What is Cyano?
Cyano is an interactive cellular metabolism simulator that traces how cells produce and consume energy through interconnected biochemical pathways. Click enzyme labels on the canvas to advance reactions step by step, or enable autoplay to watch the full metabolic network operate continuously.
Metabolic Pathways
Twelve pathways run on a shared metabolite grid. Glycolysis breaks glucose into pyruvate, generating 2 ATP and 2 NADH. The Krebs cycle oxidizes acetyl-CoA to CO&sub2;, producing GTP, NADH, and FADH&sub2;. The electron transport chain converts NADH and FADH&sub2; into a proton gradient that drives ATP synthase. Photosynthetic organisms additionally run the Calvin cycle, fixing CO&sub2; into G3P using ATP and NADPH from the light reactions.
Regulation
Every reaction is gated by allosteric regulation. Phosphofructokinase, the committed step of glycolysis, is inhibited by ATP and citrate — high energy charge slows glucose consumption. Pyruvate dehydrogenase is inhibited by its own products (acetyl-CoA and NADH). These feedback loops maintain homeostasis and prevent metabolic waste.
Reactive Oxygen Species
Complexes I and III of the electron transport chain leak electrons to molecular oxygen, forming superoxide radicals. The simulator tracks ROS accumulation and the enzymatic scavenging response (superoxide dismutase, catalase). Excessive ROS damages cell health, visible as declining cell integrity in the dashboard.
Fatty Acid Metabolism
Beta-oxidation breaks fatty acids into acetyl-CoA units, generating FADH₂ and NADH per cycle. The reverse pathway, fatty acid synthesis, consumes NADPH and ATP. Both pathways share the acetyl-CoA pool with the Krebs cycle, creating the metabolic intersection that determines whether a cell burns or stores fat.
Organism Presets
Five organism presets configure the metabolic network for different cell types: a generic eukaryote, an obligate aerobe, an anaerobic fermenter, a photosynthetic cyanobacterium, and a cancer cell (Warburg effect). Each preset enables different pathway combinations and sets initial metabolite ratios.
Accessibility
Cyano supports keyboard navigation for all controls, high-contrast mode via the theme toggle, and ARIA labels on toolbar buttons and enzyme labels. Metabolite levels are displayed as numerical values in the sidebar dashboard. Known hazards: continuous particle motion in the electron transport chain visualization. Users sensitive to motion can use step-by-step mode instead of autoplay.
See also: Geon for particle physics, Shoals for options trading, Gerry for electoral fairness.
Learning Outcomes
After using Cyano, students should be able to: trace the flow of carbon from glucose through glycolysis, the Krebs cycle, and the electron transport chain to CO2 and ATP; explain how the proton motive force couples electron transport to ATP synthesis; describe how allosteric regulation at phosphofructokinase and pyruvate dehydrogenase maintains metabolic homeostasis; compare ATP yield between aerobic respiration (~30-32 ATP per glucose), anaerobic fermentation (2 ATP), and photosynthesis; and identify the sources and consequences of reactive oxygen species at ETC Complexes I and III.
Prerequisites
Basic chemistry (atoms, molecules, chemical bonds, redox reactions). Familiarity with cell structure (mitochondria, chloroplasts) is helpful but not required — the simulator introduces each organelle through its organism presets.
References
P. Mitchell, "Coupling of phosphorylation to electron and hydrogen transfer by a chemi-osmotic type of mechanism" (1961). J. M. Berg, J. L. Tymoczko, and L. Stryer, Biochemistry, 9th ed. (W.H. Freeman, 2019).