Weirdly, [this exact question was posted 30 minutes ago](https://www.reddit.com/r/explainlikeimfive/comments/v7fu1d/eli5_why_is_the_heat_you_feel_from_eating/ibkjs5m) too. I’m copying my answer from there:
Because their spiciness comes from two different chemicals! We call them both “heat” because they both kind of burn, but that’s a big generalization. They’re two different flavours. It’s like saying “Why is the fruitiness of a strawberry different from the fruitiness of a cherry?”
Hot-sauce hot comes from capsaicin, a thick oily liquid. It activates pain receptors, not taste buds. We call the sensation “burning” because to your brain it actually registers as burning, not as a flavour. The thick oiliness is also why hot sauce heat can linger longer than horseradish heat.
Horseradish and wasabi get their spiciness from “allyl isothiocyanate”, which is a volatile (thin and easily evaporating) liquid. That’s why horseradish heat gets into your nose and sinuses so easily – it’s evaporating from your mouth. It’s also why it doesn’t stay in your mouth as long as the thick oily hotsauce-spice.
[https://www.pepperscale.com/pepper-heat-vs-horseradish-heat/](https://www.pepperscale.com/pepper-heat-vs-horseradish-heat/)
Chilis are spicy due to the chemical called Capsaicin. It is specifically a chemical meant to deter mammals from eating it so that more of the fruit is available for birds to eat and thus allowing the seeds to be spread further afield.
isothiocyanate is the chemical that makes horseradish hot. This chemical is more of an insect deterrent to protect the root bulb from being eaten by burrowing insects. Wasabi has a variant of the chemical.
They hit you differently because the spicy flavor is from different chemicals.
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