Atlas One · Human · Level 03

Molecular

Proteins, lipids, nucleic acids, metabolites — the functional machinery of the cell.

This is the mechanistic layer: where hormones bind receptors, enzymes catalyze reactions, ion channels gate current, and transcription factors read the genome. Every drug target in modern medicine is a molecule at this scale.

45Entries
~20KUnique proteins (proteome)
6Subsections

The molecular scale is where biology becomes mechanism. Insulin binds its receptor tyrosine kinase and triggers a phosphorylation cascade. Cortisol enters the nucleus, displaces Hsp90 from the glucocorticoid receptor, and directly rewrites gene expression. Troponin C binds calcium and pivots the thin filament to let myosin cross-bridge. NF-κB translocates on pathogen recognition and induces cytokine transcription within minutes. Every pharmacological intervention — every drug, every biologic, every gene therapy — works by targeting a molecule at this scale. The entries below are organized by functional class.

Level 03 — Molecular

Signalling & Hormones

Endocrine, paracrine, and autocrine signals that coordinate physiology across organs and time.

Signalling & Hormones

PI3K-Akt-GLUT4; FOXO1 suppression; glycogen synthesis; T2DM; hypoglycaemia GR nuclear translocation; anti-inflammatory; gluconeogenesis; Cushing syndrome; adrenal insufficiency cAMP-PKA; hepatic glycogenolysis/gluconeogenesis; GLP-1 agonist target rationale; glucagonoma Hypothalamic JAK2-STAT3; POMC/AgRP balance; leptin resistance in obesity; congenital deficiency AQP2 insertion in collecting duct; vasoconstriction V1; SIADH; diabetes insipidus; terlipressin Basal metabolic rate; cardiac chronotropy/inotropy; myelination; hypothyroidism; Graves disease; T4→T3 via DIO1/2 JAK2-STAT5 erythroid differentiation; anaemia of CKD; recombinant EPO; polycythaemia vera; doping AT1R vasoconstriction; aldosterone secretion; ROS; cardiac fibrosis; ACEI/ARB targets; ACE2 counter-axis sGC-cGMP vasodilation; PDE5 target; iNOS in macrophage killing; septic shock; erectile dysfunction PGE2 fever/pain/inflammation; PGI2 vasodilation; TXA2 platelet aggregation; NSAID targets; misoprostol AMP:ATP ratio sensor; fatty acid oxidation; autophagy (ULK1); metformin target; mTORC1 inhibition

Receptors & Transcription Factors

IRS-1/2-PI3K-Akt-GLUT4 translocation; MAPK growth; IR-A/IR-B isoforms; T2DM resistance; hyperinsulinism GRE-driven transcription; NF-κB transrepression; GRα/GRβ isoforms; steroid resistance; GILZ induction TLR-TNFR-IL-1R canonical pathway; IκK-β phosphorylation; cytokine induction; NF-κB in cancer; bortezomib IL-6/IL-10/LIF signaling; oncogenic STAT3 in solid tumors; ruxolitinib; Bcl-2/VEGF/c-Myc targets cAMP-PKA; SERCA/PLN phosphorylation; β-blocker target; heart failure desensitization; GRK2 downregulation

Structural & Transport

Colloid oncotic pressure; fatty acid/bilirubin/drug carrier; negative acute-phase; hypoalbuminaemia in liver/renal disease Tensile strength ECM; fibrosis pathway; EDS/OI genetic disorders; Vitamin C requirement for hydroxylation; scurvy Cooperative O&sub2; binding (Hill n≈2.8); Bohr effect; 2,3-BPG; sickle cell (HbS); thalassaemias; CO poisoning Thrombin cleavage → fibrin polymerization; Factor XIII cross-linking; DIC; afibrinogenaemia; clot biomarker Membrane lipid raft; precursor to steroids/bile acids/Vitamin D; LDL-R/PCSK9 pathway; statin targets; atherosclerosis IgG1–4 subclasses; FcRn neonatal transfer; ADCC; FcγR effector functions; therapeutic mAb scaffold; autoimmune IgG Invariant chain/CLIP processing; HLA associations (T1DM, RA, coeliac); allograft rejection; vaccine APC targeting C3b opsonisation; C3a anaphylatoxin; MAC formation via C5-C9; paroxysmal nocturnal haemoglobinuria; eculizumab

Neurotransmitters

Mood regulation; gut motility (90% in enterochromaffin cells); SSRI/SNRI targets; carcinoid syndrome; platelet release Reward/motivation; nigrostriatal motor; mesocortical cognition; Parkinson (SNc loss); schizophrenia (mesolimbic excess) Sympathetic tone; fight-or-flight vasoconstriction; arousal/attention; SNRI target; pheochromocytoma; TCA mechanism Anaphylaxis first-line treatment; cardiac arrest; glycogenolysis; bronchodilation (β2); vasopressor (α1) NMJ motor activation; parasympathetic; memory (basal forebrain); AChEI in Alzheimer; myasthenia gravis (anti-AChR) Principal inhibitory NT; Cl− influx hyperpolarization; benzodiazepine/barbiturate targets; epilepsy; GABA deficiency in anxiety LTP/LTD; NMDA Mg²&sup+; block; excitotoxicity in stroke/TBI; ketamine NMDA antagonism; ALS glutamate excess Allergic response (H1); gastric acid (H2); neuronal arousal (H3); H1 antihistamines; H2 blockers (ranitidine); anaphylaxis SSRI primary target; 5-HTTLPR polymorphism; serotonin syndrome; platelet 5-HT uptake; NET co-inhibition by SNRIs

Cardiac Ion Channels & Contractile Proteins

AP propagation between cardiomyocytes; lateralization in heart failure; arrhythmia substrate; ischaemic uncoupling I&sub⊂ funny current; pacemaker depolarisation; ivabradine target; sick sinus syndrome; β-blocker interaction Ca²&sup+; extrusion in diastole; reverse mode in ischaemia; digoxin indirect NCX enhancement; heart failure NCX upregulation PKA-Ser16 / CaMKII-Thr17 phosphorylation releases SERCA2a inhibition; PLN gain-of-function DCM mutations; lusitropic target CICR; CPVT (RyR2 gain-of-function); FKBP12.6 stabilisation; dantrolene; SR Ca²&sup+; spark genesis; arrhythmia substrate 2Ca²&sup+; pumped per ATP; PLN inhibited; downregulated in heart failure; SERCA2a gene therapy (CUPID trials) Ca²&sup+;-TnC activates cross-bridge cycling; cTnI/cTnT cardiac biomarkers for MI; HCM TnT mutations; omecamtiv mechanism

Cytokines & Metabolism

Acute-phase response; B-cell differentiation; CRS marker; tocilizumab (RA/COVID); IL-6 trans-signalling; muscle myokine NF-κB; apoptosis (TNFR1 TRADD/FADD); SMAD/MAPK; TNF inhibitors (adalimumab/etanercept) for RA/IBD/SpA Phosphoanhydride bond hydrolysis (-30.5 kJ/mol); kinase substrate; P2X/P2Y purinergic signaling; AMPK energy sensor; ATP depletion in ischaemia

Help expand the Molecular Atlas

Many entries are planned but not yet written — mTOR, HIF-1α, p53, VEGF, TGF-β, Wnt/β-catenin, and the full suite of coagulation factors. Each entry follows the same open schema with peer-reviewed citations and cross-atlas links.