You remap the animation frames of the MD3 to a sprite name.
frame 0 -> LAPHA1
frame 1 -> LAPHB1
etc
Better and clearer examples by clicking
MODELDEFOf course the actual sprite lumps can be anything, they don't have to contain useful graphics (though software renderer users will see blank actors). You can use this dummy sprite template Gez helped me generate for lots of dummy frames, should be plenty enough for smoothly animated models. Copy and paste into your TEXTURES lump.
EDIT: I just re-read your question. Seems like you have no experience in modeling. I suggest you pick your modeling package of choice and stick with one. I would suggest 3ds Max. You can download it for free and legally too if you're a student. 3ds Max is widely supported and there are literally thousands of tutorials available online, on Youtube, etc. Even the built-in tutorial movies are a great help, and the help files also cover a lot on low poly modeling.
I'm probably going to get a lot of fire for this, but I'd suggest skipping things like Blender and stuff. 3ds Max is the industry standard anyway and you can get jobs easier IF you decide to go that route, cuz most studios favour those well-versed in 3ds Max. So why bother learning something redundant, it's better to start on the right track right away.
As for actual animation, here's a generic answer: model with good topology and edge flow, model in quads, keep your triangle count in check because the MD3 format has limits. Mastery of this takes time...
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