Chapter 1: The Foundations of Biochemistry PDF

8885d_c01_01-46 10/27/03 7:48 AM Page 1 mac76 mac76:385_reb: chapter...

8885d_c01_01-46 10/27/03 7:48 AM Page 1 mac76 mac76:385_reb: chapter 1 THE FOUNDATIONS OF BIOCHEMISTRY 1.1 Cellular Foundations 3 life arose—simple microorganisms with the ability to ex- 1.2 Chemical Foundations 12 tract energy from organic compounds or from sunlight, which they used to make a vast array of more complex 1.3 Physical Foundations 21 biomolecules from the simple elements and compounds 1.4 Genetic Foundations 28 on the Earth’s surface. 1.5 Evolutionary Foundations 31 Biochemistry asks how the remarkable properties of living organisms arise from the thousands of differ- ent lifeless biomolecules. When these molecules are iso- With the cell, biology discovered its atom... To lated and examined individually, they conform to all the characterize life, it was henceforth essential to study the physical and chemical laws that describe the behavior cell and analyze its structure: to single out the common of inanimate matter—as do all the processes occurring denominators, necessary for the life of every cell; in living organisms. The study of biochemistry shows how the collections of inanimate molecules that consti- alternatively, to identify differences associated with the tute living organisms interact to maintain and perpetu- performance of special functions. ate life animated solely by the physical and chemical —François Jacob, La logique du vivant: une histoire de l’hérédité laws that govern the nonliving universe. (The Logic of Life: A History of Heredity), 1970 Yet organisms possess extraordinary attributes, properties that distinguish them from other collections We must, however, acknowledge, as it seems to me, that of matter. What are these distinguishing features of liv- man with all his noble qualities... still bears in his ing organisms? bodily frame the indelible stamp of his lowly origin. A high degree of chemical complexity and —Charles Darwin, The Descent of Man, 1871 microscopic organization. Thousands of differ- ent molecules make up a cell’s intricate internal structures (Fig. 1–1a). Each has its characteristic ifteen to twenty billion years ago, the universe arose F as a cataclysmic eruption of hot, energy-rich sub- atomic particles. Within seconds, the simplest elements sequence of subunits, its unique three-dimensional structure, and its highly specific selection of binding partners in the cell. (hydrogen and helium) were formed. As the universe Systems for extracting, transforming, and expanded and cooled, material condensed under the in- using energy from the environment (Fig. fluence of gravity to form stars. Some stars became 1–1b), enabling organisms to build and maintain enormous and then exploded as supernovae, releasing their intricate structures and to do mechanical, the energy needed to fuse simpler atomic nuclei into the chemical, osmotic, and electrical work. Inanimate more complex elements. Thus were produced, over bil- matter tends, rather, to decay toward a more lions of years, the Earth itself and the chemical elements disordered state, to come to equilibrium with its found on the Earth today. About four billion years ago, surroundings. 1 8885d_c01_002 11/3/03 1:38 PM Page 2 mac76 mac76:385_reb: 2 Chapter 1 The Foundations of Biochemistry This is true not only of macroscopic structures, such as leaves and stems or hearts and lungs, but also of microscopic intracellular structures and indi- vidual chemical compounds. The interplay among the chemical components of a living organism is dy- namic; changes in one component cause coordinat- ing or compensating changes in another, with the whole ensemble displaying a character beyond that of its individual parts. The collection of molecules carries out a program, the end result of which is (a) reproduction of the program and self-perpetuation of that collection of molecules—in short, life. A history of evolutionary change. Organisms change their inherited life strategies to survive in new circumstances. The result of eons of evolution is an enormous diversity of life forms, superficially very different (Fig. 1–2) but fundamentally related through their shared ancestry. Despite these common properties, and the funda- mental unity of life they reveal, very few generalizations (b) about living organisms are absolutely correct for every organism under every condition; there is enormous di- versity. The range of habitats in which organisms live, from hot springs to Arctic tundra, from animal intestines to college dormitories, is matched by a correspondingly wide range of specific biochemical adaptations, achieved (c) FIGURE 1–1 Some characteristics of living matter. (a) Microscopic complexity and organization are apparent in this colorized thin sec- tion