These variables are located immediately after defining a local copy of jQuery in the jQuery source.
// Map over jQuery in case of overwrite
_jQuery = window
If you look through the jquery.js file you will find that they start by saving the previous definition (line 31-32 v1.4.4):
// Map over the $ in case of overwrite
_$ = window.$,
Then if you call noConflict it just sets the value back (line 397-398)
noConflict: function( deep ) {
window.$ = _$;
You can add something similar to your own project to protect the name space. The concept holds for more than just javascript.
If these lines were not included, then you wouldn't be able to run jQuery and Prototype on the same page as both use the $ operator - nothing bad may happen, it's just that your code won't work and possibly cause errors.