《生物化学》课程教学资源（书籍文献）经典教材 Lehninger Principles of Biochemistry, SIXTH EDITION, David L. Nelson, Michael M. Cox

1.1 Cellular Foundations (a)Animal cell mfored meaes intraclula Reo55steofrbosomal omes Cytoskeleto goana2pnesto store 白 metabolites Cell wall of adjacent ce (b)Plant cell FRE 1-7 Eukaryotic cell structure.Schematiclustrations of two labeled in red are unique to animal cells;those labeled in green are nd (b) .which rom5to30m.Structures hvetohoinan

1.1 Cellular Foundations 7 FIGURE 1–7 Eukaryotic cell structure. Schematic illustrations of two major types of eukaryotic cell: (a) a representative animal cell and (b) a representative plant cell. Plant cells are usually 10 to 100 mm in diameter“ larger than animal cells, which typically range from 5 to 30 mm. Structures labeled in red are unique to animal cells; those labeled in green are unique to plant cells. Eukaryotic microorganisms (such as protists and fungi) have structures similar to those in plant and animal cells, but many also contain specialized organelles not illustrated here. Nelson/Cox Lehninger Biochemistry, 6e ISBN13: 1-4292-3414-8 Figure #1.07 Permanent figure # 111 3rd pass (a) Animal cell (b) Plant cell Ribosomes are protein￾synthesizing machines. Peroxisome oxidizes fatty acids. 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. Nucleus contains the genes (chromatin). Ribosomes Nuclear envelope Cytoskeleton Cytoskeleton supports cell, aids in movement of organelles. Golgi complex Nucleolus is site of ribosomal RNA synthesis. Rough endoplasmic reticulum (RER) is site of much protein synthesis. Mitochondrion oxidizes fuels to produce ATP. Plasma membrane separates cell from environment, regulates movement of materials into and out of cell. 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. Cell wall of adjacent cell Plasmodesma provides path between two plant cells. Nuclear envelope segregates chromatin (DNA  protein) from cytoplasm. Vacuole degrades and recycles macromolecules, stores metabolites. Glyoxysome contains enzymes of the glyoxylate cycle

The Foundations of Biochemistru leaves most of the organelles intact.The ho for separating organelles from the cytosol and from each and lysosomes differ in size and therefore sediment at dif. ferent rates a typical cell f These methods v in degr ed toestablish,fore shear.This treatment ruptures the plasma membrane but 2ameeo The Cytoplasm Is Organized by the Cytoskeleton an interlocking three-dimensional meshwork,the eyto mm) skeleton.There about 6 to 22 nm),composition,and specifie function uper vide str ctur and organization to the cyto 20.0 roduce the motion of organelles or of the whole cell. h type of cytoskelet comp of sin ent is compose to form filaments of uniform thickness.These fila not per I pro change dramatically with 1500003hi old mot ion,or changes ir membranes all types of fiaments are regulated bother proteins which serve to link or bundle the filaments or to mov those cells.) The picture that emerges s fron this brief survey of stru ure is o ork c mall vesicle enclosed con the FIGURE 1-8 Sub llular fra umen thel mouon poweredenergy-dependent notor proteins endomembra system segre n ar The on which certain enzyme-catalvzed reactions occur Exocytosis and endocytosis,mechanisms of transpor (see Fig 3).Therge and small particles in the and in respectr ey) involve m at d r p erial cytoplasm and surrounding medium.allowing for secre f cen xtra

