The default behavior of the mark and region, in which setting the mark activates it and highlights the region, is called Transient Mark mode. This is a minor mode that is enabled by default. It can be toggled with M-x transient-mark-mode, or with the ‘Active Region Highlighting’ menu item in the ‘Options’ menu. Turning it off switches Emacs to an alternative mode of operation:
The usual solution to this problem is to set the mark and then use it soon, before you forget where it is. You can also check where the mark is by using C-x C-x, which exchanges the positions of the point and the mark (see Setting Mark).
query-replace) performs replacements within the region, if the mark is active. When Transient Mark mode is off, it always operates from point to the end of the buffer. Commands that act this way are identified in their own documentation.
While Transient Mark mode is off, you can activate it temporarily using C-<SPC> C-<SPC> or C-u C-x C-x.
exchange-point-and-mark, with a prefix argument.)
These commands set or activate the mark, and enable Transient Mark mode only until the mark is deactivated. One reason you may want to use them is that some commands operate on the entire buffer instead of the region when Transient Mark mode is off. Enabling Transient Mark mode momentarily gives you a way to use these commands on the region.
When you specify a region with the mouse (see Setting Mark), or with shift-selection (see Shift Selection), this likewise activates Transient Mark mode temporarily and highlights the region.