Hi,
If you upgrade to 4.3 you will lose the Jailbreak yes.
You can back your phone up in iTunes by right clicking on the device and choosing "Backup". You can also transfer your apps to iTunes by right clicking and choosing "Transfer Paid Apps".
This won't back up your Cydia installed apps though, if you want to do that I recommend an app called PkgBackup from Cydia. It creates a contact on your phone with all of the information of the installed packages from Cydia. You can then restore those apps within PkgBackup once you are back on a JB'd phone.