CHAPTER 4OutlineAmino Acids Building Blocks of ProteinsAmino Acids Can Join Via Peptide Bonds20 Common Amino AcidsSlide 6Slide 7Slide 8Slide 9Uncommon Amino AcidsSlide 11Slide 124.2 Acid-Base ChemistrySlide 14Slide 15pKa Values of the Amino AcidsSlide 17Slide 18Titration of GlycineTitration of Glutamic AcidA Sample CalculationTitration of LysineAnother Sample CalculationReactions of Amino AcidsSlide 25Slide 26Slide 27Stereochemistry of Amino AcidsSlide 29Slide 30Slide 31Slide 32Spectroscopic PropertiesSlide 34Slide 35Slide 36Separation of Amino AcidsSlide 38Slide 39Slide 40Slide 41Slide 42Biochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyCHAPTER 4Amino Acidsto accompanyBiochemistry, 2/ebyReginald Garrett and Charles GrishamAll 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 32887-6777Biochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyOutline•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. MixturesBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyAmino AcidsBuilding Blocks of ProteinsBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyAmino Acids Can Join Via Peptide BondsBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & Company20 Common Amino AcidsYou 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 acidsBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyUncommon Amino AcidsWe'll see some of these in later chapters•Hydroxylysine, hydroxyproline - collagen•Carboxyglutamate - blood-clotting proteins•Pyroglutamate - bacteriorhodopsin•Phosphorylated amino acids - signaling deviceBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & Company4.2 Acid-Base ChemistryAmino Acids are Weak Polyprotic Acids•H2A+ + H2O  HA0 + H3O+•Ka1 = [ HA0 ] [ H3O+ ] __________________________ [H2A+ ]Biochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & Company4.2 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 & GrishamCopyright © 1999 by Harcourt Brace & CompanyBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanypKa Values of the Amino AcidsYou 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.Biochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanypKa 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 = 6.0Biochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanypKa Values of the Amino AcidsYou 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 = 10.1Biochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyTitration of GlycineBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyTitration of Glutamic AcidBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyA Sample CalculationWhat 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 = 1.523Biochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyTitration of LysineBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyAnother Sample CalculationWhat 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 = 11.0Biochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyReactions 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 chainBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyStereochemistry 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 unambiguouslyBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanyBiochemistry 2/e - Garrett & GrishamCopyright © 1999 by Harcourt Brace & CompanySpectroscopic Properties•All amino acids absorb in infrared region•Only Phe, Tyr, and