Biological Molecules 1 (incomplete)

Biological Molecules 1 (incomplete)

1. Water

   • Properties
     • High latent heat of evaporisation
       • Needs a lot of energy to evaporate water - useful for organisms in restoring body temperature.
     • Highest specific heat capacity of any common liquid
       • value: 4190 J/kg/Degree celsius
     • High cohesive forces
       • Strong cohesion makes it flow - great as a transport medium e.g. xylem in plants
     • High surface tension
       • Due to high cohesive forces. Useful for some insects walking across ponds (see pic),
   • Structure
     • composed of 2 hydrogen atom and 1 oxygen atom
     • Bonding
       • Hydrogen bonds are formed between opposite atoms
         • hydrogen bonds are 1/10th the strength of a covalent bond (individually), Collectively, they're quite significant.
   • Uses of water
     • Great metabolite
     • Good solvent

2. Proteins

   • Enzymes
     • 2 types
       • Anabolic
         • build up substances
       • Catabolic
         • break down substances
     • Factors affecting enzyme-controlled reactions
       • Substrate concentration
       • Enzyme concentration
         • As long as there is an excess of substrate , an increase in enzyme leads to a proportionate increase in rate of reaction
         • However, once substrate runs out...
       • Temperature
         • 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.
       • pH conditions
         • 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.
       • Rate of reaction
     • 2 types
       • intracellular
         • work inside the cell
       • extracellular
         • work outside the cell
     • biological catalysts and are globular proteins
       • They lower the activation energy required to start a reaction so less energy and time is needed for it.
     • models
       • induced fit model
         • more accepted model of the 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
         • suitable analogy - hand in glove
       • lock and key model
         • taught at GCSE
         • Limitation - it suggests that the enzyme structure is rigid, which is actually not true
         • This suggests that the substrate combines with the enzyme in a precise way - like a lock and key
     • Inhibitors
   • General Structure
   • Condensation (forming dipeptides and polypeptides)
     • peptide bond formed
       • This is broken in the inverse reaction called HYDROLYSIS.
   • Protein structure
     • Primary structure
       • Sequence of amino acids in a polypeptide chain
     • Secondary
       • Hydrogen bonds form between certain amino acids in the chain
         • This makes the chain automatically coil/ fold into an alpha helix or beta pleated sheet
     • Tertiary
       • More bonds form between amino acids including disulfide bridges, hydrogen and ionic bonds. This causes the chain to coil further.
     • Quaternary
       • Several different polypeptide chains join together between bonds created to form one final 3D structure.
         • Conjugated proteins
           • Proteins with more groups attached
             • Haemoglobin has haem groups attached to it's quaternary structure
   • Chemical test for protein
     • Add Biuret's solution to a protein sample
       • few drops of NaOH and CuSO_4
     • Results
       • Negative result - same blue colour
       • Positive colour - solution turns lilac colour
   • Chromatography

3. Carbohydrates

   • Monosaccharides
     • They are monomers that carbohydrates are made from
     • examples
       • glucose
         • What group are these monosaccharides classified as?
       • galactose
       • fructose
     • Glucose
       • Alpha glucose
       • Beta glucose
         • What is the structural difference between these two isomers?
           • Alpha:
           • Beta:
   • Disaccharides
     • examples
       • maltose
         • glucose + glucose
       • sucrose
         • glucose + fructose
       • lactose
         • glucose + galactose
     • Processes involved
       • condensation
         • forms one water molecule and a disaccharide
       • hydrolysis
         • breaks down the disaccharide and water to form 2 monosaccharides
     • Chemical Tests
       • Reducing sugars test
         • Method
           • Add Benedict's reagent to a sample of sugar solution then heat in water bath for 2 minutes
         • Expected results
           • Negative
           • Positive
             • colour changes
       • Non reducing sugars
         • 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.
         • Result
           • Should turn blue to orange (Benedict's)
             • Non-reducing sugars present
     • Reducing and non-reducing sugars
       • What are they?
         • Reducing sugars are sugars that can donate electrons and act as reducing agents.
         • Non-reducing sugars cannot donate electrons (opposite of reducing sugars)
       • Examples
         • Non-reducing
           • Sucrose is the only one you need to know about for this course.
         • Reducing
           • All sugars except sucrose.
     • Structure
       • Bonds present
         • Only glycosidic
           • These form between carbon-1 and carbon-4 of each monosaccharide
   • Polysaccharides
     • Chemical tests
       • Test for starch
         • 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.
         • Expected Result
           • Positive
             • Changes to a blue-black colour
           • Negative
             • Stays a browny-red colour (original colour)
     • Consists of TWO or more polysaccharides
     • Functions of polysaccharides
       • Starch
         • Mixture of 2 alpha-glucose polysaccharides
           • AMYLOSE and AMYLOPECTIN
         • Amylose
           • long, unbranched chain of alpha-glucose
           • compact - lots can be stored in small places
         • Amylopectin
           • Long, branched chain of alpha-glucose
           • easily hydrolysed due to many branches
         • Insoluble in water - doesn't affect water potential. Also helical structure - makes it compact and easy to store
       • Glycogen
         • polysaccharide of alpha-glucose
         • loads more side branches than amylopectin
         • compact molecule - good for storage
       • Cellulose
         • Long, unbranched chains of BETA glucose
         • chains linked by hydrogen bonds to form microfibrils
         • hydrogen bonds give high tensile strength

4. Chromatography

   • Rf values
   • used to identify monosaccharides and amino acids in mixtures

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