Biological Molecules - Amino Acids and Proteins

Description

  • absolute configuration at the alpha position
    • L and D amino acid configuration
    • L and D is different from R and S. L is not always S, and D is not always R.
    • If the priority of NH2 > COOH > R, then L=S and D=R. For example, L-Alanine = S-Alanine.
    • If the priority of NH2 > R > COOH, then L=R, and D=S. For example, L-Cysteine = R-Cysteine.
    • L-amino acids are the more common in nature, and are the type found in proteins. D-amino acids are less common in nature, and are never found in proteins.
  • amino acids as dipolar ions classification
    • zwitterion
    • At low pH, amino acids exist in the cationic form.
    • At high pH, amino acids exist in the anionic form.
    • At pH = pI, amino acids exist in the zwitterion form, which is overall neutral.
  • classification
    • acidic or basic
      • If the R group contains carboxylic acid, then it's an acidic amino acid. There are two acidic amino acids: aspartic acid and glutamic acid.
      • If the R group contains an amine group, then it's a basic amino acid. There are three basic amino acids: lysine, arginine, and histidine.
    • hydrophobic or hydrophilic
      • Hydrophobic: If the R group doesn't contain any of the stuff below.
      • Hydrophilic: If the R group contains acids, bases, amines or alcohols.
  • synthesis of amino acids
    • Strecker synthesis
      • starting material: R-aldehyde
      • reagents: cyanide (KCN), ammonium (NH4Cl)
      • product: amino acid with the -R group originally on the aldehyde
    • Gabriel synthesis
      • starting material: R-halide
      • reagents: 1. phthalimide, 2. NH2-NH2
      • product: amino acid with the -R group originally on the halide

Reactions

  • Sulfur linkage for cysteine and cystine
    • Cysteine = side chain with the thiol group
    • cystine = 2 cysteines forming a disulfide bond
  • peptide linkage
    • peptide bond
    • Peptide bond = amide bond.
    • The peptide bond is formed by the amine group attacking the carbonyl carbon.
  • hydrolysis
    • hydrolysis of the peptide bond
    • The peptide bond is very difficult to hydrolyze. It requires a strong base, or a biological enzyme.

General principles

  • primary structure of proteins
    • Primary structure = sequence.
    • The primary structure of proteins is read from the N-terminus to the C-terminus.
  • secondary structure of proteins
    • Secondary structure = repetitive motifs formed by backbone interactions.
    • Backbone interactions = hydrogen bonding between the NH and C=O
    • The two most common secondary structures are α helices and β pleated sheets.
    • The α helix is right-handed, with the R groups sticking outward.
    • In β sheets, R groups stick out above and below the sheet.
  • Tertiary structure
    • 3D structure of proteins
    • Caused electrostatic side chain - side chain interactions
  • Quaternary structure
    • Separate chains/subunits joining together
    • Caused by covalent disulfide bonding of cysteine side chains
  • Isoelectric point
    • pH at which the molecule is neutral
    • acidic amino acids and proteins with lots of acidic side chains have have a lower isoelectric point
    • basic amino acids and proteins with lots of basic side chains have a higher isoelectric point