Lecture 1

Question 1

What is the proteome?

Answer 1

All proteins found in living cell

Question 2

What is disease?

Answer 2

Imbalanced state of cellular protein generation and recycling. Ex. increased misfolding & aggregation, increased protein production. degradation.

Question 3

How does a cell maintain protein homeostasis (proteolysis)?

Answer 3

The cell is dynamic, assesses external and internal factors. Needs balance between production and functionalization (conformation of protein + recycling)

Question 4

Describe the protein homeostasis / proteostasis network

Answer 4

See notes

Question 5

What are the 2 major protein degradation machineries

Answer 5

1. Ubiquitin - proteasome systen (UPS).
   Substrate + ubiquitin = 26S proteasome = Degradation to oligopeptides
2. Autophagy - lysosome system.
   Isolation membrane = Autophagosome = Autolysosome (Autophagosome + lysosome) = degradation to amino acids

Question 6

Describe ubiquitination

Answer 6

See notes

Question 7

How does proteasome degrade polyubiquinated proteins?

Answer 7

Poly-ubiquitin chain + substrate –> binding —> unfolding —> unfolding —> deubiquitylation —> translocation + hydrolysis —> release of amino acid into cytoplasm.
THe diameter of protease is 20A; only degraded proteins are able to enter

Question 8

What are the 3 types of autophagy?

Answer 8

1. Macroautophagy (garbage bag). 2. Microautophagy (infold lysosome membrane sequesters, targets materials to degrade). 3. Chaperone - mediated autophagy (requires chaperone protein channeled to lysosome).

Question 9

What are the key steps of macroautophagy?

Answer 9

PAS/Isolation membrane; Phagophore + lysosome/vacuole – Nucleation —- Phagophore expansion —- Phagophore expanion —- Cargo recognition — Autophagosome. Vesicle completion —- fusion with lysosome —- Degradation and recycling

Question 10

What are the roles of autophagy?

Answer 10

Garbage removal, recycling, defense, energy management.

Question 11

What is the lysosome and how is this related to autophagy?

Answer 11

A lytic organelle containing hydrolytic enzymes which function at low pH. Proteins degraded through autophagy are eventually degraded by lysosome.

Question 12

The 6 steps of macrophagy?

Answer 12

1. Formation of phagophore.
2. Elongation and expansion of phagophore.
3. Engulf cargo/substrate/target
4. Enclose and generation of autophagosome
5. Fusion of autophagosome with lysosome
6. Breakdown and recycling of autophagosome inner membrane and content. Rate-limiting step: autophagosome formation