Cellular Foundations

The unity and diversity of organisms become apparent even at the cellular level. The smallest organisms consist of single cells and are microscopic. Larger, multicellular organisms contain many different types of cells, which vary in size, shape, and specialized function. Despite these obvious differences, all cells of the simplest and most complex organisms share certain fundamental properties, which can be seen at the biochemical level.

Cells Are the Structural and Functional Units of All Living Organisms

Cells of all kinds share certain structural features (Fig. 1–3). The plasma membrane defines the periphery of the cell, separating its contents from the surroundings. It is composed of lipid and protein molecules that form a thin, tough, pliable, hydrophobic barrier around the cell. The membrane is a barrier to the free passage of inorganic ions and most other charged or polar com pounds. Transport proteins in the plasma membrane al low the passage of certain ions and molecules; receptor proteins transmit signals into the cell; and membrane enzymes participate in some reaction pathways. Because the individual lipids and proteins of the plasma membrane are not covalently linked, the entire structure is remarkably flexible, allowing changes in the shape and size of the cell. As a cell grows, newly made lipid and protein molecules are inserted into its plasma membrane; cell division produces two cells, each with its own membrane. This growth and cell division (fission) occurs without loss of membrane integrity.

FIGURE 1–3 The universal features of living cells. All cells have a nucleus or nucleoid, a plasma membrane, and cytoplasm. The cytosol is defined as that portion of the cytoplasm that remains in the super natant after centrifugation of a cell extract at 150,000 g for 1 hour.

The internal volume bounded by the plasma mem brane, the cytoplasm (Fig. 1–3), is composed of an aqueous solution, the cytosol, and a variety of sus pended particles with specific functions. The cytosol is a highly concentrated solution containing enzymes and the RNA molecules that encode them; the components (amino acids and nucleotides) from which these macro molecules are assembled; hundreds of small organic molecules called metabolites, intermediates in biosyn thetic and degradative pathways; coenzymes, com pounds essential to many enzyme-catalyzed reactions; inorganic ions; and ribosomes, small particles (com posed of protein and RNA molecules) that are the sites of protein synthesis. All cells have, for at least some part of their life, either a nucleus or a nucleoid, in which the genome—the complete set of genes, composed of DNA—is stored and replicated. The nucleoid, in bacteria, is not separated from the cytoplasm by a membrane; the nucleus, in higher organisms, consists of nuclear material en closed within a double membrane, the nuclear envelope. Cells with nuclear envelopes are called eukaryotes (Greek eu, “true,” and karyon, “nucleus”); those without nuclear envelopes—bacterial cells—are prokaryotes (Greek pro, “before”).

Cellular Dimensions Are Limited by Oxygen Diffusion Most cells are microscopic, invisible to the unaided eye. Animal and plant cells are typically 5 to 100 m in di ameter, and many bacteria are only 1 to 2 m long (see the inside back cover for information on units and their abbreviations). What limits the dimensions of a cell? The lower limit is probably set by the minimum number of each type of biomolecule required by the cell. The smallest cells, certain bacteria known as mycoplasmas, are 300 nm in diameter and have a volume of about 10 14 mL. A single bacterial ribosome is about 20 nm in its longest dimension, so a few ribosomes take up a sub stantial fraction of the volume in a mycoplasmal cell. The upper limit of cell size is probably set by the rate of diffusion of solute molecules in aqueous systems. For example, a bacterial cell that depends upon oxygen consuming reactions for energy production must obtain   molecular oxygen by diffusion from the surrounding medium through its plasma membrane. The cell is so small, and the ratio of its surface area to its volume is so large, that every part of its cytoplasm is easily reached by O2 diffusing into the cell. As cell size increases, however, surface-to-volume ratio decreases, until metabolism consumes O2 faster than diffusion can supply it. Metabolism that requires O2 thus becomes impossible as cell size increases beyond a certain point, placing a theoretical upper limit on the size of the cell.

There Are Three Distinct Domains of Life All living organisms fall into one of three large groups (kingdoms, or domains) that define three branches of evolution from a common progenitor (Fig. 1–4). Two large groups of prokaryotes can be distinguished on bio chemical grounds: archaebacteria (Greek arche-, “ori gin”) and eubacteria (again, from Greek eu, “true”). Eubacteria inhabit soils, surface waters, and the tissues of other living or decaying organisms. Most of the well-studied bacteria, including Escherichia coli, are eu bacteria. The archaebacteria, more recently discovered, are less well characterized biochemically; most inhabit extreme environments—salt lakes, hot springs, highly acidic bogs, and the ocean depths. The available evidence suggests that the archaebacteria and eubacteria diverged early in evolution and constitute two separate

FIGURE 1–4 Phylogeny of the three domains of life. Phylogenetic relationships are often illustrated by a “family tree” of this type. The fewer the branch points between any two organisms, the closer is their evolutionary relationship.

