Fun With Enzymes

In my last post, I talked about enzymatic browning and genetic engineering. I want to follow that up with some words about affecting enzyme function in ways that are not related to genetics. Be sure you’ve read the last post before you read this one so you’re up to speed.

Enzymes, like all proteins, are a long chain of amino acids. The function of a protein is based largely on the exact 3-dimensional structure of this folded chain.

This diagram shows the intricate folding pattern of the enzyme “DNA Helicase.” Image from

If this structure is altered, the protein will not function the way it’s supposed to. When the structure of a protein is changed to the point that it no longer works, it is “denatured.” Two common factors that can cause proteins to denature are high temperature and a pH that is outside of its normal working range, either too high (basic) or too low (acidic). This is why raw, cut potatoes will turn brown when you leave them out but cooked potatoes will not. This is also why many recipes using raw avocado tell you to squeeze a lime over the top of it.

Here’s a quick experiment that demonstrates this very nicely:

I’m using potatoes for this experiment because I happen to have one on hand, but it would work just about as well to use apples, avocados, bananas, or most other fruits. Like apples, potatoes undergo enzymatic browning when exposed to air. Unlike apples, which use the enzyme polyphenol oxidase for this process, potatoes use the enzyme tyrosinase. The starting molecule is the same (catechol) and the resulting molecule is different, although it is in the same family of molecules: apples convert catechol into benzoquine whereas potatoes convert it into hydroxyquinone.

To start, I cut three slices out of my potato:

1) I put a small squirt of acid on top of the cut face of the first slice. I used very dilute hydrochloric acid because it’s what I had on hand, but this would work equally well with vinegar, lemon or lime juice, or any other acidic substance.

2) The second potato slice is plain with nothing on it.

3) The third potato slice has a small squirt of water on top of it.

Condition 1 could be called the “treatment” or “experimental” or “manipulation” group. I’m going to call it the experimental group. This is the group that I’m changing by adding acid to it.

Condition 2 is the control group. I didn’t do anything to this potato so that I will have something to compare the experimental group to at the end.

Condition 3 is the “procedure control” or the “sham treatment.” In the experimental group, I put acid on the potato, but I also put water on the potato (the acid is dissolved in water). If the water on the potato is preventing oxygen from getting to it, and if condition 1 does not turn brown, we would not be able to tell whether it was from the water or the acid.

There are eight possible outcomes to this experiment, but I will mention the three most relevant ones:

All three potatoes could turn brown. This would mean that neither acid nor water prevents enzymatic browning.

Only condition 2 could turn brown. In this case, both the treatment and sham treatment would prevent browning. In this scenario it would not be possible to conclude that the acid prevented browning, though neither could we conclude that it did not prevent browning.

Conditions 2 and 3 both turn brown. From this outcome, it would be possible to conclude that exposure to acid prevents enzyme activity.

Here is a picture of the experimental setup when it was fresh. The acid and water have been added, but not enough time has passed for anything to happen:

Potatoes at the start of the experiment.

Potatoes at the start of the experiment.

About an hour later, some enzymatic browning has occurred:

Potatoes after about 1 hour

Potatoes after about 1 hour

After a total of about four hours, the potatoes are starting to dry out a little bit, so it’s time to stop. A good deal of browning has occurred in conditions 2 and 3:

Potatoes after about 4 hours

Potatoes after about 4 hours

This experiment turned out about as perfectly as it could have. Conditions 2 and 3 had significant browning, and condition 1 came out clean as a whistle. This demonstrates fairly conclusively that acid inhibits enzyme activity. Go ahead and try this experiment on your own.

Have a topic you want me to cover in a future post? Let me know in the comments.

Follow me on twitter @CGEppig


About Christopher Eppig, Ph.D.

I have a Ph.D. in biology and a passion for sharing my knowledge and understanding of the natural world with anyone who will listen. At a time where science is permeating public life more than ever, it is especially important that the public understand what science is, and how its findings intersect with their own lives. In addition to the more practical benefits of scientific literacy, I believe strongly that understanding the natural world enriches peoples lives. The man behind the curtain is not me — it is the real world, which we can discover through science, and it is beautiful. Let me show it to you.  Follow me on twitter @CGEppig. View all posts by Christopher Eppig, Ph.D.

2 responses to “Fun With Enzymes

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