of vertebrate muscle tissue, viewed with the electron microscope. (b) A prairie falcon acquires nutrients by consuming a smaller bird. (c) Biological reproduction occurs with near-perfect fidelity. A capacity for precise self-replication and self-assembly (Fig. 1–1c). A single bacterial cell placed in a sterile nutrient medium can give rise to a billion identical “daughter” cells in 24 hours. Each cell contains thousands of different molecules, some extremely complex; yet each bacterium is a faithful copy of the original, its construction FIGURE 1–2 Diverse living organisms share common chemical fea- directed entirely from information contained tures. Birds, beasts, plants, and soil microorganisms share with hu- within the genetic material of the original cell. mans the same basic structural units (cells) and the same kinds of Mechanisms for sensing and responding to macromolecules (DNA, RNA, proteins) made up of the same kinds of alterations in their surroundings, constantly monomeric subunits (nucleotides, amino acids). They utilize the same adjusting to these changes by adapting their pathways for synthesis of cellular components, share the same genetic internal chemistry. code, and derive from the same evolutionary ancestors. Shown here Defined functions for each of their compo- is a detail from “The Garden of Eden,” by Jan van Kessel the Younger nents and regulated interactions among them. (1626–1679). 8885d_c01_003 12/20/03 7:03 AM Page 3 mac76 mac76:385_reb: 1.1 Cellular Foundations 3 within a common chemical framework. For the sake of Nucleus (eukaryotes) clarity, in this book we sometimes risk certain general- or nucleoid (bacteria) Contains genetic material–DNA and izations, which, though not perfect, remain useful; we associated proteins. Nucleus is also frequently point out the exceptions that illuminate membrane-bounded. scientific generalizations. Plasma membrane Biochemistry describes in molecular terms the struc- Tough, flexible lipid bilayer. tures, mechanisms, and chemical processes shared by Selectively permeable to all organisms and provides organizing principles that polar substances. Includes membrane proteins that underlie life in all its diverse forms, principles we refer function in transport, to collectively as the molecular logic of life. Although in signal reception, biochemistry provides important insights and practical and as enzymes. applications in medicine, agriculture, nutrition, and industry, its ultimate concern is with the wonder of life itself. In this introductory chapter, then, we describe (briefly!) the cellular, chemical, physical (thermody- namic), and genetic backgrounds to biochemistry and the overarching principle of evolution—the develop- ment over generations of the properties of living cells. Cytoplasm As you read through the book, you may find it helpful Aqueous cell contents and to refer back to this chapter at intervals to refresh your suspended particles memory of this background material. and organelles. centrifuge at 150,000 g 1.1 Cellular Foundations The unity and diversity of organisms become apparent Supernatant: cytosol even at the cellular level. The smallest organisms consist Concentrated solution of enzymes, RNA, of single cells and are microscopic. Larger, multicellular monomeric subunits, organisms contain many different types of cells, which metabolites, vary in size, shape, and specialized function. Despite inorganic ions. these obvious differences, all cells of the simplest and Pellet: particles and organelles most complex organisms share certain fundamental Ribosomes, storage granules, properties, which can be seen at the biochemical level. mitochondria, chloroplasts, lysosomes, endoplasmic reticulum. Cells Are the Structural and Functional Units of All FIGURE 1–3 The universal features of living cells. All cells have a Living Organisms nucleus or nucleoid, a plasma membrane, and cytoplasm. The cytosol Cells of all kinds share certain structural features (Fig. 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. 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 The internal volume bounded by the plasma mem- a thin, tough, pliable, hydrophobic barrier around the brane, the cytoplasm (Fig. 1–3), is composed of an cell. The membrane is a barrier to the free passage of aqueous solution, the cytosol, and a variety of sus- inorganic ions and most other charged or polar com- pended particles with specific functions. The cytosol is pounds. Transport proteins in the plasma membrane al- a highly concentrated solution containing enzymes and low the passage of certain ions and molecules; receptor the RNA molecules that encode them; the components proteins transmit signals into the cell; and membrane (amino acids and nucleotides) from which these macro- enzymes participate in some reaction