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Y1 Cellular Biochemistry and Biology > L17: Proteolysis > Flashcards

L17: Proteolysis Flashcards

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1
Q

What is proteolysis?

A

The breakdown of proteins into polypeptides or amino acids through enzymatic cleavage of peptide bonds.

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2
Q

What is the ubiquitin-proteasome system (UPS)?

A

A system controlling protein degradation via the 26S proteasome, targeting proteins for breakdown into small polypeptides and amino acids.

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3
Q

What roles does the ubiquitin-proteasome system (UPS) play?

A

It ensures protein quality control, regulates biological processes, recycles peptides and amino acids, and generates peptides for antigen presentation.

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4
Q

What is ubiquitination?

A

The process by which ubiquitin, a small protein, is covalently attached to a target protein, often tagging it for degradation.

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5
Q

What are lysine 11 and lysine 48 linkages significant for?

A

They are important in ubiquitin chains for recognition by the 26S proteasome and subsequent protein degradation.

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6
Q

How is ubiquitin activated and attached to target proteins?

A

Through a three-step process involving E1 activating enzymes, E2 conjugating enzymes, and E3 ubiquitin ligases.

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7
Q

What is the role of E3 ubiquitin ligases?

A

They determine substrate specificity in the ubiquitination process and are highly diverse, with over 700 types in the human proteome.

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8
Q

What is the 26S proteasome composed of?

A

A 20S proteolytic core capped by 19S regulatory particles that control substrate recognition, unfolding, and entry.

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9
Q

What are the proteolytic activities of the 20S core proteasome?

A

Beta subunits exhibit caspase-like, trypsin-like, and chymotrypsin-like activities to cleave specific amino acid residues.

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10
Q

What is autophagy’s role in cellular health?

A

It clears damaged organelles like mitochondria through lysosomes, recycling their components for reuse.

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11
Q

What is the lysosome, and what is its pH?

A

A membrane-bound organelle involved in macromolecule degradation with an acidic internal pH of 4.5-5.

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12
Q

How are lysosomal hydrolases targeted to lysosomes?

A

Through the mannose-6-phosphate pathway.

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13
Q

How does ubiquitin influence the lysosomal degradation pathway?

A

Mono-ubiquitination regulates protein localization and substrate targeting for lysosomal degradation.

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14
Q

What diseases are linked to dysfunctions in the ubiquitin-proteasome system?

A

Cancer, neurodegenerative disorders like Parkinson’s, and cardiovascular diseases.

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15
Q

What is the significance of pink1 and Parkin in Parkinson’s disease?

A

They mediate mitochondrial clearance via autophagy, with mutations linked to early-onset Parkinson’s.

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16
Q

What is the function of ubiquitin-specific proteases (USPs)?

A

USPs reverse ubiquitination by cleaving ubiquitin from substrates, modifying ubiquitin chains, and regulating their function.

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17
Q

What are the two main components of the 26S proteasome?

A

The 20S proteolytic core and the 19S regulatory particle.

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18
Q

How does the 19S regulatory particle assist the proteasome?

A

It recognizes ubiquitinated substrates, unfolds them using ATP, and translocates them into the 20S core for degradation.

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19
Q

What are some known functions of polyubiquitin chains with specific linkages?

A
  • Lysine 48: Targets proteins for proteasomal degradation.
    • Lysine 63: Involved in DNA repair and lysosomal targeting.
    • Mono-ubiquitination: Regulates protein localization and interactions.
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20
Q

What is the function of lysosomal hydrolases?

A

They degrade macromolecules such as proteins, lipids, and nucleic acids into simpler components for recycling.

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21
Q

What triggers the activation of the APC/C complex during mitosis?

A

Proper alignment of sister chromatids on the metaphase plate and attachment to spindle microtubules.

22
Q

What is the role of the APC/C complex in cell cycle regulation?

A

It promotes degradation of cyclins and other regulatory proteins to ensure proper mitotic progression and exit.

23
Q

What happens when the proteasome pathway is inhibited?

A

Inhibition induces cell cycle arrest and apoptosis, which can be therapeutically beneficial in cancer treatment.

24
Q

What are examples of proteasome inhibitors?

A

Peptide aldehydes, boronates, epoxy ketones, and beta-lactones, such as bortezomib, used in cancer therapy.

25
Q

What is the role of the vacuolar ATPase in lysosomes?

A

It pumps hydrogen ions into the lysosome to maintain its acidic environment, essential for enzyme activity.

