Protein section 2

Amino acids are grouped according to their physico-chemical binding structural biological( physico-chemical, binding, structural, biological ) properties and this is reflected in the genetic code

A single base change in the third first second( third, first, second ) position of the codon will often produce the same amino acid and in the second third first( second, third, first ) position often one with very similar physico-chemical properties.

Resonance is the result of delocalisation deprotonation protonation( delocalisation, deprotonation, protonation ) of electrons side chains hydrogen atoms( electrons, side chains, hydrogen atoms ) over several atoms molecules( atoms, molecules )

As we mentioned previously there is rotation allowed around N-Cα N-Cb( N-Cα, N-Cb ) and Cα-C Cb-C( Cα-C, Cb-C ) by angles phi and psi
Thus we have a polymer with rotatable covalent bonds which alternate with rigid planar ones
This restricts increases( restricts, increases ) the number of conformations bonds( conformations, bonds ) the polypeptide can adopt.

Hydrophobic Hydrophilic( Hydrophobic, Hydrophilic ) side chains engage in van der Waals interactions. They have a tendency to avoid go into( avoid, go into ) contact with water and pack against each other. This is the basis for the hydrophobic hydrophilic( hydrophobic, hydrophilic ) effect.
Tendencies: Alanine Methionine Serine( Alanine, Methionine, Serine ) and leucine Aspargine Histidine( leucine, Aspargine, Histidine )- helix favouring residues, proline -helix breaking residue

Hydrophilic Hydrophobic( Hydrophilic, Hydrophobic ) side chains are able to make hydrogen covalent( hydrogen, covalent ) bonds with each other, with the peptide bond, with polar organic molecules and with water. Also because some are charged neutral( charged, neutral ) and exhibit pKa’s pH( pKa’s, pH ) they can change their charge depending on the pH pKa( pH, pKa ) or the microenvironment.

Amphipathic Acidic Basic( Amphipathic, Acidic, Basic ) side chains have both polar and non-polar character and are ideal at interfaces and may be involved in both H-bonding Covalent bonding( H-bonding, Covalent bonding ) and van der Waals interactions. hydrophobic interactions( van der Waals interactions., hydrophobic interactions )

The atom to which the hydrogen is attached is called the H-bond donor acceptor( donor, acceptor )

To the right are some examples of H-bonding in proteins, the most important of which in the context of primary structure and its influence on the secondary structure of proteins is that between the amide donor acceptor( donor, acceptor ) and the carbonyl acceptor donor( acceptor, donor ) of the main chain peptide bond. The other shown are more important in tertiary structure.

The network of regular secondary primary( secondary, primary ) structures contributes very significantly to the stability conformation size( stability, conformation, size ) of the overall folded protein providing extensive networks of hydrogen covalent( hydrogen, covalent ) bonds in which many consecutive residues are involved. All of the hydrogen covalent( hydrogen, covalent ) bonding capability in the secondary structure of a protein is contributed from the amide nitrogen and carbonyl oxygen of the main chain peptide bond as donor acceptor( donor, acceptor ) and acceptor donor( acceptor, donor ) respectively.
This hydrogen bonding provides much of the stabilising enthalpy entropy( enthalpy, entropy ) which allows the polar backbone amide and carbonyl groups to exist in the very hydrophobic hydrophylic( hydrophobic, hydrophylic ) environment in the interior of a folded protein.

The helix forms a cylindrical tetrahedral spherical( cylindrical, tetrahedral, spherical ) structure with the walls formed by the H bonded backbone with the side chains pointing outwards inwards( outwards, inwards ).

Here we see retinol binding protein with a distinct beta barrel alpha helix( beta barrel, alpha helix ) structure.
A large anti-parallel parallel( anti-parallel, parallel ) beta sheet turns( sheet, turns ) curves all the way round with the last strand hydrogen nitrogen( hydrogen, nitrogen ) bonded to the first thus forming a closed cylinder.
The interior of the cylinder is lined with hydrophobic hydrophylic( hydrophobic, hydrophylic ) residues and can accommodate retinol which is non-polar polar( non-polar, polar ).

The simplest secondary structural element is the beta turn and usually involves just four five( four, five ) residues. It is very important in allowing compact folding of proteins and is often found connecting the strands of anti-parallel parallel( anti-parallel, parallel ) beta sheets.
The beat turn comprises a hydrogen bond from the carbonyl oxygen of one residue (n) to the amide N-H of residue n+3 n+4( n+3, n+4 ). This reverses the direction of the chain.
Beta turn are most commonly found on the surface interior( surface, interior ) of proteins in contact with the aqueous environment.
The tight geometry of the turn means that some amino acids such as glycine phenylalanine glutamine( glycine, phenylalanine, glutamine ) are found more commonly in turns than other bulkier groups.