Lecture 7 - Protein Folding II Flashcards Preview

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Flashcards in Lecture 7 - Protein Folding II Deck (21):
1

How to calculate propensity for a given 2* structure

P= frequency/all AAs

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

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?

Frequency= 5/20
= 0.25

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?

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

4

What two broad mechanisms can be used for protein denaturation?

Chemical and Physical

5

Used to break most hydrogen bonds and hydrophobic interactions

Heat

6

Changes to pH produce protein _____

denaturation

7

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

agitation

8

How do detergents denature proteins?

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

9

Acts to denature proteins by interfering with hydrogen bonds.

Chaotropic agent

10

How do organic solvents denature proteins?

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

11

How do reducing agents denature proteins?

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

12

Aromatic rings absorb UV light at ____

280 nm

13

Peptide bonds absorb UV light at _____

200 nm

14

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

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

15

Describe fluorescence analysis of protein structure

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

16

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

PDI - protein disulfide isomerase

17

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

PPI - peptidyl prolyl cis-trans isomerase

18

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

HSP-70

19

Mitochondria specific HSPs

HSP-60; HSP-70

20

Describe the GroEL/ES system

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

21

How to calculate alpha-helix frequency

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

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