Prokaryotes controls

The nomenclature for transcription factors is confusing. Depending on their mode of action, various terms are in use both for the proteins themselves and for the DNA sequences to which they bind. If a factor blocks transcription, it is referred to as a repressor otherwise, it is called an inducer. DNA sequences to which regulatory proteins bind are referred to as control elements. In prokaryotes, control elements that serve as binding sites for RNA polymerases are called promoters, whereas repressor-binding sequences are usually called operators. Control elements that bind activating factors are termed enhancers, while elements that bind inhibiting factors are known as silencers. 

In this chapter we describe the basic principles involved in the controlled production and modification of two-dimensional protein crystals. These are synthesized in nature as the outermost cell surface layer (S-layer) of prokaryotic organisms and have been successfully applied as basic building blocks in a biomolecular construction kit. Most importantly, the constituent subunits of the S-layer lattices have the capability to recrystallize into iso-porous closed monolayers in suspension, at liquid-surface interfaces, on lipid films, on liposomes, and on solid supports (e.g., silicon wafers, metals, and polymers). The self-assembled monomolecular lattices have been utilized for the immobilization of functional biomolecules in an ordered fashion and for their controlled confinement in defined areas of nanometer dimension. Thus, S-layers fulfill key requirements for the development of new supramolecular materials and enable the design of a broad spectrum of nanoscale devices, as required in molecular nanotechnology, nanobiotechnology, and biomimetics [1-3]. 

Studnicka, G. M. (1987). Nucleotide sequence homologies in control regions of prokaryotic genomes. Gene 58, 45-57. 

Physically, all these prokaryotes are small, diameter about 1.0 pm and are of rigid, simple shape. They usually have little or no internal structure so that chemical diffusion is relatively rapid. Secondary compartments are rare but vesicles and vacuoles (even nuclei) are found in a very few large bacteria. We shall see that all the prokaryote cells have controlled, autocatalytic, internal metabolism, but are relatively little affected by external circumstances, except by shortage of nutrients. 

The above description provides a possible starting background for the description of the beginning of cellular chemotypes, prokaryotes, but even this is less complicated than the only cells for which we have evidence since they have at least two additional groups of more sophisticated chemicals - coenzymes (see Tables 5.3 and 5.4) and certain metal cofactors, which we presume were additions to the most primitive cells. After we have described them, we shall return to the problem of cellular (cytoplasmic) organisation. Note that coenzyme novelty is not in basic pathways but in control of rates and in energy management. 

Some lines of prokaryote development are shown in Table 6.2 with a guide to oxidation/reduction potential ranges in Table 6.3. In all these and further changes the novel chemistry has to be built into the cooperative whole (see Section 3.9). Note again the necessity that the novel features must become part of a controlled autocatalytic restricted set of reaction paths, which become general to any further evolution. 

From this account of the protoaerobic and aerobic prokaryotes it is clear that the change of the environment from a moderately reducing to an oxidising environment with the need to maintain the reductive metabolism of the cell cytoplasm placed a burden on what was possible for these small cells. We describe another way round these problems other than protected cytoplasmic reactions before we discuss the extra problems of controlling the new activities. 

Turning to the additional metabolism that needs extra controls there was little change in basic prokaryote reductive metabolism in the cytoplasm from anaerobes to aerobes but as stated above there were added several oxidative reactions and... 

Prokaryotes Water (Cytoplasm) Coenzymes Substrates, Mg2+ Controls Fe2+ c-AMP, ATP milliseconds... 

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