Food for Thought: Enzyme Action

Nature makes use of the tools that I have been developing, and does so in the most extraordinary and subtle manner. After all, she has had about four billion years to come up with solutions to problems with which human chemists have striven seriously for only a century or so. Most of the reactions that go on in organisms—including you—are controlled by the proteins called ‘enzymes’ (a name derived from the Greek words for ‘in leaven’, as in yeast). Enzymes are biological catalysts (Reaction 11) that are extraordinarily specific and highly effective in their role. One of these complex molecules might serve as the merest foot soldier in the army of reactions going on inside you, with a role such as severing the bond between two specific groups of atoms in a target molecule. Because their function may be highly specific, enzyme molecules need to be large: they have to recognize the molecule they act on, act on it, then release it so that they can act again. Thus, they have to have several functions built into them. As you will see, enzymes are the ultimate in functional blindness: they feel around in their surroundings in order to identify their substrate, the species they can act on. Life is ultimately blind chemical progress guided by touch. I am going to introduce you to one particular group of enzymes, the ‘proteases’, and focus on one example from this group, namely chymotrypsin. A protease is a traitor to its kind: it is a protein that breaks down other proteins. It plays a role in digestion, of course, but its range is much wider. One protease enables a lucky sperm to eat through the cell wall of an egg and ensure its at least temporary immortality. Another facilitates the clotting of blood to terminate possibly fatal bleeding. Chymotrypsin itself is an enzyme that is secreted from the pancreas into the intestine, and makes an essential contribution to the process of digestion. Its name is derived slightly circuitously from the Greek words for animal fluid, a bodily ‘humour’, and rubbing, as it was obtained as a fluid by rubbing the pancreas.

Fasteners: Acid Catalysis

I explained the general basis of catalysis in Reaction 11, where I showed that it accelerated a reaction by opening a new, faster route from reactants to products. One of the ways to achieve catalysis in organic chemistry is to carry out a reaction in an acidic or basic (alkaline) environment, and that is what I explore here. In Reaction 27 you will see the enormous importance of processes like this, not just for keeping organic chemists productive but also for keeping us all alive; I give a first glimpse of that later in this section too. Various kinds of acid and base catalysis, sometimes both simultaneously, are going on throughout the cells of our body and ensuring that all the processes of life are maintained; in fact they are the very processes of life. I deal with acid catalysis in this section and base catalysis in the next. The point to remember throughout this section is that an acid is a proton donor (Reaction 2) and a proton is an aggressive, nutty little centre of positive charge. If a proton gets itself attached to a molecule, it can draw electrons towards itself and so expose the nuclei that they formerly surrounded. That is, a proton can cause the appearance of positive charge elsewhere in the molecule where the nuclei shine through the depleted fog of electrons. Because positive charge is attracted to negative charge, one outcome is that a molecule may be converted into a powerful electron-sniffing electrophile (Reaction 16). Another way of looking at the outcome of adding a proton is to note that a C atom with a positive charge is a target for nucleophilic missile attack (Reaction 15). Therefore, if a proton draws the electron cloud away from a nearby atom, then its presence is like a fifth-column agent preparing a target for later attack. Let’s shrink and watch as some acid is added to a molecule that contains a –CO– group, such as acetic acid. The protons provided by the added acid are riding on water molecules, as H3O+ ions, and arrive in the vicinity of the acetic acid molecule.

