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BIO 317 > 23 - Regulated Protein Degradation > Flashcards

23 - Regulated Protein Degradation Flashcards

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1
Q

True or false: protein degradation refers to only ending a process

A

False: protein degradation can be used as actuators of cell signaling

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2
Q

What is (generally) the most common way to transmit signals in the cell?

A

Post-translational modifications

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3
Q

What is the most drastic post-translational modification?

A

Proteolysis

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4
Q

What is proteolysis?

A

The process of breaking peptide bonds

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5
Q

What are the products of protein degradation (generally)?

A

Either smaller peptides, or single amino acids

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6
Q

True or false: proteolysis is the only process of breaking peptide bonds

A

False: protein cleavage can also break peptide bonds

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7
Q

What is protein cleavage?

A

Breaking peptide bonds at specific sites to create functional domains

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8
Q

True or false: protein cleavage is highly regulated

A

True: protein cleavage is highly regulated and occurs at very specific locations

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9
Q

What is the typical structure of a cleavage protein?

A

Long extracellular domain, small transmembrane domain, little or none intracellular domain

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10
Q

What can proteolysis or protein cleavage be used for?

A
  1. Degrade proteins to eliminate their activity at specific times and locations
  2. Generate active enzymes or signaling molecules from longer, inactive precursors
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11
Q

How does proteolysis differ from other post-translational modifications?

A

It is mostly irreversible

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12
Q

How are other post-translational modifications (besides protein degradation) reversible?

A
  1. Ion channels can open / close
  2. Phosphorylation can be added or removed
  3. Acetylation of histones can be added or removed
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13
Q

How could protein degradation be “reversed”?

A

Through translation of the protein

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14
Q

How come protein degradation is called “irreversible”, if it can be reversed by translation?

A

Translation is a very slow process, so it takes significant time to reverse protein degradation

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15
Q

What are some cell activities that require regulated proteolysis?

A

Control of the cell cycle, apoptosis, development, growth, survival, etc.

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16
Q

For what types of signaling would protein degradation be the most useful?

A

When the cell wants to make a committed decision to change its state (instead of reverting back to its starting state)

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17
Q

What are examples of irreversible commitment steps?

A

Cell cycle, apoptosis, and development/morphogenesis

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18
Q

How is the cell cycle an irreversible commitment step?

A

It needs to proceed in an orderly fashion from one step to another

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19
Q

How is apoptosis an irreversible commitment step?

A

It must proceed to completion once initiated

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20
Q

How is development/morphogenesis an irreversible commitment step?

A

Cells must make irreversible decisions to acquire a specific cell fate

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21
Q

True or false: proteolysis can only be used for irreversible commitment steps

A

False: it can also be used for reversible commitment steps

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22
Q

How can proteolysis be used for a reversible commitment step?

A

It can activate signaling or other cellular events, which can be reversible

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23
Q

What family of proteins mediate degradation or cleavage?

A

Proteases

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24
Q

What do proteases do?

A

Hydrolyze the peptide bonds of proteins

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25
Q

What are proteases?

A

Proteins that mediate degradation or cleavage of other proteins

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26
Q

True or false: proteases are evolutionarily conserved

A

True: they are important for cell function, and thus are highly conserved

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27
Q

What are the functions of proteases?

A
  1. Achieve housekeeping functions
  2. Eliminate proteins no longer needed
  3. Cleave proteins to create other functional proteins
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28
Q

What is meant by “achieving housekeeping functions” (for proteases)?

A

Need to break down food for energy and biosynthesis

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29
Q

Why would proteins no longer be needed (for proteases)?

A

They are damaged or no longer needed in that specific location

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30
Q

How are many signaling proteins generated at the cell surface?

A

As inactive precursors

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31
Q

How can inactive precursors at the cell surface become active?

A

Through cleavage (control their activation)

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32
Q

How are proteases classified?

A

Based on their reaction mechanism

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33
Q

What are the different classifications of proteases?

A

Metalloproteases, and proteases categorized based on a central amino acid in their active site

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34
Q

What are metalloproteases?

A

Proteases that contain a metal ion (zinc, cobalt) in their active site

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35
Q

What are some examples of proteases categorized based on a central amino acid in their active site?

