CHEM351, Unit 1: secondary structures

edman degredation

method of amino acid sequencing, removes the terminal residue of an amino acid one by one

what AA length works best for edman degredation?

30-40 AA

fragmentation

certain substances that cleave specific amino acids

what is the difference between configuration and conformation?

configuration describes the presence of chiral structures or double bonds, conformation describes the spacial arrangement of single bonded proteins

torsion angles

describes the rotation of bonds from your perspective

positive torsion angle

clockwise rotation

negative torsion angle

counterclockwise rotation

why can peptide bonds not rotate?

due to partial double bond character

psi angle

describes the angle of the bond from the alpha carbon to the carbonyl

phi angle

describes the angle of the bond from the amine to the alpha carbon

omega angle

describes the angle of the bond from the carbonyl to the amine

what is the omega angle of the trans a-carbon conformer

180

what is the omega angle of the cis a-carbon conformer?

0

a-helix

polypeptide is wound around an imaginary axis, r groups protrude outwards

pitch

distance between turns, 0.54 nm

rise

distance between each AA, 0.15 nm

how many AA per turn?

3.6

between what amino acids are hydrogen bonds in an a-helix?

n and n+4

what is the direction of the net helix dipole?

positive on top, negative on bottom

what is the angle between each amino acid?

100 degrees

amphipathic helix

has a polar side and a nonpolar side

what two amino acids make a-helices unstable

glycine and proline

beta-sheet

extended conformation where the backbone is extended into a zigzag formation, r groups are pointed either up or down

what are the two types of beta sheets?

antiparallel and parallel

antiparallel beta sheet?

each side has alternating termini, more stable due to having a more regular arrangement of hydrogen bonds

beta turn

4 AA connection in antiparallel beta sheets that make a 180 degree turn

what two AA are stabilizing for beta turns

glycine and proline