The biological universe consists of two types of cells: prokaryotic and eukaryotic. Prokaryotic cells such as bacteria consist of a single closed compartment that is surrounded by a plasma membrane, lack a defined nucleus, and have a relatively simple internal organization (Figure 1). Eukaryotic cells contain a defined membrane-bounded nucleus and extensive internal membranes that enclose the organelles (see Figure 2).
Fig1. 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 com posed 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.]
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, 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.
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.
Escherichia coli Is Widely Used in Biological Research
The bacterial lineage includes Escherichia coli, a favorite experimental organism, which in nature is common in soil and in animal intestines. E. coli and several other bacteria have a number of advantages as experimental organisms. They grow rapidly in a simple and inexpensive medium containing glucose and salts, in which they can synthesize all necessary amino acids, lipids, vitamins, and other essential small molecules. Like all bacteria, E. coli possesses elegant mechanisms for controlling gene activity that are now well understood. Over time, researchers have developed powerful systems for genetic analysis of this organism. These systems are facilitated by the small size of bacterial genomes, the ease of obtaining mutants, the availability of techniques for transferring genes into bacteria, an enormous wealth of knowledge about bacterial gene control and protein functions, and the relative simplicity of mapping genes relative to one another in the bacterial genome.
Bacteria such as E. coli that grow in environments as di verse as the soil and the human gut have about 4000 genes, encoding about the same number of proteins (Table 1).
Table1. Genome Sizes of Organisms Used in Molecular Cell Biology Research That Have Been Completely Sequenced
Parasitic bacteria such as the Mycoplasma species acquire amino acids and other nutrients from their host cells, and they lack the genes for enzymes that catalyze reactions in the synthesis of amino acids and certain lipids. Many bacterial genes encoding proteins essential for DNA, RNA, protein synthesis, and membrane function are conserved in all organisms, and much of our knowledge of these important cellular processes was uncovered first by studies in E. coli and other bacteria. For example, certain E. coli membrane proteins that import amino acids across the plasma mem brane are closely related in sequence, structure, and function to membrane proteins in certain mammalian brain cells that import small nerve-to-nerve signaling molecules called neurotransmitters.
Because many of its genes and proteins, as well as their functions, are conserved in all organisms, E. coli has been chosen by scientists as a favorite model organism: an experimental system in which the study of specific genes or proteins, or aspects of cell or organismal function or regulation, can provide an understanding of similar molecules or processes in other species. Throughout this chapter, we will encounter other model organisms that have been chosen because, like E. coli, they are easy to grow and study. Of course, many bacteria cause serious diseases, and research on them is often focused on understanding their unique biology and on discovering antibiotics that selectively kill them but not their human or animal hosts.
