Protein section 1

The formation of disulphide bonds in proteins is an important secondary primary teriary quaternary( secondary, primary, teriary, quaternary ) structural feature. This helps to impart stability acidity reactivity inertness( stability, acidity, reactivity, inertness ) and conformational rigidity to some proteins

Phe, Tyr and Trp Ser, Thr and Cys Val, Leu, Ile Lys, Arg, His( Phe, Tyr and Trp, Ser, Thr and Cys, Val, Leu, Ile, Lys, Arg, His ) are all highly aromatic and can absorb UV light at 280nm. Proteins have an optical density at 280nm because of these side chains

The more hydrophobic hydrophilic( hydrophobic, hydrophilic ) amino acids have a tendency to be sequestered away from the solvent towards the centre inner part outer part( centre, inner part, outer part ) of protein molecules. This provides one of the major driving forces for protein folding binding inhibition( folding, binding, inhibition )

Hydrophilic hydrophobic( Hydrophilic, hydrophobic ) residues tend to interact with the solvent more easily via hydrogen covalent( hydrogen, covalent ) bonding and thus can be on the outside inside( outside, inside ) of proteins.

Under physiological cellular( physiological, cellular ) conditions this effectively restricts the peptide ionic( peptide, ionic ) bond to one of two configurations: cis or trans
To minimise steric crowding due to close proximity of bulky groups on th carbonyl carbon and the nitrogen the trans cis( trans, cis ) form is favoursed, except where Proline Histidine( Proline, Histidine ) is involved.

Proline has an alkyl carboxyl( alkyl, carboxyl ) chain rather than a hydrogen oxygen( hydrogen, oxygen ) atom as the second third( second, third ) substituent on nitrogen
In amides containing proline the cis trabs( cis, trabs ) form is not dramatically disadvantaged
In proteins about 10% 15% 5%( 10%, 15%, 5% ) of all peptide bonds involving proline are cis.

THE SHAPE OF POLYPEPTIDES IS DEFINED BY ROTATION SPIN SIDE CHAIN MOMENTUM( ROTATION, SPIN, SIDE CHAIN, MOMENTUM ) ABOUT THE C-N AND C-C BONDS

All atoms around the peptide bond lie in a planar primary cis trans( planar, primary, cis, trans ) conformation.
This rotation is described by the torsion angles φ Phi between C-N C-C( C-N, C-C ) and ψ Psi between C-C. C-N.( C-C., C-N. )
If all psi and phi angles are the same the peptide assumes a repeated saturated( repeated, saturated ) structure.
For certain combinations of angles this can take the form of a helical stucture (the alpha helix) coil structure( helical stucture (the alpha helix), coil structure ) or a beta-sheet structure.
Clearly the peptide structure exhibits flexibility motitlity( flexibility, motitlity ) and this is important for the complex structure binding( structure, binding ) of proteins.