In a recent publication [K. Hammerer, M. Wallquist, C. Genes, M. Ludwig, F. Marquardt, P. Treutlein, P. Zoller, J. Ye, and H. J. Kimble, Phys. Rev. Lett. 103, 063005 (2009)] we have shown the possibility to achieve strong coupling of the quantized motion of a micron-sized mechanical system to the motion of a single trapped atom. In the proposed setup the coherent coupling between a SiN membrane and a single atom is mediated by the field of a high finesse cavity and can be much larger than the relevant decoherence rates. This makes the well-developed tools of cavity quantum electrodynamics with single atoms available in the realm of cavity optomechanics. In this article we elaborate on this scheme and provide detailed derivations and technical comments. Moreover, we give numerical as well as analytical results for a number of possible applications for transfer of squeezed or Fock states from atom to membrane as well as entanglement generation, taking full account of dissipation. In the limit of strong-coupling the preparation and verification of nonclassical states of a mesoscopic mechanical system is within reach.