Quarks are fundamental particles (meaning that they aren’t made up of anything smaller as far as we know) that make up protons and neutrons (although sometimes they take other configurations. There are 6 different types of quarks. Physicists first proposed that they existed in the 1960’s, and they were discovered not long after in particle accelerators. Basically, the particle accelerators smash particles together and looked at what happened, and discovered that protons and neutrons were made of smaller particles.
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