What causes PDF file size to increase when saving in Preview?

It seems that making edits, annotations, or even just opening and saving a PDF file in Preview will cause a significant increase in file size. I've noticed that for some books I've scanned this also happens to improve page rendering time. Can anyone shed some light as to what is going on to cause these changes? I am interested in synching annotations of PDF ebooks between Preview and the iPad (maybe GoodReader) but this may be too impractical with large PDF files.