The Prokaryotic Cell

Of all the types of cells that have been examined microscopically, bacteria have the simplest structure and come closest to showing us life stripped down to its essentials. Indeed, a bacterium contains no organelles other than ribosomes—not even a nucleus to hold its DNA. This property—the presence or absence of a nucleus—is used as the basis for a simple but fundamental classification of all living things. Organisms whose cells have a nucleus are called eukaryotes (from the Greek words eu, meaning “well” or “truly,” and karyon, a “kernel” or “nucleus”). Organisms whose cells do not have a nucleus are called prokaryotes (from pro, meaning “before”).

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MICROSCOPY

CONVENTIONAL LIGHT MICROSCOPY

A conventional light microscope allows us to magnify cells up to 1000 times and to resolve details as small as 0.2 μm (200 nm), a limitation imposed by the wavelike nature of light, not by the quality of the lenses. Three things are required for viewing cells in a light microscope. First, a bright light must be focused onto the specimen by lenses in the condenser. Second, the specimen must be carefully prepared to allow light to pass through it. Third, an appropriate set of lenses (objective, tube, and eyepiece) must be arranged to focus an image of the specimen in the eye.

LOOKING AT LIVING CELLS

The same unstained, living animal cell (fibroblast) in culture viewed with

(A) the simplest, brightfield optics;

(B) phase-contrast optics;

The two latter systems exploit differences in the way light travels through regions of the cell with differing refractive indices. All three images can be obtained on the same microscope simply by interchanging optical components.

FIXED SAMPLES

Most tissues are neither small enough nor transparent enough to examine directly in the microscope. Typically, therefore, they are chemically fixed and cut into thin slices, or sections, that can be mounted on a glass microscope slide and subsequently stained to reveal different components of the cells. A stained section of a plant root tip is shown here (D).

FLUORESCENCE MICROSCOPY

Fluorescent dyes used for staining cells are detected with the aid of a fluorescence microscope. This is similar to an ordinary light microscope, except that the illuminating light is passed through two sets of filters (yellow). The first (1) filters the light before it reaches the specimen, passing only those wavelengths that excite the particular fluorescent dye. The second (2) blocks out this light and passes only those wavelengths emitted when the dye fluoresces. Dyed objects show up in bright color on a dark background.

FLUORESCENT PROBES

Fluorescent molecules absorb light at one wavelength and emit it at another, longer wavelength. Some fluorescent dyes bind specifically to particular molecules in cells and can reveal their location when the cells are examined with a fluorescence microscope. In these dividing nuclei in a fly embryo, the stain for DNA fluoresces blue. Other dyes can be coupled to antibody molecules, which then serve as highly specific staining reagents that bind selectively to particular molecules, showing their distribution in the cell. Because fluorescent dyes emit light, they allow objects even smaller than 0.2 μm to be seen. Here, a microtubule protein in the mitotic spindle (see Figure 1–28) is stained green with a fluorescent antibody.

CONFOCAL FLUORESCENCE MICROSCOPY

A confocal microscope is a specialized type of fluorescence microscope that builds up an image by scanning the specimen with a laser beam. The beam is focused onto a single point at a specific depth in the specimen, and a pinhole aperture in the detector allows only fluorescence emitted from this same point to be included in the image. Scanning the beam across the specimen generates a sharp image of the plane of focus—an optical section. A series of optical sections at different depths allows a three-dimensional image to be constructed, such as this highly branched mitochondrion in a living yeast cell.

SUPER-RESOLUTION FLUORESCENCE MICROSCOPY

Several recent and ingenious techniques have allowed fluorescence microscopes to break the usual resolution limit of 200 nm. One such technique uses a sample that is labeled with molecules whose fluorescence can be reversibly switched on and off by different colored lasers. The specimen is scanned by a nested set of two laser beams, in which the central beam excites fluorescence in a very small spot of the sample, while a second beam—wrapped around the first—switches off fluorescence in the surrounding area. A related approach allows the positions of individual fluorescent molecules to be accurately mapped while others nearby are switched off. Both approaches slowly build up an image with a resolution as low as 20 nm. These new super-resolution methods are being extended into 3-D imaging and real-time live cell imaging.

Microtubules viewed with conventional fluorescence microscope (left) and with super-resolution optics (right). In the super-resolution image, the microtubule can be clearly seen at the actual size, which is only 25 nm in diameter.

