option b. biochemistry

• Amino acids can have both positive and negative charged groups called a zwitterion, often denoted as the H from the carboxyl group moving to the amino group.
• Amino acids are amphoteric meaning they can act as both acids and bases
• Each amino acid has a pH in which it is electrically neutral called the isoelectric point. When the pH is below this it will be a positive ion, above this and it will be a negative ion.
• Paper chromatography:

  1. AA will move at different rates based on solubility with solvent and molecular size
  2. made visible with locating reagent (ninhydrin)
  3. Rf is calculated (Retardation factor) = distance moved by AA / distance moved by solvent
• Gel electrophoresis:

  • Amino acids are placed in a pH buffer solution
  • An electric current is then passed through
  • Amino acids will move at different rates depending on their isoelectric point
  • Detection is made by staining, or by fluorescing under UV light
• Some proteins require co-factors to bind to them for activity. Organic co-factors such as vitamins are also called co-enzymes
• Organic enzyme:

  • Proteins (except ribosomes)
  • Highly specific
  • Maximum rate with substrate saturation
  • Homogenous (in aq state)
  • Regulated by inhibitors and  activators
  • Work within narrow limits
  • Increase rates by 1000 to 1000 000
• Inorganic catalyst:

  • Metal ions or complex molecules
  • Much less specific
  • Do not show saturation
  • Homogenous and heterogenous
  • Not regulated
  • Work at high temp and pressure
  • Relatively small increase in rate compared to enzymes
• Effect on enzyme activity:

  Temperature:

  • Initial inc in rate due to inc in temp as any normal reaction. 
  • Sudden dec in rate due to the disruption of hydrogen bonds and other forces holding the tertiary structure

  pH:

  • Reactions with the R-groups and H ion concentrations change the tertiary structure
• Effect of heavy metal ions on enzyme:

  Pb, Cu, Hg, Ag react with sulfhydryl groups –SH forming covalent bonds which many change the tertiary structure
• There are three major lipid groups:

  1. Triglycerides (fats and oils)
  2. Phospholipid
  3. Steroids
• The kink in the unsaturated fatty acid chain caused by the double bonds means less effective Van der Waals forces hence lower melting points.
• Iodine number is the number of grams of iodine that react with 100g of fat
• Rancidity is the chemical or biological decomposition of fats and oils that produces unpleasant odours.
• • Hydrolytic rancidity is caused by the hydrolysis of ester bonds on exposure to water creating unpleasant smelling short chain fatty acids and is caused by enzymes (lipases), high temperatures and organic acids (autocatalytic effect). Prevention is by sterilizing foods, keeping at low temperature and adding acidic components at the last stage of cooking.
• • Oxidative rancidity is caused by oxygen free radical reactions with double bonds and is accelerated by sunlight creating unpleasant smelling volatile aldehyde and ketones. Prevention is by blocking sunlight and adding antioxidants including vitamins A, C and E.
• Fats give high energy yields because:

  • Large numbers of reduced carbons that can be oxidized
  • Hydrophobic nature decreases water content and compacts molecules together
  • The insolubility of fat makes it slower to transport and metabolise in the body explaining why carbohydrates provide a faster source of energy
• Phospholipids (or glycerophospholipids) are derivatives of triglycerides. They have a fatty acid replaced with a phosphate group.
• • The formation of this membrane in water is called a phospholipid bilayer
  • Phospholipids are amphiphilic as the phosphate group is hydrophilic and the fatty acid group is hydrophobic.
  • The most common phospholipid is lecithin.
• • POSITIVE: Lipids are important for energy storage, insulation and protection of organs, production of components such as steroid hormones and the cell membrane, essential fatty acids reduce risk of heart disease and lower LDL levels
  • NEGATIVE: Lipids can cause obesity due to their high energy content, saturated and trans fats can increase LDL levels increasing risk of heart disease and atherosclerosis
• LDL (low density lipoproteins) associated with increasing cardiovascular disease. It appears to increase the build up of chlolesterol in the arteries. Levels are raised by consuming saturated fats and trans fats (hydrogenated fats)
• Steroids are lipids that consist of four fused rings called the steroidal backbone with three six carbon and one five carbon rings.
• HDL (high density liproproteins) associated with lowering cardiovascular disease. It appears to decrease the build up of chlolesterol in the arteries. Levels are raised by consuming unsaturated fats
• Steroid advantages

