1. chapterFifteen to twenty billion years ago, the universe aroseas a cataclysmic eruption of hot, energy-rich sub-atomicparticles. Within seconds, the simplest elements(hydrogen and helium) were formed. As the universeexpanded and cooled, material condensed under the in-fluenceof gravity to form stars. Some stars becameenormous and then exploded as supernovae, releasingthe energy needed to fuse simpler atomic nuclei into themore complex elements. Thus were produced, over bil-lionsof years, the Earth itself and the chemical elementsfound on the Earth today. About four billion years ago,life arosesimple microorganisms with the ability to ex-tractenergy from organic compounds or from sunlight,which they used to make a vast array of more complexbiomolecules from the simple elements and compoundson the Earths surface.Biochemistry asks how the remarkable propertiesof living organisms arise from the thousands of differ-entlifeless biomolecules. When these molecules are iso-latedand examined individually, they conform to all thephysical and chemical laws that describe the behaviorof inanimate matteras do all the processes occurringin living organisms. The study of biochemistry showshow the collections of inanimate molecules that consti-tuteliving organisms interact to maintain and perpetu-atelife animated solely by the physical and chemicallaws that govern the nonliving universe.Yet organisms possess extraordinary attributes,properties that distinguish them from other collectionsof matter. What are these distinguishing features of liv-ingorganisms?A high degree of chemical complexity andmicroscopic organization. Thousands of differ-entmolecules make up a cells intricate internalstructures (Fig. 11a). Each has its characteristicsequence of subunits, its unique three-dimensionalstructure, and its highly specific selection ofbinding partners in the cell.Systems for extracting, transforming, andusing energy from the environment (Fig.11b), enabling organisms to build and maintaintheir intricate structures and to do mechanical,chemical, osmotic, and electrical work. Inanimatematter tends, rather, to decay toward a moredisordered state, to come to equilibrium with itssurroundings.THE FOUNDATIONSOF BIOCHEMISTRY1.1 Cellular Foundations 31.2 Chemical Foundations 121.3 Physical Foundations 211.4 Genetic Foundations 281.5 Evolutionary Foundations 31With the cell, biology discovered its atom . . . Tocharacterize life, it was henceforth essential to study thecell and analyze its structure: to single out the commondenominators, necessary for the life of every cell;alternatively, to identify differences associated with theperformance of special functions.Franois Jacob, La logique du vivant: une histoire de lhrdit(The Logic of Life: A History of Heredity), 1970We must, however, acknowledge, as it seems to me, thatman with all his noble qualities . . . still bears in hisbodily frame the indelible stamp of his lowly origin.Charles Darwin, The Descent of Man, 187111

2. (b)A capacity for precise self-replication andself-assembly (Fig. 11c). A single bacterial cellplaced in a sterile nutrient medium can give riseto a billion identical daughter cells in 24 hours.Each cell contains thousands of different molecules,some extremely complex; yet each bacterium isa faithful copy of the original, its constructiondirected entirely from information containedwithin the genetic material of the original cell.Mechanisms for sensing and responding toalterations in their surroundings, constantlyadjusting to these changes by adapting theirinternal chemistry.Defined functions for each of their compo-nentsand regulated interactions among them.This is true not only of macroscopic structures,such as leaves and stems or hearts and lungs, butalso of microscopic intracellular structures and indi-vidualchemical compounds. The interplay amongthe chemical components of a living organism is dy-namic;changes in one component cause coordinat-ingor compensating changes in another, with thewhole ensemble displaying a character beyond thatof its individual parts. The collection of moleculescarries out a program, the end result of which isreproduction of the program and self-perpetuationof that collection of moleculesin short, life.A history of evolutionary change. Organismschange their inherited life strategies to survivein new circumstances. The result of eons ofevolution is an enormous diversity of life forms,superficially very different (Fig. 12) butfundamentally related through their shared ancestry.Despite these common properties, and the funda-mentalunity of life they reveal, very few generalizationsabout living organisms are absolutely correct for everyorganism under every condition; there is enormous di-versity.The range of habitats in which organisms live,from hot springs to Arctic tundra, from animal intestinesto college dormitories, is matched by a correspondinglywide range of specific biochemical adaptations, achieved2 Chapter 1 The Foundations of Biochemistry(a)(c)FIGURE 11 Some characteristics of living matter. (a) Microscopiccomplexity and organization are apparent in this colorized thin sec-tionof 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.FIGURE 12 Diverse living organisms share common chemical fea-tures.Birds, beasts, plants, and soil microorganisms share with hu-mansthe same basic structural units (cells) and the same kinds ofmacromolecules (DNA, RNA, proteins) made up of the same kinds ofmonomeric subunits (nucleotides, amino acids). They utilize the samepathways for synthesis of cellular components, share the same geneticcode, and derive from the same evolutionary ancestors. Shown hereis a detail from The Garden of Eden, by Jan van Kessel the Younger(16261679). 3. within a common chemical framework. For the sake ofclarity, in this book we sometimes risk certain general-izations,which, though not perfect, remain useful; wealso frequently point out the exceptions that illuminatescientific generalizations.Biochemistry describes in molecular terms the struc-tures,mechanisms, and chemical processes shared byall organisms and provides organizing principles thatunderlie life in all its diverse forms, principles we referto collectively as the molecular logic of life. Althoughbiochemistry provides important insights and practicalapplications in medicine, agriculture, nutrition, andindustry, its ultimate concern is with the wonder of lifeitself.In this introductory chapter, then, we describe(briefly!) the cellular, chemical, physical (thermody-namic),and genetic backgrounds to biochemistry andthe overarching principle of evolutionthe develop-mentover generations of the properties of living cells.As you read through the book, you may find it helpfulto refer back to this chapter at intervals to refresh yourmemory of this background material.1.1 Cellular FoundationsThe unity and diversity of organisms become apparenteven at the cellular level. The smallest organisms consistof single cells and are microscopic. Larger, multicellularorganisms contain many different types of cells, whichvary in size, shape, and specialized function. Despitethese obvious differences, all cells of the simplest andmost complex organisms share certain fundamentalproperties, which can be seen at the biochemical level.Cells Are the Structural and Functional Units of AllLiving OrganismsCells of all kinds share certain structural features (Fig.13). The plasma membrane defines the periphery ofthe cell, separating its contents from the surroundings.It is composed of lipid and protein molecules that forma thin, tough, pliable, hydrophobic barrier around thecell. The membrane is a barrier to the free passage ofinorganic ions and most other charged or polar com-pounds.Transport proteins in the plasma membrane al-lowthe passage of certain ions and molecules; receptorproteins transmit signals into the cell; and membraneenzymes participate in some reaction pathways. Be-causethe individual lipids and proteins of the plasmamembrane are not covalently linked, the entire struc-tureis remarkably flexible, allowing changes in theshape and size of the cell. As a cell grows, newly madelipid and protein molecules are inserted into its plasmamembrane; cell division produces two cells, each with itsown membrane. This growth and cell division (fission)occurs without loss of membrane integrity.1.1 Cellular Foundations 3Nucleus (eukaryotes)or nucleoid (bacteria)Contains genetic materialDNA andassociated proteins. Nucleus ismembrane-bounded.Plasma membraneTough, flexible lipid bilayer.Selectively permeable topolar substances. Includesmembrane proteins thatfunction in transport,in signal reception,and as enzymes.CytoplasmAqueous cell contents andsuspended particlesand organelles.centrifuge at 150,000 gSupernatant: cytosolConcentrated solutionof enzymes, RNA,monomeric subunits,metabolites,inorganic ions.Pellet: particles and organellesRibosomes, storage granules,mitochondria, chloroplasts, lysosomes,endoplasmic reticulum.FIGURE 13 The universal features of living cells. All cells have anucleus or nucleoid, a plasma membrane, and cytoplasm. The cytosolis defined as that portion of the cytoplasm that remains in the super-natantafter centrifugation of a cell extract at 150,000 g for 1 hour.The internal volume bounded by the plasma mem-brane,the cytoplasm (Fig. 13), is composed of anaqueous solution, the cytosol, and a variety of sus-pendedparticles with specific functions. The cytosol isa highly concentrated solution containing enzymes andthe RNA molecules that encode them; the components(amino acids and nucleotides) from which these macro-moleculesare assembled; hundreds of small organicmolecules called metabolites, intermediates in biosyn-theticand degradative pathways; coenzymes, com-poundsessential to many enzyme-catalyzed reactions;inorganic ions; and ribosomes, small particles (com-posedof protein and RNA molecules) that are the sitesof protein synthesis.All cells have, for at least some part of their life, ei-thera nucleus or a nucleoid, in which the genome 4. the complete set of genes, composed of DNAis storedand replicated. The nucleoid, in bacteria, is not sepa-ratedfrom the cytoplasm by a membrane; the nucleus,in higher organisms, consists of nuclear material en-closedwithin a double membrane, the nuclear envelope.Cells with nuclear envelopes are called eukaryotes(Greek eu, true, and karyon, nucleus); those with-outnuclear envelopesbacterial cellsare prokary-otes(Greek pro, before).Cellular Dimensions Are Limited by Oxygen DiffusionMost 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 (seethe inside back cover for information on units and theirabbreviations). What limits the dimensions of a cell? Thelower limit is probably set by the minimum number ofeach type of biomolecule required by the cell. Thesmallest cells, certain bacteria known as mycoplasmas,are 300 nm in diameter and have a volume of about1014 mL. A single bacterial ribosome is about 20 nm inits longest dimension, so a few ribosomes take up a sub-stantialfraction of the volume in a mycoplasmal cell.The upper limit of cell size is probably set by therate of diffusion of solute molecules in aqueous