MODULE 3 – Molecular interactions and energetics
Interactions between AA and those between AA and water are often weak = at the cellular level,
bonds must be broken and reformed on a continuous basis in order for large scale motion and
muscular contraction and relaxation to occur.
Gibbs free energy: - used for large quantities
ΔG = ΔH - T ΔS
o ΔG = G2 – G1
o ΔG < 0, bonds form
o ΔG > 0, bonds don’t form
o ΔG = 0, nothing happens.
2nd law of thermodynamics – during a real process, the entropy of an isolated system always
increases. Heat is released and order tends to increase when bonds are formed.
Bond formation – System favors minimum energy = ΔG is at a maximum where there is a
minimum energy and the bind is formed.
Bond breakage – Total E= U + KE
o The ratio of ΔG/RT, bond energy to KE, will determine the fraction of bonded molecules.
o If ΔG = 0, Keq = 1 and formation and breakage of bonds are equally favored
o If ΔG < 0, Keq > 1, bond formation favored
o If ΔG >0, Keq <1, bond breakage favored
o If force is -, => attractive; if force is +, = repulsive
o Dielectric constant – charges within the protein will not be evenly distributed (variable)
o Entropically driven reactions: ion-pair formation.
For aqueous solvents, the entropy of the water increases substantially so that
there is a net overall increase in entropy within the system”
ΔH for ion-pair formation is +
ΔS for ion-pair formation is –
Dipole (permanent dipoles)
o Antiparallel – attraction; parallel – repulsion.
o Examples: OH, C=O, NH, peptide bond
Van der Waals (London dispersion forces)
o Occurs between 2 fluctuating, non-permanent dipoles
o In proximity, the electron cloud distribution can shift momentarily due to unpredictable
quantum fluctuations, producing a transient dipole-like interaction.
o Fluctuations continue in such a way that a net attraction exists.
o As atoms come close together, electron orbitals start to overlap and a repulsive force
will result in keeping with the Pauli exclusion principle = called the hard sphere potential
o You can also add 2 vanderwaal forces (+) + (-) = called the Lennard-Jones potential
o Strongest weak bond with energy of up to 5 kcals/mole