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

* See Figure 1-2.

Compartments give eukaryotic cells a number of advantages. Membranes provide a barrier that allows each type of organelle to maintain novel ionic and enzymatic interior environments. Each of these special environments favors a subset of the biochemical reactions required for life. The following examples demonstrate this concept:

• Segregation of digestive enzymes in lysosomes prevents them from destroying other cellular components.

• Each of the membrane-bound organelles concentrates particular proteins and small molecules in an ionic environment specialized for certain biochemical reactions.

• Special proteins in each organelle membrane contribute to the functions of the organelle.

• ATP synthesis depends on the impermeable membrane around mitochondria; energy-releasing reactions produce a proton gradient across the membrane that enzymes in the membrane use to drive ATP synthesis.

• The nuclear envelope provides a compartment where the synthesis and editing of RNA copies of the genes can be completed before the mature messenger RNAs exit to the cytoplasm where they direct protein synthesis.

Some Universal Principles of Living Cells

This section summarizes the numerous features shared by all forms of life. Together with the following section on eukaryotic cells, these pages reprise the main points of the whole text.

1. Genetic information stored in one-dimensional chemical sequences in DNA (occasionally RNA) is duplicated and passed on to daughter cells (Fig. 1-3). The information required for cellular growth, multiplication, and function is stored in long polymers of DNA called chromosomes. Each DNA molecule is composed of a covalently linked linear sequence of four different nucleotides (adenine [A], cytosine [C], guanine [G], and thymine [T]). In the double-helical DNA molecule, each nucleotide base preferentially forms a specific complex with a complementary base on the other strand. Specific noncovalent interactions stabilize the pairing between complementary nucleotide bases: A with T and C with G. During DNA replication, the two DNA strands are separated, each serving as a template for the synthesis of a new complementary strand. Enzymes that carry out DNA synthesis recognize the structure of complementary base pairs and insert only the correct complementary nucleotide at each position, thereby producing two identical copies of the DNA. Precise segregation of one newly duplicated double helix to each daughter cell then guarantees the transmission of intact genetic information to the next generation.

2. One-dimensional chemical sequences are stored in DNA code for both the linear sequences and three-dimensional structures of RNAs and proteins (Fig. 1-4). Enzymes called polymerases copy the information stored in genes into linear sequences of nucleotides of RNA molecules. Some genes specify RNAs with structural roles, regulatory functions, or enzymatic activity, but most genes produce messenger RNA (mRNA) molecules that act as templates for protein synthesis, specifying the sequence of amino acids during the synthesis of polypeptides by ribosomes. The amino acid sequence of most proteins contains sufficient information to specify how the polypeptide folds into a unique three-dimensional structure with biological activity. Two mechanisms control the production and processing of RNA and protein from tens of thousands of genes. Genetically encoded control circuits consisting of proteins and RNAs respond to environmental stimuli through signaling pathways. Epigenetic controls involve modifications of DNA or associated proteins that affect gene expression. These epigenetic modifications can be transmitted from a parent to an offspring. The basic plan for the cell contained in the genome, together with ongoing regulatory mechanisms (see points 7 and 8), works so well that each human develops with few defects from a single fertilized egg into a complicated ensemble of trillions of specialized cells that function harmoniously for decades in an ever-changing environment.

3. Macromolecular structures assemble from subunits (Fig. 1-5). Many cellular components form by self-assembly of their constituent molecules without the aid of templates or enzymes. The protein, nucleic acid, and lipid molecules themselves contain the information that is required to assemble complex structures. Diffusion usu-ally brings the molecules together during these assembly processes. Exclusion of water from their complementary surfaces (“lock and key” pack-ing), as well as electrostatic and hydrogen bonds, provides the energy to hold the subunits together. In some cases, protein chaperones assist with assembly by preventing the precipitation of partially or incorrectly folded intermediates. Im-portant cellular structures that are assembled in this way include chromatin, consisting of nuclear DNA compacted by associated proteins; ribosomes, assembled from RNA and proteins; cytoskeletal polymers, polymerized from protein subunits; and membranes formed from lipids and proteins.

