Cell Death Flashcards
Cell death is the end of a response. True or false
No it is the beginning of an immune response
How many cells die a second
1 million
3 reasons cell death is used in normal physiology
Development/ ageing
Immune system
To protect from pathogens and tissue malfunction
What is modus operandi
Over production of excess cells in development to allow cell culling to select fittest cells and remodel
How many neurons dies in new born
60%
This is why identical twins aren’t completely identical - their neuronal network is different
Name a structure we are all born with but it only persists in females
What does it form
Mullerian duct
Uterus and oviducts
Name a structure we are all born with but it only persists in males
What does it form
Wolffian duct
Male reproductive organs
Why is cell death important in the immune system (3)
Many T lymphocytes are produced but only functional ones are selected
Those without a productive T cell receptor die by neglect
Faulty T cells that attack self are killed via negative selection
There is also T cell mediated murder (effector cytotoxic T cells initiate cell death in infected cells)
Also during an infection, T cells for that pathogen are in a very high number but after the infection this must decrease so cell death must occur
What is contraction
Reducing number of T cells after an infection is over
Cell death is important for homeostasis - Why
Balances with new cell production and well as relative fitness sensing
What happens if cell death exceeds new cell production (3)
Neurodegeneration
Immunodeficiency
Infertility
What happens if new cell production outweighs cell death
Cancer
Autoimmunity
What is relative fitness sensing and how does it relate to cell death
Every cell has a certain level of fitness which is cross referenced to the fitness standard of the organ.
If a cell is produced that is viable but doesn’t reach the fitness standard it is destroyed by the surrounding cells
Name a type of cell death that is immunologically silent and one that is immunogenic
Apoptosis = silent
Necroptosis = immunogenic
2 key aspects to consider about the cellular context of cell death
1) what was the cell death event
2) what were the underlying signalling events -> were inducible DAMPs produced?
What is a DAMP
Danger associated signalling event
4 reasons apoptosis is silent
The PM remains intact
Caspase dependant
Caspases incapacitate danger signals and ensure neat disposal of dead corpses
No DAMPs
What happens in all lytic cell deaths
Pore formation
Where aRe pores formed in a apoptosis
Mitochondrial membrane
What is the most common form of cell death
Apoptosis
Give the 5 morphological features of apoptosis
Cell shrinkage Membrane blebbing DNA fragmentation Apoptotic body formation Engulfment by neighbouring cells and phagocytes
MEMBRANE REMAIN INTACT
How long does engulfment take after apoptosis
15 mins
Give the structure of caspases
Homo dimers
Produced as inactive form and must be activated
Where do caspases cleave
After aspartate
Hence the name: cASPases
2 pathways to activate caspases
Give the key complex in each
Mitochondrial pathway - intrinsic - the apoptosome
Death receptor - extrinsic - DISC
What does DISC stand for
Death Inducing Signalling Complex
Which caspases do DISC and apoptosome activate
Apoptosome: 9
DISC: 8
2 groups of caspases
Initiator and executioner (these are subunits of initiator caspases)
Key differences between initiator and executioner caspases
Initiator:
•long pro-domain
• monomeric
• activated by dimerisation
Executioner
•obligate dimers
• activated by cleavage
3 features common to all caspases
Made of Pro enzymes
Active as dimers
Cys Asp proteases
3 targets for initiator caspases
Themselves
Effector caspases (Casp-3, and -7)
BCL-2 homology 3 (BH3) - BID
5 things effector caspases (eg Casp 3,6 and 7) do
- Dismantle cell structures
- Phenotypic changes to cell that are characteristic of apoptosis
- cleavage of ICAD, which releases CAD
- proteolysis at adhesion sites allowing cell detachment and retraction
- exposure of PS and other phagocytic signals on the cell surface
What does CAD do in cell death
Cut up the DNA
CAD = Caspase activates DNA-ase
How are initiator caspases activated
Proximity induced dimerisation
- certain ligands change the configuration of a death ligand, allowing recruitment of adapter protein with a death domain
The death domain brings in 2 Casp 8 molecules which dimerise and activate
What does cytochrome c do after it is released from the mitochondria
Binds to an Apaf-1 molecule which binds to other Apaf-1 molecules forming an apoptosome
How is Casp 9 activated
It sits on top of the apoptosome and dimerises
Why are executioner caspases activates by cleavage
The catalytic cysteine is masked and cleavage unmasks it allowing substrate entry
Is cell death assured once caspases are activated
No IAPs (inhibitor of apoptosis proteins) can inhibit caspases
Where were IAPs discovered
In viruses
What is the point of no return in apoptosis
MOMP
What is the anti apoptotic family that inhibits Bak (pore forming proteins)
The BCL-2 family
What do bak and bax proteins do
Form pores in the mitochondria
What do BH3-only family members do
Suppress BCL-2 family, allowing Bax and thus pore formation in the mitochondria leading to apoptosis
How many proteins in a cell can be cleaved by caspases
2000
How do extrinsic signals initiate cell death
The death ligand binds to the death receptor, causing it to trimerise
What happens after the death domain trimerises when the death ligand binds
FADD (an adapter protein) is recruited which in turn brings casp 8 molecules to be activated
How does FADD from the death receptor activate casp 8
There is a proximity induced conformational change that rotates the catalytic centre into an active position
