With the cell,biologydiscovered its atom..Tocharacterizelife, itwashenceforthessential to study thecellandanalyze its structure:tosingleoutthecommondenominators,necessaryforthelifeof everycell; alternatively,to identify differences associated with the perfor-manceofspecial functions.FrancoisJacob,La logigueduvivant:unehistoiredeI'heredite(TheLogicofLife:AHistoryofHeredity),1970The Foundations of Biochemistry1.1CellularFoundationsof matter. What are these distinguishing features ofliving organisms?1.2Chemical Foundations11A high degree of chemical complexity and mi-1.3Physical Foundations19croscopic organization. Thousands of different1.4GeneticFoundationsmolecules make up a cell's intricate internal struc27tures(Fig.1-la).Theseincludeverylongpolymers1.5EvolutionaryFoundations29eachwith itscharacteristic sequence of subunits,itsunique three-dimensional structure, and its highlyspecific selection of binding partners in the cell.bout fifteen billion years ago, the universe arose asSystems for extracting, transforming, and us.a cataclysmic eruption of hot, energy-rich sub-ingenergyfromtheenvironment(Fig.1-lb),enatomic particles.Within seconds,the simplestabling organisms to build and maintain their intricateelements (hydrogen and helium) were formed. As thestructuresand todomechanical, chemical,osmotic,universe expanded and cooled,material condensedandelectricalwork.Thiscounteractsthetendencyofunder the infuence of gravity to form stars. Some starsall matter todecay toward a more disordered state,became enormous and then exploded as supernovae,to cometoequilibriumn with its surroundings.releasing the energyneeded to fuse simpler atomicnuclei into themore complexelements.Thus were proDefined functions for each of an organism'sduced, over billions of years, Earth itself and thecomponents and regulated interactions amongchemicalelementsfound on Earth today.Aboutfourbil-them. This is true not only of macroscopic struc-lionyears ago,lifearose-simplenicroorganismswithtures, such as leaves and stems or hearts and lungs,the ability to extract energy from chemical compoundsbut also of microscopic intracellular structuresand,later, from sunlight,which theyused tomake a vastand individual chemical compounds. The interplayarrayofmorecomplexbiomoleculesfromthesimpleamongthechemicalcomponents ofa living organismelements and compounds on the Earth's surface.is dynamic;changes in one componentcause coordi-Biochemistryaskshowtheremarkableproperties ofnatingorcompensatingchangesinanother,withtheliving organismsarisefrom the thousands ofdifferentwhole ensemble displaying a characterbeyond thatbionolecules.When these molecules are isolated andof its individual parts.The collection ofmoleculesexamined individually,they conform to all the physicalcarries out a program, the end result of which is re-and chemical laws that describe the behavior of inani-production of the program and self-perpetuation ofmatematter--as do all theprocessesoccurring in livingthat collection of molecules--in short,life.organisms.The study of biochemistry shows how theMechanisms for sensing and responding to al-collections ofinanimatemoleculesthatconstitutelivingterations in their surroundings, constantly ad-organisms interact to maintain and perpetuate lifejusting to these changes by adapting their internalanimated solelyby thephysical and chemical lawsthatchemistry or their location in the environment.govern thenonliving universe.Yet organisms possess extraordinary attributes,A capacity for precise self-replication andpropertiesthatdistinguishthemfromothercollectionsself-assembly (Fig.1-lc).A single bacterial cell
1.1 1.2 1.3 1.4 1.5 The Foundations of Biochemistry Cellular Foundations 2 ChemicalFoundations 11 PhysicalFoundations 19 Genetic Foundations 27 EvolutionaryFoundations 29 bout fifteen billion years ago, the universe arose as a cataclysmic eruption of hot, energy-rich subatomic particles. Within seconds, the simplest elements (hydrogen and helium) were formed. As the universe expanded and cooled, material condensed under the influence of gravity to form stars. Some stars became enormous and then exploded as supernovae, releasing the energy needed to fuse simpler atomic nuclei into the more complex elements. Thus were produced, over billions of years, Earth itself and the chemical elements found on Earth today. About four billion years ago, life arose-simple microorganisms with the ability to extract energy from chemical compounds and, later, from sunlight, which they used to make a vast array of more complex biomolecules from the simple elements and compounds on the Earth's surface. Biochemistry asks how the remarkable properties of living organisms arise from the thousands of different biomolecules. When these molecules