Apples are living things---just like us.
It's hard to remember that fruits and vegetables are living organisms until we harvest them. Just like any other living organism on the planet, they have a lifespan and several different factors contribute to their decomposition.
Mold, bacteria, and fungi
Plant pathogens account for a large percent of crop disease. A plant pathogen will either be biotrophic, meaning that it can establish a relationship with the apple cells that allows it to feed without damaging the apple, or necrotrophic, meaning that the pathogen will violently invade and kill plant tissues as it feeds. Mold, bacteria and fungi can enter the apple in a number of different ways, given that cell walls in the apple are broken (such as dropping an apple on the ground or biting into it). Different types of fungi degrade the apple in different ways, perhaps by making it dry and brown or soft and wet.
After harvest
Once an apple is picked it will experience biochemical changes, as the harvester is cutting it off from its life-source, the tree from which it drew its nutrients. There will be a breakdown in carbohydrates in the apple and the production of the gases carbon dioxide and methane. Enzymes inside the apple accelerate the breakdown process. If one simply picks and apple and lets it sit on the counter, it will eventually turn brown whether or not the skin is broken. Harvesting an apple is the beginning of the end to its life---after that, it only has several weeks of ripeness before it begins to brown.
Oxidation
An apple has millions of cells inside of it. When an apple is dropped, bitten into, cut open or damaged in any other way, many of those cell walls will be broken. The inside of the apple is now vulnerable to oxygen---the apple's enzymes and iron-containing phenols will react to that oxygen and as a result the inside of the apple will turn brown.
Prevention
You can stop apples from turning brown by putting them in the refrigerator to lessen their exposure to bacteria, mold and fungi. Once an apple is cut, you can place it in water or any kind of citrus juice (which contains antioxidants) to prevent browning. The best way to keep an apple fresh is to prevent breakage and exposure to oxygen and plant pathogens. Remember that even one bad apple can ruin a bagful in a chain reaction.
Summary
When apples turn brown, it may appear that they did so simply because they were exposed to oxygen. However, there are several other possible factors in apple degradation. First, an apple that was harvested a long time ago may be at the end of its lifespan, and therefore naturally rotted away. Any apple that has even a slight break in it is not only exposed to oxygen, which will ignite a chemical reaction with the iron and enzymes inside an apple, but to pathogens as well. Bacteria, mold and fungi will not only turn an apple brown but dry it out or make it wet and soft. Any of these things can occur separately and at the same time.
Tags: inside apple, turn brown, apple that, bacteria fungi, cell walls, different ways