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BM 210: Introduction to Biochemistry > Block E Part 2: How and why Cells Die > Flashcards

Block E Part 2: How and why Cells Die Flashcards

1
Q

During development, what helps determine the size and shapes of limbs?

A

Carefully orchestrated patterns of cell death
(Lecture 2, Slide 3)

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2
Q

Is cell death random?

A

No, cell death is programmed
(Lecture 2, Slide 3)

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3
Q

What proteins trigger apoptosis?

A

Specialised intracellular proteases (called caspases)
(Lecture 2, Slide 5)

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4
Q

How do specialised intracellular proteases trigger apoptosis?

A

By cleaving specific sequences in numerous proteins inside the cell, bringing about dramatic changes the lead to cell death and engulfment
(Lecture 2, Slide 5)

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5
Q

Why are the specialised intracellular proteases called caspases?

A

As they have a cysteine at their active site and they cleave their target protein at specific aspartic acids they are called caspases as c for cysteine + asp for aspartic acid
(Lecture 2, Slide 5)

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6
Q

Are caspases active when synthesised in the cell?

A

No, they are activated only during apoptosis
(Lecture 2, Slide 5)

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7
Q

What are the 2 major types of apoptotic caspases?

A

Initiator and executioner caspases
(Lecture 2, Slide 5)

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8
Q

What does an initiator caspase contain in its carboxy terminal region?

A

A protease domain
(Lecture 2, Slide 6)

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9
Q

What does an initiator caspase contain near its amino terminus?

A

A small protein interaction domain
(Lecture 2, Slide 6)

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10
Q

What form is an initiator caspase initially made in?

A

An inactive, monomeric form
(Lecture 2, Slide 6)

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11
Q

What is the inactive form of a caspase sometimes called?

A

Procaspase
(Lecture 2, Slide 6)

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12
Q

What do adaptor proteins assembled by apoptotic signals carry?

A

Multiple binding sites for the caspase amino-terminal small protein interaction domain
(Lecture 2, Slide 6)

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13
Q

What happens to the initiator caspases upon binding to adaptor proteins?

A

They dimerize (form a dimer) which activates them, leading to a cleavage of a specific site in their protease domain
(Lecture 2, Slide 6)

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14
Q

What happens to the protease domains of caspases after they are cleaved by the caspase forming a dimer?

A

They rearrange into a large and small subunit
(Lecture 2, Slide 7)

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15
Q

What form are executioner caspases originally formed as?

A

Inactive dimers
(Lecture 2, Slide 7)

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16
Q

What happens to an executioner caspase after cleavage at a site in the protease domain by an initiator caspase?

A

The executioner caspase dimer undergoes an activating conformational change
(Lecture 2, Slide 7)

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17
Q

What do executioner dimers do after undergoing their conformational change?

A

They cleave a variety of key proteins, leading to the controlled death of the cell
(Lecture 2, Slide 7)

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18
Q

How many proteins have scientists found to be cleaved by caspases during apoptosis?

A

Over 1,000
(Lecture 2, Slide 8)

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19
Q

What are 4 types of proteins which are cleaved by caspases?

A

Lamins
Cytoskeleton proteins
Cell-cell adhesion proteins
DNA degrading proteins
(Lecture 2, Slide 8)

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20
Q

What is caspase-activated DNase (CAD)?

A

A protein in humans encoded by the DFFB gene
(Lecture 2, Slide 9)

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21
Q

What does caspase-activated DNase (CAD) do during apoptosis?

A

It breaks up DNA
(Lecture 2, Slide 9)

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22
Q

What form is caspase-activated DNase (CAD) usually found in?

A

Inactive monomer inhibited by iCAD
(Lecture 2, Slide 9)

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23
Q

How do caspases mediate the intracellular proteolytic cascade that apoptosis depends on?

A

As executioner caspases cleave iCAD, leading to CAD becoming activated and start breaking up DNA
(Lecture 2, Slide 9)

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24
Q

What are the 2 main forms of apoptosis?

A

Extrinsic pathway
Intrinsic pathway
(Lecture 2, Slide 11)

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25
Q

What cascade occurs in extrinsic apoptosis and where does it begin?

A

Caspase 8 cascade, beginning outside the cell
(Lecture 2, Slide 11)

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26
Q

What cascade occurs in intrinsic apoptosis?

