Chapter 4. Amino acids - - / 2007-08-31آ  Chapter 4. Amino acids • The amino acids of...

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Transcript of Chapter 4. Amino acids - - / 2007-08-31آ  Chapter 4. Amino acids • The amino acids of...

  • Chapter 4. Amino acids

    • The amino acids of proteins • Optical activity • “Nonstandard” amino acids

  • Structure of an α-Amino Acid

  • Zwitterion

  • 3-D structure of amino acids

  • Non-polar amino acids

    • Center of globular proteins • Transmembrane domains • Non-polar (hydrophobic) interactions

  • Uncharged polar amino acids

    • Stabilizing protein structure • Protein-protein interactions • Enzyme substrate interactions

    Participate in hydrogen bonding

  • 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

  • Proline

  • Hydroxyl-containing amino acids

  • Condensation of two amino acids

    Peptide bond

    Dipeptide

    Hydrolysis Condensation

  • “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

  • Disulfide-Bond Formation

    Cystine

  • Ionization of amino acids

  • 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

  • Titration of alanine

  • Net charge = +1 Net charge = 0 Net charge = -1

    pI = pK1 + pK2 2

    = 2

    2.3 + 9.7 = 6.0

  • pI = pK1 + pKR 2

    = 2

    2.0 + 3.9 = 3.0

  • Nomenclature

  • Nomenclature

    (N-terminus) (C-terminus)

    alanyltyrosylaspatylglycine AYDG

    Amino terminus Carboxyl terminus

  • Enantiomers

  • Same Configurations

  • The Fischer Convention

  • “CORN crib” mnemonic of L-amino acids

  • Diastereomers

  • The Cahn-Ingold-Prelog System (The RS System)

    All the L-amino acids from proteins are (S)-amino acids except L-cysteine

  • Prochiral center

  • Prochiral center

    re face si face

  • 21st and 22nd amino acids

    (UGA codon) (UAG codon)

  • Modified amino acids in proteins

  • Biologically active amino acids

  • D-Amino acids

    • Bacterial cell wall • Peptide antibiotics

  • Biologically important peptides