lecture 6 Flashcards
apoptosis
1
Q
what does apoptosis do
A
physiological method to eliminate unwanted/unnecessary cells
2
Q
example of apoptosis
A
during development, paws/hands have extra tissue which is webbing between digits; to get rid of it is apoptosis is triggered
3
Q
define apoptosis
A
controlled, polite cell death
4
Q
define necrosis
A
bad; uncontrolled cell death
5
Q
what happens in necrosis
A
cells burst, release intracellular contents into extracellular space (which is bad because harmful enzymes spill out into space which is dangerous and can trigger more necrotic death)
6
Q
what else can necrosis trigger
A
can trigger immune response by promoting inflammation; white blood cells infiltrate which is damaging to normal tissues
7
Q
what happens in apoptosis
A
cells don’t burst and release; they are broken into small components so they dissasemble
8
Q
describe apoptosis (how regulated it is)
A
highly regulated; everything in cell remains contained in barrier; b/c job of machinery is to make sure stuff remains where its supposed to be
9
Q
how does stuff get taken away in apoptosis
A
when broken into chunks, things like macrophages come in and phagocytose, clean up dead cell, make sure tissue operates as healthily as possible
10
Q
irreversible injury
A
cell can no longer function, structural integrity is disrupted
11
Q
what happens in irreversible injruy
A
cell needs to die; prefers to do so through apoptosis
12
Q
what happens in normal cell injury
A
cells usually bounce back; thru homeostasis they upregulate or downregulate certain genes
13
Q
when does necrosis happen
A
if you have a massive injury, happens very quickly, not enough time for cells to undergo apoptosis
14
Q
what are signs of reversible cell injury
A
reduced oxphos (E production) and depletion of ATP –> sign that mitochondria is injured
physical injury –> cell swelling
morphological changes to cell as injuries accumulate –> ER, mitochondria, cytoskeleton change function and appearance
15
Q
what’s the end result if these things are allowed to progress
A
cell death
16
Q
how can u tell necrosis happens
A
cell burst
17
Q
how can u tell apoptosis happened
A
cellular fragmentation, not bursting
18
Q
what does apoptosis depend on / what molecular mechanisms allow it to occur
A
depends on intracellular proteolytic cascade mediated by caspases
19
Q
important mediator of apoptotic process
A
caspase
20
Q
what happens when apoptosis is triggered
A
apoptotic signal –> caspase becomes active, initiate apoptotic signaling cascade resulting in morphological changes like cell fragmentation & packing into smaller pieces for engulfment by macrophages
21
Q
what are caspases
A
proteases
22
Q
what happens when caspases are activated
A
bind and cleave other proteins within cytoplasm
23
Q
what is caspase / how does it transmit signal
A
caspase is a signaling protein, transmits signals by cleaving downstream proteins
24
Q
how are caspases activated
A
cleave themselvse
25
describe inactivated caspases
monomers floating around in cytoplasm; intact, full length
26
what happens when cell decides to undergo apoptosis
apoptotic signal arrives, signal is gonna assemble an adaptor complex --> a dimer
27
what is the adaptor complex
2 identical dimers that can each bind and recruit a caspase to the complex
28
what is the job of adaptor
to bring caspases close enough together so they can cleave each otehr
29
what is this cleavage analagous to
trans autophosphorylation
30
what happens after the dimerization event hapens
proteins enzymatic activity gets close enough to act on their neighbors (in RTKs thats a phosphate group added) (in caspases, one cleaves the other)
31
what does cleavage do
initiates activation
32
what is this cleavage process called, and where is it in
cross cleavage; common to all mechanisms of caspase activation
33
what happens once cleaved
active caspase dimers are released, labeled as mature active caspases
34
what do mature active caspases do
cleave other proteins downstream in apoptotic pathway
35
initiator caspases
caspases that are initially activated; these are caspases that get things going
36
what do initiator caspases do
start process in response to upstream signal; go and activate executioner caspases next
37
executioner caspases
go and cleave all downstream targets needed for apoptosis to occur
38
what's on top of next step of pathway
active initiator caspase that's been cleaveed
39
what do active initiator caspases do next