pathways. Be- molecules are assembled; hundreds of small organic cause the individual lipids and proteins of the plasma molecules called metabolites, intermediates in biosyn- membrane are not covalently linked, the entire struc- thetic and degradative pathways; coenzymes, com- ture is remarkably flexible, allowing changes in the pounds essential to many enzyme-catalyzed reactions; shape and size of the cell. As a cell grows, newly made inorganic ions; and ribosomes, small particles (com- lipid and protein molecules are inserted into its plasma posed of protein and RNA molecules) that are the sites membrane; cell division produces two cells, each with its of protein synthesis. own membrane. This growth and cell division (fission) All cells have, for at least some part of their life, ei- occurs without loss of membrane integrity. ther a nucleus or a nucleoid, in which the genome— 8885d_c01_01-46 10/27/03 7:48 AM Page 4 mac76 mac76:385_reb: 4 Chapter 1 The Foundations of Biochemistry the complete set of genes, composed of DNA—is stored molecular oxygen by diffusion from the surrounding and replicated. The nucleoid, in bacteria, is not sepa- medium through its plasma membrane. The cell is so rated from the cytoplasm by a membrane; the nucleus, small, and the ratio of its surface area to its volume is in higher organisms, consists of nuclear material en- so large, that every part of its cytoplasm is easily reached closed within a double membrane, the nuclear envelope. by O2 diffusing into the cell. As cell size increases, how- Cells with nuclear envelopes are called eukaryotes ever, surface-to-volume ratio decreases, until metabo- (Greek eu, “true,” and karyon, “nucleus”); those with- lism consumes O2 faster than diffusion can supply it. out nuclear envelopes—bacterial cells—are prokary- Metabolism that requires O2 thus becomes impossible otes (Greek pro, “before”). as cell size increases beyond a certain point, placing a theoretical upper limit on the size of the cell. Cellular Dimensions Are Limited by Oxygen Diffusion There Are Three Distinct Domains of Life Most cells are microscopic, invisible to the unaided eye. Animal and plant cells are typically 5 to 100
m in di- All living organisms fall into one of three large groups ameter, and many bacteria are only 1 to 2
m long (see (kingdoms, or domains) that define three branches of the inside back cover for information on units and their evolution from a common progenitor (Fig. 1–4). Two abbreviations). What limits the dimensions of a cell? The large groups of prokaryotes can be distinguished on bio- lower limit is probably set by the minimum number of chemical grounds: archaebacteria (Greek arche-, “ori- each type of biomolecule required by the cell. The gin”) and eubacteria (again, from Greek eu, “true”). smallest cells, certain bacteria known as mycoplasmas, Eubacteria inhabit soils, surface waters, and the tissues are 300 nm in diameter and have a volume of about of other living or decaying organisms. Most of the well- 10
14 mL. A single bacterial ribosome is about 20 nm in studied bacteria, including Escherichia coli, are eu- its longest dimension, so a few ribosomes take up a sub- bacteria. The archaebacteria, more recently discovered, stantial fraction of the volume in a mycoplasmal cell. are less well characterized biochemically; most inhabit The upper limit of cell size is probably set by the extreme environments—salt lakes, hot springs, highly rate of diffusion of solute molecules in aqueous systems. acidic bogs, and the ocean depths. The available evi- For example, a bacterial cell that depends upon oxygen- dence suggests that the archaebacteria and eubacteria consuming reactions for energy production must obtain diverged early in evolution and constitute two separate Eubacteria Eukaryotes Animals Ciliates Green Fungi Gram- positive nonsulfur Plants Purple bacteria bacteria bacteria Flagellates Cyanobacteria Flavobacteria Microsporidia Thermotoga Extreme halophiles Methanogens Extreme thermophiles Archaebacteria 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. 8885d_c01_005 12/20/03 7:04 AM Page 5 mac76 mac76:385_reb: 1.1 Cellular Foundations 5 All organisms Phototrophs Chemotrophs (energy from (energy from chemical light) compounds) Autotrophs Heterotrophs Heterotrophs (carbon from (carbon from (carbon from organic CO2) organic compounds) compounds) Examples: Cyanobacteria Examples: Plants Purple bacteria Green bacteria Lithotrophs Organotrophs (energy from (energy from inorganic organic compounds) compounds) Examples: Examples: Sulfur bacteria Most prokaryotes FIGURE 1–5 Organisms can be classified according to their source Hydrogen bacteria All nonphototrophic of energy (sunlight or oxidizable chemical compounds) and their eukaryotes source of carbon for the synthesis of cellular