Electronic Warfare: Electrophilic Substitution

Benzene, 1, is a hard nut to crack. The hexagonal ring of carbon atoms each with one hydrogen atom attached has a much greater stability than its electronic structure, with an alternation of double and single carbon–carbon bonds, might suggest. But for reasons fully understood by chemists, that very alternation, corresponding to a continuous stabilizing cloud of electrons all around the ring, endows the hexagon with great stability and the ring persists unchanged through many reactions. The groups of atoms attached to the ring, though, may come and go, and the reaction type responsible for replacing them is commonly ‘electrophilic substitution’. Whereas the missiles of Reaction 15 sniff out nuclei by responding to their positive electric charge shining through depleted regions of electron clouds, electrophiles, electron lovers, are missiles that do the opposite. They sniff out the denser regions of electron clouds by responding to their negative charge. Let’s suppose you want to make, for purposes you are perhaps unwilling to reveal, some TNT; the initials denote trinitrotoluene. You could start with the common material toluene, which is a benzene ring with a methyl group (–CH3) in place of one H atom, 2. Your task is to replace three of the remaining ring H atoms with nitro groups, –NO2, to achieve 3. And not just any of the H atoms: you need the molecule to have a symmetrical array of these groups because other arrangements are less stable and therefore dangerous. It is known that a mixture of concentrated nitric and sulfuric acids contains the species called the ‘nitronium ion’, NO2+, 4, and this is the reagent you will use. Before we watch the reaction itself, it is instructive to see what happens when concentrated sulfuric acid and nitric acid are mixed. If we stand, suitably protected, in the mixture, we see a sulfuric acid molecule, H2SO4, thrust a proton onto a neighbouring nitric acid molecule, HNO3. (Funnily enough, according to the discussion in Reaction 2, nitric ‘acid’ is now acting as a base, a proton acceptor! I warned you of strange fish in deep waters.) The initial outcome of this transfer is unstable; it spits out an H2O molecule which wanders off into the crowd. We see the result: the formation of a nitronium ion, the agent of nitration and the species that carries out the reaction for you.

Carbon Footprints: The Wittig Reaction

As a molecular architect working on an atomic construction site you need to be able to build up the carbon skeleton of your project, not merely decorate it with foreign atoms. There are dozens of different ways of doing that, and in this and the next section I shall introduce you to just two of them to give you a taste of what is available. A secondary point is that throughout chemistry you will find reactions denoted by proper nouns, recognizing the chemists who have invented or developed them. One example is that of the ‘Wittig reaction’, which is named after the German chemist Georg Wittig (1897–1987; Nobel Prize 1979). The reaction is used to replace the oxygen atom of a CO group in a molecule by a carbon atom, so that what starts out as decoration becomes part of a growing network of carbon atoms. You need to know that phosphine, PH3, 1, the phosphorus cousin of ammonia, NH3, is a base (Reaction 2). When it accepts a proton it becomes the ion PH4+. The H atoms in that ion can be replaced with other groups of atoms. A replacement that will be of interest is when three of the H atoms have been replaced by benzene rings and the remaining H atom has been replaced by –CH3. The resulting ion is 2. In the presence of a base, such as the hydroxide ion, OH–, the –CH3 group can be induced to release one of its protons, so the positive ion becomes the neutral molecule, 3. Note that there is a partial positive charge on the P atom and a partial negative charge on the C atom of the CH2 group. The presence of that partial negative charge suggests that the species could act as a nucleophile (Reaction 15), a seeker out of positive charge, with the CH2 group the charge-seeking head of the missile. Let’s watch what happens when 3 attacks a molecule with a CO group, specifically 4: perhaps you want to sprout a carbon chain out from the ring and intend to begin by replacing the O atom with a C atom.

Zippers: Base Catalysis

A base, you should recall from Reaction 2, is the second hand clapping to the acid’s first. That is, whereas an acid is a proton donor, a base is its beneficiary as a proton acceptor. The paradigm base is a hydroxide ion, OH–, which can accept a proton and thereby become H2O. However, in the context of catalysis, the topic of this section, its role is rather different: instead of using its electrons to accept the proton, it uses them to behave as a nucleophile (Reaction 15), a searcher out of positive charge. Instead of forming a hydrogen–oxygen bond with an incoming proton, it sets the electronic fox among the electronic geese of a molecule by forming a new carbon–oxygen bond and thereby loosening the bonds to neighbouring atoms so that they can undergo rearrangement. The OH– ion in effect unzips the molecule and renders it open to further attack. Base catalysis has a lot of important applications. An ancient one is the production of soap from animal fat. To set that scene, I shall consider a simple model system, the ‘hydrolysis’ (severing apart by water) of the two components of an ester, 1 (the same compound I used in Reaction 17, a combination of acetic acid and ethanol), and then turn to soap-making itself. You saw in Reaction 17 how esters can be broken down into their components, a carboxylic acid and an alcohol, by an acid; here we see the analogous reaction in the presence of a base. To be specific, the reagent is a solution of sodium hydroxide, which provides the OH– ions that catalyse the reaction. We watch what happens when a solution of sodium hydroxide is added to an ester and the mixture is boiled. The O oxygen atoms of the ester have already ripened the molecule for nucleophilic attack by drawing some of the electron cloud away from the C atom to which they are both attached, leaving it with a partial positive charge, 2. The negatively charged OH– ion sniffs out that positive charge and jostles in to do its business.

