The hops cones or flowers are rich in resins, oils, tannins, proteins, and sugars among other things. The alpha and beta acids that are at the forefront of the packaged products are contained in the resins. Humulones, or alpha acids, are the most prominent bittering agent in hops. As the wort is heated, along with the hops, these alpha acids change in form and result in iso alpha acids, or isohumulones. These iso alpha acids tend to increase in bitterness. This is in contrast to the beta acids, or lupulones, which tend to convert into some bitter and non-bitter agents.
When you see hops labeled with an alpha hops percentage this refers to the measurement for the composition of alpha acids compared in weight to the rest of the elements in hops. This is shown in percent, and indicates the % weight of the primary bittering agent.
AAUs or alpha acid units are then used for creating recipes that can be followed regardless of volume. HBU refers to Homebrew Bittering Units. HBU's are calculated by taking the weight in hops multiplied by the alpha acid %. HBUs were created as a tool to use when calculating the amount of hops to use in say 5 gallons of homebrew. One ounce of 10 AAU hops will result in 10 HBUs. IBU stands for International Bitterness Units and is actual measurement for bitterness.