Levels of protein conformation

Question 1

where are cis bonds usually found?

Answer 1

in a surface-accessible bend, coil, or turn conformation

Question 2

what are prolyl isomerases?

Answer 2

function as protein folding chaperones; the X-prolyl bond does not go to cis on its own, needs help from a prolyl isomerase; PI may functiom to regulate the function of the protein that the X-prolyl bond is in
--proline trans to cis may be the RLS of protein folding

Question 3

where is the phi bond?

Answer 3

between the alpha carbon and the nitrogen;

Question 4

where is the psi bond?

Answer 4

between the alpha carbon and the carboxyl carbon

Question 5

what are the six atoms in a peptide bond, and what conformation are they?

Answer 5

Calpha, C, O, N, H, and Calpha; planar

Question 6

what is the difference between conformation and configuration?

Answer 6

conf=no bonds broken

config= bonds broken

Question 7

most proteins have a large difference in Free e between cis and trans–but proline has smaller free e–> more tolerant of cis conformation/ or the activation energy might be lower/higher

Answer 7

ya

Question 8

having an equal number of H-bnd donors (N-H) and acceptors (=O) in a peptide bond is important from the perspective of optimizing H bonds

Answer 8

ya