Topic 1, Lecture 3 Flashcards
What is the structure of proteasome? And what is the components…
keeps the entire substrate bound until all of it is converted into short polypeptides, 19S cap and 20S core
describe the 19S cap, what it must have,
clips off ubiquitin and sends it back to be used again
Ubiquitin hydrolase, cap must have ubiquitin receptor, hydrolase, and unfoldase ring
what is the unfoldase ring (hexameric ring)
it is 6 proteins with loop that sticks out in the middle loop catch. completely denatures the proteins to allow the protease to reach the amino acids
what is ubiquitin receptor?
ensures that protein is recognized by their ubiquitin tag
what is ubiquitin hydrolase?
clips off ubiquitin from target protein as it is pulled into proteasome
what is a degron
a minimal element within a protein that is sufficient for degradation by a proteolytic system
what does the degron do?
binds to E3, and ubiquitin binds on the side, polymerizes when enough ubiquitin is added
what 2 things must happen in the degron process?
activated degron signal, activate E3
what could the degron be?
phosphorylation by protein kinases, unmasking by protein dissociation, creation of destabilizing n-terminus
what percent of human proteins will have an exposed acetylated protein on the n-terminus
80%
How many E3 ligase genes to ensure that the wide variety of proteins to be polyubiquitinated, can be modified when necessary?
over 600
how many distinct E2 molecules
30
Ubiquitin ligase can also signal the degron via E3 by
phosphorylation by protein kinases, allosteric transition caused by ligand binding, allosteric transition caused by protein subunit addition
what is allosteric regulation and what does it do?
shape change, it adopts multiple (slightly different) conformations
what is kinase? what does it need?
enzyme that phosphorylates proteins can be inactive or active, it needs phosphate binding loop (catalytic loop)
what is the function of phosphatase?
it takes the phosphate off
what is the purpose of kinase families?
changing the function of a protein, and translocation, activity, interactions with other proteins
how can we alter affinity?
by conformation change
Describe cyclic AMP
it is bound to the folded protein, multiple covalent bonds present, h-bond between amino and side chain of cyclic amp, cyclic amp has a high affinity for binding site.
what is GTP
the active hydrolysis
what is GDI
guanine dissociation inhibitor, binds to GDP bound form
what is GDP
inactive dissociation
what is GEF
guanine exchange factor GDP to GTP increasing activation
what is GAP
GTPase activation (accelerating protein, inactivate protein by speeding up hydrolysis
have to add what to make active again?
GTP
What is GDI’s purpose to GDP ?
it locks GDP in site so it cannot be replaced (it keeps it inactive
on the picture of the switch helix which is in position and which is out of position?
GTP is in postion and GDP is out of position
what controls how active/ inactive a protein is?
a spectrum of covalent modifications that produces a regulatory protein code
what are the covalent modifications?
activity
location
interaction with other proteins