4. Membranes grow by expansion of preexisting membranes (Figs. 1-5 and 1-6). Biological membranes composed of phospholipids and proteins do not form de novo in cells; instead, they grow only by expansion of preexisting lipid bilayers. As a consequence, organelles, such as mitochondria and endoplasmic reticulum, form only by growth and division of preexisting organelles and are inherited maternally starting from the egg. The endoplasmic reticulum (ER) plays a central role in membrane biogenesis as the site of phospholipid synthesis. Through a series of budding and fusion events, membrane made in the ER provides material for the Golgi apparatus, which, in turn, provides lipids and proteins for lysosomes and the plasma membrane.

5. Signal-receptor interactions target cellular constituents to their correct locations (Fig. 1-6). Specific recognition signals incorporated into the structures of proteins and nucleic acids route these molecules to their proper cellular compartments. Receptors recognize these signals and guide each molecule to its compartment. For example, most proteins destined for the nucleus contain short sequences of amino acids that bind receptors that facilitate their passage through nuclear pores into the nucleus. Similarly, a peptide signal sequence first targets lysosomal proteins into the lumen of the ER. Subsequently, the Golgi apparatus adds a sugar-phosphate group recognized by receptors that secondarily target these proteins to lysosomes.

6. Cellular constituents move by diffusion, pumps, and motors (Fig. 1-7). Most small molecules move through the cytoplasm or membrane channels by diffusion. Energy is required for movements of small molecules across membranes against concentration gradients and movements of larger objects, like organelles, through cytoplasm. Electrochemical gradients or ATP hydrolysis provides energy for molecular pumps to drive molecules across membranes against concentration gradients. ATP-burning motor proteins move organelles and other cargo along microtubules or actin filaments. In a more complicated example, protein molecules destined for mitochondria diffuse from their site of synthesis in the cytoplasm to a mitochondrion (Fig. 1-6), where they bind to a receptor. An energy-requiring reaction then transports the protein into the mitochondria.

7. Receptors and signaling mechanisms allow cells to adapt to environmental conditions (Fig. 1-8). Environmental stimuli modify cellular behavior and biochemistry. Faced with an unpredictable environment, cells must decide which genes to express, which way to move, and whether to proliferate, differentiate into a specialized cell, or die. Some of these choices are programmed genetically or epigenetically, but minute-to-minute decisions generally involve the reception of chemical or physical stimuli from outside the cell and processing of these stimuli to change the behavior of the cell. Cells have an elaborate repertoire of receptors for a multitude of stimuli, including nutrients, growth factors, hormones, neurotransmitters, and toxins. Stimulation of receptors activates diverse signal-transducing mechanisms that amplify the stimulus and also generate a wide range of cellular responses, including changes in the electrical potential of the plasma membrane, gene expression, and enzyme activity. Basic signal transduction mechanisms are ancient, but receptors and output systems have diversified by gene duplication and divergence during evolution. Thus, humans typically have a greater number of variations on the general themes than simpler organisms do.

8. Molecular feedback mechanisms control molecular composition, growth, and differentiation (Fig. 1-9). Living cells are dynamic, constantly undergoing changes in composition or activity in response to external stimuli, nutrient availabil-ity, and internal signals. Change is constant, but through well-orchestrated recycling and renewal, the cell and its constituents remain relatively stable. Each cell balances production and degradation of its constituent molecules to function optimally. Some “housekeeping” molecules are used by most cells for basic functions, such as intermediary metabolism. Other molecules are unique and are required for specialized functions of differentiated cells. The supply of each of thousands of proteins is controlled by a hierarchy of mechanisms: by epigenetic mechanisms that designate whether a particular region of a chromosome is active or not, by regulatory proteins that turn specific genes on and off, by the rate of translation of messenger RNAs into protein, by the rate of degradation of specific RNAs and proteins, and by regulation of the distribution of each molecule within the cell. Some proteins are enzymes that determine the rate of synthesis or degradation of other proteins, nucleic acids, sugars, and lipids. Molecular feedback loops regulate all of these processes to ensure the proper levels of each cellular constituent.

Figure 1-3 dna structure and replication. The genes that are stored as the sequence of bases in DNA are replicated enzymatically, forming two identical copies from one double-stranded original.

