Pre-Med Club BBQ , TODAY @ 4pm @ Marine Park .

1. Pre-Med Club BBQ , TODAY @ 4pm @ Marine Park . Come join the fun, eat free food, and make new friends!!! Also, at the BBQ there will be sign up sheets for volunteer opportunities for Make A Difference Day (Saturday, Oct. 28th from 8am-1pm ) Also at the BBQ, sign up to buy a WWU Pre-Med Club T-shirt!!! If you did not receive an Ocotber Events Calender, you can pick one up at the Chemistry Office.

2. Exam W 10/11 Review Session?

3. Stryer Fig. 3.11: Phe absorbs a little as well. This phenomenon is the basis of one method to determine protein concentration in a non-destructive manner using Beer’s Law. Beer Beer Beer

4. Stryer Fig.3.13

5. Stryer Fig. 3.20

6. Basic Amino Acids     Stryer Fig.3.14

7. Figure 4-9 Greek lettering scheme used to identify the atoms in the glutamyl and lysyl R groups. Page 71

8. Acidic AA’s    Stryer Fig.3.16

9. Figure 4-22 Some uncommon amino acid residues that are components of certain proteins. Page 77

10. Figure 4-23 Some biologically produced derivatives of “standard” amino acids and amino acids that are not components of proteins. Page 77

11. Ionic properties of amino acids impart ionic properties to proteins • in general these are SURFACE properties (i.e. charged sidechains are on solvent-exposed outside of folded structure) • affect protein-ligand binding (e.g. DNA-binding proteins) or catalysis • average charge on protein is an important consideration in the design of a purification process

13. Table 4-1 (left) Covalent Structures and Abbreviations of the “Standard” Amino Acids of Proteins, Their Occurrence, and the pK Values of Their Ionizable Groups. Page 66

14. Table 4-1 (right)Covalent Structures and Abbreviations of the “Standard” Amino Acids of Proteins, Their Occurrence, and the pK Values of Their Ionizable Groups. Page 67

15. Figure 4-6 Titration curve of glycine. Page 70

16. This is IMPORTANT!!! • If pH = pKa, then [A-] = [HA] then [deprotonated] = [protonated] • If pH < pKa, then [A-] < [HA] then [deprotonated] < [protonated] • If pH > pKa, then [A-] > [HA] then [deprotonated] > [protonated]

18. pKa3 pKa2 pKa1

19. Using Henderson-Hasselbalch • at pH values +3 pH units from pKa the group is essentially fully deprotonated or fully protonated, so the average charge = 0 or +1. • at pH = pKa the group is 50% protonated, thus it carries an average charge = + 0.5 • H-H equation can be used to calculate the average charge on any ionizable group at any pH.

20. You should be able to determine the net charge on any amino acid at any pH. What is the net charge of glu at pH 6? Determine charge on each ionizable group:  carboxyl: -1  carboxyl: -1  amino: +1 Net charge is -1. If you’re within 1 pH unit of a pK, you must calculate the charge with the HH equation.

21. What is the net charge on his at pH 6.8?  carboxyl: -1  amino: +1 Net charge = 0.14 + Imidazole N = ? Imidazole N = 0.14+ Which form has the charge? pH = pK + log A/HA HA = + 6.8 = 6.0 + log A/HA xHA= HA = 1 = 0.14 A + HA 6.3 + 1 0.8 = log A/HA 6.3 = A/HA DOES THIS MAKE SENSE?

22. Isoelectric Point: pI pI = pH at which a molecule has 0 net charge For amino acids with no ionizable R groups, pI = pK1 + pK2 2 For all others, you must determine which 2 pKs determine the pI by inspection. What is the pI for asp?

24. Other Properties of Amino Acids • Stereochemistry (all biosynthetic proteins made up of L-isomer) • Hydropathy (partitioning between polar and nonpolar solvents as indicator of polarity) these two properties are major determinants of peptide conformation

25. Figure 4-7 Titration curves of the enzyme ribonuclease A at 25°C. Page 71

26. Bloody Fact: • If 1 mL of 10 N HCl is added to 1 liter of saline solution at pH = 7.0, the pH will decrease to roughly pH = 2. • If 1 mL of 10 N HCl is added to 1 liter of blood plasma at pH = 7.4, the pH will decrease to pH = 7.2. • Why? Blood is buffered (in this case by the H2CO3/HCO3 system).

27. Figure 4-3 Condensation of two a-amino acids to form a dipeptide. Page 68

28. Figure 4-8 The tetrapeptide Ala-Tyr-Asp-Gly. Page 71

29. Stryer Fig.3.19

30. Stryer Fig.3.20

31. Glutathione -E-C-G 2 Glut-SH Glut-S-S-Glut + 2H+ + 2e-