Fe (II) enzymes Zn (III enzymes M g ATP
Cu oxidases Mo oxidases (flavins)
Superoxide generator (Fe) (flavin)
Fig. 7.5. A schematic indication of some of the different membrane separated compartments in an advanced cell. PEROX is a peroxisome; MITOCHLORO is either a mitochondrion or a chloroplast; CHROMO is a vesicle of, say, the chromaffin granule; ENDO is a reticulum, e.g. the endoplasmic reticulum. Other compartments are lysosomes, vacuoles, calcisomes and so on. Localised metal concentrations are shown. The figure is of a transverse section. To appreciate a cell fully it is necessary to have serial plane sections in parallel along the z-direction.
vesicles nor their apparently "purposeful" design for protection. The endoplasmic reticulum is also used for storage of calcium, and other vesicles, the vacuoles, are used to store or remove heavy metal ions, the value of which is seen in Section 7.12. All such features seem to appear suddenly in the record of life. As we observed before, the absence of well-defined precursors is often a grave problem in evolutionary connectivity.
There are other compartments, called peroxysomes, in which peroxide is produced to destroy unwanted bacteria or large particles. They remain a part of the defense mechanisms of later eukaryotes. This is another example of the advantage of the eukaryote compartments - keeping the cytoplasm as free as possible from risk while introducing new, especially high redox potential, chemistry, compare the advantages of the periplasm of aerobic bacteria.
As stressed earlier, the vesicle and organelle membranes are in themselves extra compartments, as is the cytoplasmic membrane containing pumps and enzymes as well as detectors/receptors. It is important to observe that the vesicle membrane pumps face in the inverse direction to those of the outer membrane, so that vesicles take up free Ca2+, CI", Na+ and Mn2+, often protons, and later excess free Ni2+ and Zn2+, for example. Of special interest are the so-called V-type ATP-ases, some of which pump protons. Thus the interior of vesicles can be of much lower pH than the cytoplasm, as low as pH 2. This pH hydrolyses many proteins and hence is helpful in digestion. The V-type ATP-ases that pump ions are strongly "irreversible" in contrast with the F^-type ATP-ases of organelle energy transduction (see Appendix 4C). The compartments often have therefore a very novel inorganic content giving rise in part to the novelty of eukaryote chemotypes. Each also have a controlled protein and modified protein content, so that there has to be designed trafficking of proteins directed selectively to many compartments. Now all these compartments have to be managed and shortly we turn to communication using messengers between them and the cytoplasmic components and especially DNA and RNA. We shall see that these compartments aid response to external events, providing a means of protection and of selection of environments. A general property of all the eukaryote membranes appears to be flexibility but use of them requires mechanical devices and energy often linked to the internal filaments.
Before we describe the chemistry of the compartments involved, note that like prokaryotes, a number of oxidative enzymes are found in the cytoplasm but they do not release damaging chemicals (see Section 6.10). We also observed that such kinds of kinetic "compartments" are not enclosed by physical limitations such as membranes. We have also mentioned that increased size itself makes for kinetic "compartments" if diffusion is restricted. In this section, we see many additional advantages of eukaryotes from those given in Section 7.4. How deceptive it can be to use just the DNA, the all-embracing proteome, metabolome or metallome in discussing evolution without the recognition of the thermodynamic importance of compartments and their concentrations? These data could be useful both here and in simpler studies of single-compartment bacteria even in the analysis of species but not much information is available.
7.6. Reproduction, Growth and Form
A further set of complications are involved in the simple description of eukaryotes. They reproduce sexually by a combination of male and female gametes (half-cells); they grow and change form and their form may be mobile, especially that of the more animal-like, as animals are motile in a directed, sensed, way. We cannot describe the advantages and disadvantages of these features here, but the reader should be aware of the huge diversity of patterns of growth, of form and of behaviour of unicellular eukaryotes. We can give them morphological labels and analyse their genotype, but we are far from being able to discuss their chemotypes today except in the broadest groupings, plants, fungi and animals. In fact, simple analytical data of element content are not available for most cell compartments. However, given our stress on flowing systems, we can note some additional general features of these single-cell eukaryotes that appear during growth. In many, if not in all, of the adult cells there is cytoplasmic directed flow for the distribution of chemicals. This flow occurs over or through the organisation of larger units, filaments and vesicles, but all these units can be re-arranged to increase efficiency under a given circumstance. The state of energisation of mitochondria and thylakoids clearly alters their shape within the cell. We stress that as chemotypes the plant-like organisms are individually very efficient in capturing light while fungal- and animal-like organisms are very efficient in digestion, both increase efficiency by circulation of material as well as by readjustment of form, external and internal, opposite circumstances. Digestion requires capture of food, and here motility of the whole cell or of parts can be aids as we see in the way an amoeba can catch other organisms. We deal with these topics in somewhat more detail in Section 8.6.