goes and cleaves executioner caspases to activate them
40
how are executioners different from initiator caspases
executioners are already dimerized, but inactive
41
why don't executioners do cross cleavage
if they did, they wouldn't be able to exist as inactive dimers b/c they would just cleave each other
42
who cleaves executioner caspases
initiator caspases
43
what happens when initiator caspases cleave executioner caspases
similar rearrangement; executioners go and cleave multiple types of cell proteins
44
what does this process of cleavage by executioners result in
process of apoptosis
45
how many pathways needed for apoptosis to occur
MANY; we are just looking at one specific oen
46
how many targets do executioners have
multiple
47
how much does one set of initiator caspase activate
multiple dimers of executioner caspase; not a one to one
48
what does each downstream step represent
amplification where one upstream protein can activate multiple copies of downstream proteins amplifying signal
49
describe example pathway of what an executioner caspase is gonna do
dna cleaved into regular sized fragments
50
what is one hallmark of apoptosis
dna structure of cells undergoing apoptosis is cleaved in regular sized fragments
51
what does this dna cleaving allow you to determine
help determine when cell undergoes apoptosis vs necrossi
52
what is the end result of this specific pathway
it cuts DNA b/w histones [histones are regularly spaced in genomic DNA, cuts regularly spaced, so you get spaced out DNA ladders]
53
what happens if this dna cleavage pathway happens in healthy cells
NEVER want this to happen; cells will die if you cleave DNA ; hella rightly regulated
54
what are key players in executioner caspases controlling cleavage of DNA
CAD proteins, caspase activated DNase
55
what is activated by executioner caspase
CAD
56
what is CAD activity
DNase activity; cuts DNA
57
what happens when there's no apoptosis
CAD is inhibited by the inhibitor iCAD --> held in place
58
what does active executioner caspase do to CAD
it cleaves iCAD or inhibitor of CAD; CAD is ready
59
what happens when iCAD / CAD inhibitor is degraded
CAD is released and becomes active
60
what can CAD do when its active
cleaves DNA between histones, resulting in regular DNA pattern
61
what is net result of inhibiting the inhibitor
activation of protein
62
what is the normal resting state
it's held in inactive inhibited state; to activate you inhibit the inhibitor
63
what does CAD degrade
degrades DNA between histones to begin orderly destruction of nuclear contents
64
what does CAD convert
converts genomic DNA into ladder of regularly sized pieces (experimental hallmark of cells undergoing apoptosis)
65
why is immune system good at triggering apoptosis
immune cells kill cancer cells; T cells kill tumor cells; tumor cells have ways to evade apoptotic signals, so immune system needs to get good at triggering apoptosis
66
two pathways of apoptosis triggered by immune cells
extrinsic and intrinsic pathway
67
extrinsic pathway
cell receives apoptosis signal from outside / external environment
68
example scenario of extrinsic pathway
imagine a virus infected cell that's gonna be taken out by T cell
69
what are key players in extrinsic pathway
caspase 8, adaptor protein: FADD, Fas death receptors
70
what is caspase 8
initiator caspase of extrinsic apoptotic pathway
71
what are adaptor proteins
bring inactive initiator caspases together so they can close cleave each other to become activated
72
what is specific adaptor protein in extrinsic apoptosis
FADD protein
73
what is the other key thing in extrinsic apoptosis
needs to be a receptor involved since signal is coming from outside; receptor need to be able to recognize signal to transmit info across hydrophobic barrier of plasma membrane
74
specific receptor in extrinsic pathway
Fas death receptor
75
describe receptors in cell when it's normal and not undergoing extrinsic apoptosis
death receptors at surface; inactive, not bound
76
describe adaptor proteins in cell when it's normal and not undergoing extrinsic apoptosis
adaptor proteins in cytoplasm; folded up & inactive, not bringing anything together
77
describe caspases in cell when it's normal and not undergoing extrinsic apoptosis
caspase 8 is monomer, floating around cytoplasm, inactive
78
what comes from top
signal; killer lymphocyte or killer T cell
79
job of killer T cell
go in and trigger death of cells (cancer cells, infected or damaged cells, etc.)
