Attack of the Killer Water Molecule (AKA hydrolysis)

Water fills our oceans, lakes, rivers and streams. It comes out of our taps. We swim in the stuff, and we drink it. For these reasons we tend to think of water as being inert. It isn’t. Water is an aggressively reactive molecule. Consider what happens when you stir salt into water: the water destroys the salt crystals. But why is water so ferocious? Read on to find out.

The Nature of Water 

In a molecule of water (H2O), two hydrogen atoms are attached to an oxygen atom. Oxygen has a much greater pull on electrons, or electronegativity, than hydrogen. In part this is because the oxygen atom has eight positively charged protons in its nucleus, and hydrogen only has one. Oxygen’s highly charged nucleus tugs electrons away from hydrogen, resulting in a partial negative charge (δ-) on the oxygen and a partial positive charge (δ+) on each hydrogen.

Figure 1 shows two views of a water molecule. Notice that the oxygen atom is surrounded by four pairs of electrons: two bonding pairs and two nonbonding, or lone pairs (Figure 1, left). The four electron pairs, which have a negative charge, repel each other and exist as far apart as possible around the spherical oxygen atom. In effect, to two bonding pairs are pushed to one side by the lone pairs, giving water a bent, or V shape (Figure 1, right).

Figure 1. Water has a bent shape

A partial negative charge exists at the point of the V and a partial positive charge exists at each tip. As a result, each water molecule behaves like a tiny magnet and is attracted to other charged particles. In some cases this attraction is so strong that water is able to break the bonds that hold other particles together. A reaction in which water attacks another compound is called hydrolysis. Hydro means “water” and lysis means “to unbind”, so hydrolysis literally means “to unbind with water”.

Hydrolysis Reactions

Hydrolysis of salt Consider a crystal of table salt (NaCl). The crystal contains positively charged sodium (Na+) ions and negatively charged chlorine (Cl-) ions. These charged particles interact with each other, holding the crystal together. Water, which is attracted to the charged particles, can disrupt this interaction and cause the salt crystal to dissolve (Figure 2).

Figure 2. Salt dissolving in water

Our oceans are salty because water attacks salt, but salt isn’t the only compound that water attacks. Water can also attack certain molecules.

Hydrolysis of molecules We have already established that oxygen is an electron bully. But oxygen doesn’t just tug electrons away from hydrogen. It tugs electrons away from other atoms as well, including carbon. A bond between oxygen and carbon possesses a dipole moment that can attract molecules of water. In some cases water attacks the molecule, causing it to split apart.

If you’ve eaten recently, hydrolysis is occurring right now, in your stomach and intestines. Digestion of fats, carbohydrates, and proteins is a hydrolysis reaction. Figure 3 shows hydrolysis of the ester bond in a fat.

Figure 3. Hydrolysis of the ester bond in a fat.

Of course, our bodies don’t just break down fats, carbohydrates, and proteins; they build new ones, too. To build new molecules water must be added in a type of reaction called dehydration. Dehydration is the reverse of hydrolysis.

So it turns out that water is a very good solvent for life, not because it is inert, but because it is highly reactive. Our very clever cells have learned to harness this reactivity so that they can build or break molecules on an as-needed basis.



What is a Greenhouse Gas?

These lambs, bathed in the reddish glow of an infrared lamp, are taking advantage of a property of infrared light: it causes electrons to vibrate. When electrons vibrate the molecules they hold together move as well. And we are quite adept at noticing an increase in molecular movement: we call it an increase in temperature.

Any moving object, whether it is a hammer or a molecule, has energy associated with it. Energy associated with the movement of large objects is called kinetic energy. When you a drop a hammer on your foot, kinetic energy in the hammer is transferred to your foot. That’s why it hurts.

Energy associated with the movement of atoms and molecules is called thermal energy. Thermal energy that is transferred to an object (for example, a lamb sitting under an infrared lamp) is called heat.

In the atmosphere some gases absorb infrared and produce heat. But not all gases are greenhouse gases. To make a good greenhouse gas, a molecule must possess an uneven charge distribution, called a dipole moment.

When a molecule with a dipole moment vibrates, the opposite charges alternately move closer together and farther apart. It takes energy to move the charges farther apart, which can be supplied by infrared light. Energy is released as heat when the charges move closer together, causing an increase in temperature. The water molecule has partial negative (δ-) and partial positive (δ+) charges and therefore possesses a dipole and is a potent greenhouse gas (Figure 1).

Figure 1: Water has a dipole moment and acts as a greenhouse gas (left). Oxygen does not possess a dipole and does not act as a greenhouse gas (right).

Carbon dioxide possessed two dipole moments but the molecule is linear, so the dipole moments cancel each other out. For this reason you might not expect carbon dioxide to act as a greenhouse gas. However, certain vibrations can torque the molecule, producing a temporary induced dipole (Figure 2). When the induced dipole disappears, energy is re-released as heat. In other words, carbon dioxide acts as a greenhouse gas.

Figure 2. Carbon dioxide is a greenhouse gas because molecular vibration can torque the molecule, producing an induced dipole.

