Chapter 2
1.) Properties of water, hydrogen bonding and the hydrophobic effect
2.) Other important intramolecular interactions
3.) Acid/base chemistry
Liquid water Ice
Hydrogen bonding
D-H---A
Water is a “locally structured transient gel.”
While the conformational entropy (# of possible arrangements) of the lipid is decreased by sequestering it, the overall system entropy increases due to the dramatically increased number of ways that the HOH molecules can be arranged.
This is a direct result of the transient nature of HB networks…meaning, they are continuously fluctuating and any number of HOH molecules can occur within a given ‘location.’
time
Diffusion is from high to low concentration!
Chapter 2
1.) Properties of water, hydrogen bonding and the hydrophobic effect
2.) Other important intramolecular interactions
3.) Acid/base chemistry
Intramolecular H-bonds
Relative strength of the chemicalinteractions that we are interested in
Covalent bonds
Salt bridges (aka ionic bonds)
Hydrogen bonds
Dipole-dipole interactions
van der Waals interactions (aka,
London forces)
Incre
asin
g s
tren
gth
Note that the hydrophobic effect is NOT a direct force between nuclei.
Rather, it is a bulk colligative property arising from the overall number of degrees of freedom within the system (as already discussed).
Notes
Hooke’s law, U = 1/2k·l2
Hooke’s law, U = 1/2k·2
We will ignore improper torsions
Sinusoidal potential. Note the three minima, which depending on the local chemistry, may or may not be equally deep.
U = q1q2 / (4·rij)Positive (destabilizing) values when ++ or --.
Morse curve.
Dissecting the force field
What is a torsion angle?
CH3-CH2-CH2-CH3
While the hydrophobic effect is NOT a direct chemical interaction…
…it does contribute to increased propensity for chemical species of similar polarity to aggregate.
Hydrophilic surface
Hydrophobic core
Chapter 2
1.) Properties of water, hydrogen bonding and the hydrophobic effect
2.) Other important intramolecular interactions
3.) Acid/base chemistry
(alkaline)
Consider the halide diatomic acids (HF, HCl, etc.)Q: Which are “strong” acids? Which are not? Why?
Nomenclature of common acid/conjugate base pairs
Amino acid sidechain pKa values*Q: Why is there an asterisk here?
Residue pKa values:CT: 3.8 (R-CO2H)
Asp: 4.0 (R-CO2H)Glu: 4.4 (R-CO2H)
His: 6.5 (imidazole)NT: 8.0 (R-NH3
+) Cys: 8.5 (R-SH)
Tyr: 10.0 (Ph-OH)Lys: 10.0 (R-NH3
+)Arg: 12.0 (guanidinium)
The answer is yes! You must know these values.
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