POLYPEPTIDES

amino acids joined by peptide bonds = polypeptide

amino acids in a polypeptide chain are called residues with a name change from -ine to -yl
peptide bonds (or amide) are formed via a condensation reaction
the equilibrium favors hydrolysis, but ribosomes catalyse the condensation increasing the rate
the hydrolysis reaction is in fact very slow so proteases are required to break bonds
primary structure = the sequence of amino acids
polypeptides are linear (not branched) with a specific polarity (direction) from N- to C- terminal
only the end termini groups have a charge so they contribute little to overall polarity
it is the R groups on every residue that determines the charge status
sanger was the first to determine the primary structure of a protein and proved that:
proteins have a precisely defined amino acid sequence
all amino acids were L amino acids
amino acids were linked by peptide bonds
the peptide bond links (carboxylic acid) C N (amino group)
planar as the bond resonates between single and double bond character
but the other bonds in the backbone (N C) and (C C) are single and can rotate
three dihedral angles (, and ) define the conformation along the backbone
defines the conformation of the petide bond and is constrained to planar (+/-180 degrees)
it is normally in the trans formation 99.6% of time
steric clashes between groups attached to C inhibit the cis formation
specific enzymes can transform between trans and cis
X-Pro bonds are the most common cis peptide bonds
and determine the conformation of the backbone and how the protein folds
theoretically allows any angle between -180 and 180 but in reality there are few combinations
many combinations of values are prohibited due to steric clashes
the Ramachandran plot is a tool to test if and values are sterically allowed
nb. glycine has many more angles it can form as its R group is only a H (no beta C)
nb. proline has a very narrow range of values because of its rare structure with a cyclic ring
disulphide bonds are covalent and are important in protein structure
only a pair of cysteines form a disulphide bond if close enough due to their reactive -SH group
keratins are durable structural proteins that form hair, horns, nails and feathers
they are found in mammals, providing protective structures
the polypeptide chain forms helices which wrap around each other to form a coiled coil
the chains are rich in cysteine so can form disulphide bonds
the number of disulphide bonds determines its hardness (e.g. horns) or flexibility (e.g. wool)
most proteins contain between 50 and 2000 residues
polypeptide chains of less than 50 residues are referred to as peptides
daltons (Da) is a unit of mass similar to that of a hydrogen atom
the average amino acid weighs 110 Da