L17: Proteolysis Flashcards
What is proteolysis?
The breakdown of proteins into polypeptides or amino acids through enzymatic cleavage of peptide bonds.
What is the ubiquitin-proteasome system (UPS)?
A system controlling protein degradation via the 26S proteasome, targeting proteins for breakdown into small polypeptides and amino acids.
What roles does the ubiquitin-proteasome system (UPS) play?
It ensures protein quality control, regulates biological processes, recycles peptides and amino acids, and generates peptides for antigen presentation.
What is ubiquitination?
The process by which ubiquitin, a small protein, is covalently attached to a target protein, often tagging it for degradation.
What are lysine 11 and lysine 48 linkages significant for?
They are important in ubiquitin chains for recognition by the 26S proteasome and subsequent protein degradation.
How is ubiquitin activated and attached to target proteins?
Through a three-step process involving E1 activating enzymes, E2 conjugating enzymes, and E3 ubiquitin ligases.
What is the role of E3 ubiquitin ligases?
They determine substrate specificity in the ubiquitination process and are highly diverse, with over 700 types in the human proteome.
What is the 26S proteasome composed of?
A 20S proteolytic core capped by 19S regulatory particles that control substrate recognition, unfolding, and entry.
What are the proteolytic activities of the 20S core proteasome?
Beta subunits exhibit caspase-like, trypsin-like, and chymotrypsin-like activities to cleave specific amino acid residues.
What is autophagy’s role in cellular health?
It clears damaged organelles like mitochondria through lysosomes, recycling their components for reuse.
What is the lysosome, and what is its pH?
A membrane-bound organelle involved in macromolecule degradation with an acidic internal pH of 4.5-5.
How are lysosomal hydrolases targeted to lysosomes?
Through the mannose-6-phosphate pathway.
How does ubiquitin influence the lysosomal degradation pathway?
Mono-ubiquitination regulates protein localization and substrate targeting for lysosomal degradation.
What diseases are linked to dysfunctions in the ubiquitin-proteasome system?
Cancer, neurodegenerative disorders like Parkinson’s, and cardiovascular diseases.
What is the significance of pink1 and Parkin in Parkinson’s disease?
They mediate mitochondrial clearance via autophagy, with mutations linked to early-onset Parkinson’s.
What is the function of ubiquitin-specific proteases (USPs)?
USPs reverse ubiquitination by cleaving ubiquitin from substrates, modifying ubiquitin chains, and regulating their function.
What are the two main components of the 26S proteasome?
The 20S proteolytic core and the 19S regulatory particle.
How does the 19S regulatory particle assist the proteasome?
It recognizes ubiquitinated substrates, unfolds them using ATP, and translocates them into the 20S core for degradation.
What are some known functions of polyubiquitin chains with specific linkages?
- Lysine 48: Targets proteins for proteasomal degradation.
• Lysine 63: Involved in DNA repair and lysosomal targeting.
• Mono-ubiquitination: Regulates protein localization and interactions.
What is the function of lysosomal hydrolases?
They degrade macromolecules such as proteins, lipids, and nucleic acids into simpler components for recycling.
What triggers the activation of the APC/C complex during mitosis?
Proper alignment of sister chromatids on the metaphase plate and attachment to spindle microtubules.
What is the role of the APC/C complex in cell cycle regulation?
It promotes degradation of cyclins and other regulatory proteins to ensure proper mitotic progression and exit.
What happens when the proteasome pathway is inhibited?
Inhibition induces cell cycle arrest and apoptosis, which can be therapeutically beneficial in cancer treatment.
What are examples of proteasome inhibitors?
Peptide aldehydes, boronates, epoxy ketones, and beta-lactones, such as bortezomib, used in cancer therapy.
What is the role of the vacuolar ATPase in lysosomes?
It pumps hydrogen ions into the lysosome to maintain its acidic environment, essential for enzyme activity.
