3.13 Amino Acids, Proteins and DNA

• What do amino acids contain?

  An amino group (-NH2) and a carboxyl group (-COOH)
• What is meant by amino acids are amphoteric?

  They have acidic and basic properties
• Why are amino acids chiral?

  As they have 4 different groups around a central carbon atom and therefore rotate plane polarised light
• How to name amino acids using IUPAC rules?

  1. Find the longest carbon chain

  2. Number the carbons

  3. Note the number where the NH2 group(s) sit

  4. Name any other groups

  5. Name it
• What are zwitterions?


  A molecule with both positive and negative ions. They not exist at the amino acid's isoelectric point
• What is the isoelectric point?

  The pH at which the average overall change is zero. This dependant on the 'R' group
• What happens if the isoelectric point is at a low pH?

  The COO- is likely to accept an H+
• What happens if the isoelectric point is at a high pH?

  Then NH3+ is likely to lose an H+
• Why do we use thin layer chromatography?

  Allows us to separate and identify amino acids as they have different solubilities
• How does TLC work?

  - the amino acid mixture spots dissolve n the solvent

  - some chemicals in the mixture may not dissolve as much and stick to the stationary phase quickly
• How do you identify amino acids as they are colourless?

  Using iodine/ninhydrin solution or fluorescent dyes and UV light
• How do you calculate Rf?

  Rf = distance travelled by spot / distance travelled by solvent
• What are proteins?


  Polymers that are made up of amino acid monomer units joined together by peptide links. They are condensation polymers and therefore the chain can be broken via hydrolysis
• What is the primary structure of a protein?

  The individual sequence of amino acids that makes the protein
• What is the secondary structure of a protein?

  - hydrogen bonds exist between the peptide links in the polymer chain and this pulls a straight chain into alpha helix chain or beta pleated sheet
• What is the tertiary structure of a protein?

  - the protein chain is long and often it coils itself up giving a unique shape for that protein

  - this is known as the tertiary protein structure and additional bonds hold the long coiled chain together
• What holds the proteins specific shape?

  Intermolecular forces (disulphide bonds and hydrogen bonding) create the twisting feature which gives proteins a specific 3D shape that is vital as this determines basic functions
• What are enzymes?


  Biological catalysts that speed up chemical reactions by catalysing metabolic reactions
• What do enzymes have?

  A 3D active site which is part of the tertiary protein structure. This is where chemical reactions occur and substrates can interact with the enzyme
• How do active sites work?

  - Enzymes work by receiving the correct shaped substrate into the active site. The shapes must match otherwise the reaction won't be catalysed

  - enzymes have chiral centres this is because they are made up of amino acids

  - this means that only one enantiomer in the substrate will fit into the active site. We say that active sites are stereospecific
• How do inhibitors work to slow down rate of reaction?

  - inhibitors are substances that has a similar shape to the substrate that fits into the active site of an enzyme

  - an inhibitor blocks the active site from a substrate to enter. The higher the concentration of inhibitor the more active sites will be blocked and so the rate of reaction decreases

  - another factor to consider is how strongly the inhibitor binds to the active site. If it binds poorly then rate of reaction will not be reduced much
• What is DNA?


  Polymer that is made up of monomers called nucleotides
• What are nucleotides made up of?

  A phosphate, a sugar and a base
• How is the sugar-phosphate backbone formed?

  Via condensation polymerisation using nucleotides as monomers. A phosphodiester bond is formed and water is eliminated
• How is DNA formed?

  - Two polynucleotide strands are twisted together to form a double helix. The polynucleotide strands are held together by hydrogen bonds between the bases

  - both strands in DNA are complementary which means there is adenine on one strand it will align and bond with thymine and cytosine with guanine
• How are bases paired?

  By hydrogen bonding between a delta positive hydrogen and an electronegative element with a lone pair such as an oxygen or nitrogen
• What is cis-platin?


  An anti-cancer drug which is a square planar complex with a platinum metal ion, 2 ammonia ligands and 2 chloride ion ligands
• What is cancer?


  Many cells multiplying in an uncontrollable fashion to form a tumour. They do this by replicating its DNA
• How does cis-platin work?

  - binds to DNA in cancer cells

  - as the complex is attached to the DNA it prevents the cell reproducing through cell division. The cell dies as it is unable to repair itself