Like Clockwork

By David Alan Walker

The angels all were singing out of tune And hoarse with having little else to do Excepting to wind up the sun and the moon Byron

Introduction
Pray my dear, quoth my mother, have you not forgot to wind up the clock? Laurence Sterne
Once upon a time everything ran like clockwork; or so it seemed. Now, very little does; not even clocks. There is no longer much need to wind up clocks and watches. The hand-wound gramophones of my childhood have long since gone to antique shops. But, if they are to run at all, such things still need energy. Almost invariably, be they new clocks, cars, computers, or old gramophones, rabbits or people, their energy comes from the same source. Hence the titleLike Clockwork. And what is it about? It is to do with where our energy comes from, how we get our hands on it and what happens in consequence. Well, yes, I dare say it also owes a little to The Blind Watchmaker but what is wrong with that?

Chapter 1

Winding the Mainspring

Winding the Mainspring

I live in Biddlestone, an English village seven miles to the south of the Scottish border. It lies very close to the Harden Quarry, certainly too close for comfort.
No. 6 Biddlestone Village with Harden Quarry in the background

The history of the manor of Biddlestone is rather difficult to unravel for, not withstanding the oft-quoted copy of the grant of Vissards lands to Sir Walter Selby, knight , by Edward 1., dated October 24, 1272, it is somewhat puzzling and disappointing. David Dippie Dixon, 1903

Chapter 1

Robin Hill

Despite its modest six houses and a mere handful of residents, Biddlestone has two claims to fame. Reputedly, when Sir Walter Scott stayed with the Selby family at the old hall, which once graced the nearby slopes, it prompted him to invent Osbaldistone Hall in Rob Roy. Secondly the quarry, which provides the village with more than its fair share of noise and dust, is renowned for the red stone which it exports as far afield as Japan. Nearer to home, this stone paves The Mall, the London avenue, which leads from Admiralty Arch to Buckingham Palace. Red stone is not all that unusual but that from Harden Quarry is undoubtedly special. I once took a piece to show to Robin Hill, doyen of photosynthesis and my scientific mentor for 35 years. How did it become so oxidised? he wondered. Neither of us ever answered that question but it was typical of the man and it relates to a matter central to our very existence.

Robert Hill 1899- 1991

Robert Hill will always be remembered for his fundamental contributions to the study of Photosynthesis ----He was almost invariably known as Robin, by family, friends and colleagues alike He is perhaps best known for the Hill Reaction and the Zscheme which provided a thermodynamic framework for the whole electron transport system of the chloroplast and thus added an extra dimension to the description of electron transfer. The Z-scheme has stood the test of time and repulsed all attempts, including those of Robin himself, to over turn it. ---D. S. Bendall (1994)

We are mostly aware, if only subconsciously, that iron can turn red when exposed to oxygen (O2). Rusting iron is common enough. In school we learn that blood is red because of its haemoglobin (which contains iron, Fe).

Chapter 1

Oxidation/Reduction

Ha e m

We are also told that blood is redder as it leaves the lungs than it is on its return journey, stripped of much of its oxygen. This sort of thing has been going on since very early in biological time but right at the beginning there was plenty of iron and no oxygen. Then, as the first green organisms evolved, and oxygen was produced, the world went rusty.

Oxidation and Reduction

Oxidation is a familiar concept. At least in the everyday sense, it simply means combining oxygen with something. When we burn things we oxidise them. When we make toast we oxidise bread a little. If we burn the toast we oxidise it a bit more. When we eat the toast our bodies continue the process of oxidation. If we leave a piece of unprotected iron out in the rain it rusts. Iron (Fe) atoms react with oxygen molecules (O2) in the air to form molecules of iron oxide (Fe2O3) The weights of two iron atoms and three oxygen atoms give the weight of one molecule of iron oxide. The atomic weight of iron is fifty-six, and the atomic weight of oxygen is sixteen. The molecular weight of iron oxide is therefore one hundred and sixty.