TRANSMISSION ELECTRON MICROSCOPY

The electron micrograph below shows a small region of a cell in a thin section of testis. The tissue has been chemically fixed, embedded in plastic, and cut into very thin sections that have then been stained with salts of uranium and lead.

The transmission electron microscope (TEM) is in principle similar to a light microscope, but it uses a beam of electrons, whose wavelength is very short, instead of a beam of light, and magnetic coils to focus the beam instead of glass lenses. Because of the very small wavelength of electrons, the specimen must be very thin. Contrast is usually introduced by staining the specimen with electron-dense heavy metals. The specimen is then placed in a vacuum in the microscope. The TEM has a useful magnification of up to a million-fold and can resolve details as small as about 1 nm in biological specimens.

SCANNING ELECTRON MICROSCOPY

In the scanning electron microscope (SEM), the specimen, which has been coated with a very thin film of a heavy metal, is scanned by a beam of electrons brought to a focus on the specimen by magnetic coils that act as lenses. The quantity of electrons scattered or emitted as the beam bombards each successive point on the surface of the specimen is measured by the detector, and is used to control the intensity of successive points in an image built up on a video screen. The microscope creates striking images of three-dimensional objects with great depth of focus and can resolve details down to somewhere between 3 nm and 20 nm, depending on the instrument.

Question 1–4

A bacterium weighs about 10^–12 g and can divide every 20 minutes. If a single bacterial cell carried on dividing at this rate, how long would it take before the mass of bacteria would equal that of the Earth (6 × 10²⁴ kg)? Contrast your result with the fact that bacteria originated at least 3.5 billion years ago and have been dividing ever since. Explain the apparent paradox. (The number of cells N in a culture at time t is described by the equation N = N₀ × 2^t/G, where N₀ is the number of cells at zero time, and G is the population doubling time.)

Prokaryotes are typically spherical, rodlike, or corkscrew-shaped (Figure 1–10). They are also small—generally just a few micrometers long, although some giant species are as much as 100 times longer than this. Prokaryotes often have a tough protective coat, or cell wall, surrounding the plasma membrane, which encloses a single compartment containing the cytoplasm and the DNA. In the electron microscope, the cell interior typically appears as a matrix of varying texture, without any obvious organized internal structure (Figure 1–11). The cells reproduce quickly by dividing in two. Under optimum conditions, when food is plentiful, many prokaryotic cells can duplicate themselves in as little as 20 minutes. In only 11 hours, a single prokaryote can therefore give rise to more than 8 billion progeny (which exceeds the total number of humans currently on Earth). Thanks to their large numbers, rapid proliferation, and ability to exchange bits of genetic material by a process akin to sex, populations of prokaryotic cells can evolve fast, rapidly acquiring the ability to use a new food source or to resist being killed by a new antibiotic.

An illustration shows three types of bacteria with examples. They are on the order of 1 to 10 micrometers in diameter. — Figure 1–10 Bacteria come in different shapes and sizes. Typical spherical, rodlike, and spiral-shaped bacteria are drawn to scale. The spiral cells shown are the organisms that cause syphilis.

A micrograph shows a longitudinal section of an Escherichia coli bacterium. — Figure 1–11 The bacterium Escherichia coli (E. coli) has served as an important model organism. An electron micrograph of a longitudinal section is shown here; the cell’s DNA is concentrated in the lightly stained region. Note that E. coli has an outer membrane and an inner (plasma) membrane, with a thin cell wall in between. The many flagella distributed over its surface are not visible in this micrograph. (Courtesy of E. Kellenberger.)

In this section, we offer an overview of the world of prokaryotes. Despite their simple appearance, these organisms lead sophisticated lives—occupying a stunning variety of ecological niches. We will also introduce the two distinct classes into which prokaryotes are divided: bacteria and archaea (singular, archaeon). Although they are structurally indistinguishable, archaea and bacteria are only distantly related.

Prokaryotes Are the Most Diverse and Numerous Cells on Earth

Most prokaryotes live as single-celled organisms, although some join together to form chains, clusters, or other organized, multicellular structures. In shape and structure, prokaryotes may seem simple and limited, but in terms of chemistry, they are the most diverse class of cells on the planet. Members of this class exploit an enormous range of habitats, from hot puddles of volcanic mud to the interiors of other living cells, and they vastly outnumber all eukaryotic organisms on Earth. Some are aerobic, using oxygen to oxidize food molecules; some are strictly anaerobic and are killed by the slightest exposure to oxygen. As we discuss later in this chapter, mitochondria—the organelles that generate energy in eukaryotic cells—are thought to have evolved from aerobic bacteria that took to living inside the anaerobic ancestors of today’s eukaryotic cells. Thus our own oxygen-based metabolism can be regarded as a product of the activities of bacterial cells.

