L6: protein turnover and autophagy Flashcards
(10 cards)
what is cellular rubbish?
- Errors during protein folding
- Mechanically damaged proteins
- Short-lived proteins (cell cycle)
- Aggregation of e.g. mutant proteins
protein folding
When you synthesise your amino acid chain, start with N-terminus, goes to C-terminus, different responses to water. Hydrophobic aa prefer to be inside the fold, not in contact with water, while hydrophillic prefer to be outside. Alot of proteins do this fine but it can go wrong. Proteins that facillitate folding are chaperones. They can occasionally dix it but if not the cell realises it has to get rid of the non-functional protein. If you have a multiprotein complex, if a component is missing, the leftover ones have to be degraded. For example the head of the myosin molecule require chaperons. Need to interact with 3 types of chaperones: UNC-45, Hsp70, Hsp90. If canot fold properly, tails cant assemble to filaments and you get aggregates.
how to mark a protein for degradation?
Phosporylation by a protein kinase: can tell the cell to go towards the ubuqutin protease pathway.
another way: unmasking by protein dissociation.
Also creation of destabilising N-terminal (arg, asp, glu)
ubiquitylation cascade
ATP is required to mount these ubiquitin chains onto the proteins that are to be degraded. more atp for transferring the proteins to the proteasome. To put these ubiqutin chains on your target protein you need a cascade of ubiquitination enzymes. The 3 classes: E1 ubiquitin activating enzyme (Uba1) that brings in ubuiqutin protein under the consumption of atp transfers that to the next step. Next: E1 ubiqutuin ligase that transfers with the help of ubqiutin E3, build up chains and these are recognised by proteasome. E3 selects the target.
- Ubiquitin-E1 activating enzyme (Uba1)
E3
E2 Ubiquitin-E2 conjugating enzymes (several)
Ubiquitin-E3 protein ligases (often cell-type specific, RING-type; HECT-type; U-box type)
ubuiquitin
11 kili dalton protein. To make the ubqiutin chains you use lysine resides in the ubqiutin protein. Depending which lysine resides you use, different effect on the ubqiutin. classical lysine to mark protein for degradation is lysin 48 or lysine 63, which can also have effect on protein activity, not always degradtion (for 63).
proteasome structure
diameter: 10 nm
multiprotein complex
core particle is put together from alpha and beta subunits
mw: 2.5 mw
how does ptoeasome work
has to recognise the targeted protein through the ubiquitin chain. Once its lid has caught the substrate, and degradation route, the chains of ubqituin are cut off by deubiqutilation enzyme that cuts off ubiquitin so only substrate will go into mouth of bin and ubiqutins stay outside to be reused (recycling). need atp for subsrate to go in.
The UPS
Proteins that are to be degraded are “marked” by phosphorylation,
unmasking of binding sites or destabiliation of the N-terminus.
They are subsequently conjugated to ubiquitin. This is achieved in
a cascade of reactions that involves the use of ATP and E1-, E2- and
E3-ubiquitin enzymes.
Final degradation into peptides and recycling of ubiquitin happens
in the proteasome and also requires ATP.
Proteins can be mono-, multi- and poly-ubiquitinylated.
Ubiquitylation does not always mean doom and gloom but can also
affect a protein’s subcellular localisation and activity.
Ubiquitin K48 usually means degradation and K63 means activity.
second way to deal with rubbish?
autophagy. ‘ self eating’
evolution: more of a way to survive. like in yeast cells, can survive by self degrading proteins to use the amino acids for proteins that arent as essential and make important proteins. so in yeast, starvation leads to the formation of the phagophore,using the membrane from the er or golgi, making a cup that starts to engulf proteins that have been marked tas not essential for surviva. form a ring around it called the autophagosome. means that stuff that needs to be recycled is sitting in a separate compartment in the cell. the autophagosome fuses with the lyosome making an autolyosome. the lysosome brings in the proteases.Autophagy not only to get rid of damaged proteins but also damaged organelles such as mitochondria which are prone to oxidative stress damage or even bacteria and viruses can be rid of through the autophagosome.
how does the autophagosome work?
LC3 is a marker for autophagy. LC3 is inserted in the membrane of a membrane to catch things that need engulfing. Other proteins: P62 or MVA1 that bin ubiquitin chains and in turn recognised by LC3.
