protein secondary structure Flashcards
what favorable interactions in proteins create the native fold?
hydrophobic effect
hydrogen bonds
London dispersion
electrostatic interactions
what are phi and psi bonds/angles? draw a peptide bond and identify them
slide 6-7
phi: angle around the alpha C – N bond
psi: angle around the alpha C – O bond
what atoms determine the dihedral angle?
a dihedral angle is a measure of the angle around the phi or psi bonds and so is determined by the alpha C, peptide N, and peptide bond C. each angle is determined by 4 atoms
it’s easier to visualize drawn out. draw peptide bond and label phi and psi bonds and atoms used to determine angles
what does a ramachandran plot show?
the distribution of phi and psi dihedral angles that are found in a protein. be able to recognize roughly where each type of secondary structure is found on these plots. slide 9
what creates the backbone structure of alpha helices?
hydrogen bonds between the amides H and carbonyl O of an n and n+4 amino acids
how can sequence affect helix stability?
interactions between R groups of AAs 3-4 residues apart and bulkiness of R groups can affect. Appearance of Pro and Gly residues will break helix because Pro does not allow rotation around the N-Calpha bond and Gly has a tiny R group that can support other conformations
does the alpha helix have a dipole?
yes is has a large macroscopic dipole moment with a + charged amino terminus and - charged carboxyl terminus. negatively charged residues often occur near the positive end of the helix dipole ??
what interactions create Beta sheets?
the planarity of the peptide bond and tetrahedral geometry of the alpha carbon create a pleated sheet like structure. Sheet like arrangement is held together by hydrogen bonds between amides H and carbonyls O in different strands
describe the two possible formations of beta sheets?
parallel: H bonded strands run in the same direction, results in bent H bonds
antiparallel: H bonded strands run in opposite directions, results in linear H bonds
see slide 18-20 for visualization of H bonding patterns
how are beta turns allowed?
a beta turn is a 180 degree turn accomplished one 4 amino acids. the turn is stabilized by a H bond from a carbonyl O to amine H three residues down the sequence. Pro in pos 2 or Gly in pos 3 are common
why are Pro and Gly found in beta turns in position 2 and 3?
Pro: peptide bonds involving proline may have a cis configuration which allows for 180 degree turns
Gly: the very small R group allows for conformations that other AA’s can’t have. This includes a conformation allowing beta turns
what is CD and what does it look like for alpha helix vs beta sheet vs random coil?
Circular Dichroism analysis measures the molar absorption difference of left and right circularly polarized light (?? I don’t think that part is important). Beta has dip at 215 and alpha has two dips at 208 and 222. see slide 26 for how each type of structure looks
