When a neutral atom lose an electron, it becomes a positively charged ion. That means the atom change when the electron is lost or gained. Hence, if the atom undergoes a change and becomes a positive ion, in this process the lost subatomic particle is electron.
The alkaline/alkaline results could indicate that only the protein was utilized by the organism, but it could also be a result of prolonged incubation. The organisms could have exhausted that available sugar and then reverted to protein catabolism.