80
how does killer T cell trigger death
expresses fast ligand on its surface --> contact dependent signaling
81
describe fast ligand
ligand is a trimer; binds to 3 Fas death receptors
82
what does fast ligand bind to
Fas death receptors
83
what happens once fast ligand activates fas death receptors
can now bind and unfold FADD adaptor proteins
84
what happens when FADD adaptor proteins are unfolded
they are active can bind to initiator caspases
85
what do adaptor proteins do
bring caspases close enough together so they can cleave each other to activate
86
what happens when caspase 8s are cleaved
release as dimers (caspase-8 dimer), go and activate executioner caspases
87
what are executioner caspases in extrinsic pathways
caspases 3 and 7
88
what happens after to killer T cell
job is done; gonna go and find other affected cells
89
general features that show up in apoptosis pathways
adaptor proteins, cross-cleavage, initiator caspases activate downstream executioners
90
what do adaptor proteins do
bring initiator caspases close enough together for cross cleavage
91
what is specific to extrinsic pathway
caspase 8, trimers of receptors, signal comes from T cell, specific FADD adaptor proteins
92
where does extrinsic pathway occur
contained within cell
93
what is intrinsic pathway
even more polite way to die; cell decides for itself to die for betterment of group
94
what is central regulatory node of intrinsic apoptotic pathway
mitochondria
95
what happens to mitochondria in intrinsic pathway
mitochondria can't function as efficiently, ATP production drops, cell homeostasis goes out the window
96
what happens if ATP production drops
cell is metabolically not active enough and dies
97
what is key factor cell is gonna listen to in inactive pathway
when ATP can't be produced in enough abundance
98
what does intrinsic pathway of apoptosis depend on
mitochondria
99
how do cells know mitochondria isn't working properly
if mitochondria is leaky
100
what happens if mitochondria membrane is leaky
proton gradient of oxphos is gonna be destroyed --> ATP production is gonna crater; apoptosis
101
what should mitochondrial membrane be for regular cell
intact
102
how does cell know when mitochondria membrane is leaky
cytochrome c
103
what's up w/ cytochrome c in healthy mitochondria
cytochrome C always held within mitochondria; never exposed to cytoplasm [good thing; membrane is intact and fully producing ATP]
104
how is mitochondria damaged
UV radiation, triggers oxygen radicals that damage membranes and make them leaky
105
where is cytochromes not supposed to be
in cytoplasm (green)
106
what is trigger for intrinsic apoptotic pathway
cytochromes in cytoplasm (supposed to be in membrane)
107
describe damaged mitochondria in signaling pathway
cytochrome c released into cytoplasm
108
what detects cytochrome c in cytoplasm
adaptor protein Apaf1
109
job of adaptor protein
assemble initiator caspases so they are close enough to cleave each other
110
what does Apaf1 do
binds cytochrome c
111
what does Apaf1-cytochrome c binding do
triggers conformational change in adaptor that allows it to assemble into oligomerized form
112
what does cytochrome c do (important)
cytochrome c binds one copy of adaptor, triggers conformational change that allows it to form higher order oligomer
113
what happens once oligomer is formed
recruits initiator caspases
114
what is caspase for intrinsic pathway
caspase 9
115
what happens after cross-cleaving (intrinsic)
activated caspase 9 dimers are released, cleave & activate executioner caspases & trigger apoptosis
116
what happens in some situations w/ intrinsic pathway (in diagram apoptotic stimulus pointing at mitochondria)
some signaling pathways purposefully cause release of cytochrome c (even tho mitochondria is healthy)
117
what pathway can trigger intrinsic pathway
PI 3-kinase pathway AKA survival signaling pathway
