Proteins 3 Flashcards
primary protein structure
sequence of a chain of amino acids
secondary protein structure
regular, local arrangement of polypeptide chain
tertiary protein structure
complete folding of a single chain
quaternary protein structure
association of multiple chains into multi-subunit structures
residue
an amino acid in a polypeptide chain
no. of peptide bonds in a polypeptide chain
no. of residues - 1
features of polypeptides in 3D
- flexible yet conformationally restricted
- peptide bond is essentially planar
- peptide bond is uncharged
2 configurations for a planar peptide bond
Trans, Cis
Cis causes steric clashes to arise, so Trans is strongly favoured
Alpha helix
This conformation is formed when the polypeptide chain is twisted by the same amount about phi and psi rotation
a helix may be characterized by the number, n, of peptide units per helical turn, by its pitch, p, the distance the helix rises along its axis per turn and by helical rise per repeating unit, d=p/n
define a repeat unit
a single turn of the helix
what is an alpha helix stabilised by?
hydrogen bonds between the NH and CO groups of the main chain
if the helix has a positive value for n
Right-handed helix, anticlockwise
if the helix has a negative value for n
Left-handed helix, clockwise
helical structures
only one helical polypeptide conformation has simultaneously allowed conformation angles and a favourable hydrogen bonding patter –> the alpha helix
the polypeptide made from L-alpha amino acid residues is …
right handed
torsion angles (phi)= -57 (psi) = -47 n=3.6 residues per turn p=5.4 Å d=1.5 Å
the polypeptide made from D-alpha amino acids residues is …
left handed
torsion angles phi = 57 psi = 47 n= -3.6 residues per turn p=5.4 Å d=1.5 Å
are essentially all alpha helices in proteins right or left-handed?
right handed
are alpha helices common in fibrous or globular proteins?
both
the combination of multiple alpha helices by loop and turn can construct large proteins such as Ferrin
Beta pleated sheet
composed of two or more polypeptide chains called β strands.
- common structural motifs in proteins
- β strand is almost fully extended. A range of extended structures are sterically allowed
antiparallel β sheet
neighbouring hydrogen bonded polypeptide chains run in opposite directions
parallel β sheet
hydrogen bonded chains extend in the same direction
how do β sheets compare with alpha helices
β sheets are structurally diverse more than α helices
what is a dipole moment
the product of magnitude of electronic charge of the molecule and the internuclear distance between the atoms in a molecule
which type of secondary structure has dipole moments?
alpha helices have a dipole moment, beta sheets have no dipole moment
