cells - labs.icb.ufmg.brlabs.icb.ufmg.br/lbcd/prodabi3/integrantes/cibele/lehn02.pdf · the human...

20

Cells

chapter

2Cells are the structural and functional units of all living organisms. Thesmallest organisms consist of single cells and are microscopic, whereaslarger organisms are multicellular. The human body, for example, containsat least 1014 cells. Unicellular organisms are found in great variety through-out virtually every environment from Antarctica to hot springs to the innerrecesses of larger organisms. Multicellular organisms contain many differ-ent types of cells, which vary in size, shape, and specialized function. Yet nomatter how large and complex the organism, each of its cells retains someindividuality and independence.

Despite their many differences, cells of all kinds share certain struc-tural features (Fig. 2–1). The plasma membrane defines the periphery ofthe cell, separating its contents from the surroundings. It is composed ofenormous numbers of lipid and protein molecules, held together primarilyby noncovalent hydrophobic interactions (p. 17), forming a thin, tough, pli-able, hydrophobic layer around the cell. The membrane is a barrier to thefree passage of inorganic ions and most other charged or polar compounds.Transport proteins in the plasma membrane allow the passage of certainions and molecules. Other membrane proteins include receptors that trans-mit signals from the outside to the inside of the cell and enzymes that par-ticipate in membrane-associated reaction pathways.

Because the individual lipids and proteins of the plasma membrane arenot covalently linked, the entire structure is remarkably flexible, allowingchanges in the shape and size of the cell. As a cell grows, newly made lipidand protein molecules are inserted into its plasma membrane; cell divisionproduces two cells, each with its own membrane. Growth and fission occurwithout loss of membrane integrity. In a reversal of the fission process, twoseparate membrane surfaces can fuse, also without loss of integrity. Mem-brane fusion and fission are central to mechanisms of transport into and outof cells known as endocytosis and exocytosis, respectively.

The internal volume bounded by the plasma membrane, the cyto-

plasm, is composed of an aqueous solution, the cytosol, and a variety ofinsoluble, suspended particles (Fig. 2–1). The cytosol is a highly concen-trated aqueous solution with a complex composition and gel-like consis-

figure 2–1The universal features of living cells. All cells have anucleus or nucleoid, a plasma membrane, and cyto-plasm. The cytosol is defined operationally as that portionof the cytoplasm that remains in the supernatant aftercentrifugation of a cell extract at 150,000 g for 1 hour.

Nucleus (eukaryotes)or nucleoid (bacteria)Contains genetic material–DNA andassociated proteins. Nucleus is membrane-bounded.

Plasma membrane Tough, flexible lipid bilayer. Selectively permeable to polar substances. Includes membrane proteins that function in transport, in signal reception, and as enzymes.

CytoplasmAqueous cell contents andsuspended particlesand organelles.

Supernatant: cytosolConcentrated solutionof enzymes, RNA, monomeric subunits, metabolites, inorganic ions.

Pellet: particles and organellesRibosomes, storage granules,mitochondria, chloroplasts, lysosomes,endoplasmic reticulum.

centrifuge at 150,000 g

Chapter 2 Cells 21

tency. Dissolved in the cytosol are many enzymes and the RNA moleculesthat encode them; the monomeric subunits (amino acids and nucleotides)from which these macromolecules are assembled; hundreds of small or-ganic molecules called metabolites, intermediates in biosynthetic anddegradative pathways; coenzymes, compounds of Mr 200 to 1,000 that areessential participants in many enzyme-catalyzed reactions; and inorganicions.

Among the particles suspended in the cytosol are supramolecular com-plexes and, in almost all nonbacterial cells, a variety of membrane-boundedorganelles containing specialized metabolic machinery. Ribosomes, smallparticles 18 to 22 nm in diameter (1 nm is 10�9 m) that are composed ofover 50 different protein and RNA molecules, are the sites at which proteinsynthesis occurs. Ribosomes engaged in protein synthesis often occur inclusters called polysomes (polyribosomes) held together by a strand ofmessenger RNA. Also present in the cytoplasm of many cells are granulesor droplets containing stored nutrients such as starch and fat.

