Silicates, which constitute about one third of all the minerals and around 90 percent of the Earth's crust are molecules built on the elements of Silicon and Oxygen. Silicate molecules are the building blocks in Quartz, Amethyst, Carnelian and many other Quartz minerals. (Trace elements of Iron or other elements are responsible for the varying colors and properties of the colored Quartz minerals.)

Two Silica tetrahedron can bond together by sharing an oxygen atom between themselves at one of their points. This forms Silicate.

Two Silica tetrahedron can also bond together by sharing an atom of an element other than oxygen. In an Aquamarine, the shared oxygen molecule shown in the illustration above would be an atom of Beryllium.

Science - Mysteries - Silicate Chemistry