Primary protein structure

peptide bond

carboxyl group of first amino acid reacts with amino group of second, condensation reaction produces water

peptide unit

carbon, nitrogen and peptide bond

direction of amino acid sequence

N --> C

why is rotation around peptide bond rigid

peptide bond has a partial double bond - because of electron distribution within the peptide unit, there is no free rotation around it - protein chain can only rotate around the bonds on either side of the peptide unit

psi angle

rotation around C-C bond angle

phi angle

rotation around N-C bond angle

most combinations of psi and phi angles aren't allowed because of …

steric collisions between side chains and the main polypeptide chain

main driving force in protein folding?

to attain an energetically stable structure

how do hydrophobic side chains behave in protein configuration

packed into protein interior to hide them from surrounding water - forms a hydrophobic core

Why is the main polypeptide chain hydrophilic?

polar C=O and NH groups

protein needs structures to neutralise this