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, 6277 Sea Harbor Drive, Orlando, Florida 32887-6777

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

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

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+ ]

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 ]

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.

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

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

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