Amino acids, proteins and DNA

• Amino acid features

  • Amino group, carboxyl group, H and R group
  • Amphoteric
  • Chiral
• Zwitterions

  • Both positive and negative ions at the ions isoelectric point (The pH where the average overall charge is 0)

  
• Zwitterion at different pH levels

  Low pH: The COO- will accept a H+

  High pH: The NH3+ will lost a H+
• TLC method

  • Separate and identify amino acids as they have different solubilities
  • Stationary phase of silica of alumina mounated on a glass/metal plate. A pencil base line is drawn and drops of amino acid mixtures are added
  • Place the plate in a solvent below the pencil line so amino acids dont dissolve
  • Leave until solvent has moved up to near he top of the plate, remove and mark the solvent front
  • Lower down on the chromatogram are less soluble
• TLC analysis

  Fluroscent dyes and UV light: Adding a fluroescent dye to the silicia/alumina can be seen using UV, colourless spots will block any glow from the fluorescent dye, which are then drawn around to mar where they are

  Iodine/ninhydrin: Place chromatogram in a sealed jar with a few iodine crystals, iodine vapour sticks to chemicals and dyes them purple; locating agent
• Rf values

  • Identify the amino acids
  • N.o. spots tell you how many amino acids make up the mixture
  • Distance travelled by spot/Distance travelled by solvent
  • Compare value to a data book, same temperature solvent and TLC make up must be used
• Proteins

  • Polymers made up of amino acid monomer units, condensation polymer
  • Peptide link
  • Broken down via hydrolysis
  • 2 amino acids = dipeptide
  • 6 moldm3 HCl, 110 degrees and reflux for hydrolysis

  
• Proteins structure

  Primary: Sequence of amino acids that make up the protein

  Secondary: Hydrogen bonds which determine an alpha helix or beta pleated sheet

  Tertiary: unique shape of protein determined by ionic bonds, hydrogen bonds and disulfide bridges; changed by temperature and pH
• Enzymes

  • Biological catalysts that speed up chemical reactions
  • Enzymes have an active site in their tertiary structure which will be complementary to the substrate
  • Enzymes are stereospecific as they have chiral centres (Only one enantiomer is complementary)
  • Inhibitors can block active site of a substrate and slow rate of reaction, will also be complementary to the active site: depending on concentration and how strongly the inhibitor binds
• Antibiotics

  Will work as an inhibitor by blocking the active site of the enzyme that is responsible for making the cell wall of a bacteria cell, if this cant be formed the bacteria will burst and die.
• DNA

  • Polymer that is made up of nucleotides
  • 2 polynucleotide strands are twisted together to form a double helix, held together by hydrogen bonds
• Nucleotides

  Made up of a: Phosphate group, 2-deoxyribose group and a nitrogenous base (ATCG)

  • Bottom NH on each base is what bonds with deoxyribose

  
• What provides strength to the DNA

  • Sugar phosphate backbone which is covalently bonded (Phosphodiester bond) to join nucleotides using condensation polymerisation and protects the nitrogenous bases

  
• Which bases bond together and what is the number of hydrogen bonds

  • AT; 2 bonds
  • CG; 3 bonds

  
• Cis-platin

  • Anti-cancer drug with a square planar complex
  • Cancer is uncontrollable multiplication of cells, replicating DNA
  • Cis-platin binds to DNA in cancer cells and prevents reproduction of DNA
  • Chloride is displaced and platinum binds to guanine base causing distortion which casues DNA to be unable to unwind
  • Cis-platin can also prevent healthy cells from reproducing, supressing the immune system and increasing risk of infection and kidney damage
  • Reduced through lower doses and targeted deliveries directly to tumours
  • Long term benefits