1. Amino Acids

2. Amino Acid Structure Basic Structure: – (α) Carbon – Carboxylic Acid Group – Amino Group – R-group Side Chain Determines properties of Amino Acid R | H 2 N — C —COOH | H R Group Classification: - Non-polar, Polar, Aromatic, Acidic, and Basic

3. Non-Polar; Hydrophobic Glycine (G) Alanine (A) Proline (P) Valine (V) Leucine (L) Isoleucine (I) Methionine (M)

4. Polar; Hydrophilic Serine (S) Threonine (T) Cysteine (C) Asparagine (N) Glutamine (Q)

5. Aromatic Phenylalanine (F) – Hydrophobic Tyrosine (Y) – Hydrophilic Tryptophan (W) – Hydrophobic

6. Charged R-Groups Acidic (positively-charged) – Aspartate (D) – Glutamate (E) Basic (negatively charged) – Lysine (K) – Arginine (R) - strongly – Histidine (H) - weakly

7. 7 The Peptide Bond Amide bond formed by the –COOH of an amino acid and the –NH 2 of the next amino acid O CH 3 + | | + | NH 3 –CH 2 –COH + H 3 N–CH–COO – O CH 3 + | | | NH 3 –CH 2 –C – N–CH–COO – | peptide bond H

8. 8 Peptides Amino acids linked by amide (peptide) bonds Gly Lys Phe Arg Ser H 2 N- -COOH endPeptide bonds end Glycyllysylphenylalanylarginylserine

9. Isoelectric Point Each amino acid has an isoelectric point, (pI) numerically equal to the pH at which the zwitterion concentration is at a maximum. The amino acid has no NET charge at its pI; it has one positive and one negative charge. At a pH less than the value of the isoelectric point, the amino acid is protonated and has a POSITIVE charge; at a pH greater than the pI the amino acid is deprotonated and has a NEGATIVE charge. CationNeutralAnion (zwitterion form)

10. Prentice Hall c2002Chapter 310 Fig 3.6 Titration curve for alanine Titration curves are used to determine pK a values pK 1 = 2.4 pK 2 = 9.9 pI Ala = isoelectric point

11. Prentice Hall c2002Chapter 311 Fig 3.7 Ionization of Histidine (a) Titration curve of histidine pK 1 = 1.8 pK 2 = 6.0 pK 3 = 9.3

12. Derivatization with Ninhydrin Ninhydrin (2 mol) reacts with one mol of ANY amino acid to give the SAME blue colored product. This reaction is performed post-column, after Ion Exchange Chromatography separation of a mixture of amino acids. The area of each peak in the chromatogram is proportional to the relative molar amount of the amino acid of that retention time.

13. Disulfide bonding in peptides [O]

14. Sanger’s Reagent: N-terminal Amino Acid Analysis

15. Sanger’s Reagent, cont’d

16. Carboxypeptidase: C-terminal AA Analysis

17. Prentice Hall c2002Chapter 317 Acid-catalyzed hydrolysis of a peptide