118
what regulatory proteins have the job of controlling if cytochrome c is released or not from mitochondria
Bcl2 family (Bcl2, Bak, Bad)
119
how do Bcl2 family of proteins regulate intrinsic apoptosis
by controlling mitochondrial permeability
120
3 varieties of Bcl2 fam
anti-apoptotic fam proteins, 2 pro-apoptotic fam proteins
121
name the anti-apoptotic fam protein
Bcl2
122
name the pro-apoptotic proteins
Bak and Bad
123
what do these apoptotic proteins do
control permeability of mitochondria in response to upstream signals
124
what happens when Bak is activated
cell is gonna wanna undergo apoptosis (b/c it's pro apoptotic)
125
where is Bak found
outermembrane of mitochondria
126
describe inactive Bak
exists as monomers in outer membrane of mitochondria
127
describe inactive Bak again
membrane is intact, no cytochrome c is leaking out, bak is inactive
128
what does bak directly control
permeability of outermembrane
129
what happens when apoptotic stimulus acts on Bak
activation of Bak, it clusters into an oligomer that forms a channel thru which cytochrome c floods cytoplasm
130
what does Bak channel cytochrome cytoplasm trigger
Apaf1 adaptor protein complex, caspase 9 activation, all steps necessary for intrinsic apoptosis
131
what about Bcl2
anti-apoptitic; when active it sits in outer membrane of mitochondria
132
what does Bcl2 do
Bcl2 binds Bak and blocks cytochrome channels from forming
133
what is Bcl2 similar to
safety mechanism; when safety is engaged, Bak can never fire
134
what happens when you take out Bcl2
remove safety, when trigger is pulled Bak makes channels --> apoptosis
135
basically what does Bak do
pro-apoptotic; forms channels and increases permeability of membrane
136
basically what does Bcl2 do
anti-apoptotic; blocks Bak and formation of channel
137
what is 3rd apoptotic regulator protein
Bad; pro-apoptotic
138
what does active Bad do
inhibits Bcl2
139
what does Bad inhibiting Bcl2
inhibits inhibitor of Bak; causes activation of Bak and apoptosis
140
what does PI 3-kinase signaling pathway
prevents apoptosis
141
what does trans autophosphorylation of RTK provide
docking site for PI 3-kinase
142
what does PI 3 kinase do
phosphorylates PI (4,5)P2 into PI(3,4,5)P3; which provides docking site in plasma membrane for downstream kinases PDK1 and AKt
143
what does PDK1 do
helps activate Akt
144
what happens when AKt is activated
released from plasma membrane, goes into cytoplasm
145
what does Akt phosphorylate
Bad
146
what does Bad phosphorylation do
releases active apoptosis inhibitory protein
147
what happens when Bad is phosphorylated
can't inhibit the inhibitor Bcl2 (meaning Bcl2 is free to inhibit apoptosis)
148
what happens to Bcl2 when PI 3 Kinase pathway is active
Bcl2 can bind to Bak and prevent cytochrome channel from forming (cytochrome can't go into cytoplasm)
149
describe PI 3 kinase pathway
survival pathway; if in right env. cells don't need to go in apoptosis
150
what happens if survival signal for PI-3-kinase pathway is withdrawn or cell is in wrong place and needs to self-destruct
Bad is gonna be de-phosphorylated, can inhibit the inhibitor Bcl2 and allow Bak to trigger apoptosis (thru cytochrome channel formation)
151
what does this survival signaling pathway regulate
intrinsic mechanism of apoptosis
152
when do cells stay alive
when pathway is active
153
why do we need survival signaling
we have more neurons early in dev. than as adult; more cells than the survival factor can keep alive
154
describe abundance of survival signal
kinda limited; some cells are gonna die so it leaves cells that remain to enjoy benefits of limiting survival signal
155
what causes apoptosis via PI3-kinase mechanism acting on regulation of intrinsic apoptotic pathway
apoptosis adjusts number of nerve cells to size of target; more nerve cells than survival factors released by target cells
