Amino Acids

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CHAPTER 4

• Amino Acids
• to accompany
• Biochemistry, 2/e
• by
• Reginald Garrett and Charles Grisham

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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

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Amino AcidsBuilding Blocks of Proteins
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Amino Acids Can Join Via Peptide Bonds
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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

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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

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4.2 Acid-Base Chemistry

• Amino Acids are Weak Polyprotic Acids
• H2A H2O ? HA0 H3O
• Ka1 HA0 H3O
• __________________________
  H2A

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4.2 Acid-Base Chemistry

• The second dissociation (the amino group in the
  case of glycine)
• HA0 H2O ? A H3O
• Ka2 A H3O
• _______________________
  HA0

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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.

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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

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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

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Titration of Glycine
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Titration of Glutamic Acid
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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

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Titration of Lysine
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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

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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

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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

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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

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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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