FIGURE 1–5 Organisms can be classified according to their source of energy (sunlight or oxidizable chemical compounds) and their source of carbon for the synthesis of cellular material.

domains, sometimes called Archaea and Bacteria. All eu karyotic organisms, which make up the third domain, Eukarya, evolved from the same branch that gave rise to the Archaea; archaebacteria are therefore more closely related to eukaryotes than to eubacteria. Within the domains of Archaea and Bacteria are sub groups distinguished by the habitats in which they live. In aerobic habitats with a plentiful supply of oxygen, some resident organisms derive energy from the trans fer of electrons from fuel molecules to oxygen. Other environments are anaerobic, virtually devoid of oxy gen, and microorganisms adapted to these environments obtain energy by transferring electrons to nitrate (forming N2), sulfate (forming H₂S), or CO₂ (forming CH₄). Many organisms that have evolved in anaerobic environments are obligate anaerobes: they die when ex posed to oxygen.

We can classify organisms according to how they obtain the energy and carbon they need for synthesizing cellular material (as summarized in Fig. 1–5). There are two broad categories based on energy sources: phototrophs (Greek trophe-, “nourishment”) trap and use sunlight, and chemotrophs derive their energy from oxidation of a fuel. All chemotrophs require a source of organic nutrients; they cannot fix CO2 into organic com pounds. The phototrophs can be further divided into those that can obtain all needed carbon from CO2 (autotrophs) and those that require organic nutrients (heterotrophs). No chemotroph can get its carbon

atoms exclusively from CO2 (that is, no chemotrophs are autotrophs), but the chemotrophs may be further classified according to a different criterion: whether the fuels they oxidize are inorganic (lithotrophs) or organic (organotrophs). Most known organisms fall within one of these four broad categories—autotrophs or heterotrophs among the photosynthesizers, lithotrophs or organotrophs among the chemical oxidizers. The prokaryotes have several general modes of obtaining carbon and energy. Escherichia coli, for example, is a chemo organoheterotroph; it re quires organic compounds from its environment as fuel and as a source of carbon. Cyanobacteria are photo Lith autotrophs; they use sunlight as an energy source and convert CO₂ into biomolecules. We humans, like E. coli, are chemo organoheterotrophs.

Escherichia coli Is the Most-Studied Prokaryotic Cell

Bacterial cells share certain common structural features, but also show group-specific specializations (Fig. 1–6). E. coli is a usually harmless inhabitant of the hu man intestinal tract. The E. coli cell is about 2 m long and a little less than 1 m in diameter. It has a protective outer membrane and an inner plasma membrane that encloses the cytoplasm and the nucleoid. Between the inner and outer membranes is a thin but strong layer of polymers called peptidoglycans, which gives the cell its shape and rigidity. The plasma membrane and the

FIGURE 1–6 Common structural features of bacterial cells. Because of differences in the cell envelope structure, some eubacteria (gram positive bacteria) retain Gram’s stain, and others (gram-negative bacteria) do not. E. coli is gram-negative. Cyanobacteria are also eubacteria but are distinguished by their extensive internal membrane system, in which photosynthetic pigments are localized. Although the cell envelopes of archaebacteria and gram-positive eubacteria look similar under the electron microscope, the structures of the membrane lipids and the polysaccharides of the cell envelope are distinctly different in these organisms.

layers outside it constitute the cell envelope. In the Archaea, rigidity is conferred by a different type of poly mer (pseudopeptidoglycan). The plasma membranes of eubacteria consist of a thin bilayer of lipid molecules penetrated by proteins. Archaebacterial membranes have a similar architecture, although their lipids differ strikingly from those of the eubacteria. The cytoplasm of E. coli contains about 15,000 ribosomes, thousands of copies each of about 1,000 different enzymes, numerous metabolites and cofactors, and a variety of inorganic ions. The nucleoid contains a single, circular molecule of DNA, and the cytoplasm (like that of most bacteria) contains one or more smaller, circular segments of DNA called plasmids. In nature, some plasmids confer resistance to toxins and antibiotics in the environment. In the laboratory, these DNA segments are especially amenable to experimental manipulation and are extremely useful to molecular geneticists. Most bacteria (including E. coli) lead existences as individual cells, but in some bacterial species cells tend to associate in clusters or filaments, and a few (the myxobacteria, for example) demonstrate simple social behavior.

