Structure and Function of Proteins

• Amino acids


  The building blocks of proteins and there are 20 naturally occurring amino acids
• Amino acids


  • They all share the same structure but have different R groups, which give different properties: negatively charged (acidic), positively charged (basic), polar, but uncharged (hydrophilic) and non-polar (hydrophobic)
  • The two arrangements of 4 groups around tetrahedral Cα give L (levulo) or D (dextro) configurations but usually only L amino acids are found in proteins
• Proteins are formed


  Linking amino acids through peptide bonds
• Peptide bonds


  • Partial double bond character means bond is planar and rigid
  • Oxygen is trans to hydrogen attached to nitrogen
  • No freedom of rotation around the peptide bond
• Peptide


  Chain of amino acids without structure
• Protein


  Polypeptide chain with structure
• Residue


  An amino acid in a peptide chain
• Protein structure


  • Primary structure — sequence of amino acid residues in a polypeptide chain N terminus to C terminus)
  • Secondary structure — local structures of the polypeptide chain, e.g. a α helix, β sheet (hydrogen bonds)
  • Tertiary structure — occurs due to the bending and twisting of the secondary structure into a more compact shape (disulphide bonds, ionic bonds, hydrogen bonds)
  • Quaternary structure — the combination of a number or different polypeptide chains and/or associated non-protein groups
• Amino acid sequence (sequence of the gene) determines secondary, tertiary and quaternary structure
• α helix


  • Right handed: 3.6 amino acid residues per turn
  • Formed by the backbone of the protein chain, side-chains extend outwards
  • Formed and stabilised by hydrogen bonds: the oxygen of the CO group is hydrogen bonded to the hydrogen of the NH group that is situated 4 residues further towards the C terminus of the sequence
• β sheet


  • Sheet-like structure
  • Also formed by the backbone of the protein chain, with side-chains extend above and below the sheet
  • Formed and stabilised by hydrogen bonds: oxygen of the CO group is hydrogen bonded to the hydrogen of NH group in different polypeptide chains or in the same chain further away
  • Adjacent chains can run in the same direction (parallel β sheet) or in opposite direction (antiparallel β sheet)
• Globular proteins


  • myoglobin, haemoglobin, cytochrome c, insulin, most enzymes (e.g. Lysozyme)
• Fibrous proteins


  • collagen, elastin, α-keratin
• Proteins that form filaments or tubes

  • actin, tubulin
• Quaternary structure


  • The combination of a number or different polypeptide chains and/or associated non-protein groups (e.g. haemoglobin has 4 chains: 2 α and 2 β chains, plus iron-containing haem group)
• Forces/bonds important in determining protein tertiary and quaternary structure

  • Covalent bonds (disulfide bonds): strong
  • Ionic bonds: weak in water
  • Hydrogen bonds: weak
  • Van der Waals attractions: very weak
  • Hydrophobic interactions
• Loss of protein folding is known as denaturation and is caused by heat, acids and alkalis, organic solvent, mechanical force etc.
• Mutation of proteins is the cause of inherited diseases such as cystic fibrosis (chloride channel), phenylketonuria (phenylalanine hydroxylase) and sickle cell anaemia (beta globin of haemoglobin — glu to val mutation)