$).

$CH_3COOH \leftrightarrow H^+ + CH_3COO^-$ $K_a = \frac{[H^+][CH_3COO^-]}{[CH_3COOH]}$ $pK_a = -\log K_a$

Titration Curves and Buffering

• The ratio of acid to conjugate base changes during titration.

• When $pH = pK_a$, $[A^-] = [HA]$ and the solution best resists changes in pH.

• Buffering region extends one pH unit on either side of the $pK_a$ point.

Example: For acetic acid ($pK_a = 4.76$), the buffering range is $3.76$ to $5.76$.

Buffers in Biological Systems

Importance of Buffers

• Organisms must maintain constant pH to preserve biomolecular structure and function.

• Weak acids serve as buffers; e.g., the bicarbonate buffer system in blood.

$CO_2 + H_2O \leftrightarrow H_2CO_3$ $H_2CO_3 \leftrightarrow HCO_3^- + H^+$

The Henderson-Hasselbalch Equation

• Relates pH, $pK_a$, and the ratio of conjugate base to acid.

$pH = pK_a + \log \left( \frac{[A^-]}{[HA]} \right)$

Example Calculation: For a mixture of 0.01 M acetic acid and 0.1 M sodium acetate ($pK_a = 4.76$): $pH = 4.76 + \log \left( \frac{0.1}{0.01} \right) = 4.76 + 1 = 5.76$

Additional info:

• Notes include critical context for biochemistry students, such as the role of water in protein folding, the importance of non-covalent interactions, and the application of buffer systems in physiology.

• Tables have been recreated and expanded for clarity.