Eukaryotic Cells Have a Variety of Membranous Organelles, Which Can Be Isolated for Study Typical eukaryotic cells (Fig. 1–7) are much larger than prokaryotic cells—commonly 5 to 100 m in diameter, with cell volumes a thousand to a million times larger than those of bacteria. The distinguishing characteristics of eukaryotes are the nucleus and a variety of membrane bounded organelles with specific functions: mitochondria, endoplasmic reticulum, Golgi complexes, and lysosomes. Plant cells also contain vacuoles and chloroplasts (Fig. 1–7). Also present in the cytoplasm of many cells are granules or droplets containing stored nutrients such as starch and fat. In a major advance in biochemistry, Albert Claude, Christian de Duve, and George Palade developed methods for separating organelles from the cytosol and from each other—an essential step in isolating biomolecules and larger cell components and investigating their

FIGURE 1–7 Eukaryotic cell structure. Schematic illustrations of the two major types of eukaryotic cell: (a) a representative animal cell and (b) a representative plant cell. Plant cells are usually 10 to 100 m in diameter—larger than animal cells, which typically range from 5 to 30 m. Structures labeled in red are unique to either animal or plant cells.

structures and functions. In a typical cell fractionation (Fig. 1–8), cells or tissues in solution are disrupted by gentle homogenization. This treatment ruptures the plasma membrane but leaves most of the organelles intact. The homogenate is then centrifuged; organelles such as nuclei, mitochondria, and lysosomes differ in size and therefore sediment at different rates. They also differ in specific gravity, and they “float” at different levels in a density gradient.

Differential centrifugation results in a rough fraction ation of the cytoplasmic contents, which may be further purified by isopycnic (“same density”) centrifugation. In this procedure, organelles of different buoyant densities (the result of different ratios of lipid and protein in each type of organelle) are separated on a density gradient. By carefully removing material from each region of the gradient and observing it with a microscope, the biochemist can establish the sedimentation position of each organelle

FIGURE 1–8 Subcellular fractionation of tissue. A tissue such as liver is first mechanically homogenized to break cells and disperse their contents in an aqueous buffer. The sucrose medium has an osmotic pressure similar to that in organelles, thus preventing diffusion of water into the organelles, which would swell and burst. (a)The large and small particles in the suspension can be separated by centrifugation at different speeds, or (b)particles of different density can be separated by isopycnic centrifugation. In isopycnic centrifugation, a centrifuge tube is filled with a solution, the density of which increases from top to bottom; a solute such as sucrose is dissolved at different concentrations to produce the density gradient. When a mixture of organelles is layered on top of the density gradient and the tube is centrifuged at high speed, individual organelles sediment until their buoyant density exactly matches that in the gradient. Each layer can be collected separately.

and obtain purified organelles for further study. For example, these methods were used to establish that lysosomes contain degradative enzymes, mitochondria contain oxidative enzymes, and chloroplasts contain photosynthetic pigments. The isolation of an organelle enriched in a certain enzyme is often the first step in the purification of that enzyme. The Cytoplasm Is Organized by the Cytoskeleton and Is Highly Dynamic Electron microscopy reveals several types of protein filaments crisscrossing the eukaryotic cell, forming an inter locking three-dimensional meshwork, the cytoskeleton. There are three general types of cytoplasmic filaments— actin filaments, microtubules, and intermediate filaments (Fig. 1–9)—differing in width (from about 6 to 22 nm), composition, and specific function. All types provide structure and organization to the cytoplasm and shape to the cell. Actin filaments and microtubules also help to produce the motion of organelles or of the whole cell. Each type of cytoskeletal component is composed of simple protein subunits that polymerize to form filaments of uniform thickness. These filaments are not permanent structures; they undergo constant disassembly  into their protein subunits and reassembly into fila ments. Their locations in cells are not rigidly fixed but may change dramatically with mitosis, cytokinesis, amoeboid motion, or changes in cell shape. The assem bly, disassembly, and location of all types of filaments are regulated by other proteins, which serve to link or bundle the filaments or to move cytoplasmic organelles along the filaments. The picture that emerges from this brief survey of cell structure is that of a eukaryotic cell with a meshwork of structural fibers and a complex system of membrane-bounded compartments (Fig. 1–7). The filaments disassemble and then reassemble elsewhere. Membranous vesicles bud from one organelle and fuse with another. Organelles move through the cytoplasm along protein filaments, their motion powered by energy de pendent motor proteins. The endomembrane system segregates specific metabolic processes and provides surfaces on which certain enzyme-catalyzed reactions occur. Exocytosis and endocytosis, mechanisms of transport (out of and into cells, respectively) that involve membrane fusion and fission, provide paths between the cytoplasm and surrounding medium, allowing for secretion of substances produced within the cell and uptake of extracellular materials.