are isolated and examined individually, they conform to all the physical and chemical laws that describe the behavior of inanimate matter-as do all the processes occurring in living organisms. The study of biochemistry shows how the collections of inanimate molecules that constitute living organisms interact to maintain and perpetuate life animated solely by the physical and chemical laws that govern the nonliving universe. Yet organisms possess extraordinary attributes, properties that distinguish them from other collections of matter. What are these distinguishing features of IMng organisms? A hrgh degree of chemical complexity and microscopic organization. Thousands of different molecules make up a cell's intricate internal structures (Fig. l-la). These include very long pol}rmers, each with its characteristic sequence of suburLits, its urLique three-dimensional structure, and its higNy specific selection of binding partners in the cell. Systems for extraeting, tlansforming, and using energy from the environment (Fig 1- lb), enabling organisms to build and maintain their intricate structures and to do mechanical, chemical, osmotic, and electrical work. This counteracts the tendency of all matter to decay toward a more disordered state, to come to equilibrium with its surroundings. Defined functions for each of an organism's components and regulated interactions arnong them. This is true not only of macroscopic structures, such as leaves and stems or hearts and lungs, but also of microscopic intracellular structures and individual chemical compounds. The interplay among the chemical components of a living organism is dpamic; changes in one component cause coordinating or compensating changes in another, with the whole ensemble displaying a character beyond that of its individual parts. The collection of molecules carries out a program, the end result of which is reproduction of the program and self-perpetuation of that collection of molecules-in short, life. Mechanisms for sensing and responding to alterations in their surroundings, constantly adjusting to these changes by adapting their internal chemistry or their location in the environment. A capacity for precise self-replication and self-assembly (Fig 1-1c). A single bacterial cell
TheFoundations of Biochemistrywithin a common chemical framework.For the sake ofclarity,inthisbook we sometimesrisk certaingeneral-izations, which, though not perfect, remain useful; wealsofrequentlypoint outtheexceptions tothesegener-alizations,whichcanproveilluminatingBiochemistry describes in molecular terms thestructures,mechanisms,andchemical processessharedby all organisms and provides organizing principles thatunderlie life in all its diverse forms,principles wereferto collectively as the molecular logic of life.Althoughbiochemistryprovides importantinsights andpractical(a)(b)applications in medicine,agriculture,nutrition,andindustry,itsultimate concern iswith the wonder oflifeitself.In this introductory chapter we give an overviewof the cellular, chemical, physical,and genetic back-groundstobiochemistry andtheoverarchingprincipleof evolution-the development over generations ofthe properties of living cells. As you read through thebook, you may find it helpful to refer back to this chap-ter at intervals to refresh your memory of this back-ground material.1.1 CellularFoundations(c)Theunity and diversityof organisms becomeapparentFIGURE1-1 Some characteristics of living matter.(a)Microscopiceven at the cellular level.Thesmallest organisms consistcomplexity and organization are apparent in this colorized thin sec-of singlecells and aremicroscopic.Larger,multicellulartionofvertebratemuscletissue,viewedwiththeelectronmicroscopeorganismscontainmanydifferenttypesofcells,which(b)Aprairie falcon acquires nutrients by consuming a smaller bird.vary in size, shape,and specialized function.Despite(c) Biological reproduction occurs with near-perfectfidelity.placed in a sterile nutrient medium can give rise toa billion identical"daughter"cells in 24 hours.Eachcell contains thousands of different molecules,some extremely complex; yet each bacterium isafaithful copy of the original, its construction di-rected entirely from information contained in thegenetic material of the original cell.A capacity to change over time bygradual evo-lution. Organisms change their inherited lifestrategies,in very small steps, to survive in new cir-cumstances.The result of eons of evolution is anenormous diversity of life forms,superficially verydifferent (Fig.1-2)but fundamentally relatedthrough their shared ancestry. This fundamentalunity of living organisms is reflected atthe molecular level in the similarity of gene sequences andprotein structures.FIGURE1-2Diverse living