Prokaryotes Comprise Two Kingdoms: Archaea and Eubacteria
In recent years, detailed analysis of DNA sequences from a variety of prokaryotic organisms has revealed two distinct kingdoms: the Eubacteria, often simply called “bacteria,” and the Archaea. Eubacteria are single-celled organisms; they include the cyanobacteria, or “blue-green algae,” which can be unicellular or filamentous chains of cells. Figure 1-11 illustrates the general structure of a typical eubacterial cell; archaeal cells have a similar structure. Bacterial cells are commonly 1–2 μm in size and consist of a single closed compartment containing the cytoplasm and bounded by the plasma membrane. The genome is composed of a single circular DNA molecule; many prokaryotes contain additional small circular DNA molecules called plasmids. Although bacterial cells do not have a defined nucleus, the DNA is extensively folded and condensed into the central region of the cell, called the nucleoid. In contrast, most ribosomes are found in the cytoplasm. Some bacteria also have an invagination of the cell membrane, called a mesosome, which is associated with synthesis of DNA and secretion of proteins. Many proteins are precisely localized within the cytosol or in the plasma membrane, indicating the presence of an elaborate internal organization. Unlike those in eukaryotes (see Figure 1-9), bacterial mRNAs undergo limited if any processing. And because there is no membrane barrier between bacterial DNA and cytoplasm, ribosomes are able to bind to an mRNA as soon as part of it has been synthesized by RNA polymerase; thus in prokaryotes, transcription and translation occur contemporaneously.
FIGURE 1-11 Prokaryotic cells are have a relatively simple structure. (Left) Electron micrograph of a thin section of Escherichia coli, a common intestinal bacterium. The nucleoid, consisting of the bacterial DNA, is not enclosed within a membrane. E. coli and other gram-negative bacteria are surrounded by two membranes separated by the periplasmic space. The thin cell wall is adjacent to the inner membrane. (Right) This artist’s drawing shows the nucleoid (blue) and a magnification of the layers that surround the cytoplasm. Most of the cell is composed of water, proteins, ions, and other molecules that are too small to be depicted at the scale of this drawing.
[Electron micrograph courtesy of I. D. J. Burdett and R. G. E. Murray.]
Bacterial cells possess a cell wall, which lies adjacent to the external side of the plasma membrane. The cell wall is composed of layers of peptidoglycan, a complex of proteins and oligosaccharides; it helps protect the cell and maintain its shape. Some bacteria (e.g., E. coli) have a thin inner cell wall and an outer membrane separated from the inner cell wall by the periplasmic space. Such bacteria are not stained by the Gram technique and thus are classified as gram-negative. Other bacteria (e.g., Bacillus polymyxa) that have a thicker cell wall and no outer membrane take the Gram stain and thus are classified as Gram-positive.
In addition to DNA sequence distinctions that separate them from eubacteria, archaea have cell membranes that differ dramatically in composition from those of eubacteria and eukaryotes. Many archaeans grow in unusual, often extreme, environments that may resemble the ancient conditions that existed when life first appeared on Earth. For instance, halophiles (“salt lovers”) require high concentrations of salt to survive, and thermoacidophiles (“heat and acid lovers”) grow in hot (80 °C) sulfur springs, where a pH of less than 2 is common. Still other archaeans live in oxygen-free milieus and generate methane (CH4) by combining water with carbon dioxide.