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Biochemistry > Protein Folding And Proteasome > Flashcards

Protein Folding And Proteasome Flashcards

1
Q

Interior of chaperone is ___ and has 7 ____ subunits inside

A

Interior of chaperone is HYDROPHOBIC and has 7 ATPase subunits inside

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2
Q

3 Functions of Chaperone during Protein Synthesis

A
  • protection of nascent chain
  • guidance during folding
  • avoidance of kinetic dead ends
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3
Q

Proteasome Structure

A

19 S regulatory cap made up of alpha subunits

20s chamber

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4
Q

Proteasome assembly requires ____ chaperone

A

Ump1

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5
Q

Types of interactions that promote folding

A 
Hydrophobic core
Electrostatic interactions
Van der Waals interactions
Disulfide bonds
Metal coordination
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6
Q

What is a molten globule?

A
  • 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
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7
Q

What happens to polypeptide with CFTR delta508 mutation?

A

Protein folds too slowly, it’s captured by proteolytic system and degraded, so intracellular levels of the protein are depleted.

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8
Q

eEIF1As Role in Protein Degradation

A

It facilitates degradation when folding is incorrect

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9
Q

In neurodegenerative diseases, aggregates form in ____ region, and _______ are usually copresent within aggregates

A

In neurodegenerative diseases, aggregates form in PERINUCLEAR region, and PROTEASOMES are usually copresent within aggregates

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10
Q

Examples of Amyloid Diseases

A
  • most aggregates contain B-pleated sheets
  • Alzheimers
  • Parkinsons
  • ALS (aggregation of SOD)
  • Huntingtons (CAG repeats)
  • Machado Joseph Disease (CAG repeats)
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11
Q

3 Ways to Regulate Proteolysis

A
  • Proteases are usually zymogens, need hormonal activation or autocatalysis
  • Activities are compartmentalized
  • pH/phosphorylation/substrate induced.
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12
Q

Distinguishing structural features of Ubiquitin

A
  • 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
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13
Q

Ub Carboxy Terminal Hydrolase

A

Cleaves polyubiqutin to expose the C-terminal tail

-mutations in this enzyme cause Parkinsons

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14
Q

Ub Activating Enzyme E1

A

Binds 2 Ubs as a UB-adenylate via thioester bond

  • ATP Dependent
  • Always has 2 mol of Ub
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15
Q

Ub-Conjugating Enzyme E2

A

Mediates the transfer of Ub from E1 to either E3 or substrate
-contributes to combinatorial diversity of Ub degradation pathway

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16
Q

Ub-Protein Ligase E3

A

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

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17
Q

How does Ub attach to conjugating enzymes?

A

Via thioester bond b.w. Ub C-terminal glycine and cysteine on enzyme

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18
Q

How does Ub attach to substrate?

A

Via Ub’s C-terminal glycine, ISOPEPTIDE bond to lysine on substrate.
-Isopeptide bond is reversible

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19
Q

Importance of Ub’s C-terminal Glycine

A

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)

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20
Q

Significance of multi-Ub cahin

A

Hydrophobic patches which create an extended hydrophobic stripe, which will interact with proteasome

21
Q

Significance of K-63

A

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

22
Q

20S catalytic core has __ stacked, __ subunit rings forming a _____

3 ________ activities are sequestered within ___ subunits

Chamber of entry is ______

A

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

23
Q

___ 19S particles bind to each end of 20S

Functions in binding _______ proteins and can release them

Contains _____ enzymes that require ____

A

TWO 19S particles bind to each end of 20S

Functions in binding UBIQUITIN proteins and can release them

Contains UNFOLDING enzymes that require ATP

24
Q

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

A

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

25
Q

Roles of 19S Regulatory Particle

A
  • Poly-Ub chain binding via hydrophobic stripe and disassembly for recycling
  • Substrate unfolding for channel entry
  • Regulates axial channel
  • Binds regulatory protiens
26
Q

Proteasome Regulation

A

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

27
Q

Parkin might bind and translocate _____ enzymes to the _____

A

Parkin might bind and translocate E2 enzymes to the PROTEASOME

28
Q

____, a HPV protein captures the _______ complex and attaches to _____, leading to the polyubiquination of ____ and it’s degradation, which results in loss of ______.

A

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.

29
Q

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.

A

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.

30
Q

____ 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.

A

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.

31
Q

_____ protein in Xeroderma pigmentosum is a protein that is degraded by the proteasome

A

Xpc

32
Q

Fancomi anemia

A

8/13 FA proteins are involved in protein degradation

33
Q

Machado Joseph Disease

A

Ataxin-3 is a proteasome subunit that can bind multi-Ub chains

34
Q

VHL Syndrome

A

Failure to degrade Hif-1 causes tumors on the skin

35
Q

Hypoxia-inducible factors are ____dimers. Has 3 __________ and a constiutive _____ subunit that is present in the _____.

A

Hypoxia-inducible factors are heterodimers. Has 3 oxygen labile alpha subunits and a constiutive Beta subunit that is present in the nucleus.

36
Q

Hif1 protein synthesis is promoted by _____/_____ and it’s degradation is controlled by _____ and _____.

A

Hif1 protein synthesis is promoted by mTOR/S6 kinaseand it’s degradation is controlled by VDL and VDU.

37
Q

Post-translational modifications of Hif1 include _____ and ______, which promote degradation, and _____ that promotes transcription. Hif1 degradation occurs by _____ dependent and independent mechanisms.

A

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.

38
Q

_____ 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 ______

A

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

39
Q

VDU2

A

Enzyme that can dismantle a multi-Ub chain conjugated to Hif1

40
Q

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

A

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

41
Q

____ enzyme can be activated and dismantle the Ub chain, allowing for hypoxia response

A

VDU enzyme can be activated and dismantle the Ub chain, allowing for hypoxia response

42
Q

During mitochondrial failure, [__] increases, which can bind PDH1,2,3, and Hif1 does not get ____, activating the hypoxia response.

A

During mitochondrial failure, [Fe2+] increases, which can bind PDH1,2,3, and Hif1 does not get hydroxylated, activating the hypoxia response.

43
Q

When Hif dimerizes in nucleus, induction of _____ expression which shuts down expression of ____, leading to _____, ______, and _____.

A

When Hif dimerizes in nucleus, induction of mir-210 miRNA expression which shuts down expression of normoxia, leading to angiogenesis, energy metabolism, and inflammation.

44
Q

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).

A

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).

45
Q

Symptoms of altitude sickness/hypoxia at varying altitudes:
2000-4000 m: ________________
4000-6000 m: ________________
6000-9000 m: ________________

A

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

46
Q

mTOR inhibitors in cancer therapy

A

Rapamycin

Everolimus

47
Q

Proteasome inhibitor in cancer therapy

A

Bortezomib

Carfilzomib

48
Q

Symptoms of normal acclimatization response

A
  • fatigue
  • sob
  • increased BP
  • increased urination
  • poor mental and physical performance
  • weight loss
  • poor sleep
49
Q

Altitude sickness symptoms

A
  • acute mountain sickness
  • sleep disordered breathing
  • high altitude pulmonary edema
  • high altitude cerebral edema
  • high altitude retinal hemorrhage
  • chronic mountain illness

Biochemistry (35 decks)

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