All living organisms fall into one of the three great groups (kingdoms or domains) that define three branches of evolution from a common ancestor (Fig. 14). For biochemical reasons, two large groups of prokaryotes can be distinguished: archaebacteria (from the Greek arche, “ori gin”) and eubacteria (again from the Greek eu, “true”). Eubacteria inhabit soil, surface water, and the tissue of other living or decaying organisms. Most of the well-studied bacteria, including Escherichia coli) are Eu bacteria. The newly discovered archaebacteria are less biochemically characterized; most live in extreme environments, salty lakes, hot springs, highly acidic moors, and the depths of the ocean. Available evidence suggests that archaebacteria and eubacteria diverged early in evolution, forming two separate domains, sometimes referred to as archaea and bacteria. All the eukaryotic organisms that make up the third domain, eukarya, evolved from the same branch from which the archaea arose; Therefore, archaebacteria are more closely related to eukaryotes.
Within the domains of Archaea and Bacteria are sub groups distinguished by the habitats in which they live. In aerobic habitats with a plentiful supply of oxygen, some resident organisms derive energy from the trans fer of electrons from fuel molecules to oxygen. Other environments are anaerobic, virtually devoid of oxy gen, and microorganisms adapted to these environments. obtain energy by transferring electrons to nitrate (form ing N₂), sulfate (forming H₂S), or CO₂ (forming CH₂). Many organisms that have evolved in anaerobic envi ronments are obligate anaerobes: they die when ex posed to oxygen.
We can classify organisms according to how they obtain the energy and carbon they need for synthesiz ing cellular material. There are two broad categories based on energy sources: pho totrophs (Greek trophe, “nourishment”) trap and use sunlight, and chemotrophs derive their energy from oxidation of a fuel. All chemotrophs require a source of organic nutrients; ey cannot fix CO₂ into organic com pounds. The phototrophs can be further divided into those that can obtain all needed carbon from CO₂ (au totrophs) and those that require organic nutrients (heterotrophs). No chemotroph can get its carbon atoms exclusively from CO₂ (that is, no chemotrophs are autotrophs), but the chemotrophs may be further classified according to a different criterion: whether the fuels they oxidize are inorganic (lithotrophs) or or ganic (organotrophs).
Biochemistry describes in molecular terms the struc tures, mechanisms, and chemical processes shared by all organisms and provides organizing principles that underlie life in all its diverse forms, principles we refer to collectively as the molecular logic of life. Although biochemistry provides important insights and practical applications in medicine, agriculture, nutrition, and industry, its ultimate concern is with the wonder of life itself.
Most known organisms fall within one of these four broad categories-autotrophs or heterotrophs among the photosynthesizers, lithotrophs or organotrophs among the chemical oxidizers. The prokaryotes have several gen eral modes of obtaining carbon and energy. Escherichia coli, for example, is a chemoorganoheterotroph; it re quires organic compounds from its environment as fuel and as a source of carbon. Cyanobacteria are photo lithoautotrophs; they use sunlight as an energy source and convert CO₂ into biomolecules. We humans, like E. coli, are chemoorganoheterotrophs.