A

Caspase 9 mitochondrial pathways
(Lecture 2, Slide 11)

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27
Q

What do both the extrinsic and intrinsic pathways of apoptosis function to do?

A

Activate the executioner caspases
(Lecture 2, Slide 11)

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28
Q

How is the extrinsic pathway of apoptosis activated?

A

By extracellular proteins binding to cell surface death receptors
(Lecture 2, Slide 12)

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29
Q

What type of protein complex are death receptors?

A

Homotrimers
(Lecture 2, Slide 12)

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30
Q

What is a homotrimer?

A

A structure composing of 3 identical subunits
(Lecture 2, Slide 12)

31
Q

What are death receptors characterised by?

A

The presence of a death domain
(Lecture 2, Slide 12)

32
Q

Are death receptor ligands trimeric?

A

Yes
(Lecture 2, Slide 12)

33
Q

How is the fas death receptor activated on the surface of a target cell?

A

By the fas-ligand on the surface of a cytotoxic T cell lymphocyte binding to the receptor
(Lecture 2, Slide 12)

34
Q

How do fas ligands lead to several ligand-bound receptor trimers clustering?

A

Trimeric fas ligands on the surface of a cytotoxic kill T cell interact with trimeric fas receptors on the surface of the target cell, leading to clustering of several ligand-bound receptor trimers
(Lecture 2, Slide 13)

35
Q

What does clustering of fas receptors activate?

A

Death domains on the receptor tails
(Lecture 2, Slide 14)

36
Q

What do death domains activated by receptor clustering interact with?

A

Similar domains on the adaptor protein FADD (Fas-associated death domain)
(Lecture 2, Slide 14)

37
Q

What does each FADD (Fas-associated death domain) protein recruit after interacting with death domains?

A

An initiator caspase (caspase-8)
(Lecture 2, Slide 15)

38
Q

How do FADD (Fas-associated death domain) proteins recruit caspase-8?

A

Via a death effector domain on both FADD and the caspase
(Lecture 2, Slide 15)

39
Q

What does FADD proteins recruiting caspases form?

A

A death-inducing signalling complex
(DISC)
(Lecture 2, Slide 15)

40
Q

How do adjacent initiator caspases (caspase 8) in the death-inducing signalling complex (DISC) form an activated protease dimer?

A

By interacting and cleaving one another
(Lecture 2, Slide 16)

41
Q

What does the activated protease dimer in the death-inducing signalling complex (DISC) do?

A

It cleaves itself
(Lecture 2, Slide 16)

42
Q

What does the activated protease dimer in the death-inducing signalling complex (DISC) cleaving itself result in?

A

The protease dimer being linked to the death effector domain
(Lecture 2, Slide 16)

43
Q

What does the activated protease dimer being linked to the death effector domain do?

A

It stabilises and releases the active protease (caspase) dimer into the cytosol
(Lecture 2, Slide 16)

44
Q

What does the activated protease dimer activate once released into the cytosol and how does it do this?

A

Executioner caspases by cleaving them
(Lecture 2, Slide 16)

45
Q

What do many cells produce to restrain the extrinsic pathway of apoptosis?

A

Inhibitory proteins
(Lecture 2, Slide 17)

46
Q

How is the intrinsic pathway of apoptosis activated?

A

From within the cell, usually in response to a signal such as DNA damage that cannot be repaired, cellular stress or in response to a developmental cue (such as the formation of digits)
(Lecture 2, Slide 18)

47
Q

What does the intrinsic pathway of apoptosis depend on?

A

Mitochondria releasing cytochrome c into the cytosol
(Lecture 2, Slide 20)

48
Q

What causes mitochondria to release cytochrome c?

A

Intracellular apoptotic stimuli
(Lecture 2, Slide 20)

49
Q

What does cytochrome c bind to after being released by mitochondria into the cytosol?

A

Apaf1
(Lecture 2, Slide 20)

50
Q

What does the binding of cytochrome c to Apaf1 cause?

A

Apaf1 to unfold partly
(Lecture 2, Slide 20)

51
Q

What does Apaf1 unfolding partly in response to cytochrome c binding it cause?

A

A domain to be exposed, which interacts with the same domain in other Apaf1 molecules
(Lecture 2, Slide 20)

52
Q

How many Apaf1 molecules interacting does it take to form a large ring complex called the apoptosome?

A

7
(Lecture 2, Slide 20)

53
Q

How are caspase-9 molecules recruited into the apoptosome and activated ?

