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01 Foundations of Biochemistry
PART I: STRUCTURE AND CATALYSIS
02 Water
03 Amino Acids, Peptides, and Proteins
04 Three-Dimensional Structure of Proteins
05 Protein Function
06 Enzymes
07 Carbohydrates and Glycobiology
08 Nucleotides and Nucleic Acids
09 DNA-Based Information Technologies
10 Lipids
11 Biological Membranes and Transport
12 Biosignaling
PART II: BIOENERGETICS AND METABOLISM
13 Principles of Bioenergetics
14 Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway
15 Principles of Metabolic Regulation: Glucose and Glycogen
16 Citric Acid Cycle
17 Fatty Acid Catabolism
18 Amino Acid Oxidation and the Production of Urea
19 Oxidative Phosphorylation and Photophosphorylation
20 Carbohydrate Biosynthesis in Plants and Bacteria
21 Lipid Biosynthesis
22 Biosynthesis of Amino Acids, Nucleotides, and Related Molecules
23 Hormonal Regulation and Integration of Mammalian Metabolism
PART III: INFORMATION PATHWAYS
24 Genes and Chromosomes
25 DNA Metabolism
26 RNA Metabolism
27 Protein Metabolism
28 Regulation of Gene Expression
8885d_c01_01-46 10/27/03 7:48 AM Page 1 mac76 mac76:385_reb: 1 chapter THE FOUNDATIONS OF BIOCHEMISTRY 1.1 Cellular Foundations 3 1.2 Chemical Foundations 12 1.3 Physical Foundations 21 1.4 Genetic Foundations 28 1.5 Evolutionary Foundations 31 With the cell, biology discovered its atom . . . To characterize life, it was henceforth essential to study the cell and analyze its structure: to single out the common denominators, necessary for the life of every cell; alternatively, to identify differences associated with the performance of special functions. —François Jacob, La logique du vivant: une histoire de l’hérédité (The Logic of Life: A History of Heredity), 1970 We must, however, acknowledge, as it seems to me, that man with all his noble qualities . . . still bears in his bodily frame the indelible stamp of his lowly origin. —Charles Darwin, The Descent of Man, 1871 F ifteen to twenty billion years ago, the universe arose as a cataclysmic eruption of hot, energy-rich sub- atomic particles. Within seconds, the simplest elements (hydrogen and helium) were formed. As the universe expanded and cooled, material condensed under the in- fluence of gravity to form stars. Some stars became enormous and then exploded as supernovae, releasing the energy needed to fuse simpler atomic nuclei into the more complex elements. Thus were produced, over bil- lions of years, the Earth itself and the chemical elements found on the Earth today. About four billion years ago, life arose—simple microorganisms with the ability to ex- tract energy from organic compounds or from sunlight, which they used to make a vast array of more complex biomolecules from the simple elements and compounds on the Earth’s surface. Biochemistry asks how the remarkable properties of living organisms arise from the thousands of differ- ent lifeless biomolecules. When these molecules are iso- lated and examined individually, they conform to all the physical and chemical laws that describe the behavior of inanimate matter—as do all the processes occurring in living organisms. The study of biochemistry shows how the collections of inanimate molecules that consti- tute living organisms interact to maintain and perpetu- ate life animated solely by the physical and chemical laws that govern the nonliving universe. Yet organisms possess extraordinary attributes, properties that distinguish them from other collections of matter. What are these distinguishing features of liv- ing organisms? A high degree of chemical complexity and microscopic organization. Thousands of differ- ent molecules make up a cell’s intricate internal structures (Fig. 1–1a). Each has its characteristic sequence of subunits, its unique three-dimensional structure, and its highly specific selection of binding partners in the cell. Systems for extracting, transforming, and using energy from the environment (Fig. 1–1b), enabling organisms to build and maintain their intricate structures and to do mechanical, chemical, osmotic, and electrical work. Inanimate matter tends, rather, to decay toward a more disordered state, to come to equilibrium with its 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 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 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 (a) (b) (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 directed entirely from information contained within the genetic material of the original cell. Mechanisms for sensing and responding to alterations in their surroundings, constantly adjusting to these changes by adapting their internal chemistry. Defined functions for each of their compo- nents and regulated interactions among them. FIGURE 1–2 Diverse living organisms share common chemical fea- tures. Birds, beasts, plants, and soil microorganisms share with hu- mans the same basic structural units (cells) and the same kinds of macromolecules (DNA, RNA, proteins) made up of the same kinds of monomeric subunits (nucleotides, amino acids). They utilize the same pathways for synthesis of cellular components, share the same genetic code, and derive from the same evolutionary ancestors. Shown here is a detail from “The Garden of Eden,” by Jan van Kessel the Younger (1626–1679).