systems.For example, a bacterial cell that depends upon oxygen-consumingreactions for energy production must obtainmolecular oxygen by diffusion from the surroundingmedium through its plasma membrane. The cell is sosmall, and the ratio of its surface area to its volume isso large, that every part of its cytoplasm is easily reachedby O2 diffusing into the cell. As cell size increases, how-ever,surface-to-volume ratio decreases, until metabo-lismconsumes O2 faster than diffusion can supply it.Metabolism that requires O2 thus becomes impossibleas cell size increases beyond a certain point, placing atheoretical upper limit on the size of the cell.There Are Three Distinct Domains of LifeAll living organisms fall into one of three large groups(kingdoms, or domains) that define three branches ofevolution from a common progenitor (Fig. 14). Twolarge groups of prokaryotes can be distinguished on bio-chemicalgrounds: archaebacteria (Greek arche-, ori-gin)and eubacteria (again, from Greek eu, true).Eubacteria inhabit soils, surface waters, and the tissuesof other living or decaying organisms. Most of the well-studiedbacteria, including Escherichia coli, are eu-bacteria.The archaebacteria, more recently discovered,are less well characterized biochemically; most inhabitextreme environmentssalt lakes, hot springs, highlyacidic bogs, and the ocean depths. The available evi-dencesuggests that the archaebacteria and eubacteriadiverged early in evolution and constitute two separate4 Chapter 1 The Foundations of BiochemistryEubacteria EukaryotesPurple bacteriaCyanobacteriaFlavobacteriaThermotogaGram-positivebacteriaExtremehalophilesGreennonsulfurbacteriaMethanogens Extreme thermophilesMicrosporidiaPlantsFlagellatesFungiAnimals CiliatesArchaebacteriaFIGURE 14 Phylogeny of the three domains of life. Phylogenetic relationships are often illustrated by a family treeof this type. The fewer the branch points between any two organisms, the closer is their evolutionary relationship. 5. Heterotrophs(carbon fromorganiccompounds)Examples:Purple bacteriaGreen bacteriadomains, sometimes called Archaea and Bacteria. All eu-karyoticorganisms, which make up the third domain,Eukarya, evolved from the same branch that gave riseto the Archaea; archaebacteria are therefore moreclosely related to eukaryotes than to eubacteria.Within the domains of Archaea and Bacteria are sub-groupsdistinguished by the habitats in which they live.In aerobic habitats with a plentiful supply of oxygen,some resident organisms derive energy from the trans-ferof electrons from fuel molecules to oxygen. Otherenvironments are anaerobic, virtually devoid of oxy-gen,and microorganisms adapted to these environmentsobtain energy by transferring electrons to nitrate (form-ingN2), sulfate (forming H2S), or CO2 (forming CH4).Many organisms that have evolved in anaerobic envi-ronmentsare obligate anaerobes: they die when ex-posedto oxygen.We can classify organisms according to how theyobtain the energy and carbon they need for synthesiz-ingcellular material (as summarized in Fig. 15). Thereare two broad categories based on energy sources: pho-totrophs(Greek trophe-, nourishment) trap and usesunlight, and chemotrophs derive their energy fromoxidation of a fuel. All chemotrophs require a source oforganic nutrients; they cannot fix CO2 into organic com-pounds.The phototrophs can be further divided intothose that can obtain all needed carbon from CO2 (au-totrophs)and those that require organic nutrients(heterotrophs). No chemotroph can get its carbon1.1 Cellular Foundations 5atoms exclusively from CO2 (that is, no chemotrophsare autotrophs), but the chemotrophs may be furtherclassified according to a different criterion: whether thefuels they oxidize are inorganic (lithotrophs) or or-ganic(organotrophs).Most known organisms fall within one of these fourbroad categoriesautotrophs or heterotrophs among thephotosynthesizers, lithotrophs or organotrophs amongthe chemical oxidizers. The prokaryotes have several gen-eralmodes of obtaining carbon and energy. Escherichiacoli, for example, is a chemoorganoheterotroph; it re-quiresorganic compounds from its environment as fueland as a source of carbon. Cyanobacteria are photo-lithoautotrophs;they use sunlight as an energy sourceand convert CO2 into biomolecules. We humans, like E.coli, are chemoorganoheterotrophs.Escherichia coli Is the Most-Studied Prokaryotic CellBacterial cells share certain common structural fea-tures,but also show group-specific specializations (Fig.16). E. coli is a usually harmless inhabitant of the hu-manintestinal tract. The E. coli cell is about 2 m longand a little less than 1 m in diameter. It has a protec-tiveouter membrane and an inner plasma membranethat encloses the cytoplasm and the nucleoid. Betweenthe inner and outer membranes is a thin but strong layerof polymers called peptidoglycans, which gives the cellits shape and rigidity. The plasma membrane and theAutotrophs(carbon fromCO2)Examples:CyanobacteriaPlantsHeterotrophs(carbon from organiccompounds)Phototrophs(energy fromlight)Chemotrophs(energy from chemicalcompounds)All organismsLithotrophs(energy frominorganiccompounds)Examples:Sulfur bacteriaHydrogen bacteriaOrganotrophs(energy fromorganiccompounds)Examples:Most prokaryotesAll nonphototrophiceukaryotesFIGURE 15 Organisms can be classified according to their sourceof energy (sunlight or oxidizable chemical compounds) and theirsource of carbon for the synthesis of cellular material. 6. layers outside it constitute the cell envelope. In theArchaea, rigidity is conferred by a different type of poly-mer(pseudopeptidoglycan). The plasma membranes ofeubacteria consist of a thin bilayer of lipid moleculespenetrated by proteins. Archaebacterial membraneshave a similar architecture, although their lipids differstrikingly from those of the eubacteria.The cytoplasm of E. coli contains about 15,000ribosomes, thousands of copies each of about 1,000different enzymes, numerous metabolites and cofac-tors,and a variety of inorganic ions. The nucleoidcontains a single, circular molecule of DNA, and thecytoplasm (like that of most bacteria) contains one ormore smaller, circular segments of DNA called plas-mids.In nature, some plasmids confer resistance totoxins and antibiotics in the environment. In the labo-ratory,these DNA segments are especially amenableto experimental manipulation and are extremely use-fulto molecular geneticists.Most bacteria (including E. coli) lead existences asindividual cells, but in some bacterial species cells tendto associate in clusters or filaments, and a few (themyxobacteria, for example) demonstrate simple socialbehavior.Eukaryotic Cells Have a Variety of MembranousOrganelles, Which Can Be Isolated for StudyTypical eukaryotic cells (Fig. 17) are much larger thanprokaryotic cellscommonly 5 to 100 m in diameter,with cell volumes a thousand to a million times larger thanthose of bacteria. The distinguishing characteristics ofeukaryotes are the nucleus and a variety of membrane-boundedorganelles with specific functions: mitochondria,endoplasmic reticulum, Golgi complexes, and lysosomes.Plant cells also contain vacuoles and chloroplasts (Fig.17). Also present in the cytoplasm of many cells aregranules or droplets containing stored nutrients such asstarch and fat.In a major advance in biochemistry, Albert Claude,Christian de Duve, and George Palade developed meth-odsfor separating organelles from the cytosol and fromeach otheran essential step in isolating biomoleculesand larger cell components and investigating their6 Chapter 1 The Foundations of BiochemistryRibosomes Bacterial ribosomes are smaller thaneukaryotic ribosomes, but serve the same functionprotein synthesis from an RNA message.Nucleoid Contains a single,simple, long circular DNAmolecule.Pili Providepoints ofadhesion tosurface ofother cells.FlagellaPropel cellthrough itssurroundings.Cell envelopeStructure varieswith type ofbacteria.Outer membranePeptidoglycan layerInner membraneGram-negative bacteriaOuter membrane;peptidoglycan layerPeptidoglycan layerInner membraneGram-positive bacteriaNo outer membrane;thicker peptidoglycan layerCyanobacteriaGram-negative; tougherpeptidoglycan layer;extensive internalmembrane system withphotosynthetic pigmentsArchaebacteriaNo outer membrane;peptidoglycan layer outsideplasma membraneFIGURE 16 Common structural features of bacterial cells. Becauseof differences in the cell envelope structure, some eubacteria (gram-positivebacteria) retain Grams stain, and others (gram-negativebacteria) do not. E. coli is gram-negative. Cyanobacteria are alsoeubacteria but are distinguished by their extensive internal membranesystem, in which photosynthetic pigments are localized. Although thecell envelopes of archaebacteria and gram-positive eubacteria looksimilar under the electron microscope, the structures of the membranelipids and the polysaccharides of the cell envelope are distinctly dif-ferentin these organisms. 7. 1.1 Cellular Foundations 7Ribosomes are protein-synthesizingmachinesPeroxisome destroys peroxidesCytoskeleton supports cell, aidsin movement of organellsLysosome degrades intracellulardebrisTransport vesicle shuttles lipidsand proteins between ER, Golgi,and plasma membraneGolgi complex processes,packages, and targets proteins toother organelles or for exportSmooth endoplasmic reticulum(SER) is site of lipid synthesisand drug metabolismNucleus contains thegenes (chromatin)Ribosomes CytoskeletonGolgicomplexNucleolus is site of ribosomalRNA synthesisRough endoplasmic reticulum(RER) is site of much proteinsynthesisMitochondrion oxidizes fuels toproduce ATPPlasma membrane separates cellfrom environment, regulatesmovement of materials into andout of cellChloroplast harvests sunlight,produces ATP and carbohydratesStarch granule temporarily storescarbohydrate products ofphotosynthesisThylakoids are site of light-drivenATP synthesisCell wall provides shape andrigidity; protects cell fromosmotic swellingPlasmodesma provides path Cell wall of adjacent cellbetween two plant cellsNuclear envelope segregateschromatin (DNAprotein)from cytoplasmVacuole degrades and recyclesmacromolecules, storesmetabolites(a) Animal cellGlyoxysome contains enzymes ofthe glyoxylate cycle(b) Plant cellFIGURE 17 Eukaryotic cell structure. Schematic illustrations of thetwo major types of eukaryotic cell: (a) a representative animal celland (b) a representative plant cell. Plant cells are usually 10 to100 m in diameterlarger than animal cells, which typicallyrange from 5 to 30 m. Structures labeled in red are unique toeither animal or plant cells. 