Biochemistry

• Conjugated proteins


  Globular proteins that contain a prosthetic group (e.g. haemoglobin)
• Globular proteins


  Spherical, compact, water soluble proteins that fold into their tertiary structure with hydrophobic r-groups kept on the inside of the protein (e.g. insulin)
• Breakdown of peptides

  Proteases catalyse the breakdown of proteins by hydrolysis with a water molecule being used to break the peptide bond and reform the amine and carboxylic acid groups
• Hydrophobic and hydrophilic interactions in protein structure

  Proteins are made in the aqueous cytoplasm so hydrophilic r-groups fold on the outside and hydrophobic r-groups fold on the inside
• Quaternary structure

  - Interactions between polypeptide subunits using the same interactions as in tertiary structure but between protein molecules rather than within one

  - Not all proteins reach this level of structure
• Interactions between r-groups

  - hydrophobic and hydrophilic interactions - weak interactions between polar and non-polar R groups

  - hydrogen bonds

  - ionic bonds - stronger than H bonds and formed between R-groups with opposite charge

  - Disulfide bonds - the strongest bonds, they are covalent and only form between R-groups containing sulfur atoms
• Tertiary structure


  - The overall 3d shape of the protein determined by folding due to R-groups interacting
• Secondary structure

  - Alpha helix or beta pleating (pattern of coiling)

  - The O, H and N atoms of the basic, repeating structure of the amino acids interact and form hydrogen bonds within the amino acid chain, pulling it into a coil shape called an alpha helix

  - Alternatively, polypeptide chains can lie parallel to each other joined by hydrogen bonds to form sheet-like structures with the pattern formed by individual amino acids making the structure appear pleated. This is beta pleating.
• Layers of protein structure

  Primary, secondary, tertiary and quaternary
• Primary structure


  - Sequence in which amino acids are joined

  - This influences how the polypeptides will fold, impacting the protein's final shape
• Peptide bond


  A chemical bond formed between amino acids and water
• How many amino acids are there?

  25 with 5 being non-essential
• R-groups


  - Variable groups on amino acids

  - Different r-groups interact with each other, allowing proteins to fold
• Peptides


  Short polymer of amino acids
• Roles of lipids

  - Membrane creation and creation of hydrophobic barriers

  - Hormone production

  - Electrical insulation necessary for impulse transmission

  - Waterproofing

  - Thermal insulation

  - Cushioning

  - Buoyancy
• Sterols (Steroid alcohols)


  - Complex alcohol lipids with a very different structure to oils and fatty acids, based on a 4 carbon ring structure with a hydroxyl group.

  - They have dual hydrophobic/hydrophilic characteristics with the hydroxyl group being polar while the rest is not

  - Cholesterol is a sterol and Vitamin D, Steroid hormones and bile are all manufactured using cholesterol
• Hydrophillic


  Attracts and attracted to water, soluble
• Hydrophobic

  Repels and repelled by water, insoluble
• Unsaturated fats


  Lipids with a double bond, causing them to have less than the maximum number of hydrogens and to be less compact with more bends in the carbon chain (Oils)
• Saturated lipids

  Lipids with no double bonds, causing them to have the maximum number of hydrogens and to be more compact (Fatty acids)
• Lipids

  - Non-polar molecules made up of carbon, hydrogen and oxygen without polar regions, making it unable to mix with water

  - Lipids are large, complex molecules known as macromolecules built from monomers
• Difference between oils and fats

  Fats are solid at room temperature while oils are liquid at room temperature
• Display

  The change by the transducer will then produce a visible, qualitative or quantitative change on a test strip or on a test machine
• Transduction


  The interaction from molecular recognition will cause a change in a transducer (which detects changes such as change in pH) and it will produce a response such as the release of an immobilised dye on a test strip or an electric current in a glucose-testing machine
• Molecular recognition


