Monthly Archives: January 2014

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 http://www.wikimedia.org

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

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GMO Apples

The other day I read an article about a genetically modified apple that doesn’t turn brown when you leave it out. At first glance, this sounds like they created an apple that doesn’t rot, which may sound scary. While it’s true that GMOs frequently sound scary to people, the point of this post is not to advocate for or against them, but to illuminate some of the science that is going on with this particular one.

When most fruits or vegetables are cut or bruised, the exposed bit will turn brown and that makes many people not want to eat it. The brown color is caused in part by one of a couple of enzymes — in the case of apples, it is “polyphenol oxidase.” Fruit will also turn brown when it rots, but that is not what is going on here. The spokesperson for the company that created these apples is quick to point out that the apples will still rot as normal, but will not discolor due to what is broadly called “enzymatic browning.”

On the left is a normal apple, with slight browning. On the right is the GMO apple with no browning. Image from http://www.npr.org

An enzyme is a type of protein that functions a little bit like a piece of machinery in a factory. It is not a reactant in a chemical reaction, just as machinery is not a construction material, so it is not consumed by a chemical reaction. Also like some machines, each enzyme has only one function — the enzyme “catalase” can only break down hydrogen peroxide, and the enzyme “DNA helicase” can only separate the two strands of a DNA molecule.

Back to our apples.

The skin of a fruit is its first line of defense against bacteria. If the skin of a fruit is damaged, bacteria may get in and feed on the sugar present inside. To combat this, apples produce a chemical called “catechol” and the enzyme polyphenol oxidase. When exposed to oxygen (such as when the skin is damaged or removed) polyphenol oxidase allows catechol to convert into the chemical “benzoquine,” which is an antimicrobial agent, and usually looks brown on the fruit. Many plants have a system just like this, although the exact chemicals and enzymes involved may differ slightly. While most people don’t like to eat food that has discolored this way, it is still perfectly safe to eat.

Given the fairly simple process that causes fruit to turn brown when damaged, it’s not so hard to engineer one that doesn’t — you just have to disrupt the short series of events that leads it to happen. There are three obvious ways to interrupt this process via genetic engineering. First, you could disrupt the production of the enzyme so it can’t convert catechol into benzoquine. Second, you could disrupt the production of catechol so there is nothing for the enzyme to convert into benzoquine. The third way is through the production of an enzyme inhibitor. These are chemicals produced by the organism that help regulate the activity of the enzyme. To slow down a reaction, an inhibitor is produced that prevents the enzyme from working at all or just slows it down. To speed up the reaction again, the inhibitor is removed and the enzymes go about their business. If you modify a plant to produce more of a particular enzyme’s inhibiter, the enzyme will be present but will not function.

Of these three methods, the genetic engineers chose option 2. Paradoxically, they engineered the plants to produce more enzyme, rather than less, which causes the plant to “decide” on its own to shut down the production of the enzyme. Because I’m not a geneticist, I cannot tell you why this method is better than simply removing the gene that codes for polyphenol oxidase, but the people who ARE geneticists decided that this was the way to go. The end result is the same, and it creates an apple that does not produce benzoquine when the flesh is exposed to air.

These are the facts. How you feel about genetic engineering is still up to you.

Have a topic that you want me to cover? Let me know in the comments section.

Follow me on twitter @CGEppig


Why do we have sex?

When posed with this question, most people will answer some combination of “to make babies” or “it feels good.” These answers are both true, but they are only part of the story — they describe what biologists call “proximate causes.” A proximate cause is one that explains the presence of a trait during the lifetime of the individual, compared to “ultimate causes” which are the reason why the trait evolved in the first place.

Take, for example, the opposable thumb. The proximate causes for this trait include the genes that code for it and the developmental processes that create the right environment for it to occur. The ultimate cause of the trait is that it allows us to manipulate objects in our environment with greater dexterity, therefore allowing us to get more food and survive better. All traits have an ultimate cause and a proximate cause, and both are integral to understanding the trait.

To make things a little bit more complicated, “to make babies” can be both a proximate and an ultimate cause. One thing that motivates people to have sex is the intention of making a baby. This motivation is a proximate cause. Making babies is also the ultimate cause of sexual reproduction. But even this is not the whole story. There are two basic methods of reproduction: sexual and asexual. Across all life, sexual reproduction is not the default position. Of the three lineages of life — bacteria, archaea and eukarya — only one (eukarya; the lineage to which we belong) typically reproduces sexually, and there are many species in this lineage that are asexual. Why do some types of organisms reproduce sexually and others asexually?

