Introduction to Cells

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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.

Figure 1-1 simplified phylogenetic tree. This tree shows the common ancestor of all living things and the three main branches of life that diverged from this cell: Archaea, Bacteria, and Eukaryotes. Note that eukaryotic mitochondria and chloroplasts originated as symbiotic Bacteria.

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.

Living things differ in size and complexity and are adapted to life in environments as extreme as deep-sea hydrothermal vents at temperatures of 113°C or pockets of water at 0°C in frozen Antarctic lakes. Organisms also differ in strategies to extract energy from their environments. Plants, algae, and some Bacteria derive energy from sunlight for photosynthesis. Some Bacteria and Archaea oxidize reduced inorganic compounds, such as hydrogen, hydrogen sulfide, or iron, as an energy source. Many organisms in all parts of the tree, including animals, extract energy from reduced organic compounds.

As the molecular mechanisms of life become clearer, the underlying similarities are more impressive than the external differences. Retention of common molecular mechanisms in all parts of the phylogenetic tree is remarkable, given that the major phylogenetic groups have been separated for vast amounts of time and subjected to different selective pressures. The biochemical mechanisms in the branches of the phylogenetic tree could have diverged radically from each other, but they did not.

All living organisms share a common genetic code, store genetic information in nucleic acids (usually DNA), transfer genetic information from DNA to RNA to protein, employ proteins (and some RNAs) to catalyze chemical reactions, synthesize proteins on ribosomes, derive energy by breaking down simple sugars and lipids, use adenosine triphosphate (ATP) as energy currency, and separate their cytoplasm from their environment by means of phospholipid membranes containing pumps, carriers, and channels. These ancient biochemical strategies are so well adapted for survival that they have been retained during natural selection of all surviving species.

A practical consequence of common biochemical mechanisms is that one may learn general principles of cellular function by studying any cell that is favorable for experimentation. This text cites many examples in which research on bacteria, insects, protozoa, or fungi has revealed fundamental mechanisms shared by human cells. Humans and baker’s yeast have similar mechanisms to control cell cycles, to guide protein secretion, and to segregate chromosomes at mitosis. Human versions of essential proteins can often substitute for their yeast counterparts. Biologists are confident that a limited number of general principles, summarizing common molecular mechanisms, will eventually explain even the most complex life processes in terms of straightforward chemistry and physics.

Many interesting creatures have been lost to extinction during evolution. Extinction is irreversible because the cell is the only place where the entire range of life-sustaining biochemical reactions, including gene replication, molecular biosynthesis, targeting, and assembly, can go to completion. Thus, cells are such a special environment that the chain of life has required an unbroken lineage of cells stretching from each contemporary organism back to the earliest forms 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.

Figure 1-2 basic cellular architecture. A, A section of a eukaryotic cell showing the internal components. B, Comparison of cells from the major branches of the phylogenetic tree.

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.

Table 1-1 INVENTORY OF EUKARYOTIC CELLULAR COMPONENTS ^*

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