Chapter 1

Rusting Iron

56 + 56 + 16 + 16 + 16 = 160 of which 2 x 56 =112 is iron and 3 x 16 = 48 is oxygen. As a percentage, 70% (112/160 x 100) of rust is iron and 30% (48/160 x 100) is oxygen So, if we were to start with seven grams of iron, we would eventually have ten grams of rust. Although the percentages would differ when oxygen is combined with other substances there is always an increase in weight. This may not always be immediately apparent. If we set fire to a piece of newspaper we start with something and are seemingly left with next to nothing. This is because most of the newspaper is made of carbon (C) and most of the end product of combustion is an invisible gas, carbon dioxide (CO2). Nevertheless, were we able to weigh the CO 2 (molecular weight = 44) we would find that it was substantially heavier than carbon (atomic weight = 12). This makes it easier to appreciate why the reverse of oxidation is called reduction. As in everyday speech, reduction implies a decrease, a diminution. In chemistry, if oxygen is removed from a molecule there is a readily discernible loss in weight. Just as iron can be oxidised, so can rust (i.e. iron oxide, Fe2O3) be reduced to iron. In the process of smelting, iron ore is heated with a source of carbon such as charcoal. The oxygen atoms migrate to the carbon atoms so that they become molecules of CO2, and iron is left behind. 2Fe2O3 + 3C 2Fe + 3CO2

Every ten grams of iron oxide reduced yields seven grams of metal. Until green organisms started to produce oxygen, the iron in Earths crust existed as the metal. Then, of course, it started to rust. Only when the iron exposed to the atmosphere had rusted did oxygen levels build up towards the levels that we enjoy today. For many thousands of years people have been putting this process in reverse, smelting iron to make implements. At first this had little impact on the environment but, even by the sixteenth century, Queen Elizabeth the First of England, anxious about the wood needed to build her ships, sought to restrict charcoal burning. When new machines were invented in the early nineteenth century the release of CO2 accelerated considerably. Steam engines made it easier to make more iron and more steam-driven machines. Farm machines made it possible to grow more food. More food made it possible to feed more people. More people made more machines. More machines produced even more carbon dioxide.

Chapter 1

Energy

By now, oxidation of carbon has increased to such an extent that it is affecting global climate. So far we have considered oxidation and reduction only in terms of addition and removal of oxygen but oxygen may not be involved in either. Oxidation may result from the removal of hydrogen atoms or electrons; reduction from the addition of hydrogen atoms or electrons. The one common feature in all of these processes is movement of electrons. It also follows that if something is oxidised something else must be reduced (and vice versa).

Energy
It would help at this point if you and I had Ph.D.s in physics but, since I dont, I shall just have to do my best and, if you dont, we shall just have to sit around together and see what sense we can make of it.

For starters, lets see what mutual comfort we can extract from Albert Einsteins famous equation: E = mc2

Chapter 1

Albert Einsteins Equation

This embodies the concept that energy (E) and matter (m) are interconvertible. They can be converted from one form into another but neither can be destroyed. So we can make a tree into a piece of furniture or we can cut it into little pieces or we can burn it. Even if we burn it, however, it hasnt been destroyed. At least not in the fullest sense of the word. It has been changed beyond recognition, its constituents scattered to the winds. Where there was once a nice piece of wood there may now be little more than a pile of ash, some more carbon dioxide in the atmosphere and a lot of hot air. The atoms that once made up the tree still exist. They have been spread around and combined with other things to make new molecules but not one atom has actually gone forever. Similarly, there must have been some sort of latent energy within the tree and burning it has converted this chemical energy into heat and light. So one form of energy, like one form of matter, was changed into other. According to Einsteins equation, what doesnt change in all of this, is the speed of light, c. What is more, neither m nor E can be destroyed but only converted into one another. It follows that, if m gets smaller, E must get bigger (and vice versa). This, as you might guess, has a lot to do with where we get our energy from, and with life, the universe and the beginning of things. There are relatively recent (and reasonably well understood) beginnings and beginnings so distant that they can scarcely be contemplated. So for now, let us suppose that our solar system already exists and that planet earth, devoid of all life except for a few bacteria, is circling around the sun. Earths core is still very hot, maybe 4200 degrees C, as volcanoes and hot springs and the like, periodically remind us today. Heat radiates out through the crust which, by now, would have cooled to about -35oC had it not been for the blanket of water vapour and carbon dioxide wrapped around it and a daily influx of radiant energy from the sun In Einsteins equation, c is the speed of light; the unchanging constant. In the sun, when four atoms of hydrogen fuse to form one atom of helium there is a decrease in mass. One atom of helium weighs slightly less than four atoms of hydrogen. The decrease in mass is only 0.7% but, the corresponding increase in energy is very large. So much so that, when one gram of hydrogen atoms give rise to helium in this way, the energy released is equivalent to burning 15,000 kilograms of fuel oil. This is the biological mainspring. This is where our energy comes from. The next question is how this energy gets to us from the sun and is then converted into forms that we can use. Before we can answer this we really need to venture a little further into the world of atoms and molecules. By now, few of us will remember the Hindenburg disaster and the sad fate of its British counterpart, the R100. I remember as a child, being called to the

