Lecture 12 ubiquitin Flashcards
What is selectivity?
The ways of achieving the correct binding
What is avidity and affinity?
The ways of achieving tight binding
What is the half life of proteins definition?
The time it takes for the copy number to fall by half due to a specific protein system e.g., ubiquitination. Cyclins and transcription factors have half lives of seconds due to the quick signal pathway.
What percentage of proteins is turned over every day?
5%. Every single protein in the body is replaced every 6-12 months.
What is ubiquitin?
A covalent modifier that can signal selective degradation of other proteins via the UPS.
What is autophagy?
The other major intracellular pathway of protein degradation-ubiquitin plays a role here as well. Lysosome mediated degradation.
How does ubiquitin exert its effects?
By establishing new non-covalent protein protein interactions with the modified protein (alters interaction landscape).
How does neurons being post mitotic affect them?
They can’t divide to relieve themselves of pathological protein burden. Therefore they have incredibly active protein degradation systems. Ubiquitin aims to prevent those misfolding events from forming pathological proteins that lead to neurodegeneration.
What residue protrudes from the globular structure?
C-terminus (glycine 76) protrudes from the globular structure.
How many different PTMs have been found?
Between 300-400 PTMs that have been described. Reversible PTMs.
How does ubiquitin bind to proteins?
Side chains of selected lysine (K) residues (At NH2 group) in a modified protein become involved in a covalent isopeptide bond with the C terminal -COOH group of ubiquitin Gly76.
How do polyubiquitin chains form?
All of the 7 lys residues of ubiquitin (and Met at the N-terminus) can be used to form chains with different topologies and structures. This gives rise to the formation of Lys48-polyubiquitin chains.
What are the lysines?
Acceptor sites of ubq modification.
What is the proximal ubiquitin called?
The ubiquitin bound to the target protein.
What is the distal ubiquitin?
The last ubiquitin in the chain.
Why can N terminus methionine also be ubiquited?
It has a free amino group. This forms a peptide bond not an isopeptide bond.
How can western blots show how common ubq is as a PTM?
Many bands. Smear of activity with a free ubiquitin band at the bottom at 8.5kDa. The smear shows ubiquitinated proteins.
What is a covalent thiolester linkage?
S-Cys
What is the explanation of what the covalent thiolester linkage looks like?
A free sulf-hydryl group on a cysteine residue side chain and an S-H group interacting or forming a covalent bond with the free carboxyl group in glycine 76 at the C terminus of ubq.
What does ATP do in the ubq pathway?
Allows ubiquitin to bind to E1 and E2.
What are deubiquitinating enzymes?
Reverse ubiquitination (about 90 genes in humans). Associated with many human cancers.
What does monoubiquitylation lead to?
Endocytosis, protein sorting, subnuclear trafficking, gene expression.
What does polyubiquitylation lead to?
Degradation, DNA repair, signal transduction, proteolysis-independent unknown functions, proteosome binding.
How is ubiquitin recycled?
By proteosome associated DUBs
What does the proteosome do?
Unfold proteins using ATPases. Feed protein through catalytic core of proteosome. Protease residues cut the target protein into shorter peptides. These get released and degraded by amino acids.
What is the 26S proteosome?
Has a 19S cap or regulator. 19S binds to the Lys48-polyubiquitin chain on a substrate: uses ATP to unfold the substrate. 20S core contains (threonine) protease subunits which digest the substrate.
What is ERAD endoplasmic reticulum associated degradation?
E3 ubiquitin ligase recognise ER membrane proteins so they get unfolded and translocated into the cytoplasm to the UPS.
What residues other than Lys on target proteins can be bound to ubiquitin?
Ser, Thr in rare cases (presumed ester bonds).
What else expands the ubiquitin code?
The phosphorylation (ser) and acetylation (lys) of ubiquitin.
What are unanchored polyubiquitin chains?
Chains of ubiquitin that are substrate free. Eg., RIG-I can recognise viral RNA through recognising unanchored polyubiquitin chains that are there due to the viral RNA using it.
What can lysine 63 ubq binding lead to?
Kinase activation, DNA repair, trafficking, translation.