  A protein (enzyme or antibody) or a singular strand of DNA is immobilised to a surface (e.g. a glucose test strip). This will interact/bind with the the specific molecule under investigation
• Biosensors


  Detecting devices that can detect the presence and quantity of specific substances in cells using biological components
• Colorimetry method for Benedict's test

  1. A filter was placed in the colorimeter

  2. The colour was calibrated using distilled water

  3. Benedict's test was performed on a range of known concentrations of glucose

  4. The resulting solutions were filtered to remove the precipitate

  5. The % transmission of each of the solutions of glucose was measured using the colorimeter and recorded in a table

  6. Using this information, a calibration curve was plotted. Steps 3-6 were then repeated on an unknown concentration and the calibration curve was used to identify the concentration.
• Method for Iodine test for starch

  1. Obtain sample with expected trace of starch

  2. Dissolve in solvent e.g. ethanol or water

  3. Add iodine (iodine dissolved in potassium iodide) solution to test for starch

  4. If present, the starch will cause the iodine solution to turn purple-black. If not, the iodine will stay yellow-brown.
• Method for Benedict's test for non-reducing sugars

  1. Place the sample to be tested in a boiling tube. If it is not in a liquid form, grind it up or blend it in water.

  2. Add dilute hydrochloric acid and boil the solution

  3. Allow the solution to cool

  2. Add an equal volume of Benedict's reagent

  3. Heat the mixture gently in a boiling water bath for five minutes

  4. Check the solution and note its colour. Blue = no reducing sugars, green = very low, yellow = low, orange = medium, red = high (reverse traffic lights)
• Benedict's test for non-reducing sugars

  - Non-reducing sugars do not react with Benedict's solution and so change in solution colour will be seen. Sucrose is the most common non-reducing sugar

  - If sucrose is first boiled with dilute hydrochloric acid to hydrolyse the sucrose into glucose and fructose (both reducing sugars), it will then give a positive result when warmed with Benedict's solution
• How Benedict's test works

  - Tests for reducing sugars, meaning they can donate electrons and reduce other molecules (all monosaccharides and some disaccharides, e.g. maltose and lactose)

  - This test uses Benedict's reagent, an alkaline solution of copper (II) sulphate

  - Reducing sugars react with the copper ions in the solution, adding electrons to the blue Cu2+ ions and reducing them to brick red Cu+ ions. When a reducing sugar is mixed with Benedict's reagent and warmed, a brick red precipitate is formed indicating a positive result.

  - The more reducing sugar present, the more precipitate formed and the less blue Cu2+ ions formed, so the actual colour seen will be a mixture of the two and will depend on the present concentration of reducing sugars. This makes the test qualitative.
• Method for Benedict's test (Reducing sugars)

  1. Place the sample to be tested in a boiling tube. If it is not in a liquid form, grind it up or blend it in water.

  2. Add an equal volume of Benedict's reagent

  3. Heat the mixture gently in a boiling water bath for five minutes

  4. Check the solution and note its colour. Blue = no reducing sugars, green = very low, yellow = low, orange = medium, red = high (reverse traffic lights)
• Macrofibrils


  Many microfibrils joined together
• Microfibrils

  Fibres of cellulose bonded with hydrogen
• Similarities and differences between glycogen and amylopectin

  Similarities

  - Both are insoluble

  - Both are branched and compact

  - Both are made from a hexose monosaccharide

  
  

  Differences

  - Glycogen is used in animals and fungi, amylopectin is used in plants

  - Glycogen forms more branches and is more compact than amylopectin

  - Glycogen is made of alpha glucose whereas amylopectin is made of beta glucose
• Examples of polysaccharides


  starch, glycogen, cellulose
• Examples of dissacharides

  sucrose, lactose, maltose
• Examples of monosaccharides

  glucose, fructose, galactose
• Polysaccharide


  Carbohydrates that are made up of more than two monosaccharides
• Dissacharide


  A molecule made of two monosaccharides.