Model answers for PPS96 Assignment 2

1. CHIRAL CENTRES IN AMINO ACIDS

• Chiral molecules are those which cannot be superimposed on
  their mirror images.
  
• Organic molecules which contain at least one tetrahedral carbon
  atom bound to four different substituent groups are chiral. That
  carbon atom is a "chiral centre". All amino acids except
  glycine are chiral (the alpha carbon is a chiral centre).
  
• Threonine and isoleucine also have a chiral centre at the
  beta carbon.
  
  
  
  
  
  

2. B FACTORS

• B factors are "temperature factors" - atoms with
  high B factors have high mobility or are disordered.
  
• In proteins, residues lying on the outside of the protein,
  in contact with the solvent, are likely to have high B factors
  - as will residues at the extreme N and C termini. Residues on
  the surface are more likely to be polar or charged.
  
• Residues with long, flexible side chains (such as Lysine),
  and particularly the atoms at the end of those chains, are also
  likely to have high B factors.
  
  
  
  
  
  

3. BETA-ALPHA-BETA MOTIFS

Two kinds of beta-alpha-beta motif

1. Singly wound topology - alpha/beta barrels (e.g. TIM barrel).
   Helices on one side of the sheet, which forms a barrel with the
   helices on the outside.
   
2. Doubly wound topology - twisted open sheet (e.g. Rossman fold).
   Helices on both sides of the sheet.
   
   

4. CALCIUM BINDING MOTIFS

The calcium binding motif associated with an E-F hand consists
of about 12 residues, encompassing the loop region of a helix-turn-helix
motif.

The two helices are almost perpendicular to each other. The loop
region binds calcium, which is octahedrally coordinated: it is
bound to five oxygen atoms in the motif and to one water molecule.
Glycine at the 6th position of the motif is conserved for structural
reasons. Some hydrophobic and polar positions are also conserved.

5. HELIX KINKING

Proline is the amino acid which causes alpha helices to kink or
distort.

• It has no NH group (i.e. it is an imino acid) so cannot take
  part in H-bonding through its main chain nitrogen.
  
• It is the most rigid of all the amino acids. Its (phi, psi)
  angles are (almost) fixed close to positions which are near, but
  not identical with,those of alpha-helices.
  
  

6. QUATERNARY STRUCTURE SYMMETRY TYPES

• Cyclic
  
• Dihedral
  
• "Higher" symmetries: tetrahedral, octahedral, icosahedral
  
• Helical
  
  

7. HYDROPHOBIC AMINO ACIDS

This is a difficult decision: there are several different ways
of comparing hydrophobicities.

1. hydrophobicity scales based on free energy of transfer of
   each amino acid between water and a hydrophobic solvent
   
2. hydrohobicity scales based on chemical properties of amino
   acid side chains, such as surface area and lack of polar atoms.
   
3. scales based on the tendency of an amino acid to be found
   in the interior of a protein, based on actual crystal structures.
   

In practice, it was possible to score full marks from a well argued
position based on one or more of these principles, using an established
hydrophobicity scale (or more) and highlighting amino acids such
as I, F, L, and W. I was the most
popular choice.

Another useful point: an aromatic amino acid is usually considered
less hydrophobic than an aliphatic one with a similar surface
area (and no polar atoms) due to electron delocalisation.