Although generalizations in biology usually lack the theoretical underpinnings found in physics, there are very clear commonalities among living systems that give biology a unity. One is the style of cellular construction. The biological universe consists of two types of cells - prokaryotic cells, which lack a defined nucleus and have a simplified internal organization, and eukaryotic cells, which have a more complicated internal structure including a defined, membrane-limited nucleus. Detailed analysis of the DNA from a variety of prokaryotic organisms in recent years has revealed two distinct types: bacteria (often called “true” bacteria or eubacteria) and archaea (also called archaebacteria or archaeans). As we discuss in Chapter 7, the archaea are in some respects more similar to eukaryotic organisms than to the true bacteria.
Based on the assumption that organisms with more similar genes evolved from a common progenitor more recently than those with more dissimilar genes, researchers have developed the lineage tree shown in Figure 1-5. According to this tree, the archaea and eukarya (eukaryotes) are thought to have diverged from the bacteria before they diverged from each other. Despite the differences in the organization of prokaryotic and eukaryotic cells, all cells share certain structural features and carry out many complicated processes in basically the same way.
A cell, because it is a limited space, must have an outer border. The construction of that border represents one of the most fundamental considerations in biological organization. The outer shell of cells, like any shell, is built to keep the interior contents from leaking out into the surrounding environment. The chemical processes of cellular life generally take place in a watery solution, and the intracellular constituents of cells are largely molecules that are easily dissolved in water. Similarly, the environment around cells is a watery one, the blood and other bodily fluids being solutions in water. Cells then, in order to maintain their integrity, need to be surrounded by an environment through which water cannot flow. A membrane composed of fatty molecules serves this purpose.
We all know from common experience that “oil and water don’t mix.” That maxim is all one needs to appreciate how a cell is constructed. When oil is poured on water, the oil spreads into a thin film; that film is analogous to the film of fat that surrounds cells, called the plasma membrane (Figure 1-6). Biological membranes differ from a pure oil film in that the molecules that make the membrane have both oily and watery portions; they have long fatty chains, but they also have a head group that is water-soluble by virtue of being electrically charged. Thus membranes are formed because these bipartite molecules, called phospholipids, spontaneously orient themselves to form a double layer, or bilayer, having a fatty interior with external surfaces bonded to the surrounding water by the charged head groups. The membrane is given rigidity by interspersion of cholesterol, a molecule we have come to hate because of its association with heart disease, but one that is required to build the outer membrane of all our cells. Hence from an understanding of the contrasting properties of watery solutions and oily layers, an understanding of cellular construction emerges.
In spite of the rigidity provided by cholesterol, membranes composed of fat are not very strong, so numerous mechanisms for strengthening the borders of cells have evolved. In plants the plasma membrane is surrounded by a rigid cell wall. Although most animal cells lack a cell wall, proteins attached to their exterior surfaces provide some stability; the linking of cells together through these proteins helps maintain the integrity of tissues. Tissues and organs are often covered by strong networks of proteins and other molecules that strengthen and protect them, and also wall off the various compartments of the body. Single-celled organisms, like bacteria, have special outer coats to protect them.
Although membranes are valuable as a way to segregate the watery interior of the cell from its environment, or to segregate intracellular events from one another, they have other important functions, including energy storage. Because membranes separate watery compartments from one another, if an ion or a molecule dissolved in water is moved through a membrane into a new cellular compartment, it will not be able to diffuse freely out of the compartment into which it was moved. It takes energy to move the molecule, but once moved, the molecule stores that energy by virtue of its entrapment. Formally, this storage of energy is just like the storage of energy in a battery. Therefore, membranes not only delineate compartments, but also serve as active participants in the cell’s dynamism.
The functions of many proteins depend on their mode of association with membranes. For instance, the passage of water-soluble molecules through membranes is carried out by protein transporters that are embedded in the membrane. Also, cells send information to one another by releasing signaling molecules. The outer membranes of cells have proteins, known appropriately as receptors, that bind the circulating signaling molecules. These signaling molecules allow the individual activities of the many cells in the body to be coordinated. The receipt of a signaling molecule by a receptor causes the transient organization of particular types of intracellular proteins, called signal-transduction proteins, into an activated complex at the interior face of the cell’s outer membrane, from which it directs alterations of events in the cell’s cytoplasm or nucleus (Chapter 20).
All prokaryotes are single-celled organisms, or protists. The bacterial lineage includes Escherichia coli, found in animal intestines and a favorite experimental organism, and the photosynthetic organisms formerly known as blue-green algae but better known today as cyanobacteria. (Because most prokaryotes studied in laboratories are bacteria, discussions of prokaryotic structure or metabolism throughout this book refer to these organisms, not archaeans, unless noted otherwise.) Many members of the archaeal lineage grow in unusual, often extreme, environments. For instance, the halophiles require high concentrations of salt to survive, and the thermoacidophiles grow in hot (80°C) sulfur springs, where a pH of less than 2 is common. Other archaeans, called methanogens, live in oxygen-free milieus and generate methane (CH4) by the reduction of carbon dioxide.