All living cells have, for at least some part of their life, either a nucleus

or a nucleoid, in which the genome (the complete set of genes, composedof DNA) is stored and replicated. The DNA molecules are always far longerthan the cells themselves and are tightly folded and packed within the nu-cleus or nucleoid as supramolecular complexes of DNA with specific pro-teins. The bacterial nucleoid is not separated from the cytoplasm by a mem-brane, but in higher organisms the nuclear material is enclosed within adouble membrane, the nuclear envelope. Cells with nuclear envelopes arecalled eukaryotes (Greek eu, “true,” and karyon, “nucleus”); those with-out nuclear envelopes—bacterial cells—are prokaryotes (Greek pro, “be-fore”).

Unlike bacteria, eukaryotes have a variety of other membrane-boundedorganelles in their cytoplasm, including mitochondria, endoplasmic reticu-lum, Golgi complexes, lysosomes and vacuoles (related organelles found inanimal and plant cells, respectively), and, in photosynthetic cells, chloro-plasts.

In this chapter we briefly review the evolutionary relationships amongsome commonly studied cells and organisms and the structural featuresthat distinguish cells of various types. Our main focus is on eukaryotic cells.Also discussed in brief are the cellular parasites known as viruses.

Cellular DimensionsMost cells are microscopic, invisible to the unaided eye. Animal and plantcells are typically 5 to 100 mm in diameter, and many bacteria are only 1 to2 mm long (1 mm is 10�6 m).

What limits the dimensions of a cell? The lower limit is probably set bythe minimum number of each type of biomolecule required by the cell. Thesmallest cells, certain bacteria known as mycoplasmas, are 300 nm in diam-eter and have a volume of about 10�14 mL. A single bacterial ribosome isabout 20 nm in its longest dimension, so a few ribosomes take up a sub-stantial fraction of the volume in a mycoplasmal cell. In a cell of this size, a1 mM solution of a compound (a typical concentration for some smallmetabolites) represents only 6,000 molecules.

The upper limit of cell size is probably set by the rate of diffusion ofsolute molecules in aqueous systems. A bacterial cell that depends uponoxygen-consuming reactions for energy production (an aerobic cell) mustobtain molecular oxygen (O2) from the surrounding medium by diffusionthrough its plasma membrane. The cell is so small, and the ratio of its sur-face area to its volume is so large, that every part of its cytoplasm is easily

0.5 mm

22 Part I Foundations of Biochemistry

reached by O2 diffusing into the cell. As cell size increases, however, sur-face-to-volume ratio decreases, until metabolism consumes O2 faster thandiffusion can supply it. Aerobic metabolism thus becomes impossible as cellsize increases beyond a certain point, placing a theoretical upper limit onthe size of the aerobic cell.

There are interesting exceptions to the generalization that cells mustbe small. The green alga Nitella has giant cells several centimeters long. Toassure the delivery of nutrients, metabolites, and genetic information(RNA) to all of its parts, each cell is vigorously “stirred” by active cytoplas-mic streaming (see Fig. 2–18). The shape of a cell can also help to com-pensate for its large size. A smooth sphere has the smallest surface-to-volume ratio possible for a given volume. Many large cells, although roughlyspherical, have highly convoluted surfaces (Fig. 2–2a), creating larger sur-face areas for the same volume and thus facilitating the uptake of fuels andnutrients and the release of waste products to the surrounding medium.Other large cells (neurons, for example) have large surface-to-volume ratios because they are long and thin, star-shaped, or highly branched (Fig. 2–2b), rather than spherical.

Cells and Tissues Used in Biochemical StudiesBecause all living cells have evolved from the same progenitors, they sharecertain fundamental similarities. Careful biochemical study of just a fewtypes of cells, however different in biochemical details and varied in super-ficial appearance, should therefore yield general principles applicable to allcells and organisms. The burgeoning of biological knowledge over the past150 years has repeatedly supported these propositions. Certain cells, tis-sues, and organisms have proved more amenable to experimental studiesthan others. Knowledge in biochemistry is derived primarily from a few rep-resentative tissues and organisms, such as the bacterium Escherichia coli,

50 mm(a) (b)

figure 2–2Convolutions of the plasma membrane, or long, thinextensions of the cytoplasm, increase the surface-to-volume ratio of cells. (a) In cells of the intestinal mucosa(the inner lining of the small intestine), the plasma mem-brane facing the intestinal lumen is folded into microvilli,

increasing the area for absorption of nutrients from theintestine. (b) Neurons of the hippocampus of the rat brainare several millimeters long, but the long extensions(axons) are only about 10 nm wide.

