1. Reginald Garrett and Charles Grisham
CHAPTER 4
Amino Acids
to accompany
Biochemistry, 2/e by
Reginald Garrett and Charles Grisham
All rights reserved. Requests for permission to make copies of any part of the work should be mailed to: Permissions Department, Harcourt Brace & Company, Sea Harbor Drive, Orlando, Florida

2. Outline 4.1: Amino Acids: Building Blocks of Proteins
4.2: Acid-Base Chemistry of Amino Acids
4.3: Reactions of Amino Acids
4.4: Optical Activity and Stereochemistry of Amino Acids
4.5: Spectroscopic Properties of Amino Acids
4.6: Separation and Analysis of a.a. Mixtures

3. Amino Acids Building Blocks of Proteins

4. Amino Acids Can Join Via Peptide Bonds

5. 20 Common Amino Acids
You should know names, structures, pKa values, 3-letter and 1-letter codes
Non-polar amino acids
Polar, uncharged amino acids
Acidic amino acids
Basic amino acids

10. We'll see some of these in later chapters
Uncommon Amino Acids
We'll see some of these in later chapters
Hydroxylysine, hydroxyproline - collagen
Carboxyglutamate - blood-clotting proteins
Pyroglutamate - bacteriorhodopsin
Phosphorylated amino acids - signaling device

13. Amino Acids are Weak Polyprotic Acids
4.2 Acid-Base Chemistry
Amino Acids are Weak Polyprotic Acids
H2A+ + H2O  HA0 + H3O+
Ka1 = [ HA0 ] [ H3O+ ]
__________________________ [H2A+ ]

14. The second dissociation (the amino group in the case of glycine):
4.2 Acid-Base Chemistry
The second dissociation (the amino group in the case of glycine):
HA0 + H2O  A¯ + H3O+
Ka2 = [ A¯ ] [ H3O+ ]
_______________________ [ HA0 ]

16. pKa Values of the Amino Acids
You should know these numbers and know what they mean!
Alpha carboxyl group - pKa = 2
Alpha amino group - pKa = 9
These numbers are approximate, but entirely suitable for our purposes.

17. pKa Values of the Amino Acids
You should know these numbers and know what they mean
Arginine, Arg, R: pKa(guanidino group) = 12.5
Aspartic Acid, Asp, D: pKa = 3.9
Cysteine, Cys, C: pKa = 8.3
Glutamic Acid, Glu, E: pKa = 4.3
Histidine, His, H: pKa = 6.0

18. pKa Values of the Amino Acids
You should know these numbers and know what they mean
Lysine, Lys, K: pKa = 10.5
Serine, Ser, S: pKa = 13
Threonine, Thr, T: pKa = 13
Tyrosine, Tyr, Y: pKa = 10.1

19. Titration of Glycine

20. Titration of Glutamic Acid

21. A Sample Calculation
What is the pH of a glutamic acid solution if the alpha carboxyl is 1/4 dissociated?
pH = 2 + log10 [1]
¯¯¯¯¯¯¯
[3]
pH = 2 + (-0.477)
pH = 1.523

22. Titration of Lysine

23. Another Sample Calculation
What is the pH of a lysine solution if the side chain amino group is 3/4 dissociated?
pH = log10 [3]
¯¯ ¯¯¯¯¯
[1]
pH = (0.477)
pH = = 11.0

24. Reactions of Amino Acids
Carboxyl groups form amides & esters
Amino groups form Schiff bases and amides
Side chains show unique reactivities
Cys residues can form disulfides and can be easily alkylated
Few reactions are specific to a single kind of side chain

28. Stereochemistry of Amino Acids
All but glycine are chiral
L-amino acids predominate in nature
D,L-nomenclature is based on D- and L-glyceraldehyde
R,S-nomenclature system is superior, since amino acids like isoleucine and threonine (with two chiral centers) can be named unambiguously

33. Spectroscopic Properties
All amino acids absorb in infrared region
Only Phe, Tyr, and Trp absorb UV
Absorbance at 280 nm is a good diagnostic device for amino acids
NMR spectra are characteristic of each residue in a protein, and high resolution NMR measurements can be used to elucidate three-dimensional structures of proteins

37. Separation of Amino Acids
Mikhail Tswett, a Russian botanist, first separated colorful plant pigments by ‘chromatography’
Many chromatographic methods exist for separation of amino acid mixtures
Ion exchange chromatography
High-performance liquid chromatography