I think I need to restore my MacBook Pro but I am unsure how. When I turn it on, safari and iTunes do not show in the dock there is just question marks in its slot. Please help

Not even had it on in a month and turned it on this morning and my dock is all messed up and I can't even open Finder

Pull the question marks off the Dock and let go,  drag new icons of the app  down  to the Dock from the Applications folder.
Try another restart in Recovery command R.
Run the DiskUtility repair disk and repair permissions
http://support.apple.com/kb/HT4718

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