8885d_c01_003 12/20/03 7:03 AM Page 3 mac76 mac76:385_reb: within a common chemical framework. For the sake of clarity, in this book we sometimes risk certain general- izations, which, though not perfect, remain useful; we also frequently point out the exceptions that illuminate scientific generalizations. Biochemistry describes in molecular terms the struc- tures, mechanisms, and chemical processes shared by all organisms and provides organizing principles that underlie life in all its diverse forms, principles we refer to collectively as the molecular logic of life. Although biochemistry provides important insights and practical 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. As you read through the book, you may find it helpful to refer back to this chapter at intervals to refresh your memory of this background material. 1.1 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. Be- cause the individual lipids and proteins of the plasma membrane are not covalently linked, the entire struc- ture 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. 1.1 Cellular Foundations 3 Nucleus (eukaryotes) or nucleoid (bacteria) Contains genetic material–DNA and associated proteins. Nucleus is membrane-bounded. Plasma membrane Tough, flexible lipid bilayer. Selectively permeable to polar substances. Includes membrane proteins that function in transport, in signal reception, and as enzymes. Cytoplasm Aqueous cell contents and suspended particles and organelles. centrifuge at 150,000 g Supernatant: cytosol Concentrated solution of enzymes, RNA, monomeric subunits, metabolites, inorganic ions. Pellet: particles and organelles Ribosomes, storage granules, mitochondria, chloroplasts, lysosomes, endoplasmic reticulum. 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, ei- 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 and replicated. The nucleoid, in bacteria, is not sepa- rated 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 with- out nuclear envelopes—bacterial cells—are prokary- otes (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, how- ever, surface-to-volume ratio decreases, until metabo- lism 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 evi- dence suggests that the archaebacteria and eubacteria diverged early in evolution and constitute two separate Eubacteria Eukaryotes Purple bacteria Gram- positive bacteria Green nonsulfur bacteria Animals Ciliates Fungi Plants Cyanobacteria Flavobacteria Thermotoga Flagellates Microsporidia 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 (energy from light) Autotrophs (carbon from CO2) Examples: •Cyanobacteria •Plants Heterotrophs (carbon from organic compounds) Examples: •Purple bacteria •Green bacteria Chemotrophs (energy from chemical compounds) Heterotrophs (carbon from organic compounds) 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 (form- ing N2), sulfate (forming H2S), or CO2 (forming CH4). Many organisms that have evolved in anaerobic envi- ronments 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 synthesiz- ing cellular material (as summarized in Fig. 1–5). There are two broad categories based on energy sources: pho- totrophs (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 (au- totrophs) and those that require organic nutrients (heterotrophs). No chemotroph can get its carbon Lithotrophs (energy from inorganic compounds) Examples: •Sulfur bacteria •Hydrogen bacteria Organotrophs (energy from organic compounds) Examples: •Most prokaryotes •All nonphototrophic eukaryotes 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 or- ganic (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 gen- eral modes of obtaining carbon and energy. Escherichia coli, for example, is a chemoorganoheterotroph; it re- quires organic compounds from its environment as fuel and as a source of carbon. Cyanobacteria are photo- lithoautotrophs; they use sunlight as an energy source and convert CO2 into biomolecules. We humans, like E. coli, are chemoorganoheterotrophs. Escherichia coli Is the Most-Studied Prokaryotic Cell Bacterial cells share certain common structural fea- tures, 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 protec- tive 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
