How do I use OpenGL 3.x VBOs to render a dynamic world?

Question

Although there seem to be very few up to date references for OpenGL 3.x itself, the actual low level manipulation of OpenGL is relatively straight forward. However I am having serious trouble trying to even conceptualise how one would manipulate VBOs in order to render a dynamic world.

Obviously the immediate mode ways of old are non applicable, but from there where do I go? Do I write some kind of scene structure and then convert that to a set of vertices and stream that to the VBO, how would I store translation data? If so how would that look code wise?

Basically really unsure how to continue.