Micrographs A and B show cross sections of the bacteria Anabaena cylindrica and Phormidium laminosum, respectively. — Figure 1–12 Some bacteria are photosynthetic. (A) Anabaena cylindrica forms long, multicellular chains. This light micrograph shows specialized cells that either fix nitrogen (that is, capture N₂ from the atmosphere and incorporate it into organic compounds; labeled H), fix CO₂ through photosynthesis (labeled V), or become resistant spores (labeled S) that can survive under unfavorable conditions. (B) An electron micrograph of a related species, Phormidium laminosum, shows the intracellular membranes where photosynthesis occurs. As shown in these micrographs, some prokaryotes can have intracellular membranes and form simple multicellular organisms. (A, courtesy of David Adams; B, courtesy of D.P. Hill and C.J. Howe.)

Virtually any organic, carbon-containing material—from wood to petroleum—can be used as food by one sort of bacterium or another. Even more remarkably, some prokaryotes can live entirely on inorganic substances: they can get their carbon from CO₂ in the atmosphere, their nitrogen from atmospheric N₂, and their oxygen, hydrogen, sulfur, and phosphorus from air, water, and inorganic minerals. Some of these prokaryotic cells, like plant cells, perform photosynthesis, using energy from sunlight to produce organic molecules from CO₂ (Figure 1–12); others derive energy from the chemical reactivity of inorganic substances in the environment (Figure 1–13). In either case, such prokaryotes play a unique and fundamental part in the economy of life on Earth, as other living organisms depend on the organic compounds that these cells generate from inorganic materials.

A micrograph shows Beggiatoa. — Figure 1–13 A sulfur bacterium gets its energy from H₂S. Beggiatoa, a prokaryote that lives in sulfurous environments, oxidizes H₂S to produce sulfur and can fix carbon even in the dark. In this light micrograph, yellow deposits of sulfur can be seen inside two of these bacterial cells. (Courtesy of Ralph S. Wolfe.)

Plants, too, can capture energy from sunlight and carbon from atmospheric CO₂. But plants unaided by bacteria cannot capture N₂ from the atmosphere. In a sense, plants even depend on bacteria for photosynthesis: as we discuss later, it is almost certain that the organelles in the plant cell that perform photosynthesis—the chloroplasts—have evolved from photosynthetic bacteria that long ago found a home inside the cytoplasm of a plant-cell ancestor.

The World of Prokaryotes Is Divided into Two Domains: Bacteria and Archaea

Traditionally, all prokaryotes have been classified together in one large group. But molecular studies have determined that there is a gulf within the class of prokaryotes, dividing it into two distinct domains—the bacteria and the archaea—which are thought to have diverged from a common prokaryotic ancestor approximately 3.5 billion years ago. Remarkably, DNA sequencing reveals that, at a molecular level, the members of these two domains differ as much from one another as either does from the eukaryotes. Most of the prokaryotes familiar from everyday life—the species that live in the soil or make us ill—are bacteria. Archaea are found not only in these habitats but also in environments that are too hostile for most other cells: concentrated brine, the hot acid of volcanic springs, the airless depths of marine sediments, the sludge of sewage treatment plants, pools beneath the frozen surface of Antarctica, as well as in the acidic, oxygen-free environment of a cow’s stomach, where they break down ingested cellulose and generate methane gas. Many of these extreme environments resemble the harsh conditions that must have existed on the primitive Earth, where living things first evolved before the atmosphere became rich in oxygen.

eukaryote
An organism whose cells have a distinct nucleus and cytoplasm.
prokaryote
Major category of living cells distinguished by the absence of a nucleus; includes the archaea and the eubacteria (commonly called bacteria).
bacterium
Microscopic organism that is a member of one of the two divisions of prokaryotes; some species cause disease. The term is sometimes used to refer to any prokaryotic microorganism, although the world of prokaryotes also includes archaea, which are only distantly related to each other. (See also archaeon.)
archaeon
Microscopic organism that is a member of one of the two divisions of prokaryotes; often found in hostile environments such as hot springs or concentrated brine. (See also bacterium.)