In the last two decades significant progress has been made in developing methodologies (fabrication and analysis) for organic functionalization of semiconductors, in view of applications in molecular electronics, nano-bio devices, and surface nanopatterning in general. A strategic route is the functionalization of Si surfaces to exploit both the existing Si technology and the strength of the Si-C bond. It is also interesting to take advantage of Si-O chemistry, creating Si-O-C covalent bridges and trying at the same time to protect the interface from spurious oxidation. The microscopic understanding of interactions at the organic/semiconductor interfaces, required to proceed in these directions is, however, still poor. Theoretical studies can thus be very helpful to identify relevant model systems, and predict the effects on the electronic structure. Here, we use state-of-the-art ab initio methods to investigate alkyl monolayers on the perfectly hydrogenated Si(100) surface, bonded through single Si-C or double Si-OO-C bridges. Our results point to structural differences between bridging mechanisms, leading to different overall surface orderings. We find also relevant electronic differences. Our results always show a sharp frontier between the organic and inorganic electronic states, with a well defined energy barrier. For configurations with a Si-C bridge the top valence states are free from molecular contributions, while in the case of bonding through the Si-OO-C double bridge the results point to a contribution from the interface oxygen atoms.