Figure 1-4 Genetic information contained in the base sequence of DNA determines the amino acid sequence of a protein and its three-dimensional structure. Enzymes copy (transcribe) the sequence of bases in a gene to make a messenger RNA (mRNA). Ribosomes use the sequence of bases in the mRNA as a template to synthesize (translate) a corresponding linear polymer of amino acids. This polypeptide folds spontaneously to form a three-dimensional protein molecule, in this example the actin-binding protein profilin. (PDB file: 1ACF.) Scale drawings of DNA, mRNA, polypeptide, and folded protein: The folded protein is enlarged at the bottom and shown in two renderings—space filling (left); ribbon diagram showing the polypeptide folded into blue α-helices and yellow β-strands (right).

Figure 1-5 macromolecular assembly. Many macromolecular components of cells assemble spontaneously from constituent molecules without the guidance of templates. This figure shows the assembly of chromosomes from DNA and proteins, a bundle of actin filaments in a filopodium from proteins, and the plasma membrane from lipids and proteins. A, Atomic scale. B, Molecular scale. C, Macromolecular scale. D, Organelle scale. E, Cellular scale.

Figure 1-6 protein targeting. Signals built into the amino acid sequences of proteins target them to all compartments of the eukaryotic cell. A, Proteins synthesized on free ribosomes can be used locally in the cytoplasm or guided by different signals to the nucleus, mitochondria, or peroxisomes. B, Other signals target proteins for insertion into the membrane or lumen of the endoplasmic reticulum (ER). From there, a series of vesicular budding and fusion reactions carry the membrane proteins and lumen proteins to the Golgi apparatus, lysosomes, or plasma membrane.

Figure 1-7 molecular movements by diffusion, pumps, and motors. Diffusion: Molecules up to the size of globular proteins diffuse in the cytoplasm. Concentration gradients can provide a direction to diffusion, such as the diffusion of Ca²⁺ from a region of high concentration inside the endoplasmic reticulum through a membrane channel to a region of low concentration in the cytoplasm. Pumps: ATP-driven protein pumps can transport ions up concentration gradients. Motors: ATP-driven motors move organelles and other large cargo along microtubules and actin fila-ments.

Figure 1-8 receptors and signals. Activation of cellular metabolism by an extracellular ligand, such as a hormone. In this example, binding of the hormone (A) triggers a series of linked biochemical reactions (B–E), leading through a second messenger molecule (cyclic adenosine monophosphate, or cAMP) and a cascade of three activated proteins to a metabolic enzyme. The response to a single ligand is multiplied at steps B, C, and E, leading to thousands of activated enzymes. GTP, guanosine triphosphate.

Figure 1-9 molecular feedback loops. A, Control of the synthesis of aromatic amino acids. An intermediate and the final products of this biochemical pathway inhibit three of nine enzymes (Enz) in a concentration-dependent fashion, automatically turning down the reactions that produced them. This maintains constant levels of the final products, two amino acids that are essential for protein synthesis. B, Control of the cell cycle. The cycle consists of four stages. During the G1 phase, the cell grows in size. During the S phase, the cell duplicates the DNA of its chromosomes. During the G2 phase, the cell checks for completion of DNA replication. In the M phase, chromosomes condense and attach to the mitotic spindle, which separates the duplicated pairs in preparation for the division of the cell at cytokinesis. Biochemical feedback loops called checkpoints halt the cycle (blunt bars) at several points until the successful completion of key preceding events.

Overview of Eukaryotic Cellular Organization and Functions

This section previews the major constituents and processes of eukaryotic cells. This overview is intended to alleviate a practical problem arising in any text on cell biology—the interdependence of all parts of cells. The material must be divided into separate chapters, each on a particular topic. But to appreciate the cross-references to material in other chapters, the reader needs some basic knowledge of the whole cell.

Nucleus

The nucleus (Fig. 1-10) stores genetic information in extraordinarily long DNA molecules called chromosomes. Surprisingly, the coding portions of genes make up only a small fraction (<2%) of the 3 billion nucleotide pairs in human DNA, but more than 50% of the 97 million nucleotide pairs in a nematode worm. Regions called telomeres stabilize the ends of chromosomes, and centromeres ensure the distribution of chromosomes to daughter cells when cells divide. The functions of most of the remaining DNA are not yet known. The DNA and its associated proteins are called chromatin (Fig. 1-5). Interactions with histones and other proteins fold each chromosome compactly enough to fit inside the nucleus. During mitosis, chromosomes condense further into separate structural units that one can observe by light microscopy (Fig. 1-7). Between cell divisions, chromosomes are decondensed but occupy discrete territories within the nucleus.

