MacBook Pro not booting from hard drive
The question mark means that it cannot find its boot partition.  On any OS X drive, you are going to have several partitions.  It might look something like:

 #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:     Apple_partition_scheme                        *55.9 Gi    disk0
   1:        Apple_partition_map                         31.5 Ki    disk0s1
   2:                 Apple_Boot Boot OSX                128.0 Mi   disk0s2
   3:                 Apple_HFSX Macintosh HD0           25.0 Gi    disk0s3
   4:                 Apple_Boot                         128.0 Mi   disk0s4


Using this drive as an example, you can probably see what is on "Macintosh HD0" which is disk0s3.  To boot, you need the "Apple_Boot" partition or disk0s4 partition.

You should be able to fix this by running the installer and having it repair the OS X installation.  

Make sure you back up your files first (it sounds like you did).