It shouldn't, if you are updating via your computer's iTunes then it should take a backup as part of the update process (the contents of the Music and Videos apps aren't included in a backup, and neither are photos synced from a computer).
But to try and minimise lots content if the update process doesn't go smoothly, you should connect the iPad to your computer's iTunes and copy any purchases off it to your computer via File > Transfer Purchases. You may also want to copy photos and any important documents off the iPad as well 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 force a backup of the iPad by right-clicking the iPad 'Device' on the left-hand side of iTunes and selecting 'Backup'.
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
Your iPad should be updated to iOS 6.0.1 (which is the only version that is 'signed' by Apple), so you will lose the built-in YouTube app and the Maps app will change.