Apoptosis and Inflammation

Comprehensive vocabulary flashcards covering the molecular mechanisms of apoptosis (intrinsic, extrinsic Type I and Type II, caspase cascades, mitochondrial regulation), the cellular stages and mediators of acute and chronic inflammation (leukocyte extravasation, cytokines, PAMPs, DAMPs, inflammasomes), and laboratory detection assays.

Apoptosis

A regulated form of programmed cell death characterized by cellular condensation, intact cell membranes, dependence on $ATP$, ladder-like DNA fragmentation, and non-inflammatory phagocytosis affecting individual cells in vivo.

Necrosis

An unprogrammed form of cell death caused by acute cellular injury, characterized by cellular swelling, membrane rupture, $ATP$ depletion, random or smeared DNA fragmentation, and cell lysis that releases cellular contents to elicit an acute inflammatory reaction across whole tissue areas.

Apoptosis vs. Necrosis (Cellular Features)

Apoptosis leads to cell shrinkage, apoptotic body formation, and neat phagocytosis without inflammation, whereas necrosis involves cellular swelling, plasma membrane breakdown, enzymatic digestion, and leakage of cellular contents triggering inflammation.

Intrinsic Apoptotic Pathway

An intracellular apoptotic pathway initiated by internal lethal stimuli such as reactive oxygen species (ROS), DNA damage, ER stress, hypoxia, and metabolic stress, leading to BAX and BAK activation and mitochondrial outer membrane permeabilization.

Extrinsic Apoptotic Pathway

A cell death pathway triggered by extracellular signals through transmembrane death receptors (such as Fas/CD95, TNFR1, and DR4/DR5) binding to trimeric ligands (FasL, TNF-\alpha, and TRAIL).

Death-Inducing Signaling Complex (DISC)

A multiprotein complex formed upon death receptor trimerization when intracellular death domains (DD) recruit adaptor proteins (FADD or TRADD) to bind and activate initiator procaspase-8 and procaspase-10.

Initiator Caspases

Upstream caspases that initiate the proteolytic cascade of apoptosis, specifically Caspase-9 in the intrinsic pathway and Caspase-8 and Caspase-10 in the extrinsic pathway.

Executioner Caspases

Terminal effector proteases, primarily Caspase-3 and Caspase-7 (along with Caspase-6), that cleave essential cellular substrates to cause DNA laddering, protein degradation, organelle dismantling, cell blebbing, and final cell death.

Apoptosome

A wheel-like cytosolic protein complex composed of cytochrome c and oligomerized APAF-1 (Apoptotic Protease Activating Factor-1) that recruits and activates procaspase-9 into active Caspase-9.

Mitochondrial Outer Membrane Permeabilization (MOMP)

The central committed step of intrinsic apoptosis, induced by pore-forming pro-apoptotic proteins BAX and BAK translocating from the cytosol to the mitochondrial outer membrane, facilitating the release of cytochrome c and SMAC into the cytosol.

Mitochondrial Permeability Transition Pore (MPTP)

A inner mitochondrial membrane pore whose opening increases permeability; rapid opening across most mitochondria causes severe $ATP$ depletion and necrosis, while slow and asynchronous opening releases cytochrome c and activates Caspases-9 and -3 to drive apoptosis.

BCL-2 Family (Anti-Apoptotic Proteins)

A group of survival proteins, including BCL-2, BCL-XL, and MCL1, that inhibit apoptosis upstream by binding and neutralizing BH3-only proteins and blocking the activation and oligomerization of BAX and BAK.

XIAP (X-Linked Inhibitor of Apoptosis Protein)

An anti-apoptotic protein that directly binds to and inhibits active Caspase-9 as well as executioner Caspases-3 and -7, blocking pro-apoptotic caspase cleavage and downstream execution.

SMAC / DIABLO

Second Mitochondria-derived Activator of Caspase; a mitochondrial protein released alongside cytochrome c that binds to and neutralizes XIAP, relieving caspase inhibition and amplifying pro-apoptotic signaling.

Type I vs. Type II Extrinsic Pathways

Two death receptor signaling modes: Type I directly activates executioner Caspases-3 and -7 via Caspase-8; Type II relies on Caspase-8 cleaving BID to tBID, engaging BAX/BAK-mediated MOMP, cytochrome c release, and Caspase-9 activation before executing cell death.

Cardinal Signs of Inflammation (PRISH / PRESI)

The five principal clinical manifestations of acute inflammation: Pain (P, prostaglandins stimulating nerves), Redness (R, vasodilation), Immobility (I, oedema from increased vascular permeability), Swelling (S, oedema), and Heat (H, vasodilation).

Margination

The initial stage of leukocyte extravasation in which slowed blood flow pushes leukocytes to the vascular periphery; inflammatory cytokines IL-1 and TNF-\alpha released by macrophages and mast cells stimulate endothelial and leukocyte adhesion molecule expression.

