Opacities and thus local chemical composition play a key role when characterizing exoplanet atmospheres from observations. When the gas is in chemical equilibrium the chemical abundances depend strongly on the temperature profile. Grey models tend to overestimate the temperatures in the upper atmosphere. We present a new analytical model with a more realistic description of the radiative cooling in the infrared. Mechanisms like quenching and cold traps can drive the upper atmosphere far from its chemical equilibrium. The efficiency of these mechanisms depends on the strength of the vertical mixing. Using 3D global circulation models of HD209458b including passive tracers, we show that, although Hot Jupiter atmospheres are stably stratified, they are strongly mixed by planetary scale circulation patterns. We provide a rough estimate of the effective vertical mixing coefficient in Hot Jupiter atmosphere which can be used in 1D models.