I have searched the definition of what life is and it says that something living is something that can repriduce, grow and evolve. However viruses are not classed as living but do the same. We say we are living creatures but how is it that we are living if we are made up of atoms which are not living, so we are essentially an organic machine, atoms are made up of quarks but what are they made of? I've read that it is some form of energy but if we are made of energy how do we exist as physical beings? My questop is how are we actually living from something that is dead so are we already dead or not living? I'm just intrigued as to how everything is how it is yet such small things as atoms that can't think mean we are how we are

Viruses are not considered alive because while they can reproduce and evolve they can only do so inside a host and not on their own.
While we are organic machines and made up of molecules, atoms, etc that's just chemistry. The biology is how all these molecules work together, interact with each other, using energy, to make things happen. This doesn't happen in dead things. Only the chemical processes can take place in dead things (degradation).