Lecture 6: Protein folding II

Question 1

LO1: Know how to predict the secondary structure of a protein based on conformational preferences of AA residues

Answer 1

• Secondary structures- alpha helixes and B sheets
• **Chou-Fasman predicts secondary structures in proteins
• AA have diff propensities for forming secondary structures

Question 2

Chou-Fasman

Answer 2

Method for prediction of secondary structures in proteins
P=Propensity/Natural inclination
f= aa in alpha helix/ all aa
P=f/All aa

Question 3

Tertiary structure

Answer 3

Spatial arrangement of AA residues that are far apart in the sequence and to the pattern of DISULFIDE (S-S) BONDS
Ex: myoglobin

Question 4

Protein disulfide isomerase (PDI)

Answer 4

Rearranges the polypeptide’s non-native S-S bonds

[incorrect disulfide bonds –> via PDI –> correct disulfide bonds]

Question 5

Accessory Proteins

Answer 5

• PDI (Protein Disulfide Isomerases)
• PPI (Peptidyl prolyl cis-trans isomerases)
• Molecular chaperones (HSP70, HSP40, HSP90, HSP27)

Question 6

Molecular chaperones

Answer 6

1. HSP70 (HSP40) - ATP driven
2. Chaperonins- HSP90 (sig transduction proteins)
3. Nucleoplasmins - HSP27, alpha crystallin (Small-HSP

Question 7

Bovine insulin

Answer 7

Consists of 2 chains linked by disulfide bonds; alpha chain has an intra-chain disulfide bond

–> Note protein folding: ALL OR NONE PROCESS

Question 8

Quaternary Structure

Answer 8

Spatial arrangement of subunits and nature of their interaction
Ex: Hb

Question 9

Protein denaturation (conditions and chemicals)

Answer 9

1. Conditions (heat, pH, agitation)
2. Chemicals:
   - Detergents-SDS
   - Chaotropic agents (urea, guanidine hydrochloride)
   - Organic solvents (TCA)

Question 10

Protein denaturation (Method of analysis)

Answer 10

• Turbidity
• Circular dichroism (CD)
• UV absorption
• Fluorescence
• Biological activity

Question 11

Chaperones

Answer 11

Soluble –> partial misfolding

Insoluble–> terminal misfolding

Question 12

Molecular chaperones

Answer 12

1. Heat Shock Proteins (HsP)

2. Chaperonins (protein folding container)

Question 13

HSP

Answer 13

Hsp70 family- coordinates cellular function by directing substrates for unfolding, disaggregation, refolding or degradation

Hsp90 family- integrates signaling functions, acting at a late stage of folding of substrates

Question 14

Chaperonins

Answer 14

• Hsp 60 (GroEL)

- Hsp10 (GroES/co-chap)

Question 15

Protein turnover

Answer 15

• Every cell has lifespan
• Cell must remove aged proteins as well as damaged proteins
• # of pathological diseases are associated with protein aggregation