Quarks make up everything we know of, but the universe is a complicated place. Let's start with molecules. Molecules are made of different kinds of atoms forming together. Atoms have a very small nucleus in the center which is surrounded by electrons. The nucleus is composed of protons and neutrons and the protons and neutrons are made of quarks. There are other particles around us such as electrons and photons. See the Subatomic Roadmap to learn more.
The space around us is not empty, but is full of energy. At the subatomic scale, the particles can also be waves that fill space. Some of these particles/waves carry forces. The more the particles interact with space, the more mass they obtain. Einstein's E=mc2 equation tells us that mass and energy are equivalent. Scientists are working to understand matter to help us find new ways to use the energy all around us.