Amino Acids

• structure of an amino acid:

  A) amino group

  B) acid group

  
• • all amino acids are optically active except glycine
  • this is because there is a chiral carbon, which has 4 different groups around it
  • they rotate plane polarised light
• amino acids are amphoteric - they can act as an acid or a base
• zwitterions:

  • amino acids in their solid states
  • dipolar ion - both positive and negative
  • high melting and boiling points
  • strong intermolecular forces
• structure of a zwitterion:

  
• reactions of amino acids:

  • amine group gives it basic properties
  • carboxyl group gives it acidic properties
  • can react with acids or bases to form salts
• calculating Rf value:

  A) distance travelled by amino acid

  B) distance travelled by solvent

  
• thin layer chromatography (TLC) allows separation and identification of amino acids as they have different solubilities
• TLC:

  1. draw a base line in pencil on a TLC plate
  2. place a concentrated spot of amino acid on base line
  3. put the plate in a beaker of solvent, making sure base line is above solvent level
  4. when the solvent is near the top of the plate, remove the plate and mark the solvent front
• the chromatography plate has thin layer of silica or alumina
• to identify an amino acid, calculate the Rf value and compare this with a database of known Rf values
• amino acids join together in condensation reactions to make polypeptides
• amino acid condensation reaction:

  A) peptide link

  
• • proteins and poly/dipeptides can be broken back down into amino acids by hydrolysis
• primary structure - sequence of amino acids
• secondary structure - polypeptide chain folds into an alpha helix or a beta pleated sheet
• tertiary structure is the 3D structure of a protein that is determined by the interactions between the R groups of amino acids. interactions include hydrogen bonds, disulphide bonds and ionic
• temperature and pH change the shape of the protein by affecting hydrogen bonding and formation of disulphide bonds
• bonds to keep proteins in shape:

  • hydrogen bonds - between polar groups, stabilise the secondary and tertiary structure
  • disulphide bonds - link different parts of the protein chain
• • enzymes have chiral carbons because they are made up of amino acids
  • the active sites are stereospecific which means that if the substrate is chiral, only one enantiomer will be complementary to the active site
• inhibitors:

  • similar shape to substrate
  • can fit active site of enzyme
  • blocks the active site from the substrate
• a higher concentration of inhibitor blocks more active sites so there is a lower rate of reaction
• drugs as inhibitors:

  • antibiotics
  • block active site of enzymes responsible for making the cell wall of bacteria cells
  • if the cell wall can't be made, the bacteria cell will burst and die
• • computer modelling is used by scientists to speed up the designing of new drugs to act as inhibitors
  • quicker and cheaper than making the drug
• structure of DNA:

  • phosphate group, pentose sugar and a base

  A) phosphate group

  
• structures of DNA

  A) pentose sugar

  
• condensation of nucleotides:

  A) phosphodiester bond

  
• polynucleotide chain formation:

  • joining nucleotides together
  • phosphate on one nucleotide covalently bonds to the sugar on another
  • creates a sugar-phosphate backbone
  • condensation reaction
• base pairings:

  A) guanine

  B) cytosine

  
• base pairings:

  A) adenine

  B) thymine

  
• cisplatin structure:

  A) Cl

  B) Cl

  
• • G-C are paired by 3 Hydrogen bonds
  • A-T are paired by 2 Hydrogen bonds
• cisplatin:

  • anti-cancer drug
  • always has 2 Cl groups next to each other
  • binds to the DNA in cancer cells and prevents cell division and DNA replication
  • cells die
• • cisplatin is not specific or targeted, so it also kills healthy cells
  • side effects are minimised by giving cis-platin in small doses
• how cis-platin works:

  • chloride ions can easily detach from the cis-platin complex
  • Pt can bond to N atoms on guanine in DNA
  • ligand replacement reaction - dative covalent bond is formed between platinum and the N on guanine
• the distance travelled by the amino acid in TLC is determined by its solubility in the mobile phase and its retention in the stationary phase
• explain why different amino acids have different Rf values:

  • different polarities
  • they have different retention times in the stationary phase and different solubilities in the mobile phase
• explain why J and K can be separated by gas chromatography

  • different retention times/dipeptides appear at different times
  • different balance between solubility in the mobile phase and retention in the stationary phase

  
• suggest why urea is effective at separating the complementary strands in DNA

  the amino groups in urea can substitute for the Hydrogen bonds in DNA (can form hydrogen bonds with DNA strands)