Figure 1-10 ELECTRON MICROGRAPH OF A THIN SECTION OF A NU-CLEUS.

(Courtesy of Don Fawcett, Harvard Medical School, Boston, Massachusetts.)

Proteins of the transcriptional machinery turn specific genes on and off in response to genetic, developmental, and environmental signals. Enzymes called polymerases make RNA copies of active genes. Messenger RNAs specify the amino acid sequences of proteins. Other RNAs have structural, regulatory, or catalytic functions. Most newly synthesized RNAs must be processed extensively before they are ready for use. Processing involves removal of noncoding intervening sequences, alteration of bases, or addition of specific structures at either end. For cytoplasmic RNAs, this processing occurs before RNA molecules are exported from the nucleus through nuclear pores. The nucleolus assembles ribosomes from more than 50 different proteins and 3 RNA molecules. Genetic errors resulting in altered RNA and protein products cause or predispose individuals to many inherited human diseases.

The nuclear envelope is a double membrane that separates the nucleus from the cytoplasm. All traffic into and out of the nucleus passes through nuclear pores that bridge the double membranes. Inbound traffic includes all nuclear proteins, such as transcription factors and ribosomal proteins. Outbound traffic in-cludes messenger RNAs and ribosomal subunits. Some macromolecules shuttle back and forth between the nucleus and cytoplasm.

Cell Cycle

Cellular growth and division are regulated by an integrated molecular network consisting of protein kinases (enzymes that add phosphate to the side chains of proteins), specific kinase inhibitors, transcription factors, and highly specific proteases. When conditions inside and outside a cell are appropriate for cell division (Fig. 1-9B), changes in the stability of key proteins allow specific protein kinases to escape from negative regulators and to trigger a chain of events leading to DNA replication and cell division. Once DNA replication is initiated, specific destruction of components of these kinases allows cells to complete the process. Once DNA replication is complete, activation of the cell cycle kinases such as Cdk1 pushes the cell into mitosis, the process that separates chromosomes into two daugh-ter cells. Three controls sequentially activate Cdk1 through a positive feedback loop: (1) synthesis of a regulatory subunit, (2) transport into the nucleus, and (3) removal of inhibitory phosphate groups.

Phosphorylation of proteins by Cdk1 leads directly or indirectly to disassembly of the nuclear envelope (in most but not all cells), condensation of mitotic chromosomes, and assembly of the mitotic spindle. Selective proteolysis of Cdk1 regulatory subunits and key chromosomal proteins then allows segregation of identical copies of each chromosome and their repackaging into daughter nuclei as the nuclear envelope reassembles on the surface of the clustered chromosomes. Then daughter cells are cleaved apart by the process of cytokinesis.

A key feature of the cell cycle is a series of built-in quality controls, called checkpoints (Fig. 1-9), which ensure that each stage of the cycle is completed successfully before the process continues to the next step. These checkpoints also detect damage to cellular constituents and block cell cycle progression so that the damage may be repaired. Misregulation of checkpoints and other cell cycle controls is a common cause of cancer. Remarkably, the entire cycle of DNA replication, chromosomal condensation, nuclear envelope breakdown, and reformation, including the modulation of these events by checkpoints, can be carried out in cell-free extracts in a test tube.

Ribosomes and Protein Synthesis

Ribosomes catalyze the synthesis of proteins, using the nucleotide sequences of messenger RNA molecules to specify the sequence of amino acids (Figs. 1-4, 1-6, and 1-11). If the protein being synthesized has a signal sequence for receptors on the endoplasmic reticulum (ER), the ribosome binds to the ER, and the protein is inserted into the ER membrane bilayer or into the lumen of the ER as it is synthesized. Otherwise, ribosomes are free in the cytoplasm, and newly synthesized proteins enter the cytoplasm for routing to various destinations.

Figure 1-11 ELECTRON MICROGRAPH OF A THIN SECTION OF A LIVER CELL SHOWING ORGANELLES.

(Courtesy of Don Fawcett, Harvard Medical School, Boston, Massachusetts.)