organisms share common chemical features.Despite these common properties, and the funda.Birds, beasts, plants, and soil microorganisms share with humans themental unity of life they reveal, it is difficult to makesamebasic structural units (cells)andthesamekindsof macromoleculesgeneralizations about living organisms. Earth has an(DNA, RNA, proteins)made up of the same kinds of monomeric subunitsenormous diversity of organisms.Therange of habitats,(nucleotides, amino acids). They utilize the same pathways for synthesisfrom hotsprings toArctictundra,from animal intestinesofcellular components,share the same genetic code, and derivefrom theto collegedormitories,is matched by a correspondinglysameevolutionaryancestors.Shownhereisadetail fromrTheGardenofwiderangeofspecificbiochemicaladaptations,achievedEden, by Jan van Kessel the Younger (1626-1679)
(c) FIGURE l-1 Some characteristics of living matter. (a) Microscopic complexity and organization are apparent in this colorized thin section of vertebrate muscle tissue, viewed with the electron microscope. (b) A prairie falcon acquires nutrients by consuming a smaller bird. (c) Biological reproduction occurs with near-perfect fidelity. placed in a sterile nutrient medium can give rise to a billion identical "daughter" cells in 24 hours. Each cell contains thousands of different molecules, some extremely complex; yet each bacterium is a faithful copy of the original, its construction directed entirely from information contained in the genetic material of the original cell. A capacity to change over time by gradual evolution. Organisms change their inherited life strategies, in very small steps, to survive in new circumstances. The result of eons of evolution is an enorrnous diversity of Me forms, superflcially very different (Fig. 1-2) but fundamentally related through their shared ancestry. This fundamental unity of living organisms is reflected at the molecular level in the similarity of gene sequences and protein structures. Despite these common properties, and the fundamental unity of life they reveal, it is difflcult to make generalizations about living organisms. Earth has an enorrnous diversity of organisms. The range of habitats, from hot springs to Arctic tundra, from animal intestines to college dormitories, is matched by a correspondingly wide range of speci-flc biochemical adaptations, achieved within a corrmon chemical framework. For the sake of clarity, in this book we sometimes risk certain generalizations, which, though not perfect, remain useftil; we also frequently point out the exceptions to these generalizations, which can prove illuminating. Biochemistry describes in molecular terms the structures, mechanisms, and chemical processes shared by all organisms and provides organizing principles that underlie life in all its diverse forms, principles we refer to collectively as the molecular logi,c oJ life. I.Jthorgh biochemistry provides important insights and practical applications in medicine, agriculture, nutrition, and industry, its ultimate concern is with the wonder of life itself. In this introductory chapter we give an overview of the cellular, chemical, physical, and genetic backgrounds to biochemistry and the overarching principle of evolution-the development over generations of the properties of living cells. As you read through the book, you may find it helpful to refer back to this chapter at intervals to refresh your memory of this background material. 1.1 (ellularFoundations The unity and diversity of organisms become apparent even at the cellular level. The smallest organisms consist of single cells and are microscopic. Larger, multicellular organisms contain many different types of cells, which vary in size, shape, and specialized function. Despite FIGURE 1-2 Diverse living organisms share common chemical features. Birds, beasts, plants, and soil microorganisms share with humans the same basic structural units (cells) and the same kinds of macromolecules (DNA, RNA, proteins) made up of the same kinds of monomeric subunits (nucleotides, amino acids). They utilize the same pathways for synthesis of cellular components, share the same genetic code, and derive from the same evolutionary ancestors. Shown here is a detail from "The Carden of Eden," bylan van Kessel theYounger (1626-1679)