A

Serine proteases, cysteine proteases, and aspartyl proteases

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36
Q

Besides their reaction mechanism, how can proteases be further classified?

A

By their substrate specificity

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37
Q

How are most proteases synthesized?

A

As an inactive precursor (zymogen)

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38
Q

What is a zymogen?

A

An inactive precursor of the protease

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39
Q

Why are proteases synthesized as zymogens?

A

The cell does not want active proteases running around the cell at all times

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40
Q

How are zymogens activated?

A

Through protein cleavage

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41
Q

What signals can activate zymogens?

A

Extracellular signals

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42
Q

True or false: a protease can activate its own zymogen

A

True: this creates a positive feedback loop for a rapid response

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43
Q

Which steps of protease activation are irreversible?

A
  1. Activation of enzymes from inactive zymogens

2. Proteolytic degradation of proteins

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44
Q

True or false: protein degradation offers a unique temporal feature of cell signaling

A

True: based on its irreversible nature, it offers unique temporal features

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45
Q

What are the unique temporal features of protein degradation in cell signaling?

A

Degradation occurs rapidly, but translation occurs slowly

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46
Q

How can protein degradation or cleavage be used to sculpt signaling (5 ways)?

A
  1. Secretion of an extracellular ligand upon cleavage of a membrane precursor
  2. Activation of cell-surface receptor upon cleavage
  3. Removal of cell-surface receptors to down-regulate their signaling
  4. Degradation of damaged/”old”/inactive proteins (signaling attenuation)
  5. Degradation of proteins at specific cellular locations to localize signaling
47
Q

What is an example of secretion of an extracellular ligand upon cleavage of a membrane precursor?

A

Neurotrophins such as BDNF

48
Q

How is BDNF (and other neurotrophins) secreted into the extracellular space?

A

As immature proteins (pro-BDNF)

49
Q

How is pro-BDNF activated?

A

By specific cleavage

50
Q

What is the importance of the signal peptide in pro-BDNF?

A

It trafficks pro-BDNF to be secreted by the cell

51
Q

True or false: only mature BDNF can generate signaling

A

False: pro-BDNF can also generate signaling

52
Q

What is an example of activation of cell-surface receptors upon cleavage?

A

Notch-Delta signaling

53
Q

When is Notch cleaved?

A

When it binds to its ligand delta

54
Q

What type of protein is delta?

A

A cell surface ligand

55
Q

What happens when Notch is cleaved?

A

The intracellular domain goes to the nucleus to regulate gene expression

56
Q

What type of protein is Notch?

A

A cell surface receptor

57
Q

What is signaling attenuation?

A

Reducing the strength of the signal

58
Q

How can signaling attenuation be achieved?

A

By down regulating cell surface receptors through proteolysis

59
Q

Why would a cell use protein degradation for localization?

A

They may not have other mechanisms, such as scaffold proteins, to accomplish this

60
Q

How can protein degradation be used for localization?

A

They can degrade proteins in areas where they shouldn’t be acting, thus restricting their activity to specific locations in the cell

61
Q

What are the (3) roles of metalloproteases?

A
  1. Degrade ECM proteins to regulate migration
  2. Generate active signaling molecules (ligands) from large precursors
  3. Cleave receptors for their activation or down regulation
62
Q

What does MMP stand for?

A

Matrix metalloprotease

63
Q

What does ADAM stand for?

A

A disintegrin and metalloprotease

64
Q

True or false: MMPs are found at the cell surface

A

False: they are found in the intracellular space

65
Q

How come MMPs are not found at the cell surface?

A

They have no transmembrane and intracellular domain

66
Q

True or false: ADAMs are found at the cell surface?

A

True: they are anchored to the cell membrane

67
Q

How come ADAMs are found at the cell surface?

A

They have a transmembrane and intracellular domain

68
Q

For most metalloproteases, which domain is the largest?

A

The extracellular domain

69
Q

How are MMPs and ADAMs synthesized?

A

As inactive precursors (zymogens)

70
Q

How are MMPs and ADAMs activated?

A

Through cleavage events

71
Q

True or false: MMPs are only active during development

A

False: they are active all throughout life for cell migration

72
Q

Besides development, what is an example of a process that require MMPs?