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 eukaryotic ribosomes, but serve the same function— protein synthesis from an RNA message. Nucleoid Contains a single, simple, long circular DNA molecule. Pili Provide points of adhesion to surface of other cells. Flagella Propel cell through its surroundings. Cell envelope Structure varies with type of bacteria. Outer membrane Peptidoglycan layer Inner membrane Inner membrane Peptidoglycan layer Inner membrane Gram-negative bacteria Outer membrane; peptidoglycan layer Gram-positive bacteria No outer membrane; thicker peptidoglycan layer Cyanobacteria Gram-negative; tougher peptidoglycan layer; extensive internal membrane system with photosynthetic pigments Archaebacteria No outer membrane; peptidoglycan layer outside plasma membrane 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 dif- ferent 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 cofac- tors, 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 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 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 meth- ods for separating organelles from the cytosol and from each other—an essential step in isolating biomolecules and larger cell components and investigating their
8885d_c01_007 1/15/04 3:28 PM Page 7 mac76 mac76:385_reb: (a) Animal cell 1.1 Cellular Foundations 7 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 Nucleolus is site of ribosomal RNA synthesis Nucleus contains the genes (chromatin) Ribosomes Cytoskeleton Golgi complex Nuclear envelope segregates chromatin (DNA ⫹ protein) from cytoplasm Plasma membrane separates cell from environment, regulates movement of materials into and out of cell Rough endoplasmic reticulum (RER) is site of much protein synthesis Mitochondrion oxidizes fuels to produce ATP 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 between two plant cells Cell wall of adjacent cell 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. Glyoxysome contains enzymes of the glyoxylate cycle (b) Plant cell
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 (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 in- tact. 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 gra- dient and observing it with a microscope, the biochemist can establish the sedimentation position of each organelle (a) Differential centrifugation Tissue homogenization ❚ ❚ ❚ Low-speed centrifugation (1,000 g, 10 min) ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚❚ ▲ ▲ ▲ ▲ ▲ ▲ ❚❚ ❚ ▲ ▲ ▲ ❚❚ ▲ ▲ ❚❚ ❚❚ ▲ ❚ ❚ ❚❚ ▲ ❚❚ ❚❚ ▲ ▲ ❚❚ ❚❚ ❚❚ ❚❚ ▲ ▲ ▲ ▲ ▲ ❚❚ ▲ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ Tissue homogenate ❚ ❚❚ ▲ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ Supernatant subjected to medium-speed centrifugation (20,000 g, 20 min) ❚ ❚❚ ❚❚ ❚❚ ❚❚ ▲ ▲ ❚❚ ❚❚ ▲ ❚❚ ❚❚ ❚❚ ▲ ❚❚ ▲ ▲▲ ❚❚ ❚❚ ❚❚ ❚❚ ❚❚ ❚❚ ▲ ❚❚ ❚❚ ▲ ▲▲ ▲ ▲▲ ▲ ▲ ▲ Pellet contains whole cells, nuclei, cytoskeletons, plasma membranes Supernatant subjected to high-speed centrifugation (80,000 g, 1 h) Supernatant subjected to very high-speed centrifugation (150,000 g, 3 h) ❚❚ ❚❚ ❚❚ ❚❚ ❚❚ ❚❚ ❚❚ ❚❚ ❚❚ ❚❚ ❚❚ ▲▲ ▲ ▲▲ ▲ ▲▲ ▲ Pellet contains mitochondria, lysosomes, peroxisomes ❚ ❚ ❚❚ ❚ ❚❚ ❚ ❚❚ ❚❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ Pellet contains microsomes (fragments of ER), small vesicles ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ ❚ Pellet contains ribosomes, large macromolecules Supernatant contains soluble proteins 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 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. (b) Isopycnic (sucrose-density) centrifugation Centrifugation Sample Sucrose gradient Less dense component More dense component Fractionation 8 7 6 5 4 3 2 1
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