I should REALLY finish this video tutorial on particles that I have sitting on my computer.
Both color and transparency of particles can be animated over time. You just have to activate automatic keyframes (just as you would for normal animation), scrub the timeline slider to the desired frame and change the paramter(s) (e.g. color) to the new values. A red box should appear around the parameter to indicate that it is animated. When you've finished just turn off automatic keyframes again.
It's important to keep in mind that only the first 10 frames are used for particle material animation. So the material properties of the very first frame are used when a new particle is born. And the settings at the 10th frame are used when the particle dies. Whatever is in between those frames gets interpolated over the lifetime of the particle.
EDIT: And yes, you can also stop the emission of new particles without killing all active ones. To do that animate the "Birthrate (per sec)" value in the parameters of the ParticleSystem component that you've assigned to your emitter.
If you then want to trigger this animation (for example when the player klicks a button) assign an Animation component to the emitter and set up the animation using the Notes Track in TrackView (have a look at
THIS tutorial if you don't know how to do that). When you now trigger the animation component it will stop the particle emission.
As an additional tip: if you want to activate the emitter again later on, have the animation component that you've just set up play backwards. This will turn the value of particles back up and the particle system is active again.