Lecture 15 Flashcards
What is the protein half life?
this is the time that half the population of protein remains or the time that half of the original populations of protein has been degraded
What are 5 reasons that proteins are degraded?
- to regulate the ________/________ of a ________ and therefore the ________ eg. ______ channels and transporters in epithelia to change _______ transport pathways
- to allow _______ with new proteins
- to _________ them e.g., ligands, cell cycle proteins
- to recycle ________ ________ of ___________ proteins e.g., _________ or _________ proteins in the ER
- as they are _______ proteins from pathogens
- to regulate the function/activity of a protein and therefore the cell eg. ion channels and transporters in epithelia to change ion transport pathways
- to allow replacement with new proteins
- to inactivate them e.g., ligands, cell cycle proteins
- to recycle amino acids of nonfunctional proteins e.g., misfolded or misassembled proteins in the ER
- as they are extracellular proteins from pathogens
What does the lifetime of a protein depend on?
the function of the protein and the cellular pathway it is involved in
Where are proteins degraded?
in the lysosome or the proteasome
What do lysosomes break down?
- extracellular or transmembrane proteins brought into the cell and
- aged or defective organelles (autophagy)
(tyrosine, leucine motifs and ubiquitination)
What do lysosomes contain?
enzymes that work best at acidic pH
What do the enzymes in the lysosomes breakdown?
proteins, sugars and nucleic acids
Two transport proteins pump H+ and Cl- into the lysosome to do what?
maintain low pH
Describe the process of autophagy
- there is uptake of a random area of cytoplasm of cytoplasm or defective organelles (this is called the phagophore)
- the phagophore forms a complete vesicle called the autophagosome
- the autophagosome begins to fuse with the lysosome
- an autophagosome is formed and degradation begins
- organelles and any uptake substances degraded and recycled
What is the ubiquitin-proteasome system for protein degradation?
this is a highly controlled process for degrading unwanted proteins, terminating or activating signalling pathways, regulating the cell cycle and providing an important source of amino acids for new protein synthesis
What is ubiquitination?
this is when proteins are covalently tagged with a small 8kDa protein called ubiquitin
Ubiquitination occurs through a series of enzymes called what? What do these enzymes do?
E1 (activating enzyme)
E2 (conjugating enzyme)
E3 (ligase)
these catalyse the covalent attachment of ubiquitin to target proteins
Describe how the ubiquitination process occurs
E1 catalyses the breakdown of ATP to AMP which will transfer ubiquitin to E2, then this repeats to get it to E3 and then E3 transfers it to the protein
During endocytosis, proteins are deubiquitinated. What is involved in this?
this is done by deubiquitinating enzymes or DUBS which remove ubiquitin from proteins
Describe the role of the proteasome in the process of degradation
Ubiquitin binds to the proteasome and orients the protein. The protein is degraded in the proteasome by a peptidase (break the peptide bonds between amino acids) and the peptides and amino acids are recycled
What does ubiquitin tagging promote?
endocytosis of ion channels
Give an example of Ubiquitin tagging promoting endocytosis of ion channels?
- ENaC and ROMK1 are monoubiquitinated, promoting endocytosis to the apical sorting endosome
- Ubiquitinated proteins trafficked onto common endosome where fate of the channel is determined
- Deubiquitination leads to recycling. If they are not deubiquitinated, the ubiquitinated proteins move on to lysosome for degradation
What happens in Liddle’s syndrome?
ENaC cannot be tagged with ubiquitin due to loss of the binding site for an E3 ubiquitin ligase. Therefore less ENaC endocytosis, more ENaC at the plasma membrane and more Na+ reabsorption leading to high ECF volume and pressure
What are the 3 main types of ubiquitination?
- monoubiquitination
- multiubiquitination
- polyubiquitination
Describe monoubiquitination
This is the single addition of ubiquitin
What is multiubiquitination?
The single addition of ubiquitin at multiple different sites
What is polyubiquitination?
the binding of a ubiquitination chain on a single site
How and to what is ubiquitin binded?
It is covalently linked to lysines or to the N-terminal amino acid of the target/substrate protein
What is ubiquitination a signal for?
endocytosis
What is polyubiquitination a signal for?
degradation in the proteosome
Where can a good summary and comparison on lysosome, autophagy and proteosome-mediated degradation be found?
slide 13 lecture 15
Which method of degradation involves E1, E2, E3?
proteasome
Lysosomes only degrade proteins BECAUSE monoubiquitin is used as a tag for degradation in the endocytosis pathway. A. Both statements true and causal. B. Both statements true but not causal. C. First statement true, second false. D. First statement false, second true. E. Both statements are false
false, true
What enzymes are in lysosomes?
Acid hydrolases
What enzymes are in Proteasomes?
Peptidases
What enzymes are involved in Autophagy?
Acid hydrolases
What do lysosomes degrade?
proteins, sugars, DNA/RNA
What do proteasomes degrade?
Proteins (ubiquitin recycled)
What does autophagy degrade?
Damaged organelles, microbes, cytosolic components
Describe the regulation of the lysosome degradation
it is Somewhat random, ubiquitin tagging
Describe the regulation of the proteasome degradation
Highly regulated
Describe the regulation of the autophagy degradation
Random, but some regulation
What are the cofactors required in lysosome degradation?
NA
What are the cofactors required in proteasome degradation?
Requires a series of three enzymes: E1,E2 and E3
What are the cofactors required in autophagy degradation?
NA
What are the general targets for lysosome degradation?
Cell surface and extracellular proteins
What are the general targets for proteasome degradation?
Cytoslic, nuclear, ER proteins (ERAD)
What are the general targets for autophagy degradation?
Cytosolic components
Describe the structure of the autophagy
Double- membraned autophagosome
