Flashcards in Protein Folding And Proteasome Deck (49):
Interior of chaperone is ___ and has 7 ____ subunits inside
Interior of chaperone is HYDROPHOBIC and has 7 ATPase subunits inside
3 Functions of Chaperone during Protein Synthesis
-protection of nascent chain
-guidance during folding
-avoidance of kinetic dead ends
19 S regulatory cap made up of alpha subunits
Proteasome assembly requires ____ chaperone
Types of interactions that promote folding
Van der Waals interactions
What is a molten globule?
-Term describng a polypeptide chain that has achieved near-final secondary structure but is looser and more open.
-Not a defined structure, refers to family of related structures taht are fluid and interchangeable
-Driving force is water exclusion
What happens to polypeptide with CFTR delta508 mutation?
Protein folds too slowly, it's captured by proteolytic system and degraded, so intracellular levels of the protein are depleted.
eEIF1As Role in Protein Degradation
It facilitates degradation when folding is incorrect
In neurodegenerative diseases, aggregates form in ____ region, and _______ are usually copresent within aggregates
In neurodegenerative diseases, aggregates form in PERINUCLEAR region, and PROTEASOMES are usually copresent within aggregates
Examples of Amyloid Diseases
-most aggregates contain B-pleated sheets
-ALS (aggregation of SOD)
-Huntingtons (CAG repeats)
-Machado Joseph Disease (CAG repeats)
3 Ways to Regulate Proteolysis
-Proteases are usually zymogens, need hormonal activation or autocatalysis
-Activities are compartmentalized
Distinguishing structural features of Ubiquitin
-7 lysines on surface which attach to other Ubs
-highly reactive carboxy terminus which is involved in all covalent interactions that Ub makes
-hydrophobic patches on surface
-always initially expressed as fusion protein
Ub Carboxy Terminal Hydrolase
Cleaves polyubiqutin to expose the C-terminal tail
-mutations in this enzyme cause Parkinsons
Ub Activating Enzyme E1
Binds 2 Ubs as a UB-adenylate via thioester bond
-Always has 2 mol of Ub
Ub-Conjugating Enzyme E2
Mediates the transfer of Ub from E1 to either E3 or substrate
-contributes to combinatorial diversity of Ub degradation pathway
Ub-Protein Ligase E3
Attaches Ub to substrate via isopeptide bond
-Parkin is an E3 enzyme
-Poly-Ub chain must be at least 4 in order to be targeted for degradation
How does Ub attach to conjugating enzymes?
Via thioester bond b.w. Ub C-terminal glycine and cysteine on enzyme
How does Ub attach to substrate?
Via Ub's C-terminal glycine, ISOPEPTIDE bond to lysine on substrate.
-Isopeptide bond is reversible
Importance of Ub's C-terminal Glycine
It makes thioester bond with conjugating enzymes
Forms isopeptide bond with substrate
Forms isopeptide bond with lysine residues in Ub (to make multi-Ub chain)
Significance of multi-Ub cahin
Hydrophobic patches which create an extended hydrophobic stripe, which will interact with proteasome
Significance of K-63
Multi-Ub via K-63 is important for DNA repair, but does not promote degradation via proteasome
-short chains assembled via k-63 promote translocation of plasma membrane proteins to lysosome for degradation
20S catalytic core has __ stacked, __ subunit rings forming a _____
3 ________ activities are sequestered within ___ subunits
Chamber of entry is ______
20S catalytic core has 4 stacked, 7 BETA subunit rings forming a BARREL
3 HYDROLYTIC activities are sequestered within BETA subunits
Chamber of entry is NARROW
___ 19S particles bind to each end of 20S
Functions in binding _______ proteins and can release them
Contains _____ enzymes that require ____
TWO 19S particles bind to each end of 20S
Functions in binding UBIQUITIN proteins and can release them
Contains UNFOLDING enzymes that require ATP
Maturation of the 20S consists of:
The 3 beta subunits that have ________ activities are expressed as ________
Following assembly of the _____ barrel, the _____________ are cleaved
The proteasome is now fully active and ____ is the first substrate
Maturation of the 20S consists of:
The 3 beta subunits that have HYDROLYTIC activities are expressed as PRECURSORS
Following assembly of the ALPHABETA/BETAALPHA barrel, the PRO-SEQUENCES are cleaved
The proteasome is now fully active and UMP1 is the first substrate
Roles of 19S Regulatory Particle
-Poly-Ub chain binding via hydrophobic stripe and disassembly for recycling
-Substrate unfolding for channel entry
-Regulates axial channel
-Binds regulatory protiens
Allosteric: bite and chew
ATP Hydrolysis: for assembly, stability, and substrate unfolding
Recycling and peptide release: chew and spew
Combinatorial diversity with E2-E3 combinations
Parkin might bind and translocate _____ enzymes to the _____
Parkin might bind and translocate E2 enzymes to the PROTEASOME
____, a HPV protein captures the _______ complex and attaches to _____, leading to the polyubiquination of ____ and it's degradation, which results in loss of ______.
