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CORE Block 4 > Protein degradation > Flashcards

Protein degradation Flashcards

1
Q

Define quality control.

A

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

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2
Q

What are the two aims of proteolysis?

A
  1. quality control: to remove unwanted proteins by protein re-folding and proteolysis
  2. to regulate various cellular processes
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3
Q

Where does non-selective proteolysis take place?

A

lysosome

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4
Q

Where are extracellular proteins degraded?

A

lysosome

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5
Q

where are intracellular proteins degraded?

A

proteosome

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6
Q

where does selective proteolysis take place?

A

proteosome

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7
Q

List several lysosomal storage diseases.

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

**all defects in breakdown of certain materials

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8
Q

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

A

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

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9
Q

List the neurodegnerative diseases caused by protein aggregation.

A
  1. alzheimer’s
  2. parkinson’s
  3. huntingtons
  4. ALS
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10
Q

Describe the ER unfolded protein response.

A
  • 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
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11
Q

Define selective proteolysis.

A

Degradation in proteosome by ubiquitinated proteins

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12
Q

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

A
  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)
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13
Q

what does the proteosome antechamber do?

A

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

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14
Q

What are the subunits of the proteosome chamber ring?

A

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

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15
Q

Describe ubiquitin

A

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

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16
Q

How is ubiquitin linked to the protein?

A

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

17
Q

Roles of ubiqutiin.

A
  1. histone regulation (mono-ub)
  2. endocytosis (multi-ub)
  3. proteosomal degradation (poly-ub at lys 48)
  4. DNA repair (poly-ub)
18
Q

Where is ATPase used in ubiquitination?

A

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

19
Q

Ubiquitin conjugating enzyme

A

E2

20
Q

Ubiquitin ligase

A

E3

21
Q

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

A

E3

22
Q

Poly-ub chain conjugating factor

A

E4

23
Q

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

A

E4

24
Q

Optimal ubiquitin chain length

A

4-6

25
Q

What type of structure is formed from prion disease?

A

cross-beta filament aggregate

26
Q

Conformational change of prion protein when it is infectious

A

two alpha helices to four beta sheets

27
Q

How can E3 ligases be activated?

A

modifications: phosphates, ligands, allosteric binding

28
Q

How are degradation signals activated

A

phosphorylation, unmasking, destabilizing N-terminus

29
Q

Consequences of ubiquitination

A
  1. changing conformation to modulate protein activity
  2. creating protein binding sites (i.e. to E3 ligase)
  3. masking protein binding sites
30
Q

Ubiquitin domain protein

A

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

31
Q

Ubiquitin like modifier

A

functions in analagous manner to ubiqutiin

have similar structure to ubiqutiin

all have C-term glycine and go through same conjugation process

32
Q

some types of ubiquitin like modifier

A

sumoylation

nedylation

Atg

Urm

33
Q

how are ubiquitin like modifiers processed

A

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

34
Q

How are sumoylation and ub different

A

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
35
Q

Function of 19S proteosome cap

A

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

36
Q

True or false. the proteosome is very large

A

true. 26S

CORE Block 4 (8 decks)

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