Protein Folding and Unfolding

Question 1

Pauling

Answer 1

alpha and beta is enough to fold-all from one polymer

Question 2

Anfinsen

Answer 2

all needed to fold is in polypeptide sequence

Question 3

Levinthals

Answer 3

some sort of process that drives folding preferred way

Question 4

A4- principal of minimum frustration

Answer 4

amino acids position themselves in way to do folding

Question 5

Why can’t all proteins self fold

Answer 5

locailzed high energy transition state

Question 6

groEL chaperone

Answer 6

conserved across evolution

Question 7

protein repair vs deg

Answer 7

try repair numerous times, then degrade

Question 8

chaperone abilities

Answer 8

matchmaker, trafficker, quality control, protein disassembly, molecular CPR, complex assembly (subunits in proper place)

Question 9

chaperone role during protein syn

Answer 9

guide during folding (much done by RNA itself however), protect nascent dna, avoid kinetic dead ends

Question 10

cotranslational protein degradation

Answer 10

irreversibly damaged protein brought immediately from synthesis site to protease

Question 11

proteosome strcuture

Answer 11

four rings, outer are identical (alpha subunit), inner are identical, hydrolytic activity (beta unit)

Question 12

UMP1

Answer 12

chaperone for proteasome synthesis, first target of proteasome

Question 13

interactions that impact folding

Answer 13

hydrophobic core, electrostatic, VDW forces, disulfide bonds, metal coordination

Question 14

Molten globule+final 2 steps

Answer 14

Almost completely folded-hydrophobic collapse and water exclusion

Question 15

Hierarchical, nucleation, and hydrophobic collapse protein folding models

Answer 15

Secondary structures form first then combine, cascade, obvious

Question 16

disulfide bond

Answer 16

even if things are cut one way-as long as held close together (by disulfide bond in this case) can re attach

Question 17

RING Motif

Answer 17

Zinc coordation domain, coordinates metal atom which traps conformation in many TFs

Question 18

Agents that promote unfolding

Answer 18

Temp, pH, Urea, pressure, guanidine, organic solvents

Question 19

Fold to tertiary or quaternary proteins (in sequence)

Answer 19

Use chaperones to not immediately bind with proximal protein-instead move on to tertiary/quat

Question 20

Isomerase chaperones

Answer 20

Clip protein and reform

Question 21

ERAD

Answer 21

Endoplasmic retiduclum assocated degradation

1. Ribo and chap dock onto ER membrane (send in unfolded=presence of ER chaperones)
2. Something doesn’t work out-send unfolded protein back out way it came in
3. Proteasome waiting at other end of tunnel

Question 22

CFTR Delta 508

Answer 22

Protein folds extremely slowly-protease destroys before full folding complete

Question 23

Protein aggregation

Answer 23

Common cause of many neurodegen diseases (ex Parkinsons/Huntingtons)

Question 24

chaperone and protease

Answer 24

very similar structure (non polar barrel in both) also subunit congruency is the same

Question 25

Key features of chaperone

Answer 25

not all need ATP, leave after doing job

Question 26

Important determinants for protein folding

Answer 26

hydrophobic core, electrostatic, VDW forces, disulfide bonds, metal coordination

Question 27

Sig of water exclusion

Answer 27

hydrophobic collapse results in very close but not final-then water exlcuion is final driving force in folding

Question 28

Biochem activités that require chaperones

Answer 28

3 main-assembling large complex, secretion, repairing damaged but many more

Question 29

Different forces that stabilize native protein structure

Answer 29

Hierarchical , Nucleation/Condensation, Hydrophobic Collapse

Question 30

Proteasome/rearrageing scaffolding mech

Answer 30

bind with non polar residues, use 7 ATP, shift non polar residues away pulling apart molecule