1.1 Cellular Foundationsthese obvious differences, all cells of the simplest andways.Because the individual lipids and proteins of themost complex organisms share certain fundamentalplasmamembranearenotcovalentlylinkedthe entireproperties, which can be seen at the biochernical level.structureis remarkablyflexible,allowing changes in theshape and size of the cell. As a cell grows, newly madeCells Are the Structural and Functional Units oflipidandproteinmoleculesareinsertedintoitsplasmamembrane; cell division producestwo cells, each withAll LivingOrganismsits ownmembrane.This growthand cell division (fis-Cells of all kinds share certain structural featuression)occurs without loss ofmembrane integrity.(Fig.1-3).Theplasma membrane definesthepe-Theinternal volume enclosed bythe plasma mem-riphery of the cell, separating its contents from the sur-brane,thecytoplasm(Fig.1-3),iscomposedofanaque-roundings.It is composed of lipidandproteinmoleculesous solution,the cytosol.and a variety of suspendedthat form a thin,tough,pliable,hydrophobic barrierparticleswithspecificfunctionsThecytosolisahighlyaround the cell. The membrane is a barrier to the freeconcentrated solution containing enzymes and the RNApassage of inorganic ions and most other charged or po-moleculesthat encode them;the components (aminolarcompounds.Transportproteinsintheplasmamem-acidsandnucleotides)fromwhichthesemacromoleculesbraneallowthepassage of certain ions andmolecules;are assembled; hundreds of small organic moleculesreceptor proteins transmit signals into the cell; andcalledmetabolites.intermediatesinbiosymtheticandmembraneenzymesparticipateinsomereactionpath-degradativepathways;coenzymes,compounds essentialtomany enzyme-catalyzed reactions;inorganic ions;andsuch supramolecular structures as ribosomes,the sitesNucleus (eukaryotes)or nucleoid (bacteria, archaea)of protein synthesis, and proteasomes,which degradeContains genetic material-DNA andproteins no longerneeded bythecell.associated proteins.Nucleus isAll cells have, for at least some part of their life,membrane-enclosed.either a nucleus oranucleoid,in which thegenomePlasmamembranethecompletesetofgenes,composedofDNA-isstoredTough, flexible lipid bilayer.and replicated. The nucleoid, in bacteria and archaea, isSelectively permeable tonotseparated fromthecytoplasmby amembrane;thepolarsubstances.Includesmembrane proteins thatnucleus,in eukaryotes, consists of nuclear material en-function intransport,closed withinadoublemembrane,thenuclearenvelope.in signal reception,Cells with nuclear envelopes make up the large groupand as enzymes.Eukarya (Greek eu, "true," and karyon, "nucleus")Microorganisms without nuclear envelopes,formerlygrouped together as prokaryotes (Greek pro,"be-fore"),arenow recognized as comprising two very dis-tinctgroups, Bacteria and Archaea,described below.CellularDimensionsAreLimitedbyDiffusionMost cells are microscopic, invisible to the unaided eye.CytoplasmAqueous cell contents andAnimal and plant cells are typically 5 to100 μm in diam-suspended particleseter, and many unicellularmicroorganisms are only1 toand organelles.2μmlong (seethe insideback coverfor information onunits and their abbreviations).What limits the dimen-centrifuge at 150,000gsions of a cell? The lower limit is probably set by theminimumnumberofeachtypeofbiomoleculerequiredSupernatant: cytosolbythecell.Thesmallestcells,certainbacteriaknownasConcentrated solutionmycoplasmas,are300nm in diameter and have avol-ofenzymes,RNA,ume of about 10-14 mL. A single bacterial ribosome ismonomeric subunits,metabolites,about20nminitslongestdimensionsoafewribosomesinorganic ions.take up a substantial fraction of the volume in a my-coplasmal cell.Pellet: particles and organellesThe upper limit of cell size is probably set by theRibosomes, storage granules,mitochondria,chloroplasts,lysosomes,rateofdiffusionofsolutemoleculesinaqueoussystemsendoplasmic reticulum.For example, a bacterial cell that depends on oxygen-consumingreactionsfor energyproductionmust obtainFIGURE1-3The universal features of living cells.All cells have a nu-molecular oxygen by diffusion from the surroundingcleus or nucleoid, a plasma membrane, and cytoplasm.The cytosol ismediumthrough its plasma membrane.The cell is sodefined as thatportion of the cytoplasm that remains in the supernatantsmall, and the ratio of its surface area to its volume is soafter gentle breakage of the plasma membrane and centrifugation oflarge,that everypartof itscytoplasmiseasilyreachedthe resulting extract at 150,000 g for 1 hour