material. domains, sometimes called Archaea and Bacteria. All eu- atoms exclusively from CO2 (that is, no chemotrophs karyotic organisms, which make up the third domain, are autotrophs), but the chemotrophs may be further Eukarya, evolved from the same branch that gave rise classified according to a different criterion: whether the to the Archaea; archaebacteria are therefore more fuels they oxidize are inorganic (lithotrophs) or or- closely related to eukaryotes than to eubacteria. ganic (organotrophs). Within the domains of Archaea and Bacteria are sub- Most known organisms fall within one of these four groups distinguished by the habitats in which they live. broad categories—autotrophs or heterotrophs among the In aerobic habitats with a plentiful supply of oxygen, photosynthesizers, lithotrophs or organotrophs among some resident organisms derive energy from the trans- the chemical oxidizers. The prokaryotes have several gen- fer of electrons from fuel molecules to oxygen. Other eral modes of obtaining carbon and energy. Escherichia environments are anaerobic, virtually devoid of oxy- coli, for example, is a chemoorganoheterotroph; it re- gen, and microorganisms adapted to these environments quires organic compounds from its environment as fuel obtain energy by transferring electrons to nitrate (form- and as a source of carbon. Cyanobacteria are photo- ing N2), sulfate (forming H2S), or CO2 (forming CH4). lithoautotrophs; they use sunlight as an energy source Many organisms that have evolved in anaerobic envi- and convert CO2 into biomolecules. We humans, like E. ronments are obligate anaerobes: they die when ex- coli, are chemoorganoheterotrophs. posed to oxygen. We can classify organisms according to how they Escherichia coli Is the Most-Studied Prokaryotic Cell obtain the energy and carbon they need for synthesiz- ing cellular material (as summarized in Fig. 1–5). There Bacterial cells share certain common structural fea- are two broad categories based on energy sources: pho- tures, but also show group-specific specializations (Fig. totrophs (Greek trophe-, “nourishment”) trap and use 1–6). E. coli is a usually harmless inhabitant of the hu- sunlight, and chemotrophs derive their energy from man intestinal tract. The E. coli cell is about 2
m long oxidation of a fuel. All chemotrophs require a source of and a little less than 1
m in diameter. It has a protec- organic nutrients; they cannot fix CO2 into organic com- tive outer membrane and an inner plasma membrane pounds. The phototrophs can be further divided into that encloses the cytoplasm and the nucleoid. Between those that can obtain all needed carbon from CO2 (au- the inner and outer membranes is a thin but strong layer totrophs) and those that require organic nutrients of polymers called peptidoglycans, which gives the cell (heterotrophs). No chemotroph can get its carbon its shape and rigidity. The plasma membrane and the 8885d_c01_006 11/3/03 1:39 PM Page 6 mac76 mac76:385_reb: 6 Chapter 1 The Foundations of Biochemistry Ribosomes Bacterial ribosomes are smaller than FIGURE 1–6 Common structural features of bacterial cells. Because eukaryotic ribosomes, but serve the same function— of differences in the cell envelope structure, some eubacteria (gram- protein synthesis from an RNA message. positive bacteria) retain Gram’s stain, and others (gram-negative bacteria) do not. E. coli is gram-negative. Cyanobacteria are also Nucleoid Contains a single, simple, long circular DNA eubacteria but are distinguished by their extensive internal membrane molecule. system, in which photosynthetic pigments are localized. Although the cell envelopes of archaebacteria and gram-positive eubacteria look Pili Provide similar under the electron microscope, the structures of the membrane points of lipids and the polysaccharides of the cell envelope are distinctly dif- adhesion to ferent in these organisms. surface of other cells. Flagella layers outside it constitute the cell envelope. In the Propel cell Archaea, rigidity is conferred by a different type of poly- through its surroundings. 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 Cell envelope different enzymes, numerous metabolites and cofac- Structure varies tors, and a variety of inorganic ions. The nucleoid with type of contains a single, circular molecule of DNA, and the bacteria. cytoplasm (like that of most bacteria) contains one or more smaller, circular segments of DNA called plas- mids. In nature, some plasmids confer resistance to toxins and antibiotics in the environment. In the labo- ratory, these DNA segments are especially amenable to experimental manipulation and are extremely use- ful to molecular geneticists. Most bacteria (including E. coli) lead existences as individual cells, but in some bacterial species cells tend Outer membrane Peptidoglycan layer to associate in clusters or filaments, and a few (the Peptidoglycan layer Inner membrane myxobacteria, for example) demonstrate simple social Inner membrane behavior. Eukaryotic Cells Have a Variety of Membranous Organelles, Which Can Be Isolated for Study Gram-negative bacteria Gram-positive bacteria Typical eukaryotic cells (Fig. 1–7) are much larger than Outer membrane; No outer membrane; prokaryotic cells—commonly 5 to 100
