Lecture 2 - Biomolecular Interactions

Why can’t a model prove a hypothesis?

• Consistency with hypothesis is not sufficient (but is necessary)

• Need to make predictions that are experimentally testable

• Find limitations/boundary conditions (try to “break” model)

Hydrogen bonding

• Non-covalent force

• H donor (is often N in proteins)

• H acceptor is often O or lone electron pair

• In water, each molecule participates in 4 H bonds

Electrostatics

• Attraction between unlike charges

• Repulsion between like charges

• Can allow for specificity

Van der Waals forces (dispersion forces)

• Weak interaction at close range

• Attractive at ≥0.4 nm

• Induced dipole win nonpolar atoms:

  • Dipole-induced dipole

  • Induced dipole-induced dipole

• Think of gecko

Hydrophobic interactions

• Not actual bonds

• Structure water around a molecule

• When a hydrophobic surface frees itself from solvation there is a gain in entropy

• Can be a dominating energy term

∆G

• ∆Gº = ∆Hº - T∆Sº

• Total free energy

• Contributions from both enthalpy and entropy

• Determines if a reaction will occur

∆H

Enthalpy - energy in molecular bonds

∆S

Entropy - disorder, j