CHMI 2227E Biochemistry I

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CHMI 2227EBiochemistry I

• Amino acids
• Structure
• General chemical properties

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Proteins Building blocks of life!

• Proteins are extremely complex molecules
• Proteins are involved in a vast variety of
  biological structures and phenomena

• Silk
• Spider web
• Horns
• Antibiotics
• Toxins

• Enzymes
• Antibodies
• Hormones
• Membrane transporters
• Haemoglobin

• The building block for all proteins are amino
  acids.

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Amino acids

• An amino acid is a molecule in which a carbon
  atom (Ca) is bonded simultaneously to a
  carboxylic acid (COOH) and an amine group (NH2)
• Hundreds of amino acids exist in nature
• However, only 20 amino acids are used by the cell
  to make proteins.

• Each amino acid differs from all the others by
  the nature of the R group.
• Each R group differs from the others in several
  ways
• Size
• Charge
• Water solubility

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General properties of amino acids.

• Note that the Ca is bonded to 4 different groups
  and is chiral
• Two stereoisomers are distinguished
• L-amino acids
• D-amino acids
• Only the L-amino acids are found in proteins.

• L amino group is on the left in the Fisher
  representation.
• L and D arbitrary. Has nothing to do with the
  direction of rotation of polarised light by the
  amino acid.

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General properties of amino acids.

• Every amino acids has at least two chemical
  groups that can be ionized
• Carboxylic Acid (COOH)
• Amino (NH2)

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Amino acid titration1. simplest scenario

• pI isoelectric point pH where 100 zwitterion
• pI pKa1 pKa2
• 2
• The fraction of COOH or NH2 group that is charged
  at any given pH can be determined with the
  Henderson-Hasselbach equation
• pH pKa log A-
• HA

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The twenty amino acids
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Structure of the 20 amino acids1. Hydrophobic
amino acids

• All these amino acids are NOT soluble in water.
• Note glycine is NOT optically active. Why?

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Structure of the 20 amino acids1. Hydrophobic
amino acids

• Proline is the only cyclic amino acid

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Structure of the 20 amino acids2. Aromatic amino
acids
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Structure of the 20 amino acids2. Aromatic amino
acids

• Tyr, Trp and Phe are very useful
• Their aromatic ring absorb UV light at 260-280
  nm.
• Form the basis of protein detection at 280 nm.

Absorbance Absorbance
?max (nm) Molar Absorbance (M-1 cm-1)
Phenylalanine 257.4 197
Tyrosine 274.6 1420
Tryptophan 279.8 5690
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Structure of the 20 amino acids3. polar,
uncharged amino acids
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Structure of the 20 amino acidsCysteine and
cystine
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Structure of the 20 amino acids Tyr, Ser, Thr
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Structure of the 20 amino acids4. Negatively
charged amino acids
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Structure of the 20 amino acids4. Negatively
charged amino acids
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Structure of the 20 amino acids5. Positively
charged amino acids
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Structure of the 20 amino acids5. Positively
charged amino acids His
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Structure of the 20 amino acidspKa values of
amino acids
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Analysis of amino acids1. Ion exchange
chromatography

• Different types of ion exchange resins exist
• Cation exchange negatively charged/separation of
  cations
• Anion exchange positively changed/separation of
  anions.
• Obviously, the type of resin to be used will
  depend on the charge of the amino acid on
  interest, itself dependent on the pH of the
  solution.

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Analysis of amino acids2. Detection of amino
acids ninhydrin reagent

• While Trp, Phe and Tyr can be detected by their
  A260-280nm, the other amino acids cannot
• Ninhydrin reacts with the amine group of amino
  acids, generating a purple product (yellow in the
  case of Pro).
• The ninhydrin reaction allows one to detect and
  quantify (A570nm) the amino acids contained in
  the fractions of the IEX column.