To put this question into perspective, let’s talk about the down-sides of sexual reproduction:

First, there is the problem of males. What exactly do males do? In a population of asexually-reproducing organisms, every individual is reproducing. Because males cannot have babies, a population of sexually-reproducing organisms can only reproduce half as quickly (because only half of the individuals are capable of reproducing). Males consume resources that would otherwise be available for females and young. Males provide parental care in relatively few species.

Second, there is the efficiency of passing on genes. Everyone knows that reproduction is about passing on your genes. When reproducing asexually, each offspring is a genetic clone of you, meaning that you are related to each offspring by 100%. With sexual reproduction, each offspring is only related to you by 50%, meaning that you need to have twice the number of offspring when reproducing sexually to match what you would have when reproducing asexually. For accounting purposes, each offspring only counts as a half.

Third, there is the problem of finding mates. In an asexual species, an individual may spend all of their energy on survival and reproduction. In a sexual species, individuals must expend energy on finding mates at the expense of survival and actually producing offspring.

I could make this list longer, but I hope I’ve convinced you that sexual reproduction has it’s shortcomings. So why on earth would the most complex organisms on earth reproduce this way?

The answer is genetic diversity. Sexually reproducing organisms are much less vulnerable to changes in the environment than asexual ones, especially when it comes to infectious diseases. Normally, individuals of a species differ in their susceptibility to a particular pathogen, and a large part of this variation is due to genetics. Some people don’t usually get the flu, whereas other people get it often and badly. This is because people are physiologically different, and therefore the flu virus cannot infect all people equally well. When two individuals reproduce sexually, their genes get mixed together in new ways. This creates a constantly moving target for pathogens. Asexual organisms do not need another individual to mate with, but all of their offspring are genetic clones of the parent. When there is lower genetic diversity, a pathogen can evolve to be better at infecting the host species to devastating effect. For example, the “regular” bananas that we buy in the store are a single strain called “cavendish” bananas. Not only are they a single strain, but every tree that produces them are genetic clones of each other. There is essentially zero genetic diversity among them, and as a result, a fungal disease is currently decimating the world’s crops.

Infectious disease is one of the biggest problems for life on earth — even many organisms that are themselves diseases can become infected by diseases. The costs of sexual reproduction may be high, but not as high as the costs of reproducing asexually when there are infectious diseases around.


Variations in the Sex Chromosomes FAQ

One thing I’ve always enjoyed about teaching is that students ask me questions that I never would have thought of myself. This is a reminder that everyone thinks differently and interacts with knowledge in different ways. One particular subject that frequently gets a lot of questions is unusual arrangements of the human sex chromosomes.

Let’s start at the beginning. All of our DNA is divided into 23 pairs of chromosomes, or 46 in total. Our chromosomes are numbered 1-23 by size, with the smallest being the sex chromosomes. In the sex chromosome “slot” (#23), typical human males have an “X” and a “Y” chromosome (XY) and typical human females have two “X” chromosomes (XX). All chromosomes are actually shaped like an “X” except for the “Y” chromosome — which is really shaped more like a “v” — but “X” and “Y” chromosomes are so named to distinguish the sex chromosomes from one another and from the other 22 pairs.

Typical human male chromosomes. Image from http://www.intropsych.com/ch10_development/10karyotype.jpg

Sometimes people are born with a number of chromosomes other than 46 — either too many or too few. Having too few or too many of chromosomes 1-22 can be pretty bad for you, causing, for example, Edwards, Patau and Down syndromes. Too many or too few sex chromosomes, on the other hand, frequently come with some characteristic physical and psychological traits, but they tend to be within the typical range of human variation.

Here are some questions that I’ve frequently been asked about chromosomal anomalies (the original wording of the questions was preserved to the extent possible):

Question #1: “Are women with three ‘X’ chromosomes super hot?”

Short answer: No.

This isn’t a question that would have occurred to me, but I understand where it comes from. Typical human females have two “X” chromosomes, and are usually more feminine looking than typical human males, who have only one “X” chromosome. Following this trend, females with three “X” chromosomes should be extra feminine and therefore extra attractive (if that’s what you’re into), right?

Not really. When an individual has more than one “X” chromosome, only one is active. The other/s is/are condensed into structures called “barr bodies.” When the DNA is condensed to this extent, it does not function. Females with three “X” chromosomes have two barr bodies instead of one, and therefore don’t have any extra chromosomes from a functional standpoint, and most of these people are totally unaware of the extra one. There are no morphological or psychological traits that are typical of the “XXX” condition, including increased attractiveness.

Question #2: “Are men with extra ‘Y’ chromosomes unusually masculine or violent?”