Chapter 2 Cells 23

the yeast Saccharomyces cerevisiae, photosynthetic algae such asChlamydomonas, spinach leaves, rat liver, and the skeletal muscle of sev-eral vertebrates. Some biochemical studies focus on the isolation, purifica-tion, and characterization of cellular components; other research investi-gates the metabolic and genetic pathways of living cells.

An experimenter ideally begins the isolation of enzymes and other cel-lular components with a plentiful and homogeneous source of the material.The component of interest (such as an enzyme or nucleic acid) often rep-resents only a miniscule fraction of the total material, and grams or evenkilograms of starting material are needed to obtain a few micrograms of thepurified component. A homogeneous source of an enzyme or nucleic acid,in which all the cells are genetically and biochemically identical, leaves nodoubt about which cell type yielded the purified component and makes itsafer to extrapolate the results of in vitro studies to the situation in vivo. A large culture of bacterial or protistan cells (E. coli, S. cerevisiae, orChlamydomonas, for example), all derived by division from the same par-ent and therefore genetically identical, meets the requirement for a plenti-ful and homogeneous source. Individual tissues from laboratory animals(rat liver, pig brain, rabbit muscle) are plentiful sources of similar, thoughnot identical, cells. Some animal and plant cells proliferate in cell culture,producing populations of identical (cloned) cells in quantities suitable forbiochemical analysis.

Genetic mutants in which a defect in a single gene produces a defectiveprotein, which causes a specific functional defect in the cell or organism,are extremely useful in establishing that a certain protein is essential to aparticular cellular function. Because it is technically much simpler to pro-duce and detect mutants in bacteria and yeast, these organisms (E. coli andS. cerevisiae, for example) have been favorite experimental targets for bio-chemical geneticists. Once the gene for a protein has been isolated, it canoften be inserted into a bacterial or yeast cell, which then acts as a biologi-cal factory, overproducing the protein. With genetic engineering tech-niques, experimenters can introduce specific mutations into such genes anddetermine their effects on protein structure and function.

An organism that is easy to culture in the laboratory, and has a shortgeneration time, offers significant advantages to the research biochemist.An organism that requires only a few simple precursor molecules in itsgrowth medium can be cultured in the presence of a radioisotopically la-beled precursor, and the metabolic fate of that precursor can then be con-veniently traced by following the incorporation of the radioactive atoms intoits metabolic products. The short generation time of microorganisms (min-utes or hours) allows the investigator to follow a labeled precursor or a ge-netic defect through many generations in a few days. In organisms with gen-eration times of months or years, this is virtually impossible.

Some highly specialized tissues of multicellular organisms are remark-ably enriched in some particular component related to their specializedfunction. For studies on such specific components or functions, biochemistscommonly choose the specialized tissue for their experimental systems. Forexample, vertebrate skeletal muscle is a rich source of actin and myosin;pancreatic secretory cells contain high concentrations of rough endoplas-mic reticulum; sperm cells are rich in DNA; liver contains high concentra-tions of many enzymes of biosynthetic pathways; and spinach leaves con-tain large numbers of chloroplasts.

Sometimes it is simplicity of structure or function that makes a partic-ular cell or organism attractive as an experimental system. For studies ofplasma membrane structure and function, the mature erythrocyte (redblood cell) has been a favorite, because it has no internal membranes to

0.6 m�

A dividing Escherichia coli cell.

4 m�

Dividing Saccharomyces cerevisiae (baker’s yeast) cells.


complicate purification of the plasma membrane. Some bacterial viruses(bacteriophages) have few genes. Their DNA molecules are thereforesmaller and much simpler than those of humans or maize plants. It hasproved easier to study DNA replication with these viruses than with eu-karyotic chromosomes because when a virus infects a bacterial cell, there isa synchronous burst of DNA synthesis, often accompanied by increased lev-els of the enzymes of DNA replication.

The biochemical description of living cells in this book is a composite,based on studies of many types of cells. Biochemists must always exercisecaution in generalizing from results obtained in studies of selected cells, tis-sues, and organisms and in relating what is observed in vitro to what hap-pens within the living cell.

