Proteins

• What is the general structure of an amino acid

  ~COOH carboxyl/carboxylic acid group

  ~R variable side group consists of carbon chain and may include other functional groups

  ~NH2 amine/amino group
• Describe the test for proteins in a sample

  ~Biuret test confirms presence of peptide bond

  ~Add equal volume of sodium hydroxide to sample at room temperature

  ~Add drops of dilute copper (II) sulfate solution. Swirl to mix

  ~Positive result: colour changes from blue to purple

  ~Negative result: solution remains blue
• How many amino acids are there and how do they differ from one another

  ~20

  ~Differ only by side 'R' group
• How do dipeptides and polypeptides form

  ~Condensation reaction forms peptide bond and eliminates molecule of water

  ~Dipeptide: two amino acids

  ~Polypeptide: three or more amino acids
• How many levels of protein structure are there

  four
• Define primary structure of a protein

  ~Sequence, number and 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 attached to -C=O and H attached to -NH
• Describe the two 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 and C=O groups alternate from one side to the other
• Define tertiary structure of a protein. Name the bonds present

  ~3D structure formed by further folding of polypeptide

  ~Disulfide bridges

  ~Ionic bonds

  ~Hydrogen bonds
• Describe each type of bond in the tertiary structure of proteins

  ~Disulfide bridges: strong covalent S-S bonds between molecules of amino acid cysteine

  ~Ionic bonds: relatively strong bonds between charged R groups

  ~Hydrogen bonds: numerous and 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
• Describe the structure and function of globular proteins

  ~Spherical and compact

  ~Hydrophilic R groups face outwards and hydrophobic R groups face inwards = usually water soluble

  ~Involved in metabolic processes
• Describe the structure and function of fibrous proteins

  ~Can form long chains or fibres

  ~Insoluble in water

  ~Useful for structure and support
• Outline how chromatography could be used to identify the amino acids in a mixture

  ~Use capillary tube to spot mixture onto pencil origin line and place chromatography paper in solvent

  ~Allow solvent to run until it almost touches other end of paper. Amino acids move different distances based on relative attraction to paper and solubility in solvent

  ~Use revealing agent or UV light to see spots

  ~Calculate Rf values and match to database
• What are enzymes


  ~Biological catalysts for intra and extracellular reactions

  ~Specific tertiary structure determines shape of active site, complementary to a specific substrate

  ~Formation of enzyme-substrate (ES) complexes lowers activation energy of metabolic reactions
• Explain the induced fit model of enzyme action

  ~Shape of active site is not directly complementary to substrate and is flexible

  ~Conformational changes enables (ES) complexes to form

  ~This puts strain on substrate bonds, lowering activation energy
• How have models of enzyme action changed

  ~Initially lock and key model: rigid shape of active site complementary to only one substrate

  ~Currently induced fit model: also explains why binding at allosteric sites can change shape of active site
• Name five factors that affect the rate of enzyme-controlled reactions

  ~Enzyme concentration

  ~Substrate concentration

  ~Concentration of inhibitors

  ~pH

  ~Temperature
• Outline 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
• Outline 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 and 'end product inhibition'