The cell is the basic unit of life. Cells grow, replicate, and interact with their environment. Living organisms can be as simple as a single cell or as complex as a human body, which is composed of approximately 100 trillion cells. Every cell is delineated by a membrane that separates the inside of the cell from its environment. A membrane is a lipid bilayer: two layers of lipids organized with their hydrophobic chains interacting with one another and the hydrophilic head groups interacting with the environment (Figure 1.9).

There are two basic types of cells: eukaryotic cells and prokaryotic cells (Figure 1.10). The main difference between the two is the existence of membrane-enclosed compartments in eukaryotes and the absence of such compartments in prokaryotes. Prokaryotic cells, exemplified by the human gut bacterium Escherichia coli, have a relatively simple structure. They are surrounded by two membranes separated by the periplasmic space. Although human beings are composed of 100 trillion cells, we carry more than 10 times that number of bacteria in us and on us. For the most part, our attitude toward our prokaryotic colleagues is to “live and let live.” For example, the prokaryotes living in our intestines assist us in the process of digestion. Prokaryotes are responsible for making our lives richer in other ways. Various prokaryotes provide us with buttermilk, yogurt, and cheese. Nevertheless, prokaryotes also cause a wide array of diseases.

Regardless of cell type—eukaryotic or prokaryotic, plant or animal—two biochemical features minimally constitute a cell: there must be (1) a barrier that separates the cell from its environment and (2) an inside that is chemically different from the environment and that accommodates the biochemistry of living. The barrier is called the plasma membrane, and the fundamental intracellular material is called the cytoplasm.

The plasma membraneThe plasma membrane separates the inside of the cell from the outside, one cell from another cell. This membrane is impermeable to most substances, even to substances such as fuels, building blocks, and signal molecules that must enter the cell. Consequently, the barrier function of the membrane must be mitigated to permit the entry and exit of molecules and information. In other words, the membrane must be rendered semipermeable but in a very selective way. This selective permeability is the work of proteins that are embedded in the plasma membrane or associated with it (Figure 1.11). These proteins facilitate the entrance of fuels, such as glucose, and building blocks, such as amino acids, and they transduce information—for example, that insulin is in the blood stream.

The plant cell wallThe plasma membrane of a plant is itself surrounded by a cell wall (Figure 1.12). The cell wall is constructed largely from cellulose, a long, linear polymer of glucose molecules. Cellulose molecules interact with one another as well as with other cell-wall components to form a sturdy protective wall for the cell.

The cytoplasmThe inner substance of the cell, the material that is surrounded by the plasma membrane, is called the cytoplasm. The cytoplasm is the site of a host of biochemical processes, including the initial stage of glucose metabolism, fatty acid synthesis, and protein synthesis. Formerly, the cytoplasm was believed to be a “soup” of important biomolecules, but it is becoming increasingly clear that the biochemistry of the cytoplasm is highly organized by a network of structural filaments called the cytoskeleton. In many eukaryotes, the cytoskeleton is a network of three kinds of protein fibers—actin filaments, intermediate filaments, and microtubules—that support the structure of the cell, help to localize certain biochemical activities, and even serve as “molecular highways” by which molecules can be shuttled around the cell (Figure 1.13).

A key difference between eukaryotic cells and prokaryotic cells is the presence of a complex array of intracellular, membrane-bounded compartments called organelles in eukaryotes (Figure 1.10B). We will now tour the cell to investigate prominent organelles, which we will see many times in our study of biochemistry.

The nucleusThe largest organelle is the nucleus, which is a double-membrane-bounded organelle (Figure 1.14). The nucleus is the information center of the cell, the location of an organism’s genome. The nuclear membrane is punctuated with pores that allow transport into and out of the nucleus. For instance, the molecular machines that synthesize DNA and RNA are formed in the cytoplasm, but function in the nucleus. The nucleus is where the genomic information is selectively expressed at the proper time and in the proper amount.

The mitochondrionThe mitochondrion (plural, mitochondria) has two membranes—an outer mitochondrial membrane that is in touch with the cytoplasm and an inner mitochondrial membrane that defines the matrix of the mitochondrion—the mitochondrial equivalent of the cytoplasm. The inner mitochondrial membrane is highly invaginated (Figure 1.15). The space between the two membranes is the intermembrane space. In mitochondria, fuel molecules undergo combustion into carbon dioxide and water with the generation of cellular energy, adenosine triphosphate (ATP). Approximately 90% of the energy used by a typical cell is produced in this organelle. Poisons such as cyanide and carbon monoxide are so deadly precisely because they shut down the functioning of mitochondria. When we study the biochemistry of this organelle in detail, we will see that the structure of the mitochondrion plays an intimate role in its biochemical functioning.