8. structures and functions. In a typical cell fractionation(Fig. 18), cells or tissues in solution are disrupted bygentle homogenization. This treatment ruptures theplasma membrane but leaves most of the organelles in-tact.such as nuclei, mitochondria, and lysosomes differ insize and therefore sediment at different rates. They alsodiffer in specific gravity, and they float at differentlevels in a density gradient. The homogenate is then centrifuged; organelles Centrifugation Differential centrifugation results in a rough fraction-ationof the cytoplasmic contents, which may be furtherpurified by isopycnic (same density) centrifugation. Inthis procedure, organelles of different buoyant densities(the result of different ratios of lipid and protein in eachtype of organelle) are separated on a density gradient. Bycarefully removing material from each region of the gra-dientand observing it with a microscope, the biochemistcan establish the sedimentation position of each organelle8 Chapter 1 The Foundations of Biochemistry FractionationSampleSucrosegradientLess densecomponentMore densecomponent8 7 6 5 4 3 2 1 Isopycnic(sucrose-density)centrifugation(b) Low-speed centrifugation(1,000 g, 10 min)Supernatant subjected tomedium-speed centrifugation(20,000 g, 20 min)Supernatant subjectedto high-speedcentrifugation(80,000 g, 1 h)Supernatantsubjected tovery high-speedcentrifugation(150,000 g, 3 h)DifferentialcentrifugationTissuehomogenizationTissuehomogenatePelletcontainsmitochondria,lysosomes,peroxisomesPelletcontainsmicrosomes(fragments of ER),small vesiclesPellet containsribosomes, largemacromoleculesPelletcontainswhole cells,nuclei,cytoskeletons,plasmamembranesSupernatantcontainssolubleproteins(a)FIGURE 18 Subcellular fractionation of tissue. A tissue such as liveris first mechanically homogenized to break cells and disperse theircontents in an aqueous buffer. The sucrose medium has an osmoticpressure similar to that in organelles, thus preventing diffusion of wa-terinto the organelles, which would swell and burst. (a) The large andsmall particles in the suspension can be separated by centrifugationat different speeds, or (b) particles of different density can be sepa-ratedby isopycnic centrifugation. In isopycnic centrifugation, a cen-trifugetube is filled with a solution, the density of which increasesfrom top to bottom; a solute such as sucrose is dissolved at differentconcentrations to produce the density gradient. When a mixture oforganelles is layered on top of the density gradient and the tube iscentrifuged at high speed, individual organelles sediment until theirbuoyant density exactly matches that in the gradient. Each layer canbe collected separately. 9. and obtain purified organelles for further study. Forexample, these methods were used to establish thatlysosomes contain degradative enzymes, mitochondriacontain oxidative enzymes, and chloroplasts containphotosynthetic pigments. The isolation of an organelle en-richedin a certain enzyme is often the first step in thepurification of that enzyme.The Cytoplasm Is Organized by the Cytoskeletonand Is Highly DynamicElectron microscopy reveals several types of protein fila-mentscrisscrossing the eukaryotic cell, forming an inter-lockingthree-dimensional meshwork, the cytoskeleton.There are three general types of cytoplasmic filamentsactin filaments, microtubules, and intermediate filaments(Fig. 19)differing in width (from about 6 to 22 nm),composition, and specific function. All types providestructure and organization to the cytoplasm and shapeto the cell. Actin filaments and microtubules also help toproduce the motion of organelles or of the whole cell.Each type of cytoskeletal component is composedof simple protein subunits that polymerize to form fila-mentsof uniform thickness. These filaments are not per-manentstructures; they undergo constant disassembly1.1 Cellular Foundations 9into their protein subunits and reassembly into fila-ments.Their locations in cells are not rigidly fixed butmay change dramatically with mitosis, cytokinesis,amoeboid motion, or changes in cell shape. The assem-bly,disassembly, and location of all types of filamentsare regulated by other proteins, which serve to link orbundle the filaments or to move cytoplasmic organellesalong the filaments.The picture that emerges from this brief surveyof cell structure is that of a eukaryotic cell with ameshwork of structural fibers and a complex system ofmembrane-bounded compartments (Fig. 17). The fila-mentsdisassemble and then reassemble elsewhere. Mem-branousvesicles bud from one organelle and fuse withanother. Organelles move through the cytoplasm alongprotein filaments, their motion powered by energy de-pendentmotor proteins. The endomembrane systemsegregates specific metabolic processes and providessurfaces on which certain enzyme-catalyzed reactionsoccur. Exocytosis and endocytosis, mechanisms oftransport (out of and into cells, respectively) that involvemembrane fusion and fission, provide paths between thecytoplasm and surrounding medium, allowing for secre-tionof substances produced within the cell and uptakeof extracellular materials.Actin stress fibers(a)Microtubules(b)Intermediate filaments(c)FIGURE 19 The three types of cytoskeletal filaments. The upper pan-elsshow epithelial cells photographed after treatment with antibodiesthat bind to and specifically stain (a) actin filaments bundled togetherto form stress fibers, (b) microtubules radiating from the cell center,and (c) intermediate filaments extending throughout the cytoplasm. Forthese experiments, antibodies that specifically recognize actin, tubu-lin,or intermediate filament proteins are covalently attached to afluorescent compound. When the cell is viewed with a fluorescencemicroscope, only the stained structures are visible. The lower panelsshow each type of filament as visualized by (a, b) transmission or(c) scanning electron microscopy. 10. Although complex, this organization of the cyto-plasmis far from random. The motion and the position-ingof organelles and cytoskeletal elements are undertight regulation, and at certain stages in a eukaryoticcells life, dramatic, finely orchestrated reorganizations,such as the events of mitosis, occur. The interactions be-tweenthe cytoskeleton and organelles are noncovalent,reversible, and subject to regulation in response to var-iousintracellular and extracellular signals.Cells Build Supramolecular StructuresMacromolecules and their monomeric subunits differgreatly in size (Fig. 110). A molecule of alanine is lessthan 0.5 nm long. Hemoglobin, the oxygen-carrying pro-teinof erythrocytes (red blood cells), consists of nearly600 amino acid subunits in four long chains, folded intoglobular shapes and associated in a structure 5.5 nm indiameter. In turn, proteins are much smaller than ribo-somes(about 20 nm in diameter), which are in turnmuch smaller than organelles such as mitochondria, typ-ically1,000 nm in diameter. It is a long jump from sim-plebiomolecules to cellular structures that can be seen10 Chapter 1 The Foundations of Biochemistry(a) Some of the amino acids of proteinsCOOOC AOHOOH OC AOH OC ACHHNOOHCHNUracil ThymineNH2CN CHNAdenine GuanineOHOCH2HNH HOHNH2OHOHH2CHCytosineHOHHONHOCH2 HH H-D-Ribose 2-Deoxy- -D-riboseHOHOHOHCOOCH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2 CH2CH2 CH3CH2OleateCH2PalmitateCH2OHCHOHCH2OHCH3 CH2CH2OHCH3CH2OHH HHHOHOOHHOHOH-D-Glucose(b) The components of nucleic acids (c) Some components of lipids(d) The parent sugarOHO POOHPhosphoric acidNCholineCH3GlycerolCH2CH3CH2CH2COOCH2CH2CH2CHCHCCCHHCN NHOCCCHCN NH NCOCHCNHOCHCNHCOCHCNHH2NCH3Nitrogenous basesFive-carbon sugarsH3NH3NH3NH3NOC ACOO COOCOOH3NCOOH3NCOOCOOACH3ACH2OHACAH2Alanine SerineAspartateOC AACASHCysteineHistidineC AH2OHTyrosineOC AACAH2C HCHHCNNHFIGURE 110 The organic compounds from which most cellularmaterials are constructed: the ABCs of biochemistry. Shown here are(a) six of the 20 amino acids from which all proteins are built (theside chains are shaded pink); (b) the five nitrogenous bases, two five-carbonsugars, and phosphoric acid from which all nucleic acids arebuilt; (c) five components of membrane lipids; and (d) D-glucose, theparent sugar from which most carbohydrates are derived. Note thatphosphoric acid is a component of both nucleic acids and membranelipids. 11. Chromosomewith the light microscope. Figure 111 illustrates thestructural hierarchy in cellular organization.The monomeric subunits in proteins, nucleic acids,and polysaccharides are joined by covalent bonds. Insupramolecular complexes, however, macromoleculesare held together by noncovalent interactionsmuchweaker, individually, than covalent bonds. Among thesenoncovalent interactions are hydrogen bonds (betweenpolar groups), ionic interactions (between chargedgroups), hydrophobic interactions (among nonpolargroups in aqueous solution), and van der Waals inter-actionsall of which have energies substantially smallerthan those of covalent bonds (Table 11). The natureof these noncovalent interactions is described in Chap-ter2. The large numbers of weak interactions betweenmacromolecules in supramolecular complexes stabilizethese assemblies, producing their unique structures.In Vitro Studies May Overlook Important Interactionsamong MoleculesOne approach to understanding a biological process isto study purified molecules in vitro (in glassin thetest tube), without interference from other moleculespresent in the intact cellthat is, in vivo (in the liv-ing).Although this approach has been remarkably re-vealing,we must keep in mind that the inside of a cellis quite different from the inside of a test tube. The in-terferingcomponents eliminated by purification maybe critical to the biological function or regulation of themolecule purified. For example, in vitro studies of pure1.1 Cellular Foundations 11Level 4:The celland its organellesLevel 3:SupramolecularcomplexesLevel 2:MacromoleculesLevel 1:Monomeric unitsNucleotidesDNA OO P O OO HAmino acidsProteinCellulosePlasma membraneCell wallSugarsOCH2NH2NNHH HOH HHH3N C COOCH3OHHOHCH2OHHHOOHOHHCH2OHOHFIGURE 111 Structural hierarchy in the molecular organization ofcells. In this plant cell, the nucleus is an organelle containing severaltypes of supramolecular complexes, including chromosomes. Chro-mosomesconsist of macromolecules of DNA and many different pro-teins.Each type of macromolecule is made up of simple subunitsDNA of nucleotides (deoxyribonucleotides), for example.enzymes are commonly done at very low enzyme con-centrationsin thoroughly stirred aqueous solutions. Inthe cell, an enzyme is dissolved or suspended in a gel-likecytosol with thousands of other proteins, some ofwhich bind to that enzyme and influence its activity.TABLE 11 Strengths of Bonds Commonin BiomoleculesBond Bonddissociation dissociationType energy* Type energyof bond (kJ/mol) of bond (kJ/mol)Single bonds Double bondsOOH 470 CPO 712HOH 435 CPN 615POO 419 CPC 611COH 414 PPO 502NOH 389COO 352 Triple bondsCOC 348 CmC 816SOH 339 NmN 930CON 293COS 260NOO 222SOS 214*The greater the energy required for bond dissociation (breakage), the stronger the bond. 12. Some enzymes are parts of multienzyme complexes inwhich reactants are channeled from one enzyme to an-otherwithout ever entering the bulk solvent. Diffusionis hindered in the gel-like cytosol, and the cytosolic com-positionvaries in different regions of the cell. In short,a given molecule may function quite differently in thecell than in vitro. A central challenge of biochemistry isto understand the influences of cellular organization andmacromolecular associations on the function of individ-ualenzymes and other biomoleculesto understandfunction in vivo as well as in vitro.SUMMARY 1.1 Cellular