8 The Foundations of Biochemistry 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 investigating their structures and functions. In a typical cell fractionation (Fig. 1–8), cells or tissues in solution are gently disrupted by physical shear. This treatment ruptures the plasma membrane but 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 simi￾lar to that in organelles, thus balancing diffusion of water into and out of the organelles, which would swell and burst in a solution of lower osmo￾larity (see Fig. 2“13). The large and small particles in the suspension can be separated by centrifugation at different speeds. Larger particles sedi￾ment more rapidly than small particles, and soluble material does not sediment. By careful choice of the conditions of centrifugation, subcellular fractions can be separated for biochemical characterization. Nelson/Cox Principles of Biochemistry, 6e ISBN13: 1-4292-3414-8 Figure 01.08 Permanent figure # 112 ISBN13: 1-4292-3414-8 02-26-2012 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 dif￾ferent rates. These methods were used to establish, for example, that lysosomes contain degradative enzymes, mitochon￾dria 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 Fluorescence microscopy reveals several types of pro￾tein filaments crisscrossing the eukaryotic cell, forming an interlocking three-dimensional meshwork, the cyto￾skeleton. There are three general types of cytoplasmic filaments—actin filaments, microtubules, and interme￾diate 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 cyto￾plasm and shape to the cell. Actin filaments and micro￾tubules 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 associate noncovalently to form filaments of uniform thickness. These fila￾ments are not permanent structures; they undergo constant disassembly into their protein subunits and reassembly into filaments. Their locations in cells are not rigidly fixed but may change dramatically with mitosis, cytokinesis, amoeboid motion, or changes in cell shape. The assembly, 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. (Bacteria contain actinlike proteins that serve similar roles in those cells.) The picture that emerges from this brief survey of eukaryotic cell structure is of a cell with a meshwork of structural fibers and a complex system of membrane￾enclosed compartments (Fig. 1–7). The filaments disas￾semble 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-dependent motor proteins. The endomembrane system segre￾gates 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 mem￾brane fusion and fission, provide paths between the cytoplasm and surrounding medium, allowing for secre￾tion of substances produced in the cell and uptake of extracellular materials. macromolecules Low-speed centrifugation (1,000 g, 10 min) Supernatant subjected to medium-speed centrifugation (20,000 g, 20 min) Supernatant subjected to high-speed centrifugation (80,000 g, 1 h) Supernatant subjected to very high-speed centrifugation (150,000 g, 3 h) Tissue Tissue homogenate Pellet contains mitochondria, lysosomes, peroxisomes Pellet contains microsomes (fragments of ER), small vesicles Pellet contains ribosomes, large Differential centrifugation ▲ ▲ ▲ ▲▲ ▲ ▲ ▲ ▲ ▲ ▲ ▲ ▲ ▲ ▲ ▲ ▲ Pellet contains whole cells, nuclei, cytoskeletons, plasma membranes Supernatant contains soluble proteins ❚ homogenization

1.1 Cellular Foundations 9 between the cytoskeleton and organelles are noncova Cells Build Supramolecular Structures alanine m tes (red blood cells). globuar shapes and ate somes (about 20 nm in diameter).which are in turn muc microscope.Figure 1-11 the structural hierar chyinoelhlarorganzation ucleic acid and polysaccharides are ioi证 alent bonds.In owever. macromolecules by non ons noncovalent interactions are hydrogen bonds (betweer polar groups),ionic interactions (between groups) smaller than those of covalent bonds.The non in supramolecular complexes stabilize these assemblies producing their unique structures In Vitro Studies May Overlook Important Interactions FIGURE 1-9 TH type among Molecules ibody (that recognizes a characteristic protein cova 1 erstand ell is viewed with a fluc test tube),without interference from other molecules present he inta cel lis from the bovine pulmonary artery.Bundle ach s. in vivo ("in t the cell chromosomes (in the nuleus)are stained blue.(b)Anewt lung cell undergoing mitosis.Microtubule is quite different from the inside of a test tube.Th terfer densed chro osomes(blue).pull the chromomes to pposite poles. the molecule purified For example.in vitro studies of pure enzymes are commonly done at very low enzyme mn the ce ed in th Although complex,this organization of the cyto- gel-like cyt ol with thousands of other proteins,some f which bind to that enzyme and ce its activity ain s in its life redramatic,incly orcheatrater never entering the bulk solvent zations,such as the events of mitosis. The interaction of the known macromolecules in a cell an

