Lecture 7: Protein Folding II

Question 0

What are the main contributing factors to protein stability?

Answer 0

Disulfide Bonding- Occurs outside the cell, b/c the protein is no longer protected and needs to become more stable to survive in the extracellular environment
Hydrophobic Effect- This causes the fat to stay inside the protein (fat-fat interactions)
Oligomers- Formation of dimers, tetramers, etc. creates added stability

Question 1

What is protein turnover?

Answer 1

How quickly proteins are translated (created) or degraded (broken down) by ribosomes

Question 2

What are UPS and UPR?

Answer 2

UPS- Unfolded Protein Stress
UPR- Unfolded Protein Response
Where a protein is unfolded, undergoes a stress and can no longer fold into its natural form

Question 3

Conditions for protein denaturation

Answer 3

Heat
pH
Agitation

Question 4

Chemicals that cause protein denaturation

Answer 4

Detergents
Organic Solvents (alcohol)
Chaotropic Agents (urea & guanidinium chloride): unravel proteins

Question 5

Methods of analysis of denatured proteins

Answer 5

Turbidity: look at protein and raise temp. until cloudy substance appears
Circular Dichroism: look at secondary structure and determine number of alpha-helices
UV Absorption/Fluorescence: absorbance and fluorescence will change depending on folder/unfolded protein
Biological Activity: does the protein function as it’s supposed to

Question 6

PDI (protein disulfide isomerases)

Answer 6

An accessory protein that recognizes incorrect disulfide linkages within proteins that are going to be exported, then corrects the errors so the protein can be exported

Question 7

PPI (protein cis/trans prolyl isomerases)

Answer 7

An accessory protein that corrects the cis/trans direction of a proline in a chain

Question 8

Molecular Chaperones

Answer 8

HSP70: ATP-driven and it reverses misfolds and allows unfolding/refolding for protein to slither into mitochondria (through membrane)
Small-HSP: Prevent aggregation then bring in HSP70 to allow proper folding
HSP90: For signal transduction molecules and to assist unstructured proteins
Chaperonins: XXXXX
Nucleoplasmins: Nucleosome formation and ribosome biogenesis

Question 9

What are the 2 mechanisms used by Chaperonins

Answer 9

Passive (Anfinsen cage): Put protein in a cage, away from other proteins and allow it to unfold and refold on its own until it’s correct
Active (iterative annealling): Inner portion of basket interacts with misfolded area and pulls it apart repetitively until it finds the correct folding structure