Protein Degradation

Question 1

What is the types of protein and how are they different?

Answer 1

Structural and regulatory protein

They differ in:
- Lifelines: Structural > regulatory
- Role they play

Question 2

What is the purpose of protein degradation?

Answer 2

Ensure proper regulation of cell signaling pathways through maintaining normal protein turnovers

Removing misfolded / damaged protein that can cause abnormal cellular activity

Question 3

Qn. The HIF-1 alpha is responsible for inducing expression of genes involved in angiogenesis, cell migration and glycolytic pathway. What happens if it is not degraded properly?

Answer 3

Accumulation of HIF-1 alpha can lead to increase in transcriptional activity

Increases expression of target genes such as VEGF and MMP

This ultimately leads to an increase in invasion, metastasis and angiogenesis

Question 4

What are the two ways protein degradation occurs?

Answer 4

Lysosomal degradation and proteosomal degradation

Question 5

What is the difference between lysosomal degradation and protein degradation?

HINT: Consider who is involved, the specificity of the process and what are the criteria for it to be degraded

Answer 5

Lysosomal degradation:
- Happens in lysosomes
- Non specific process
- Needs to be internalized by endocytosis before being degraded by lysosomes

Protein degradation
- Degraded by 26S proteosome
- Specific
- Ubiquitinated and some non ubitiquinated proteins

Question 6

Define endocytosis

Answer 6

Process involving cells taking in extracellular substances by internalizing them in a vesicle

Question 7

What are the 3 ways endocytosis can take place?

Answer 7

Phagocytosis
Pinocytosis
Receptor mediated endocytosis

Question 8

What do phagocytosis targets and how do they function?

Answer 8

Target large solid particles such as debris, dead cells, protein aggregates, pathogenic microorganisms

Function: Cell eating by phagosomes

Question 9

What do pinocytosis target and how do they undergo endocytosis?

Answer 9

Fluids and solute dissolved in fluids

Do so by cell drinking of ECF through budding of small vesicles from membrane

Question 10

How does receptor mediated endocytosis target specific molecules and how do they undergo endocytosis?

Answer 10

Receptors recognize the ligands expressed on cell membrane of cell

Work by binding with extracellular macromolecules with receptors
Internalizing them into coated vesicles
Fuse with endosomes and then they are send to lysosomes for degradation

Question 11

What is the function of a proteosome?

Answer 11

Responsible for specific degradation of regulatory proteins and removal of misfolded and damaged proteins

Question 12

What are the two parts of the proteosome and how do they work?

Answer 12

19S regulatory particle: Provide entrance to degradation channel. Helps with substrate recognition, unfolding and translocation

20S core: Act as degradation chamber

Question 13

How does the proteosome degrades proteins?

Answer 13

Enters the narrow entrance to channel at 13A

Folded proteins then partially unfold before they can be translocated into 20S core particle

Upon entering the channel, protein unfolds and stretches along channel

Unfolded protein is hydrolyzed to short peptides and released from opposite end of the channel

Question 14

How do the 19S regulatory particles help?

Answer 14

Contains ATPase subunits which gates entrance to degradation channel and help with substrate recognition

Question 15

Is the proteolysis of substances selective?

Answer 15

Yes

Question 16

What is the minimal signal necessary for protein targeting?

Answer 16

Chain of 4 Ub monomers linked with Lys48 as target

Question 17

Describe what is monoubiquitination

Answer 17

Act as regulatory modification for molecules

Question 18

Provide some examples of monoubiquitination

Answer 18

Histones and transcription factors: used to regulate transcription

Surface cell receptors: signal for endocytosis and degradation of lysosomes

Question 19

How is the polyubiquitin tag made

Answer 19

Ubiquitin tag is cleaved by deubiquitinating enzymes into monomers first

When monomers escape from proteasome, it is recycled to label other protein substrates

Question 20

What are the ways proteins are delivered to proteasomes?

Answer 20

1. Binding directly to proteasome through direct interaction with 19S regulatory protein
2. Brought to proteasome by adaptor protein binding both proteasome and polyubiquitin chain
3. Degraded by proteasome without being ubiquitinated (RARE)

Question 21

What happens when misfolded / damaged proteins undergo degradation?

Answer 21

Ub molecules are removed from the target protein

Target protein then unfolds

Unfolded protein gets transferred into 20S proteasome core to be broken to smaller fragments

Released at other end of 19S