Cell Death (Freid)

programmed cell death (apoptosis)

An intrinsic regulatory mechanism in all metazoans that is an equally regulated and controlled process in biology, equal in importance to cell division. It is defined by a specific morphology of the process, where cells shrink and are phagocytized without causing an inflammatory response

necrosis

Death of a cell by lysis or exploding, often caused by a traumatic event or stress that damages the cell (e.g., sulfuric acid, organic solvents, radiation).

It is characterized by cell swelling, rupture of the plasma membrane, dissolution of cellular structures, and the release of cellular contents, which can attract and activate an inflammatory response. It is not dependent on caspase activation

programmed cell death (apoptosis)

An intrinsic regulatory mechanism in all metazoans that is an equally regulated and controlled process in biology, equal in importance to cell division. It is defined by a specific morphology of the process, where cells shrink and are phagocytized without causing an inflammatory response

necrosis

Death of a cell by lysis or exploding, often caused by a traumatic event or stress that damages the cell (e.g., sulfuric acid, organic solvents, radiation).

It is characterized by cell swelling, rupture of the plasma membrane, dissolution of cellular structures, and the release of cellular contents, which can attract and activate an inflammatory response. It is not dependent on caspase activation

apoptosis vs. necrosis (morphology)

Apoptosis involves cell shrinking, chromatin condensation, blebbing, formation of apoptotic bodies, and phagocytosis by neighboring cells. Necrosis involves cell swelling, rupture of the plasma membrane, and lysis

apoptosis vs. necrosis (inflammation)

Apoptosis does not release cytokines or activate an inflammatory response. Necrosis does release cellular contents that can attract and activate the inflammatory response

life is controlled by cell death

The concept that life is not just controlled by cell division but also by controlled cell death, which is equally important for biological stasis, involving a balance between synthesis and degradation, birth and death

apparatus for death

The idea that every cell in metazoans already contains all the components (genes and proteins) within it for that cell to die by apoptosis. The regulation of the functional activation of these components determines whether a cell lives or dies

caspases

A family of specific proteases that are the central executioners of apoptosis and most other forms of programmed cell death and inflammatory responses. They are constitutively present in cells as inactive zymogens

caspase activation

The process by which inactive pro-caspases (zymogens) are converted into active enzymes through specific proteolytic processing (cleavage of their inactive form). The regulation of this processing determines cell fate

active caspase structure

function as heterotetramers, composed of two large (e.g., 20k) and two small (e.g., 10k) subunits. These subunits often originate from a single polypeptide chain that is cleaved during activation

caspase active site

contains a cysteine residue, which is crucial for their protease activity. They cleave peptide bonds on the C-terminal side of Aspartic acid residues

caspase sequence specificity

Individual members of the caspase family have sequence specificity at their cleavage sites, meaning they recognize and cleave proteins at specific amino acid sequences containing aspartic acid. Examples of recognition motifs include DMQDx and IETDx

inhibitor caspases

(e.g., Caspase 8, 9, 10) whose primary function is to activate executioner caspases by cleaving their inactive forms. They are typically present in the cell as inactive monomers and require dimerization for activation

executioner (effector) caspases

(e.g., Caspase 3) that, once activated by initiator caspases, dismantle the cell by cleaving various cellular proteins. They are present in the cytosol as inactive dimers

caspase 3

key executioner caspase that is activated by cleavage by initiator caspases. Once active, it cleaves numerous cellular targets, leading to the dismantling of the cell

caspase 3 targets

cleaves proteins like lamins (leading to nuclear membrane disassembly), MAPs (disassembling microtubules), actin-binding proteins (dismantling the actin filament network), and ICAD (activating CAD). It also cleaves the plasma membrane "flippase”

CAD (caspase-activated DNase)

when activated by Caspase 3 cleavage of its inhibitor ICAD, cleaves DNA between nucleosomes, resulting in a characteristic ladder of nucleosome-protected DNA fragments, a molecular hallmark of apoptosis ***?

ICAD

inhibtor of CAD

binds to and prevents CAD from cleaving DNA. It is cleaved and inactivated by activated Caspase 3 during apoptosis, allowing CAD to become active

DNA fragmentation in apoptosis

A process caused by the activation of CAD, resulting in the cleavage of chromosomal DNA into fragments of characteristic sizes (nucleosome ladders), which can be detected by techniques like gel electrophoresis

TUNEL Assay

used to detect fragmented DNA, a hallmark of apoptosis. It labels the 3'-hydroxyl ends of DNA breaks created during apoptosis with modified nucleotides.

plasma membrane ‘flippase’

