24 - Regulated Protein Degradation in Neuronal Development

Question 1

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

Answer 1

The cells need to physically separate

Question 2

What is the most important mediator of repulsive ephrin signaling?

Answer 2

ADAM-10

Question 3

What does ADAM-10 do?

Answer 3

Causes cleavage of the ephrin ligand

Question 4

Where is ADAM-10 expressed?

Answer 4

At the cell surface, near the Eph receptor

Question 5

What is the significance of ADAM-10?

Answer 5

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

Question 6

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

Answer 6

Upon binding of Eph to ephrin

Question 7

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

Answer 7

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

Question 8

What is the phenotype of deleting ADAM-10?

Answer 8

Disorganized array of axons at the tectum (no repulsion)

Question 9

What is an example of ripping?

Answer 9

Notch signaling

Question 10

What processes utilize Notch signaling?

Answer 10

Embryonic development, especially neurogenesis and neuronal development

Question 11

What is the structure of Notch?

Answer 11

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

Question 12

What type of molecules are Notch ligands?

Answer 12

Single pass cell surface proteins

Question 13

What are the names of some Notch ligands?

Answer 13

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

Question 14

What happens when Notch binds to Delta?

Answer 14

It induces proteolytic cleavage of the intracellular domain of Notch

Question 15

What does NICD stand for?

Answer 15

Notch intracellular domain

Question 16

Where is Notch cleaved?

Answer 16

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

Question 17

What does the NICD do after cleavage?

Answer 17

It translocates to the nucleus to activate gene expression

Question 18

Which cleavage of Notch does ADAM-10 mediate?

Answer 18

Cleavage at the extracellular domain

Question 19

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

Answer 19

ADAM-10

Question 20

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

Answer 20

Cleavage at the transmembrane domain

Question 21

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

Answer 21

The presenilin / gamma-secretase complex

Question 22

What is the order of cleavages for Notch?

Answer 22

First the extracellular cleavage, then the transmembrane cleavage

Question 23

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

Answer 23

By binding of Notch to Delta

Question 24

How is the presenilin / gamma-secretase complex actiavted?

Answer 24

Upon cleavage of Notch by ADAM-10

Question 25

What is ripping?

Answer 25

Regulated intramembrane proteolysis

Question 26

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

Answer 26

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

Question 27

What types of decisions are not suited for Notch signaling?

Answer 27

Rapid, repeat changes in stimulus over time

Question 28

What types of decisions are suited for Notch signaling?

Answer 28

Strong, decisive decisions (cell fate)

Question 29

Why is Notch signaling not suited for amplification?

Answer 29

One activated receptor only generates one active transcription factor

Question 30

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

Answer 30

False: it can be a transcription factor for many genes

Question 31

How is Notch signaling a direct signaling pathway?

Answer 31

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

Question 32

What proteins can MMPs degrade?

Answer 32

Collagen, fibronectin, etc.

Question 33

What events (4) do MMPs participate in?

Answer 33

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

Question 34

What is the broad function of MMPs?

Answer 34

Remodeling of the extracellular environment

Question 35

How are MMPs and ADAMs regulated?

Answer 35

Through transcription / translation, or proteolytic activation

Question 36

How are MMPs and ADAMs regulated through transcription / translation?

Answer 36

A tight regulation that occurs only under specific conditions

Question 37

How are MMPs and ADAMs regulated through proteolytic activation?

Answer 37

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

Question 38

What does the ubiquitin pathway regulate?

Answer 38

Regulated degradation of cytosolic proteins

Question 39

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

Answer 39

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

Question 40

What is the nature of the proteasome pathway?

Answer 40

Rapid and irreversible regulation of cell signaling

Question 41

What is the purpose of ubiquitin?

Answer 41

Tag proteins for degradation

Question 42

What is the purpose of the proteasome?

Answer 42

Degrade cytosolic proteins into short peptides

Question 43

Why must misfolded proteins be removed?

Answer 43

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

Question 44

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

Answer 44

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

Question 45

What do lysosomes do?

Answer 45

Mediate the degradation of proteins derived from endocytosis

Question 46

How does a lysosome shield proteolysis from the cytosol?

Answer 46

Through a lipid membrane

Question 47

What is the structure of the proteasome?

