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Chapter 4. Amino acids
• The amino acids of proteins• Optical activity• “Nonstandard” amino acids
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Structure of an α-Amino Acid
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Zwitterion
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3-D structure of amino acids
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Non-polar amino acids
• Center of globular proteins• Transmembrane domains• Non-polar (hydrophobic) interactions
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Uncharged polar amino acids
• Stabilizing protein structure• Protein-protein interactions• Enzyme substrate interactions
Participate in hydrogen bonding
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Charged amino acids• Present on the surface of proteins• Ionic interactions
– other protein– membrane
• Histidine - pKR is 6.04– 10% is positively charged at pH 7.0– pKa can be affected by the local environment– Can donate or accept protons during
catalysis
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Proline
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Hydroxyl-containing amino acids
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Condensation of two amino acids
Peptide bond
Dipeptide
Hydrolysis Condensation
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“Peptides”
• Dipeptides, tripeptides, oligopeptides and polypeptides
• Polypeptide- Linear polymers • Potential diversity = 20n
• Proteins – One or more polypeptide chains• Estimation of molecular mass of proteins:
Average mass of amino acid (110D) x Number of amino acids
500 aa protein x 110 ≈ 55,000 Daltons or 55 kD
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Disulfide-Bond Formation
Cystine
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Ionization of amino acids
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Isoelectric point (pI)The pH at which a molecule carries no net charge
pI = pK1 + pK2
2
• Amino acids with acidic side chains
pI = pK1 + pKR
2
• Amino acids with uncharged side chains
• Amino acids with basic side chains
pI = pK2 + pKR
2
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Titration of alanine
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Net charge = +1 Net charge = 0 Net charge = -1
pI = pK1 + pK2
2=
22.3 + 9.7
= 6.0
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pI = pK1 + pKR
2=
22.0 + 3.9
= 3.0
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Nomenclature
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Nomenclature
(N-terminus) (C-terminus)
alanyltyrosylaspatylglycineAYDG
Amino terminus Carboxyl terminus
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Enantiomers
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Same Configurations
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The Fischer Convention
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“CORN crib” mnemonic of L-amino acids
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Diastereomers
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The Cahn-Ingold-Prelog System(The RS System)
All the L-amino acids from proteins are (S)-amino acids except L-cysteine
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Prochiral center
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Prochiral center
re face si face
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21st and 22nd amino acids
(UGA codon) (UAG codon)
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Modified amino acids in proteins
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Biologically active amino acids
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D-Amino acids
• Bacterial cell wall• Peptide antibiotics
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Biologically important peptides