A

Wound healing

73
Q

Which metalloproteases are anchored at the cell surface?

A

ADAMs

74
Q

Which metalloproteases are secreted by the cell?

A

MMPs

75
Q

What do ADAMs do?

A

Cleave membrane-associated proteins at the cell surface (ectodomain shedding)

76
Q

What is ectodomain shedding?

A

The cleavage of membrane-associated proteins at the cell surface

77
Q

How can ADAMs promote signaling?

A

By releasing an active ligand

78
Q

How can ADAMs regulate signaling?

A

By cleaving the extracellular ligand-binding domain of a receptor

79
Q

What is another name for ADAM-17?

A

TACE

80
Q

What is another name for TACE?

A

ADAM-17

81
Q

What is one substrate of TACE?

A

EGF

82
Q

What does TACE stand for?

A

Tumor necrosis factor-alpha-converting enzyme

83
Q

True or false: the only substrate of TACE is EGF

A

False: TACE has a wide range of substrates

84
Q

What happened when TACE was deleted in cells?

A

It had similar phenotypes to EGFR mutations

85
Q

How does TACE interact with EGFR?

A

TACE cleaves pro-EGF to release it and allow it to bind to EGFR

86
Q

In what mechanisms is TACE important for?

A

Juxtacrine signaling, and establishment of a gradient

87
Q

Why is the TACE mechanism important for juxtacrine signaling?

A

It generates localized signaling, so only the cells in the vicinity respond to it

88
Q

What is juxtacrine signaling?

A

Signaling to the same or neighboring cells

89
Q

How can the TACE mechanism lead to a gradient of cues?

A

Cues can diffuse away from the cell to create a gradient

90
Q

How is EGF synthesized?

A

As an inactive cell surface protein

91
Q

What happens if a protease is absent?

A

The downstream signaling of that extracellular cue is also absent

92
Q

What can be done to rescue the deletion of a protease?

A

Need to activate the pathway genetically or pharmacologically

93
Q

How do cells influence axon pathfinding?

A

They can present cell surface ligands to help guide the axon

94
Q

What axon guidance cues are found on the cell surface?

A

Ephrins

95
Q

What receptors bind to ephrins?

A

Eph receptors

96
Q

What type of signaling do ephrins mediate?

A

Repulsive (sometimes attractive) signaling

97
Q

What is meant by “ephrin bi-directional signaling”?

A

Ephrins can also act as receptors, and transmit signals when binding to an Eph ligand

98
Q

What type of proteins are Eph receptors?

A

RTKs

99
Q

What are topographic maps?

A

Precise innervations of axons from specific neurons in one tissue to another

100
Q

What is the RetinoTectal projection?

A

The patterning of axons from the retina (eye) to the tectum

101
Q

What is the tectum?

A

The part of the brain (in chickens, frogs, and fish) responsible for auditory and visual response)

102
Q

What brain structure in humans is analogous to the tectum?

A

The visual cortex

103
Q

If an axon is anterior in the retina, where will it be found in the tectum?

A

More posterior

104
Q

If an axon is posterior in the retina, where will it be found in the tectum?

A

More anterior

105
Q

If an axon is posterior in the tectum, where did it originate in the retina?

A

More anterior

106
Q

If an axon is anterior in the tectum, where did it originate in the retina?

A

More posterior

107
Q

What is the gradient of Eph receptors in the retina?

A

Lower anterior to higher posterior

108
Q

What is the gradient of ephrins in the tectum?

A

Lower anterior to higher posterior

109
Q

How come axons that start more anterior in the retina end up more posterior in the tectum?

A

They have less Eph receptors, so they are less affected by ephrin signaling

110
Q

How come axons that start more posterior in the retina end up more anterior in the tectum?

A

They have more Eph receptors, so they are more affected by ephrin signaling

111
Q

Which region of the RetinoTectal projection has a gradient of Eph receptors?

A

The retina

112
Q

Which region of the RetinoTectal projection has a gradient of ephrin?

A

The tectum

113
Q

What does “anterior” refer to?

A

Front

114
Q

What does “posterior” refer to?

A

Back

BIO 317 (27 decks)

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