Key to this is the harmonics of the note. If you just play a 440Hz perfect sine wave it doesn't sound very exciting at all, but add in some of the harmonics and it starts to come alive.
If you add in the waveforms at 3x and 5x the fundamental, or at 2x the fundamental you will get a very different tonal effect. Varying the relative amplitude of these also alters the tone. Adding in frequencies which are not a multiple can lead to more atonality (think bells or cymbals)
If you translate the waveform into the frequency domain (ie look at the output of a frequency analyser which has your sounds fed into it) you can see how much these harmonics shape the sounds we hear.
Bass and Treble (or wah and other filters) just boost or cut a particular range of frequencies.
have a look at this wikipedia article for a great starting point, and also search for fourier transform to understand how the time and frequency domains are equivalent.