Divorce and Reconciliation: Radical Recombination

In Reaction 3 you saw that a radical is a species with at least one unpaired electron. An ‘unpaired electron’ is a single electron that is present in the molecule but not playing a role in bonding. The French word celebataire conveys the sense of the electron’s forlorn loneliness very well. However, it is capable of joining forces with another unpaired electron on another radical to form a bond. Two examples of radicals are ·OH (1, a hydroxyl radical), and ·CH3 (2, a methyl radical). The dot denotes the unpaired electron. In most cases, radicals are highly reactive and aggressively attack other species in order to use their unpaired electron to pair with an electron on the second species and so form a bond. The most primitive type of radical reaction is simply the clunking together of two radicals, each donating its unpaired electron to the formation of an electron-pair bond, as in the combination of two ·CH3 radicals to form ethane, CH3–CH3, 3. Some species might have more than one unpaired electron that they can use for biting into other molecules. If they are double-fanged, the most common case after ordinary single-fanged radicals, then the species is known as a ‘biradical’. To continue the partnering analogy: the two electrons cohabit but are platonic in their relationship. A very important example is an oxygen atom, O, which is a biradical. For the purposes of this section I shall write it ·O· with two dots for its two relevant electrons. An O2 molecule is also a sort of biradical, so when I want to emphasize its radical nature I shall denote it ·O–O·. There are a lot of reasons why you should be interested in radical reactions. One is that, as I explained in Reaction 3, they take part in the combustion reactions of the everyday world. Combustion reactions include the reactions that take place inside internal combustion and jet engines and move us around the world. Radical reactions occur wherever there is fire. Because fire is sometimes unintended, if the reactions that contribute to it are understood, then better ways to control and quench it can be devised.

Civil Partnerships: Lewis Acid–Base Reactions

One of the most remarkable chemists of the twentieth century, Gilbert Lewis (1875–1946), who died in a rather peculiar event involving cyanide (which will figure further in this account) took the story of acids and bases that I described in Reaction 2, extended its reach, and thereby captured a further huge swathe of chemical countryside. As I remarked in that section, chemists seek patterns of behaviour, partly because it systematizes their subject but also because it gives insight into the molecular events accompanying a reaction. Lewis contributed greatly to this enlargement of chemistry’s vision, as I shall unfold in this section. I explained in Reaction 2 how Lowry and Brønsted had extended Arrhenius’s vision of acids and bases by proposing that all reactions between acids and bases involve the transfer of a proton (a hydrogen ion, H+) from the acid, the proton donor, to the base, the proton acceptor. For instance, hydrochloric acid, HCl, can provide a proton that sticks to an ammonia molecule, NH3, 1, converting it into NH4+, 2. The Lowry–Brønsted account of an acid–base reaction involves a proton as an essential part of the definition: if protons aren’t around, then Lowry and Brønsted are silent on whether a substance is an acid or a base. There are, however, many reactions that resemble acid–base reactions but in which no protons are transferred. I will give what might seem to be a rather esoteric example, but it makes the point in a simple and direct way, so please bear with me; you will soon see the relevance of this presentation to everyday life. The esoteric example I have in mind is a reaction in which a boron trifluoride molecule, BF3, 3, sticks to an ammonia molecule to form NH3BF3, 4. This reaction clearly resembles the proton transfer reaction in which H+ attaches to NH3 to form NH4+, but with BF3 playing the role of H+. Lewis brought these aspects together in a very simple idea in 1923, at about the same time as Lowry and Brønsted made their proposals. A base, he proposed, is any species that can use two of its electrons to attach to an incoming species.