Chapter 1

Molecular Structures

window by mother to get a glimpse of the R100 as it flew over. These huge airships lifted machinery and people into the air because they where filled with hydrogen. Molecular hydrogen (H2) is fourteen times lighter than the molecular nitrogen (N2) which constitutes about 81% of our present atmosphere. Atomic hydrogen (H) is four times as light as the helium (He) which results from nuclear fusion of hydrogen ions (H+) in the sun. Of course an awful lot of hydrogen on this planet is combined with other atoms and molecules. The most familiar of these substances is our old friend H2O; two atoms of hydrogen (H) combined with one of oxygen (O) to give water. That was the big problem for the Hindenburg because hydrogen gas (H2), which is very good for lifting balloons into the air is also very keen to combine with O2 and, when it is permitted to do so in an uncontrolled fashion, the resulting explosion or conflagration can release a great deal of heat in a very short time. Helium, on the other hand, which is not so different from hydrogen, at least in the sense that it is also good for putting into balloons, is not at all anxious to react with O2 . Why is this? Well if we side step this question we can respond by saying that this is an intrinsic quality of the elements concerned. Iron rusts, gold doesnt. Of course intrinsic qualities of this sort have to do with molecular structures and, in the case of O2 and H2, the structures are such that these two molecules lie at opposite ends of a scale. Just as in a familiar temperature scale, to do with freezing and boiling water, 0oC is cold and 100oC is hot, oxygen is very oxidising and hydrogen is just the opposite - i.e. very reducing.
It is my opinion that the student of chemistry may well benefit from the study of modern structural chemistry early in his career; for example, as an undergraduate. I have thought it wise to change the character of this book somewhat in order to increase its value to such a student. The theory of the chemical bond, as presented in this book, is still far from perfect. Most of the principles that have been developed are crude, and only rarely can they be used in making an accurate quantitative prediction. However, they are the best that we have, as yet, and I agree with Poincare that it is far better to foresee, even without certainty, than not to foresee at all. Linus Pauling 1959

Chapter 1

Breaking Bonds

In this context, these particular opposites strive to get together and, when they combine, they generate a great deal of heat. This brings us to a concept that we cant escape any longer.

Chemical Bonds
When either similar or dissimilar atoms combine with one another, to form molecules, they are then held together by chemical bonds. Energy is released as these bonds are formed. Conversely, energy (bond dissociation energy) must be consumed if these bonds are to be broken (Chap 3).

Breaking bonds takes energy

There are different sorts of bonds, some weak and some strong. In water, hydrogen is bound tightly to oxygen. If we mix together two parts of hydrogen and one part of oxygen and ignite the mixture the release of energy is immediate and considerable. In our vehicles, our aircraft, our turbines, we contain the violence of such explosions and use them to drive machinery. In our own bodily metabolism, hydrogen can be joined to oxygen in very controlled and gentle fashion. Nevertheless, whether we are thinking about energy in relation to people; in relation to other living organisms or our environment at large, this is what it all boils down to in the end. It all starts up there in the sun as hydrogen atoms fuse to form helium in a nuclear furnace.

Chapter 1

Atomic Structure

The manner in which the Suns energy, gets to earth, as light, is complex (page 20) but it works. After that, green organisms use this energy to take hydrogenoxygen bonds apart and people (who are much better at this than the Kings men who failed Humpty Dumpty) proceed to put these bonds back together in a variety of ways.

..the release of energy is immediate and considerable

Atomic Structure
What does an atom of hydrogen look like? No one really knows. We can see some very tiny things with the help of a good microscope but atoms are far too small to be seen this way and, although there are other ways of visualising very tiny things, there is a big difference between visualising what something is like and actually seeing it. Never mind, physicists have a good idea of what an atom is like even if they cant see it. Moreover, they have never been afraid of drawing pictures. Im going to take liberties here and offer an older and less satisfactory picture than a contemporary physicist would like. Still, it was good enough in its time and it will do for our present purpose. It is called the BohrRutherford atom (after two famous, but no longer living, physicists) and, in the

Chapter 1

J. J. Thomson

10

case of hydrogen, it is very easy to visualise even without a drawing, because it is a bit like a planet with a single satellite in orbit around it or an Olympic athlete swinging the hammer at the end of a chain..