E6, a HPV protein captures the E2-E3 complex and attaches to P53, leading to the polyubiquination of P53 and it's degradation, which results in loss of GROWTH CONTROL.
When _____ tumor suppressor protein is mutated, _____ does not get degraded, so hypoxia genes remain active. This happens in tumors so tumors can get more vasculature.
When VHL tumor suppressor protein is mutated, Hif-1 does not get degraded, so hypoxia genes remain active. This happens in tumors so tumors can get more vasculature.
____ is an inflammatory protein, made as precursor. The precursor is processed by ________, which makes ___, which forms complex with ____, which is inhibited by ____. _______ (which is activated by stress and Ub factors) will phosphorylate ______, it will be degraded. _____ will then be active, and will activate inflammatory response.
NFK is an inflammatory protein, made as precursor. The precursor is processed by proteasome, which makes p65, which forms complex with p50, which is inhibited by IKB alpha. KINASE (which is activated by stress and Ub factors) will phosphorylate IKB, it will be degraded. NFK will then be active, and will activate inflammatory response.
_____ protein in Xeroderma pigmentosum is a protein that is degraded by the proteasome
8/13 FA proteins are involved in protein degradation
Machado Joseph Disease
Ataxin-3 is a proteasome subunit that can bind multi-Ub chains
Failure to degrade Hif-1 causes tumors on the skin
Hypoxia-inducible factors are ____dimers. Has 3 __________ and a constiutive _____ subunit that is present in the _____.
Hypoxia-inducible factors are heterodimers. Has 3 oxygen labile alpha subunits and a constiutive Beta subunit that is present in the nucleus.
Hif1 protein synthesis is promoted by _____/_____ and it's degradation is controlled by _____ and _____.
Hif1 protein synthesis is promoted by mTOR/S6 kinaseand it's degradation is controlled by VDL and VDU.
Post-translational modifications of Hif1 include _____ and ______, which promote degradation, and _____ that promotes transcription. Hif1 degradation occurs by _____ dependent and independent mechanisms.
Post-translational modifications of Hif1 include prolyl hydroxylation and lysyl acetylation, which promote degradation, and cystine nitrosylation that promotes transcription. Hif1 degradation occurs by VHL dependent and independent mechanisms.
_____ is a component of a complex E3 ligase.
Hif1 ____ causes binding to ____.
____ can dismantle a multi-Ub chain conjugated to Hif
Multi-Ub Hif is degraded by the ______
VHL is a component of a complex E3 ligase.
Hif1 hydroxylation causes binding to VHL.
VDU2 can dismantle a multi-Ub chain conjugated to Hif
Multi-Ub Hif is degraded by the proteasome
Enzyme that can dismantle a multi-Ub chain conjugated to Hif1
In normoxia, PDH1,2,3 _____ Hif1, leading to recognition by _____ on E3 ligase, causing polyubiquitination, leading to degradation.
PDH1,2,3 can also be ubiquitinated
_____-E3 can also be ubiquitinated
In normoxia, PDH1,2,3 hydroxylate Hif1, leading to recognition by VHL on E3 ligase, causing polyubiquitination, leading to degradation.
PDH 1,2,3 can also be ubiquitinated
VHL-E3 can also be ubiquitinated
____ enzyme can be activated and dismantle the Ub chain, allowing for hypoxia response
VDU enzyme can be activated and dismantle the Ub chain, allowing for hypoxia response
During mitochondrial failure, [__] increases, which can bind PDH1,2,3, and Hif1 does not get ____, activating the hypoxia response.
During mitochondrial failure, [Fe2+] increases, which can bind PDH1,2,3, and Hif1 does not get hydroxylated, activating the hypoxia response.
When Hif dimerizes in nucleus, induction of _____ expression which shuts down expression of ____, leading to _____, ______, and _____.
When Hif dimerizes in nucleus, induction of mir-210 miRNA expression which shuts down expression of normoxia, leading to angiogenesis, energy metabolism, and inflammation.
In normoxia, Hif1 is ______ synthesized, but degraded.
Hypoxia inhibits _______. Transcription activation of specific _____ shuts off expression of normoxia genes. However, energy metabolism regulators, including ___ promote synthesis of Hif1.
Growth promoter ____ and _____ promote Hif1 translation (O2 independent).
In normoxia, Hif1 is constitutively synthesized, but degraded.
Hypoxia inhibits global protein synthesis.
Transcription activation of specific miRNAs shuts off expression of normoxia genes. However, energy metabolism regulators, including Akt promote synthesis of Hif1.
Growth promoter mTOR and S6-kinase promote Hif1 translation (O2 independent).
Symptoms of altitude sickness/hypoxia at varying altitudes:
2000-4000 m: ________________
4000-6000 m: ________________
6000-9000 m: ________________
Symptoms of altitude sickness/hypoxia at varying altitudes:
2000-4000 m: altered night vision
4000-6000 m: dizziness or tingling
6000-9000 m: loss of consciousness
mTOR inhibitors in cancer therapy
Proteasome inhibitor in cancer therapy
Symptoms of normal acclimatization response
-poor mental and physical performance