these obvious differences, all cells of the simplest and most complex organisms share certain fundamental properties, which can be seen at the biochemicalevel. {e[is Are the Strurturai afid Falnrti*n*f Uni{s cl{ Altl-iuing Organi*ms Cells of all kinds share certain structural features (f ig. [-3). The plasma membrane defines the periphery of the cell, separating its contents from the surroundings. It is composed of lipid and protein molecules that form a thin, tough, pliable, hydrophobic barrier around the cell. The membrane is a barrier to the free passage of inorganic ions and most other charged or polar compounds. T?ansport proteins in the plasma membrane allow the passage of certain ions and molecules; receptor proteins transmit signals into the cell; and membrane enzpes participate in some reaction pathNucleus (eukaryotes) or nucleoid (bacteria, archaea) Contains genetic material-DNA and associated proteins. Nucleus is membrane-enclosed. Plasma membrane Tough, fledble lipid bilayer. Selectively permeable to polar substances. Includes membrane proteins that 1.1 Cellular Foundations 3 ways. Because the individual lipids and proteins of the plasma membrane are not covalently lirked, the entire structure is remarkably flexible, allowing changes in the shape and size of the cell. As a cell grows, newly made lipid and protein molecules are inserted into its plasma membrane; cell division produces two cells, each with its own membrane. This growth and cell division (flssion) occurs without loss of membrane integrity. The internal volume enclosed by the plasma membrane, the cytoplasm (F g 1-3), is composed of an aqueous solution, the c5rtosol, and a variety of suspended particles with specific functions. The cytosol is a highly concentrated solution containing enzlirnes and the RNA molecules that encode them; the components (amino acids and nucleotides) from which these macromolecules are assembled; hundreds of small organic molecules called metabolites, intermediates in biosynthetic and degradative pathways ; coenz5rmes, compounds essential to many enzyme-catalyzed reactions; inorganic ions; and such supramolecular structures as ribosomes, the sites of protein sSmthesis, and proteasomes, which degrade proteins no longer needed by the cell. All cells have, for at least some part of their life, either a nucleus or a nucleoid, in which the genomethe complete set of genes, composed of DNA-is stored and replicated. The nucleoid, in bacteria and archaea, is not separated from the cytoplasm by a membrane; the nucleus, in eukaryotes, consists of nuclear material enclosed within a double membrane, the nuclear envelope. Cells with nuclear envelopes make up the large group Eukarya (Greek eLL, "trte," and karyon, "nucleus"). Microorganisms without nuclear envelopes, formerly grouped together as prokaryotes (Greek pro, "before"), are now recognized as comprising two very distinct groups, Bacteria and Archaea, described below. {ellu}ar ftimensions Are [innited by Dlffusion Most cells are microscopic, invisible to the unaided eye. Animal and plant cells are typically 5 to 100 pm in diameter, and many unicellular microorganisms are only 1 to 2 g,m long (see the inside back cover for information on units and their abbreviations). What limits the dimensions of a cell? The Iower limit is probably set by the minimum number of each type of biomolecule required by the cell. The smallest cells, certain bacteria known as mycoplasmas, are 300 nm in diameter and have a volume of about 10-14 mL. A single bacterial ribosome is about 20 nm in its longest dimension, so a few ribosomes take up a substantial fraction of the volume in a mycoplasmal cell. The upper limit of cell size is probably set by the rate of diffusion of solute molecules in aqueous systems. For example, a bacterial cell that depends on oxygenconsuming reactions for energy production must obtain molecular oxygen by diffusion from the surrounding medium through its plasma membrane. The cell is so small, and the ratio of its surface area to its volume is so Iarge, that every part of its cytoplasm is easily reached Cytoplasm ; Aqueous cell contents and suspended particles and organelles. I centrifuge at 150,0009 | V Pellet: particles and organelles Ribosomes, storage granules, mitochondria, chloroplasts, lysosomes, endoplasmic reticulum. FI6URE 1- 3 The universal features of living cells, All cells have a nucleus or nucleoid, a plasma membrane, and cytoplasm. The cytosol is defined as that portion ofthe cytoplasm that remains in the supernatant after gentle breakage of the plasma membrane and centrifugation of the resulting extract at 1 50,000 g for .l hour
TheFoundations of BiochemistryEukaryaAnimalsGreenSlimeEntamoebaenonsulfurmolds1BacteriaArchaeabacteriaFungiGram-MethanosarcinapositivePlantsMethanobacteriumProteobacteriabacteriaCiliatesHalophiles(Purple bacteria)ThermoproteusMethanococcusThermococcusPyrodictiumCyanobacteriacelerFlagellatesFlavobacteriaTrichomonadsThermotogalesMicrosporidiaDiplomonadsFIGURE1-4 Phylogeny of the three domains of life.Phylogenetic rela-beconstructed fromsimilaritiesacross species of the amino acid setionships are often illustrated by a"family tree"of this type. The basis forquences of a single protein. For example, sequences of the proteinthis tree is the similarity in nucleotide sequences of the ribosomal RNAsGroEL (a bacterial protein that assists in protein