Protein Folding

Question 1

Disfavorable energy changes from protein folding

Answer 1

random coil to folded protein

Question 2

Favorable entropy changes

Answer 2

• hydrophobic effect
• favorable enthalpy changes (stronger H-bonds, salt bridges, dipole interactions, and VDW)

Question 3

what provides most of the reduction in free energy that stabilizes the folded conformation over unfolded

Answer 3

hydrophobic effect

Question 4

hydrophilic surface contribution to stabilization

Answer 4

small, bc already well satisfied by waters in the unfolded state

Question 5

Buried H-bonds benefits

Answer 5

not full benefit bc already partially satisfied by water in unfolded state

Question 6

buried salt bridges are stronger where

Answer 6

low dielectric (inside proteins)

Question 7

hydrophobic effect contributes to ______ of compact structure

Answer 7

stability

Question 8

noncovalent interactions contribute to the _______ of unique folded structure

Answer 8

specificity

Question 9

how do disulfide bonds affect protein stability

Answer 9

no change to entropy

Question 10

domain

Answer 10

independently folding segment of protein sequence

Question 11

motif

Answer 11

small section of three dimensional structure
usually pretty important (common interacting domain, catalysis)

Question 12

rossman fold

Answer 12

binds to nucleotides

Question 13

quaternary structure show that many proteins form oligomeric complexes that ______

Answer 13

do not repeat to form fibers

Question 14

4 structures is stabilized by

Answer 14

noncovalent interactions or disulfide bondsbetween different polypeptides

Question 15

Levinthal’s Paradox

Answer 15

if stretch out pp, when refold, tons of diff ways to fold. not enuff time to reford in the world

Question 16

what to apply to unfold protein

Answer 16

heat
chemical denaturants (urea and guanidinium chloride)

Question 17

order of protein folding

Answer 17

1. formation of local secondary structure
2. local protein domains
3. hydrophobic collapse to molten globule (hydrophobic core comes together, clathrate cage)
4. native side chain interactions between domains between domains the crystalline packing of hydrophic core

Question 18

disulfide isomerases

Answer 18

speed up exchange of incorrect with correct disulfides

Question 19

prolyl cis-trans isomerases

Answer 19

flip proline between cis and trans isomers affecting backbone

Question 20

molecular chaperones

Answer 20

binds misfolded/partially unfolded proteins, uses ATP to unfold