3.1.4 Proteins

• The twenty universal amino acids differ only in their side group
• A condensation reaction between the two amino acids forms a peptide bond.

  • Dipeptides; condensation of two amino acids
  • Polypeptides; condensation of many amino acids
• A functional protein may contain one or more amino acids
• Amino Acid

  Monomers containing:

  • Amine group (NH2)
  • Carboxyl group (COOH)
  • Variable R group
• Structure of proteins is determined by the order and number of amino acids, bonding present and the shape of the protein
• Primary Structure

  Sequence/order of amino acids joined by peptide bonds.

  • Protein specific; determines the protein function.
  • Determined by DNA
• Alpha-helix

  When a hydrogen bond forms between every fourth peptide bond in a helix
• Beta-pleated sheet

  The protein folds so two parts are parallel to one another

  • Hydrogen bonds form between parallel peptide bonds.
• Biuret Test

  Tests for presence of peptide bonds

  1. Add Biuret
  2. r.t.p

  • Blue to violet/purple
• Enzymes

  Increase rate of reaction by lowering the activation energy of the reaction they catalyse
• Active Site

  Area of the enzyme that is made up of only a few amino acids.

  • Made of Tertiary structure
• Enzymes are specific to substrates they bind to; only one type of substrate fits into the active site.
• Induced fit model

  1. Substrate binds to active site
  2. Puts stress on the bonds
  3. Causes conformational changes on active site
  4. Active site changes shape to become complementary to the substrate
  5. Lowers activation energy
• Factors affecting enzyme-controlled reactions

  • Temperature
  • pH
  • Enzyme Concentration
  • Substrate Concentration
  • Competitive Inhibitors
  • Non-competitive Inhibitors
• Competitive inhibition

  Binds to the active site and prevents the substrate from forming the Enzyme-substrate complex

  • Has similar shape to substrate.
• Non-competitive inhibition

  Alters the shape of the enzyme and active site; substrate cannot bond.

  1. Binds to allosteric site
  2. Puts stress on bonds, causes conformational change on active site
• How the structure of a protein depends on the amino acids it contains

  1. Structure is determined by positions of amino acid/R group
  2. Primary Structure; sequence/order of amino acids
  3. Secondary structure; H bonds between amino acids
  4. Tertiary structure; R group interactions
  5. Creates active site in enzymes
• Universal

  The same codons (amino acid triplets) code for the same amino acids in all living things
• Secondary Structure

  The folding of primary structure into a-helix or b-pleated sheets held in place by hydrogen bonds.
• Tertiary structure

  The further folding of the secondary structure to create a unique 3D structure held in place by hydrogen, ionic and disulfide bonds.
• Quaternary Structure

  A protein made up of more than one polypeptide chain.
• Disulfide bonds

  Strong covalent bonds between two cysteine R groups

  • Strongest, helps stabilise the protein
  • Broken by reduction
  • Sulfur - Sulfur bond
• Ionic bond

  Forms between positively charged amine and negatively charged carboxylic acid R groups

  • Stronger than H-bonds, not common
  • Broken by pH changes