Evolution and Structure of Prokaryotic CellsTwo large groups of extant prokaryotes can be distinguished on biochemi-cal grounds: archaebacteria (Greek arche, “origin”) and eubacteria

(Greek eu, “true”). Eubacteria inhabit soils, surface waters, and the tissuesof other living or decaying organisms. Most common and well-studied bac-teria, including Escherichia coli, are eubacteria. The archaebacteria aremore recently discovered and less well characterized biochemically. Mostinhabit more extreme environments—salt lakes, hot springs, bogs, and theocean depths. The available evidence suggests that the archaebacteria andeubacteria diverged early in evolution and constitute two separate ur-king-doms or domains, sometimes called Bacteria and Archaea. All eukaryoticorganisms, which constitute the third domain, Eukarya, evolved from thesame branch that gave rise to the Archaea; archaebacteria are thereforemore closely related to eukaryotes than to eubacteria. As complete genomicsequences have become available for archaebacteria (such as Methanococ-

cus jannaschii) and eubacteria (E. coli), the extent of the divergence be-tween these domains of life has become starkly apparent: less than half thegenes of M. jannaschii have recognizable homologs in E. coli! Further-more, the genes that encode the proteins required for DNA replication,RNA transcription, and protein synthesis in the archaebacterium M. jan-

naschii are of the same general type as those found in eukaryotes and dis-tinctly different from those involved in the same processes in eubacteria.

Within the domains of Bacteria and Archaea are subgroups distin-guished by the habitats in which they live. In aerobic habitats with a plenti-ful supply of oxygen, some resident organisms live by aerobic metabolism;their catabolic processes ultimately result in the transfer of electrons fromfuel molecules to oxygen. Other environments are anaerobic, virtually de-void of oxygen, and microorganisms adapted to these environments carryout catabolism without it. These bacteria transfer electrons to nitrate(forming N2), sulfate (forming H2S), or CO2 (forming methane, CH4). Manyorganisms that have evolved in anaerobic environments are obligate anaer-

obes; they die when exposed to oxygen.Organisms can be divided into two broad categories according to their

energy sources: phototrophs (Greek trophe, “nourishment”) trap sunlight,whereas chemotrophs derive their energy from oxidation of a fuel. Thephototrophs can be further divided into those that can obtain all neededcarbon from CO2 (autotrophs) and those that require organic nutrients(heterotrophs). No chemotroph can get its carbon atoms exclusively fromCO2 (that is, there are no autotrophs in this group), but the chemotrophsmay be further classified according to a different criterion: whether the fuels they oxidize are inorganic (lithotrophs) or organic (organotrophs).

Most known organisms fall within one of these four broad categories—autotrophs or heterotrophs among the photosynthesizers; lithotrophs or

0.25 m�

Nostoc sp., a photosynthetic cyanobacterium. This lightmicrograph shows long strings of the individual roundcells.

Chapter 2 Cells 25

figure 2–3Organisms can be classified according to their source ofenergy (sunlight or oxidizable chemical compounds) andtheir source of carbon for the synthesis of cellular material.

Heterotrophs(carbon from

organiccompounds)

Examples:•Purple bacteria•Green bacteria

Autotrophs(carbon from

CO2)

Examples:•Cyanobacteria

•Plants

Heterotrophs(carbon from organic

compounds)

Phototrophs(energy from

light)

Chemotrophs(energy from chemical

compounds)

All organisms

Lithotrophs(energy from

inorganiccompounds)

Examples:•Sulfur bacteria

•Hydrogen bacteria

Organotrophs(energy from

organiccompounds)

Examples:•Most prokaryotes

•All nonphototrophiceukaryotes

organotrophs among the chemical oxidizers (Fig. 2–3). Thus the prokary-otes have several general modes of obtaining carbon and energy. E. coli, forexample, is a chemoorganoheterotroph; it requires organic compoundsfrom its environment as fuel and as a source of carbon. Cyanobacteria arephotolithoautotrophs; they use sunlight as an energy source and convertCO2 into biomolecules.