What are the 2 different forms of extrinsic induced apoptosis
Type I: activated casp 8 activates casp 3 and 7, directly leading to apoptosis (no MOMP required)
Type II: casp 8 cleaves BID, which activates Bak and MOMP for pore formation in the mitochondria
What happens to XIAP in Type I and Type II cells in apoptosis
What XIAP do
Type I: XIAP rapidly decreases upon activation of death receptor
Type II: SMAC is released from mitochondria after pore formation and inhibits XIAP
XIAP inhibits apoptosomes and casp 3 and 7, ultimately inhibiting apoptosis
What is special about the TNF death receptor
It can send 2 different signals: one for cell survival (the dominant outcome) and one for cell death
What molecule is activated by a TNF death receptor to initiate cell death
When is this released
RIPK1
If the cell is not fit enough / under stress as TNF tests cells for fitness
What do TRADD and RIPK1 recruit
What is important about these
TRAF1, cIAP, LUBAC
They recruit ubiquitin chains - different chains either determine cell death or gene expression
If RIPK1 recruits a ubiquitin chain NOT for cell death, what recognises the ubiquitin chain
What about for TRADD
What does this eventually lead to
TAB2
NEMO
Activation of NF-κB
What is the ubiquitin checkpoint
If RIPK1 and TRADD, bound the the TNF death receptor, have a ubiquitin chain not signalling cell death, the complex remains attached the the plasma membrane
If the ubiquitin chain signals cell death, the RIPK1 is released and RIPK1 oligomerises and binds to FADD, allowing casp 8 to be activated by proximity. This leads to apoptosis
When RIPK1 oligomerises and activates Casp 8, what is this complex called
If this is formed, is cell death certain
Complex 2
No - cFLIP can mediate complex 2 activity
What is FLIP
A pseudo caspase
Like a caspase in structure but with a mutated catalytic centre
It can dimerise with casp 8
What does FLIP do
Dimerises and tethers casp 8 so it cannot cleave you activate effector caspases
What can The dimer of FLIP + casp 8
Cleave RIPK1 and RIPK3 to disable them and allowing survival
Does the RIPK1 complex 2 always lead to apoptosis
No it can activate MLKL pathway for necropotosis
When virus prevent cell death what do they target
The extrinsic apoptosis pathway, often targeting caspases
Which viral proteins attack casp 8
CrmA and vFLIP
Which viral proteins attack executioner proteins
vIAP
When does necroptosis occur
When caspases like casp 8 are blocked
Does necroptosis affect the mitochondria
No it makes holes in the PM instead
What is the main trigger of necroptosis
Pathogens
Cell stress damage
What are the 2 domains of RIPK1
Death domain and kinase domain
What is a ripoptosome
What inhibits it
The RIPK-FADD complex that can activate either casp 8 or MLKL as well as NF-κΒ for danger signals
cIAP1 and 2
XIAP
How does MLKL work
It is a pseudo kinase that is activated via phosphorylation by the ripoptosome
How does phosphorylation activate MLKL
A 4HB disengages, exposing the domain allowing dimerisation and thus pore formation
Other than TNF what can initiate necroptosis (3)
When ZBP1 senses a virus and uses its RHIM domains to bind and activate RIPK3
IFNs initiate necroptosis when FADD is absent
LPS binds TLR4 to initiate necroptosis via TRIF
What are the 3 outcomes of a death receptor pathway
Survival
Apoptosis
Necroptosis
What is RHIM
RIP homology interact motifs
They allow RIPK1 and RIPK3 to interact
Give the sequence of events of necroptosis starting with RIPK1 and RIPK3 interaction
RIPK1 and 3 interact through their RHIMs
Activated RIPK3 phosphorylates MLKL
MLKL undergoes conformational change to allow oligomerisation and then pore formation in PM
How does RIPK1 interact with Casp 8
Casp 8 is cleaved and Inactivated
Do carnivores have MLKL
Why?
No
Pathogens have won the race?
Is pyroptosis caspase dependant
Yes- it mainly uses casp 1 and 11
How does pyroptosis blow up the cell
Gasdermin- D forms pores in the PM and water comes in to swell the cell
What does casp 1 activate in pyroptosis
IL-1β and IL-18
It also cleaves DNA so other casp can become active
What are always the final 3 steps leading to pyroptosis
What is different
ASC activates casp 1 which activates IL-1β and IL-18
Different stresses have different triggers and sensors
How is casp 1 activated
NLRP3 oligomises to form an inflammasome and ASC forms filaments which recruit and activate casp 1
What is PAMP vs DAMP
PAMP is a pathogen induces danger signal where as DAMP is endogenous
What is the back up system for pyroptosis
When is it needed
Inflammasome instead drives activation of casp 8
If casp 1 is deactivated
What happens if NKRP3 is spontaneously activated
Chronic inflammation etc
Give 3 initiator caspases
2
8
9
Give 3 executioner caspases
3
6
7
What does TNF do
Tests the fitness of cells
How does casp 8 block necroptosis
What happens if casp 8 is low? When can this also happen?
By cleaving RIPK1 and RIPK3
RIPK1 activates RIPK3 which in turn activates MLKL. This will also happen if IAP is low
What is the key effector of necroptosis
MLKL
In which form of cell death is nuclear integrity maintained
Pyroptosis
How are initiator caspases activated?
Why
Dimerisation
Can only be properly activated when there are enough present
Key casp for pyroptosis
Casp 1
What activates casp 1
What do interleukins do
Inflammasome
Create Gasdermin D pores
Which cell death modality uses lipid peroxidation?
Ferroptosis
What is SMAC / DIABLO
Inhibitors of apoptosis
What is BH3 present in
BCL-2 (anti apoptotic)
But also BID (pro apoptotic)
Describe the domains of the Bcl2 family
All anti apoptotic members have all BH domains (1-4)
All pro apoptotic have at least BH3 (BID has only BH3, Bak has several BH domains)
