7 - Proteasomes and Exosomes Flashcards
Why does so much degradation take place in the cell?
- Cell regulation - signals must be degraded so they can act as time dependent factors. (switch off signals)
- For adaption to environmental conditions
- Inflammatory signalling
- Clearance of misfolded, mutated or damaged proteins, hence the prevention of aggregation.
What does the lysosome degrade? How does it do this?
It degrades, proteins non-selectivity (membrane and endocytose proteins) as well as whole organelles. It is acidic and full of proteases.
What is autophagy?
- Autophagy is an intracellular degradation system that delivers cytoplasmic constituents to the lysosome.
- Autophagy is where a membrane bag wraps around organelles or the cytoplasm.
- This process is not that selective - Then the pieces from the degradation are recycled.
- Autophagy is upregulated when nutrients are low, during fasting and when there is low insulin levels.
What are the products of the proteasome?
3-22 amino acid long peptides. These can be used either for:
- antigen presentation in immune proteasome
- In other proteasomes, peptidases chop these up into amino acids to be recycled.
What is the role of the AAA+ protein?
AAA+ protein which is an ATPase, unfolds the proteins and threads it through the tube of the proteasome.
What are the differences between the eukaryotic, TB bacteria and archaea proteasome?
Eukaryotic proteasome has the protease domain, then another regulatory subunit followed by the ATPase subunit and finally the lid domain. TB bacteria proteasome is similar to archaea’s proteasome. Instead of a ubiquitin tag, TB uses a Pup tag.
What is the structure of the core particle?
Core particle is made up of 2 copies of 14 different proteins: 2 x β7 and 2 x α7. These 4 rings of 7 proteins are stacked on top of one another.
Why must the proteins must be unfolded before entering the proteasome?
The tunnel is too narrow for ubiquitin (a small protein) to fit through folded, so proteins must be unfolded to enter the tunnel (13 Å wide)
What is the structure of the regulatory particle of the proteasome?
There are 2 identical regulatory particles per proteasome. Each made up of 18 different proteins including 6 ATPases. Some of the subunits have sites that recognise ubiquitin.
What are β ring subunit structure? How was this identified?
Each protein of the proteasome was tagged to identify different subunits of the 20S core particle complex of the 2 stacked rings - β ring, three subunits were active these are the protease subunits. Eukaryotic 20S proteasomes have 3 types of proteolytic sites: Trypsin like (cleaves after basic residues), caspase-like (cleaves after acidic residues) and chymotrypsin-like (cleaves after hydrophobic residues).
What is the functions of the exosome?
The exosome is the complex that is responsible for degrading RNA, thus it controls:
- Expression of mRNA (or levels of mRNA)
- RNA quality control - nonsense mediated decay etc. are degraded by the exosome.
What is the structure of the Exosome?
Common structural core has 9 subunits, with 6 RNAse PH-like ring and a trimeric cap
What is the difference between the Archaea and eukaryotic exosome’s nuclease subunits?
Eukaryotic nuclease subunits are Rrp44 and Rrp6 (only in the nucleus). In archaea there are 3 active subunits, the other 3 are just structural. Eukaryotic exosome, Rrp44 has an endonuclease function.
What are the functions of Hsp100?
Hsp100 proteins can completely unfold their target proteins in order to deliver them to associated proteases or with Hsp70 dissolve large aggregates.
What is the mechanistic steps of Hsp100’s action?
Hsp100’s ATPase ring has a spiral action so operates sequentially. Tyrosine loops are involved in polypeptide binding. There is sequential binding of tyrosine loops as these subunits move down the polypeptide as it is pulled.