Endoplasmic Reticulum

The endoplasmic reticulum is a continuous system of flattened membrane sacks and tubules (Fig. 1-11) that is specialized for protein processing and lipid biosynthesis. Motor proteins move along microtubules to pull the ER membranes into a branching network spread throughout the cytoplasm. ER also forms the outer bilayer of the nuclear envelope. ER pumps and channels regulate the cytoplasmic Ca²⁺ concentration, and ER enzymes metabolize drugs.

Ribosomes synthesizing proteins destined for insertion into cellular membranes or for export from the cell associate with specialized regions of the ER, called rough ER owing to the attached ribosomes (Fig. 1-6). These proteins carry signal sequences of amino acids that guide their ribosomes to ER receptors. As a polypeptide chain grows, its sequence determines whether the protein folds up in the lipid bilayer or translocates into the lumen of the ER. Some proteins are retained in the ER, but most move on to other parts of the cell.

Endoplasmic reticulum is very dynamic. Continuous bidirectional traffic moves small vesicles between the ER and the Golgi apparatus. These vesicles carry soluble proteins in their lumens, in addition to membrane lipids and proteins. Proteins on the cytoplasmic surface of the membranes catalyze each membrane budding and fusion event. The use of specialized proteins for budding and fusion of membranes at different sites in the cell prevents the membrane components from getting mixed up.

Golgi Apparatus

The Golgi apparatus processes the sugar side chains of secreted and membrane glycoproteins and sorts the proteins for transport to other parts of the cell (Figs. 1-6 and 1-11). The Golgi apparatus is a stack of flattened, membrane-bound sacks with many associated vesicles. Membrane vesicles come from the ER and fuse with the Golgi apparatus. As a result of a series of vesicle-budding and fusion events, the membrane molecules and soluble proteins in the lumen pass through the stacks of Golgi apparatus from one side to the other. During this passage, Golgi enzymes, retained in specific layers of the Golgi apparatus by transmembrane anchors, modify the sugar side chains of secretory and membrane proteins. On the downstream side of the Golgi apparatus, processed proteins segregate into different vesicles destined for lysosomes or the plasma membrane. The Golgi apparatus is characteristically located in the middle of the cell near the nucleus and the centrosome.

Lysosomes

An impermeable membrane separates degradative enzymes inside lysosomes from other cellular components. Lysosomal proteins are synthesized by rough ER and transported to the Golgi apparatus, where enzymes recognize a three-dimensional site on the proteins’ surface that targets them for addition of the modified sugar, phosphorylated mannose (Fig. 1-6). Vesicular transport, guided by phosphomannose receptors, delivers lysosomal proteins to the lumen of lysosomes.

Membrane vesicles, called endosomes and phagosomes, deliver ingested microorganisms and other materials destined for destruction to lysosomes. Fusion of these vesicles with lysosomes exposes their cargo to lysosomal enzymes in the lumen. Deficiencies of lysosomal enzymes cause many congenital diseases. In each of these diseases, a deficiency in the ability to degrade a particular biomolecule leads to its accumulation in quantities that can impair the function of the brain, liver, or other organs.

Plasma Membrane

The plasma membrane is the interface of the cell with its environment (Fig. 1-12). Owing to the hydrophobic interior of its lipid bilayer, the plasma membrane is impermeable to ions and most water-soluble molecules. Consequently, they cross the membrane only through transmembrane channels, carriers, and pumps, which provide the cell with nutrients, control internal ion concentrations, and establish a transmembrane electrical potential. A single amino acid change in one plasma membrane pump and Cl⁻ channel causes cystic fibrosis.

Figure 1-12 structure and functions of an animal cell plasma membrane. The lipid bilayer forms a permeability barrier between the cytoplasm and the extracellular environment. Transmembrane adhesion proteins anchor the membrane to the extracellular matrix (A) or to like receptors on other cells (B) and transmit forces to the cytoskeleton (C). ATP-driven enzymes (D) pump Na⁺ out and K⁺ into the cell against concentration gradients (E) to establish an electrical potential across the lipid bilayer. Other transmembrane carrier proteins (F) use these ion concentration gradients to drive the transport of nutrients into the cell. Selective ion channels (G) open and shut transiently to regulate the electrical potential across the membrane. A large variety of receptors (H) bind specific extracellular ligands and send signals across the membrane to the cytoplasm.