A membrane protein that is cleaved and inactivated by Caspase 3 during apoptosis. Its inactivation leads to the accumulation of phosphatidylserine (PS) on the outer surface of the cell.

phosphatidyl serine as an ‘eat me’ signal

Phosphatidylserine, normally on the inner leaflet of the plasma membrane, is exposed on the outer surface of apoptotic cells and cell fragments due to flippase inactivation. This exposed PS acts as an "eat me" signalrecognized by both professional and amateur phagocytic cells, leading to the engulfment and removal of apoptotic bodies.

extrinsic pathway of apoptosis

A pathway initiated by extracellular signals binding to death receptors (members of the TNF receptor family) on the cell surface. Ligand binding causes receptor trimerization, leading to the recruitment of adaptor proteinslike FADD and the activation of initiator caspases (Caspase 8 and 10).

death receptors

Specific receptors on the cell surface (e.g., FAS receptor) that, when bound by their respective ligands (e.g., FAS ligand), undergo conformational changes and trimerize, initiating the extrinsic apoptotic pathway.

FADD (Fas-associated death domain protein)

An adaptor protein that contains a death domain (DD) and a death effector domain (DED). In the extrinsic pathway, it binds to the activated death receptor via its DD and recruits pro-caspase 8/10 via DED-DED interactions.

death domain

A protein domain present in death receptors and adaptor proteins like FADD, involved in protein-protein interactions that facilitate the assembly of signaling complexes in the extrinsic apoptotic pathway.

death effector domain

A protein domain present in adaptor proteins like FADD and initiator caspases (pro-caspase 8/10) in the extrinsic pathway. DED-DED interactions promote the recruitment and dimerization of pro-caspase 8/10, leading to their autoactivation.

activation of initiator caspase 8 and 10 (extrinsic)

Recruitment of inactive monomeric pro-caspase 8/10 to the death receptor complex via DED-DED interactions leads to their dimerization at high local concentrations. This proximity induces autocatalytic cleavage and activation, forming active heterotetrameric initiator caspases.

intrinsic pathway of apoptosis

A pathway activated by intracellular stresses or damage (e.g., DNA damage, mitochondrial dysfunction). It involves changes in the mitochondria, leading to the release of cytochrome C into the cytoplasm, formation of the apoptosome, and activation of initiator Caspase 9.

mitochondrial outer membrane permeability (MOMP)

The process by which the outer mitochondrial membrane becomes permeable, allowing the release of intermembrane space proteins like cytochrome C into the cytoplasm. This is regulated by the Bcl-2 family of proteins.

cytochrome c release

The release of cytochrome C from the space between the inner and outer mitochondrial membranes into the cytoplasm, a key event in the intrinsic apoptotic pathway. It is triggered by MOMP, often regulated by pro-apoptotic Bcl-2 family members.

apoptosome

A large protein complex formed in the cytoplasm when released cytochrome C binds to APAF1 (Apoptotic Protease Activating Factor 1) in the presence of dATP. The apoptosome facilitates the activation of initiator Caspase 9.

APAF1 (apoptotic protease activating factor 1)

A protein in the cytoplasm that contains a CARD (Caspase Recruitment Domain). When it binds to cytochrome C and dATP, it unfolds and oligomerizes, exposing its CARD domain to interact with the CARD domain of pro-caspase 9, forming the apoptosome.

CARD (caspase recruitment domain)

A protein domain present in APAF1 and initiator Caspase 9 in the intrinsic pathway. CARD-CARD interactions within the apoptosome bring multiple pro-caspase 9 molecules into close proximity, facilitating their dimerization and autoactivation.

activation of initiator caspase 9 (intrinsic)

Within the apoptosome, the close proximity of pro-caspase 9 molecules due to CARD-CARD interactions promotes their dimerization and autocatalytic activation, forming active heterotetrameric Caspase 9.

BCL2 family of proteins

A family of proteins that regulate MOMP and play a crucial role in the intrinsic apoptotic pathway. It includes anti-apoptotic proteins (e.g., Bcl-2) and pro-apoptotic proteins (e.g., Bax, Bak, BH3-only proteins).

BCL2

antiapoptotic

A member of the Bcl-2 family that inhibits apoptosis by binding to and preventing the oligomerization of Bax and Bak, thus stabilizing the outer mitochondrial membrane and preventing cytochrome C release.

BAX and BAK

pro-apoptotic

Pro-apoptotic members of the Bcl-2 family that can be mobilized to the mitochondrial outer membrane where they oligomerize to form pores, leading to MOMP and the release of cytochrome C.

BH3 domain proteins

pro apoptotic

A subfamily of pro-apoptotic Bcl-2 family members that contain only the BH3 homology domain (e.g., Bid, Bad, Puma). They can promote apoptosis by activating Bax/Bak or by inhibiting anti-apoptotic Bcl-2 proteins.

