Self-assembled organic monolayers serve for modifying the workfunction of inorganic substrates. We examined the role of the molecular backbone in determining the monolayer-adsorbed work function, by considering the adsorption of dithiols with either a partially conjugated or a saturated backbone on the GaAs(001) surface. Using a combination of first principles electronic structure calculations, together with chemically resolved electrical measurements based on x-ray photoelectron spectroscopy and contact potential difference, we were able to distinguish quantitatively between the contributions of the band bending and surface dipole components. We find that while the substrates coated by partially conjugated layers possess a larger band-bending, relative to that of the substrates coated by saturated layers, this is offset by a difference in interface dipole, found to result primarily from an extended charge rearrangement on the molecular backbone. The combination of the two effects leads to a significant net change in work function. Thus, design of the molecular backbone emerges as an additional and important degree of freedom in the design of potential profiles and charge injection barriers in monolayer-based structure and devices.