proteostasis

Question 1

regulation of proteostasis largely controlled by

Answer 1

access, since degradative enzymes are sequestered into compartments

Question 2

why does protein degradation matter? (3)

Answer 2

allows cells to respond to changing conditions or stress, ditch misfolded or mutated proteins, and rapidly turn cellular processes on or off

Question 3

two examples of processes which are acutely regulated by protein degradation

Answer 3

cell cycle progression, response to stimuli

Question 4

lysosomal degradation is inhibited by

Answer 4

weak bases (ie chloroquine or ammonium chloride

Question 5

proteosome specific inhibitors

Answer 5

MG-132, etc

Question 6

EGFR internalization and degradation pathway

Answer 6

ligand binding, internalization by clathrin-coated vesicles, deliver to lysosome for degradation. Receptor down regulation terminates signal

Question 7

What happens to internalized receptors between the early endosome and the lysosome?

Answer 7

Internalized receptors are incorporated into multi-vesicular bodies - AKA late endosomes

Question 8

What are vesicles called within the MVBs?

Answer 8

Intra-lumenal vesicles, which bud inward from the surface to the lumen, away from cytosol

Question 9

What are the coats for ILV formation?

Answer 9

ESCRT complexes

Question 10

how does HIV recruit ESCRT for its own purposes?

Answer 10

to exit the cell, gag protein something

Question 11

autophagy

Answer 11

allows cells to break down its own material and dispose of or re-use obsolete parts of the cell itself

Question 12

autophagy steps (4)

Answer 12

1. Starvation signal
2. Formation of a double membrane around cytosolic components to form an autophagosome
3. Autophagosome fuses with lysosome
4. Lysosomal hydrolases break down autophagic body, allowing recycling

Question 13

Which E is the ubiquitin ligase?

Answer 13

E3

Question 14

what results in ubiquitin smear

Answer 14

lots of heterogeneity in MW in targeted proteins

Question 15

26S proteosome made up of what two major structural components

Answer 15

20S core proteolysis, 19S cap regulatory

Question 16

20S core structure

Answer 16

four 7 membered rings with alpha and beta subunits, proteolyticaly active sites are on the beta subunits and face inside.

Question 17

T/F. Unfolded proteins can enter proteolytic channel

Answer 17

False, they must be unfolded and threaded through

Question 18

19s cap roles (3)

Answer 18

Ub receptor binds ubiquitinated proteins
Unfolds protein and feeds into 20S core
Deubiquitinates substrate to recycle

Question 19

isopeptide

Answer 19

branched polypeptide, ub is linked to substrates through an isopeptide bond

Question 20

What is recognized by 19S proteosome cap

Answer 20

K48 chain >4

Question 21

E1-Ub function

Answer 21

Ubiquitin activating enzyme, ATP dependent rxn. Can transfer Ub to E2

Question 22

E2-Ub function

Answer 22

receive Ub from E1 and eith help of E3 specificity factor conjugate Ub to target proteins

Question 23

Specificity factor in Ub cascade

Answer 23

E3-ligase

Question 24

Two classes of E3s

Answer 24

HECT (covalent intermediate) and RING (no covalent intermediate)

Question 25

Three ways proteins can be recognized for degradation

Answer 25

1. Motifs (PEST, destruction boxes)
2. Destabilizing N-terminal residues
3. Exposed hydrophobic patch (can bind E3 directly, or indirectly thorugh a chaperone bridge)

Question 26

Three types of ub chains and their distinct fates

Answer 26

1. K48 chains direct a substrate to the proteosome
2. K63 chains play a role in DNA repair and autophagy
3. Mono-ubiquitin plays trafficking roles, ie endocytosis

Question 27

SCF E3 ubiquitin ligase

Answer 27

cyclin-dependent kinase inhibitor, target is marked for degradation by phosphorylation

Question 28

APC/C

Answer 28

involved in separating sister chromatids in anaphase, E3 ligase

Question 29

how are virally infected cells recognized by cytotoxic T cells

Answer 29

they present fragments of viral proteins on Class I MHC molecules, after antigenic peptides are ubiquitinated and digested by the proteasome

Question 30

ERAD

Answer 30

ER-associated degradation, where misfolded proteins in ER are retro-translocated from ER to cytosol, where they are ubiquitinated on the cytosolic face of the ER membrane and then degraded by proteasome

Question 31

Mono-ubiquitin as an endocytosis tag leads to degradation where

Answer 31

lysosome

Question 32

ubiquitin binding domains

Answer 32

motifs within adapter and receptor proteins that bind Ub on cargoes and link them to downstream effectors

Question 33

how is monoubiquitination related to lysosomal trafficking

Answer 33

Signal to sort cargo into ILVs of MVB

Question 34

ubiquitin-like proteins

Answer 34

have structural homology, although often no strong sequence homology - Sumo, APG, etc

Question 35

sumo

Answer 35

nuclear functions, common beta-grasp fold to ub, can be conjugated to lysine via glycine.

Question 36

why is Ub and UBLs so good at regulating target activity/localization?

Answer 36

1. High info content - diverse surfaces available for interactions
2. Mono Ub or topologically distinct chains
3. Same site can be modified by distinct Ub or Ubl mods