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Why do apples turn brown after you cut them, or when they rot? Basically for the same reason that human hair, eyes and skin is brown, too. Not that we're calling you rotten. Quick Questions explains!
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Sources:
CITATIONS
http://www.scientificamerican.com/article/experts-why-cut-apples-turn-brown/
http://www.ncbi.nlm.nih.gov/books/NBK9921/
http://recipes.howstuffworks.com/question168.htm
http://www.worthington-biochem.com/TY/default.html
http://www.food-info.net/uk/colour/enzymaticbrowning.htm
http://health.howstuffworks.com/skin-care/problems/medical/albinism1.htm
http://www.scitechnol.com/tyrosinase-and-tyrosinase-inhibitors-xGSY.php?article_id=285
http://www.nature.com/milestones/skinbio4/pdf/melanocytes.pdf
http://pwp.surfglobal.net/rmangile/Pigeons/Biosynthesis%20of%20Eumelanin%20and%20Pheomelanin.html
http://www.bcerc.org/COTCpubs/BCERC.FactSheet_Phenols.pdf
Let's say you've got an apple and it looks delicious, and then you bite into it and you find out it's all gross and brown inside. Or maybe you just want to eat half an apple, so you slice it and leave the other half on the counter. An hour later, it's a brown mealy mess. All I wanted was an apple, and now all I have is a mouthful of disappointment!

What happened? Well, different kinds of cells have different kinds of enzymes. One enzyme that's found in the flesh of fruits, as well as the flesh of people, is polyphenol oxidase, or PPO.

Its job is to interact with phenols, simple organic chemical compounds that can be found in pretty much everything alive. Specifically, PPO oxidizes these phenols wherever it can. That just means it encourages them to bond with oxygen atoms, and it will do this as long as it has access to both phenols and oxygen.

Now, the oxidation of phenols kicks off a long and complicated chain reaction that ends in a protein you've probably heard of: melanin. The same pigment that controls your hair and skin color is also produced by fruits and veggies. It's what you're seeing when your apple turns brown.

And actually melanins are a lot more widespread in plant tissue than in our own tissue. We can only really produce them in our hair, eyes, and in the bottom layer of our skin, whereas plants have them practically everywhere. And the melanin that plants make serves a different purpose.

So, when plant cells are damaged, melanin is produced to surround and slow down any possible infection. That is why if you cut open a rotten apple, the rotten spot is usually surrounded by brown flesh. It's essentially the apple's immune response to rot.

Unfortunately for us, it's also the apple's response to any kind of damage. Drop an apple on the floor; it kills some apple cells and starts cranking out melanin to protect itself. And when you cut an apple into slices and serve them with crackers and cheese, those slices are going to brown really, really fast because not only are those cells damaged, but they've been exposed to air, which as you may have noticed is full of oxygen. It allows the PPO and those cells to basically throw a big oxidation party. It'll oxidize all the phenols. That apple is going to be so safe!

Except it's not going to be safe at all. You're either going to eat it or you're going to throw it away when it gets all brown and nasty. Those nice fresh phenols are really tasty, but the melanin, not so much.

But, on the bright side, the brown color in cocoa, raisins, coffee, and tea are all caused by this exact same oxidation reaction. And that actually gives those things the taste we like about them.

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