We study the quantum dynamics of the cavity optomechanical system formed by a Fabry-Perot cavity with a thin vibrating membrane at its center. We first derive the general multimode Hamiltonian describing the radiation pressure interaction between the cavity modes and the vibrational modes of the membrane. We then restrict the analysis to the standard case of a single cavity mode interacting with a single mechanical resonator and we determine to what extent optical absorption by the membrane hinder reaching a quantum regime for the cavity-membrane system. We show that membrane absorption does not pose serious limitations and that one can simultaneously achieve ground state cooling of a vibrational mode of the membrane and stationary optomechanical entanglement with state-of-the-art apparatuses.