An atom of of hydrogen seen in human terms, the nucleus of the athlete is a proton and the orbiting hammer an electron.

The date was Friday, April 30, 1897. The place was the lecture theater of the Royal Institute of Great Britain. By the desk in the center of the theater stood a man with a pince-nez, a straggling mustache, and a receding hairline. He was Joseph John Thomson, director of the Cavendish Laboratory . he had made a surprising discovery. He had found a particle of matter a thousand times smaller than the atom. Today we call them electrons, from the Greek word for amber. .. Janine Adler Parker
The proton is 500 times larger than the electron. The proton can exist by itself and it is then often called a hydrogen ion and written H+. The electron, tiny

Chapter 1

Orbitals & Energy Levels

11

by comparison (mass = 9.109 x 10-31 kg) can be thought of simply as a negatively charged particle of electricity (e-). When we throw a switch, and have electric currents flowing through wires, these currents are made up of the selfsame electrons. Energy has to be expended by the athlete to swing the hammer about his body and, the longer the chain, the more energy is required to swing it at the same rate. Similarly, the electron may be considered to circle the nucleus at a specific energy level. More energy would be required to lift it further from the nucleus and energy would be released if it dropped to a lower level. Until he releases it, the chain binds the hammer to the athlete. Similarly, electrons circling an atomic nucleus are maintained in orbit by the electrical attraction between positive and negative charges. When the athlete finally releases his grip, the hammer may a fly a great distance. Electrons can also exist as independent entities and, indeed, electron transport (electricity) is of fundamental importance to most aspects of biology and physics. It is central to the transfer of energy. For example, in a metal conductor (e.g. a copper wire), electrons can separate from their parent atoms and move freely through the metal, while the atoms which have temporarily lost their electrons, now positively charged, remain in a fixed position. The conductor will offer resistance to this flow of electrons as they collide with stationary atoms in the metal. In such a collision, the electron will transfer the energy of its motion to the atoms in the conductor. The vibration of these atoms manifests itself as heat. For this reason, conductors tend to become hot as electrons flow through them as in electric fires or heating elements. The thinner the conductor or wire, the greater the frequency of collision and the greater the internal generation of heat. Very thin wires may become so hot that they burn (like overloaded fuses) or, if there is no oxygen surrounding them, become incandescent (as in electric lights). We are all very familiar with these phenomena just as we are aware that we live in an electronic age. Telephones, television, radio, computers all rely on electron movement. Less obviously, perhaps, we and other living organisms depend on electron transport for most of our functions and, in many respects, electricity, electron transport and oxidation/reduction are all part and parcel of the same thing. Given this, it is hard to imagine a parcel more worth opening and looking in to.

Chapter 1

Transferring Hydrogen Atoms

12

Making omelets and moving hydrogen atoms

In plants and animals, oxidation often involves the actual addition of oxygen. Frequently, however, the oxidative reactions which constitute metabolism proceed by removal of hydrogen. If we represent a metabolite (i.e. .a compound such as a sugar, undergoing metabolism) by MH2 we can write an equation MH2 + A M + AH2 In which two hydrogen atoms are transferred to a hydrogen acceptor (A) which becomes reduced. As we are so often reminded, we cant make omelets without breaking eggs. Similarly, since hydrogen atoms (H) are made of protons (H+) and electrons H
Hydrogen atom

H+ + eproton electron

(e-), it is not possible to move hydrogen atoms without moving electrons.

Transferring Hydrogen Atoms

Accordingly, electrons are transferred, or transported from the substance which is being oxidized to the substance which is being reduced. In metabolism, there are often long sequences, or chains, of hydrogen (or electron) acceptors. It is partly for this reason that burning a sugar in respiration, although it eventually involves the addition of oxygen, does not liberate energy quite so dramatically as it does if sugar is burned on a fire.

Chapter 1

Electron Transfer

13

Instead, energy is released in a trickle rather than a flood. In addition, much of the energy is not released at all, immediately, but is conserved, as chemical energy, in molecules of ATP ( page 37).