As shown in Figure 2–4, the earliest cells arose about 3.5 billion (3.5 �109) years ago in the rich mixture of organic compounds, the “primordialsoup,” of prebiotic times; they were almost certainly chemoheterotrophs.The organic compounds they required were originally synthesized fromsuch components of the early earth’s atmosphere as CO, CO2, N2, and CH4

by the nonbiological actions of volcanic heat and lightning (Chapter 3).Early heterotrophs gradually acquired the ability to derive energy from cer-tain compounds in their environment and to use that energy to synthesizemore and more of their own precursor molecules, thereby becoming lessdependent on outside sources of these compounds. A very significant evo-lutionary event was the development of pigments capable of capturing vis-ible light from the sun, allowing the cell to use light energy to reduce or “fix”CO2 into more complex, organic compounds. The original electron donor forthese photosynthetic organisms was probably H2S, yielding elemental sul-fur or sulfate (SO4

2�) as the byproduct, but later cells developed the enzy-matic capacity to use H2O as the electron donor in photosynthetic reac-tions, eliminating O2 as waste. Cyanobacteria are the modern descendantsof these early photosynthetic oxygen producers.

The atmosphere of the earth in the earliest stages of biological evolu-tion was nearly devoid of oxygen, and the earliest cells were thereforeanaerobic. Under these conditions, chemoheterotrophs could oxidize or-ganic compounds to CO2 by passing electrons not to O2, but to acceptors

0

4,500 Formation of Earth

4,000 Formation of oceans and continents

3,500 Photosynthetic O2-producing cyanobacteriaPhotosynthetic sulfur bacteriaMethanogens

2,500 Aerobic bacteriaDevelopment of O2-rich atmosphere

1,500 Protists, the first eukaryotes

Red and green algae1,000

Endosymbionts (mitochondria, plastids)

500Diversification of multicellular eukaryotes (plants, fungi, animals)

3,000

2,000

Mil

lion

s of

yea

rs a

go

figure 2–4 Landmarks in the evolution of life on Earth.


figure 2–5Common structural features of bacterial cells.Because of differences in cell envelope structure, someeubacteria (gram-positive bacteria) retain Gram’s stain,and others (gram-negative bacteria) do not. E. coli isgram-negative. Cyanobacteria are also eubacteria butare distinguished by their extensive internal membranesystem, in which photosynthetic pigments are localized.Although the cell envelopes of archaebacteria andgram-positive eubacteria look similar under the electronmicroscope, the structures of the membrane lipids andthe polysaccharides of the cell envelope are distinctlydifferent in these organisms.

Ribosomes Bacterial ribosomes are smaller thaneukaryotic ribosomes, but serve the same function—protein 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.

Gram-negative bacteriaOuter membrane andpeptidoglycan layer

Outer membrane

Peptidoglycan layer

Inner membraneInner membrane

Gram-positive bacteriaThicker peptidoglycanlayer; outer membraneabsent

CyanobacteriaType of gram-negativebacteria with tougherpeptidoglycan layer andextensive internal mem-brane system containingphotosynthetic pigments

ArchaebacteriaPseudopeptidoglycan layeroutside plasma membrane;outer membrane absent

Peptidoglycan layerInner membrane

such as SO42�, yielding H2S as the product. With the rise of O2-producing

photosynthetic bacteria, the earth’s atmosphere became progressivelyricher in oxygen—a powerful oxidant and deadly poison to anaerobesadapted to a milder environment. Responding to the evolutionary pressureof the so-called “oxygen holocaust,” some lineages of microorganisms gaverise to aerobes that obtained energy by passing electrons from fuel mole-cules to oxygen. Because the transfer of electrons from organic moleculesto O2 releases a great deal of energy (the reaction is strongly exergonic; seeChapter 1), aerobic organisms had an energetic advantage over their anaer-obic counterparts when both competed in an environment containing oxy-gen. This advantage translated into the predominance of aerobic organismsin O2-rich environments.

