Proteins

• What is the general structure of an amino acid?

  • carboxyl group
  • amine group
  • R group

  
• What is an amino acid?

  The monomers from which proteins are made. A condensation reaction between two amino acids forms a peptide bond.
• Describe how to test for proteins in a sample

  Biuret test confirms presence of a peptide bond

  1. add equal volume of sodium hydroxide to sample at room temperature
  2. add drops of dilute copper (II) sulfate solution. Swirl to mix
  3. positive result: colour change from blue to purple

  negative result: solution remains blue
• How many amino acids are there and how do they differ from each other?

  20

  Only differ by side 'R' group
• How do dipeptides and polypeptides form?

  .

  • condensation reaction forms peptide bond & eliminates molecule of water
  • dipeptide: 2 amino acids
  • polypeptide: 3 or more amino acids
• How many levels of protein structure are there?

  4
• Define 'primary structure' of a protein

  .

  • sequence, number & type of amino acids in the polypeptide
  • determined by sequence of codons on mRNA
• Define 'secondary structure' of a protein

  Hydrogen bonds form between O (delta negative) attached to C=O and H (delta positive) attached to NH
• Describe the 2 types of secondary protein structure

  alpha-helix:

  • all N-H bonds on same side of protein chain
  • spiral shape
  • H-bonds parallel to helical axis

  Beta-pleated sheet:

  • N-H & C=O groups alternate from one side to the other
• Define the 'tertiary structure' of a protein. Name the bonds present

  3D structure formed by further folding of polypeptide

  • disulphide bridges
  • ionic bonds
  • hydrogen bonds
• Describe each type of bond in the tertiary structure of proteins

  .

  • disulphide bridges: strong covalent S-S bonds between molecules of the amino acid cysteine
  • ionic bonds: relatively strong bonds between charged R groups (pH changes cause these bonds to break)
  • hydrogen bonds: numerous & easily broken
• Define 'quaternary structure' of a protein

  .

  • functional proteins may consist of more than one polypeptide
  • precise 3D structure held together by the same types of bond as tertiary structure
  • may involve addition of prosthetic groups e.g metal ions or phosphate groups
• Describe the structure and function of globular proteins

  .

  • spherical & compact
  • hydrophilic R groups face outwards & hydrophobic R groups face inwards = usually water-soluble
  • involved in metabolic processes e.g enzymes & haemoglobin
• Describe the structure and function of fibrous proteins

  .

  • can form long chains or fibres
  • insoluble in water
  • useful for structure and support e.g collagen in skin
• Outline how chromatography could be used to identify the amino acids in a mixture

  .

  1. use capillary tube to spot mixture onto pencil origin line and place chromatography paper in solvent
  2. allow solvent to run until it almost touches other end of paper - amino acids move differently based off relative attraction to paper & solubility in solvent
  3. use revealing agent or UV light to see spots
  4. calculate Rf values & match to a database
• What are enzymes?

  .

  • biological catalysts for intracellular and extracellular reactions
  • specific tertiary structure determines shape of active site, complementary to a specific substrate
  • formation of enzyme-substrate complexes lowers activation energy of metabolic processes
• Explain the induced fit model of enzyme action

  .

  • shape of active site is not directly complementary to substrate and is flexible
  • conformational change enables ES complexes to form
  • this puts strain on substrate bonds, lowering activation energy
• How have models of enzyme action changed?.

  .

  • Initially lock & key model: rigid shape of active site complementary to only 1 substrate
  • currently induced fit model: explains why binding at allosteric sites can change shape of active site
• Name 5 factors that affect the rate of enzyme-controlled reactions

  .

  • enzyme concentration
  • substrate concentration
  • concentrations of inhibitors
  • pH
  • temperature
• How does substrate concentration affect rate of reaction?

  .

  • rate increases proportionally to substrate concentration
  • rate levels off when maximum number os ES complexes form at any given time
• How does enzyme concentration affect rate of reaction?

  .

  • rate increases proportionally to enzyme concentration
  • rate levels off when maximum number of ES complexes form at any given time
• How does temperature affect rate of reaction?

  .

  • rate increases as kinetic energy increases & peaks at optimum temperature
  • above optimum, ionic bonds & H-bonds in tertiary structure break = active site no longer complementary to substrate (denaturation)
• How does pH affect rate of reaction?

  .

  • Enzymes have a narrow optimum pH range
  • outside range, H+/OH- ions interact with H-bonds &ionic bonds in tertiary structure = denaturation
• Contrast competitive and non-competitive inhibitors


  .

  
• How to calculate rate of reaction from a graph

  .

  • calculate gradient of line or gradient of tangent to a point
  • initial rate: draw tangent at t=0
• How to calculate rate of reaction from raw data

  Change in concentration of product or reactant / time
• Why is it advantageous to calculate initial rate?

  represents maximum rate of reaction before concentration of reactants decreases & 'end product inhibition'