An accessible PDF is comprised of three layers:
This is the layer you see on the screen or would see if you printed out the PDF. It is essentially a picture of your document.
This layer allows for searching and basic editing of the PDF document. It contains all the content text and text for elements such as alternative text represented in the visual layer. There is no formatting in this document, and if you were to print it, it would be all the same font size, read top to bottom, left to right, according to the layout of the physical document. It would not have a structure such as paragraph breaks, lists, columns, etc.
This layer exists to work in union with assistive technology such as screen readers. This layer includes markup components called "tags," which are similar in function as is HTML markup for websites. This markup allows assistive technology to distinguish what are headings, lists, non-text elements, and more. This layer also dictates the order of the document for the assistive technology if it is different than top to bottom, left to right (multiple columns, sidebars, etc.).