T8: Cell death

Question 1

Different classifications of cell death + main description (4)

Answer 1

1. Necrosis: passive, unplanned cell death due to extrinsic factors
2. Apoptosis: active planned cell death due to intrinsic (intracellular) factors
3. Autophagy: active programmed cell death due to intrinsic (extracellular) factors
4. Necroptosis: intermediate situation, an alternative method for planned cell death with features of both autophagy and apoptosis

Question 2

compare and contrast apoptosis and autophagy
(3 similarities, 7 differences)

Answer 2

Similarities:
-both are programmed cell death
-both are triggered by intrinsic factors
-both can be reversed before the final stage is reached

Differences:
-autophagy is slow and apoptosis is fast
-apoptosis is controlled by cascade activation whereas autophagy is triggered by cell starvation (lack of nutrients)
-apoptosis works via activation of molecular cascades to modify intracellular substrates and cause cell fragmentation whereas autophagy works via downregulation of metabolic processes leading to cell digestion.
-apoptosis forms apoptotic bodies and autophagy forms autophagic bodies
-apoptosis doesn’t induce inflammation whereas macrophages in autophagy induce inflammation
-apoptosis can only lead to cell death, autophagy can lead either to the cell adapting to stress OR death
-autophagy balances cellular energy sources whereas apoptosis controls ratio of proliferation: death in organisms

Question 3

Compare and contrast necrosis and apoptosis

Answer 3

-N has an extracellular cause (injury), AP has intracellular cause (cascades)
-N is unplanned and passive, AP is planned and active
-N has degeneration of organelles, swelling of ER and disruption to plasma membrane, AP has no membrane degeneration but is characterised by condensing of chromatin and apoptotic body formation
-N causes inflammatory response and AP doesnt
-

Question 4

Reasons why cell death is important to organisms (5)

Answer 4

1. cells that evade it are transformed, become cancerous, or allow viral infections to worsen (because apoptosis expels virions from cells)
2. organ sculpting such as shapes of (fetal body parts in development), and establishing of neural networking
3. controls ratio between cell proliferation and cell death, hence controlling size of organism
4. death by apoptosis ensures lack of inflammatory response
5. removal of organs in other animals (like a tadpole losing its tail as it matures into a frog)

Question 5

Caspases: function, structure and different families in the context of cell death

Answer 5

-Proteases involved in cell death cascades
-contain cysteine residues in their active sites
-cleave their target molecules at the specific level of aspartic acid residues
-2 families : initiators (2,8,9,10) and executioners (3,6,7)
-CARD DOMAIN: present in caspases 2 and 9
-DED DOMAIN: present in caspases 8 and 10

!! can either degrade substrates or activate certain molecules within cascades

Question 6

Substrates of caspase degradation and activation respectively

Answer 6

1. DEGRADATION:
   -nuclear lamins: role in fragmentation of nuclear envelope
   -cytoskeletal elements: filaments (eg. tubulin) which affect cell shape and motility
   -DNA endonuclease inhibitor: act on caspase activated DNAse which can degrade DNA molecules
   -Adhesion molecules: adhere cells to substrates
   -Focal adhesion kinases: induce detachment of apoptotic cells from surrounding viable cells
2. ACTIVATION:
   -cytokines
   -protein kinases
   -protein phosphatases
   !! all play a role in their corresponding cell cascades

Question 7

EXTRINSIC apoptotic pathway cause detailed mechanism

Answer 7

CAUSE: triggered by extracellular signal proteins of the TNF (tumour necrosis factor) ligand

PROCESS:
1. binding of FAS/TNF ligand (trimeric proteins found attached to cell membrane of immune cells) to the trimeric death receptors via cell contact.

