chapter 2 1.)properties of water, hydrogen bonding and the hydrophobic effect 2.)other important...

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.