Lecture 7 - Protein Folding II

Question 1

How to calculate propensity for a given 2* structure

Answer 1

P= frequency/all AAs

Ex: P of beta-sheets=0.23/19 AA long protein
=0.012

Question 2

A given peptide is 20 amino acids long. 5 of those amino acids form an alpha-helix. What is the frequency of alpha-AAs?

Answer 2

Frequency= 5/20

= 0.25

Question 3

A given peptide has an alpha helix frequency of 0.25. Given that the protein is 13 amino acids long, what is the propensity for alpha-helices?

Answer 3

P = freq/all AA
= 0.25/13
= 0.019

Question 4

What two broad mechanisms can be used for protein denaturation?

Answer 4

Chemical and Physical

Question 5

Used to break most hydrogen bonds and hydrophobic interactions

Answer 5

Heat

Question 6

Changes to pH produce protein _____

Answer 6

denaturation

Question 7

Aside from changes to pH and addition of heat, what is the third thing to denature proteins?

Answer 7

agitation

Question 8

How do detergents denature proteins?

Answer 8

There are three “parts” to a detergent: (-) charged polar head, fatty acid tails, and a (+) ion to balance the (-) polar head. SDS acts to disrupt non-covalent bonds

Question 9

Acts to denature proteins by interfering with hydrogen bonds.

Answer 9

Chaotropic agent

Question 10

How do organic solvents denature proteins?

Answer 10

The electronegative oxygen in solvents functions to disrupt hydrogen bonding (denatures 2* structure)

Question 11

How do reducing agents denature proteins?

Answer 11

-S-S- bonds are part of the 2* structure; the reducing agents reduce disulfide bonds to thiols (from -S-S- to -SH and HS-)

Question 12

Aromatic rings absorb UV light at ____

Answer 12

280 nm

Question 13

Peptide bonds absorb UV light at _____

Answer 13

200 nm

Question 14

How does circular dichromism (CD) act to determine protein structure?

Answer 14

Amino acids will rotate polarized light clockwise (+) or counter-clockwise (-)

Question 15

Describe fluorescence analysis of protein structure

Answer 15

Aromatic AAs (W, F, Y) all have natural fluorescence. This is measured to determine the presence of aromatic AAs.

Question 16

Corrects misfolding and adds -S-S- bonds to newly synthesized proteins

Answer 16

PDI - protein disulfide isomerase

Question 17

Reduces steric hindrance by moving large groups from cis to trans position

Answer 17

PPI - peptidyl prolyl cis-trans isomerase

Question 18

Reverses mis-folded proteins; acts to unfold/refold proteins that are being trafficked; utilizes ATP

Answer 18

HSP-70

Question 19

Mitochondria specific HSPs

Answer 19

HSP-60; HSP-70

Question 20

Describe the GroEL/ES system

Answer 20

1) Unfolded protein attaches to GroEL cavity
2) 7ATP bind to GroEL and GroES cap binds
3) Protein undergoes new folding with loss of 7 Pi
4) 7 additional ATP bind to “swell” GroEL, GroES cap dissociates
5) Newly folded protein released

Question 21

How to calculate alpha-helix frequency

Answer 21

F-alpha= (AA-alpha/all AAs)

Ex: F-alpha= (13 AA-alpha/19 AA long protein)
F-alpha= 0.68