The chloroplastAnother double-membrane-bounded organelle vital to all life, but found only in plant cells, is the chloroplast (Figure 1.12). Chloroplasts power the plant cell, the plant, and the rest of the living world. A chloroplast is the site of a remarkable biochemical feat: the conversion of sunlight into chemical energy, a process called photosynthesis. Every meal that we consume, be it a salad or a large cut of juicy steak, owes its existence to photosynthesis. If photosynthesis were to halt, life on Earth would cease in about 25 years. The mass extinction of the Cretaceous period (65.1 million years ago), in which the dinosaurs met their demise, is believed to have been caused by a large meteor strike that propelled so much debris into the atmosphere that sunlight could not penetrate and photosynthesis ceased.

Let us briefly examine other eukaryotic organelles (Figure 1.10B) in the context of how they cooperate with one another to perform vital biochemical tasks.

The endoplasmic reticulumThe endoplasmic reticulum is a series of membranous sacs. Many biochemical reactions take place on the cytoplasmic surface of these sacs as well as in their interiors, or lumens. The endoplasmic reticulum comes in two types: the smooth endoplasmic reticulum (smooth ER, or SER) and the rough endoplasmic reticulum (rough ER, or RER), as illustrated in Figure 1.16 (also Figure 1.10). The smooth endoplasmic reticulum plays a variety of roles, but an especially notable role is the processing of exogenous chemicals (chemicals originating outside the cell) such as drugs. The more drugs, including alcohol, ingested by an organism, the greater the quantity of smooth endoplasmic reticulum in the liver.

The rough endoplasmic reticulum appears rough because ribosomes are attached to the cytoplasmic side (Figure 1.14). Ribosomes that are free in the cytoplasm take part in the synthesis of proteins for use inside the cell. Ribosomes attached to the rough endoplasmic reticulum synthesize proteins that will either be inserted into cellular membranes or be secreted from the cell.

Proteins synthesized on the rough endoplasmic reticulum are transported into the lumen of the endoplasmic reticulum during the process of translation. Inside the lumen of the rough endoplasmic reticulum, a protein folds into its final three-dimensional structure, with the assistance of other proteins called chaperones, and is often modified, for instance, by the attachment of carbohydrates. The folded, modified protein then becomes sequestered into regions of the rough endoplasmic reticulum that lack ribosomes. These regions bud off the rough endoplasmic reticulum as transport vesicles.

The Golgi complexThe transport vesicles from the rough endoplasmic reticulum are carried to the Golgi complex—a series of stacked membranes—and fuse with it (Figure 1.17). Further processing of the proteins that were contained in the transport vesicles takes place in the Golgi complex. In particular, a different set of carbohydrates is added. Proteins with different fates are sorted in the Golgi complex.

Secretory granulesA secretory granule, or zymogen granule, is formed when a vesicle filled with the proteins destined for secretion buds off the Golgi complex. The granule is directed toward the cell membrane. When the proper signal is received, the secretory granule fuses with the plasma membrane and dumps its cargo into the extracellular environment, a process called exocytosis (Figure 1.18).

The endosomeMaterial is taken into the cell when the plasma membrane invaginates and buds off to form an endosome (not shown in Figure 1.10B). This process is called endocytosis, which is the opposite of exocytosis. Endocytosis is used to bring important biochemicals such as iron ions, vitamin B₁₂, and cholesterol into the cell. Endocytosis takes place through small regions of the membrane, such as when a protein is taken into the cell (Figure 1.19). Alternatively, large amounts of material can also be taken into the cell. When large amounts of material are taken into the cell, the process is called phagocytosis. Figure 1.20 shows an immune-system cell, called a macrophage, phagocytizing bacteria. Macrophages phagocytize bacteria as a means of protecting an organism from infection. What is the fate of the vesicles formed by endocytosis or phagocytosis?

LysosomesThe lysosome is an organelle that contains a wide array of digestive enzymes. Lysosomes form in a manner analogous to the formation of secretory granules, but lysosomes fuse with endosomes instead of the cell membrane. After fusion has taken place, the lysosomal enzymes digest the material, releasing small molecules that can be used as building blocks or fuel by the cell. Lysosomes do not just degrade extracellular material, however. Another role is the digestion of damaged intracellular organelles (Figure 1.21).

Plant vacuolesAnother organelle unique to plant cells, in addition to the chloroplast, is a large vacuole. In some plant cells, this single-membrane-bounded organelle may occupy as much as 80% of a cell’s volume (Figure 1.12). These vacuoles store water, ions, and various nutrients. For instance, the vacuoles of citrus fruits are rich in citric acid, which is responsible for the tart taste of these fruits. Proteins transport the molecules across the vacuolar membrane.

Cellular organization attests to the high information content of the cell. But this brief overview has only touched the surface of the information processing that must take place to construct something as sophisticated as a cell. In the rest of this textbook, we will examine the biochemical energy and information pathways that construct and maintain living systems.