Protein structure Flashcards
how are peptide bonds formed in terms of orientation of the amino acids
one has to invert
reduce steric clashes between R groups
why does the backbone of a polypeptide have high hydrogen-bonding potential
C=O hydrogen bond acceptor
NH hydrogen bond donor
peptide
<50 amino acids
mass of an amino acid
110 Da
1Da
1g/mol
why can polypeptides for tightly packed globular structures
peptide bonds are uncharged
characteristics of peptide bonds
planar
cannot rotate freely due to partial double bond character that shortens the bond
why do peptide bonds have double bond character
electrons in the nitrogen can be delocalised into the peptide bond
why are trans isomers more common
cis isomers are unfavourable due to steric clashes
proline isomers
both cis and trans have steric clashes as the side chain is bonded both to the alpha carbon and the amino group to form a five membered ring
how can proteins fold if there is no rotation about the peptide bond
alpha carbon-carboxyl bond and alpha carbon-amine bond are single bonds that can freely rotate
dihedral angles
phi
psi
phi
angle of rotation about the bond between the nitrogen and the alpha carbon atom
psi
angle of rotation about the bond between the carbonyl atom and the alpha carbon atom
Ramachandran plot
shows which combinations of phi and psi do not cause steric clashes so are possible.
secondary structures
alpha helix
beta sheet
loop
alpha helix
rod like structure of a tightly coiled backbone and a helical array of side chains
how many residues per helical turn?
distance of a turn?
3.6
5.4A
dihedral angles of amino acids in an alpha helix
phi=-57
psi=-47
why are left handed alpha helices rare
L amino acids would clash
why do alpha helices have a dipole moment
all amino groups point up and all carbonyl groups point down: N terminus and C terminus
how many degrees is each residue separated by
100
structure of beta pleated sheets
2 or more polypeptide chains called beta strands
almost fully extended
Side chains of adjacent amino acids point in opposite directions
distance between adjacent amino acids in beta strand
3.5A
dihedral angles of amino acids in a beta strand
phi -120
psi+120
why can large side chains be accepted on beta strands
7A between amino acids orientated the same way so chance of steric clashes is low
how do beta sheets form
linking two or more beta strands by hydrogen bonds
antiparallel beta sheet
adjacent chains run in opposite directions
H bonds between NH and CO connect each amino acid to a single amino acid on adjacent strand (one amino acid on one strand forms 2H bonds with another)
parallel beta sheet
adjacent strands run in the same direction
each amino acid on one strand hydrogen bonds with two amino acids on the adjacent strand
why dont beta sheets have a dipole
dipoles on adjacent amino acids cancel out as they are in opposite orientation
why arent beta sheets perfectly planar?
twist slightly due to tug of war between conformational energies of the side chain (minimising steric clashes) and maximal H-bonding
why don’t proline or glycine exist in these secondary structures
glycine is too flexible so not energetically favourable
proline forms kinks in the chain
loops
join secondary structures together and change the direction of a polypeptide chain
type 1 loop
proline in the second position- kink allows hydrogen bond between 1 and 4 amino acids
type 2 loop
glycine in position 3- flexibility allows it to form different conformations, H bond between 1 and 4 amino acids