Rolling (Leukocyte Adhesion)

The second step in leukocyte extravasation where endothelial selectins (Selectin E and Selectin P) bind reversibly to leukocyte sialyl Lewis proteins, slowing leukocyte transit and causing them to roll along the endothelium.

Firm Adhesion (Leukocyte Adhesion)

The third step of leukocyte extravasation where leukocyte surface integrins bind tightly to endothelial cell adhesion molecules, such as VCAM-1 and ICAM-1, in response to IL-1 and TNF-\alpha stimulation.

Transmigration (Diapedesis)

The fourth step of leukocyte extravasation where adherent leukocytes migrate through endothelial cell junctions into the extravascular space, mediated by PECAM-1 (CD31) and directed by chemokine gradients via chemotaxis.

Stages of Leukocyte Extravasation

The multi-step recruitment of circulating leukocytes across the vascular wall into inflamed tissues, sequentially involving capture, rolling, slow rolling, firm adhesion (integrin-mediated), and transmigration.

Temporal Leukocyte Dynamics in Acute Inflammation

The sequential infiltration pattern where neutrophils (PMNs) dominate the initial acute inflammatory infiltrate during the first $6\text{--}24\,\text{hours}$, followed by monocytes and macrophages between $24\text{--}48\,\text{hours}$.

TGF-\beta (Transforming Growth Factor-Beta)

A profibrogenic cytokine existing in $5$ isoforms that signals through the TGF-\beta receptor to stimulate fibroblast conversion to myofibroblasts, induce expression of collagen types I, II, and III, and produce fibronectin.

Matrix Metalloproteinases (MMPs) and TIMPs

Enzymes regulating extracellular matrix degradation, including homeostatic MMP-2 and inducible MMP-9; their proteolytic activity is inhibited by TIMPs (tissue inhibitors of metalloproteinases), where reduced MMPs and elevated TIMPs produce permanent fibrotic scars.

Pathogen-Associated Molecular Patterns (PAMPs)

Conserved exogenous microbial molecules (such as LPS, flagellin, peptidoglycans, and microbial nucleic acids) detected by pattern recognition receptors (TLRs and NODs) that drive NF-\kappa B, MAPK, and IRF signaling to induce pro-inflammatory cytokines and interferons.

Damage-Associated Molecular Patterns (DAMPs)

Endogenous danger signals released from stressed, injured, or necrotic cells (including mitochondrial DNA, formyl peptides, HMGB1, ATP, and uric acid) that bind PRRs like TLR-9 to trigger a sterile inflammatory response.

Acute vs. Chronic Inflammation

Acute inflammation begins within minutes to hours and is characterized by fluid exudation, neutrophil infiltration, and chemical mediators; chronic inflammation lasts days to years and features macrophages, T cells, fibroblast proliferation, and permanent ECM tissue remodeling.

Inflammasome

A cytosolic multiprotein complex (such as NLRP1b, NLRP3, NAIP/NLRC4, or AIM2) assembled upon sensing PAMPs or DAMPs that activates Caspase-1, cleaves pro-IL-1\beta and pro-IL-18 into mature cytokines, and initiates lytic programmed cell death termed pyroptosis.

Annexin V Binding Assay

An apoptosis assay utilizing Annexin V, a $35\text{--}36\,\text{kDa}$, $\text{Ca}^{2+}$-dependent protein that binds with high affinity to phosphatidylserine (PS) when it is translocated from the inner leaflet to the outer leaflet of the plasma membrane in apoptotic cells.

Caspase-3/7 DEVD Assay

An assay that detects apoptosis by monitoring the enzymatic activity of Caspase-3 and Caspase-7, relying on their specific ability to recognize and cleave the tetrapeptide motif DEVD (e.g., releasing a fluorogenic DNA-binding dye).

JC-1 Dye Assay

A cationic carbocyanine dye assay for mitochondrial membrane potential; in healthy polarized mitochondria, JC-1 forms J-aggregates emitting red fluorescence ($590\,\text{nm}$), while in depolarized apoptotic mitochondria, it remains a monomer emitting green fluorescence ($527\,\text{nm}$).

TUNEL Assay

Terminal deoxynucleotidyl transferase (TdT) dUTP Nick-End Labeling; an in situ assay that selectively detects internucleosomal DNA fragmentation in apoptotic cells by catalyzing the enzymatic addition of labeled dUTP to the exposed $3'$ ends of cleaved DNA.

Caspase-Glo 1 Inflammasome Assay

A homogeneous bioluminescent assay designed to measure active Caspase-1 by cleavage of a specific Z-WEHD-aminoluciferin substrate, releasing free aminoluciferin that reacts with luciferase to generate a luminescent signal proportional to inflammasome activity.

Bio-Plex Suspension Array (Th17 Cytokine Assay)

A multiplex bead-based sandwich immunoassay measuring cytokines (such as IL-17) using antibody-conjugated magnetic capture beads, biotinylated detection antibodies, and a streptavidin-phycoerythrin (SA-PE) reporter analyzed on a dual-laser suspension array reader.