Other plasma membrane proteins mediate interactions of cells with their immediate environment. Transmembrane receptors bind extracellular signaling mole-cules, such as hormones and growth factors, and trans-duce their presence into chemical or electrical signals that influence the activity of the cell. Genetic defects in signaling proteins, which turn on signals for growth in the absence of appropriate extracellular stimuli, contribute to some human cancers.

Adhesive glycoproteins of the plasma membrane allow cells to bind specifically to each other or to the extracellular matrix. These selective interactions allow cells to form multicellular associations, such as epithelia. Similar interactions allow white blood cells to bind bacteria so that they can be ingested and digested in lysosomes. In cells that are subjected to mechanical forces, such as muscle and epithelia, adhesive proteins of the plasma membrane are reinforced by association with cytoskeletal filaments inside the cell. In skin, defects in these attachments cause blistering diseases.

ER synthesizes phospholipids and proteins for the plasma membrane (Fig. 1-6). After insertion into the lipid bilayer of the ER, proteins move to the plasma membrane by vesicular transport through the Golgi apparatus. Many components of the plasma membrane are not permanent residents; receptors for extracellular molecules, including nutrients and some hormones, can recycle from the plasma membrane to endosomes and back to the cell surface many times before they are degraded. Defects in the receptor for low-density lipoproteins cause arteriosclerosis.

Mitochondria

Mitochondrial enzymes convert most of the energy released from the breakdown of nutrients into the synthesis of ATP, the common currency for most energy-requiring reactions in cells (Fig. 1-11). This efficient mitochondrial system uses molecular oxygen to complete the oxidation of fats, proteins, and sugars to carbon dioxide and water. A less efficient glycolytic system in the cytoplasm extracts energy from the partial breakdown of glucose to make ATP. Mitochondria cluster near sites of ATP utilization, such as sperm tails, membranes engaged in active transport, nerve terminals, and the contractile apparatus of muscle cells.

Mitochondria also have a key role in cellular responses to toxic stimuli from the environment. In response to drugs such as many that are used in cancer chemotherapy, mitochondria release into the cytoplasm a toxic cocktail of enzymes and other proteins that brings about the death of the cell. Defects in this form of cellular suicide, known as apoptosis, lead to autoimmune disorders, cancer, and some neurodegenerative diseases.

Mitochondria form in a fundamentally different way from the ER, Golgi apparatus, and lysosomes (Fig. 1-6). Free ribosomes synthesize most mitochondrial proteins, which are released into the cytoplasm. Receptors on the surface of mitochondria recognize and bind signal sequences on mitochondrial proteins. Energy-requiring processes transport these proteins into the lumen or insert them into the outer or inner mitochondrial membranes.

DNA, ribosomes, and messenger RNAs located inside mitochondria produce a small number of the proteins that contribute to the assembly of the organelle. This machinery is left over from an earlier stage of evolution when mitochondria arose from symbiotic Bacteria (Fig. 1-1). Defects in the maternally inherited mitochondrial genome cause several diseases, including deafness, diabetes, and ocular myopathy.

Peroxisomes

Peroxisomes are membrane-bound organelles containing enzymes that participate in oxidative reactions. Like mitochondria, peroxisomal enzymes oxidize fatty acids, but the energy is not used to synthesize ATP. Peroxisomes are particularly abundant in plants as well as some animal cells. Peroxisomal proteins are synthesized in the cytoplasm and imported into the organelle using the same strategy as mitochondria but using different targeting sequences and transport machinery (Fig. 1-6). Genetic defects in peroxisomal biogenesis cause several forms of mental retardation.

Cytoskeleton and Motility Apparatus

A cytoplasmic network of three protein polymers—actin filaments, intermediate filaments, and microtubules (Fig. 1-13)—maintains the shape of a cell. Each polymer has distinctive properties and dynamics. Actin filaments and microtubules also provide tracks for the ATP-powered motor proteins that produce most cellular movements (Fig. 1-14), including cellular locomotion, muscle contraction, transport of organelles through the cytoplasm, mitosis, and the beating of cilia and flagella. The specialized forms of motility exhibited by muscle and sperm are exaggerated, highly organized versions of the motile processes used by most other eukaryotic cells.