m in diameter, peptidoglycan layer thicker peptidoglycan layer 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. Cyanobacteria Archaebacteria In a major advance in biochemistry, Albert Claude, Gram-negative; tougher No outer membrane; peptidoglycan layer; peptidoglycan layer outside Christian de Duve, and George Palade developed meth- extensive internal plasma membrane ods for separating organelles from the cytosol and from membrane system with each other—an essential step in isolating biomolecules photosynthetic pigments and larger cell components and investigating their 8885d_c01_007 1/15/04 3:28 PM Page 7 mac76 mac76:385_reb: 1.1 Cellular Foundations 7 (a) Animal cell Ribosomes are protein- synthesizing machines Peroxisome destroys peroxides Cytoskeleton supports cell, aids in movement of organells Lysosome degrades intracellular debris Transport vesicle shuttles lipids and proteins between ER, Golgi, and plasma membrane Golgi complex processes, packages, and targets proteins to other organelles or for export Smooth endoplasmic reticulum (SER) is site of lipid synthesis and drug metabolism Nuclear envelope segregates Nucleolus is site of ribosomal chromatin (DNA
protein) RNA synthesis from cytoplasm Nucleus contains the Rough endoplasmic reticulum (RER) is site of much protein genes (chromatin) Plasma membrane separates cell synthesis from environment, regulates movement of materials into and Ribosomes Cytoskeleton out of cell Mitochondrion oxidizes fuels to produce ATP Golgi complex Chloroplast harvests sunlight, produces ATP and carbohydrates Starch granule temporarily stores carbohydrate products of photosynthesis Thylakoids are site of light- driven ATP synthesis Cell wall provides shape and rigidity; protects cell from osmotic swelling Vacuole degrades and recycles macromolecules, stores metabolites Plasmodesma provides path Cell wall of adjacent cell between two plant cells Glyoxysome contains enzymes of the glyoxylate cycle FIGURE 1–7 Eukaryotic cell structure. Schematic illustrations of the (b) Plant cell 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.  8885d_c01_01-46 10/27/03 7:48 AM Page 8 mac76 mac76:385_reb: 8 Chapter 1 The Foundations of Biochemistry structures and functions. In a typical cell fractionation Differential centrifugation results in a rough fraction- (Fig. 1–8), cells or tissues in solution are disrupted by ation of the cytoplasmic contents, which may be further gentle homogenization. This treatment ruptures the purified by isopycnic (“same density”) centrifugation. In plasma membrane but leaves most of the organelles in- this procedure, organelles of different buoyant densities tact. The homogenate is then centrifuged; organelles (the result of different ratios of lipid and protein in each such as nuclei, mitochondria, and lysosomes differ in type of organelle) are separated on a density gradient. By size and therefore sediment at different rates. They also carefully removing material from each region of the gra- differ in specific gravity, and they “float” at different dient and observing it with a microscope, the biochemist levels in a density gradient. 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 wa- ter 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 sepa- rated by isopycnic centrifugation. In isopycnic centrifugation, a cen- trifuge tube is filled with a solution, the density of which increases (a) Differential from top to bottom; a solute such as sucrose is dissolved at different centrifugation concentrations to produce the density gradient. When a mixture of ❚ organelles is layered on top of the density gradient and the tube is ❚ Tissue centrifuged at high speed, individual organelles sediment until their ❚ ❚ homogenization ❚ buoyant density exactly matches that in the gradient. Each layer can ❚ be collected separately. ❚ ❚ ❚ ❚ ❚ Low-speed centrifugation ❚ ❚ ❚ ❚ ❚ ❚ (1,000 g, 10 min) ❚ ❚ ❚ ❚ ▲▲ ❚ ❚ ❚ ❚ ▲ ▲ ▲❚ ▲ ❚ ❚ ▲ Supernatant subjected to ❚ ❚ ❚ ❚ ❚ ❚ ▲ (b) Isopycnic medium-speed centrifugation ❚ ▲ ❚▲ ▲ ❚ ▲ ❚ ▲❚ (20,000 g, 20 min) (sucrose-density) ❚ ▲ ❚ ❚ ❚ ❚ ❚ centrifugation ❚ ▲ ❚ ▲ ❚ ❚ ❚ ▲ ▲ ❚ ❚▲ ❚ ▲ Supernatant subjected ▲ ❚ ▲ ▲ ❚ ❚ ❚ ❚ ▲ to high-speed ❚ ❚ ▲ ❚ ❚ ❚ centrifugation ▲ Tissue ❚ Centrifugation ❚ ❚ ▲ ❚▲ (80,000 g, 1 h) homogenate ❚ ▲ ▲ ❚ ❚ ❚ ❚ ❚ ▲ ❚ ▲ Supernatant ▲❚ ▲ ❚ ▲ ▲ ❚ ❚ subjected to ▲ ▲ ❚ ▲ ❚ ❚❚ ❚ ❚ ❚ very