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Biology
Enzymes: specificity, saturation and denaturation
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Change substrates and conditions, explore a 3D enzyme and measure reaction rate.
An enzyme has an active-site pocket. A suitable substrate binds and splits into products; a differently shaped one cannot fit. Drag to rotate.
Preparing the 3D scene…
Schematic · slowed cycle
1 · Substrate approaches
Whole batch · estimate
Free 33.3%Bound 66.7%Denatured 0%
Changing ingredients starts a fresh batch.
Change this batch; lost enzyme activity will not recover.
Reaction rate
5.33 u S/s
- Product
- 0.0 u S
- Substrate remaining
- 20.0 u S
- Active enzyme
- 100.0 %
- Time
- 0.0 s
What is happening
A suitable substrate binds at the active site and becomes product. The enzyme can be reused.
Save a measurement, change conditions and compare (up to 3).
Reaction rate8.00 u S/s
0Substrate (u S)100
Curve at current conditions; the dot marks this batch. The vertical axis rescales to the ceiling; compare rates numerically.
Model notes
- This hypothetical enzyme uses 37°C as a comparison reference, not a measured optimum. Constants and denaturation times are chosen for observation, not to predict real enzymes.
- Batch volume is fixed. u S denotes relative substrate amount; product is measured in converted-substrate equivalents. u E is a separate enzyme scale, not the same molar scale as S and not the international activity unit U.
- The Michaelis–Menten approximation assumes enzyme is dilute relative to substrate on a molar scale, after the initial complex-formation transient. Reverse reaction, product inhibition and environmental changes to Km are omitted. The curve shows instantaneous rates, not a series of initial-rate measurements.
- The bound fraction of surviving enzyme is estimated as S/(Km+S). Free + bound + denatured fractions total 100% of the initial enzyme population; bound enzyme remains active.
- Temperature/pH change rate immediately; extreme conditions also cause cumulative activity loss. Denaturation is irreversible here; real proteins can have additional reversible inactivation mechanisms.
- The 3D surface and folded strand are schematics, not a real protein structure. The slowed cycle follows reaction progress, not molecule counts. Shape matching omits induced fit and active-site chemistry.
- Changing ingredients starts a fresh batch; temperature/pH preserve batch history. New batch replaces enzyme and clears product while keeping settings. The sample is shown denatured below 60% active enzyme purely for illustration; the whole-batch bar is the quantitative representation.