An interesting problem is how does the final internal organisation and external form it arise? There is an undoubted contribution from the genetic information expressed as proteins. However, as we have seen in Chapter 3, form is dependent on physico-chemical fields, the environment, and transfer of energy and information between all the different flows of material and energy to which a eukaryote but not a prokaryote cell is sensitive. A considerable part of spontaneous formation of dynamic structure lies in this interaction with the environment, i.e. its information content and the metabolism of organisms which does not involve genetic (DNA) response of necessity. Another part concerns the degree of flexibility of internal self-organisation, for example, of proteins once produced. This question of the involvement of factors other than those directly genetic has exercised scientists for many generations and is not yet solved (see Thompson D. and also Harold F. and references therein in Further Reading).
Finally, no matter how the organisation arose, it has to be related to the restricted and controlled pathways, new and old, and they must be autocatalytic since their active species, proteins, are made from their own substrates or ions. There is a unity of purpose in the cell to aid survival.
We now turn to the major purpose in this book - the description of these organisms in chemical terms, their chemotypes.
7.7. The Threat of Dioxygen : The Chemistry of Protection
Looking again at the evolution of eukaryotes and its link to the increasing concentration of molecular oxygen, we note that the threat from this gas was to the more vulnerable reactants in the cytoplasm as in earlier prokaryote cells. Outstanding amongst these are the Fe/S, pterin and flavin containing enzymes inherited from prokaryotes. As we have stated, protection is the first way forward to assist survival and, as in aerobic prokaryotes, eukaryotes have devices for nullifying the greatest danger from 02 in its reduced forms, 02~ and H202. A very interesting fact is that while prokaryotes remove 02~ using an iron or a manganese superoxide dismutase and both mitochondria and chloroplast still do so, the cytoplasm of all eukaryotes has a superoxide dismutase containing copper and zinc. Now divalent iron and manganese enzymes dissociate readily, but since divalent copper and zinc enzymes do not (see Irving-Williams series in Section 2.20), the latter are to be preferred in this function. Zinc and copper binding also stabilises protein folds, and so bound forms of these metal ions are of low risk. Note that as we have stressed, the metals, zinc and copper, are late additions to the environment, requiring the oxidation of their sulfides by oxygen to increase their availability, so that these enzymes indicate again the late arrival of eukaryotes and the increased complexity of their chemistry. By contrast, prokaryotes and eukaryotes have similar systems for the removal of H202 by iron-containing catalases. We draw attention to the development of H2Oz into a very useful protective chemical in vesicles (see peroxysomes above), especially in plants, and superoxide is also employed in this manner here and there in animals and plants. These are clearly examples of the development from a poison to a useful reagent. In all the above we see again a further advantage of eukaryotes in keeping oxidation reactions away from the cytoplasm generally, only allowing them there in protected enzymes, while using them extensively in vesicles and outside cells.
The vulnerability of Fe/S, flavin and pterin enzymes to molecular oxygen did not just lead directly to a flavin Fe/S based way of removing this threat, but it also led, as stated above, to use of oxygen, for example, in the production of cholesterol (Figure 7.6), by a pterin protein. This appears to be a vital contributing step to evolution. In this oxygen chemistry, we see again the progression where the earliest step was the removal of 02 via NADH and flavins or pterins:
We have observed this sequence earlier and will do so later, and it probably applies to the uses of both zinc and copper, in all aerobes, and to calcium generally (Section 7.11), and even to sodium and chloride (see Chapter 9), and it may even apply to the impact of light (see Chapter 11).
The difficulty of handling oxygen appears to have led on the other hand to another case of cooperation in metabolism but now in true symbiosis. The vast majority of eukaryotes cannot metabolise N2 and rely on bacteria for a conversion
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