Foundations All cells are bounded by a plasma membrane;have a cytosol containing metabolites,coenzymes, inorganic ions, and enzymes; andhave a set of genes contained within a nucleoid(prokaryotes) or nucleus (eukaryotes). Phototrophs use sunlight to do work;chemotrophs oxidize fuels, passing electrons togood electron acceptors: inorganic compounds,organic compounds, or molecular oxygen. Bacterial cells contain cytosol, a nucleoid, andplasmids. Eukaryotic cells have a nucleus andare multicompartmented, segregating certainprocesses in specific organelles, which can beseparated and studied in isolation. Cytoskeletal proteins assemble into longfilaments that give cells shape and rigidity andserve as rails along which cellular organellesmove throughout the cell. Supramolecular complexes are held together bynoncovalent interactions and form a hierarchyof structures, some visible with the lightmicroscope. When individual molecules areremoved from these complexes to be studiedin vitro, interactions important in the livingcell may be lost.1.2 Chemical FoundationsBiochemistry aims to explain biological form and func-tionin chemical terms. As we noted earlier, one of themost fruitful approaches to understanding biologicalphenomena has been to purify an individual chemicalcomponent, such as a protein, from a living organismand to characterize its structural and chemical charac-teristics.By the late eighteenth century, chemists hadconcluded that the composition of living matter is strik-inglydifferent from that of the inanimate world. AntoineLavoisier (17431794) noted the relative chemical sim-plicityof the mineral world and contrasted it with thecomplexity of the plant and animal worlds; the latter,he knew, were composed of compounds rich in the ele-mentscarbon, oxygen, nitrogen, and phosphorus.During the first half of the twentieth century, par-allelbiochemical investigations of glucose breakdown inyeast and in animal muscle cells revealed remarkablechemical similarities in these two apparently very dif-ferentcell types; the breakdown of glucose in yeast andmuscle cells involved the same ten chemical intermedi-ates.Subsequent studies of many other biochemicalprocesses in many different organisms have confirmedthe generality of this observation, neatly summarized byJacques Monod: What is true of E. coli is true of theelephant. The current understanding that all organismsshare a common evolutionary origin is based in part onthis observed universality of chemical intermediates andtransformations.Only about 30 of the more than 90 naturally occur-ringchemical elements are essential to organisms. Mostof the elements in living matter have relatively lowatomic numbers; only five have atomic numbers abovethat of selenium, 34 (Fig. 112). The four most abun-dantelements in living organisms, in terms of percent-ageof total number of atoms, are hydrogen, oxygen,nitrogen, and carbon, which together make up morethan 99% of the mass of most cells. They are the light-estelements capable of forming one, two, three, and fourbonds, respectively; in general, the lightest elements12 Chapter 1 The Foundations of Biochemistry1 2H HeBulk elementsTrace elements3 4 5 6 7 8 9 10Li Be B C N O F Ne11 12 13 14 15 16 17 18Na Mg Al Si P S Cl Ar19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe55 56 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86Cs Ba Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn87 88Fr RaLanthanidesActinidesFIGURE 112 Elements essential to animallife and health. Bulk elements (shadedorange) are structural components of cellsand tissues and are required in the diet ingram quantities daily. For trace elements(shaded bright yellow), the requirements aremuch smaller: for humans, a few milligramsper day of Fe, Cu, and Zn, even less of theothers. The elemental requirements forplants and microorganisms are similar tothose shown here; the ways in which theyacquire these elements vary. 13. form the strongest bonds. The trace elements (Fig. 112)represent a miniscule fraction of the weight of the hu-manbody, but all are essential to life, usually becausethey are essential to the function of specific proteins,including enzymes. The oxygen-transporting capacityof the hemoglobin molecule, for example, is absolutelydependent on four iron ions that make up only 0.3% ofits mass.Biomolecules Are Compounds of Carbon witha Variety of Functional GroupsThe chemistry of living organisms is organized aroundcarbon, which accounts for more than half the dryweight of cells. Carbon can form single bonds with hy-drogenatoms, and both single and double bonds withoxygen and nitrogen atoms (Fig. 113). Of greatest sig-nificancein biology is the ability of carbon atoms to formvery stable carboncarbon single bonds. Each carbonatom can form single bonds with up to four other car-bonatoms. Two carbon atoms also can share two (orthree) electron pairs, thus forming double (or triple)bonds.The four single bonds that can be formed by a car-bonatom are arranged tetrahedrally, with an angle of1.2 Chemical Foundations 13(a) (b)109.5C109.5(c)CC120XCCABYabout 109.5 between any two bonds (Fig. 114) and anaverage length of 0.154 nm. There is free rotationaround each single bond, unless very large or highlycharged groups are attached to both carbon atoms, inwhich case rotation may be restricted. A double bondis shorter (about 0.134 nm) and rigid and allows littlerotation about its axis.Covalently linked carbon atoms in biomolecules canform linear chains, branched chains, and cyclic struc-tures.To these carbon skeletons are added groups ofother atoms, called functional groups, which conferspecific chemical properties on the molecule. It seemslikely that the bonding versatility of carbon was a ma-jorfactor in the selection of carbon compounds for themolecular machinery of cells during the origin and evo-lutionof living organisms. No other chemical elementcan form molecules of such widely different sizes andshapes or with such a variety of functional groups.Most biomolecules can be regarded as derivativesof hydrocarbons, with hydrogen atoms replaced by a va-rietyof functional groups to yield different families oforganic compounds. Typical of these are alcohols, whichhave one or more hydroxyl groups; amines, with aminogroups; aldehydes and ketones, with carbonyl groups;and carboxylic acids, with carboxyl groups (Fig. 115).Many biomolecules are polyfunctional, containing twoor more different kinds of functional groups (Fig. 116),each with its own chemical characteristics and reac-tions.The chemical personality of a compound is de-terminedby the chemistry of its functional groups andtheir disposition in three-dimensional space.H C H HCOCCOOC O C ON C NNC N NC CC C C C C C C CCCCCCCCOCCCNCC CCCFIGURE 113 Versatility of carbon bonding. Carbon can form cova-lentsingle, double, and triple bonds (in red), particularly with othercarbon atoms. Triple bonds are rare in biomolecules.FIGURE 114 Geometry of carbon bonding. (a) Carbon atoms havea characteristic tetrahedral arrangement of their four single bonds.(b) Carboncarbon single bonds have freedom of rotation, as shownfor the compound ethane (CH3OCH3). (c) Double bonds are shorterand do not allow free rotation. The two doubly bonded carbons andthe atoms designated A, B, X, and Y all lie in the same rigid plane. 14. Carbonyl(aldehyde)HHR COCarbonyl(ketone)HCHHCHC1 R2R COCarboxyl R COEther R1 O R2FIGURE 115 Some common functional O O Rgroups of biomolecules. In this figureand throughout the book, we use R torepresent any substituent. It may be assimple as a hydrogen atom, but typicallyit is a carbon-containing moiety. Whentwo or more substituents are shown in amolecule, we designate them R1, R2, andso forth.Cells Contain a Universal Set of Small MoleculesDissolved in the aqueous phase (cytosol) of all cells isa collection of 100 to 200 different small organic mole-cules(Mr ~100 to ~500), the central metabolites in themajor pathways occurring in nearly every cellthemetabolites and pathways that have been conservedthroughout the course of evolution. (See Box 11 for anexplanation of the various ways of referring to molecu-larC R2NC CHCHO P R2Mixed anhydride R C OPPweight.) This collection of molecules includes thecommon amino acids, nucleotides, sugars and theirphosphorylated derivatives, and a number of mono-,di-, and tricarboxylic acids. The molecules are polar orcharged, water soluble, and present in micromolar tomillimolar concentrations. They are trapped within thecell because the plasma membrane is impermeable tothemalthough specific membrane transporters cancatalyze the movement of some molecules into and out14 Chapter 1 The Foundations of BiochemistryHHydroxyl R O H(alcohol)OO OOMethyl R CHHEthyl R CHCHHEster R1 COO R2Sulfhydryl R S HDisulfide R1 S S R2Phosphoryl R O POOHThioester R1 COS R2Anhydride R1 CO O(two car-boxylicacids)OImidazole RNHNHGuanidino R NCNHHHAmino R NHHAmido R CONHHPhenyl R C CHCH(carboxylic acid andOphosphoric acid;also called acyl phosphate)OHPhosphoanhydride R1OOOO 15. P amidoCH3O C O CH2OO A OOOCH2OCH2ONHOCBOof the cell or between compartments in eukaryotic cells.The universal occurrence of the same set of compoundsin living cells is a manifestation of the universality ofmetabolic design, reflecting the evolutionary conserva-tionof metabolic pathways that developed in the earli-estcells.There are other small biomolecules, specific to cer-taintypes of cells or organisms. For example, vascularplants contain, in addition to the universal set, smallmolecules called secondary metabolites, which playa role specific to plant life. These metabolites includecompounds that give plants their characteristic scents,and compounds such as morphine, quinine, nicotine,and caffeine that are valued for their physiological ef-fectson humans but used for other purposes by plants.The entire collection of small molecules in a given cellhas been called that cells metabolome, in parallel withthe term genome (defined earlier and expanded on in1.2 Chemical Foundations 15CH3OOOPOOOCH2NH2NEimidazolePONSection 1.4). If we knew the composition of a cellsmetabolome, we could predict which enzymes and meta-bolicpathways were active in that cell.Macromolecules Are the Major Constituents of CellsMany biological molecules are macromolecules, poly-mersof high molecular weight assembled from rela-tivelysimple precursors. Proteins, nucleic acids, andpolysaccharides are produced by the polymerization ofrelatively small compounds with molecular weights of500 or less. The number of polymerized units can rangefrom tens to millions. Synthesis of macromolecules isa major energy-consuming activity of cells. Macromol-eculesthemselves may be further assembled intosupramolecular complexes, forming functional unitssuch as ribosomes. Table 12 shows the major classesof biomolecules in the bacterium E. coli.SOCH2OCH2ONHOCBOBOOC A HAOHO C AACH3BOABOOHNKC H B CANAOOPOHaminophosphoanhydrideAcetyl-coenzyme AHNCHCC HOOHmethylhydroxylmethylthioester amidophosphorylC CCHCHAAOO OFIGURE 116 Several common functional groupsin a single biomolecule. Acetyl-coenzyme A (oftenabbreviated as acetyl-CoA) is a carrier of acetylgroups in some enzymatic reactions.BOX 11 WORKING IN BIOCHEMISTRYMolecular Weight, Molecular Mass, and TheirCorrect UnitsThere are two common (and equivalent) ways to de-scribemolecular mass; both are used in this text. Thefirst is molecular weight, or relative molecular mass,denoted Mr. The molecular weight of a substance is de-finedas the ratio of the mass of a molecule of that sub-stanceto one-twelfth the mass of carbon-12 (12C).Since Mr is a ratio, it is dimensionlessit has no asso-ciatedunits. The second is molecular mass, denotedm. This is simply the mass of one molecule, or the mo-larmass divided by Avogadros number. The molecu-larmass, m, is expressed in daltons (abbreviated Da).One dalton is equivalent to one-twelfth the mass ofcarbon-12; a kilodalton (kDa) is 1,000 daltons; a mega-dalton(MDa) is 1 million daltons.Consider, for example, a molecule with a mass1,000 times that of water. We can say of this moleculeeither Mr18,000 or m18,000 daltons. We can alsodescribe it as an 18 kDa molecule. However, the ex-pressionMr18,000 daltons is incorrect.Another convenient unit for describing the massof a single atom or molecule is the atomic mass unit(formerly amu, now commonly denoted u). Oneatomic mass unit (1 u) is defined as one-twelfth themass of an atom of carbon-12. Since the experimen-tallymeasured mass of an atom of carbon-12 is1.99261023 g, 1 u1.66061024 g. The atomicmass unit is convenient for describing the mass of apeak observed by mass spectrometry (see Box 32). 