1. On a FREE AMINO ACID, what functional groups will accept or donate protons at pH 7, and hence are normally charged in water? side chain groups -OH -CH 3 -C O -NH 2 -COOH

2. the group “COOH” would be a very strong acid in fact, this group is always deprotonated, and thus exists as a weak base, COO- AA’s are zwitterions at pH 7, because they have oppositely charged groups amino acids are salts with high melting points, because as they crystallize, ionic interactions stabilize the crystal lattice

3. Titration curve for alanine pK 1 = 2.4 pK 2 = 9.9 pI Ala = isoelectric point

4. pKa values of amino acid ionizable groups

5. Which amino acid side chains are positively charged at pH 7?

6. Which amino acid side chains are negatively charged at pH 7?

7. Which amino acid side chains can act as H-bond donors?

8. Which amino acid side chains can act as H-bond acceptors?

9. Aliphatic side chains

10. Aromatic side chains

11. Proline has a nitrogen in an aliphatic ring system Proline (Pro, P) - has a three carbon side chain bonded to the  -amino nitrogen The heterocyclic pyrrolidine ring restricts the geometry of polypeptides

12. Methionine and cysteine Cys can participate in S-S bonds that covalently link different parts of a polypeptide chain to stabilize the 3D structure of a protein

13. Side Chains with Alcohol Groups - can donate & accept H-bonds, but are NOT charged! - can be phosphorylated by kinase enzymes

14. Acidic or polar side chains

15. Basic amino acids

16. Due to resonance, all lone pairs are partially occupied by the proton in its normal, positively charged state Side chain of arginine

17. Peptide bond between two amino acids

18. Peptide bond shown as a C-N single bond Peptide bond shown as a double bond Actual structure is a hybrid of the two resonance forms w/ delocalized electrons

19. Planar peptide groups in a protein Rotation around C-N bond is restricted due to 40% double-bond nature of the resonance hybrid form Peptide groups (blue planes) are therefore planar; restrict conformations possible in protein chains

20. features of the peptide backbone

21. What parts of this polypeptide are charged at pH 7 ? What groups can accept H-bonds? What groups can donate H-bonds? [ Hint: what is different for a peptide versus a free amino acid? ] draw your amino acids as part of a peptide backbone, not as free aa’s, on your homework and quizzes!!

22. Both backbone and side chain groups participate in important intra- and inter- molecular binding interactions - some are responsible for folding protein into correct 2D and 3D shape - others bind to small molecules like enzyme cofactors & substrates

23. Features of protein secondary structure (commonly encountered folding patterns) like b-sheets are due to repeated H-bonding between backbone groups of a protein