4.1. Introduction 125
4.2. Organisms: Their Classification as Thermodynamic Chemotypes 127
4.3. Organisms: Their Generalised Element Content 131
4.4. The Functional Value of the Elements in Organisms: Introduction to
Biological Compounds 137
4.5. Non-Metal Chemistry and Its Basic Biological Pathways: Coding 138
4.6. Informed Systems of Organic Molecules 149
4.7. Pathways and Efficiency 153
4.8. Structures and Maintained Flow: Containment 154
4.9. The Selection of Coded Molecules: DNA(RNA) 156
4.10. RNA and the Possible RNA World 157
4.11. Proteins: Folding, Catalysts and Transcription Factors 160
4.12. Proteins: Biological Machines in Water 164
4.13. Proteins in Membranes 165
4.13.2. Electronic and Electrolytic Devices, Energy Transduction 167
4.14. Summary of Non-Metal Functions in Cells 168
4.15. Why were Metal Ions Required? 170
4.15.1. Reduction and Oxidation Catalysts 170
4.15.2. Energy and Group Transfer 172
4.15.3. Condensation and Hydrolysis Reactions 173
4.15.4. Osmotic and Electrolytic Balance in Cells 174
4.15.5. Controls of Metabolism 175
4.15.6. Preventing Inhibition: Rejection 175
4.16. Combining Metal and Non-Metal Chemistry: Structures and Activities 176
4.17. The Biological Properties of Hydrogen 177
4.18. Cell Organisation and Constraints: Equilibria 178
4.19. Kinetic Controls and Networks and Their Energetics 179
4.20. Summary 181
Appendix 4A. The Magnitudes of Equilibrium Constraints in Cell Systems 183
Appendix 4B. Equilibrium Redox Potential Controls 186
Appendix 4C. Molecular Machines - Efficiency and Effectiveness 187
References to Appendix 4C 190
Further Reading 191
In Chapter 1 we have given an outline of the geochemistry of the Earth and its evolution in chemical terms. This is purely a limited inorganic chemistry at or moving towards equilibrium in the vast majority of its surface activities. The Earth is irradiated by the Sun's energy, but this has had little direct effect on geochemical inorganic activity except through the cycle of water and its consequences and later the creation of the ozone layer. It has, however, contributed to an approximately fixed temperature on Earth's surface even while some gases were being lost continuously (Table 1.1). There are then very few minerals in energised states on Earth's surface due to the direct effect of the Sun's radiation. Some energised minerals have been thrown up mainly by volcanic activity and they were one possible immediate source of the required energy for the first forms of life. However, the Sun's radiation has indirectly affected slowly and considerably Earth's surface chemistry through the chemical changes produced in and by living organisms, which is mainly "cellular" organic compounds with the slow release of dioxygen giving products of its reactions in the environment. There has also been the deposition, on death of organisms, of debris such as organic compounds in soils, and as gas, coal and oil. We described the environmental chemical changes from the primitive to the present day times in Section 1.14. Before we explained the origin of dioxygen and organic compounds in Chapters 2 and 3 we needed to discuss in brief the important chemical principles of non-equilibrium states of energised chemicals, pointing out that organic chemicals together with oxygen fall into this category. The organic chemicals were incorporated into cells together with many inorganic environmental elements generating the combination which produced life. To explain the differences between equilibrium and non-equilibrium states we also described in Chapter 3 the way energy interacted with matter to produce both stationary and/7owing energised chemicals, that is, energised with respect to the original environment and even more so with respect to any changed environment produced by the flow. The major flow system for producing any such chemicals remains that of living organisms. In fact, they were the only such organic systems known until mankind developed industry. We stressed that we shall examine the surface geological and biological chemistry open to light and the atmosphere in this and in Chapters 5-10, and only in Chapter 11 do we refer again to other zones of the Earth.
Now in both Chapters 1 (on the environment) and 2 (on the major chemical reactions), the flows examined were the one-way (downhill energetically) transformations of energised chemicals in the direction of equilibrium though at intermediate steps material could be trapped.
These flows of chemicals can be in a steady-state condition, provided the reactants A + B + C (etc.) are part of a very large resource and the reaction is relatively slow. Energy, as applied here, that is even in laboratory organic chemistry, generally acted so as to increase the rate of reaction by increase in temperature. In Chapter 3, we also introduced uphill steady states of flowing chemicals taking up energy and these are a major part of the combination of interactive geochemistry and the biological chemistry of organisms. It is the biological chemistry of particular components of cells and their interactions, produced by this energisation, that are to be described as an outline in this chapter. We shall be dealing here with components of biological chemistry as a whole and we shall not refer to any particular groups of organisms or to the divisions of space in them, i.e. compartments, which are so much a part of evolution, leaving those matters to Chapters 5-9. Much of the chapter is therefore about the functions of particular units of cells and not of organised activity and is close in content to traditional molecular biology. We shall ask repeatedly about the suitability, i.e. fitness, of individual types of unit, nucleotides, proteins, metal ions and so on for the tasks they perform. We leave on one side largely geological chemistry much though this is a partner in life's evolution. From the outset we must stress that in contrast to the general chemistry described in Chapters 1-3, we have to see that biological chemical systems can only use geologically available elements and energy from two sources, the Earth and the Sun, and not the full ranges of either chemicals or energy resources open today for use by mankind (see Chapter 10).
To start our approach we divide this chapter into parts. In the first part we outline the general chemical element content of all organisms (Sections 4.2^1.4); next, we look at the uses of non-metal elements and their in small molecule combinations (Sections 4.5-4.8); while in the third part we extend this description to their major biopolymers (Sections 4.9-4.13). Section 4.14 is a summary of these sections. In Sections 4.15 and 4.16 we examine the metal ion content of cells and combinations of these ions with organic molecules. The final sections integrate these descriptions with those of the principles of bioenergetics outlined in Chapter 3.
4.2. Organisms: Their Classification as Thermodynamic Chemotypes
We observe immediately that all organisms are based on controlled energised chemistry essentially in physically confined and organised flow systems, that is, in cells. Elements are concentrated as free ions or in energised compounds in the cells. To this end, we shall describe cellular evolution as being at all times within an energised advancing environment (see Chapter 1). Now the organisms evolved (a) in chemical content and use of chemicals, (b) in the ways they obtained and used energy, (c) in the space they occupied, and (d) in their organisation. In Chapters 5-10 we shall examine evolution with a broad outlook following in order these factors, stressing the differences in the early and later prokaryotes, single-cell eukary-otes, multi-cell eukaryotes, animals with nerves, and mankind with respect to these four chemical and thermodynamic characteristics (see Table 4.2). Looking at all such organisms, either in parts or as a whole, one primary need for understanding by chemists is then their composition. This might appear to be an unreasonable approach in that every species is somewhat chemically different and especially since the conventional way of looking at organisms is by functional specialisation - for example, modern plants are stationary and photosynthetic while animals forage and digest. However, we shall find that even in this example, the plants use closely similar elements and compounds but in different proportions from those used by animals and by bacteria. Most importantly, we wish to examine if the whole of life and the development of its chemical properties, i.e. of all the organisms together, had one overall chemical compositional direction from the origin of life. By introducing this simplifying approach to chemical composition at first, we proceed to give at the end of this chapter a very general impression of the chemical thermodynamics of organisms in given environments.
Immediately we see that we cannot use the conventional ways of describing organisms, for example, by morphology (see Tables 4.1(a) and (b)), or by molecular
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