16. Molecular Components of anTABLE 12E. coli CellProteins, long polymers of amino acids, constitutethe largest fraction (besides water) of cells. Some pro-teinshave catalytic activity and function as enzymes;others serve as structural elements, signal receptors, ortransporters that carry specific substances into or outof cells. Proteins are perhaps the most versatile of allbiomolecules. The nucleic acids, DNA and RNA, arepolymers of nucleotides. They store and transmit geneticinformation, and some RNA molecules have structural andcatalytic roles in supramolecular complexes. The poly-saccharides,polymers of simple sugars such as glucose,have two major functions: as energy-yielding fuel storesand as extracellular structural elements with specificbinding sites for particular proteins. Shorter polymers ofsugars (oligosaccharides) attached to proteins or lipidsat the cell surface serve as specific cellular signals. Thelipids, greasy or oily hydrocarbon derivatives, serve asstructural components of membranes, energy-rich fuelstores, pigments, and intracellular signals. In proteins,nucleotides, polysaccharides, and lipids, the number ofmonomeric subunits is very large: molecular weights inthe range of 5,000 to more than 1 million for proteins,up to several billion for nucleic acids, and in the millionsfor polysaccharides such as starch. Individual lipid mol-eculesare much smaller (Mr 750 to 1,500) and arenot classified as macromolecules. However, large num-bersof lipid molecules can associate noncovalently intovery large structures. Cellular membranes are built ofenormous noncovalent aggregates of lipid and proteinmolecules.Proteins and nucleic acids are informationalmacromolecules: each protein and each nucleic acidhas a characteristic information-rich subunit sequence.Some oligosaccharides, with six or more different sug-arsconnected in branched chains, also carry informa-tion;on the outer surface of cells they serve as highlyspecific points of recognition in many cellular processes(as described in Chapter 7).Three-Dimensional Structure Is Describedby Configuration and ConformationThe covalent bonds and functional groups of a biomol-eculeare, of course, central to its function, but so alsois the arrangement of the molecules constituent atomsin three-dimensional spaceits stereochemistry. Acarbon-containing compound commonly exists asstereoisomers, molecules with the same chemicalbonds but different stereochemistrythat is, differentconfiguration, the fixed spatial arrangement of atoms.Interactions between biomolecules are invariably stereo-specific,requiring specific stereochemistry in the in-teractingmolecules.Figure 117 shows three ways to illustrate the stereo-chemicalstructures of simple molecules. The perspec-tivediagram specifies stereochemistry unambiguously,but bond angles and center-to-center bond lengths arebetter represented with ball-and-stick models. In space-16 Chapter 1 The Foundations of BiochemistryApproximatenumber ofPercentage of differenttotal weight molecularof cell speciesWater 70 1Proteins 15 3,000Nucleic acidsDNA 1 1RNA 6 3,000Polysaccharides 3 5Lipids 2 20Monomeric subunitsand intermediates 2 500Inorganic ions 1 20MCOH2N#CDOHHOCAH!HOH(a)(c)(b)FIGURE 117 Representations of molecules. Three ways to representthe structure of the amino acid alanine. (a) Structural formula in per-spectiveform: a solid wedge (!) represents a bond in which the atomat the wide end projects out of the plane of the paper, toward thereader; a dashed wedge (^) represents a bond extending behind theplane of the paper. (b) Ball-and-stick model, showing relative bondlengths and the bond angles. (c) Space-filling model, in which eachatom is shown with its correct relative van der Waals radius. 17. HGDHDGCOOHGHDGCOOHfilling models, the radius of each atom is proportionalto its van der Waals radius, and the contours of themodel define the space occupied by the molecule (thevolume of space from which atoms of other moleculesare excluded).Configuration is conferred by the presence of either(1) double bonds, around which there is no freedom ofrotation, or (2) chiral centers, around which substituentgroups are arranged in a specific sequence. The identi-fyingcharacteristic of configurational isomers is thatthey cannot be interconverted without temporarilybreaking one or more covalent bonds. Figure 118ashows the configurations of maleic acid and its isomer,fumaric acid. These compounds are geometric, or cis-trans,isomers; they differ in the arrangement of theirsubstituent groups with respect to the nonrotating dou-blebond (Latin cis, on this sidegroups on the sameside of the double bond; trans, acrossgroups on op-positesides). Maleic acid is the cis isomer and fumaricacid the trans isomer; each is a well-defined compoundthat can be separated from the other, and each has itsown unique chemical properties. A binding site (on anenzyme, for example) that is complementary to one ofthese molecules would not be a suitable binding site forthe other, which explains why the two compounds havedistinct biological roles despite their similar chemistry.1.2 Chemical Foundations 1711In the second type of configurational isomer, fourdifferent substituents bonded to a tetrahedral carbonatom may be arranged two different ways in spacethatis, have two configurations (Fig. 119)yielding twostereoisomers with similar or identical chemical proper-tiesbut differing in certain physical and biological prop-erties.A carbon atom with four different substituentsis said to be asymmetric, and asymmetric carbons arecalled chiral centers (Greek chiros, hand; somestereoisomers are related structurally as the right handis to the left). A molecule with only one chiral carboncan have two stereoisomers; when two or more (n) chi-ralcarbons are present, there can be 2n stereoisomers.Some stereoisomers are mirror images of each other;they are called enantiomers (Fig. 119). Pairs ofstereoisomers that are not mirror images of each otherare called diastereomers (Fig. 120).As Louis Pasteur first observed (Box 12), enan-tiomershave nearly identical chemical properties butdiffer in a characteristic physical property, their inter-actionwith plane-polarized light. In separate solutions,two enantiomers rotate the plane of plane-polarizedlight in opposite directions, but an equimolar solutionof the two enantiomers (a racemic mixture) shows nooptical rotation. Compounds without chiral centers donot rotate the plane of plane-polarized light.CHOOCPCMaleic acid (cis)CH3OJC11-cis-RetinallightCHOOCDHPCFumaric acid (trans)All-trans-RetinalH3CH3GCH910 12H3CH3C9121011CH3CJOGHCH3 CH3 GD(b)(a)CH3 CH3 GDFIGURE 118 Configurations of geometric isomers. (a) Isomers suchas maleic acid and fumaric acid cannot be interconverted withoutbreaking covalent bonds, which requires the input of much energy.(b) In the vertebrate retina, the initial event in light detection is theabsorption of visible light by 11-cis-retinal. The energy of the absorbedlight (about 250 kJ/mol) converts 11-cis-retinal to all-trans-retinal,triggering electrical changes in the retinal cell that lead to a nerveimpulse. (Note that the hydrogen atoms are omitted from the ball-and-stickmodels for the retinals.) 18. Given the importance of stereochemistry in reac-tionsbetween biomolecules (see below), biochemistsmust name and represent the structure of each bio-moleculeso that its stereochemistry is unambiguous.For compounds with more than one chiral center, themost useful system of nomenclature is the RS system.In this system, each group attached to a chiral carbonis assigned a priority. The priorities of some commonsubstituents areOOCH2OOHONH2OCOOHOCHOOCH2OHOCH3OHFor naming in the RS system, the chiral atom is viewedwith the group of lowest priority (4 in the diagram onthe next page) pointing away from the viewer. If the pri-orityof the other three groups (1 to 3) decreases inclockwise order, the configuration is (R) (Latin rectus,right); if in counterclockwise order, the configuration18 Chapter 1 The Foundations of BiochemistryYYCB(a)Mirrorimage oforiginalmoleculeChiralmolecule:Rotatedmoleculecannot besuperimposedon its mirrorimageOriginalmoleculeAACX BYACBXXXACXBACX BX(b)Achiralmolecule:Rotatedmoleculecan besuperimposedon its mirrorimageMirrorimage oforiginalmoleculeOriginalmoleculeXACXBFIGURE 119 Molecular asymmetry: chiral and achiral molecules.(a) When a carbon atom has four different substituent groups (A, B,X, Y), they can be arranged in two ways that represent nonsuperim-posablemirror images of each other (enantiomers). This asymmetriccarbon atom is called a chiral atom or chiral center. (b) When a tetra-hedralcarbon has only three dissimilar groups (i.e., the same groupoccurs twice), only one configuration is possible and the molecule issymmetric, or achiral. In this case the molecule is superimposable onits mirror image: the molecule on the left can be rotated counter-clockwise(when looking down the vertical bond from A to C) to cre-atethe molecule in the mirror.CH3CH3Diastereomers (nonmirror images)CH3CCH3HC HXYEnantiomers (mirror images) Enantiomers (mirror images)CCH3XC YHHCCH3HC Y YXHCH3CCH3HCXHFIGURE 120 Two types of stereoisomers. There are four different2,3-disubstituted butanes (n2 asymmetric carbons, hence 2n4stereoisomers). Each is shown in a box as a perspective formula anda ball-and-stick model, which has been rotated to allow the reader toview all the groups. Some pairs of stereoisomers are mirror images ofeach other, or enantiomers. Other pairs are not mirror images; theseare diastereomers. 