Protein degradation

Question 1

Define quality control.

Answer 1

The cellular mechanisms that recognize and remove the hydrophobic patches on proteins.

Question 2

What are the two aims of proteolysis?

Answer 2

1. quality control: to remove unwanted proteins by protein re-folding and proteolysis
2. to regulate various cellular processes

Question 3

Where does non-selective proteolysis take place?

Answer 3

lysosome

Question 4

Where are extracellular proteins degraded?

Answer 4

lysosome

Question 5

where are intracellular proteins degraded?

Answer 5

proteosome

Question 6

where does selective proteolysis take place?

Answer 6

proteosome

Question 7

List several lysosomal storage diseases.

Answer 7

1. hurler’s disease
2. tay-sach’s disease
3. gaucher disease
4. fabry disease

**all defects in breakdown of certain materials

Question 8

What are the steps from misfolding of a protein to cell damage/disease?

Answer 8

misfolding -> aggregation -> precipitation -> cell damage/disease

Question 9

List the neurodegnerative diseases caused by protein aggregation.

Answer 9

1. alzheimer’s
2. parkinson’s
3. huntingtons
4. ALS

Question 10

Describe the ER unfolded protein response.

Answer 10

• after protein synthesis on rough ER, ER proteins are directly translocated into the lumen and ER chaperones help protein folding into final conformation
• correctly folded proteins are packaged into vesicles and targeted to their final destinations
• incorrectly folded or misfolded proteins are targeted to the proteosome for degradation

Question 11

Define selective proteolysis.

Answer 11

Degradation in proteosome by ubiquitinated proteins

Question 12

Describe the beta subunits that give the proteolytic chamber its activity.

Answer 12

1. chymotrypsin-like (preference for tyrosine or phenylalanine)
2. trypsin-like (preference for arginine or lysine)
3. post-glutamyl (preference for glutamate or other acidic residue)

Question 13

what does the proteosome antechamber do?

Answer 13

It is a place for unfolded proteins to be stored before they enter the central chamber

Question 14

What are the subunits of the proteosome chamber ring?

Answer 14

a1-a7/b1-b7/b1-b7/al-a7

Question 15

Describe ubiquitin

Answer 15

76 amino acid peptide with seven internal lysines (for polyubiquitnation)

Question 16

How is ubiquitin linked to the protein?

Answer 16

carboxy-terminal glycine of ubiqutin is linked to lysine of the protein of interest. Other ubiqutiins are then added to internal lysines of the first ubiqutiin

Question 17

Roles of ubiqutiin.

Answer 17

1. histone regulation (mono-ub)
2. endocytosis (multi-ub)
3. proteosomal degradation (poly-ub at lys 48)
4. DNA repair (poly-ub)

Question 18

Where is ATPase used in ubiquitination?

Answer 18

activation of ubiquitin by ubiquitin activating enzyme, E1 (C-term glycine linked to cysteine of E1)

Question 19

Ubiquitin conjugating enzyme

Answer 19

E2

Question 20

Ubiquitin ligase

Answer 20

E3

Question 21

To what protein does the ub degradation signal of a protein bind?

Answer 21

E3

Question 22

Poly-ub chain conjugating factor

Answer 22

E4

Question 23

Which enzyme does poly-ub proofreading and targetng to 26S proteosome?

Answer 23

E4

Question 24

Optimal ubiquitin chain length

Answer 24

4-6

Question 25

What type of structure is formed from prion disease?

Answer 25

cross-beta filament aggregate

Question 26

Conformational change of prion protein when it is infectious

Answer 26

two alpha helices to four beta sheets

Question 27

How can E3 ligases be activated?

Answer 27

modifications: phosphates, ligands, allosteric binding

Question 28

How are degradation signals activated

Answer 28

phosphorylation, unmasking, destabilizing N-terminus

Question 29

Consequences of ubiquitination

Answer 29

1. changing conformation to modulate protein activity 2. creating protein binding sites (i.e. to E3 ligase) 3. masking protein binding sites

Question 30

Ubiquitin domain protein

Answer 30

domains related to ubiqutiin in sequence but are otherwise unrelated. these domains are responsible for recruitment of ubiquitinated substrates to the proteosome

Question 31

Ubiquitin like modifier

Answer 31

functions in analagous manner to ubiqutiin have similar structure to ubiqutiin all have C-term glycine and go through same conjugation process

Question 32

some types of ubiquitin like modifier

Answer 32

sumoylation nedylation Atg Urm

Question 33

how are ubiquitin like modifiers processed

Answer 33

many UBLs are synthesized as precursors and need to be processed by UBL-specific isopeptidases to expose C-terminal glycine that is activated and linked to E1

Question 34

How are sumoylation and ub different

Answer 34

cause different consequences to protein functions - ub of PCNA clamp causes error-free DNA repair - sumoylation of PCNA clamp causes DNA replication and inhibits repair

Question 35

Function of 19S proteosome cap

Answer 35

six subunit protein ring and ATPases to unfold protein after binding to Ub signal and cleaving it. proteins AAA called unfoldases

Question 36

True or false. the proteosome is very large

Answer 36

true. 26S