Biophysical Chemistry
Biophysical chemistry applies principles of physics and chemistry to understand biological systems — particularly how molecules interact, how energy flows through biochemical reactions, and how thermodynamics governs life processes.
pH and Ionization
The Henderson-Hasselbalch equation: pH = pKa + log([A⁻]/[HA]). At pH = pKa, 50% of the acid is ionized. Amino acids exist as zwitterions at their isoelectric point (pI). At pI, net charge = 0; migration in electric field = 0 (important for electrophoresis and isoelectric focusing).
Buffer Systems
Buffers resist pH change upon addition of acid or base. Effective within ±1 pH unit of pKa.
- Bicarbonate buffer (blood): CO₂/HCO₃⁻, pKa = 6.1. Most important extracellular buffer. Regulated by lungs (CO₂) and kidneys (HCO₃⁻).
- Phosphate buffer (intracellular): H₂PO₄⁻/HPO₄²⁻, pKa = 6.8. Important in urine and intracellular fluid.
- Protein buffer: Side chains of His (imidazole, pKa ~6) act as buffers in blood (Hb is major blood buffer).
Thermodynamics in Biochemistry
- Gibbs Free Energy (ΔG): ΔG = ΔH - TΔS. If ΔG < 0, reaction is spontaneous (exergonic). If ΔG > 0, reaction requires energy input (endergonic).
- Standard Free Energy (ΔG°'): At pH 7, 25°C, 1 M concentrations. Used to compare reactions thermodynamically.
- ATP hydrolysis: ΔG°' = -30.5 kJ/mol. ATP acts as the universal energy currency coupling exergonic & endergonic reactions.
- Coupled reactions: Unfavorable reactions driven by coupling with ATP hydrolysis (or other favorable reactions).
Molecular Forces in Biomolecules
- Covalent bonds: Strongest (peptide, glycosidic, phosphodiester bonds). Form the backbone of biomolecules.
- Hydrogen bonds: Responsible for DNA base pairing, protein secondary structure, water's properties.
- Hydrophobic interactions: Nonpolar groups cluster away from water → drives protein folding and membrane formation.
- Van der Waals forces: Weak, transient dipole interactions. Important in enzyme-substrate fitting.
- Ionic interactions (salt bridges): Electrostatic attractions between charged groups — important in protein structure.
Colligative Properties & Osmosis
Osmolality of body fluids is ~290 mOsm/kg H₂O. Osmotic pressure drives water across membranes. Oncotic pressure (due to plasma proteins, mainly albumin) keeps fluid in blood vessels. Low albumin → edema.
Spectroscopy
- UV absorption: Proteins absorb at 280 nm (Trp, Tyr); nucleic acids at 260 nm.
- Beer-Lambert Law: Absorbance = ε × c × l. Used in all colorimetric lab assays.
- CD (Circular Dichroism): Detects protein secondary structure (α-helix vs β-sheet).