Electron Transfer
So hydrogen transfer always involves electron transfer (because a hydrogen atom contains an electron) but electrons can also be transferred by themselves i.e. without an accompanying hydrogen ion, or proton (H+). Both in respiration and in photosynthesis, cytochromes of different sorts are important electron carriers (constituents of the electron transport chain. Cytochromes are a type of protein which, like haemoglobin, contain iron (Fe) in the heart (page 3), of their molecular structure. This iron can be represented as Fe++ (in its reduced or ferrous state) and by Fe+++ (in its oxidized or ferric state). The increase in the number of positive signs (in this case from two to three) indicates the loss of one electron just as it does in H+). (a hydrogen atom which has lost an electron and therefore one negative charge). When a reduced cytochrome (Cyt Fe++) is oxidized (to Cyt Fe+++), only electrons are transferred and the reduced electron acceptor can be written A- to indicate that it is now the proud possessor of an electron carrying a negative charge. Cyt Fe++ + A Cyt Fe+++ + AAs it happens, electron acceptors are particular about what they will, or will not, accept. Some, like cytochromes, will only accept and donate electrons. Others, like quinones (which are also important electron carriers) like to have both an electron and a proton; i.e. they are electron carriers only in the sense that they are hydrogen carriers and because accepting a hydrogen atom necessarily involves the acceptance of an electron. Much of this account may seem unnecessarily detailed and I an not one for getting into fine structure for its own sake In this instance, however we really do need to get into the detail if we are to make any sense at all of how it is possible to conserve energy in a chemical form. If a cytochrome is offered a hydrogen atom (H) by a quinone (or a quinol as a quinone is more properly

Chapter 1

Electron Transfer &Chemiosmosis

14

called when it is in the reduced state) it can only accept the electron (e-) which is a constituent of that hydrogen atom.

Hydrogen Atoms offered, only electrons Accepted

The proton (H+) is left behind and the surrounding solution becomes more acidic (page 35) because of this increase in hydrogen ion concentration. Conversely, if the cytochrome seeks, in turn, to offer its newly acquired electron to yet another acceptor which is only prepared to accept hydrogen atoms, a proton must be taken up from solution along with each electron accepted.

Electron offered, proton taken up to complete hydrogen atom demanded

When such acceptors are contained within a membrane this can result in protons being moved from one side of the membrane to the other during electron transport. This is the essence of Mitchells Chemiosmotic Hypothesis which offers an explanation of the way in which proton gradients are established across membranes and how these gradients are then used in the synthesis of from ADP and inorganic phosphate (see pages 37 et seq).

Chapter 1

Oxidation & Electron Transport

15

Oxidation always involves electron transport. Electrons are transported from the atoms or molecules which are being oxidised to corresponding acceptors which therefore become reduced (and, in the sense that they have acquired electrons, more negative).

Oxidation always involves electron transport

However, it is not immediately obvious why this is equally true when we set light to a piece of wood or paper. What predominates in these circumstances is the addition of oxygen to carbon to give carbon dioxide. Oxygen does not normally exist as a free atom (O) but as an oxygen molecule (O2) so we can write an equation C + O2 CO2 In its outer orbit (electron shell) an atom of carbon has four electrons and an atom of oygen has six. A molecule (2 atoms) of oxygen shares two of its electrons with its partner (O=O) so that they both have eight electrons (x) in their outer shell. On oxidation, an atom of carbon (C) comes to share its electrons (x) with those of each atom of oxygen so that a molecule of carbon dioxide (O=C=O) has a similarly stable complement of eight electrons in its outer shell. Nevertheless the shared electrons are drawn towards the oxygen. Thus, in this and similar oxidations, the electrons are transported within the molecule; away from carbon towards oxygen.

carbon atom

oxygen molecule

carbon dioxide

This is because oxygen is intrinsically more attractive to electrons (more oxidising) than carbon. The extent to which substances attract or repel electrons (their oxidation/reduction potential) is very important in biology and helps to determine the manner in which electron carriers are organised within membranes.

Chapter 1

Summary

16

Summary
Breaking chemical bonds always requires energy and energy is always released when chemical bonds are formed. In living organisms, oxidation and its converse reduction, are of paramount importance. One cannot occur without the other. As one substance is oxidised another must be reduced and vice versa . Common to both, is the transfer of electrons. Electrons move away from a substance being oxidised, towards a substance being reduced.