BID

A BH3-only protein that is present in an inactive pro-form in the cell. It can be activated by proteolytic cleavage (e.g., by activated Caspase 8 in extrinsic-intrinsic crosstalk) to expose its BH3 domain, which can then promote MOMP by inhibiting Bcl-2 and/or activating Bax/Bak.

BAD

A BH3-only protein that is constitutively present but kept inactive by phosphorylation and sequestration by the 14-3-3 protein. Dephosphorylation (e.g., by Calcineurin when calcium levels rise) releases active Bad, which can then promote apoptosis by interacting with Bcl-2 family proteins.

Puma

A BH3 domain protein whose expression is induced by p53 in response to cellular stress. It can promote apoptosis by inhibiting anti-apoptotic Bcl-2 proteins, allowing Bax/Bak to induce MOMP.

extrinsic-intrinsic crosstalk

The ability of the extrinsic apoptotic pathway (activated by death receptors) to influence the intrinsic pathway. For example, activated Caspase 8 can cleave Bid into its active form, linking the extrinsic signal to mitochondrial changes.

IAPs (inhibitors of apoptosis)

A family of endogenous proteins (e.g., XIAP, Survivin) that inhibit caspases and prevent apoptosis, providing a threshold that must be overcome for cell death to occur.

XIAP

An Inhibitor of Apoptosis (IAP) family member that directly inhibits the activity of certain caspases.

Survivin

An Inhibitor of Apoptosis (IAP) family member that is found abundantly in tumor cells, where it helps to block apoptosis. Its synthesis can be repressed by p53.

Diablo

An anti-IAP protein located in the inner mitochondrial space that is released into the cytoplasm along with cytochrome C during MOMP. It binds to and inhibits IAPs, allowing caspases to become active and proceed with apoptosis.

p53

A transcription factor constitutively expressed in cells that regulates the expression of over 9,000 genes involved in various cellular processes, including cell cycle arrest and cell death. Stress can increase p53 levels, leading to the expression of pro-apoptotic proteins like PUMA and the repression of anti-apoptotic proteins like Survivin. Mutations inactivating p53 are common in cancers.

viral inhibition of apoptosis

The ability of some viruses to express proteins that inhibit the host cell's apoptotic pathway, allowing the virus more time to replicate. Examples include Bcl-2 homologs from Epstein-Barr virus and CrmA (an IAP) from Cow Pox virus, as well as interference with cellular p53.

robert horvitz

A researcher who studied the nematode C. elegans and discovered that a precise number of cells (131 out of 1090) die during normal development in a genetically programmed manner. His genetic approach identified genes required for these cell deaths (e.g., ced-3, ced-4, ced-9).

Ced-3 and Ced-4

Genes identified in C. elegans whose protein products are necessary to execute the cell death program. Mutations or knockouts of these genes prevent the 131 developmental cell deaths. Ced-3 has homology to caspases, and Ced-4 has homology to APAF1.

CED-9

A gene identified in C. elegans whose protein product acts as a suppressor of cell death. Loss of ced-9 leads to all cells dying, while overexpression prevents cell death. It has homology to the anti-apoptotic protein BCL2.

BCL2 discovery (B cell lymphoma)

The gene BCL2 was discovered in studies of B cell lymphoma, where a chromosomal translocation led to its constitutive expression. BCL2 was found to be a suppressor of cell death in B cells.

conservation of apoptotic pathways

The finding that genes involved in apoptosis in C. elegans (e.g., ced-3, ced-4, ced-9) have homologs in higher metazoans (e.g., caspases, APAF1, BCL2) indicates that the apoptotic pathway is conserved through evolution.

apoptotic bodies

Membrane-enclosed fragments of a dying apoptotic cell that contain cytoplasm, organelles, and sometimes nuclear material. They are formed by blebbing of the plasma membrane and are subsequently phagocytized by neighboring cells.

initiator caspase activation mechanism

Initiator caspases (like 8, 9, 10) are typically activated by induced proximity leading to dimerization and subsequent autocatalytic cleavage. This dimerization is facilitated by upstream signaling events, such as the recruitment to death receptor complexes (for Caspase 8/10) or assembly within the apoptosome (for Caspase 9). They are not active as monomers or inactive dimers.

regulation of apoptosis

Apoptosis is tightly regulated at multiple levels, including the balance between pro-apoptotic and anti-apoptotic Bcl-2 family members, the activation of initiator caspases, the activity of executioner caspases, and the presence of endogenous inhibitors of apoptosis (IAPs). Cellular checkpoints and viral interference also play roles in controlling this process