Do photons "lose energy" when they are absorbed? Recently in my biology class I learned about an experiment in which isolated and illuminated chlorophyll pigments fluoresce in the red part of the spectrum, but also, the solution of the pigments gets hotter. Are the photons that are reflected as the electrons fall back to their ground states lower in energy than the photons absorbed?
 A: Strictly speaking: when a photon is absorbed, it ceases to exist, so it doesn't make sense to ask whether it loses its energy.
In the experiment that you describe the green light photons are absorbed, and red photons (having lower energy) are emitted as fluorescence. The likely reason for this is that the energy of an absorbed photon is distributed between the electron and other degrees of freedom of the molecule (e.g., its internal vibrations or the overall kinetic energy - these are expressed as heating of the material). So, when the electron relaxes to its ground state, it reemits as a photon only the part of the energy of the original green photons.
A: You use "absorbed" in the title, and "reflected" in the text, so I'm not clear on what your conception of the process is.  In fluorescence the incoming photon is completely destroyed, and a new photon of lower energy is generated.  This is evident because the incoming light is typically blue or ultraviolet, and the emitted light is green, or yellow, or red, ... some color that is associated with photons of lower energy than blue.   The energy deficit between the incident and emitted light has to go somewhere.  In the situation you described, it eventually ends up in the thermal energy of the system.
