Lecture 8: Regulation of the Proteome Flashcards
(15 cards)
Define Proteosome
An abundant protein complex found in the cytosol and nucleus
hollow cylinder with an active site at its core and caps at each end that protect cellular proteins from degradation
Acts on proteins that have been tagged with a polyubiquitin chain, The longer the chain, the more likely the protein will get destroyed
Describe the ubiquitin conjugating system
E1: ATP-dependant ubiquitin-activating enzyme binds to ubiquitin with thioester bonds
E2: ubiquiting-conjugating enzyme accepts ubiquitin from E1 and exists as a complex with
E3: the ubiquitin ligase that binds to specific degradation sequences in substrates
How des ubiquitin attach to a target and what types of attachments exist
- ubiquitin from ubiquitin ligase complex is transferred to a Lysine (K) residue on target protein
Types of modifications:
monoubiquitinylation: histone regulation
multiubiquitinylation: endocytosis
polyubiquitinylation: protosomal degradation (chain forms on Lys48 of each ubiquitin) or DNA repair (chain forms on Lys63 of each ubiquitin)
How many different types of each part of the ubiquitin-conjugating system are there
a couple E1s
around 30 E2s
100s of E3s
therefore a modification to any E1 will have the greatest effect on the system
What are three methods of activation of a ubiquitin ligase
- phosphorylation by a protein kinase
- allosteric transition caused by ligand binding
- allosteric transition caused by protein subunit addition
What are three methods of activation of a protein degradation signal
- phosphorylation of the signal by protein kinase
- unmasking of the signal by protein dissociation
- creation of a destabilizing N-terminus
What are some covalent modifications that can occur on a protein
- phosphorylation
- acetylation
- SUMOfication
- ubiquitinylation
- methylation
What are seven examples of ways a gene regulatory protein can become activated
- protein synthesis
- ligand binding
- covalent modification
- addition of a second subunit
- unmasking
- stimulation of nuclear entry
- release from membrane
Describe the inactive state of PKA, how it is activated, and its active state
inactive: in the cytosol, has two regulatory subunits and two catalytic subunits
activation: binding of cAMP to the regulatory subunits causes a conformational change that releases the active catalytic subunits
active: catalytic subunits translocate to the nucleus and phosphorylate specific substrate proteins
How does PKA activate target genes
- activated PKA phosphorylates inactive CREB (CRE Binding Protein)
- active CREB binds CREB-Binding Protein (CBP) - a coactivator
- complex binds to cAMP responsive element (CRE) upstream of a target gene, activating transcription
Describe the epinephrine/glycogen pathway and the effect of PKA
1) epinephrine activates GCPR
2) GCPR a subunit activates Adenylyl Cyclase
3) Adenylyl cyclase converts ATP to cAMP
4) cAMP activates PKA
5) PKA phosphorylates glycogen phosphorylase and glycogen synthase
What does PKA phosphorylate in the epinephrine pathway and what affect does each have on glycogen breakdown
- glycogen phosphorylase kinase: increased phosphorylation increases glycogen breakdown
- glycogen phosphorylase: increased phosphorylation increases glycogen breakdown
- glycogen synthase: phosphorylation inhibits glycogen synthase action so that no more glycogen is formed
What is glycogen broken down into
glucose-1-phosphate to glucose-6-phosphate
Describe an interactome map
Represents te complete collection of static and transient interactions between proteins within an organism
each dot = protein node
each line = interactome edge
How do protein studies use guilt by association
you study the proteins that a protein interacts with. First assume that it has the same function as any protein it interactions then confirm experimentally later
