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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 Da
(Saturday, Oct. 28th from 8am-1pm )
Also at the BBQ, sign up to buy a WWU Pre-Med
Club T-shirt!!!
you did not receive an Ocotber Events Calender, you can
ick one up at the Chemistry Office.

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. Stryer Fig.3.14
β
γ
δ
ε
Basic
Amino
Acids

7. Figure 4-9 Greek lettering
scheme used to identify the
atoms in the glutamyl and lysyl R
groups.
Page71

8. α
β
γ
Acidic
AA’s

9. Figure 4-22 Some
uncommon amino acid residues
that are components of certain
proteins.
Page77

10. Figure 4-23 Some biologically produced
derivatives of “standard” amino acids and
amino acids that are not components of
proteins.
Page77

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.
Page66

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.
Page67

15. Figure 4-6 Titration curve of
glycine.
Page70

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]

17. pK assignments? HCHO
Stryer Fig. 3.6

18. pKa1
pKa2
pKa3

19. • 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.
Using Henderson-Hasselbalch

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:
α carboxyl: -1
γ carboxyl: -1
α 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?
α carboxyl: -1
α amino: +1
Imidazole N = ?
pH = pK + log A/HA
6.8 = 6.0 + log A/HA
0.8 = log A/HA
6.3 = A/HA
Which form has the charge?
HA = +
xHA= HA = 1 = 0.14
A + HA 6.3 + 1
Imidazole N = 0.14+
Net charge = 0.14 +
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?

23. Steps for determining pI.
Identify all ionizable groups and assign pK values
Set up a table and estimate the charges on each group at various pHs
pH αCOOH pK =2 βCOOH pK=4 α NH3
+
pK=10 Net charge
0 0 0 +1 +1
3 ~-0.9 ~-0.1* +1 ~0
6 -1 -1 +1 -1
10 -1 -1 +0.5 -1.5
13 -1 -1 0 -2
At ~pH 1 the α COOH starts to ionize. At ~pH 2 the β COOH starts to ionize.
The α-amino group won’t ionize until aroun pH 9.
The isoelectric point will be the average of the pK values surrounding the
pH where we estimate the isoelectric point is 0. Thus, for asp, the pI will be
the average of pK1+pK2.
Looking up these pK values we find in Segel that pK1= 2.01 and pK2= 3.86.
Therefore the pI=2.93.

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.
Page71

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
α-amino acids to form a
dipeptide.
Page68

28. Figure 4-8 The tetrapeptide Ala-
Tyr-Asp-Gly.
Page71

29. Stryer Fig.3.19

30. Stryer Fig.3.20

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