  • Can be used medically to stimulate bone growth and appetite and induce puberty
  • Estrogen supplements after menopause help older women from getting osteoporosis (HRT Hormone Replacement Therapy)
  • Help patients wasting away from chronic diseases
  • Quick recovery from injuries
• Steriod disadvantages:

  • Increases LDL decreases HDL
  • High blood pressure
  • Liver damage
  • Aggressive behavior
  • Cheating in sport? (Testosterone is an anabolic steroid – which means it builds up tissues including muscle cf. catabolic steroids which do the opposite)
• Straight chain sugars are unstable and become cyclical by intramolecular nucleophilic addition (AN) forming 5 or 6 membered rings. The reaction occurs between the carbonyl group and one of the hydroxyl groups.
• Monosaccharides contain a carbonyl group (C=O) either in the form of a aldehyde (aldose) or ketone (ketose).
• Aldoses (glucose) are called reducing sugars as the can be oxidized.
• Test for starch: Iodide and iodine forms triiodide ions, which react with amylose to make blue black complex.
• Water soluble vitamins:

  Need daily supply as can be eliminated from 30min to several weeks.

  Fat soluble vitamins:

  Accumulate in liver and fat tissue. Can be stored for up to several months. Excess can cause vitamin poisoning.
• Solutions to malnutrition:

  • providing food rations that are composed of fresh and vitamin- and mineral-rich foods

  • fortification - adding nutrients missing in commonly consumed foods (eg I2 to salt, Vit A to margarine, Vit B, D and C to cereals)

  • genetic modification of food

  • providing nutritional supplements

  • providing selenium supplements to people eating foods grown in selenium-poor soil
• Xenobiotics are chemical compounds that are found in a living organism, but which are foreign to that organism. Xenobiotics that remain the in environment for long periods of time without being metabolised are called persistent organic pollutants (POPs).
• Xenobiotics and related problems:

  1. Bioaccumulation (eg. DDT, Hg)
  2. Pharmaceutically active compounds – PACs (eg. xenoestrogens )
  3. Non-biodegradable plastics
• An insecticide created to prevent malaria, DDT, accumulated and increased in concentration up the food chain (increasing trophic levels) causing egg shells to be thin and so break which caused a large reduction in the numbers of birds of prey in the 1960s.
• Biodegradable plastics consist of over 50% starch based polymers. By creating polymers from starch or cellulose it not only decreases the use of fossil fuels, but allows the use of microorganisms in the environment to break it down.
• Strains of microorganisms have been found that can break down hydrocarbons and have been used to help clean up oil spills – also called bioremediation. Enzymes used in detergents allow for fast and effective breakdown of fats, carbohydrates and lipids even in cold water
• Induced fit model:

  • Active site is flexible as a stable enzyme-substrate complex can be achieved.
  • The slight change of shape weakens some bonds lowering the activation energy of the transition state allowing the chemical reaction to take place.
• The maximum velocity Vmax, is the maximum rate of an enzyme under particular pH and temperature conditions.

  The Michaelis constant Km, is the substrate concentration at half of the Vmax.
• Protein assays determine the concentration of protein in a sample. A UV-vis spectrophotometer in the UV range of 280nm absorbs light due to the aromatic rings in the amino acids of the protein.
• To identify a particular protein, it first needs to be separated out by high-performace liquid chromatography (HPLC) and then compared to a database with information from UV-vis spectra, gel electrophoresis, HNMR, and mass spectrometry.