Biological Molecules

• Starch

  • Polymer of alpha glucose
  • Mixture of 2 polysaccharides:
  • amylose - unbranched
  • amylopectin - branched
  • Coiled/helical so can fit into small spaces - compact for storage
  • Branched so glycosidic bonds can be easily hydrolysed to release glucose for respiration
  • Insoluble so doesn't affect water potential
  • Large so doesn't leave cell
• Test for reducing sugar

  • Add Benedict's reagent
  • Heat/boil in a water bath
  • If positive blue -> brick red precipitate
• Test for non reducing sugar

  • Test for a reducing sugar initially and discard when negative
  • Boil solution with dilute hydrochloric acid
  • Neutralise with sodium hydrogen carbonate
  • Repeat reducing sugar test
• Starch test

  • Test with iodine
  • Orange -> blue/black
• Glycogen

  • Similar to starch but highly branched so easier hydrolysis of glycosidic bonds therefore making it easier to release glucose for respiration to make ATP
  • Compact molecule so good for storage
  • Insolube so doesn't affect water potential of a cell
  • Large so doesn't leave cell
• Cellulose

  • Long straight chains of beta glucose molecules each alternate one is flipped
  • The chains are cross-linked by many hydrogen bonds to form microfibrils
  • This gives strength to the cell wall
• Polysaccharide bonds

  • Starch - 1,4 and 1,6 glycosidic bonds
  • Glycogen - 1,4 and 1,6 glycosidic bonds
  • Cellulose - 1,4 glycosidic bonds
• Fatty acids

  • Saturated - fatty acids contain single bonds which a fully saturated with hydrogen. Triglycerides containing saturated fatty acids tend to be a solid at room temperature
  • Unsaturated - fatty acids have a double bond and are not fully saturated with hydrogen. The unsaturated causes the fatty acid chain to kink and causes the melting point to lower. Triglycerides containing double bonds tend to be oils at room temperature.
• Triglyceride

  • 3 fatty acids + glycerol
  • Broken down by lipase - hydrolyses ester bond
  • Energy store
  • Insulation
  • Protection
  • Insoluble in water
  • Contain elements carbon, hydrogen and oxygen
• Phospholipid

  • Glycerol + 2 fatty acids + phosphate group
  • Main constituent of the cell membrane
  • Polar molecules - they have hydrophobic fatty acid tails and hydrophilic phosphate heads. They form a bilayer which is the main constituent of plasma membranes
• Test for lipids

  • Add sample to ethanol - shake well
  • Carefully add to water
  • If positive then a white emulsion results
• Proteins

  • 20 amino acids - monomers of proteins
  • Elements of amino acids - carbon, hydrogen, oxygen, nitrogen and sometimes sulfur
  • Peptide bond between amino acids - between carbon and nitrogen atom
  • Amino acids have amino, variable and carboxyl group
• Protein formation

  • Primary structure - order/sequence of amino acids
  • Secondary structure - polypeptide chain starts to fold. Hydrogen bonds between amino acids form and alpha helices and beta pleated sheets are produced
  • Tertiary structure - formed after more folding has occurred. More hydrogen bonds occur along with ionic bonds and disulfide bridges. The 3D shape which results is very specific to the different proteins
  • Quaternary structure - some proteins have a quaternary structure. This is when there are 2 or more polypeptide chains often associated with a prosthetic (non-protein) group
• Test for proteins

  • Add Biuret's reagent
  • Blue -> purple
• Enzymes and reaction rate

  Enzymes are biological catalysts which lower the activation energy of a reaction without being used up
• Induced fit model

  The induced fit model of enzyme action states that the enzyme and substrate are not initially complementary but the active site changes shape, moulding around the substrate and putting pressure on its bond. This bends the bonds which lowers the activation energy of the reaction.
• Enzyme activity and temperature

  • As the temperature increases, the rate of reaction increases until the optimum temperature. After this there is a decrease in enzyme activity
  • As the temperature increases, the particles have more kinetic energy so more successful collisions occur - there are more enzyme-substrate complexes
  • After the optimum temperature, the bonds (hydrogen/ionic/disulfide bridges) start to break and the tertiary structure of the enzyme and therefore the shape of its active site changes
  • It will no longer be complementary and therefore no enzyme-substrate complexes will form
• As pH increases


  Enzyme activity also increases up until the optimum pH
• After the optimum pH, as pH increases