A

The caspase recruitment domain (CARD) in Apaf1 bind similar domains in multiple caspase-9 molecules
(Lecture 2, Slide 21)

54
Q

What does caspase-9 do once activated?

A

Cleaves and activates downstream executioner caspases
(Lecture 2, Slide 21)

55
Q

What are the key regulators of the intrinsic pathway of apoptosis?

A

The Bcl2 family
(Lecture 2, Slide 22)

56
Q

How does the mammalian Bcl2 family regulate the intrinsic pathway of apoptosis?

A

By controlling the release of cytochrome c and other intermembrane mitochondrial proteins into the cytosol
(Lecture 2, Slide 22)

57
Q

What are the 2 different types of Bcl 2 family proteins and what are their fuctions?

A

Pro-apoptotic proteins which promote apoptosis by enhancing release of cytochrome c and other intermembrane mitochondrial proteins and anti-apoptotic which inhibit apoptosis by blocking the release
(Lecture 2, Slide 22)

58
Q

What can pro-apoptotic and anti-apoptotic Bcl2 family proteins form by binding to each other in various combinatons?

A

Heterodimers
(Lecture 2, Slide 22)

59
Q

What happens when pro-apoptotic and anti-apoptotic Bcl2 family proteins form heterodimers with each other?

A

They inhibit each other’s function
(Lecture 2, Slide 22)

60
Q

What are the 3 different classes of Bcl2 proteins?

A

Anti-apoptotic
Pro-apoptotic effector
Pro-apoptotic BH3 only
(Lecture 2, Slide 23)

61
Q

What Bcl-2 homology (BH) domains does the anti-apoptotic Bcl 2 family protein contain?

A

BH1, BH2, BH3 and BH4
(Lecture 2, Slide 23)

62
Q

What Bcl-2 homology (BH) domains does the pop-apoptotic effector Bcl2 family protein contain?

A

BH1, BH2 and BH3
(Lecture 2, Slide 23)

63
Q

What Bcl-2 homology (BH) domains does the pro-apoptotic BH3-only Bcl2 family protein contain?

A

BH3 only (clues in the name)
(Lecture 2, Slide 23)

64
Q

How can complex inter-play occur between the 3 classes of Bcl 2 proteins?

A

Through the BH3 domain, the only domain they have in common
(Lecture 2, Slide 23)

65
Q

What happens to the effector Bcl2 family proteins when they are activated by an apoptotic stimulator?

A

They aggregate on the outer mitochondrial membrane
(Lecture 2, Slide 24)

66
Q

What is the effector Bcl2 family proteins aggregating on the outer mitochondrial membrane thought to do?

A

Make a channel which allows the release of cytochrome c and other proteins from the mitochondrial intermembrane space into the cytosol
(Lecture 2, Slide 24)

67
Q

What do the anti-apoptotic Bcl 2 family proteins do to the pro-apoptotic effector proteins in the absence of an apoptotic stimulus?

A

They bind to and inhibit them
(Lecture 2, Slide 25)

68
Q

What do BH3-only proteins do in the presence of an apoptotic stimulator?

A

They are activated and bind to the anti-apoptotic Bcl 2 family proteins so that they can no longer inhibit the effector Bcl2 family proteins
(Lecture 2, Slide 26)

69
Q

What does the body need survival factors?

A

They ensure that individual cells behave for the good or the organism as a whole - by surviving when needed and killing themselves when not
(Lecture 2, Slide 27)

70
Q

What are 3 ways in which survival factors block apoptosis?

A

Increase production of anti-apoptotic Bcl2 family proteins
Inactive of pro-apoptotic BH3-only protein
Inactivation of anti-IAPs (counteract the activity of inhibitors of apoptosis proteins)
(Lecture 2, Slide 28)

71
Q

What happens to a cell after it has been through apoptosis?

A

The cell and its fragments do not break open and release contents, but instead remain intact and they are phagocytosed
(Lecture 2, Slide 29)

72
Q

Why are cells that have undergone apoptosis phagocyotsed?

A

As it does not trigger an inflammatory response
(Lecture 2, Slide 29)

73
Q

What regulates phagocytosis?

A

A balance of “eat me” and “don’t eat me” signals displayed on the cell surface
(Lecture 2, Slide 30)

74
Q
A

BM 210: Introduction to Biochemistry (12 decks)

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