You don’t need fancy lab equipment to observe carbon dioxide behaving as a greenhouse gas. Just take two, 2-liter soda bottles and fill each half way with water. Drop an Alka-Seltzer tablet in one (the tablet produces carbon dioxide when it dissolves). Cap the bottles and place in the warm sun, measuring the temperature at the beginning and again an hour later. The Alka-Seltzer bottle, which contains more carbon dioxide, will be several degrees warmer than the bottle with water only.

Arsenic: The King of Poisons

Was Napoleon murdered with arsenic? Probably not–historians now think that Napoleon died from stomach cancer. But arsenic was found in his hair. How did it get there? At the time arsenic was present in many products. A swatch of wallpaper from Napoleon’s home was shown to contain a popular, arsenic-based green pigment. Under the right conditions, arsenic fumes could have been produced. These fumes would not have contained enough arsenic to kill Napoleon, but they could have caused adverse health effects (2).

Many arsenic compounds are colorless, odorless, and tasteless, and before the mid-eighteen hundreds arsenic could not be easily detected in the body. For these reasons arsenic was the poison of choice in the Middle Ages. In fact, so many aristocrats were offed by arsenic that it became known as “the king of poisons, and the poison of kings” (1). But why is arsenic poisonous? To answer this question, we need to take a look at arsenic’s chemistry.


Arsenic chemistry

Arsenic is an element, meaning that it is composed of a single type of atom. The arrangement of electrons in the arsenic (As) atom and another atom, called phosphorus (P), is shown in the Bohr models below. Notice a similarity?

Bohr models show the arrangement of electrons in phosphorous and arsenic. These two elements are in the same group (or column) of the periodic table, which means that they have the same number of valence electrons and behave in a similar way.

In both phosphorous and arsenic the outermost electrons shell, called the valence shell, is partly filled with five valence electrons. A partly filled valence shell is less stable than a full shell, and atoms with a partly filled shell tend to transfer or share electrons to achieve a more stable electron configuration. When electrons are transferred or shared, a compound is formed.

Since arsenic and phosphorous have the same number of valence electrons, they tend to form similar compounds. For example, phosphorous forms a compound called phosphate, and arsenic forms an analogous compound called arsenate.

Phosphate is found in many biological molecules, including DNA and an important cellular fuel called ATP.


Phosphate forms the backbone of DNA.

Arsenate can be accidentally incorporated into biological molecules in place of phosphate. If arsenate was exactly the same as phosphate this wouldn’t matter. But it’s not. Look again at the Bohr models. The arsenic atom has a whole extra row of electrons, which means that it is slightly bigger. And this slightly bigger size makes a really big difference.

To see why, let’s consider a reaction called hydrolysis. Hydro means “water” and lysis means “unbind”, so hydrolysis literally means “to unbind with water”. In the hydrolysis reaction shown below, a water molecules removes (or unbinds) a phosphate from ATP.

ATP hydrolysis. An ATP molecule has an adenine (A) and three phosphates. In the reaction shown, the terminal phosphate is removed.

A lot of energy is released when the phosphate is removed. But often, the water molecule just can’t get close enough to react. This means that the ATP fuel is pretty stable: it sits there in the cell, until the cell is ready to use it.

Now, let’s consider what happens when arsenate replaces the terminal phosphate of ATP. Arsenic is a little bit bigger than phosphorus, and the As-O bond is a little bit longer than the P-O bond. This means that there is a bit more space between the oxygen atoms. A water molecule can get close more easily, and the hydrolysis reaction is faster. Not a little faster. A lot faster (3). As a result, the arsenic-containing fuel falls apart as soon as it is made.

Imagine what would happen if you filled your car’s tank and the gasoline was ruined before you finished pumping. You wouldn’t get anywhere, right? Likewise, a cell can’t do anything when its cellular fuel is ruined, which is what happens when the fuel is made from arsenate rather than phosphate. The cell keeps trying to make more fuel, and in so doing eventually exhaust its energy supply. Arsenate-containing DNA falls apart as well, and so do other molecules in which arsenate replaces phosphate. If enough arsenate is present, the cell dies.

Arsenate isn’t the only toxic form of arsenic. In fact, arsenite, which has one less oxygen than arsenate, is even more toxic for different reasons. Unfortunately arsenate turns to arsenite more easily than phosphate turns to the phosphite, all because the arsenic atom is a little bit different than the phosphorus atom (4).

Arsenic tolerance

Can living organisms ever use arsenate in place of phosphate? In 2010 scientists reported that GFAJ-1, a bacterium isolated from an arsenic-laced lake, could. However, subsequent studies showed that this bacterium always used phosphate, not arsenate, in DNA and other biological molecules even when the arsenic concentration was extraordinarily high (5).

To date, no life form is known that can substitute arsenate for phosphate. Nevertheless, certain organisms such as GFAJ-1 have adapted the ability to survive in high arsenic environments. A couple of different strategies for surviving in arsenic are described below.