FIGURE 1–9 The three types of cytoskeletal filaments. The upper panels show epithelial cells photographed after treatment with antibodies that bind to and specifically stain (a) actin filaments bundled together to form “stress fibers,” (b) microtubules radiating from the cell center, and (c) intermediate filaments extending throughout the cytoplasm. For these experiments, antibodies that specifically recognize actin, tubulin, or intermediate filament proteins are covalently attached to a fluorescent compound. When the cell is viewed with a fluorescence microscope, only the stained structures are visible. The lower panels show each type of filament as visualized by (a, b) transmission or (c) scanning electron microscopy.

Although complex, this organization of the cyto plasm is far from random. The motion and the position ing of organelles and cytoskeletal elements are under tight regulation, and at certain stages in a eukaryotic cell’s life, dramatic, finely orchestrated reorganizations, such as the events of mitosis, occur. The interactions be tween the cytoskeleton and organelles are noncovalent, reversible, and subject to regulation in response to various intracellular and extracellular signals.

Cells Build Supramolecular Structures Macromolecules and their monomeric subunits differ greatly in size (Fig. 1–10). A molecule of alanine is less than 0.5 nm long. Hemoglobin, the oxygen-carrying protein of erythrocytes (red blood cells), consists of nearly 600 amino acid subunits in four long chains, folded into globular shapes and associated in a structure 5.5 nm in diameter. In turn, proteins are much smaller than ribosomes (about 20 nm in diameter), which are in turn much smaller than organelles such as mitochondria, typically 1,000 nm in diameter. It is a long jump from simple biomolecules to cellular structures that can be seen

FIGURE 1–10 The organic compounds from which most cellular materials are constructed: the ABCs of biochemistry. Shown here are (a) six of the 20 amino acids from which all proteins are built (the side chains are shaded pink); (b) the five nitrogenous bases, two five carbon sugars, and phosphoric acid from which all nucleic acids are built; (c) five components of membrane lipids; and (d)D-glucose, the parent sugar from which most carbohydrates are derived. Note that phosphoric acid is a component of both nucleic acids and membrane lipids.

FIGURE 1–11 Structural hierarchy in the molecular organization of cells. In this plant cell, the nucleus is an organelle containing several types of supramolecular complexes, including chromosomes. Chro with the light microscope. Figure 1–11 illustrates the structural hierarchy in cellular organization. The monomeric subunits in proteins, nucleic acids, and polysaccharides are joined by covalent bonds. In supramolecular complexes, however, macromolecules are held together by noncovalent interactions—much weaker, individually, than covalent bonds. Among these noncovalent interactions are hydrogen bonds (between polar groups), ionic interactions (between charged groups), hydrophobic interactions (among nonpolar groups in aqueous solution), and van der Waals inter actions—all of which have energies substantially smaller than those of covalent bonds (Table 1–1). The nature of these noncovalent interactions is described in Chapter 2. The large numbers of weak interactions between macromolecules in supramolecular complexes stabilize these assemblies, producing their unique structures.

In Vitro Studies May Overlook Important Interactions among Molecules One approach to understanding a biological process is to study purified molecules in vitro (“in glass”—in the test tube), without interference from other molecules present in the intact cell—that is, in vivo (“in the living”). Although this approach has been remarkably revealing, we must keep in mind that the inside of a cell is quite different from the inside of a test tube. The “interfering” components eliminated by purification may be critical to the biological function or regulation of the molecule purified. For example, in vitro studies of pure mosomes consist of macromolecules of DNA and many different proteins. Each type of macromolecule is made up of simple subunits— DNA of nucleotides (deoxyribonucleotides), for example. enzymes are commonly done at very low enzyme concentrations in thoroughly stirred aqueous solutions. In the cell, an enzyme is dissolved or suspended in a gel like cytosol with thousands of other proteins, some of which bind to that enzyme and influence its activity.

Some enzymes are parts of multienzyme complexes in which reactants are channeled from one enzyme to another without ever entering the bulk solvent. Diffusion is hindered in the gel-like cytosol, and the cytosolic com position varies in different regions of the cell. In short, a given molecule may function quite differently in the cell than in vitro. A central challenge of biochemistry is to understand the influences of cellular organization and macromolecular associations on the function of individual enzymes and other biomolecules—to understand function in vivo as well as in vitro.

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Physical Foundations:- Energy Coupling Links Reactions in Biology

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Physical Foundations:- Organisms Transform Energy and Matter from Their Surroundings

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Organocopper reagents undergo conjugate addition

Hydroboration

تثبيت النتروجين Nitrogen Fixation

دورة اليوريا urea cycle

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