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Amino Acids: Building Blocks and Chemistry of Proteins

This chapter provides an overview of amino acids, including their structures, acid-base chemistry, reactions, spectroscopic properties, and separation techniques. Essential information on 20 common amino acids and their pKa values is also covered.

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Amino Acids: Building Blocks and Chemistry of Proteins

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  1. 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

  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 AcidsBuilding 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 acid • Polar, uncharged amino acids • Acidic amino acids • Basic amino acids

  6. 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

  7. 4.2 Acid-Base Chemistry Amino Acids are Weak Polyprotic Acids • H2A+ + H2O  HA0 + H3O+ • Ka1 = [ HA0 ] [ H3O+ ] __________________________ [H2A+ ]

  8. 4.2 Acid-Base Chemistry The second dissociation (the amino group in the case of glycine): • HA0 + H2O  A¯+ H3O+ • Ka2 = [ A¯ ] [ H3O+ ] _______________________ [ HA0 ]

  9. 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.

  10. 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

  11. 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

  12. Titration of Glycine

  13. Titration of Glutamic Acid

  14. 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

  15. Titration of Lysine

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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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