19. BOX 12 WORKING IN BIOCHEMISTRYis (S) (Latin sinister, left). In this way each chiral car-bonis designated either (R) or (S), and the inclusionof these designations in the name of the compound pro-videsan unambiguous description of the stereochem-istryat each chiral center.142 3Counterclockwise(S)143 2Clockwise(R)Another naming system for stereoisomers, the D and Lsystem, is described in Chapter 3. A molecule with a sin-glechiral center (glyceraldehydes, for example) can benamed unambiguously by either system.4COOHH OHHC 3OHH(2R,3R)-Tartaric acid (2S,3S)-Tartaric acid(dextrorotatory) (levorotatory)CHO1.2 Chemical Foundations 19C 3(2)2CHOOC1OH2CHOOC1HO4COHOHHO C H H OHCH2OHCHO(4) (1)CH2OH(3)L-Glyceraldehyde (S)-GlyceraldehydeDistinct from configuration is molecular confor-mation,the spatial arrangement of substituent groupsthat, without breaking any bonds, are free to assumedifferent positions in space because of the freedom ofrotation about single bonds. In the simple hydrocarbonethane, for example, there is nearly complete freedomof rotation around the COC bond. Many different, in-terconvertibleconformations of ethane are possible,depending on the degree of rotation (Fig. 121). Twoconformations are of special interest: the staggered,which is more stable than all others and thus predomi-nates,and the eclipsed, which is least stable. We cannotisolate either of these conformational forms, becauseLouis Pasteur and Optical Activity:In Vino, VeritasLouis Pasteur encountered the phenome-nonof optical activity in 1843, during hisinvestigation of the crystalline sedimentthat accumulated in wine casks (a form oftartaric acid called paratartaric acidalsocalled racemic acid, from Latin racemus,bunch of grapes). He used fine forcepsto separate two types of crystals identicalin shape but mirror images of each other.Both types proved to have all the chemi-calproperties of tartaric acid, but in solu-tionone type rotated polarized light to theleft (levorotatory), the other to the right(dextrorotatory). Pasteur later described the experi-mentand its interpretation:In isomeric bodies, the elements and the propor-tionsin which they are combined are the same, onlythe arrangement of the atoms is different . . . Weknow, on the one hand, that the molecular arrange-mentsof the two tartaric acids are asymmetric, and,on the other hand, that these arrangements are ab-solutelyidentical, excepting that they exhibit asym-metryin opposite directions. Are the atoms of thedextro acid grouped in the form of a right-handedspiral, or are they placed at the apex of an irregu-lartetrahedron, or are they disposed according tothis or that asymmetric arrangement? We do notknow.*Now we do know. X-ray crystallo-graphicstudies in 1951 confirmed that thelevorotatory and dextrorotatory forms oftartaric acid are mirror images of eachother at the molecular level and establishedthe absolute configuration of each (Fig. 1).The same approach has been used todemonstrate that although the amino acidalanine has two stereoisomeric forms (des-ignatedD and L), alanine in proteins existsexclusively in one form (the L isomer; seeChapter 3).FIGURE 1 Pasteur separated crystals of two stereoisomers of tartaricacid and showed that solutions of the separated forms rotated po-larizedlight to the same extent but in opposite directions. Thesedextrorotatory and levorotatory forms were later shown to be the(R,R) and (S,S) isomers represented here. The RS system of nomen-clatureis explained in the text.Louis Pasteur18221895*From Pasteurs lecture to the Socit Chimique de Paris in 1883,quoted in DuBos, R. (1976) Louis Pasteur: Free Lance of Science,p. 95, Charles Scribners Sons, New York. 20. mol)kJ/(12energy 84Potential 12.1kJ/molthey are freely interconvertible. However, when one ormore of the hydrogen atoms on each carbon is replacedby a functional group that is either very large or elec-tricallycharged, freedom of rotation around the COCbond is hindered. This limits the number of stable con-formationsof the ethane derivative.Interactions between BiomoleculesAre StereospecificBiological interactions between molecules are stereo-specific:the fit in such interactions must be stereo-chemicallycorrect. The three-dimensional structure ofbiomolecules large and smallthe combination of con-figurationand conformationis of the utmost impor-tancein their biological interactions: reactant withenzyme, hormone with its receptor on a cell surface,antigen with its specific antibody, for example (Fig.122). The study of biomolecular stereochemistry withprecise physical methods is an important part of mod-ernresearch on cell structure and biochemical function.In living organisms, chiral molecules are usuallypresent in only one of their chiral forms. For example,the amino acids in proteins occur only as their L iso-mers;glucose occurs only as its D isomer. (The con-ventionsfor naming stereoisomers of the amino acidsare described in Chapter 3; those for sugars, in Chap-ter7; the RS system, described above, is the mostuseful for some biomolecules.) In contrast, when a com-poundwith an asymmetric carbon atom is chemicallysynthesized in the laboratory, the reaction usually pro-ducesall possible chiral forms: a mixture of the D and Lforms, for example. Living cells produce only one chiralform of biomolecules because the enzymes that syn-thesizethem are also chiral.Stereospecificity, the ability to distinguish betweenstereoisomers, is a property of enzymes and other pro-teinsand a characteristic feature of the molecular logicof living cells. If the binding site on a protein is com-plementaryto one isomer of a chiral compound, it willnot be complementary to the other isomer, for the samereason that a left glove does not fit a right hand. Twostriking examples of the ability of biological systems todistinguish stereoisomers are shown in Figure 123.SUMMARY 1.2 Chemical Foundations Because of its bonding versatility, carbon canproduce a broad array of carboncarbonskeletons with a variety of functional groups;these groups give biomolecules their biologicaland chemical personalities. A nearly universal set of several hundred smallmolecules is found in living cells; the interconver-sionsof these molecules in the central metabolicpathways have been conserved in evolution. Proteins and nucleic acids are linear polymersof simple monomeric subunits; their sequencescontain the information that gives eachmolecule its three-dimensional structure andits biological functions.20 Chapter 1 The Foundations of Biochemistry0 60 120 180 240 300 3600Torsion angle (degrees)FIGURE 121 Conformations. Many conformations of ethane are pos-siblebecause of freedom of rotation around the COC bond. In theball-and-stick model, when the front carbon atom (as viewed by thereader) with its three attached hydrogens is rotated relative to the rearcarbon atom, the potential energy of the molecule rises to a maximumin the fully eclipsed conformation (torsion angle 0, 120, etc.), thenfalls to a minimum in the fully staggered conformation (torsion angle60, 180, etc.). Because the energy differences are small enough toallow rapid interconversion of the two forms (millions of times per sec-ond),the eclipsed and staggered forms cannot be separately isolated.FIGURE 122 Complementary fit between a macromolecule and asmall molecule. A segment of RNA from the regulatory region TAR ofthe human immunodeficiency virus genome (gray) with a bound argin-inamidemolecule (colored), representing one residue of a protein thatbinds to this region. The argininamide fits into a pocket on the RNAsurface and is held in this orientation by several noncovalent interac-tionswith the RNA. This representation of the RNA molecule is pro-ducedwith the computer program GRASP, which can calculate theshape of the outer surface of a macromolecule, defined either by thevan der Waals radii of all the atoms in the molecule or by the solventexclusion volume, into which a water molecule cannot penetrate. 21. NH3H3 Molecular configuration can be changed only bybreaking covalent bonds. For a carbon atomwith four different substituents (a chiralcarbon), the substituent groups can bearranged in two different ways, generatingstereoisomers with distinct properties. Onlyone stereoisomer is biologically active.Molecular conformation is the position of atomsin space that can be changed by rotation aboutsingle bonds, without breaking covalent bonds. Interactions between biological molecules arealmost invariably stereospecific: they require acomplementary match between the interactingmolecules.1.3 Physical FoundationsLiving cells and organisms must perform work to stayalive and to reproduce themselves. The synthetic reac-tionsthat occur within cells, like the synthetic processesin any factory, require the input of energy. Energy is alsoconsumed in the motion of a bacterium or an Olympicsprinter, in the flashing of a firefly or the electrical dis-chargeof an eel. And the storage and expression ofinformation require energy, without which structuresrich in information inevitably become disordered andmeaningless.In the course of evolution, cells have developedhighly efficient mechanisms for coupling the energyobtained from sunlight or fuels to the many energy-consumingprocesses they must carry out. One goal of1.3 Physical Foundations 21(R)-Carvone (S)-Carvone(spearmint) (caraway)(a)CH3O CCH2CCCH3 CCH2CHCH2HCH3O CCH2CCCHCH2H CCH2CH3(b)CHCH2CH2biochemistry is to understand, in quantitative and chem-icalterms, the means by which energy is extracted,channeled, and consumed in living cells. We can considercellular energy conversionslike all other energy con-versionsin the context of the laws of thermodynamics.Living Organisms Exist in a Dynamic Steady State,Never at Equilibrium with Their SurroundingsThe molecules and ions contained within a living or-ganismdiffer in kind and in concentration from those inthe organisms surroundings. A Paramecium in a pond,a shark in the ocean, an erythrocyte in the human blood-stream,an apple tree in an orchardall are different incomposition from their surroundings and, once theyhave reached maturity, all (to a first approximation)maintain a constant composition in the face of con-stantlychanging surroundings.Although the characteristic composition of an or-ganismchanges little through time, the population ofmolecules within the organism is far from static. Smallmolecules, macromolecules, and supramolecular com-plexesare continuously synthesized and then brokendown in chemical reactions that involve a constant fluxof mass and energy through the system. The hemoglo-binmolecules carrying oxygen from your lungs to yourbrain at this moment were synthesized within the pastmonth; by next month they will have been degradedand entirely replaced by new hemoglobin molecules.The glucose you ingested with your most recent mealis now circulating in your bloodstream; before the dayis over these particular glucose molecules will have beenOOC CH2CCON HCHOOCH3OOCCH2CCONCHCOOCH3HCCHCHHCCCHNHCCHCHHCCCHH HL-Aspartyl-L-phenylalanine methyl ester(aspartame) (sweet)L-Aspartyl-D-phenylalanine methyl ester(bitter)FIGURE 123 Stereoisomers distinguishable by smelland taste in humans. (a) Two stereoisomers of carvone:(R)-carvone (isolated from spearmint oil) has thecharacteristic fragrance of spearmint; (S)-carvone (fromcaraway seed oil) smells like caraway. (b) Aspartame,the artificial sweetener sold under the trade nameNutraSweet, is easily distinguishable by taste receptorsfrom its bitter-tasting stereoisomer, although the twodiffer only in the configuration at one of the two chiralcarbon atoms. 