Biological molecules

• beta pleated sheets

  • Due to hydrogen bonding between amino acids
  • Between NH (group of one amino acid) and C=O (group)

  
• Tertiary structure of a protein


  • 3D folding of polypeptide chain
  • Due to interactions between amino acid R groups (dependent on sequence of amino acids)
  • Forming hydrogen bonds, ionic bonds and disulfide bridges
• Quaternary structure of a protein

  • More than one polypeptide chain
  • Formed by interactions between polypeptides (hydrogen bonds, ionic bonds, disulfide bridges)
• Test for proteins


  1. Add biuret reagent (sodium hydroxide + copper (II) sulphate)

  2. Positive result = purple / lilac colour (negative stays blue) → indicates presence of peptide bonds
• Proteins have a variety of functions within all living organisms. You need to be able to relate the structure of proteins to properties of proteins named throughout the specification eg. enzymes / antibodies.
• Amino acids contain DNA triplets.
• A dipeptide has a primary structure.
• All hydrogen bonds are between R groups.
• All proteins have a quaternary structure.
• Quaternary structure is made of four polypeptides.
• Quaternary structure is multiple tertiary structures.
• Enzymes act as biological catalysts


  • Each enzyme lowers activation energy of reaction it catalyses
  • To speed up rate of reaction
• Induced-fit model of enzyme action

  1. Substrate binds to (not completely complementary) active site of enzyme

  2. Causing active site to change shape (slightly) so it is complementary to substrate

  3. So enzyme-substrate complex forms

  4. Causing bonds in substrate to bend / distort, lowering activation energy
• Models of enzyme action

  • Initially lock and key model (now outdated) - Active site a fixed shape, complementary to one substrate
  • Now induced-fit model
• Specificity of enzymes


  • Specific tertiary structure determines shape of active site, dependent on sequence of amino acids (primary structure)
  • Active site is complementary to a specific substrate
  • Only this substrate can bind to active site, inducing fit and forming an enzyme-substrate complex
• Enzyme concentration increases


  Rate of reaction increases
• Substrate concentration increases


  Rate of reaction increases
• Temperature increases up to optimum


  Rate of reaction increases
• Temperature increases above optimum


  Rate of reaction decreases
• pH increases / decreases above / below an optimum

  Rate of reaction decreases
• Concentration of competitive inhibitor increases


  Rate of reaction decreases

  
• Concentration of non-competitive inhibitor increases


  Rate of reaction decreases
• Variables that could affect the rate of an enzyme-controlled reaction

  • Enzyme concentration / volume
  • Substrate concentration / volume
  • Temperature of solution
  • pH of solution
  • Inhibitor concentration
• Controlling temperature


  1. Use a thermostatically controlled water bath

  2. Monitor using a thermometer at regular intervals and add hot / cold water if temperature fluctuates
• Controlling pH


  1. Use a buffer solution

  2. Monitor using a pH meter at regular intervals
• Enzyme & substrate solutions left in the water bath for 10 mins before mixing so solutions equilibrate / reach the temperature of the water bath
• Measuring the rate of an enzyme-controlled reaction

  1. Measure time taken for reaction to reach a set point, eg. concentration / volume / mass / colour of substrate or product

  2. Measure concentration / volume / mass / colour of substrate or product at regular intervals (or using a continuous data logger) throughout reaction
• Initial rate of reaction = change in y / change in x; example units = cm3s-1
• Handling enzymes may cause an allergic reaction
• Using a colorimeter to measure colour change is better than comparison to colour standards as it is not subjective and more accurate
• Procedures to stop each reaction

  1. Boil / add strong acid / alkali → denature enzyme

  2. Put in ice → lower kinetic energy so no E-S complexes form

  3. Add high concentration of inhibitor → no E-S complexes form
• Presenting processed data as a graph


  1. Independent variable on x axis, rate of reaction on y axis, including units

  2. Linear number sequence on axis, appropriate scale (graph should cover at least half of grid)

  3. Plot coordinates accurately as crosses

  4. Join point to point with straight lines if cannot be certain of intermediate values OR draw a smooth curve but do not extrapolate

  
• The rate of reaction decreases over time throughout each experiment as the initial rate is highest as substrate concentration not limiting / many E-S complexes form, but the reaction slows as substrate used up and often stops as there is no substrate left
• Functions of DNA and RNA

  • DNA holds genetic information which codes for polypeptides (proteins)
  • RNA transfers genetic information from DNA to ribosomes
• Components of a ribosome

  RNA and proteins
• DNA nucleotide


  • Pentose sugar is deoxyribose
  • Base can be thymine
• RNA nucleotide


  • Pentose sugar is ribose
  • Base can be uracil
• Nucleotides joining to form polynucleotides

  1. Condensation reactions, removing water molecules

  2. Between phosphate group of one nucleotide and deoxyribose/ribose of another

  3. Forming phosphodiester bonds
• Many scientists initially doubted that DNA carried the genetic code due to the relative simplicity of DNA - chemically simple molecule with few components
• Structure of DNA


  • Polymer of nucleotides (polynucleotide)
  • Each nucleotide formed from deoxyribose, a phosphate group and a nitrogen-containing organic base
  • Phosphodiester bonds join adjacent nucleotides
  • 2 polynucleotide chains held together by hydrogen bonds
  • Between specific complementary base pairs - adenine / thymine and cytosine / guanine
  • Double helix