Amino acids

• What are the two functional groups of amino acids

  NH2 and COOH

  Amine and carboxylic acid
• How many naturally occurring amino acids are there in the body

  20
• What type of amino acids are found in the body

  • Alpha amino acids
  • It means that the NH2 is ALWAYS on the CARBON next to the COOH
• Draw a general formula for alpha amino acids 


  ,

  
• Are alpha amino acids CHIRAL

  • YES
  • One carbon has four different substituents
  • EXCEPT GLYCINE where R=H
• Which enatiomer do alpha amino acids exist as in nature

  NEGATIVE enantiomer
• How can amino acids be synthesised industrially

  • RCHO + NH4CN -> RCH(NH2)CH via NUCLEOPHILLIC ADDITION
  • RCH(NH2)CN + HCl + 2H2O -> RCH(NH2)COOH + NH4Cl
  • Hydrolysis and HCl is DILUTE
  • Need to REFLUX the reaction mixture
• Is the product from amino acids being synthesised naturally optically active

  • NO
  • A racemic mixture is formed when CN- ions can attack from above and below the planar C=C bond with equal likelihood
  • An equal amount of each enantiomer is formed, so no net effect on plane polarised light
• In what form do amino acids exist as solids

  • ZWITTERIONS
  • because it is an ionic lattice they have a HIGH melting and boiling point
• What colour solids are most zwitterions at room temperature

  white solid
• Do zwitterions dissolve in water

  • YES
  • But NOT in NON-POLAR solvents
  • Due to the ionic nature and polar bonds
• define a zwitterion

  Ions which have both a permanent positive and negative charge, but are overall NEUTRAL
• How do zwitterions occur in amino acids

  • COOH is DEPROTONATED -> COO-
  • NH2 is protonated -> NH3+

  
• What happens to amino acids in ACIDIC conditions

  GAINS A PROTON ON NH2 GROUP

  
• What happens to amino acids in ALKALINE conditions

  LOSES A PROTON FROM THE COOH GROUP
• What is the peptide linkage

  -CONH-

  
• What is a dipeptide

  Two amino acids bonded together

  
• What name is given to chains of amino acids up to 50 amino acids

  polypeptides
• What is the name given to chains of amino acids with more than 50 amino acids

  proteins
• What are polypeptides used for

  • Enzymes
  • Wool
  • Hair
  • Muscles
• What is the process called where polypeptides are broken down

  hydrolysis
• What conditions are needed for hydrolysis to occur

  • 6 moldm^-3 HCl
  • Reflux for 24 hours
• What is the primary structure of a protein

  the sequence of amino acids along the protein chain, bonded by Covalent bonds
• How is the primary structure represented

  Sequence of 3 letters abbreviations of the amino acids
• How can the primary structure of a protein be broken up

  • Hydrolysis
  • 6M HCl
  • 24 hour reflux
• What is the secondary structure of a protein

  the shape of the protein chain
• What are the two shapes an amino acid can form in the secondary structure

  • Alpha helix shape
  • Beta pleated sheets
• How is the secondary structure held together

  • Hydrogen bonding
  • E.g between C=O and N-H groups
• What is the tertiary shape of a protein

  • Alpha helix or beta pleated sheets is folded into a COMPLEX 3D shape
• How is the tertiary structure held together

  • Hydrogen bonding
  • Ionic interactions between R groups
  • Disulfide bridges
  • Van der waals forces of attraction
• Why is the tertiary structure important

  The shape of protein molecules is vital in their function e.g enzymes
• How can amino acids be attracted to each other

  • Hydrogen bonding
  • Ionic interactions between groups on the side chain
  • Disulfide bridges -> 2 S atoms oxidised to form an S-S bond
• What is wool

  • A protein fibre in the secondary structure of alpha-helix
  • held together by hydrogen bonds
• What does wool's structure and bonding mean for wools properties

  • Can be stretched, as H bonds extend
  • You can release it after stretching it and it returns to its original shape
  • If you wash it TOO hot the H bonds PERMANENTLY break so the clothes will lose its shape
• What is a TLC plate made of

  • Plastic sheet coated with silica, SiO2
  • This is the stationary phase
• Describe how you would carry out THIN LAYER CHROMATOGRAPHY

  • spot the samples onto a pencil line a few cm above the base of the TLC plate
  • Place this in a beaker, with solvent level below the pencil line
  • Ensure there is a lid on the beaker to keep the inside saturated with solvent vapour
  • Wait until the solvent front is almost at the top of the TLC plate; then remove it from the beaker then analyse
• Why does TLC separate amino acids

  • Solvent carries amino acids up the TLC plate
  • The rate of movement depends on the balance between the amino acid's affinity for the solvent and the affinity for the stationary phase
• What do you often have to do to enable the amino acid to be seen on the chromatogram

  • Shine UV light
• How do you calculate an Rf value

  • Distance moved by the substance / distance moved by solvent front
• How can Rf values which amino acid is which

  • Compare the experimental Rf Values to known/accepted values in the same solvent