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BIO 317 > 24 - Regulated Protein Degradation in Neuronal Development > Flashcards

24 - Regulated Protein Degradation in Neuronal Development Flashcards

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1
Q

For cell surface receptors / ligands to mediate repulsive signaling, what needs to happen?

A

The cells need to physically separate

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2
Q

What is the most important mediator of repulsive ephrin signaling?

A

ADAM-10

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3
Q

What does ADAM-10 do?

A

Causes cleavage of the ephrin ligand

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4
Q

Where is ADAM-10 expressed?

A

At the cell surface, near the Eph receptor

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5
Q

What is the significance of ADAM-10?

A

It allows the cell to physically separate, which is needed for repulsive signaling

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6
Q

How is ADAM-10 activated (in ephrin signaling)?

A

Upon binding of Eph to ephrin

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7
Q

True or false: overexpression of Eph and ephrin can rescue the deletion of ADAM-10

A

False: overexpression would not lead to cleavage, which is necessary for the proper phenotype

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8
Q

What is the phenotype of deleting ADAM-10?

A

Disorganized array of axons at the tectum (no repulsion)

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9
Q

What is an example of ripping?

A

Notch signaling

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10
Q

What processes utilize Notch signaling?

A

Embryonic development, especially neurogenesis and neuronal development

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11
Q

What is the structure of Notch?

A

A single pass transmembrane receptor with a large extracellular domain, and a small transmembrane and intracellular domain

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12
Q

What type of molecules are Notch ligands?

A

Single pass cell surface proteins

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13
Q

What are the names of some Notch ligands?

A

Delta and Serrate (flies), Delta-like and Jagged (mammals)

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14
Q

What happens when Notch binds to Delta?

A

It induces proteolytic cleavage of the intracellular domain of Notch

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15
Q

What does NICD stand for?

A

Notch intracellular domain

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16
Q

Where is Notch cleaved?

A

Once close to the extracellular leaflet, and once at the transmembrane region

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17
Q

What does the NICD do after cleavage?

A

It translocates to the nucleus to activate gene expression

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18
Q

Which cleavage of Notch does ADAM-10 mediate?

A

Cleavage at the extracellular domain

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19
Q

Which enzyme catalyzes the cleavage of Notch at the extracellular domain?

A

ADAM-10

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20
Q

Which cleavage of Notch does the presenilin / gamma-secretase complex mediate?

A

Cleavage at the transmembrane domain

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21
Q

Which enzyme catalyzes the cleavage of Notch at the transmembrane domain?

A

The presenilin / gamma-secretase complex

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22
Q

What is the order of cleavages for Notch?

A

First the extracellular cleavage, then the transmembrane cleavage

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23
Q

How is ADAM-10 activated (in Notch signaling)?

A

By binding of Notch to Delta

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24
Q

How is the presenilin / gamma-secretase complex actiavted?

A

Upon cleavage of Notch by ADAM-10

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25
Q

What is ripping?

A

Regulated intramembrane proteolysis

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26
Q

What are the specific characteristics (3) of the Notch signaling pathway?

A
  1. Release of NCID is irreversible
  2. Not a good pathway for signal amplification
  3. Directness
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27
Q

What types of decisions are not suited for Notch signaling?

A

Rapid, repeat changes in stimulus over time

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28
Q

What types of decisions are suited for Notch signaling?

A

Strong, decisive decisions (cell fate)

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29
Q

Why is Notch signaling not suited for amplification?

A

One activated receptor only generates one active transcription factor

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30
Q

True or false: NCID is a transcription factor for a particular gene

A

False: it can be a transcription factor for many genes

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31
Q

How is Notch signaling a direct signaling pathway?

A

There are no intermediates between cell-surface receptor engagement and nuclear activity

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32
Q

What proteins can MMPs degrade?

A

Collagen, fibronectin, etc.

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33
Q

What events (4) do MMPs participate in?

A
  1. Cell migration
  2. Wound healing / cell protrusion
  3. Ovulation
  4. Angiogenesis
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34
Q

What is the broad function of MMPs?

A

Remodeling of the extracellular environment

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35
Q

How are MMPs and ADAMs regulated?

A

Through transcription / translation, or proteolytic activation

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36
Q

How are MMPs and ADAMs regulated through transcription / translation?

A

A tight regulation that occurs only under specific conditions

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37
Q

How are MMPs and ADAMs regulated through proteolytic activation?

A

They are produced as inactive zymogens, that need to be activated by MMPs or other proteases

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38
Q

What does the ubiquitin pathway regulate?

A

Regulated degradation of cytosolic proteins

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39
Q

Why would a cell want to degrade cytosolic proteins (3 reasons)?

A
  1. When the protein is old/damaged/inactive
  2. When the protein is unable to fold correctly or is damaged
  3. Protein removal for attenuation of cell signaling
40
Q

What is the nature of the proteasome pathway?

A

Rapid and irreversible regulation of cell signaling

41
Q

What is the purpose of ubiquitin?

A

Tag proteins for degradation

42
Q

What is the purpose of the proteasome?

A

Degrade cytosolic proteins into short peptides

43
Q

Why must misfolded proteins be removed?

A

Their accumulation and aggregation can be toxic to the cell, so they must be removed

44
Q

What considerations (2) need to be considered when degrading proteins?

