It is unlikely that they will do this. If the GA doesn't do it (likely), you will have to pick up you bags in IST and re-check them (and go through security again). If your flight is late, etc etc, and you do not show up for your FRA flight, that entire ticket with all future segments will be auto-cancelled and you'll end up having to buy a new ticket home as you will not be accommodated on later flights. Sorry to sound harsh, but these are the realities/dangers of buying separate tickets.