1.1 Cellular Foundations 9 between the cytoskeleton and organelles are noncova￾lent, 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). An alanine molecule is less than 0.5 nm long. A molecule of 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 ribo￾somes (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 biomol￾ecules to cellular structures that can be seen with the light microscope. Figure 1–11 illustrates the structural hierar￾chy in cellular organization. The monomeric subunits of 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 interac￾tions (London forces)—all of which have energies much smaller than those of covalent bonds. These noncova￾lent interactions are 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 enzymes are commonly done at very low enzyme concentrations in thoroughly stirred aqueous solutions. In the cell, an enzyme is dissolved or suspended in the gel-like cytosol with thousands of other proteins, some of which bind to that enzyme and influence its activity. Some enzymes are components of multienzyme com￾plexes in which reactants are channeled from one enzyme to another, never entering the bulk solvent. When all of the known macromolecules in a cell are Although complex, this organization of the cyto￾plasm is far from random. The motion and positioning of organelles and cytoskeletal elements are under tight regulation, and at certain stages in its life, a eukaryotic cell undergoes dramatic, finely orchestrated reorgani￾zations, such as the events of mitosis. The interactions FIGURE 1–9 The three types of cytoskeletal filaments: actin filaments, microtubules, and intermediate filaments. Cellular structures can be labeled with an antibody (that recognizes a characteristic protein) cova￾lently attached to a fluorescent compound. The stained structures are visible when the cell is viewed with a fluorescence microscope. (a) Endothelial cells from the bovine pulmonary artery. Bundles of actin fila￾ments called “stress fibers” are stained red; microtubules, radiating from the cell center, are stained green; and chromosomes (in the nucleus) are stained blue. (b) A newt lung cell undergoing mitosis. Microtubules (green), attached to structures called kinetochores (yellow) on the con￾densed chromosomes (blue), pull the chromosomes to opposite poles, or centrosomes (magenta), of the cell. Intermediate filaments, made of keratin (red), maintain the structure of the cell. (b) (a)

10 The Foundations of Biochemistry function ofindividual enzymes and other biomolecules- crowded and that diffusion of macromolecules within to understan unction in vivo as well as in vitro. the cytosol must be slowed by collisions with other large SUMMARY 1.1 Cellular Foundations a have organization and macromolecular associations on the inorganic ions,and enzymes;and have a set of (a)Some of the amino acids of proteins romchemotrpchemi el c00 C00 passing electrons to good electron acceptors: -H H HN-C-H 「cH s contain cytos Serin envelope.Eukaryotic cells have a nucleus and are multicompartmented,with certain processes H.N- C-H 00 FIGURE 1-10 The orga ater mistry.Sh NE o here are (a) ugars,and phosphate ion from which all nu OH Tyrosin omponent of both nucleic acids and membrane lipids b)The (e)So C00 -CH.CH OH HO -0H Phosphate (d)The parent sugar a-o-Ribo -Deoxy-a--ribose H OH a--Glucose

10 The Foundations of Biochemistry function of individual enzymes and other biomolecules— to understand function in vivo as well as in vitro. SUMMARY 1.1 Cellular Foundations u All cells are bounded by a plasma membrane; have a cytosol containing metabolites, coenzymes, inorganic ions, and enzymes; and have a set of genes contained within a nucleoid (bacteria and archaea) or nucleus (eukaryotes). u All organisms require a source of energy to perform cellular work. Phototrophs obtain energy from sunlight; chemotrophs oxidize chemical fuels, passing electrons to good electron acceptors: inorganic compounds, organic compounds, or molecular oxygen. u Bacterial and archaeal cells contain cytosol, a nucleoid, and plasmids, all contained within a cell envelope. Eukaryotic cells have a nucleus and are multicompartmented, with certain processes represented at their known dimensions and concentra￾tions (Fig. 1–12), it is clear that the cytosol is very crowded and that diffusion of macromolecules within the cytosol must be slowed by collisions with other large structures. In short, a given molecule may behave quite differently in the cell and in vitro. A central challenge of biochemistry is to understand the influences of cellular organization and macromolecular associations on the FIGURE 1–10 The organic compounds from which most cellular materi￾als 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 light red); (b) the five nitrogenous bases, two five-carbon sugars, and phosphate ion from which all nucleic acids are built; (c) five components of membrane lipids; and (d) d-glucose, the simple sugar from which most carbohydrates are derived. Note that phosphate is a component of both nucleic acids and membrane lipids. H3  N H3  N H3   N H3  N OC A COO COO COO COO H3  N COO H3  N COO COO A CH3 OH OC A A CH2OH OH OC A A C A H2 OH Alanine Serine Aspartate OC A A C A SH H2 OH Cysteine Histidine C A OC A OH H2 OH Tyrosine OC A A C A H2 OH C H CH HC N NH (a) Some of the amino acids of proteins Uracil Thymine -D-Ribose 2-Deoxy- -D-ribose O H OH NH2 HOCH2 Cytosine H HH OH H O H OH HOCH2 H HH OH OH Adenine Guanine COO Oleate Palmitate H CH2OH O HO OH -D-Glucose H H H OH OH H (b) The components of nucleic acids (c) Some components of lipids (d) The parent sugar HO P O O OH Phosphate N Choline  CH2CH2OH CH3 CH3 CH3 Glycerol CH2OH CHOH CH2OH CH2 CH3 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH3 CH2 CH2 CH2 CH2 CH2 CH2 COO CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH CH    C NH2 C C CH HC N N N H N C O C C CH C HN N N H N C O O CH CH C HN N H O CH CH C N N H C O O CH C C HN N H H2N CH3 Nitrogenous bases Five-carbon sugars

