Death by apoptosis is an event that characterizes all phylogenetic levels (not only higher organisms), in fact the description of these mechanisms has been made through studies on the nematode (also called Caenorhabditis elegans, worm).  

It is also called "programmed cell death" due to the fact that it is part of the developmental program of all organisms, and is a programmed event. It is therefore a physiological event as part of the program of development and maintenance of homeostasis. Cells actively participate in the program of death (it is also called "suicide").  In necrosis are all situations that the cell undergoes, while in apoptosis the cell participates: it expresses particular genes and produces proteins in order to die. Death by apoptosis is an event that characterizes all phylogenetic levels (not only higher organisms), in fact the description of these mechanisms has been made through studies on nematode (Caenorhabditis elegans).

Starting observation for apoptosis studies: during the development of all C. elegans always 131 cells die by apoptosis and it is therefore a programmed event during its development.  

Apoptosis works to eliminate those cells that are no longer needed within the homeostasis of the organism itself. Cells in tissues that are defined as labile, also known as tissues with high cell turnover, die by apoptosis. It serves to maintain tissue homeostasis and also to eliminate cells that have suffered irreversible damage, such as DNA damage that cannot be repaired or when they have been infected. In order to keep the genetic heritage intact, it is better to eliminate a cell with altered DNA than to keep it with the risk that it may give rise to a clone of altered cells. 

Death by apoptosis does not produce an inflammatory process and can be triggered by extracellular (extrinsic pathway, starts from something exogenous) and intracellular (intrinsic pathway) signals.

 Definitions of apoptosis:

- without repercussion → does not produce an inflammatory process because it does not release any cellular components; in fact, apoptotic bodies are formed, which are then phagocytosed;

- selective → even only two or three cells die by apoptosis, only the cells that need to be eliminated from the tissue;

- regulated → it has a gene regulation, so there are genes that induce or inhibit it.  

Physiological conditions in which apoptosis plays an important role

Apoptosis is part of the embryonic developmental program, even in humans. Here, apoptosis events also occur quite early.

• In humans, cells die by apoptosis before and during implantation of the embryo because they have accomplished their task.  
• During the developmental stage we go through a phase in which we have interdigital membranes that in the next phase are eliminated by apoptosis.
• Apoptosis also occurs during the formation of hollow organs (including the heart), because it is easier to form a full ball and then make it hollow by apoptosis.
• Apoptosis also occurs to CNS cells at the end of its development. In fact, during CNS development more cells are formed than will be needed so that there is a redundancy of cells in case something happens in development and cells are lost (if nothing happens and I don't use the reserve I send them to death by apoptosis at the end of development).

Maintenance of homeostasis of rapidly turnover tissues, e.g., epithelium.

Elimination of cells by cessation of a stimulus:

• involution when a hormone-type stimulus ceases (example of breast and uterus at end of pregnancy and lactation; previously they are hypertrophic and hyperplastic);
• during the inflammatory process the number of granulocytes increases and, when this ends, they are eliminated by apoptosis;
• the same is true for the immune response with involvement of lymphocytes that undergo cloning.

Phases of apoptosis

The event of apoptosis is marked by the succession of phases:   

• Activation of the death program itself 
• Activation of pro-apoptotic proteins.
• During death by apoptosis, cellular components are degraded in a highly regulated manner by the activation of special proteins that are termed pro-apoptotic.  
• Activation of apoptosis executing proteins. 
• They are referred to as caspases and each caspase results in degradation of very specific cellular substrates (each element is degraded by a specific protein). Caspases are pepsidases and degrade specific target proteins.

 Morphological changes

Let us examine what happens at the level of cytoplasmic membranes, nucleus, and mitochondria.  

At the membrane level, the "earliest" events of apoptosis occur. 

• Cells initially isolate themselves from the tissue of which they are a part, they enclose themselves.
• All cell organelles condense, while remaining intact.
• The cell as a whole undergoes a decrease in volume.
• It then emits membrane eversions called blebs.

Thus, it first compacts and then emits membrane eversions. 

In the nucleus, changes are quite early and consist of an initial compaction; this compaction also corresponds to a condensation of chromatin. 

Hematoxylin-eosin staining of the nucleus is diffuse bluish, except in the nucleolus. In apoptosis, chromatin condenses and is arranged in segments below the membrane, so it is no longer uniform. When chromatin is condensed, fragmentation of the nucleus also occurs.

At the mitochondrial level during death by apoptosis there is a change in membrane potential. So their normal permeability or non-permeability also changes. 

This means that they release molecules that are pro-apoptotic, such as cytochrome C.

The cell loses its contact elements, becomes compact, and after the formation of the half-moons in the nucleus it undergoes fragmentation (a number n of fragments are formed); however, all the pieces are always surrounded by the nuclear membrane.  The nuclear fragments will become part of cellular fragments, in the cell will form a number n of fragments with or without fragments of the nucleus inside. These cell fragments are what are called apoptotic bodies (with or without nucleus they are always surrounded by intact plasmamembrane, with no loss of cellular components).  The fate of apoptotic bodies is to be phagocytosed by professional phagocytes (neutrophil granulocytes and macrophages) or by normal cells not affected by the process of apoptosis that are close to dead cells.  

Biochemical changes

A cell that dies by apoptosis synthesizes new proteins in order to go to death. This is a difference from death by necrosis, such as a finger on a hot oven plate. In this case, the cell does not have time to synthesize new proteins. In apoptosis, the cell contributes to its own death program by synthesizing new proteins.

Studies

In the development of a new drug active in cancer cells and able to induce the death of cancer cells. apoptosis avoids the induction of the inflammatory process, hoping to kill them selectively. The different types of fragments that are formed as a result of apoptosis or necrosis can be useful in research for the study of anticancer molecules and to understand if they determine the death of cancer cells by apoptosis (what is expected) or by necrosis (to be avoided because it develops an inflammatory response).

In vitro studies on cultured cells to test the new substance clarify what kind of death occurs. DNA is extracted and electrophoresed by depositing it in wells and analyzing how the DNA fragments arrange and run on the agarose gel. It is important to understand how they are arranged. You deposit the fragments in the wells and then turn on the electric field. Migration depends on the size and charges of the components themselves.