Biol/Chem 5310

Lecture: 5

September 5, 2002

Amino Acids

Proteins were the first studied macromolecules. The roles of proteins include:

  • enzymes
  • binding/transport
  • structural
  • mechanical
  • gene expression/protein synthesis
  • hormones
  • antibodies

    • Proteins consist of one or more polypeptides.

  • Polypeptides are linear polymers of amino acids.
  • 20 standard amino acids in proteins
  • General structure of an amino acid, zwitterionic form
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  • Peptide bond: amide linkage of amino acids, head to tail, called a peptide bond
  • Note reduction in charge when peptide bond forms.
  • Amino acids are always charged at pH 7
  • Polypeptides are reduced to one amino group and one carboxyl group per chain, plus the side chains of each amino acid residue.
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    Classification of amino acids

    Structures

  • Nonpolar side chains
  • Glycine, Gly, G
  • smallest, no side chain, only nonchiral aa, flexible in protein chain
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  • Alanine, Ala, A
  • side chain aliphatic (methyl), small, common aa
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  • Valine, Val, V
  • side chain aliphatic (isopropyl), somewhat hydrophobic, branched at b-carbon
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  • Leucine, Leu, L
  • side chain aliphatic, hydrophobic, common, branched at g-carbon
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  • Isoleucine, Ile, I
  • isomer of Leu, side chain aliphatic, hydrophobic, branched at b-carbon
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  • Methionine, Met, M
  • side chain thioether, hydrophobic, flexible like straight chain aliphatic, first amino acid in synthesized protein chain
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  • Proline, Pro, P
  • an imino acid, side chain is a ring that forms a secondary amine, properties in proteins dominated by the restrictions imposed by the ring
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  • Phenylalanine, Phe, F
  • side chain aromatic (phenyl), hydrophobic, absorbs uv
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  • Typtophan, Trp, W
  • side chain aromatic (indole), hydrophobic, 1 H-bond donor (N-H), absorbs uv
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  • Polar uncharged side chains
  • Tyrosine, Tyr, Y
  • side chain aromatic (phenolic), hydrophobic and polar, OH is H-bond donor and acceptor, absorbs uv, side chain can ionize, pKa = 10.5
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  • Cysteine, Cys, C
  • side chain somewhat hydrophobic (sulfhydryl), weak H-bonds, usually as acceptor, -SH can ionize, pKa = 8.4, found in enzymes at active sites, 2 SH groups can form a disulfide bond
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  • Serine, Ser, S
  • side chain alcohol, small, very polar, H-bond donor and acceptor, structural analog of Cys, but does not ionize, sometimes found in enzymes at active site
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  • Threonine, Thr, T
  • side chain alcohol, somewhat polar, branched at b-carbon, isosteric with valine, like Ser H-bond donor and acceptor but not as likely to be at active site
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  • Asparagine, Asn, N
  • side chain amide, very polar, extensive H-bonding, does not ionize, but can deamidate in acid (Asx)
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  • Glutamine, Gln, Q
  • similar to Asn, side chain amide, very polar, extensive H-bonding, does not ionize, but can deamidate in acid (Glx)
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  • Charged polar side chains
  • Aspartic acid, Asp, D (aspartate)
  • side chain carboxyl, small, negative when ionized (pH 7), pKa = 3.9, isosteric with Asn
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  • Glutamic acid, Glu, E (glutamate)
  • side chain carboxyl, similar to Asp, pKa = 4.1, isosteric with Gln
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  • Lysine, Lys, K
  • side chain, long flexible aliphatic, e-amino group, positive charge at pH 7, pKa = 10.5
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  • Arginine, Arg, R
  • side chain contains guanidinium group, positive charge at pH 7, pKa = 12.5, multiple H-bond donors
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  • Histidine, His, H
  • side chain imidazole, weak base, pKa = 6.0, partially ionized at pH 7, positive charge when ionized, commonly found in enzymes
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  • QUIZ of properties
  • Quiz of structure
  • Ionization of amino acids
  • Side chain does not ionize
  • charge +1, pKa = 2-3, charge 0, pKa = 9-10, charge -1
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  • pI= pH at which net charge is zero, called isoelectric point
  • here it is the average of pKa1 and pKa2
  • Side chain ionizes, e.g. Asp
  • charge +1, pKa1=2.0, charge 0, pKa2=3.9, charge -1, pKa3=9.9, charge -2
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  • The positive species (A) must exactly cancel the two negative species (C and D).
  • If A is present, the pH must be low, near the pKa1.
  • In this case, D will be extremely low. About 10 to the 8th less than C
  • What is pI?Average of pKa1 and pKa2.
  • When the pH equals the pI, the net charge of the molecule is zero.
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    • Stereochemistry of amino acids

  • The a-carbon is a chiral center (except Gly)
  • Gly has 2-hydrogens bonded to its a-carbon, it is superimposable on its mirror image.
  • All other amino acids have 4 different substituents
  • The 20 standard amino acids are L-form, enantiomers are called D-form (Fischer convention)
  • Ile and Thr have a 2nd chiral center

    • RS system (Cahn-Ingold-Prelog)

  • Rank the 4 substituents of a chiral center
  • -SH> -OH> -NH2> -COOH> -CHO> -CH2OH> -C6H5> -CH3> H
  • Orient the lowest priority group away
  • If decreasing priority is clockwise: R
  • If decreasing priority is counterclockwise: S
  • All L-amino acids are S, except Cys

    Try a quiz in Chapter 4.

    Comments/questions: svik@mail.smu.edu

    Copyright 2002, Steven B. Vik, Southern Methodist University