Biological Molecules 1 (incomplete)

Water
1. Properties
  1. High latent heat of evaporisation
    1. Needs a lot of energy to evaporate water - useful for organisms in restoring body temperature.
  2. Highest specific heat capacity of any common liquid
    1. value: 4190 J/kg/Degree celsius
  3. High cohesive forces
    1. Strong cohesion makes it flow - great as a transport medium e.g. xylem in plants
  4. High surface tension
    1. Due to high cohesive forces. Useful for some insects walking across ponds (see pic),
2. Structure
  1. composed of 2 hydrogen atom and 1 oxygen atom
  2. Bonding
    1. Hydrogen bonds are formed between opposite atoms
      2. hydrogen bonds are 1/10th the strength of a covalent bond (individually), Collectively, they're quite significant.
3. Uses of water
  1. Great metabolite
  2. Good solvent
Proteins
1. Enzymes
  1. 2 types
    1. Anabolic
      1. build up substances
    2. Catabolic
      1. break down substances
  2. Factors affecting enzyme-controlled reactions
    1. Substrate concentration
    2. Enzyme concentration
      1. As long as there is an excess of substrate , an increase in enzyme leads to a proportionate increase in rate of reaction
      2. However, once substrate runs out...
    3. Temperature
      1. As temperature increases, enzyme and substrate molecules gain more kinetic energy so they collide more frequently. this means that more ES complexes are formed so there is a faster rate of reaction.
    4. pH conditions
      1. Changes alter the charges on the amino acids making up the active site of the enzyme
        This causes hydrogen and ionic bonds to break that maintain the tertiary structure and makes it reform in different places.
        The active site has changed shape and the substrate will not fit - the enzyme has denatured.
    5. Rate of reaction
  3. 2 types
    1. intracellular
      1. work inside the cell
    2. extracellular
      1. work outside the cell
  4. biological catalysts and are globular proteins
    1. They lower the activation energy required to start a reaction so less energy and time is needed for it.
  5. models
    1. induced fit model
      1. more accepted model of the 2
      2. suggests that the enzyme active site and substrate are NOT exactly complementary to begin with but when a substrate binds to an enzyme it induces change in enzyme structure.
        The active site of the enzyme is said to be complementary as the active site moulds itself around the substrate to make an enzyme-substrate complex
      4. suitable analogy - hand in glove
    2. lock and key model
      1. taught at GCSE
      2. Limitation - it suggests that the enzyme structure is rigid, which is actually not true
      3. This suggests that the substrate combines with the enzyme in a precise way - like a lock and key
  6. Inhibitors
2. General Structure
3. Condensation (forming dipeptides and polypeptides)
  2. peptide bond formed
    1. This is broken in the inverse reaction called HYDROLYSIS.
4. Protein structure
  1. Primary structure
    1. Sequence of amino acids in a polypeptide chain
  2. Secondary
    1. Hydrogen bonds form between certain amino acids in the chain
      1. This makes the chain automatically coil/ fold into an alpha helix or beta pleated sheet
  3. Tertiary
    1. More bonds form between amino acids including disulfide bridges, hydrogen and ionic bonds. This causes the chain to coil further.
  4. Quaternary
    1. Several different polypeptide chains join together between bonds created to form one final 3D structure.
      1. Conjugated proteins
        Proteins with more groups attached
        Haemoglobin has haem groups attached to it's quaternary structure
5. Chemical test for protein
  1. Add Biuret's solution to a protein sample
    1. few drops of NaOH and CuSO_4
  2. Results
    1. Negative result - same blue colour
    2. Positive colour - solution turns lilac colour
6. Chromatography
Carbohydrates
1. Monosaccharides
  1. They are monomers that carbohydrates are made from
  2. examples
    1. glucose
      1. What group are these monosaccharides classified as?
    2. galactose
    3. fructose
  3. Glucose
    1. Alpha glucose
    2. Beta glucose
      1. What is the structural difference between these two isomers?
        Alpha:
        Beta:
2. Disaccharides
  1. examples
    1. maltose
      1. glucose + glucose
    2. sucrose
      1. glucose + fructose
    3. lactose
      1. glucose + galactose
  2. Processes involved
    1. condensation
      1. forms one water molecule and a disaccharide
    2. hydrolysis
      1. breaks down the disaccharide and water to form 2 monosaccharides
  3. Chemical Tests
    1. Reducing sugars test
      1. Method
        Add Benedict's reagent to a sample of sugar solution then heat in water bath for 2 minutes
      2. Expected results
        Negative
        Positive
        colour changes
    2. Non reducing sugars
      1. Method
        Add dilute HCl to a sample of sugar in test tube then boil in a water bath for 5 mins. Remove and cool. Neutralise acid by adding few drops of NaOH. Dip a glass rod in then transfer a drop onto indicator paper. If paper BLUE add Benedict's reagent then heat for 2 minutes.
      2. Result
        Should turn blue to orange (Benedict's)
        Non-reducing sugars present
  4. Reducing and non-reducing sugars
    1. What are they?
      1. Reducing sugars are sugars that can donate electrons and act as reducing agents.
      2. Non-reducing sugars cannot donate electrons (opposite of reducing sugars)
    2. Examples
      1. Non-reducing
        Sucrose is the only one you need to know about for this course.
      2. Reducing
        All sugars except sucrose.
  5. Structure
    1. Bonds present
      1. Only glycosidic
        These form between carbon-1 and carbon-4 of each monosaccharide
3. Polysaccharides
  1. Chemical tests
    1. Test for starch
      1. Method
        Add some iodine solution to a sample of starch. Iodine will change from a browny-red to a specific colour that shows whether sample has starch present.
      2. Expected Result
        Positive
        Changes to a blue-black colour
        Negative
        Stays a browny-red colour (original colour)
  2. Consists of TWO or more polysaccharides
  3. Functions of polysaccharides
    1. Starch
      1. Mixture of 2 alpha-glucose polysaccharides
        AMYLOSE and AMYLOPECTIN
      2. Amylose
        long, unbranched chain of alpha-glucose
        compact - lots can be stored in small places
      3. Amylopectin
        Long, branched chain of alpha-glucose
        easily hydrolysed due to many branches
      4. Insoluble in water - doesn't affect water potential. Also helical structure - makes it compact and easy to store
    2. Glycogen
      1. polysaccharide of alpha-glucose
      2. loads more side branches than amylopectin
      3. compact molecule - good for storage
    3. Cellulose
      1. Long, unbranched chains of BETA glucose
      2. chains linked by hydrogen bonds to form microfibrils
      3. hydrogen bonds give high tensile strength
Chromatography
1. Rf values
2. used to identify monosaccharides and amino acids in mixtures

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Biological Molecules 1 (incomplete)

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