Modern bacteria inhabit almost every ecological niche in the biosphere,and there are bacteria capable of using virtually every type of organic com-pound as a source of carbon and energy. Photosynthetic bacteria in bothfresh and marine waters trap solar energy and use it to generate carbohy-drates and all other cell constituents, which are in turn used as food byother forms of life. A potential limit to growth in the rest of the biosphere isthe availability of nitrogen-containing compounds, and here bacteria are anessential link in the global food web. A few strains of bacteria, called di-

azatrophs, are the only organisms on Earth that can metabolically convertatmospheric nitrogen (N2) into biologically necessary compounds, in aprocess known as nitrogen fixation. Lightning-driven reactions and thefertilizer industry also contribute significantly to the global budget of fixednitrogen. However, these ultimate sources of bioavailable nitrogen are notnecessarily the immediate sources of supply for the biosphere. Most nitro-gen compounds taken up by organisms are recycled from organic waste,and here again, bacteria play an essential role in the global food web by act-ing as the ultimate consumers, degrading the organic material of deadplants and animals and recycling the end products to the environment.

Escherichia coli Is the Best-Studied Prokaryotic CellBacterial cells share certain common structural features, but also showgroup-specific specializations (Fig. 2–5). E. coli is a usually harmless in-habitant of the human intestinal tract. The E. coli cell is about 2 mm longand a little less than 1 mm in diameter. It has a protective outer membraneand an inner plasma membrane that encloses the cytoplasm and the nu-cleoid. Between the inner and outer membranes is a thin but strong layer ofpeptidoglycans (sugar polymers cross-linked by amino acids), which givesthe cell its shape and rigidity. The plasma membrane and the layers outsideit constitute the cell envelope. Differences in the cell envelope among bac-terial species account for the different affinities for the dye gentian violet,

Chapter 2 Cells 27

which is the basis for Gram’s stain; gram-positive bacteria retain the dye,gram-negative bacteria do not. The outer membrane of E. coli, like that ofother gram-negative eubacteria, is similar to the plasma membrane in struc-ture but is different in composition. Gram-positive bacteria (Bacillus sub-

tilis and Staphylococcus aureus, for example) lack an outer membrane,and the peptidoglycan layer surrounding the plasma membrane is muchthicker than that in gram-negative bacteria. In the Archaea, rigidity is con-ferred by a different type of cross-linked sugar polymer (“pseudopeptido-glycan”). The plasma membranes of eubacteria consist of a thin bilayer oflipid molecules penetrated by proteins. Archaebacterial membranes have asimilar architecture, although their lipids differ strikingly from those of theeubacteria.

The plasma membrane contains proteins capable of transporting ionsand compounds into and out of the cell. Also in the plasma membrane ofmost eubacteria are electron-carrying proteins (cytochromes) essential inthe formation of ATP from ADP (Chapter 1). In photosynthetic bacteria, in-ternal membranes derived from the plasma membrane contain chlorophylland other light-trapping pigments.

From the outer membrane of E. coli cells and some other eubacteriaprotrude short, hairlike structures called pili, by which cells adhere to thesurfaces of other cells. Strains of E. coli and other motile bacteria have oneor more long flagella (singular, flagellum), which can propel the bac-terium through its aqueous surroundings. Bacterial flagella are thin, rigid,helical rods, 10 to 20 nm thick and up to several hundred micrometers long.Each is attached to a rotary motor, a protein structure that spins in the cellenvelope, rotating the flagellum.

The cytoplasm of E. coli contains about 15,000 ribosomes, thousandsof copies of each of about 1,000 different enzymes, numerous metabolitesand cofactors, and a variety of inorganic ions. Under some conditions, gran-ules of polysaccharides or droplets of lipid accumulate. The nucleoid con-tains a single, circular molecule of DNA. Although the DNA molecule of anE. coli cell is 1,000 times longer than the cell itself, it is packaged with pro-teins and tightly folded into the nucleoid, which is less than 1 mm in itslongest dimension. As in all bacteria, no membrane surrounds the geneticmaterial. In addition to the DNA in the nucleoid, the cytoplasm of most bac-teria contains one or more smaller, circular segments of DNA called plas-

mids. In nature, some plasmids confer resistance to toxins and antibioticsin the environment. In the laboratory, these DNA segments, because theyare nonessential, are especially amenable to experimental manipulation andare extremely useful to molecular geneticists.

There is a division of labor within the bacterial cell. The cell envelope,which includes the plasma membrane, regulates the flow of materials intoand out of the cell and protects the cell from noxious environmental agents.The plasma membrane and the cytoplasm contain a variety of enzymes es-sential to energy metabolism and the synthesis of precursor molecules; theribosomes manufacture proteins; and the nucleoid stores and transmits ge-netic information. Most bacteria lead existences that are nearly indepen-dent of other cells, but in some bacterial species, cells tend to associate inclusters or filaments, and a few (the myxobacteria, for example) demon-strate simple social behavior.