A
  1. Need to avoid potential dangers of unrestrained proteolytic activity
  2. Sites of proteolysis must be confined/sequestered from other components of the cytosol
45
Q

What do lysosomes do?

A

Mediate the degradation of proteins derived from endocytosis

46
Q

How does a lysosome shield proteolysis from the cytosol?

A

Through a lipid membrane

47
Q

What is the structure of the proteasome?

A

A large multi-subunit protein structure, cylindrical in shape

48
Q

What manmade object is similar to the proteasome?

A

A paper shredder

49
Q

How is a paper shredder similar to the proteasome (2 ways)?

A
  1. It has a clear direction

2. Closed box (well protected)

50
Q

What is meant by the proteasome having a “clear direction”?

A

Proteins go in one way, and amino acids go out the other way (specified direction)

51
Q

What is meant by the proteasome being a “closed box”?

A

The proteolytic environment is well protected from the outside environment

52
Q

What does the cap protein of the proteasome do?

A

Recognize the protein for degradation

53
Q

What does the core protein of the proteasome do?

A

Performs proteolysis

54
Q

What does the regulatory protein of the proteasome do?

A

Releases the amino acids

55
Q

What is the sedimentation of the entire proteasome?

A

26S

56
Q

What is the sedimentation of the cap and regulatory proteins in the proteasome?

A

19S

57
Q

What is the sedimentation of the core protein in the proteasome?

A

20S

58
Q

How does the core protein of the proteasome mediate proteolysis?

A

It is lined by many proteases

59
Q

How do proteins enter the proteasome?

A

By binding to the lid structure

60
Q

In what state does the protein enter the proteasome?

A

As a linear chain

61
Q

How are proteins misfolded when entering the proteasome?

A

They are threaded as a linear chain into the proteasome

62
Q

What is needed for the protein to be threaded into the proteasome?

A

ATP

63
Q

What is the purpose of ATP in the proteasome?

A

Misfold the protein and thread it into the proteasome

64
Q

How does a cell mark a protein for degradation?

A

By addition of unbiquitin

65
Q

What is ubiquitin?

A

A small molecule used as a tag for protein degradation

66
Q

What mediates the binding of ubiquitin to a protein / other ubiquitins?

A

Lysine linked connections

67
Q

What does the cap protein recognize to allow a protein to go into the proteasome?

A

A polyubiquitin tag

68
Q

What class of proteins add ubiquitin to proteins?

A

Cellular ubiquitin ligases

69
Q

Which proteins conjugate ubiquitin to a molecule?

A

E1, E2, and E3

70
Q

What is E1?

A

A ubiquitin activating enzyme

71
Q

What does E1 do?

A

Activates ubiquitin to create a high energy intermediate (E1-S-ubiquitin)

72
Q

What type of protein is the high energy intermediate after E1?

A

A thiol ester (E1-S-ubiquitin)

73
Q

What is needed for E1 to create the thiol ester?

A

ATP

74
Q

What is E2?

A

Ubiquitin-carrier proteins, or UBCs

75
Q

What does UBCs stand for?

A

Ubiquitin-Conjugating enzymes

76
Q

What is another name for UBC?

A

E2

77
Q

What does E2 do?

A

Transfers the ubiquitin from E1 to the target protein

78
Q

What is E3?

A

A ubiquitin-protein ligase

79
Q

What does E3 do?

A

Binds to E2 and the target protein to facilitate transfer of ubiquitin

80
Q

Which parts of the ubiquitin conjugation pathway are general to many proteins?

A

E1 and E2

81
Q

Which parts of the ubiquitin conjugation pathway are specific to one particular protein?

A

E3

82
Q

For each turn of the ubiquitin conjugation pathway, how many ubiquitins are added to the protein?

A

One

83
Q

What processes does E3 catalyze?

A

Transfer of ubiquitin from E2 to the target protein, and covalent attachment of ubiquitin to the target protein

84
Q

What does DUB stand for?

A

Deubiquitinating enzymes

85
Q

What do DUBs do?

A

Remove ubiquitin from polyubiquitin chains

86
Q

What does Smurf1 stand for?

A

Smad ubiquitin regulatory factor 1

87
Q

What is Smurf1?

A

An E3 ligase in neuronal polarization

88
Q

What protein phosphorylated Smurf1?

A

PKA

89
Q

What does phosphorylation of Smurf1 do (generally)?

A

Changes its affinity for its substrates

90
Q

What do the two substrates of Smurf1 do?

A

They have opposing effects on axon formation

91
Q

What is the effect on its substrates when Smurf1 is phosphorylated?

A

Reduced degradation of PAR-6, and increased degradation of RhoA

92
Q

What does PAR-6 do?

A

It is a scaffold protein that helps mediate axon formation

93
Q

What does RhoA do?

A

It is a growth-inhibiting small GTPase that inhibits axon formation

94
Q

What are the downstream targets of Smurf1?

A

RhoA and PAR-6

95
Q

Which substrate of Smurf1 promotes axon formation?

A

PAR-6

96
Q

Which substrate of Smurf1 inhibits axon formation?

A

RhoA

97
Q

When Smurf1 is phosphorylated, what is the net result?

A

Promotion of axon formation

BIO 317 (27 decks)

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