cp is copy command and it functions:
cp source target
SO you can make backup for example:
Lets first change directory
cd /usr/share/hildon-desktop
And then make backup of file in this directory
cp transitions.ini transitions.backup
Now you have two files in this directory. You can check this with command:
ls
And please remember linux is case sensitive system and you can use TAB for auto completion for directories and filenames.

.edit
You probably need rootsh installed. After installation you can enable root user access in xterm with command:
sudo gainroot
Means that now you have superuser/root access (be careful) you can overwrite anything and delete anything. All the system files also which transition.ini is.