We evaluate here, using synchrotron X-ray reflectivity, hemoglobin adsorption characteristics on silicon substrates with varying chemical functionalities. Hemoglobin at isoelectronic point and at negative charge is immobilized on functionalized hydrophilic (hydroxyl, carboxylic, amine) and hydrophobic (alkylated) silicon surfaces for the study. As a control, the bare cofactor hemin (containing only the metal and porphyrin with no amino acid residues) is also studied under similar conditions. Ordered layers (grown using the Langmuir-Blodgett technique) are observed to be less affected by the surface chemistry compared to the multilayers formed by physical absorption. Surface chemistry and charge of the proteins are critical in controlling the protein adsorption characteristics on silicon, such as thickness (correlated to molecule size) and roughness. In this study, this is very well realized by varying both the hydrophobicity and hydrophilicity of the substrate. The fundamental studies discussed here provide us with a set of important guidelines as to how electrode surface functionalization can control molecular conformation/orientation, especially protein adsorption on the substrate. This in turn is expected to have a significant impact on the protein electrochemical function and response of biomolecular devices.