Peptide Bond, Change on a Peptide

protein

a polymer of L-amino acids; fold into distinct 3D shapes stabilized by non-covalent interactions (big polypeptides)

polypeptide

2 or more amino acids joined by peptide bonds

dipeptide

2 amino acids, 1 peptide bond

tripeptide

3 amino acids, 2 peptide bonds

peptides

small polypeptides (<~50 amino acids)

amino terminal

always on the left; peptides are names beginning with this

backbone

N-C-C-N-C-N-C-C same for every peptide

side chains

R groups of the amino acids; vary from one protein to the next

residue

amino acid unit within a protein/peptide

Amino (N-) terminal residue

amino acid at the end with a free amino group

Carboxyl (C-) terminal residue

amino acid at end with a free carboxyl group

planar peptide bond

peptide bond cannot rotate; amide N has unshared e- pair, e- pair of carbonyl bond shifts to O and both pairs are now shared with carbonyl C

polar peptide bond

peptide O & N carry a small charge (- & +)

trans peptide bond

peptide O & H are on opposite sides

dihedral angles

2 angles per residue along backbone of protein that are free to rotate

steric hindrance

many choices of phi and psi don’t work and cause atoms to crash into each other

Ramachandran plot

phi vs. psi plot where blue areas show allowed options for phi and psi and dots are values for a particular protein

isoelectric point

pH at which a solute has no net electric charge and does not move in an electric field