There is .bash_profile and also .bashrc. It works this way. (This is true for most shells.)
When you first log in, it looks at the .profile, .bash_profile, or whatever. For instance, at least some versions of the korn shell will look at profile and ignore the rc file unless you tell it not to (in the .profile).
Now the rc script is usually examined with each instances of the shell, that is when you're not logging in. (Sheesh, my explanations are obscure tonight. Well, if you're taking your nick from the Japanese word, you'll be brave enough to bear with me. Although, in that case, it should be konjou, sounding like a slightly longer o at the end.)
Ok, you log in. That is, you boot up the machine, or you start a new X session, or whatever--you type in your user name and password. That's when profile, .bash_profile or whatever kicks in.
Now, in that session, you open another shell. For example, you log into gnome by typing your user name and password, and then, while in gnome, you open a terminal. The terminal won't bother with your profile, it will just look at the rc file, which, in most Linux default installations, is .bashrc.
If you look at most (including Fedora's, I think--I'm on BSD right now so can't check, but can give you a similar example) it will often say something like
if [ -f ~/.bashrc ]; then source ~/.bashrc
This means that if there is a .bashrc file in your home directory, read it and use what might be in there. In many cases, that might be the entire .profile or .bash_profile line. So, this means you can put all your environment variables, any aliases and anything else in your .bashrc.
For example, in FreeBSD, which I'm using to write this, the default shell is the somewhat simple original bourne shell. I have a .profile, which contains the line
ENV=$HOME/.shrc; export ENV
This means, look at the .shrc for various environment variables, such as which editor I want to use, what is my path, and everything else.
So, practically speaking, you can usually put these things in either your .bash_profile or .bashrc.
If you look at the man page for bash, and do a search within the page for INVOCATION, it gives additional explanation of what files bash looks for when starting up and when being used interactively, e.g., in a shell script.