Proteins

• Chiral carbon atom


  • 4 different groups are attached to the central carbon atom, resulting in 2 optical isomers
• Amino acid side chains


  Vary in properties
• Only the L-isomers are incorporated into proteins
• Amino acids


  Zwitterions, pH dependent
• Physiological pH (≈7)

  Amino and carboxyl groups are ionised
• pKa


  pH at which an ionisable group is one-half charged and one-half neutral
• Ethanoic acid, CH3COOH


  • pKa of 4.8
• At lower pH


  More of the protonated form, CH3COOH
• At higher pH


  More of the ionised form, CH3COO-
• Histidine


  Special amino acid, side chain has a pKa around physiological pH
• The pKa of histidine's side chain is approximately 6.8
• Proteins are synthesised as long unbranched chains of amino acids
• Proteins carry out many diverse and essential functions in living organisms
• Protein functions

  • Enzymic
  • Transport
  • Structural
  • Movement
  • Signalling
  • Defence
  • Storage
• Primary structure

  The sequence in which the amino acids are arranged
• How can the R group affect the amino acid?

  • size and shape
  • charge
  • hydrophilicity / hydrophobicity
• What is the only amino acid with no optical isomerism?

  Glycine
• what is the difference between L and D isomerism?

  L isomers have the hydroxy group attached to the left side of the asymmetric carbon furthest from the carbonyl, while D isomers have the hydroxy group on the right sid
• amino acids are zwitterions
• Primary structure of a protein

  The sequence in which the amino acids are arranged
• Peptide bond formation

  1. Carboxyl group of first amino acid reacts with amino group of second

  2. Produces water

  3. Condensation reaction
• Polypeptides

  • Synthesised as long unbranched chains of amino acids
  • Amino acid sequence always written N to C direction
• Peptide bond has partial double bond character, so no free rotation, therefore rigid and planar
• Phi (φ) angle

  Rotation around N-C bond
• Psi (ψ) angle

  Rotation around C-C bond
• Most combinations of psi and phi angles are not allowed due to steric collisions
• Protein conformation is determined by psi and phi angles for each amino acid
• Protein folding is not a random process


  Trying every conformation would take 1.6 x 10^27 years
• Protein folding

  • Main driving force is to attain energetically stable structure
  • For water soluble proteins, need to pack hydrophobic side chains into interior to form hydrophobic core
  • Polypeptide chain is hydrophilic, so protein must adopt structures to neutralise polar C=O and N-H groups via hydrogen bonding
• Two main types of protein secondary structure: alpha helix and beta sheet
• Proteins form regular, stabilised secondary structures which are heavily hydrogen bonded