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Amino Acids

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Title: Amino Acids


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 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.

17
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

18
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

19
Titration of Glycine
20
Titration of Glutamic Acid
21
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

22
Titration of Lysine
23
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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