Short answer: No.

As in the previous question, it seems plausible at its face that the extra “Y” chromosome confers hyper-masculinity. Indeed, people used to believe that men with an extra “Y” chromosome were overrepresented in prison populations, but we now know that this isn’t true.

Biological masculinity broadly has to do with levels of testosterone, and “XYY” individuals do not have more or less testosterone than “XY” individuals. Just as in the “XXX” condition, people with the “XYY” condition are not noticeably different from people with “XY.”

Question #3: “Are people with XXY/XYY/XO sex chromosomes homosexual/transgender/intersex/hermaphrodites?”

Short answer: No.

Genetically speaking, maleness is determined by the presence of a “Y” chromosome, and femaleness is determined by the absence one. Female development is the default position that is altered by the presence of a “Y” chromosome. Unless something else is going on, too, people with no “Y” chromosome develop as females and people with at least one “Y” chromosome develop as males. So having two “X’s” and a “Y” usually leads to male development on account of the “Y” and in spite of the two “X’s.” “XO” refers to a condition called “Turner Syndrome” in which one one “X” chromosome is present and no “Y” chromosome. These individuals develop as females because there is no “Y” chromosome.

As far as we know, none of these combinations of sex chromosomes lead to a higher rate of people who are homosexual, transgender or intersex. “Hermaphrodite” isn’t a word that we use to describe humans anymore. We don’t know a whole lot about what causes people to be homosexual or transgender, and we know some (but not all) of the mechanisms that lead people to be intersex, but there isn’t any evidence that any of these are caused or influenced by unusual arrangements of the sex chromosomes.


A UFO

Let me tell you about the time I saw a UFO.

During my first year of graduate school, I took a trip to southern New Mexico. The first stop was to the UFO museum in Roswell (very disappointing). When that was a bust, the next stop was to a nearby wildlife refuge. While looking for cranes in a wetland, I happened to glance up into the sky. That’s when I saw the UFO. Most UFO sightings (and purported alien craft sightings) are a strange light in the sky or a fuzzy object in a photograph. What I saw was a fairly large, crisp, black, irregular shape hovering in the sky. As I stared at it, it changed shape continuously over the course of several seconds.

In stunned silence, I tried to make sense of what I saw. It didn’t look like any plane or bird I had ever seen, and I was sure it wasn’t some kind of optical illusion. I was completely unable to explain what I was looking at, and I couldn’t help but wonder if it was some kind of alien spacecraft. (Having nothing to do, I’m sure, with just having been to the UFO museum.) I stared for what seemed like minutes but in reality must have just been a few seconds. Spoiler alert: just a few seconds later, I figured out what I was looking at. But things could very easily have gone a different way. I could have run back to my car to tell the press. The object could have moved behind a cloud or a mountain. I could have fainted from the excitement. Any number of things could have prevented me from getting to the end of the story. If that had been the case, I would be left only with a strange, unexplained experience. Many people who experienced similar, strange phenomenon that are unexplained at the time go on to fill in the details on their own, forgetting that the “U” in “UFO” stands for “Unidentified.” “Unidentified,” of course, means that you don’t know what it is. Sometimes people will go on to conclude that what they saw was, for example, an alien space craft, and go on to attribute complex motivations to its purported crew and race. I hope it is obvious that you can’t start by admitting that you don’t know what something is, and then conclude that you know exactly what it is without adding additional information.

Back to the story. As I continued to watch in dumbfounded silence, the changing, irregular shape began to coalesce into a more recognizable form. I suddenly realized that I was looking at some type of stealth fighter, in the middle of a banking turn. It was flying away from me, which was why it appeared to be hovering, and it was turning, which caused the profile to change shape. The irregularity of the shape was due to the odd angle I was viewing it from, and the already odd shape of the aircraft. The “U” in “UFO” had just turned into an “I” for “Identified.”

The moral of this story isn’t necessarily about UFOs. (Though neither is it necessarily NOT about UFOs.) The moral of this story is more broadly to cautiously resist drawing conclusions about things until you have sufficient information to know what’s going on.

In my story above, I easily could have never figured out what really happened. Had that been the case, I would have been left only with a strange experience that I couldn’t explain. And I would have been wise to leave it at that. You may have had similar stories of your own, whether resolved or unresolved, and you will probably have more in the future. When you do, try to maintain a healthy skepticism about what it is you’re seeing. Be more interested in finding out what really happened than in having an answer. Seeking the truth means that sometimes you have to put the conclusion on the back burner until you get more information. Until then, it’s okay not to have an answer.