22. converted into something elsecarbon dioxide or fat,perhapsand will have been replaced with a fresh sup-plyof glucose, so that your blood glucose concentrationis more or less constant over the whole day. The amountsof hemoglobin and glucose in the blood remain nearlyconstant because the rate of synthesis or intake of eachjust balances the rate of its breakdown, consumption,or conversion into some other product. The constancyof concentration is the result of a dynamic steady state,a steady state that is far from equilibrium. Maintainingthis steady state requires the constant investment of en-ergy;when the cell can no longer generate energy, itdies and begins to decay toward equilibrium with its sur-roundings.We consider below exactly what is meant bysteady state and equilibrium.Organisms Transform Energy and Matterfrom Their SurroundingsFor chemical reactions occurring in solution, we can de-finea system as all the reactants and products present,the solvent that contains them, and the immediate at-mospherein short, everything within a defined regionof space. The system and its surroundings together con-stitutethe universe. If the system exchanges neithermatter nor energy with its surroundings, it is said to beisolated. If the system exchanges energy but not mat-terwith its surroundings, it is a closed system; if it ex-changesboth energy and matter with its surroundings,it is an open system.A living organism is an open system; it exchangesboth matter and energy with its surroundings. Living or-ganismsderive energy from their surroundings in twoways: (1) they take up chemical fuels (such as glucose)from the environment and extract energy by oxidizingthem (see Box 13, Case 2); or (2) they absorb energyfrom sunlight.The first law of thermodynamics, developed fromphysics and chemistry but fully valid for biological sys-temsas well, describes the principle of the conservationof energy: in any physical or chemical change, thetotal amount of energy in the universe remains con-stant,although the form of the energy may change.Cells are consummate transducers of energy, capable ofinterconverting chemical, electromagnetic, mechanical,and osmotic energy with great efficiency (Fig. 124).The Flow of Electrons Provides Energy for OrganismsNearly all living organisms derive their energy, directlyor indirectly, from the radiant energy of sunlight, whicharises from thermonuclear fusion reactions carried outin the sun. Photosynthetic cells absorb light energyand use it to drive electrons from water to carbon di-oxide,forming energy-rich products such as glucose(C6H12O6), starch, and sucrose and releasing O2 into theatmosphere:light6CO26H2O 888n C6H12O66O2(light-driven reduction of CO2)Nonphotosynthetic cells and organisms obtain the en-ergythey need by oxidizing the energy-rich products ofphotosynthesis and then passing electrons to atmos-22 Chapter 1 The Foundations of Biochemistry(a)(b)(c)(d)(e)Potential energyEnergytransductionsaccomplishwork Nutrients in environment(complex molecules such assugars, fats) SunlightChemical transformationswithin cellsCellular work: chemical synthesis mechanical work osmotic and electrical gradients light production genetic information transferHeatIncreased randomness(entropy) in the surroundingsMetabolism produces compoundssimpler than the initialfuel molecules: CO2, NH3,H2O, HPO42Decreased randomness(entropy) in the systemSimple compounds polymerizeto form information-richmacromolecules: DNA, RNA,proteinsFIGURE 124 Some energy interconversion in living organisms. Dur-ingmetabolic energy transductions, the randomness of the system plussurroundings (expressed quantitatively as entropy) increases as the po-tentialenergy of complex nutrient molecules decreases. (a) Living or-ganismsextract energy from their surroundings; (b) convert some ofit into useful forms of energy to produce work; (c) return some en-ergyto the surroundings as heat; and (d) release end-product mole-culesthat are less well organized than the starting fuel, increasing theentropy of the universe. One effect of all these transformations is (e) in-creasedorder (decreased randomness) in the system in the form ofcomplex macromolecules. We return to a quantitative treatment of en-tropyin Chapter 13. 23. pheric O2 to form water, carbon dioxide, and other endproducts, which are recycled in the environment:C6H12O6O2 888n 6CO26H2Oenergy(energy-yielding oxidation of glucose)Virtually all energy transductions in cells can be tracedto this flow of electrons from one molecule to another,in a downhill flow from higher to lower electrochem-icalpotential; as such, this is formally analogous to theflow of electrons in a battery-driven electric circuit. Allthese reactions involving electron flow are oxidation-reductionreactions: one reactant is oxidized (loseselectrons) as another is reduced (gains electrons).Creating and Maintaining Order Requires Workand EnergyDNA, RNA, and proteins are informational macromole-cules.In addition to using chemical energy to form thecovalent bonds between the subunits in these polymers,the cell must invest energy to order the subunits in theircorrect sequence. It is extremely improbable that aminoacids in a mixture would spontaneously condense into asingle type of protein, with a unique sequence. This wouldrepresent increased order in a population of molecules;but according to the second law of thermodynamics, thetendency in nature is toward ever-greater disorder in theuniverse: the total entropy of the universe is continu-allyincreasing. To bring about the synthesis of macro-moleculesfrom their monomeric units, free energy mustbe supplied to the system (in this case, the cell).The randomness or disorder of the components of achemical system is expressed as entropy, S (Box 13).Any change in randomness ofthe system is expressed asentropy change, S, which byconvention has a positive valuewhen randomness increases.J. Willard Gibbs, who devel-opedthe theory of energychanges during chemical reac-tions,showed that the free-energycontent, G, of anyclosed system can be definedin terms of three quantities:enthalpy, H, reflecting thenumber and kinds of bonds;entropy, S; and the absolute temperature, T (in degreesKelvin). The definition of free energy is GHTS.When a chemical reaction occurs at constant tempera-ture,the free-energy change, G, is determined bythe enthalpy change, H, reflecting the kinds and num-bersof chemical bonds and noncovalent interactionsbroken and formed, and the entropy change, S, de-scribingthe change in the systems randomness:GHT S1.3 Physical Foundations 23OOOHCNH2A process tends to occur spontaneously only if Gis negative. Yet cell function depends largely on mole-cules,such as proteins and nucleic acids, for which thefree energy of formation is positive: the molecules areless stable and more highly ordered than a mixture oftheir monomeric components. To carry out these ther-modynamicallyunfavorable, energy-requiring (ender-gonic)reactions, cells couple them to other reactionsthat liberate free energy (exergonic reactions), so thatthe overall process is exergonic: the sum of the free-energychanges is negative. The usual source of freeenergy in coupled biological reactions is the energy re-leasedby hydrolysis of phosphoanhydride bonds suchas those in adenosine triphosphate (ATP; Fig. 125; seealso Fig. 115). Here, each P represents a phosphorylgroup:Amino acids 888n polymer G1 is positive (endergonic)OPOP 888nOP P G2 is negative (exergonic)When these reactions are coupled, the sum of G1 andG2 is negativethe overall process is exergonic. Bythis coupling strategy, cells are able to synthesize andmaintain the information-rich polymers essential to life.Energy Coupling Links Reactions in BiologyThe central issue in bioenergetics (the study of energytransformations in living systems) is the means by whichenergy from fuel metabolism or light capture is coupledto a cells energy-requiring reactions. In thinking aboutenergy coupling, it is useful to consider a simple me-chanicalexample, as shown in Figure 126a. An objectat the top of an inclined plane has a certain amount ofpotential energy as a result of its elevation. It tends toslide down the plane, losing its potential energy of po-sitionas it approaches the ground. When an appropri-atestring-and-pulley device couples the falling object toanother, smaller object, the spontaneous downward mo-tionof the larger can lift the smaller, accomplishing aJ. Willard Gibbs,18391903O POO POO PO O CH2OHOHOHHH HP P P Ribose AdenineCHCNN C NNFIGURE 125 Adenosine triphosphate (ATP). The removal of the ter-minalphosphoryl group (shaded pink) of ATP, by breakage of a phos-phoanhydridebond, is highly exergonic, and this reaction is coupled tomany endergonic reactions in the cell (as in the example in Fig. 126b). 24. certain amount of work. The amount of energy availableto do work is the free-energy change, G; this is al-wayssomewhat less than the theoretical amount of en-ergyreleased, because some energy is dissipated as theheat of friction. The greater the elevation of the largerobject, the greater the energy released (G) as the ob-jectslides downward and the greater the amount ofwork that can be accomplished.How does this apply in chemical reactions? In closedsystems, chemical reactions proceed spontaneously un-tilequilibrium is reached. When a system is at equilib-rium,the rate of product formation exactly equals the7 moleculesO2(a gas)rate at which product is converted to reactant. Thusthere is no net change in the concentration of reactantsand products; a steady state is achieved. The energychange as the system moves from its initial state to equi-librium,with no changes in temperature or pressure, isgiven by the free-energy change, G. The magnitude ofG depends on the particular chemical reaction and onhow far from equilibrium the system is initially. Eachcompound involved in a chemical reaction contains a cer-tainamount of potential energy, related to the kind andnumber of its bonds. In reactions that occur sponta-neously,the products have less free energy than the re-24 Chapter 1 The Foundations of BiochemistryBOX 13 WORKING IN BIOCHEMISTRYEntropy: The Advantages of Being DisorganizedThe term entropy, which literally means a changewithin, was first used in 1851 by Rudolf Clausius, oneof the formulators of the second law of thermody-namics.A rigorous quantitative definition of entropyinvolves statistical and probability considerations.However, its nature can be illustrated qualitatively bythree simple examples, each demonstrating one aspectof entropy. The key descriptors of entropy are ran-domnessand disorder, manifested in different ways.Case 1: The Teakettle and the Randomization of HeatWe know that steam generated from boiling water cando useful work. But suppose we turn off the burnerunder a teakettle full of water at 100 C (the sys-tem)in