26
Q

How does parkin function in mitochondrial quality control?

A

Parkin ubiquitinates damaged mitochondrial proteins, marking them for degradation via the autophagy-lysosome pathway.

27
Q

What is the structure of the 20S core proteasome?

A

It consists of four stacked rings with alpha subunits on the outer rings and beta subunits in the inner rings containing proteolytic activity.

28
Q

What are primary and secondary lysosomes?

A
  • Primary lysosomes are formed directly from the Golgi apparatus.
    • Secondary lysosomes are formed by the fusion of primary lysosomes with endosomes or autophagosomes.
29
Q

What biological processes are regulated by ubiquitin-proteasome-mediated proteolysis?

A

Cell growth, cell cycle progression, DNA damage repair, transcription, metabolism, and immunity.

30
Q

What happens when there is dysregulation of E3 ubiquitin ligases?

A

It can lead to diseases such as cancer, neurodegenerative disorders, and cardiovascular disease due to improper protein degradation.

31
Q

What is the significance of the 26S proteasome gate?

A

It remains closed until substrate binding and ATP hydrolysis occur, ensuring controlled access to the proteolytic core.

32
Q

How does ubiquitin chain structure affect its function?

A

The type of linkage (e.g., lysine 11, 48, 63) and chain conformation determine the biological role of the ubiquitin chain.

33
Q

What are chaperone proteins’ roles in proteasome substrate targeting?

A

They assist in recruiting non-ubiquitinated substrates to the proteasome through ubiquitin-like domains.

34
Q

What is the role of the lid subunit in the 19S regulatory particle?

A

It recognizes and binds polyubiquitin chains on substrates targeted for degradation.

35
Q

How are ubiquitin molecules recycled?

A

Deubiquitinating enzymes like RPN11 remove ubiquitin en bloc, while others cleave ubiquitin one molecule at a time.

36
Q

What diseases are linked to the dysfunction of ubiquitin-mediated autophagy?

A

Parkinson’s disease, due to accumulation of damaged mitochondria and proteins, and certain cancers.

37
Q

How does ubiquitination affect the cell cycle?

A

By regulating the degradation of cyclins and other proteins, it ensures timely progression through different cell cycle phases.

38
Q

What is the structure and function of lysosomal membranes?

A

They have a bilayer containing glycosylated transport proteins and maintain an acidic environment for enzyme activity.

39
Q

What is the significance of mannose-6-phosphate in lysosomes?

A

It is a marker for targeting lysosomal hydrolases from the Golgi apparatus to lysosomes.

40
Q

How do endocytosis and lysosomal degradation interact?

A

Endocytosed ligands and receptors are sorted in endosomes, with some targeted for lysosomal degradation.

41
Q

What is the lysosome’s role in autophagy?

A

It fuses with autophagosomes to degrade damaged organelles and macromolecules, recycling their components.

42
Q

What are the hydrolase classes found in lysosomes?

A

Proteases, nucleases, lipases, phospholipases, and sulfatases, which degrade diverse biomolecules.

43
Q

What is Angelman syndrome, and how is it linked to ubiquitin?

A

A genetic disorder caused by inactivation of E3 ubiquitin ligases, highlighting the role of ubiquitin in neurological development.

44
Q

What is the role of the 20S proteasome independent of the 19S regulatory particle?

A

It can degrade non-ubiquitinated proteins under specific cellular conditions.

45
Q

How does lysosomal pH support its function?

A

The acidic pH enhances the activity of lysosomal hydrolases required for macromolecule degradation.

46
Q

What is the role of the autophagy-lysosome pathway in mitochondrial health?

A

It removes dysfunctional mitochondria through mitophagy, preventing cellular damage.

47
Q

How does ubiquitination promote NF-kB activation?

A

Specific ubiquitin chains (e.g., K63) facilitate transcription factor activation, critical for immune responses.

48
Q

What is the ubiquitin E1 enzyme’s primary function?

A

To activate ubiquitin using ATP and transfer it to an E2 conjugating enzyme.

49
Q

What are the three ubiquitin receptors in the 19S particle?

A

RPN10, RPN13, and a third variable receptor that facilitate substrate recognition.

50
Q

What is the clinical significance of proteasome inhibitors like bortezomib?

A

They are used in cancer therapy to induce apoptosis by preventing the degradation of regulatory proteins.

Y1 Cellular Biochemistry and Biology (20 decks)

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