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20 Cards in this Set

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What are the major pathways for degredation?
1. autophagy (macroautophagy, microautophagy, direct protein transfer) LYSOMAL DEPENDENT PATHWAYS

2. 26S Proteasomes and the ubiquitin dependent pathway.
what is autophagy?
the break down of cellular materials (usually dependent on lysosomes)
-involved in the intracellular destruction of endogenous proteins and the removal of damaged organelles
-necessary for cell homeostasis and cell remodeling during differentiation, metamorphasis, non-apoptotic cell death, and aging.

-very highly regulated
-the main means of degradation for long lived proteins and the only means of turn over for membrane organelles like mitochondria and peroxosomes
-the main means of degradation for long lived proteins and the only means of turn over for membrane organelles like mitochondria and peroxosomes
part of the ER forms a double membrane vesicle, that consequently fuses with a lysosome

- the inner membrane of the autophagosome along with the protein and organelle contents are then degraded by lysosomal proteases and then the products are all recycled
examples of proteins that are degraded by chaperone mediated autophagy
-glycolytic enzymes
-transcription factors
-transcription factor inhibitors
-subunits of some cytostolic proteases
a signal that means I am a protein that should be degraded by chaperone mediated autophagy

-motif recognized by a chaperone, the chaperone binds the protein and binds the lysosomal membrane through protines and then the protein is transfered into the lysomal matrix for degradation
chaperone protein that recognizes KFERQ signals in proteins that need to be degraded by chaperone-mediated autophagy.
What are the units and full units of a proteasome
caps are each 19s
the middle is 20s

total they are called a 26s
deubiquitinating enzymes - recycles the ubiquitin so that it can be reused
A key difference between lysome degradation (autophagy) and ubiquitin proteasome pathways - not obvious
proteins degraded in a proteasome are still free in the cytoplasm or the nucleoplasm, whereas proteins degraded IN lysosomes had to cross a membrane
Steps in the Ubiquitin proteasome pathway
1. substrate tagging by covalent attachment of multiple ubiquitin molecules
2. degradation of the tagged protein by the 26s proteasome complex with the release of free and reusable ubiquitin.
20s proteasome
1. a multicatalytic macromolecular complex

2. subunits have trypsin, chymotrypsin, peptidyl-glutamyl hydrolyzing activites and an isopeptidase
3. has intrinsic proteolytic activity that is ATP dependent
4. ATP is required for degradation of ubiquitinated proteins
what protein residue are ubiquitin trees attached to?
- lysine
The Ubiquitinylation multistep process?
1. Ub is activated by the enzyme E1 requires ATP
2. E2 (Ub conjugating enzyme) transfes Ub from E1 to the substrate that is already bound to E3 (ub-protein ligase)
- an isopeptide bond is formed between Ub and e-NH2 (Lysine) in the substrate protein

-a ubiquitin tree is formed by the transfer of Ub to previously bound Ub
Ub protein ligase
Ub conjugating enzyme
N end rule
proteins with arg lys phe leu trp at the n terminal end are short lived

proteins with Cys, ala, ser, thr, gly, val or met at the N terminal end are long lived
Arg -X-X-Leu-gly-x-ile-gly-asx
-near the n terminus
-targets them for destruction by UB mediated pathway
-caleld the destruction box
PEST sequence
-targeted for Ub mediated degradation

-proteins with internal sequences enriched in Pro, glutamic acid, ser, thr
Proteins that are degraded by a ubiquitin mediated pathway
-N end rule
-PEST sequence