Biochemistry 2/e - Garrett & Grisham
CHAPTER 4
Amino Acids
to accompany
Biochemistry, 2/e
by
Reginald Garrett and Charles Grisham
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Biochemistry 2/e - Garrett & Grisham
Outline
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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
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Biochemistry 2/e - Garrett & Grisham
Amino Acids
Building Blocks of Proteins
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Biochemistry 2/e - Garrett & Grisham
Amino Acids Can Join Via Peptide Bonds
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Biochemistry 2/e - Garrett & Grisham
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
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
Uncommon Amino Acids
We'll see some of these in later chapters
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Hydroxylysine, hydroxyproline - collagen
Carboxyglutamate - blood-clotting proteins
Pyroglutamate - bacteriorhodopsin
Phosphorylated amino acids - signaling
device
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
4.2 Acid-Base Chemistry
Amino Acids are Weak Polyprotic Acids
• H2A+ + H2O  HA0 + H3O+
• Ka1 = [ HA0 ] [ H3O+ ]
__________________________
[H2A+ ]
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Biochemistry 2/e - Garrett & Grisham
4.2 Acid-Base Chemistry
The second dissociation (the amino group
in the case of glycine):
• HA0 + H2O  A¯ + H3O+
• Ka2 = [ A¯ ] [ H3O+ ]
_______________________
[ HA0 ]
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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.
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Biochemistry 2/e - Garrett & Grisham
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
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Biochemistry 2/e - Garrett & Grisham
pKa Values of the Amino Acids
You should know these numbers and
know what they mean
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Lysine, Lys, K: pKa = 10.5
Serine, Ser, S: pKa = 13
Threonine, Thr, T: pKa = 13
Tyrosine, Tyr, Y: pKa = 10.1
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Titration of Glycine
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Biochemistry 2/e - Garrett & Grisham
Titration of Glutamic Acid
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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
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Titration of Lysine
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Another Sample Calculation
What is the pH of a lysine solution if the side
chain amino group is 3/4 dissociated?
• pH = 10.5 + log10 [3]
¯¯
¯¯¯¯¯
[1]
• pH = 10.5 + (0.477)
• pH = 10.977 = 11.0
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Biochemistry 2/e - Garrett & Grisham
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
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Stereochemistry of Amino Acids
• All but glycine are chiral
• L-amino acids predominate in nature
• D,L-nomenclature is based on D- and Lglyceraldehyde
• R,S-nomenclature system is superior,
since amino acids like isoleucine and
threonine (with two chiral centers) can
be named unambiguously
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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
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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
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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Biochemistry 2/e - Garrett & Grisham
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