Either all or almost all of the schools require prereqs to be finished before 'matriculation'. Meaning you're welcome to take whatever you want during the process of application. However, you may be at a disadvantage when compared to other applicants who have finished their requirements. It's impossible to tell what the adcoms will think.
I would say that if you were talking about extra courses in upper division (biochem, cell bio, etc) for prereqs, these are less of a concern. But orgo is something you need before taking the MCAT. So I would hold off, take the orgo, study for the MCAT, and next year when you've taken the April/June MCAT, you can start applications.