Figure 1-7a illustrates the general structure of a typical bacterial cell; archaeal cells have a similar structure. In general, prokaryotes consist of a single closed compartment containing the cytosol and bounded by the plasma membrane. Although bacterial cells do not have a defined nucleus, the genetic material, DNA, is condensed into the central region of the cell. In addition, most ribosomes - the cell’s protein-synthesizing particles - are found in the DNA-free region of the cell. Some bacteria also have an invagination of the cell membrane, called a mesosome, which is associated with synthesis of DNA and secretion of proteins. Thus bacterial cells are not completely devoid of internal organization.
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 cell wall and an unusual outer membrane separated from the 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.
Eukaryotes comprise all members of the plant and animal kingdoms, including the unicellular fungi (e.g., yeasts, mushrooms, molds) and protozoans. Eukaryotic cells, like prokaryotic cells, are surrounded by a plasma membrane. However, unlike prokaryotic cells, most eukaryotic cells also contain extensive internal membranes that enclose specific compartments, the organelles, and separate them from the rest of the cytoplasm, the region of the cell lying outside the nucleus (Figure 1-7b and chapter opening figure).
Most organelles are surrounded by a single phospholipid membrane, but several, including the nucleus, are enclosed by two membranes. Each type of organelle plays a unique role in the growth and metabolism of the cell, and each contains a collection of specific enzymes that catalyze requisite chemical reactions. The membranes defining these subcellular compartments control their internal ionic composition so that it commonly differs from that of the cytosol (the portion of the cytoplasm outside the organelles) and among the various organelles.
The largest organelle in a eukaryotic cell is generally the nucleus, which houses most of the cellular DNA. In addition to the nucleus, several other organelles are present in nearly all eukaryotic cells: the mitochondria, in which much of the cell’s energy metabolism is carried out; the rough and smooth endoplasmic reticula, a network of membranes in which glycoproteins and lipids are synthesized; Golgi vesicles, which direct membrane constituents to appropriate places in the cell; and peroxisomes, in which fatty acids and amino acids are degraded. Animal cells, but not plant cells, contain lysosomes, which degrade worn-out cell constituents and foreign materials taken in by the cell. Chloroplasts, where photosynthesis occurs, are found only in certain leaf cells of plants and some single-celled organisms. Both plant cells and some single-celled eukaryotes contain one or more vacuoles, large, fluid-filled organelles in which nutrients and waste compounds are stored and some degradative reactions occur.
The cytosol of eukaryotic cells contains an array of fibrous proteins collectively called the cytoskeleton (Chapters 18 and 19). Three classes of fibers compose the cytoskeleton: microtubules (20 nm in diameter), built of polymers of the protein tubulin; microfilaments (7 nm in diameter), built of the protein actin; and intermediate filaments (10 nm in diameter), built of one or more rod-shaped protein subunits. The cytoskeleton gives the cell strength and rigidity, thereby helping to maintain cell shape. Cytoskeletal fibers also control movement of structures within the cell; for example, some cytoskeletal fibers connect to organelles or provide tracks along which organelles move.
The rigid cell wall, composed of cellulose and other polymers, that surrounds plant cells contributes to their strength and rigidity. Fungi are also surrounded by a cell wall, but its composition differs from that of bacterial or plant cell walls.
The DNA in the nuclei of eukaryotic cells is distributed among 1 to more than 50 long linear structures called chromosomes. The number and size of the chromosomes are the same in all cells of an organism, but vary among different types of organisms. Each chromosome comprises a single DNA molecule associated with numerous proteins, and the total DNA in the chromosomes of an organism is referred to as its genome. Chromosomes, which stain intensely with basic dyes, are visible in the light microscope only during cell division when the DNA becomes tightly compacted (Figure 1-8).
In all prokaryotic cells, most of or all the genetic information resides in a single circular DNA molecule, about a millimeter in length; this molecule lies, folded back on itself many times, in the central region of the cell. Although the large genomic DNA molecule in prokaryotes is associated with proteins and often is referred to as a chromosome, the arrangement of DNA within a bacterial chromosome differs greatly from that within the chromosomes of eukaryotic cells.
The concept that genes are like “beads” strung on a long “string,” the chromosome, was proposed early in the 1900s based on genetic work with the fruit fly Drosophila. The early Drosophila workers could position, or map, the genes responsible for various mutant traits on a chromosome, even though they did not yet know that genes were segments of DNA or that the function of a gene was due to a protein whose sequence was encoded by that gene!