A gemstone is a mineral that has been cut, shaped and polished to enhance its natural beauty, like this piece of quartz – it has been faceted or shaped and polished so that the light is focused in to give it this beautiful brilliance. This is a natural quartz crystal that hasn’t been cut and polished and shaped; these faces are the way that nature formed it.
Gem minerals are crystals, which means they are made up of tiny atoms that are stacked together in a regular pattern. If we think of the atoms as the building blocks of the crystal, when every block is in the correct place, we end up with a perfect, transparent crystal. They also have a chemical composition, so the common mineral quartz is always made up of silicon and oxygen atoms arranged in a certain pattern to produce these beautiful crystals.
As crystals grow they often trap bubbles and little bits of other minerals, and while this makes the crystal not quite perfect, it does indicate that it hasn’t been manufactured.
So what causes colour in gem minerals? It’s complicated, and it’s related to its chemical composition. So a mineral like turquoise - a copper phosphate - is coloured by the copper. The mineral beryl has many gem varieties; the most popular are emerald and aquamarine. Emerald is coloured by trace amounts of chromium and vanadium, and aquamarine is coloured by trace amounts of iron.
One other thing that can colour gemstones is natural radiation. This quartz crystal has been turned smoky by being close to radioactive minerals in the granite in which it formed. Diamond is the hardest mineral, but it does have planes of weakness on its crystal structure, which means it can be broken. Another good example of that is the beautiful mineral topaz, which is very hard and not easily scratched, but it does have these planes of weakness and it will break, and form these flat shards of topaz.
We need perfect conditions to form perfect gem minerals; we need the right chemical ingredients and the right geological environments. This combination is unusual, which is why these beautiful gem minerals are very rare.