CHAPTER 1 Introduction to Cells
Biology is based on the fundamental laws of nature embodied in chemistry and physics, but the origin and evolution of life on earth were historical events. This makes biology more like astronomy than like chemistry and physics. Neither the organization of the universe nor life as we know it had to evolve as it did. Chance played a central role. Throughout history and continuing today, the genes of some organisms sustain chemical changes that are inherited by their progeny. Many of the changes reduce the fitness of the organism, but some changes improve fitness. Over the long term, competition between sister organisms with random differences in their genes determines which organisms survive in various environments. Although these genetic differences ensure survival, they do not necessarily optimize each chemical life process. The variants that survive merely have a selective advantage over the alternatives. Thus, the molecular strategy of life processes works well but is often illogical. Readers would likely be able to suggest simpler or more elegant mechanisms for many cellular processes described in this book.
In spite of obvious differences in size, design, and behavior, all forms of life share many molecular mechanisms because they all descended from a common ancestor that lived 3 or 4 billion years ago (Fig. 1-1). This founding organism no longer exists, but it must have utilized biochemical processes similar to the biological processes that sustain contemporary cells.
Over several billion years, living organisms diverged from each other into three great divisions: Bacteria, Archaea, and Eucarya (Fig. 1-1). Archaea and Bacteria were considered to be one kingdom until the 1970s; then ribosomal RNA sequences revealed that they were different divisions of the tree of life, having branched from each other early in evolution. The origin of eukaryotes is still uncertain, but they inherited genes from both Archaea and Bacteria. One possibility is that eukaryotes originated when an Archaea fused with a Bacterium. Note that multicellular eukaryotes (green, blue, and red in Fig. 1-1) evolved relatively recently, hundreds of millions of years after earlier, single-celled eukaryotes first appeared. Also note that algae and plants branched off before fungi, our nearest relatives on the tree of life.
This book focuses on the underlying molecular mechanisms of biological function at the cellular level. Chapter 1 starts with a brief description of the main features that set eukaryotes apart from prokaryotes and then covers the general principles that apply equally to eukaryotes and prokaryotes. It closes with a preview of the major components of eukaryotic cells. Chapter 3 covers the macromolecules that form cells, while Chapters 4 and 5 introduce the chemical and physical principles required to understand how these molecules assemble and function. Armed with this introductory material, the reader will be prepared to circle back to Chapter 2 to learn what is known of the origins of life and the evolution of the forms of life that currently inhabit the earth.
Features That Distinguish Eukaryotic and Prokaryotic Cells
Although sharing a common origin and basic biochemistry, cells vary considerably in their structure and organization (Fig. 1-2). Although diverse in terms of morphology and reliance on particular energy sources, Bacteria and Archaea have much in common, including basic metabolic pathways, gene expression, lack of organelles, and motility powered by rotary flagella. All eukaryotes (protists, algae, plants, fungi, and animals) differ from the two extensive groups of prokaryotes (Bacteria and Archaea) in having a compartmentalized cytoplasm with membrane-bounded organelles including a nucleus.
A plasma membrane surrounds all cells, and additional intracellular membranes divide eukaryotes into compartments, each with a characteristic structure, biochemical composition, and function (Fig. 1-2). The basic features of eukaryotic organelles were refined more than 1.5 billion years ago, before the major groups of eukaryotes diverged. The nuclear envelope separates the two major compartments: nucleoplasm and cytoplasm. The chromosomes carrying the cell’s genes and the machinery to express these genes reside inside the nucleus; they are in the cytoplasm of prokaryotes. Most eukaryotic cells have endoplasmic reticulum (the site of protein and phospholipid synthesis), a Golgi apparatus (an organelle that adds sugars to membrane proteins, lysosomal proteins, and secretory proteins), lysosomes (a compartment for digestive enzymes), peroxisomes (containers for enzymes involved in oxidative reactions), and mitochondria (structures that convert energy stored in the chemical bonds of nutrients into ATP in addition to other functions). Cilia (and flagella) are ancient eukaryotic specializations used by many cells for motility or sensing the environment. Table 1-1 lists the major cellular components and some of their functions.
| Cellular Component | Description |
|---|---|
| Plasma membrane | A lipid bilayer, 7 nm thick, with integral and peripheral proteins; the membrane surrounds cells and contains channels, carriers and pumps for ions and nutrients, receptors for growth factors, hormones and (in nerves and muscles) neurotransmitters, plus the molecular machinery to transduce these stimuli into intracellular signals |
| Adherens junction | A punctate or beltlike link between cells with actin filaments attached on the cytoplasmic surface |
| Desmosome | A punctate link between cells associated with intermediate filaments on the cytoplasmic surface |
| Gap junction | A localized region where the plasma membranes of two adjacent cells join to form minute intercellular channels for small molecules to move from the cytoplasm of one cell to the other |
| Tight junction | An annular junction sealing the gap between epithelial cells |
| Actin filament | “Microfilaments,” 8 nm in diameter; form a viscoelastic network in the cytoplasm and act as tracks for movements powered by myosin motor proteins |
| Intermediate filament | Filaments, 10 nm in diameter, composed of keratin-like proteins that act as inextensible “tendons” in the cytoplasm |
| Microtubule | A cylindrical polymer of tubulin, 25 nm in diameter, that forms the main structural component of cilia, flagella, and mitotic spindles; microtubules provide tracks for organelle movements powered by the motors dynein and kinesin |
| Centriole | A short cylinder of nine microtubule triplets located in the cell center (centrosome) and at the base of cilia and flagella; pericentrosomal material nucleates and anchors microtubules |
| Microvillus (or filopodium) | A thin, cylindrical projection of the plasma membrane supported internally by a bundle of actin filaments |
| Cilia/flagella | Organelles formed by an axoneme of nine doublet and two singlet microtubules that project from the cell surface and are surrounded by plasma membrane; the motor protein dynein powers bending motions of the axoneme; nonmotile primary cilia have sensory functions |
| Glycogen particle | Storage form of polysaccharide |
| Ribosome | RNA/protein particle that catalyzes protein synthesis |
| Rough endoplasmic reticulum | Flattened, intracellular bags of membrane with associated ribosomes that synthesize secreted and integral membrane proteins |
| Smooth endoplasmic reticulum | Flattened, intracellular bags of membrane without ribosomes involved in lipid synthesis, drug metabolism, and sequestration of Ca2+ |
| Golgi apparatus | A stack of flattened membrane bags and vesicles that packages secretory proteins and participates in protein glycosylation |
| Nucleus | Membrane-bounded compartment containing the chromosomes, nucleolus and the molecular machinery that controls gene expression |
| Nuclear envelope | A pair of concentric membranes connected to the endoplasmic reticulum that surrounds the nucleus |
| Nuclear pore | Large, gated channels across the nuclear envelope that control all traffic of proteins and RNA in and out of the nucleus |
| Euchromatin | Dispersed, active form of interphase chromatin |
| Heterochromatin | Condensed, inactive chromatin |
| Nucleolus | Intranuclear site of ribosomal RNA synthesis and processing; ribosome assembly |
| Lysosome | Impermeable, membrane-bound bags of hydrolytic enzymes |
| Peroxisome | Membrane-bound bags containing catalase and various oxidases |
| Mitochondria | Organelles surrounded by a smooth outer membrane and a convoluted inner membrane folded into cristae; they contain enzymes for fatty acid oxidation and oxidative phosphorylation of ADP |