folding) were comparedofeachgroup;themoresimilarthesequence,thecloserthelocationoftogeneratethetree inFigure3-32.Thetree inFigure3-33 isa"conthe branches, with the distance between branches representing the de-sensus" tree, which uses several comparisons such as these to make thegree of difference between two sequences. Phylogenetic trees can alsobest estimates of evolutionary relatedness of a group of organisms.a common progenitor (Fig.1-4).Two largegroups ofbyO2diffusing into the cell.Withincreasing cell size,however, surface-to-volume ratio decreases, until me-single-celled microorganisms can be distinguished ontabolismconsumes O2fasterthandiffusioncan supplygenetic and biochemical grounds:Bacteria andit.Metabolism that requires Ozthus becomes impossibleArchaea. Bacteria inhabit soils, surface waters, andas cell sizeincreasesbeyond a certainpoint,placingathetissues of other living or decaying organisms.Many oftheoretical upperlimit on the size of cells.the Archaea, recognized as a distinct domain by CarlWoeseinthe 1980s,inhabit extreme environments-saltlakes, hot springs, highly acidic bogs,and the oceanThere AreThreeDistinctDomains of Lifedepths.Theavailable evidence suggests that theArchaeaAll living organisms fall into one of three large groupsand Bacteriadiverged earlyin evolution. All eukarvotic(domains)thatdefinethreebranchesof evolution fromorganisms, which make up the third domain, Eukarya,AllorganismsReducedfuelPhototrophsChemotrophsOxidizedEnergy(energyfromlight)(energyfromoxidationofchemicalfuels)fuelsourceLithotrophsOrganotrophs(inorganic fuels)(organicfuels)HeterotrophsCarbonAutotrophs(carbon from organicsource(carbonfromCO2)compounds)CyanobacteriaSulfur bacteriaPurple bacteriaMost bacteriaHydrogen bacteriaVascular plantsGreen bacteriaAllnonphototrophiceukaryotesExamples滋1CFIGURE1-5Organismscanbeclassified accordingtotheirsourceofenergy(sunlightoroxidizablechemicalcompounds)and their source of carbon for the synthesis of cellular material
4 The Foundationsf Biochemistry Bacteria Proteobacteria (Purple bacteria) Cyanobacteria Flavobacteria Archaea Methanobacterium Thermoproteus Methanococcus Entamoebae Slime molds Halophiles Eukarya Animals Green nonsulfur bacteria Phototrophe (energy from light) Pyrod.ictium\Thermococcus " \ \ celer Plants Ciliates Thermotogales FIGURE 1-4 Phylogeny of the three domains of life. Phylogenetic relationships are often illustrated by a "family tree" of this type The basis for this tree is the similarity in nucleotide sequences ofthe ribosomal RNAs of each group; the more similar the sequence, the closer the location of the branches, with the distance between branches representing the degree of difference bretween two sequences. Phylogenetic trees can also by 02 diffusing into the cell. With increasing cell size, however, surface-to-volume ratio decreases, until metabolism consumes 02 faster than diffusion can supply it. Metabolism that requires 02 thus becomes impossible as cell size increases beyond a certain point, placing a theoretical upper limit on the size of cells. There Are Three Distinct Domains of Life All living organisms fall into one of three Iarge groups (domains) that define three branches of evolution from Flagellates Trichomonads Microsporidia Diplomonads be constructed from similarities across species of the amino acid sequences of a single protein. For example, sequences of the protein CroEL (a bacterial protein that assists in protein folding) were compared to generate the tree in Figure 3-32. The tree in Figure 3-33 is a "consensus" tree, which uses several comparisons such as these to make the best estimates of evolutionary relatedness ofa group of organisms. a common progenitor (Fig. 1-4). TWo large groups of single-celled microorganisms can be distinguished on genetic and biochemical grounds: Bacteria and Archaea. Bacteria inhabit soils, surface waters, and the tissues of other Living or decaying organisms. Many of the Archaea, recognized as a distinct domain by Carl Woese in the 1980s, inhabit extreme environrnents-salt lakes, hot springs, highly acidic bogs, and the ocean depths. The available evidence suggests that the Archaea and Bacteria diverged early in evolution. AII eukaryotic organisms, which make up the third domain, Eukarya, Reduced fuel Oxidized fuel Lithotrophs (inorganic fuels) Energy source Carbon source Examples Autotrophs (carbon from CO2) Cyanobacteria Vascular plants Heterotrophs (carbon from organic compounds) Purple bacteria Green bacteria Sulfur bacteria Hydrogen bacteria Most bacteria All nonphototrophic eukaryotes All organisms tlGUREl-5 Organismscanbeclassifiedaccordingtotheirsourceof energy(sunlightoroxidizablechemical compounds) and their source of carbon for the synthesis of cellular material