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Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
CHAPTER 4
Amino Acidsto accompany
Biochemistry, 2/eby
Reginald Garrett and Charles Grisham
All rights reserved. Requests for permission to make copies of any part of the workshould be mailed to: Permissions Department, Harcourt Brace & Company, 6277Sea Harbor Drive, Orlando, Florida 32887-6777
Biochemistry 2/e - Garrett & Grisham
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
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
ΑµινοξέαΔοµικές µονάδες των πρωτεϊνών
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Amino Acids Can Join Via Peptide Bonds
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
20 Αµινοξέα
• Μη-πολικά• Πολικά, µη-φορτισµένα• Όξινα• Βασικά
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Uncommon Amino AcidsWe'll see some of these in later chapters
• Hydroxylysine, hydroxyproline - collagen• Carboxyglutamate - blood-clotting proteins• Pyroglutamate - bacteriorhodopsin• Phosphorylated amino acids - signaling
device
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
4.2 Acid-Base Chemistry
Amino Acids are Weak Polyprotic Acids
• H2A+ + H2O → HA0 + H3O+
• Ka1 = [ HA0 ] [ H3O+ ] __________________________
[H2A+ ]
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
4.2 Acid-Base ChemistryThe second dissociation (the amino group
in the case of glycine):
• HA0 + H2O → A¯ + H3O+
• Ka2 = [ A¯ ] [ H3O+ ] _______________________
[ HA0 ]
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
pKa Values of the Amino Acids
You should know these numbers andknow what they mean!
• Alpha carboxyl group - pKa = 2• Alpha amino group - pKa = 9• These numbers are approximate, but
entirely suitable for our purposes.
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
pKa Values of the Amino AcidsYou 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
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
pKa Values of the Amino Acids
You should know these numbers andknow 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
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Titration of Glycine
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Titration of Glutamic Acid
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
A Sample Calculation
What is the pH of a glutamic acid solutionif the alpha carboxyl is 1/4 dissociated?
• pH = 2 + log10 [1]
¯¯¯¯¯¯¯ [3]
• pH = 2 + (-0.477)• pH = 1.523
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Titration of Lysine
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Another Sample Calculation
What is the pH of a lysine solution if the sidechain amino group is 3/4 dissociated?
• pH = 10.5 + log10 [3]
¯¯ ¯¯¯¯¯ [1]
• pH = 10.5 + (0.477)• pH = 10.977 = 11.0
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
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 canbe easily alkylated
– Few reactions are specific to a single kindof side chain
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
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 andthreonine (with two chiral centers) canbe named unambiguously
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Spectroscopic Properties
• All amino acids absorb in infraredregion
• 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 resolutionNMR measurements can be used toelucidate three-dimensional structuresof proteins
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Separation of Amino Acids
• Mikhail Tswett, a Russian botanist, firstseparated colorful plant pigments by‘chromatography’
• Many chromatographic methods existfor separation of amino acid mixtures– Ion exchange chromatography– High-performance liquid chromatography
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company
Biochemistry 2/e - Garrett & Grisham
Copyright © 1999 by Harcourt Brace & Company