Lecture 7: Protein Folding

Question 1

Amino acids that prefer alpha helix

Answer 1

M Methionine
A Alanine
L Leucine
E Glutamate
K Lysine
R Arginine
H Histidine
Q Glutamine

Question 2

Amino acids that prefer Beta sheet

Answer 2

C Cystein
F Phenylalanine
W Tryptophan
T Threonine
I Isoleucine
Y Tyrosine
V Valine

Question 3

Amino acids that prefer reverse turn

Answer 3

S Serine
N Asparagine
D Aspartic acid
G Glycine
P Proline

Question 4

Protein disulfide isomerase function

Answer 4

Properly positions sulfide bonds by re-arranging non-native S-S

Question 5

S-S bonds in intra vs extracellular proteins

Answer 5

Intracellular lack S-S bonds

Extracellular typically have a few S-S bonds

Question 6

HSP 70

Answer 6

ATP driven

Reverses misfolds; newly synthesized proteins; unfold/refold of trafficked proteins

Question 7

HSP 90

Answer 7

For signal transduction proteins

Acts at late stage of folding of proteins

Question 8

Chemicals that will denature

Answer 8

Detergents (SDS)
Chaotropic agents (Urea)
Organic solvents (TCA)

Question 9

Circular dichromism

Answer 9

Used to study conformation of proteins in solution

Question 10

Molecular chaperons

Answer 10

Bind to unfolded/partially folded polypeptide chains
Prevent improper association of hydrophobic segments
Non-native folding/aggregation will not occur
Allow misfolded proteins to refold into native conformation

Question 11

Chaperonin mechanism

Answer 11

Unfolded polypeptide enters cylinder
Cylinder is capped and creates hydrophillic environment for protein to fold
Protein is released

Question 12

Proteasome

Answer 12

Digests ubiqutinated proteins

Question 13

26S proteasome consists of

Answer 13

2- 19S regulatory units

1- 20S catalytic core

Question 14

19S

Answer 14

Recognizes ubiquitinated proteins
Isopeptidase cleaves ubiquitin
Directs protein into catalytic core 20S

Question 15

20S

Answer 15

Catalytic core composed of 28 subunits

Sealed barrel, access controlled by 19S

Question 16

Proteasome and other proteases generate

Answer 16

Free amino acids that can be re-used for biosynthetic reactions

Question 17

Accessory proteins in folding include

Answer 17

PDI (protein disulfide isomerases)
PPI (peptidyl prolyl cis-trans isomerases)
Molecular chaperones HSP 70 (40)
Chaperonins
HSP 90
Nucleoplasmins
Small-HSP (HSP 27)