high-speed ❚ ❚ Pellet ❚ centrifugation ❚ ❚ ❚ contains ❚ (150,000 g, 3 h) ❚ ❚ ❚ ❚ ❚ ❚ whole cells, ❚ ❚❚ ❚❚ ❚ ❚ ❚ ❚ ❚ ❚ nuclei, ❚ ❚ ❚ ▲ ▲ ❚ ▲ cytoskeletons, ❚ ▲▲ ❚ ▲ ▲ ❚ ❚ ▲ ❚ ❚ ❚ ▲ ❚ ❚ ❚ plasma ❚ ❚❚ ❚ ❚ ❚ ❚ membranes ❚ ❚ Pellet ❚ ❚ contains Sample ❚❚ ❚ ❚ ❚ mitochondria, ❚❚ ❚ ❚ ❚ ❚ ❚ lysosomes, Supernatant Sucrose ❚ ❚ ❚ contains peroxisomes ❚ ❚ ❚ ❚ ❚ ❚❚❚❚ ❚ gradient ❚ ❚❚ soluble ❚ ❚ ❚ ❚ ❚ Pellet proteins ❚ ❚ ❚ ❚ ❚ contains Less dense ❚❚ ❚ ❚ ❚ microsomes (fragments of ER), component ❚ ❚ small vesicles Fractionation More dense Pellet contains component ribosomes, large macromolecules 8 7 6 5 4 3 2 1 8885d_c01_009 12/20/03 7:04 AM Page 9 mac76 mac76:385_reb: 1.1 Cellular Foundations 9 and obtain purified organelles for further study. For into their protein subunits and reassembly into fila- example, these methods were used to establish that ments. Their locations in cells are not rigidly fixed but lysosomes contain degradative enzymes, mitochondria may change dramatically with mitosis, cytokinesis, contain oxidative enzymes, and chloroplasts contain amoeboid motion, or changes in cell shape. The assem- photosynthetic pigments. The isolation of an organelle en- bly, disassembly, and location of all types of filaments riched in a certain enzyme is often the first step in the are regulated by other proteins, which serve to link or purification of that enzyme. bundle the filaments or to move cytoplasmic organelles along the filaments. The Cytoplasm Is Organized by the Cytoskeleton The picture that emerges from this brief survey of cell structure is that of a eukaryotic cell with a and Is Highly Dynamic meshwork of structural fibers and a complex system of Electron microscopy reveals several types of protein fila- membrane-bounded compartments (Fig. 1–7). The fila- ments crisscrossing the eukaryotic cell, forming an inter- ments disassemble and then reassemble elsewhere. Mem- locking three-dimensional meshwork, the cytoskeleton. branous vesicles bud from one organelle and fuse with There are three general types of cytoplasmic filaments— another. Organelles move through the cytoplasm along actin filaments, microtubules, and intermediate filaments protein filaments, their motion powered by energy de- (Fig. 1–9)—differing in width (from about 6 to 22 nm), pendent motor proteins. The endomembrane system composition, and specific function. All types provide segregates specific metabolic processes and provides structure and organization to the cytoplasm and shape surfaces on which certain enzyme-catalyzed reactions to the cell. Actin filaments and microtubules also help to occur. Exocytosis and endocytosis, mechanisms of produce the motion of organelles or of the whole cell. transport (out of and into cells, respectively) that involve Each type of cytoskeletal component is composed membrane fusion and fission, provide paths between the of simple protein subunits that polymerize to form fila- cytoplasm and surrounding medium, allowing for secre- ments of uniform thickness. These filaments are not per- tion of substances produced within the cell and uptake manent structures; they undergo constant disassembly of extracellular materials. Actin stress fibers Microtubules Intermediate filaments (a) (b) (c) FIGURE 1–9 The three types of cytoskeletal filaments. The upper pan- lin, or intermediate filament proteins are covalently attached to a els show epithelial cells photographed after treatment with antibodies fluorescent compound. When the cell is viewed with a fluorescence that bind to and specifically stain (a) actin filaments bundled together microscope, only the stained structures are visible. The lower panels to form “stress fibers,” (b) microtubules radiating from the cell center, show each type of filament as visualized by (a, b) transmission or and (c) intermediate filaments extending throughout the cytoplasm. For (c) scanning electron microscopy. these experiments, antibodies that specifically recognize actin, tubu- 8885d_c01_010 1/15/04 3:28 PM Page 10 mac76 mac76:385_reb: 10 Chapter 1 The Foundations of Biochemistry Although complex, this organization of the cyto- reversible, and subject to regulation in response to var- plasm is far from random. The motion and the position- ious intracellular and extracellular signals. ing of organelles and cytoskeletal elements are under tight regulation, and at certain stages in a eukaryotic Cells Build Supramolecular Structures cell’s life, dramatic, finely orchestrated reorganizations, Macromolecules and their monomeric subunits differ such as the events of mitosis, occur. The interactions be- greatly in size (Fig. 1–10). A molecule of alanine is less tween the cytoskeleton and organelles are noncovalent, than 0.5 nm long. Hemoglobin, the oxygen-carrying pro- tein of erythrocytes (red blood cells), consists of nearly (a) Some of the amino acids of proteins 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 ribo- COO COO COO A  A  A somes (about 20 nm in diameter), which are in turn H3NOCOH H3NOCOH H3NOCOH much smaller than organelles such as mitochondria, typ- A A A CH3 CH2OH CH2 ically 1,000 nm in diameter. It is a long jump from sim- A ple biomolecules to cellular structures that can be seen
