L5-8 proteins

• 20 amino acids used to make proteins
• alpha carbon (central carbon) is chiral
• the variable side chain is different for all amino acids
• variable side chain gives different properties

  1. size
  2. shape
  3. charge
  4. hydrophilicity/hydrophobicity
• structure of amino acid

  1. amino group
  2. carboxyl group (carboxylic acid)
  3. R group
  4. hydrogen atom
• sides chains vary in chemical reactivity
• alpha carbon (central carbon) is chiral so has 2 optical isomers (L and D)
• L isomers are the only optical isomers into proteins
• if CO, R and N groups are arranged in anticlockwise direction around the chiral carbon then the amino acid is the L-isomer
• exception to chiral amino acid

  glycine (as R group is a hydrogen atom)
• amino acid zwitterion contains positive and negative charge on amino group (positive) and carboxyl group (negative)
• physiological pH is approximately 7
• reduce pH->> increase H+ concentration
• increase pH->>decrease H+ concentration
• pKa is the pH at which the ionisable group is 50% charged and 50% neutral
• at lower pH than pKa 


  more of the protonated form
• at higher pH than pKa 


  more of the ionised form
• increasing the pH by 1 above the pKa 90% will be in ionised form
• decreasing pH by 1 below the pKa 90% will be protonated
• define primary structure

  sequence of amino acids
• amino acids bond together using

  peptide bonds
• formation of amino acids releases

  water molecule as it is a condensation reaction
• peptide bond contains O=C-N-H
• amino acid sequence always written in N terminus to C terminus direction
• the peptide bond has partial double bond character meaning

  rotation is restricted so is rigid and planar
• hydrogen and oxygen atoms in peptide bond are on opposite sides
• which bonds is PSI and PHI rotation


  PSI is around alpha carbon-carbon

  PHI is around alpha carbon-nitrogen

  
• steric collisions (steric hinderance) restricts movement caused by R group
• protein folding is not a random process because

  driving force is to attain energetically stable structure
• what direction do we write out nucleotide sequences

  5' to 3'
• what direction do we write out (poly)peptide sequences

  N terminus to C terminus
• protein synthesis: the amino group of one amino acid is joined to...


  the carboxylic group of another amino acid
• certain PSI and PHI angles are not allowed because of:

  steric collisions between side chains
• what is the secondary structure?

  folding of parts of the primary sequence
• what are the 2 types of secondary structure?

  alpha helix

  beta sheet
• alpha helices length

  5-40 amino acids
• hydrogen and oxygen in different peptide bonds are hydrogen bonded together along the axis of alpha helix
• the alpha helix is very stable
• 3.6 amino acids per turn of the alpha helix
• the C=O group of the amino acid n is hydrogen bonded to the N-H group of amino acid n+4