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Polymer Breakdown
  • Polymers formed by linking together monomer subunits
    • Carbohydrates
      • Monosaccharides (simple sugars)
    • Lipid
      • Fatty acids, some lipids are not polymers, eg waxes
    • Protein
      • amino acids
    • Nucleic acids
      • nucleotides: bases GAT(U)C
  • A large number of polymers can be made from a small set of monomers
  • Synthesis is the formation of a new covalent bond between monomer units by the loss of a water molecule
    • Known as condensation polymerisation
  • Breakdown involves the addition of water to split a covalent bond
    • Eg: digestion to extract nutrients
  • Polymers and monomers are often very stable molecules and require a lot of energy to synthesise or breakdown
    • Thus a catalyst is used
    • Enzymes (which are proteins) are used as this catalyst


  • Are like LEGO, i.e. building blocks
  • Most versatile macromolecules in living systems
    • Many different functions: structural (collagen, keratin, cytoskeleton), storage (casein in milk, ovalbumin in eggs), transport (haemoglobin), hormones (insulin, many are not proteins tho), defence (antibodies), motion (actin, myosin in muscle), receptors, membrane transport, catalytic (enzymes)
  • About 100 000 different proteins in humans
  • Proteins are made from amino acids

Amino Acids

General Structure of An Amino Acid
  • Organic molecules
    • Have an amino group and an acid (carboxyl) group
    • Variation created by variable side chain
    • 20 different amino acids are encoded in DNA
  • Amino acids have stereoisomers, ie, they are chiral
    • Have a chiral centre (asymmetric carbon atom)
    • This is possible because 4 different chemical groups are attached to the chiral carbon
    • Therefore have a L(S) and D(R) stereoisomer
  • Side Chains:
    • Polar Amino Acids – create dipoles with electro-negativity through charged or neutral groups
    • Non-polar amino acids of proteins – have aliphatic and aromatic groups
  • Peptide bonds are the bonds that join amino acids together to form linear protein molecules
    • Form the backbone for proteins with the side chains branching off
    • The length of the polypeptide chain and the order of amino acids is specified in the DNA
      • Analogy: necklace with beads
    • Form by synthesis giving off water at the point where the COO- group meets the NH2+
    • Direction is also important since ends are different. Normally read from amino to the acid end.

Protein Structure

  • Primary structure – amino acids linked by peptide bonds forming polypeptide chains, order of amino acids
    • Sequence of amino acids
    • Encoded in DNA
      • Eg: order of letters (ATTAG vs. ACGGA)
  • Secondary structure – local organisation of the chain into structures such as the α-helix and β-sheet
    • Result of hydrogen bonding between C=O and NH groups in the peptide bonds
    • Do not involve side chains
    • α-helix is like a single helix with hydrogen bonds forming between the spirals
    • β-sheet is like a sheet with polypeptide chains in parallel, hydrogen bonds between them
  • Tertiary structure – compact structures that occur in water soluble proteins
    • Result of interactions between side chains – ionic, hydrogen bonding, dispersion
    • Defines the overall conformation or shape
      • i.e, the way the alpha-helix and beta-sheets fold around each other
  • Quaternary structure – chains can assemble into multi-subunit structures
    • The association of several polypeptide chains to give a functional protein
    • Correct folding of protein chains is necessary to achieve a 3D structure specific to the protein’s function
  • All polypeptide chains have primary, secondary and tertiary but not all have quaternary

Protein function

  • Proteins can be destroyed by:
    • Detergents, heating, acid/alkali, mechanical ‘shear’ forces
    • This involves the loss of secondary, tertiary (and quaternary) structure by unfolding of the molecule
      • Loss of function may be irreversible
  • Function is dependant on protein recognising another molecule at a specific binding site
    • The protein’s entire 3D structure is needed to bring together specific amino acid side chains so as to form binding sites
      • Other molecule being recognised can be another protein, a macromolecule, a small organic molecule or an inorganic ion
  • Eg: Immunoglobulin G (IgG) structure:
    • Quaternary structure containing 2 light and 2 heavy chain subunits stabilised by disulfide bonds
    • Arms contain hypervariable regions that are designed to give a wide variety of binding sites
      • These recognition sites can thus attach to different foreign molecules
    • Tail of IgG used to interact with the immune response, ie, make foreign molecule more tasty