Alanine Serine COO Aspartate

COO COO A  A
FIGURE 1–10 The organic compounds from which most cellular COO H3NOCOH H3NOCOH  A A A materials are constructed: the ABCs of biochemistry. Shown here are H3NOCOH CH2 CH2 A (a) six of the 20 amino acids from which all proteins are built (the A NH CH2 side chains are shaded pink); (b) the five nitrogenous bases, two five- C A CH SH carbon sugars, and phosphoric acid from which all nucleic acids are HC  NH built; (c) five components of membrane lipids; and (d) D-glucose, the Cysteine parent sugar from which most carbohydrates are derived. Note that OH Histidine phosphoric acid is a component of both nucleic acids and membrane Tyrosine lipids. (b) The components of nucleic acids (c) Some components of lipids O O NH2 COO
COO
CH2OH C C CH3 CH2 CH2 CHOH HN CH HN C N CH CH2 CH2 CH2OH C CH C CH C CH Glycerol O N O N O N CH2 CH2 H H H CH2 CH2 Uracil Thymine Cytosine CH3 CH2 CH2  CH3 N CH2CH2OH NH2 O CH2 CH2 CH3 C C O
CH2 CH2 Choline N N N C HN C CH CH2 CH CH HO P OH HC C C C CH CH2 N N H2N N N O H H Phosphoric acid CH2 CH2 Adenine Guanine (d) The parent sugar CH2 CH2 Nitrogenous bases CH2 CH2 HOCH2 O H HOCH2 O CH2 CH2 CH 2OH H H H CH2 CH2 O H H H H H OH H H OH CH2 CH3 OH H OH OH OH H Palmitate HO OH CH2  -D-Ribose H OH 2-Deoxy--D-ribose CH3 Five-carbon sugars Oleate  -D-Glucose 8885d_c01_011 12/20/03 7:04 AM Page 11 mac76 mac76:385_reb: 1.1 Cellular Foundations 11 Level 4: Level 3: Level 2: Level 1: The cell Supramolecular Macromolecules Monomeric units and its organelles complexes NH2 Nucleotides N DNA O
O N
O P O CH2 O O H H H H OH H Chromosome Amino acids H  H3N C COO
Protein CH3 Plasma membrane OH Cellulose CH 2 O H H H OH OH HO OH H CH Sugars H 2 OH O Cell wall FIGURE 1–11 Structural hierarchy in the molecular organization of mosomes consist of macromolecules of DNA and many different pro- cells. In this plant cell, the nucleus is an organelle containing several teins. Each type of macromolecule is made up of simple subunits— types of supramolecular complexes, including chromosomes. Chro- DNA of nucleotides (deoxyribonucleotides), for example. with the light microscope. Figure 1–11 illustrates the enzymes are commonly done at very low enzyme con- structural hierarchy in cellular organization. centrations in thoroughly stirred aqueous solutions. In The monomeric subunits in proteins, nucleic acids, the cell, an enzyme is dissolved or suspended in a gel- and polysaccharides are joined by covalent bonds. In like cytosol with thousands of other proteins, some of supramolecular complexes, however, macromolecules which bind to that enzyme and influence its activity. 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 TABLE 1–1 Strengths of Bonds Common groups), hydrophobic interactions (among nonpolar in Biomolecules groups in aqueous solution), and van der Waals inter- actions—all of which have energies substantially smaller Bond Bond than those of covalent bonds (Table 1–1). The nature dissociation dissociation of these noncovalent interactions is described in Chap- Type energy* Type energy ter 2. The large numbers of weak interactions between of bond (kJ/mol) of bond (kJ/mol) macromolecules in supramolecular complexes stabilize these assemblies, producing their unique structures. Single bonds Double bonds OOH 470 CPO 712 In Vitro Studies May Overlook Important Interactions HOH 435 CPN 615 POO 419 CPC 611 among Molecules COH 414 PPO 502 One approach to understanding a biological process is NOH 389 to study purified molecules in vitro (“in glass”—in the COO 352 Triple bonds test tube), without interference from other molecules COC 348 CmC 816 present in the intact cell—that is, in vivo (“in the liv- SOH 339 NmN 930 ing”). Although this approach has been remarkably re- CON 293 vealing, we must keep in mind that the inside of a cell COS 260 is quite different from the inside of a test tube. The “in- NOO 222 terfering” components eliminated by purification may SOS 214 be critical to the biological function or regulation of the molecule purified. For example, in vitro studies of pure *The greater the energy required for bond dissociation (breakage), the stronger the bond. 8885d_c01_01-46 10/27/03 7:48 AM Page 12 mac76 mac76:385_reb: 12 Chapter 1 The Foundations of Biochemistry Some enzymes are parts of multienzyme complexes in 1.2 Chemical Foundations which reactants are channeled from one enzyme to an- other without ever entering the bulk