SCHOCH Flashcards
Cells control the balance between ________/_________ & degradation to respond to changing cellular environments and stimuli.
transcription/translation
The balance between transcription/translation & degradation is specific to each ________/________.
gene/protein
List three reasons why a protein might be degraded.
Damage, Aggregation/Misfolding, Not currently needed
Amino acids may be needed for _________ generation (muscle) or for biosynthesis of other molecules.
energy
Protein half-lives can depend on the protein’s _______________ properties.
physicochemical
List four physicochemical properties that can affect a protein’s half-life.
-Amount of secondary structure
-Number of cellular binding partners
-Catalytic activity level
-Tissue type
Degradation can be coordinated between multiple proteins in a ________.
complex
How many E1, E2, and E3 enzymes are there in the ubiquitin proteasome system?
1 E1 enzyme, 30 E2 enzymes, >700 E3 enzymes
True or False: Each E3 recognizes only one protein for degradation.
False, less E3s than proteins
What is the size of ubiquitin?
8.6 kD
Ubiquitin has many ________ residues which serve as sites for poly-ubiquitin chain formation.
lysine
Ubiquitin is highly _________: between human, yeast, and oat there are only 3 amino acid changes.
conserved
The C-terminal ________ of ubiquitin is the residue that will be esterified to the E1 and E2 enzymes.
glycine
The E1 enzyme is comprised of two halves – each containing an ___________ domain and a catalytic _________ domain.
adenylation, cysteine
What stabilizes the interaction between ubiquitin and the E1 enzyme?
The flexible C-terminal tail extends under a loop connecting the two domains (“the crossover loop”)
________ and ________ are two structurally related proteins to ubiquitin that tag proteins for processes other than degradation.
Nedd8, SUMO
The E1 enzyme for ubiquitin has a negatively charged groove that binds ________ in the tail of ubiquitin.
arginine
The E1 enzyme for Nedd8 has a ___________ groove that binds alanine in the tail of Nedd8.
hydrophobic
The E1 enzyme for SUMO has an arginine and tyrosine-filled groove that binds __________ in the tail of SUMO.
glutamate
True or False: Nedd8 and SUMO do not lead to degradation by the proteosome.
True
The E2 enzyme acts as a ______________ binding both the E1 and E3 enzyme.
middle-man
The E2 enzyme depends upon the E1 having bound the correct ________ or ____________________.
ubiquitin, ubiquitin-like protein
What are the two major families of E3 ligases?
HECT-containing, RING-containing
RING-containing E3 ligases can be either _________ subunit or ______________.
single, multi-unit
HECT E3s contain a catalytic _________ residue in their C-lobe that accepts Ub from the E2.
cysteine
RING E3s transfer Ub directly to the __________.
substrate
One RING E3 recognizes the _________________ residue of a protein to target it for degradation.
N-terminal
Degradation rates in the N-end rule pathway are dependent on the N-terminal ___________ or on a modified N-terminus such as _______________.
amino acid, acetylation
_____ (___________) Ligases are the largest family of RING E3s.
SCF (Skp1-Cullin1-Fbox)
What are the four components of SCF ligases?
RING domain (ex. Rbx1), Scaffolding protein (Cullin1), Adaptor protein (Skp1), The E3 ligase which contains an Fbox domain
Flexibility in the ________ scaffold disrupts ubiquitination of substrates.
Cullin1
Binding to SCF ligase substrate binding domains is almost always regulated by requiring ______________________ modification or an _______________ protein.
post-translational, accessory.
RING E3s need to be _______(rigid/flexible).
rigid
The goal of SCF ligases is to bring a substrate ________ into the right proximity to catalyze Ub transfer from the E2 or E3.
lysine
Sites of ubiquitin chain attachment (on the substrate) affects the rate of substrate _____________.
degradation
Ubiquitination targets the protein to the ___________.
proteosome
The core particle of the proteasome consists of 4 ___________ rings, 2⍺ and 2β.
heptameric
The RPT hexamer is an __________ enzyme.
unfoldase
Degradation by the proteasome requires the Ub chain + an _____________ region of 20-30 aa that is positioned near the RPT hexamer.
unstructured
The proteasome is regulated by requiring assembly of the _____ regulatory particle.
19S
Fbxw7 is the most frequently mutated member of the UPS. Mutations in Fbxw7 abolish binding with all its substrates, and many of these substrates are ___________.
oncogenes
_____________ is the process by which cytosolic components are encapsulated within a single membrane which then fuses with the lysosome to degrade its components.
Autophagy
Specific autophagy requires ___ modification.
Ub (ubiquitin)
________________ is the term used to describe the balance between transcription/translation and degradation that cells use to respond to changing cellular environments and stimuli.
Proteostasis
A protein that is ________________ and/or misfolded may be degraded.
aggregated
The _________ of a protein is the time it takes for half of the protein to be degraded.
half-life
________________ E3 ligases contain a catalytic cysteine residue in their C-lobe that accepts ubiquitin from the E2 enzyme.
HECT
The _________ between the two lobes of HECT E3s is flexible, allowing the C-lobe to rotate into the proper proximity to transfer ubiquitin to the substrate.
linker
________________ E3 ligases transfer ubiquitin directly to the substrate.
RING
In the N-end rule degradation pathway, the protein is targeted for degradation based on its ________________ amino acid.
N-terminal
SCF ligases are the __________ family of RING E3s.
largest
The RING domain of an SCF ligase is also called _________.
Rbx1
_______________________ modification or the presence of an accessory protein is often required for binding to SCF ligase substrate binding domains.
Post-translational
The ____________ is a large protein complex responsible for degrading proteins that have been tagged with ubiquitin.
Proteasome
For a protein to be degraded by the proteasome, it must be tagged with a _______________ chain of a certain type.
poly-ubiquitin
True or False: Proteins that are more unfolded (less structured) are degraded faster than globular proteins.
True
If all lysines in a ubiquitin chain are linked through the same lysine, the chain is called __________.
Homotypic
