Some General Principles and Ground Rules

Foraging, broadly construed, is essentially the ‘input’ or resource acquisition function of the organism-as-system model presented in Fig. 1.2 of Chap. 1. Metabolic rules governing how energy sources and matter are acquired and processed underpin all organism functions, however, beginning with resource acquisition and ending with output of progeny. Metabolic rates largely determine the rates of most biological activities (Brown et al. 2004). Thus, before looking in more detail into the diverse lifestyles with respect to nutrition, we need to consider some common underlying processes and principles.

In an abiotic environment that is energetically disordered, living things maintain structural and functional order by converting energy from one form to another. The work done by cells operating as isothermal, homeostatic chemical engines includes such activities as biosynthesis, catabolism, osmosis and active transport, maintenance of concentration gradients, excretion, and mechanical work in the form of locomotion or contraction. In all organisms, the biochemicals and their reactions conform to chemical and physical ground rules pertaining to inanimate matter, as well as to rules governing how metabolites interact with each other in living cells. Lehninger (1970) has referred to these protocols collectively as the “molecular logic of the living state.” The most important among these are the principles of chemical thermodynamics and the physical and chemical laws pertaining to energy balance and mass. Stoichiometry is the branch of chemistry that deals with such laws. It is the rules of stoichiometry that specify allowable states (Sterner and Elser 2002; for a summary of the key axioms and theorems see their Chapter 1)

Organisms from the smallest to the largest are unified in another way: They operate according to a very similar biochemical master plan, an attribute sometimes referred to as the “universality of cellular biochemistry” (the implications of this are discussed in Chap. 4) (Neidhardt et al. 1990; Stephanopoulos et al. 1998; Lengeler et al. 1999). For example, there are core cellular features such as the conventional lipoprotein cellular envelope; DNA as the fundamental genetic material together with its transcriptional and translational machinery; and universal intermediary metabolism. Though organisms may differ with respect to specific proteins and certain other macromolecules, all cell components are built from the same building blocks, such as amino acids and nucleotides. In turn, these 75 or so building blocks originate from 12 central precursor metabolites (Table 3.1).

Table 3.1. The 12 universal precursor metabolitesa (Neidhardt et al. 1990)

Overall metabolic coordination and the precursor metabolites are universal. The reactions by which they are produced from whatever substrates are available to the cell are very similar in all organisms. With minor exception, the central key pathways and reactions, such as glycolysis, the pentose phosphate pathway, and the citric acid (Krebs) cycle are common to both prokaryotes and eukaryotes. This is generally true even though the enzymes participating in the comparable reactions may differ among organisms, or be regulated differently, or where the same substrate is processed differently in different organisms.

Metabolically speaking, reactions can be clustered with respect to their role in growth into four general groups common to all living things, even though the specifics may differ among species: fueling, biosynthesis, polymerization, and assembly (Fig. 3.1 and Neidhardt et al. 1990). For these processes to function, all organisms must have raw materials to feed the fueling reactions and an energy source to make them run. In the broad category of reactions comprising biosynthesis or anabolism, ATP is consumed in all organisms; conversely, ATP is generated from ADP and P_; universally in catabolism.

Fig. 3.1. The four universal categories of biochemical reactions in cellular metabolism. Fueling reactions produce the universal precursor metabolites (see Table 3.1), and energy and reducing power for biosynthesis. Biosynthetic reactions, which begin with one or more of the precursor metabolites, produce building blocks for polymerization and related metabolites. Polymerizations link the building blocks into large polymers. Assembly reactions use the macromolecules to construct cellular features. The example shown is for E. coli but the scheme is applicable also to eukaryotes. From Neidhardt et al. (1990). Reproduced by permission of Sinauer Associates, Inc., Sunderland, MA ©1990

The biosynthetic pathways from precursor metabolites to building blocks are, with minor exceptions, the same in all organisms. Though the fueling reactions differ, for example, depending on whether the organism is a phototroph or chemotroph (discussed below), the common thread is that they serve to generate the precursor metabolites noted above, as well as to conserve energy and reducing power. Those metabolites then enter the biosynthetic pathways. A significant contribution emerging from this era of genomics and metabolomics is that metabolites and metabolic pathways of organisms can be inferred and compared from their sequenced genomes and protein databases.

These analyses show there to be a basic, common core of interconnected, conserved enzymes across the three domains of life. This suggests, among other things, that ‘enzyme recruitment’ plays a major role in metabolic evolution (Caspi et al. 2006; Peregrin-Alvarez et al. 2009), i.e., new pathways emerge by recruiting enzymes and their metabolites from existing pathways.