1. To do list: Read chapter 2, work problems Work on amino acids
Working with molarity, pH, especially
Look at Henderson-Hasselbalch
pH = pKa + log([base]/[acid])
Work on amino acids
Names, structures, functional groups
Paper summary (due 2/23/07)

2. Paper summary Discuss more in detail on Monday
Find an *interesting* biochemical paper
Suggest Medline/Pubmed
Biochemistry, Journal of Biological Chemistry, Biochemical Journal, etc.
Recent:
Summarize the paper (1-2 pages dbl spaced)
What’s the hypothesis/question? Why is it important? How did they address it? Conclusions?
Is their conclusion valid? What are some alternative explanations?

3. Today: ‘weak’ interactions (intramolecular bonding)
Next week: osmosis, pH, water as a reactant

4. Weak interactions in biological systems
Strong: covalent bonds
Hydrogen bonds
Dipole-dipole interactions
Ionic interactions (attractive OR repulsive)
Hydrophobic interactions
van der Waals interactions

5. Electronegativity: How strongly an atom in a covalent bond
pulls the shared electrons
More electronegative: Stronger pull

6. C O Hydrogen: 2.1 Carbon: 2.5 Oxygen: 3.5 Nitrogen: 3.0 H H d+ d- 2.1
Similar electronegativities
e- shared ~ equally
Non-polar bond C H
3.5
2.1
~Big diff in electronegs
e- favor oxygen atom
Polar bond O H d+ d-

7. Two dipoles attract
A: more electronegative than B A B A B d- d+ d- d+

8. Water is a polar moleculeH O H

9. H-bond “Donor”: O-H or N-H (or F-H) H-bond “Acceptor”: O or N (or F)
Hydrogen bond (H-bond): strong (partial) positive charge
on hydrogen attracts lone electon pair on oxygen or nitrogen
H-bond “Donor”: O-H or N-H (or F-H)
H-bond “Acceptor”: O or N (or F)

10. H-bond: Strength in numbers
H-bond is weaker than a covalent bond
H-bond ~ 20 kJ/mol
H-O covalent bond in H2O ~460 kJ/mol
H-bond is stronger than a typical dipole-dipole interaction
Water (H2O) boiling point = 100°C
Hydrogen sulfide (H2S) bp = -70°C
Much stronger intermolecular forces

11. Straight H-bonds = strongest A driving force for the structures of protein and nucleic acid molecules

12. H-bond: Strength in numbers

13. “Hydrophobic force” “Hydrophobic interactions”
Formation of the lipid bilayer
Protein folding
Protein-protein interactions
Enzyme-substrate interactions

14. Water interacts with polar/charged molecules
“Interaction” = forms bonds with
Forming bonds = favorable enthalpically
Negative DH

15. Entropy can drive dissolution (DG = DH – TDS; DG < 0 for spontaneous)
~same enthalpy
Great entropy
DS > 0
Enthalpy is good (plenty of bonds)
Entropy is bad (limited freedom)

16. Dissolving of polar/charged solute
Water loses hydrogen bonds (bad enthalpy)
But makes up for them with water-solute bonds (back to ~neutral enthalpy)

17. Not all potential solutes can compensate for the lost H-bonding

18. Hydrophobic groups: DG unfavorable for dissolving
DS is negative:
Maximizing H-bonds
leads to fewer
degrees of freedom

19. Hydrophobic forces cause hydrophobic groups to assemble

20. Hydrophobic forces cause hydrophobic groups to assemble
*Positive DS!*

23. van der Waals vs. Hydrophobic

24. Two dipoles attract
A: more electronegative than B A B A B d- d+ d- d+

25. What about a non-polar molecule?

26. “Polarizability” increases with electron cloud size
Benzene rings are relatively polarizable
Nucleic acids: “stacking” of the base rings
Proteins: interactions with phenylalanine, tyrosine, tryptophan, histidine

28. Types of interactions Covalent (intramolecular, very strong) Ionic
Hydrogen
Dipole-dipole
Hydrophobic
van der Waals
‘Weak’ interactions
Not unimportant