the kitchen (the surroundings) and allowthe teakettle to cool. As it cools, no work is done, butheat passes from the teakettle to the surroundings,raising the temperature of the surroundings (thekitchen) by an infinitesimally small amount until com-pleteequilibrium is attained. At this point all parts ofthe teakettle and the kitchen are at precisely the sametemperature. The free energy that was once concen-tratedin the teakettle of hot water at 100 C, poten-tiallycapable of doing work, has disappeared. Itsequivalent in heat energy is still present in the teaket-tle kitchen (i.e., the universe) but has becomecompletely randomized throughout. This energy is nolonger available to do work because there is no tem-peraturedifferential within the kitchen. Moreover, theincrease in entropy of the kitchen (the surroundings)is irreversible. We know from everyday experiencethat heat never spontaneously passes back from thekitchen into the teakettle to raise the temperature ofthe water to 100 C again.Case 2: The Oxidation of GlucoseEntropy is a state not only of energy but of matter.Aerobic (heterotrophic) organisms extract free en-ergyfrom glucose obtained from their surroundingsby oxidizing the glucose with O2, also obtained fromthe surroundings. The end products of this oxidativemetabolism, CO2 and H2O, are returned to the sur-roundings.In this process the surroundings undergoan increase in entropy, whereas the organism itself re-mainsin a steady state and undergoes no change inits internal order. Although some entropy arises fromthe dissipation of heat, entropy also arises from an-otherkind of disorder, illustrated by the equation forthe oxidation of glucose:C6H12O66O2 On 6CO26H2OWe can represent this schematically asThe atoms contained in 1 molecule of glucose plus 6molecules of oxygen, a total of 7 molecules, are morerandomly dispersed by the oxidation reaction and arenow present in a total of 12 molecules (6CO26H2O).Whenever a chemical reaction results in an in-creasein the number of moleculesor when a solidsubstance is converted into liquid or gaseous products,which allow more freedom of molecular movementthan solidsmolecular disorder, and thus entropy,increases.Case 3: Information and EntropyThe following short passage from Julius Caesar, ActIV, Scene 3, is spoken by Brutus, when he realizes thathe must face Mark Antonys army. It is an information-richnonrandom arrangement of 125 letters of theEnglish alphabet:CO2(a gas)H2O(a liquid)Glucose(a solid)12 molecules 25. abddfisactants, thus the reaction releases free energy, which isthen available to do work. Such reactions are exergonic;the decline in free energy from reactants to products isexpressed as a negative value. Endergonic reactions re-quirean input of energy, and their G values are posi-tive.As in mechanical processes, only part of the energyreleased in exergonic chemical reactions can be used toaccomplish work. In living systems some energy is dissi-patedas heat or lost to increasing entropy.In living organisms, as in the mechanical example inFigure 126a, an exergonic reaction can be coupled toan endergonic reaction to drive otherwise unfavorable1.3 Physical Foundations 25(a) Mechanical exampleG0 G0Endergonic ExergonicReaction 2:ATP ADPPi Reaction 3:reactions. Figure 126b (a type of graph called a reac-tioncoordinate diagram) illustrates this principle for theconversion of glucose to glucose 6-phosphate, the firststep in the pathway for oxidation of glucose. The sim-plestway to produce glucose 6-phosphate would be:Reaction 1: GlucosePi On glucose 6-phosphate(endergonic; G1 is positive)2.(Pi is an abbreviation for inorganic phosphate, HPO4Dont be concerned about the structure of these com-poundsnow; we describe them in detail later in thebook.) This reaction does not occur spontaneously; GThere is a tide in the affairs of men,Which, taken at the flood, leads on to fortune;Omitted, all the voyage of their lifeIs bound in shallows and in miseries.In addition to what this passage says overtly, it hasmany hidden meanings. It not only reflects a complexsequence of events in the play, it also echoes the playsideas on conflict, ambition, and the demands of lead-ership.Permeated with Shakespeares understandingof human nature, it is very rich in information.However, if the 125 letters making up this quota-tionwere allowed to fall into a completely random,chaotic pattern, as shown in the following box, theywould have no meaning whatsoever.In this form the 125 letters contain little or no infor-mation,but they are very rich in entropy. Such con-siderationshave led to the conclusion that informationis a form of energy; information has been called neg-ativeentropy. In fact, the branch of mathematics calledinformation theory, which is basic to the programminglogic of computers, is closely related to thermodynamictheory. Living organisms are highly ordered, nonran-domstructures, immensely rich in information and thusentropy-poor.c defghiIklmnoOraefhilmnoradefhilmnoradefhilnoraefhilnoradefhilno aehilnoaehinoaeinoaeioeeieeeestTuvwWyustststtstststtttWorkdoneraisingobjectLoss ofpotentialenergy ofposition(b) Chemical exampleFree energy, GReaction 1:GlucosePi glucose 6-phosphateGlucoseATP glucose 6-phosphateADPG1G2 G3G3 = G1G2Reaction coordinateFIGURE 126 Energy coupling in mechanical and chemicalprocesses. (a) The downward motion of an object releases potentialenergy that can do mechanical work. The potential energy made avail-ableby spontaneous downward motion, an exergonic process (pink),can be coupled to the endergonic upward movement of another ob-ject(blue). (b) In reaction 1, the formation of glucose 6-phosphatefrom glucose and inorganic phosphate (Pi) yields a product of higherenergy than the two reactants. For this endergonic reaction, G is pos-itive.In reaction 2, the exergonic breakdown of adenosine triphos-phate(ATP) can drive an endergonic reaction when the two reactionsare coupled. The exergonic reaction has a large, negative free-energychange (G2), and the endergonic reaction has a smaller, positive free-energychange (G1). The third reaction accomplishes the sum of re-actions1 and 2, and the free-energy change, G3, is the arithmeticsum of G1 and G2. Because G3 is negative, the overall reactionis exergonic and proceeds spontaneously. 26. is positive. A second, very exergonic reaction can occurin all cells:Reaction 2: ATP On ADPPi(exergonic; G2 is negative)These two chemical reactions share a common inter-mediate,Pi, which is consumed in reaction 1 and pro-ducedin reaction 2. The two reactions can therefore becoupled in the form of a third reaction, which we canwrite as the sum of reactions 1 and 2, with the commonintermediate, Pi, omitted from both sides of the equation:Reaction 3: GlucoseATP Onglucose 6-phosphateADPBecause more energy is released in reaction 2 than isconsumed in reaction 1, the free-energy change for re-action3, G3, is negative, and the synthesis of glucose6-phosphate can therefore occur by reaction 3.The coupling of exergonic and endergonic reactionsthrough a shared intermediate is absolutely central to theenergy exchanges in living systems. As we shall see, thebreakdown of ATP (reaction 2 in Fig. 126b) is the ex-ergonicreaction that drives many endergonic processesin cells. In fact, ATP is the major carrier of chemicalenergy in all cells.Keq and G Are Measures of a Reactions Tendencyto Proceed SpontaneouslyThe tendency of a chemical reaction to go to completioncan be expressed as an equilibrium constant. For thereactionaAbB 888n cCdDthe equilibrium constant, Keq, is given by[ACeeqc[[]aq]Keq[DBeeqd]bq]where [Aeq] is the concentration of A, [Beq] the concen-trationof B, and so on, when the system has reachedequilibrium. A large value of Keq means the reactiontends to proceed until the reactants have been almostcompletely converted into the products.Gibbs showed that G for any chemical reaction isa function of the standard free-energy change,G a constant that is characteristic of each specificreactionand a term that expresses the initial concen-trationsof reactants and products:[ACic[[]ai]GGRT ln [DB]]iidb (11)where [Ai] is the initial concentration of A, and so forth;R is the gas constant; and T is the absolute temperature.When a reaction has reached equilibrium, no driv-ingforce remains and it can do no work: G0. Forthis special case, [Ai][Aeq], and so on, for all reactantsand products, and[ACeeqc[[]aq] [DBee]]qqdbKeq[Ci]c[Di]d[Ai]a[Bi]bSubstituting 0 for G and Keq for [Ci]c[Di]d/[Ai]a[Bi]b inEquation 11, we obtain the relationshipGRT ln Keqfrom which we see that G is simply a second way (be-sidesKeq) of expressing the driving force on a reaction.Because Keq is experimentally measurable, we have away of determining G, the thermodynamic constantcharacteristic of each reaction.The units of G and G are joules per mole (orcalories per mole). When Keq1, G is large andnegative; when Keq1, G is large and positive.From a table of experimentally determined values of ei-therKeq or G, we can see at a glance which reactionstend to go to completion and which do not.One caution about the interpretation of G: ther-modynamicconstants such as this show where the fi-nalequilibrium for a reaction lies but tell us nothingabout how fast that equilibrium will be achieved. Therates of reactions are governed by the parameters of ki-netics,a topic we consider in detail in Chapter 6.Enzymes Promote Sequences of Chemical ReactionsAll biological macromolecules are much less thermody-namicallystable than their monomeric subunits, yetthey are kinetically stable: their uncatalyzed break-downoccurs so slowly (over years rather than seconds)that, on a time scale that matters for the organism, thesemolecules are stable. Virtually every chemical reactionin a cell occurs at a significant rate only because of thepresence of enzymesbiocatalysts that, like all othercatalysts, greatly enhance the rate of specific chemicalreactions without being consumed in the process.The path from reactant(s) to product(s) almost in-variablyinvolves an energy barrier, called the activationbarrier (Fig. 127), that must be surmounted for any re-actionto proceed. The breaking of existing bonds andformation of new ones generally requires, first, the dis-tortionof the existing bonds, creating a transitionstate of higher free energy than either reactant or prod-uct.The highest point in the reaction coordinate dia-gramrepresents the transition state, and the differencein energy between the reactant in its ground state andin its transition state is the activation energy, G.An enzyme catalyzes a reaction by providing a morecomfortable fit for the transition state: a surface thatcomplements the transition state in stereochemistry, po-larity,and charge. The binding of enzyme to the transi-tionstate is exergonic, and the energy released by thisbinding reduces the activation energy for the reactionand greatly increases the reaction rate.A further contribution to catalysis occurs when twoor more reactants bind to the enzymes surface close toeach other and with stereospecific orientations that fa-26 Chapter 1 The Foundations of Biochemistry 27. vor the reaction. This increases by orders of