Biological molecules 2b

• What are proteins made up of?

  Proteins are made up of one or more chains of amino acid monomers forming polypeptides
• What are all amino acids made of?

  Amino acids are made of an amine group NH2, a carboxyl group COOH, a hydrogen atom, and a side chain (R group).
• How many different amino acids are there?

  20
• What varies in each amino acid?

  The R group so has different chemical properties
• How do amino acids join together?

  Condensation reaction forming water. A peptide bond (strong covalent bond) forms between the amine group and the carboxyl group of 2 amino acids forming a dipeptide
• Primary structure 


  Determined by the sequence of amino acids in a polypeptide chain
• Secondary structure 


  Folding of the polypeptide chain in localised regions due to H bonds. Produces an alpha helix or a beta pleated sheet.
• What type of proteins have beta pleated sheets?

  Globular
• a helix common in?

  Fibrous
• Tertiary structure


  Further folding where the whole chain folds into a specific shape. Involves bonding between R groups which stabilise the structure due to ionic bonds, hydrogen bond and disulphide bonds
• What does the specific shape of the tertiary structure determine?

  The protein function
• When a protein is subjected to high temperatures or extremes of pH, it denatures and loses its shape.
• Hydrogen bonds break first as they are very weak bonds then ionic bonds then the disulphide bonds are stronger so they can withstand higher temperatures
• When bonds broken tertiary structure is lost and the protein loses its function
• What is quaternary structure?

  Two or more polypeptide chains
• What do fibrous proteins do?

  They form long chains running parallel to each other with cross-bridges between chains. Produces very stable molecules e.g collagen. They have structural roles
• What do globular proteins do?

  Enzymes and haemoglobin carry out metabolic functions
• What’s the test for proteins?

  Biuret test. Add biuret solution (KOH and CuSO4)

  lilac colour is a positive test

  Blue is negative
• Chromatagrophy


  Used to separate mixtures of monosaccharides or amino acids. This is because the molecules have different molecular sizes and have different solubilities. Peptide and glycosidic bonds have to be broken. The smaller and more soluble the molecule, the further it will be moved in a solvent. To identify the spots that appear on the chromatogram, their Rf values must be calculated. This enables a comparison between different chromatographs run with the same solvent.
• How to calculate Rf value?

  Rf value is calculated by dividing the distance traveled by the compound by the distance traveled by the solvent.
• Why was it important to draw the line and ‘x’ on the chromatography paper in pencil

  So it doesn’t dissolve in the solvent and so separate out like ink would/ move out the paper. Pencil doesn’t run up the paper.
• Why is it important that the solvent in the bottom of the solvent tank is below the level of the line drawn on the chromatography paper?


  If the solvent is above the line drawn, it would not separate the pigments in the solution on the line.
• What is activation energy?

  Activation energy is the minimum amount of energy required for a chemical reaction to occur.
• What are enzymes?


  Biological catalysts which act by lowering the activation energy needed for the reaction to occur therefore increasing the rate of reaction
• What is metabolism?


  All the metabolic reactions in the body
• Describe enzyme structure


  enzymes are globular proteins with an active site, this has a specific tertiary structure and shape

  They usually only work on one type of substance, the substrate. The active site is said to be complementary to the substrate

  When the enzyme and substrate combine, an enzyme substrate complex forms
• Describe the lock and key model of enzyme action

  Suggests that the active site is always a complementary shape.
• Describe the induced fit model

  This model suggests that a substrate and its active site are not fully complementary to begin with. The shape of the active site changes as the substrate binds and the amino acids of the active site are moulded around the substrate to form an enzymes substrate complex. The active site changes to become complementary. This puts strain on the substrate and distorts the bonds thus reducing the activation energy needed to break the bonds.
• How to calculate rate of reaction?


  Rate of reaction can be calculated by dividing the change in concentration of a reactant or product by the change in time.
• How to calculate gradient?

  Change in y/change in x
• How do you calculate the rate of reaction at A certain point on a curve?

  Take the slope of the tangent line at that point.
• How does temperature affect enzyme activity?

  • At low temps, enzymes have little energy so collision frequency is low
  • As temp increases, enzyme and substrate molecules gain more kinetic energy so move about more quickly
  • They collide more frequently and so a greater number of enzyme substrate complexes are formed so more product is made
  • Increases rate of reaction
  • optimum Temp is maximum level of rate of reaction = usually 40°c
• What happens to enzymes once temperature is too high?

  Enzymes denature as stabilising bonds break due to over frequent collisions. Tertiary structure is lost so active site changes shape
• pH refers to the concentration of H+ ions present in a solution. Greater concentration of H+, lower pH. A pH change of 1 changes the aqueous H+ conc. by 10 times.
• How can you calculate pH of a solution?

  pH = -log10 H+
• How does pH affect enzymes activity?

  • Alters the charges on the amino acids which make up the active site.
  • The change in H+ ions affects the bonding causing the hydrogen and ionic bonds that maintain the enzymes tertiary structure to break and reform in different places
  • Alters the shape of the active site so the substrate may no longer be complementary
  • So, no e-s complexes are formed as the enzyme is denatured.
  • Optimum pH
• How does substrate concentration affect enzyme activity?

  As substrate concentration increases, enzyme activity increases as more substrates mean more e-s complexes are formed. However, as substrate conc. continues to increase, enzyme activity plateaus because there are not enough enzymes available to form e-s complexes as all active sites are occupied. Rate stays the same
• How does enzyme concentration affect enzyme activity?

  • Enzymes can be reused and work efficiently even in low concentrations
  • As long as there is an excess of substrate, the rate of reaction increases as enzyme Conc increases
  • If the substrate is limiting however, any increase in enzyme concentration has no effect on rate.
  • At this point, the rate will stabilise at a constant level
• Effect of competitive inhibitors on enzyme activity?

  Inhibitors decrease rate of reaction.

  • Competitive inhibitors have a similar shape to that of the enzyme‘s substrate
  • So it competes with the substrate as it binds to the active site of the enzyme
  • Active sites are blocked by the competitive inhibitor, substrates can’t bind so fewer e-s complexes are formed
• How do non competitive inhibitors affect enzyme activity?

  • don’t combine with active site as their shape is not similar to the substrate
  • Binds to another region of the enzyme (allosteric site)
  • Results in changes in tertiary structure of enzyme so changing shape of active site so the substrate cannot bind
  • Fewer e-s complexes are formed so rats of reaction decreases.
  • Effect of inhibitor Is not dependent on its concentration relative to the substrate
  • the inhibitor inactivates the enzyme
  • A few enzymes may remain unaffected so rate may proceed at a slow rate.