How does parkin function in mitochondrial quality control?
Parkin ubiquitinates damaged mitochondrial proteins, marking them for degradation via the autophagy-lysosome pathway.
What is the structure of the 20S core proteasome?
It consists of four stacked rings with alpha subunits on the outer rings and beta subunits in the inner rings containing proteolytic activity.
What are primary and secondary lysosomes?
- Primary lysosomes are formed directly from the Golgi apparatus.
• Secondary lysosomes are formed by the fusion of primary lysosomes with endosomes or autophagosomes.
What biological processes are regulated by ubiquitin-proteasome-mediated proteolysis?
Cell growth, cell cycle progression, DNA damage repair, transcription, metabolism, and immunity.
What happens when there is dysregulation of E3 ubiquitin ligases?
It can lead to diseases such as cancer, neurodegenerative disorders, and cardiovascular disease due to improper protein degradation.
What is the significance of the 26S proteasome gate?
It remains closed until substrate binding and ATP hydrolysis occur, ensuring controlled access to the proteolytic core.
How does ubiquitin chain structure affect its function?
The type of linkage (e.g., lysine 11, 48, 63) and chain conformation determine the biological role of the ubiquitin chain.
What are chaperone proteins’ roles in proteasome substrate targeting?
They assist in recruiting non-ubiquitinated substrates to the proteasome through ubiquitin-like domains.
What is the role of the lid subunit in the 19S regulatory particle?
It recognizes and binds polyubiquitin chains on substrates targeted for degradation.
How are ubiquitin molecules recycled?
Deubiquitinating enzymes like RPN11 remove ubiquitin en bloc, while others cleave ubiquitin one molecule at a time.
What diseases are linked to the dysfunction of ubiquitin-mediated autophagy?
Parkinson’s disease, due to accumulation of damaged mitochondria and proteins, and certain cancers.
How does ubiquitination affect the cell cycle?
By regulating the degradation of cyclins and other proteins, it ensures timely progression through different cell cycle phases.
What is the structure and function of lysosomal membranes?
They have a bilayer containing glycosylated transport proteins and maintain an acidic environment for enzyme activity.
What is the significance of mannose-6-phosphate in lysosomes?
It is a marker for targeting lysosomal hydrolases from the Golgi apparatus to lysosomes.
How do endocytosis and lysosomal degradation interact?
Endocytosed ligands and receptors are sorted in endosomes, with some targeted for lysosomal degradation.
What is the lysosome’s role in autophagy?
It fuses with autophagosomes to degrade damaged organelles and macromolecules, recycling their components.
What are the hydrolase classes found in lysosomes?
Proteases, nucleases, lipases, phospholipases, and sulfatases, which degrade diverse biomolecules.
What is Angelman syndrome, and how is it linked to ubiquitin?
A genetic disorder caused by inactivation of E3 ubiquitin ligases, highlighting the role of ubiquitin in neurological development.
What is the role of the 20S proteasome independent of the 19S regulatory particle?
It can degrade non-ubiquitinated proteins under specific cellular conditions.
How does lysosomal pH support its function?
The acidic pH enhances the activity of lysosomal hydrolases required for macromolecule degradation.
What is the role of the autophagy-lysosome pathway in mitochondrial health?
It removes dysfunctional mitochondria through mitophagy, preventing cellular damage.
How does ubiquitination promote NF-kB activation?
Specific ubiquitin chains (e.g., K63) facilitate transcription factor activation, critical for immune responses.
What is the ubiquitin E1 enzyme’s primary function?
To activate ubiquitin using ATP and transfer it to an E2 conjugating enzyme.
What are the three ubiquitin receptors in the 19S particle?
RPN10, RPN13, and a third variable receptor that facilitate substrate recognition.
What is the clinical significance of proteasome inhibitors like bortezomib?
They are used in cancer therapy to induce apoptosis by preventing the degradation of regulatory proteins.
