Is there a reason that protons are positively charged and electrons are negative?

The main difference lies in the direction that electric field lines run. The direction of electric field lines is different. They originate isotopically with positive charge and end isotopically with negative charge. The quark composition can also be different. For example, proton could have 2 up and 1 down quark. Charges for up quarks (u=+2e/3, d=-e/3).

Electrons are a separate family of leptons called leptons. Rutherford assigned the respective charges to positron and electron after the gold foil experiment.

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