Answer 47

A large multi-subunit protein structure, cylindrical in shape

Question 48

What manmade object is similar to the proteasome?

Answer 48

A paper shredder

Question 49

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

Answer 49

1. It has a clear direction | 2. Closed box (well protected)

Question 50

What is meant by the proteasome having a "clear direction"?

Answer 50

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

Question 51

What is meant by the proteasome being a "closed box"?

Answer 51

The proteolytic environment is well protected from the outside environment

Question 52

What does the cap protein of the proteasome do?

Answer 52

Recognize the protein for degradation

Question 53

What does the core protein of the proteasome do?

Answer 53

Performs proteolysis

Question 54

What does the regulatory protein of the proteasome do?

Answer 54

Releases the amino acids

Question 55

What is the sedimentation of the entire proteasome?

Answer 55

26S

Question 56

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

Answer 56

19S

Question 57

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

Answer 57

20S

Question 58

How does the core protein of the proteasome mediate proteolysis?

Answer 58

It is lined by many proteases

Question 59

How do proteins enter the proteasome?

Answer 59

By binding to the lid structure

Question 60

In what state does the protein enter the proteasome?

Answer 60

As a linear chain

Question 61

How are proteins misfolded when entering the proteasome?

Answer 61

They are threaded as a linear chain into the proteasome

Question 62

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

Answer 62

ATP

Question 63

What is the purpose of ATP in the proteasome?

Answer 63

Misfold the protein and thread it into the proteasome

Question 64

How does a cell mark a protein for degradation?

Answer 64

By addition of unbiquitin

Question 65

What is ubiquitin?

Answer 65

A small molecule used as a tag for protein degradation

Question 66

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

Answer 66

Lysine linked connections

Question 67

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

Answer 67

A polyubiquitin tag

Question 68

What class of proteins add ubiquitin to proteins?

Answer 68

Cellular ubiquitin ligases

Question 69

Which proteins conjugate ubiquitin to a molecule?

Answer 69

E1, E2, and E3

Question 70

What is E1?

Answer 70

A ubiquitin activating enzyme

Question 71

What does E1 do?

Answer 71

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

Question 72

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

Answer 72

A thiol ester (E1-S-ubiquitin)

Question 73

What is needed for E1 to create the thiol ester?

Answer 73

ATP

Question 74

What is E2?

Answer 74

Ubiquitin-carrier proteins, or UBCs

Question 75

What does UBCs stand for?

Answer 75

Ubiquitin-Conjugating enzymes

Question 76

What is another name for UBC?

Answer 76

E2

Question 77

What does E2 do?

Answer 77

Transfers the ubiquitin from E1 to the target protein

Question 78

What is E3?

Answer 78

A ubiquitin-protein ligase

Question 79

What does E3 do?

Answer 79

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

Question 80

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

Answer 80

E1 and E2

Question 81

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

Answer 81

E3

Question 82

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

Answer 82

One

Question 83

What processes does E3 catalyze?

Answer 83

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

Question 84

What does DUB stand for?

Answer 84

Deubiquitinating enzymes

Question 85

What do DUBs do?

Answer 85

Remove ubiquitin from polyubiquitin chains

Question 86

What does Smurf1 stand for?

Answer 86

Smad ubiquitin regulatory factor 1

Question 87

What is Smurf1?

Answer 87

An E3 ligase in neuronal polarization

Question 88

What protein phosphorylated Smurf1?

Answer 88

PKA

Question 89

What does phosphorylation of Smurf1 do (generally)?

Answer 89

Changes its affinity for its substrates

Question 90

What do the two substrates of Smurf1 do?

Answer 90

They have opposing effects on axon formation

Question 91

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

Answer 91

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

Question 92

What does PAR-6 do?

Answer 92

It is a scaffold protein that helps mediate axon formation

Question 93

What does RhoA do?

Answer 93

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

Question 94

What are the downstream targets of Smurf1?

Answer 94

RhoA and PAR-6

Question 95

Which substrate of Smurf1 promotes axon formation?

Answer 95

PAR-6

Question 96

Which substrate of Smurf1 inhibits axon formation?

Answer 96

RhoA

Question 97

When Smurf1 is phosphorylated, what is the net result?

Answer 97

Promotion of axon formation