1.2 Chemical Foundations 11 Macromolecule Monomeric units Amino acid plasma membrane Sugars FGURE 1-1 Structural hier archy in the molecula r org mple,the nucleus of this plan cell contains chromatin,a s other relatively ents of cells ar sists of D smaller macromolecules and even smaller molecular subunits.For proteins (amino acids). alonwhich celluar organelles move throughout the cell. 1.2 Chemical Foundations ists had concluded that the d出 (17437 41 od th tive chemical simplicity of the"mineral world"and con Duter membrane nner membrane and phosphorus. ome the first half f the wentiet century,para yeast and in animal muscle cells revealed remarkable chemical similarities in these two apparently very differ ent ce a the own 10 FIGURE 1-12 Th ates,and the same 10 enzymes.Subsequent studies of nany other biochemica proc ses in many differen ues Monod been diluted manyfold and the interactions between diffusing macro nary ongin

1.2 Chemical Foundations 11 Supramolecular complexes held together by noncovalent interactions are part of a hierarchy of structures, some visible with the light microscope. When individual molecules are removed from these complexes to be studied in vitro, interactions important in the living cell may be lost. 1.2 Chemical Foundations Biochemistry aims to explain biological form and function in chemical terms. By the late eighteenth century, chem￾ists had concluded that the composition of living matter is strikingly different from that of the inanimate world. Antoine-Laurent Lavoisier (1743–1794) noted the rela￾tive chemical simplicity of the “mineral world” and con￾trasted it with the complexity of the “plant and animal worlds”; the latter, he knew, were composed of com￾pounds rich in the elements carbon, oxygen, nitrogen, and phosphorus. During the first half of the twentieth century, paral￾lel biochemical investigations of glucose breakdown in yeast and in animal muscle cells revealed remarkable chemical similarities in these two apparently very differ￾ent cell types; the breakdown of glucose in yeast and muscle cells involved the same 10 chemical intermedi￾ates, and the same 10 enzymes. Subsequent studies of many other biochemical processes in many different organisms have confirmed the generality of this obser￾vation, neatly summarized in 1954 by Jacques Monod: “What is true of E. coli is true of the elephant.” The cur￾rent understanding that all organisms share a common evolutionary origin is based in part on this observed FIGURE 1–12 The crowded cell. This drawing by David Goodsell is an accurate representation of the relative sizes and numbers of macromol￾ecules in one small region of an E. coli cell. This concentrated cytosol, crowded with proteins and nucleic acids, is very different from the typi￾cal extract of cells used in biochemical studies, in which the cytosol has been diluted manyfold and the interactions between diffusing macro￾molecules have been strongly altered. segregated in specific organelles; organelles can be separated and studied in isolation. Cytoskeletal proteins assemble into long filaments that give cells shape and rigidity and serve as rails along which cellular organelles move throughout the cell. FIGURE 1–11 Structural hierarchy in the molecular organization of cells. The organelles and other relatively large components of cells are composed of supramolecular complexes, which in turn are composed of smaller macromolecules and even smaller molecular subunits. For example, the nucleus of this plant cell contains chromatin, a supramo￾lecular complex that consists of DNA and basic proteins (histones). DNA is made up of simple monomeric subunits (nucleotides), as are proteins (amino acids). c01TheFoundationsofBiochemistry.indd Page 11 19/06/12 1:11 PM user-F391 /Users/user-F391/Desktop Cell envelope Flagellum Outer membrane Inner membrane Ribosome DNA (nucleoid)