Sequentially explain the process of apoptosis.

I. Initiation Phase

The initiation phase of apoptosis is triggered by either intrinsic or extrinsic signals.

A. Intrinsic Pathway (Mitochondrial Pathway)

This pathway is activated by intracellular stress signals such as DNA damage, oxidative stress, or growth factor deprivation. These signals lead to:

• Mitochondrial Outer Membrane Permeabilization (MOMP): Pro-apoptotic proteins like Bax and Bak oligomerize and form pores in the mitochondrial outer membrane.
• Cytochrome c Release: Cytochrome c, normally involved in the electron transport chain, is released into the cytosol.
• Apoptosome Formation: Cytochrome c binds to Apaf-1 and pro-caspase-9, forming a complex called the apoptosome.
• Caspase-9 Activation: The apoptosome activates caspase-9, initiating the caspase cascade.

B. Extrinsic Pathway (Death Receptor Pathway)

This pathway is initiated by the binding of death ligands (e.g., TNF-α, FasL) to their corresponding death receptors (e.g., TNFR1, Fas) on the cell surface. This leads to:

• Death Receptor Trimerization: Ligand binding causes the death receptors to trimerize.
• Formation of DISC: An adaptor protein, FADD, and pro-caspase-8 are recruited to the receptor, forming the Death-Inducing Signaling Complex (DISC).
• Caspase-8 Activation: Caspase-8 is activated within the DISC, initiating the caspase cascade.

II. Execution Phase

Both intrinsic and extrinsic pathways converge on the execution phase, characterized by the activation of effector caspases.

• Caspase Cascade: Activated caspase-8 (from the extrinsic pathway) or caspase-9 (from the intrinsic pathway) activates downstream effector caspases, primarily caspase-3, -6, and -7.
• ICAD Inhibition: Caspases cleave ICAD (Inhibitor of Caspase-Activated DNase), releasing CAD.
• DNA Fragmentation: CAD enters the nucleus and fragments DNA, leading to characteristic DNA laddering observed in apoptosis.
• Cytoskeletal Disruption: Caspases cleave cytoskeletal proteins, causing cell shrinkage and blebbing.
• Protein Cleavage: Caspases cleave various cellular proteins, disrupting cellular function.

III. Clearance Phase

The final phase involves the removal of the apoptotic cell without causing inflammation.

• Phosphatidylserine (PS) Exposure: Apoptotic cells expose PS on their outer leaflet, acting as an “eat me” signal.
• Phagocytosis: Phagocytes (e.g., macrophages) recognize PS and engulf the apoptotic cell.
• Silent Removal: The apoptotic cell is degraded within the phagocyte without releasing inflammatory contents, preventing damage to surrounding tissues.

Pathway	Initiating Signal	Key Proteins	Caspase Activation
Intrinsic	Intracellular stress (DNA damage, oxidative stress)	Bax, Bak, Cytochrome c, Apaf-1	Caspase-9 → Caspase-3, -6, -7
Extrinsic	Death ligands (TNF-α, FasL)	Death receptors (TNFR1, Fas), FADD	Caspase-8 → Caspase-3, -6, -7