Phosphate selectivity Phosphate is an important nutrient, and specialized transporters allow it to move into cells. Most phosphate transporters have a hard time distinguishing phosphate from arsenate, which means that any arsenate in the environment can be transported into cells along with phosphate. Some arsenic-tolerant bacteria, such as GFAJ-1, have phosphate transporters that are highly selective for phosphate (6). These transporters don’t move arsenate into cells even if it is present at very high levels, so it doesn’t cause any problems.

Arsenic detoxification and sequestration Other arsenic-tolerant bacteria are able to convert arsenate to less toxic compounds (7). Some plants are also arsenic tolerant. Interestingly, a group of plants called arsenic hyperaccumulators actively take up arsenate from the soil. In fact, the concentration of arsenic in the fronds of a hyperaccumulator called the Chinese brake fern (Pteris vittata) can be 56-times that in the soil (8). Arsenate-tolerant plants don’t use the arsenate; instead, they convert it to less toxic forms and sequester it in locations where it can do no harm (9).

The Chinese brake fern is an arsenic hyperaccumulator.

Arsenic tolerance of these plants confers a couple of advantages (9). First, arsenic-tolerant plants are the only ones that can survive in arsenic-contaminated soil, so they are not shaded by other plants. Second, experimental studies show that insects avoid hyperaccumulators grown in arsenic-contaminated soil, but feast on the same plants if they are grown in clean soil. These results indicate that the plants use arsenic as a natural insecticide.

Plants aren’t the only ones to use arsenic to fend off pests: humans do it, too. Historically, arsenic has been used as an insecticide, fungicide, herbicide, and wood preservative (1). Unfortunately, arsenic in pesticides and other products can contaminate the environment. For this reason the United States phased out the use of arsenic treated wood for residential applications in 2003. But many arsenic-treated structures still exist, and even after they are removed, the soil beneath them may contain arsenic.

Arsenic contamination is a big problem, but a company called Edenspace Systems has found a clever solution: this company uses arsenic-hyperaccumulating plants to draw arsenic out of contaminated soils. The fronds are then harvested and safely discarded.

How stinky socks launched the biotech revolution

Actually, there were two biotech revolutions. I will only argue that the second biotech revolution, which took place in the twentieth century, was launched by stinky socks. The first biotech revolution, which took place some 6,000 years before in the neolithic period, was arguably launched by beer. 

Biotechnology is, quite simply, the manipulation of living organisms or their components to make a desired product. (10) Beer is brewed with a living organism (yeast), and as such brewing is considered a form of biotechnology. Selective breeding, another form of biotechnology, was introduced around the same time as brewing, possibly to produce a more reliable source of grains for the beer. (4)

Thanks to the skills developed by early biotechnologists, humankind was able to develop a plethora of unique products and pets, from cheese to chihuahuas. (5) But the results weren’t always reproducible and the process was often less than desirable.

Take leather tanning, a process that involves removing flesh and hair from animal skin. Historically, tanning was done using urine, feces, and brain.(1) Urine, feces, and brains are all component of a living organism, so this qualifies as biotechnology.

Fortunately for tanners everywhere, in 1907 a sharp chemist named Otto Rohm had a better idea. Flesh and hair, Rohm reasoned, are biological in origin, and mammalian digestive system very good at breaking down biological molecules. Why not use digestive juices to tan leather? Rohm made an extract of digestive juice from cow pancreas and tested whether it could tan leather. It could. (2)

Meanwhile, Rohm’s wife, Elisabeth reasoned that digestive juice could also be used to remove stains from laundry. Think about it: most clothing stains are biological in origin–coffee, ketchup, blood–so it makes sense that they could be removed by digestive juice, right? Rohm tested whether his digestive juice extract could remove stains from laundry. It could. (2)

Digestive juice digests because it contains a special class of molecules, called enzymes, which are able to speed up a reaction.  Rohm partly purified a digestive enzyme called trypsin that is able to speed up the breakdown of protein, and in 1913 patented trypsin-containing laundry presoak solution called BURNUS. (2, 11)

It would be nice to say that BURNUS was a big success, but it wasn’t. It was expensive to produce and had a short shelf life. BURNUS was important, however, in that it was the first commercial product to utilize partly purified enzyme. (9) In other words, it launched the second biotech revolution: one in which purified biological components and isolated organisms are used to make a desired product.

At the time Rohm conducted his research the biological nature of enzymes was largely unknown. But shortly thereafter scientists demonstrated that certain enzymes, including trypsin and other digestive enzymes, are composed of protein. (7) And shortly thereafter this, scientists demonstrated that instructions for making proteins are encoded on DNA. (3) With this knowledge came the ability to engineer custom-designed proteins, a process called genetic engineering.

And what is one of the most successful products of genetic engineering? Laundry detergent! Modern laundry detergent, as well as dishwasher detergent, contains digestive enzymes from bacteria, some of which have been genetically modified to increase yield, or to improve stability or performance. (5) These enzymes are completely biodegradable, (9) and enable you to get the stink our of your socks at a lower temperature and with less harsh chemicals than laundry detergents of old. (8)


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