We have observed the interacting galaxies system, the Antennae, using the Fabry-Perot interferometer GHαFaS on the 4.2m William Herschel Telescope at the Observatorio del Roque de los Muchachos, La Palma, deriving the Hα surface brightness, velocity and velocity dispersion maps, and extracting key physical parameters (mean electron density, mass, velocity dispersion, and effective radius) of 303 HII regions, using a technique for which 3D mapping, including velocity, is essential. We also derived the CO(3-2) surface brightness, velocity, and velocity dispersion maps, and extracted the relevant parameters (size, CO luminosity, velocity dispersion and mass) of ~142 GMC's, using observations from the ALMA archive.We compared the properties of HII regions with GMC's, finding that the two distinct populations of HII regions are related to two populations of GMC's, as both show bimodal mass functions with a break at 106.5 solar masses. The classical Larson scaling laws need modification for the more massive population of GMC's, as the surface gas density increases with mass, which leads to enhanced star formation efficiency.The analysis of the turbulent velocity dispersion of the regions suggests that the more massive regions are bound by their own gravity, while the less massive star forming regions are confined by external pressure. If the two population of HII regions are derived from the twopopulations of GMC's, our results show the GMC's do not dissolve after they have given birth to massive stars, at least for the regime of the population of high mass clouds.