  Enzyme activity decreases
• Low pH


  High concentration of H+ which interfere with the hydrogen bonds, changing the enzyme's tertiary structure and active site shape, resulting in fewer enzyme-substrate complexes forming
• As pH increases


  There are fewer protons (H+) and so more enzyme-substrate complexes form, reaching a maximum at optimum pH
• After the optimum pH, as pH becomes more alkali


  OH- (hydroxyl) ions interfere with the hydrogen bonds causing the tertiary structure to change so fewer enzyme-substrate complexes form
• Enzyme activity and substrate concentration

  • As the substrate concentration increases the rate of reaction also increases until the rate of reaction plateaus
  • As more substrate is added, more enzyme-substrate complexes are made so the reaction rate increases
  • When the concentration of the substrate exceeds that of the enzyme, the rate of reaction remains constant as there a no more active sites available at that time
• Enzyme activity and enzyme concentration

  • As enzyme concentration increases, the rate of reaction increases until a hypothetical plateau is reached because of no more substrate
  • As the enzyme concentration increases, the number of enzyme-substrate complexes increases unless the concentration of enzymes exceeded that of substrate
• Competitive inhibition

  • Competitive inhibitors and substrates compete to bind for the enzyme's active site
  • They are both complementary in shape to the enzyme's active site as they are a similar shape to each other
  • Competitive inhibitor binds to active site and blocks substrate so less enzyme-substrate complexes formed
• Non-competitive inhibition

  • The non-competitive inhibitor binds to the enzyme site away from the active site
  • This changes the shape of the active site
  • Substrates are no longer complementary to the active site and so no enzyme-substrate complexes can be made
• Enzyme inhibition graphs

  • In order to determine whether an inhibitor is competitive or Non-competitive, increase the concentration of substrate
  • If the reaction rate increases (to that of the reaction without inhibitor) it is a competitive inhibitor
• Nucleic acids


  The monomers of nucleic acids are nucleotides
• Structure of DNA

  Bases : Adenine - Thymine, Cytosine - Guanine

  Double stranded

  Double helix - helical structure - compact to fit in nucleus

  Anti-parallel - one of the strands is upside down compared to the other

  Longer

  Lots of hydrogen and phosphodiester bonds
• Structure of RNA

  • Bases : adenine - uracil, guanine - cytosine
  • Single stranded
  • Shorter
• Semi-conservative replication

  • DNA helicase breaks the hydrogen bonds between the 2 strands causing them to unwind
  • The 2 strands are both template strands and free-floating DNA nucleotides line up opposite their complementary base pair eg A to T, G to C
  • DNA polymerase joins the adjacent DNA nucleotides together using phosphodiester bonds
  • This replication is semi-conservative so 1 parent strand (the template) and 1 new strand wind up together
• Phosphodiester bonds

  Bonds that join adjacent nucleotides together. Formed by condensation reaction.
• Sugar phosphate backbone

  Protects the bases from being removed
• Uncertainty - Reading

  • Thermometer
  • pH meter
  • Top ban balance
  • Measuring cylinder
  • Volumetric flask
• Uncertainty - measurement

  • Ruler
  • Protractor
  • Stopwatch
  • Analogue meter
• DNA structure

  • DNA is responsible for passing information from cell to cell
  • It is very stable because of the many H bonds and phosphodiester bonds
  • The 2 separate strands are joined by H bonds so they can easily be unzipped in DNA replication and protein synthesis
  • Large molecule and coiled for storage (it's a double helix)
  • Base pairs, which code for proteins, are protected by sugar phosphate backbone
  • DNA is an information carrying molecule. Its sequence of bases determines the structure of proteins, including enzymes
• ATP - Adenosine Triphosphate

  • Energy molecule
  • Nucleotide derivative
  • Adenine base + ribose sugar + 3 phosphate groups
  • ATP hydrolysis - ATP hydrolase - ATP -> ADP + Pi - water used and energy released
  • ATP synthesis - ATP synthase - ADP + Pi -> ATP - water released and energy used
• Sources of energy for ATP synthesis

  1. Respiration (oxidative phosphorylation)
  2. Photosynthesis (photo phosphorylation)
  3. Substrate level phosphorylation
• Properties of ATP

  • ATP is hydrolysed to release energy in small, manageable amounts
  • The formation of ATP is a one step reaction (as is its hydrolysis) meaning it is very fast
  • Can't leave cell
  • It can phosphorylate other molecules to make them more reactive
• Inorganic ions

  • Found in the cytoplasm and bodily fluids eg blood and saliva
  • Have differing concentrations and roles
  • They are electrically charged