Matter Falling Out: Precipitation

I shall now introduce you to one of the simplest kinds of chemical reaction: precipitation, the falling out from solution of newly formed solid, powdery matter when two solutions are mixed together. The process is really very simple and, I have to admit, not very interesting. However, I am treating it as your first encounter with creating a different form of matter from two starting materials, so please be patient as there are much more interesting processes to come. I would like you to regard it as a warming-up exercise for thinking about and visualizing chemical reactions at a molecular level. Not much is going on, so the steps of the reaction are reasonably easy to follow. There isn’t much to do to bring about a precipitation reaction. Two soluble substances are dissolved in water, one solution is poured into the other, and—providing the starting materials are well chosen—an insoluble powdery solid immediately forms and makes the solution cloudy. For instance, a white precipitate of insoluble silver chloride, looking a bit like curdled milk, is formed when a solution of sodium chloride (common salt) is poured into a solution of silver nitrate. Now, as we shall do many times in this book, let’s imagine shrinking to the size of a molecule and watch what happens when the sodium chloride solution is poured into the silver nitrate solution. As you saw in my Preliminary remark, when solid sodium chloride dissolves in water, Na+ ions and Cl– ions are seduced by water molecules into leaving the crystals of the original solid and spreading through the solution. Silver nitrate is AgNO3; Ag denotes a silver atom, which is present as the positive ion Ag+; NO3– is a negatively charged ‘nitrate ion’, 1. Silver nitrate is soluble because the negative charge of the nitrate ion is spread over its four atoms rather than concentrated on one, 2, as it is for the chloride ion, and as a result it has rather weak interactions with the neighbouring Ag+ ions in the solid.

Green Chemistry: Photosynthesis

Each square metre of the Earth receives up to 1 kW of solar radiation, with the exact intensity depending on latitude, season, time of day, and weather. A significant amount of this energy is harnessed by the almost magical process we know as ‘photosynthesis’ in which water and carbon dioxide are combined to form carbohydrates. Thus, from the air and driven by sunlight, vegetation plucks vegetation. That new vegetation is at the start of the food chain, for its metabolism is used to forge protein and, in our brains, drive imagination. There is probably no more important chemical reaction on Earth. A large proportion of solar radiation is absorbed by the atmosphere. Ozone and oxygen molecules absorb a lot of ultraviolet radiation, and carbon dioxide and water molecules absorb some of the infrared radiation. As a result, plants, algae, and some species of bacteria have to make do with what gets through and evolved apparatus that captures principally visible radiation. The early forms of these organisms stumbled into a way to use the energy of visible radiation, which arrives in the packets we call photons, to extract hydrogen atoms from water molecules and use them and carbon dioxide to build carbohydrate molecules, which include sugars, cellulose, and starch. The oxygen left over from splitting up water for its hydrogen went to waste. Most of the oxygen currently in the atmosphere has been generated and is maintained by photosynthesis since Nature first stumbled on the process about 2 billion years ago and thereby caused the first great pollution. That pollution, in Nature’s characteristically careless and wholly thoughtless and unplanned way, was to turn out to be to our great advantage. Photosynthesis begins in the organelle (a component of a cell) known as a ‘chloroplast’, so you need to poke around inside one if you are to understand what is going on. I shall focus on the light harvesting and the accompanying ‘light reactions’. What follows them, the so called ‘dark reactions’ in which the captured energy is put to use to string CO2 molecules together into carbohydrates, is controlled in a highly complex way by enzymes.

Seeing the Light: Vision

Now for that extraordinary and wonderful sense, vision. A lot of physics and physiology goes on between the object observed and the focus of its image on the retina of the eye, but the interface of the image with the brain is photochemical. About 57 per cent of the photons that enter the eye reach the retina; the rest are scattered or absorbed by the ocular fluid, the fluid that fills the eye and helps to maintain its shape. You need to know that the ‘rods’ and ‘cones’, the physical receptors distributed over the retina, contain a molecule called retinal, 1, which is anchored to a protein, opsin, to give the aggregate known as rhodopsin. Here the primary act of vision takes place, in which that rhodopsin absorbs a photon. Rhodopsin is the primary receptor for light throughout the animal kingdom, which indicates that vision emerged very early in evolutionary history, no doubt because of its enormous value for survival. Incidentally, a retinal molecule resembles half a carotene molecule, one of the molecules that contribute to the colour of carrots, which is why there is an at least apocryphal connection between eating carrots and improving one’s vision. Let’s stand almost literally eye-to-eye and watch what happens when a retinal molecule in your eye absorbs a photon that might have bounced off this page as you read it. I have indicated the shape of the opsin molecule by ribbons which show in a general way where its numerous atoms lie. The photon passes through your pupil, negotiates the ocular fluid, and plunges into the retinal hotspot of rhodopsin. We see it stir up the electron cloud of the long chain of carbon atoms in the tail of the retinal molecule. That stirring briefly loosens the double bond character of the links between the atoms, and the molecule snaps into a new shape with the carbon tail now straight. The storm in the electron cloud subsides and all the bonds are restored, but now the retinal molecule is trapped in its new shape.