Apoptosis

Topics to be covered

In multicellular organisms, growth, development, and maintenance depends not only on the production of cells but it also depends on the mechanism to destroy them.
For the maintenance of tissue size, it requires that cells die at the same rate as they are produced.
Death of cells also occurs when the cells are infected or damaged, ensuring that they are eliminated before they threaten the health of organism.
Death of cell is not random process, it occurs by a programmed cascading molecular events, in which cell destroys itself systematically from within and is engulfed by other cells, leaving no trace.
In most of the cases, this systematic programmed cell death occurs by a process termed as apoptosis.
Apoptotic cells are engulfed or eliminated by phagocytic cells such as macrophages.
All cells having limited lifespan and completing their life span very cell enter into apoptotic phase.
Apoptosis is a natural phenomenon which leads natural death of cell.
If abnormality found in apoptosis then the lifespan of cell is increased and promotes cancer development.
All multicellular organisms require external factors that provide signal to stay alive and those factors are called tropic factors.
In absence of trophic factor or survival signal cell activates suicidal program.
Apoptosis involves elimination of cells that having irrepairable DNA damage.

Brief distinguish features of necrosis and apoptosis

Necrosis	Apoptosis
It is accidental or premature cell death which is not programmed or not by any injury. Energy independent cell death.	It is programmed cell death, death by suicide.
	Energy dependent.
It occurs hen cell are comes in contact with harmful chemicals or physical agent or conditions, stress, toxins. They are inflammatory. Necrotic events involves cell swell, rupture, and it affects surrounding cells too.	In this unwanted cells are eliminated by systematic biological process.
	Phagocytosis involved.
	Apoptosis may be through intrinsic or extrinsic pathways.
	Apoptotic events involves, cell becomes more compact, blebbing of membrane, chromatin condensation, DNA fragmentation, and cell shrink, and release of apoptotic body.
	Cell adhesion loss. Macrophage has PTS receptor.

Bcl2 a mammalian gene which was first identified as oncogene that involved in the development of cancer of B- Lymphocytes.
It was found to inhibit apoptosis.
Bcl2 family of proteins are characterized by the presence of one or more small BH domains.
There are approximately 20 proteins related to bcl2 which was encoded by mammals and these are divided into three functional groups including:
- Anti-apoptotic: it protects the cells from apoptosis, gain of function mutation in these genes, increases cellular lifespan thus causes cancer. E.g. Bcl-xl, Bcl-w and Bcl-2.
- Pro-apoptotic: it promotes apoptosis, loss function mutation in these genes, inhibits apoptosis, increases cell life span and causes cancer. E.g. Bax and Bak.
- BH only: it promotes apoptosis by indirect mechanism. E.g. Bid, Bad, Puma.

Examples of anti-apoptotic and pro-apoptotic factors

Anti-apoptotic factors	Pro-apoptotic factors
BCL-2 BCL-XL A1 BCL-W MCL-1 BCL-B NFA-1	Bax Bad Bid Bak Bim Bik Bok PUMA NOXA TRAIL Apaf-1

Caspases are group of proteases which have cysteine residue in their catalytic site and cleaves protein at the C- terminal of aspartate residues.
Caspases are cysteine dependent aspartate specific protease.
Caspases are ultimate effector of programmed cell death and involved in the apoptosis by cleaving more than 100 different target proteins.
Caspases are inhibitors of DNase, which on activation responsible for the fragmentation of nuclear DNA.
It also involves in the cleavage and activation of scramblase.
In addition caspases cleaves cytoskeletal proteins which results in the cytoskeleton disruption, irregular bulging or blabbing of plasma membrane and cell fragmentation.
Involves in the fragmentation of nucleus by cleaving nuclear Lamin protein.

Initiator caspases:

- It activated by self autocatalysis.
- Begins the process of apoptosis.
- E.g. caspase- 2,8,9,10.

Effector caspases:

- It get activated by the Initiator caspases.
- E.g. caspase- 3,6,7.
All caspases are synthesized in an inactive form known as procaspases, which are then converted into active from by cleavage of proteins catalysed by other caspases.
Caspases deficiency may results in the tumour development.
In animals, caspases are responsible for the apoptosis, while in plants and fungi, apoptosis induced bg arginine and lysine specific caspase such as metacaspase.
Not all caspases activates apoptosis.

Intrinsic pathway/ cell suicide program

This pathway is favoured in the absence of trophic factor.
Activation of intrinsic pathway is regulated by membrane bound bcl2 family protein which anti-apoptotic in nature and behave as a oncogene by promoting survival of the cell.
In absence of trophic factor PK-B (protein kinase-B) is inactive that’s why Pro-apoptotic bad protein is active.
Active Bad protein bind with Bcl-2 protein and cause its activation.
If Bcl-2 is inactive then, Pro-apoptotic Bax is polymerised and behave as a channel, through which cyt-c exported from IMS site to cytosol.
In cytosol it binds with Apaf-1 and form wheel like, hepatmeric structure called apoptosomes.
Apoptosomes activates caspase 9 which is initiator caspase.

Extrinsic pathway/ murder program

It occurs through the death signal.
TNF-alpha released by macrophages and triggered cell death.
Fas-ligand is a cell surface protein produced by activated natural killer cell and Tc cell.
These signals trigger cell death of infected cells and foreign grafted cells.
Murder signal comes from outsides of the cells and binds to cell surface receptor termed death receptor.
Death receptor is trans-membrane protein containing extracellular ligand binding domain and intracellular death domain which is required for receptor to activate apoptotic programme.
In cancerous cells death receptors are mutated.

Cell undergoes apoptosis having certain biochemical changes, which can be used as indicator or marker of the apoptotic cell.

Negatively charged phosphatidyl serine located at cytosolic leaflet of the membrane, but during stressful condition it flip out to exoplasmic leaflet in ATP dependent manner where it recognize as eat-me-signal or marker of the death signal.
Anexin-5 located at extracellular domain and it specifically binds to phosphatidyl serine and activates professional phagocytic cells like macrophages and dendritic cells.
Nuclei is condensed, DNA is fragmented by topoisomerase and protein is cleaved by protease, cleavage of DNA marked as late apoptotic nuclei or necrotic nuclei.
Nuclear condensation promotes nuclear shrinkage, cell shrinkage and forms small membrane bound apoptotic body, which is engulfed by phagocytic cells.

https://en.wikipedia.org/wiki/Apoptosis
https://www.ncbi.nlm.nih.gov/books/NBK26873/
https://quizlet.com/156316283/cell-death-and-apoptosis-flash-cards/
https://www.khanacademy.org/science/biology/developmental-biology/apoptosis-in-development/a/apoptosis
ttps://www.sciencedirect.com/topics/neuroscience/protein-bcl-2
https://www.nature.com/articles/s41419-020-2589-7
https://quizlet.com/172840400/chapter-18-apoptosis-programmed-cell-death-flash-cards/