Garrett2e Chapter04

Biochemistry 2/e - Garrett & 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, 6277
Sea Harbor Drive, Orlando, Florida 32887-6777
Copyright © 1999 by Harcourt Brace & Company
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

Amino Acids
Building Blocks of Proteins

Amino Acids Can Join Via Peptide Bonds

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





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



4.2 Acid-Base Chemistry

Amino Acids are Weak Polyprotic Acids
• H2A+ + H2O  HA0 + H3O+
• Ka1 = [ HA0 ] [ H3O+ ]

__________________________
[H2A+ ]

4.2 Acid-Base Chemistry

The second dissociation (the amino group
in the case of glycine):
• HA0 + H2O  A¯ + H3O+
• Ka2 = [ A¯ ] [ H3O+ ]
_______________________
[ HA0 ]


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.


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

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

Titration of Glycine

Titration of Glutamic Acid

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

Titration of Lysine

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

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




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




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




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

Copyright © 1999 by Harcourt Brace & Company

Copyright © 1999 by Harcourt Brace & Company

Amino Acids Can Join Via Peptide Bonds

Copyright © 1999 by Harcourt Brace & Company

20 Common Amino Acids

Copyright © 1999 by Harcourt Brace & Company

Copyright © 1999 by Harcourt Brace & Company

Copyright © 1999 by Harcourt Brace & Company

Copyright © 1999 by Harcourt Brace & Company

Copyright © 1999 by Harcourt Brace & Company

Uncommon Amino Acids

• Hydroxylysine, hydroxyproline - collagen

Copyright © 1999 by Harcourt Brace & Company

Copyright © 1999 by Harcourt Brace & Company

Copyright © 1999 by Harcourt Brace & Company

4.2 Acid-Base Chemistry

• H2A+ + H2O  HA0 + H3O+

• Ka1 = [ HA0 ] [ H3O+ ]

Copyright © 1999 by Harcourt Brace & Company

4.2 Acid-Base Chemistry

• HA0 + H2O  A¯ + H3O+

Copyright © 1999 by Harcourt Brace & Company

Copyright © 1999 by Harcourt Brace & Company

pKa Values of the Amino Acids

Copyright © 1999 by Harcourt Brace & Company

pKa Values of the Amino Acids

pKa Values of the Amino Acids

• Lysine, Lys, K: pKa = 10.5

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Copyright © 1999 by Harcourt Brace & Company

Titration of Glutamic Acid

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Another Sample Calculation

• pH = 10.5 + log10 [3]

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Reactions of Amino Acids

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Stereochemistry of Amino Acids

• All but glycine are chiral

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Copyright © 1999 by Harcourt Brace & Company

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Separation of Amino Acids

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Copyright © 1999 by Harcourt Brace & Company

Copyright © 1999 by Harcourt Brace & Company

Copyright © 1999 by Harcourt Brace & Company

Copyright © 1999 by Harcourt Brace & Company

Copyright © 1999 by Harcourt Brace & Company

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