Short answers, pulled from the story.
In physical science, matter is any substance that has mass and takes up space by having volume. All everyday objects that can be touched are ultimately composed of atoms, which are made of interacting subatomic particles. Matter generally excludes massless particles such as photons and energy phenomena such as light or heat.
At the smallest scale, ordinary matter is made of quarks and leptons, two of the four types of elementary fermions. Carithers and Grannis state that ordinary matter is composed entirely of first-generation particles, namely the up and down quarks plus the electron and its neutrino. Protons and neutrons are themselves made of quarks bound by gluon fields.
Matter takes up space because of the Pauli exclusion principle, which applies to fermions such as quarks and leptons. The principle prevents two particles from occupying the same place in the same state at the same time, which forces particles and atoms to keep their distance. White dwarf stars and neutron stars are extreme examples where this principle relates matter to the occupation of space.
Ordinary matter makes up only a small fraction of the universe. Microwave light seen by the Wilkinson Microwave Anisotropy Probe suggests that about 4.6% of the observable part of the universe is baryonic matter, while about 26.8% is dark matter and about 68.3% is dark energy. Most ordinary matter in the universe is unseen, since visible stars and gas account for less than 10 per cent of the ordinary matter contribution to the mass-energy density.
Antimatter is matter composed of the antiparticles of those that constitute ordinary matter. When a particle and its antiparticle come into contact they annihilate, converting into other particles of equal energy in accordance with Albert Einstein's equation E = mc2, often producing high-energy gamma-ray photons. Antimatter is not found naturally on Earth except very briefly and in vanishingly small quantities.
The particulate theory of matter appeared independently in ancient Greece and ancient India. Early proponents include the Indian philosopher Kanada, who lived around the 6th century BCE, and the pre-Socratic Greek philosophers Leucippus, around 490 BCE, and Democritus, around 470 to 380 BCE. Aristotle later set the conception on a sound philosophical footing in his Physics.
Most of the mass of ordinary matter comes from the binding energy of quarks within protons and neutrons, not from the quarks themselves. The sum of the masses of the three quarks in a nucleon is approximately 12.5, low compared to the nucleon mass of approximately 938. Most of the mass of everyday objects comes from the interaction energy of its elementary components.