Transcript Lehninger Principles of Biochemistry 5/e

Chapter 2
1.) Properties of water, hydrogen bonding and the hydrophobic effect
2.) Other important intramolecular interactions
3.) Acid/base chemistry
Dwater > Dice
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.’
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 chemical
interactions that we are interested in
Covalent bonds
Increasing strength
Salt bridges
(aka ionic bonds)
Hydrogen bonds
Dipole-dipole
interactions
van der Waals
interactions (aka,
London forces)
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·q2
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 / (4pe·rij)
Positive (destabilizing) values when ++ or --.
Morse curve.
Dissecting the force field
ki
ki
2
2
U(r ) =
(li - li,o ) +
(qi - qi,o ) +
2
2
bonds
angles
N
å
å
Un
(1+cos(nw - g )) +
2
torsions
å
æ
éæ
ç 4e êç s ij
ç ij êçè rij
j= i+1è
ë
åå
i=1
ö
ú+ qi q j ÷
ú 4 pe o rij ÷
û
ø
6ù
ö æs ö
ij
÷÷ - çç ÷÷
ø è rij ø
12
What is a torsion angle?
CH3-CH2-CH2-CH3
While the hydrophobic effect is NOT a direct chemical
interaction…
Hydrophobic
core
Hydrophilic
surface
…it does contribute to increased
propensity for chemical species of
similar polarity to aggregate.
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.