The vital difference of eBook and PDF files, is that eBooks will adjust how they appear to you (the reader) depending on the length of the page and screen size.
PDF files on the other hand are just an image of a page, frozen entirely. If you choose to adjust the text size on an eBook, this can be easily done just like when you use a Word document. If you do the same with a PDF, you are more or less zooming and nothing else.
You can also identify if the eBook you are reading is in a PDF format or a typical eReader format like EPUB by identifying the different characteristics of each.
If you are reading an eBook in EPUB or MOBI, and you shift the screen rotation or any other appearance characteristic, your text will readjust and look comprehensive once again. PDF files don’t have the same benefits.
EPUB file formats also tend to contain links that can take the reader out to the internet, perhaps related to explaining some of the content in the text. PDF files cannot do this because of the format base.
The general rule of thumb to remember is that eBook formats like MOBI or EPUB are typically more flexible and can be reshaped, whereas PDF files can’t.