2. recruitment of adaptor protein FADD (containing death domain and a death effector domain)
3. recruitment and activation of initiator caspases 8 and 10 (which contain the DED)
4. activated initiator caspases activate executioner caspases triggering proteolytic cascade
5. executioner caspases cleave and degrade substrates (eg. cytoskeletal elements) and activate endonucleases
6. cytoskeleton breaks down, forming a cytoplasmic bud which forms the apoptotic body
7. recognition of apoptotic body and internalization by professional phagocytes

Question 8

INTRINSIC (mitochondrial) apoptotic pathway cause and detailed mechanism

Answer 8

CAUSE: triggered by intracellular stress signals (usually derived from DNA damage). Relies on proteins of the Bcl-2 family (which can be either pro or anti apoptosis depending on the number of BH domains they contain)

PROCESS:
1. Peristimulus, the cytosolic antiapoptotic molecules (of Bcl2 family) are active: hence prevent cell death

2. Arrival of apoptotic stimulus inactivates antiapoptotic molecules and hence pro-apoptotic functions are allowed to interact
3. interactions induce formation of the MOMP (mitochondrial outer membrane permeabilization) pore)
4. Pore allows exit of certain molecules from mitochondrial space into cytoplasm (eg. cytochrome C or p53)
5. Cytochrome C binds to cytoplasmic APAF1 which is found in its inactive state
6. Binding causes a conformational shape change which causes APAF1 to exhibit a CARD domain
7. CARD domain exposure induces formation of an apoptosome (macromolecular structure)
8. recruiting of caspase 9 (initiator which shows a CARD domain) by apoptosome
9. activated caspase 9 activates executioner caspases triggering proteolytic cascade
10. executioner caspases cleave and degrade substrates (eg. cytoskeletal elements) and activate endonucleases
11. cytoskeleton breaks down, forming a cytoplasmic bud which forms the apoptotic body
12. recognition of apoptotic body and internalization by professional phagocytes

Question 9

Apoptotic body elimination general description

Answer 9

-active process by which apoptotic bodies are removed by phagocytes
-prevents inflammatory response while allowing tissue to be cleaned from cellular debris
-

Question 10

bleb definition

Answer 10

Bleb: bulge of the plasma membrane of a cell with a spherical and bulky morphology

Question 11

Phagocytosis signaling process

Answer 11

Healthy cells expose molecules that signal the cell is in a healthy condition and should not be digested (eg. CD31)

UPON APOPTOTIC SIGNAL:
1. active caspases cleave and cause and the degradation of proteins/enzymes (flipases and flopases) that actively maintain the asymmetry of the 2 leaflets in the cell membrane (via translocation of phospholipids)

2. This causes the exposure of PS from the inner cytosolic leaflet to the outer leaflet
3. This induces a loss in the membrane asymmetry and the two sides start to occur in equilibrium
4. The exposed PS recruits 2 signaling molecules: Annexin I, and MFG-E8 (milk fat globule factor 8)
5. This molecules induce a signal that promotes cell digestion which is then picked up on by the integrins (heterodimeric protein receptors) present on phagocyte surface membranes

Question 12

Pathologies induced from INCREASED APOPTOSIS

Answer 12

1. Heart and cerebral strokes: extra death of cells exacerbates effects of ischemia (low blood flow and hence cut of O2 supply)
2. Neurodegenerative diseases: death of specific neural populations that are unable to regenerate, Parkinson’s, dementia, Huntington’s, ALS and HIV associated dementia

Question 13

Pathologies induced from REDUCED APOPTOSIS

Answer 13

1. Autoimmune diseases: defects in apoptosis in lymphocytes (usually an impaired FAS ligand/receptor) causing their accumulation in the spleen/lymph nodes
2. Cancer: overexpression of Bcl2 in lymphocytes causes inhibition of apoptosis and causes B lymphoma, and mutations in p53 gene inhibits apoptosis and allows proliferation of cells despite potential DNA damage
3. Chemoresistance induced if apoptosis is defective
4. Chronic infections due to viral agents inducing anti-apoptotic effects (eg. herpes and adenoviruses)