A device's backup doesn't contain music, films, TV shows, ibooks, synced photos or the actual apps (just their content and settings) - this page lists what is contained in a backup.
You should be able to copy your iTunes purchases off the iPad to your compute's iTunes via File > Transfer Purchases (you may also want to copy photos off that were taken with the iPad as well) and then force a backup of the iPad by right-clicking the iPad 'Device' on the left-hand side of iTunes and selecting 'Backup'. You may also want to copy off the iPad any important documents, notes, files etc e.g. via the file sharing section at the bottom of the device's apps tab when connected to iTunes, via wifi, email, dropbox etc - they should be included in the backup, but it's best to have a copy of them outside of the backup just in case.
You can then start the update by selecting the iPad on the left-hand side of iTunes, and on the Summary tab on the right-hand side clicking the Check For Updates button.
Updating to iOS 5+ : http://support.apple.com/kb/HT4972