particle physics - What are quarks made of?

So atoms are formed from protons and neutrons, which are formed from quarks.

But where do these quarks come from? What makes them?

Answer

I cannot resist this mother goose quote:

What are little boys made of?

What are little boys made of?

Frogs and snails,

And puppy-dogs' tails;

That's what little boys are made of.

What are little girls made of?

What are little girls made of?

Sugar and spice,

And all that's nice;

That's what little girls are made of.

You state :

So atoms are formed from protons and neutrons, which are formed from quarks. and ask: But where do these quarks come from? What makes them?

How do we know atoms are formed from protons and neutrons? We have deep inelastic scatterings which showed that the atoms have a hard core, so they are not a uniformly distributed matter. Then we have the periodic table of elements which organizes itself well counting protons and neutrons.

How do we know that protons and neutrons are formed from quarks? We have the results from painstaking experiments that showed us once more that deep inelastic scattering shows a hard core inside the protons and neutrons. The study of the interaction products organized the particles and resonances into what is now called the standard model, a grouping in families that have a one to one correspondence with the hypothesis that the hadrons (protons neutrons resonances) are composed out of quarks.

But not only. They also have gluons which hold the quarks together due to the strong interaction, and the gluons have been seen experimentally , again with scattering experiments.

This is where we are now. The LHC is scattering protons on protons, i.e. quarks on quarks at much higher energies then ever before, and we are waiting for results. The theoretical interpretation called the Standard Model, so successful at lower energies presupposes that the quarks are elementary. Due to the gluon exchanges it is hard to see how a hard core might appear in quark quark scattering to take the onion one level lower, i.e. tell us that the quarks have a core.

Even in neutrino quark scattering the gluons will interfere, if the SM theory is correct at high energies. At the moment there is no experimental indication that the quarks are not elementary.

Nature though has surprised us before, and might do it again, once high energy lepton quark scattering experiments are designed and carried out in the future. Feynman I think had said: "to see what a watch is made of one does not throw one watch on another watch and count the gears flying off. One takes a screw driver". Leptons with their weak interactions are the equivalent of the screw driver.