solvent. Diffusion Biochemistry aims to explain biological form and func- is hindered in the gel-like cytosol, and the cytosolic com- tion in chemical terms. As we noted earlier, one of the position varies in different regions of the cell. In short, most fruitful approaches to understanding biological a given molecule may function quite differently in the phenomena has been to purify an individual chemical cell than in vitro. A central challenge of biochemistry is component, such as a protein, from a living organism to understand the influences of cellular organization and and to characterize its structural and chemical charac- macromolecular associations on the function of individ- teristics. By the late eighteenth century, chemists had ual enzymes and other biomolecules—to understand concluded that the composition of living matter is strik- function in vivo as well as in vitro. ingly different from that of the inanimate world. Antoine Lavoisier (1743–1794) noted the relative chemical sim- plicity of the “mineral world” and contrasted it with the SUMMARY 1.1 Cellular Foundations complexity of the “plant and animal worlds”; the latter, he knew, were composed of compounds rich in the ele- All cells are bounded by a plasma membrane; ments carbon, oxygen, nitrogen, and phosphorus. have a cytosol containing metabolites, During the first half of the twentieth century, par- coenzymes, inorganic ions, and enzymes; and allel biochemical investigations of glucose breakdown in have a set of genes contained within a nucleoid yeast and in animal muscle cells revealed remarkable (prokaryotes) or nucleus (eukaryotes). chemical similarities in these two apparently very dif- Phototrophs use sunlight to do work; ferent cell types; the breakdown of glucose in yeast and chemotrophs oxidize fuels, passing electrons to muscle cells involved the same ten chemical intermedi- good electron acceptors: inorganic compounds, ates. Subsequent studies of many other biochemical organic compounds, or molecular oxygen. processes in many different organisms have confirmed Bacterial cells contain cytosol, a nucleoid, and the generality of this observation, neatly summarized by plasmids. Eukaryotic cells have a nucleus and Jacques Monod: “What is true of E. coli is true of the are multicompartmented, segregating certain elephant.” The current understanding that all organisms processes in specific organelles, which can be share a common evolutionary origin is based in part on separated and studied in isolation. this observed universality of chemical intermediates and transformations. Cytoskeletal proteins assemble into long Only about 30 of the more than 90 naturally occur- filaments that give cells shape and rigidity and ring chemical elements are essential to organisms. Most serve as rails along which cellular organelles of the elements in living matter have relatively low move throughout the cell. atomic numbers; only five have atomic numbers above Supramolecular complexes are held together by that of selenium, 34 (Fig. 1–12). The four most abun- noncovalent interactions and form a hierarchy dant elements in living organisms, in terms of percent- of structures, some visible with the light age of total number of atoms, are hydrogen, oxygen, microscope. When individual molecules are nitrogen, and carbon, which together make up more removed from these complexes to be studied than 99% of the mass of most cells. They are the light- in vitro, interactions important in the living est elements capable of forming one, two, three, and four cell may be lost. bonds, respectively; in general, the lightest elements 1 2 H He FIGURE 1–12 Elements essential to animal 3 4 Bulk elements 5 6 7 8 9 10 Li Be Trace elements B C N O F Ne life and health. Bulk elements (shaded orange) are structural components of cells 11 12 13 14 15 16 17 18 Na Mg Al Si P S Cl Ar and tissues and are required in the diet in 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 gram quantities daily. For trace elements K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr (shaded bright yellow), the requirements are 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 much smaller: for humans, a few milligrams Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe per day of Fe, Cu, and Zn, even less of the 55 56 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 others. The elemental requirements for Cs Ba Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn plants and microorganisms are similar to 87 88 Lanthanides Fr Ra those shown here; the ways in which they Actinides acquire these elements vary. 8885d_c01_013 1/15/04 3:28 PM Page 13 mac76 mac76:385_reb: 1.2 Chemical Foundations 13 form the strongest bonds. The trace elements (Fig. 1–12) (a) (b) represent a miniscule fraction of the weight of the hu- man body, but all are