Figure 1-13 Electron micrograph of the cytoplasmic matrix of a fibroblast prepared by detergent extraction of soluble components, rapid freezing, sublimation of ice, and coating with metal. IF, intermediate filaments; MT, microtubules.

(Courtesy of J. Heuser, Washington University, St. Louis, Missouri.)

Figure 1-14 transport of cytoplasmic particles along actin filaments and microtubules by motor proteins. A, Overview of organelle movements in a neuron and fibroblast. B, Details of the molecular motors. The microtubule-based motors, dynein and kinesin, move in opposite directions. The actin-based motor, myosin, moves in one direction along actin filaments.

(Original drawing, adapted from Atkinson SJ, Doberstein SK, Pollard TD: Moving off the beaten track. Curr Biol 2:326–328, 1992.)

Networks of cross-linked actin filaments anchored to the plasma membrane (Fig. 1-12) reinforce the surface of the cell. In many cells, tightly packed bundles of actin filaments support finger-like projections of the plasma membrane (Fig. 1-5). These filopodia or microvilli increase the surface area of the plasma membrane for transporting nutrients and other processes, including sensory transduction in the ear. Genetic defects in a membrane-associated, actin-binding protein called dystrophin cause the most common form of muscular dystrophy.

Actin filaments participate in movements in two ways. Assembly of actin filaments produces some movements, such as the extension of pseudopods. Other movements result from force produced by the motor protein myosin moving along actin filaments (Fig. 1-14). A family of different types of myosin uses the energy from ATP hydrolysis to produce movements. Muscles use a highly organized assembly of actin and myosin filaments to produce forceful, rapid, one-dimensional contractions. Myosin also drives the contraction of the cleavage furrow during cell division. External signals, such as chemotactic molecules, can influence both actin filament organization and the direction of motility. Genetic defects in myosin cause enlargement of the heart and sudden death.

Intermediate filaments are flexible but strong intracellular tendons used to reinforce the epithelial cells of the skin and other cells that are subjected to substantial physical stresses. All intermediate filament proteins are related to the keratin molecules found in hair. Intermediate filaments characteristically form bundles that link the plasma membrane to the nucleus. Other intermediate filaments reinforce the nuclear envelope. Reversible phosphorylation regulates rearrangements of intermediate filaments during mitosis and cell movements. Genetic defects in keratin intermediate filaments cause blistering diseases of the skin. Defects in nuclear lamins are associated with some types of muscular dystrophy and premature aging.

Microtubules are rigid cylindrical polymers with two main functions. They serve as (1) mechanical reinforcing rods for the cytoskeleton and (2) the tracks for two classes of motor proteins. They are the only cytoskeletal polymer that can resist compression. The polymer has a molecular polarity that determines the rate of growth at the two ends and the direction of movement of motor proteins. Virtually all microtubules in cells have the same polarity relative to the organizing centers that initiate their growth (e.g., the centrosome) (Fig. 1-2). Their rapidly growing ends are oriented toward the periphery of the cell. Individual cytoplasmic microtubules are remarkably dynamic, growing and shrinking on a time scale of minutes.

Two classes of motor proteins use the energy liberated by ATP hydrolysis to move along the microtubules. Kinesin moves its associated cargo (vesicles and RNA protein particles) out along the microtubule network radiating from the centrosome, whereas dynein moves its cargo toward the cell center. Together, they form a two-way transport system in the cell that is particularly well developed in the axons and dendrites of nerve cells. Toxins can impair this transport system and cause nerve malfunctions.

During mitosis, the cell assembles a mitotic apparatus of highly dynamic microtubules and uses microtubule motor proteins to separate the chromosomes into the daughter cells. The motile apparatus of cilia and flagella is built from a complex array of stable microtubules that bends when dynein slides the microtubules past each other. A genetic absence of dynein immobilizes these appendages, causing male infertility and lung infections (Kartagener’s syndrome).

Microtubules, intermediate filaments, and actin filaments each provide mechanical support for the cytoplasm that is enhanced by interactions between these polymers. Associations of microtubules with intermediate filaments and actin filaments unify the cytoskeleton into a continuous mechanical structure that resists forces applied to cells. These polymers also maintain the organization of the cell by providing a scaffolding for some cellular enzyme systems and a matrix between the membrane-bound organelles.