Evolution of Eukaryotic CellsAll fossils older than 1.5 billion years are the remains of small and relativelysimple organisms, similar in size and shape to modern prokaryotes. Startingabout 1.5 billion years ago, the fossil record begins to show evidence of


larger and more complex organisms, probably the earliest eukaryotic cells(Fig. 2–4). Details of the evolutionary path from prokaryotes to eukaryotescannot be deduced from the fossil record alone, but morphological and bio-chemical comparisons of modern organisms have suggested a reasonablesequence of events consistent with the fossil evidence.

Eukaryotic Cells Evolved from Prokaryotes in Several StagesThree major changes must have occurred as prokaryotes gave rise to eu-karyotes (Fig. 2–6). First, as cells acquired more DNA, the mechanisms re-quired to fold it compactly into discrete complexes with specific proteinsand to divide it equally between daughter cells at cell division became moreelaborate. These DNA-protein complexes, chromosomes (Greek chroma,

“color,” and soma, “body”), become especially compact at the time of celldivision, when they can be visualized with the light microscope as threadsof chromatin.

Second, as cells became larger, a system of intracellular membranes de-veloped, including a double membrane surrounding the DNA. This mem-brane segregated the nuclear process of RNA synthesis on a DNA templatefrom the cytoplasmic process of protein synthesis on ribosomes. Finally,

figure 2–6Evolution of eukaryotes. Modern organisms may havederived from a common ancestral prokaryote by a seriesof endosymbiotic associations. The early anaerobiceukaryote derived its nuclear structures (red) from anarchaebacterium and its motile apparatus (not shown)from an anaerobic eubacterium with which it fused. Thisearly eukaryote later acquired endosymbiotic purple bac-teria (orange), which brought their capacity for aerobiccatabolism and became, over time, mitochondria. Whenphotosynthetic cyanobacteria (green) subsequentlybecame endosymbionts of some aerobic eukaryotes,these cells became the photosynthetic precursors ofmodern green algae and plants.

Ancestralprokaryote

Eubacteria

Purplebacteria(aerobic)

Cyanobacteria(photosynthetic)

Ancestraleukaryotes

Moderndescendants

Plants

Synecoccus

Paracoccus

Protists

Animals

Fungi

Thermoplasma

Archaebacteria

Earlyeukaryotes(anaerobic)

Aerobiceukaryotes

Time

Chapter 2 Cells 29

early eukaryotic cells, which were incapable of photosynthesis or aerobicmetabolism, enveloped aerobic bacteria or photosynthetic bacteria to formendosymbiotic associations that became permanent. Some aerobic bacte-ria evolved into the mitochondria of modern eukaryotes, and some photo-synthetic cyanobacteria became plastids, such as the chloroplasts of greenalgae, the likely ancestors of modern plant cells. Prokaryotic and eukaryoticcells are compared in Table 2–1.

Early Eukaryotic Cells Gave Rise to Diverse ProtistsWith the rise of early eukaryotic cells, further evolution led to a tremendousdiversity of unicellular eukaryotic organisms (protists). Some of these(those with chloroplasts) resembled modern photosynthetic protists suchas Euglena and Chlamydomonas; other, nonphotosynthetic protists weremore like Paramecium or Dictyostelium. Unicellular eukaryotes are abun-dant, and the cells of all multicellular organisms—animals, plants, andfungi—are eukaryotic.

Major Structural Features of Eukaryotic CellsTypical eukaryotic cells (Fig. 2–7) are much larger than prokaryotic cells—commonly 5 to 100 mm in diameter, with cell volumes a thousand to a mil-lion times larger than those of bacteria. The distinguishing characteristic ofeukaryotes is the nucleus, which has a complex internal structure sur-rounded by a double membrane. Another striking difference between eu-karyotes and prokaryotes is that eukaryotes contain a number of othermembrane-bounded organelles. The following sections describe the struc-tures and roles of the components of eukaryotic cells in more detail.

table 2–1Comparison of Prokaryotic and Eukaryotic Cells

Characteristic Prokaryotic cell Eukaryotic cell

Size Generally small (1–10 mm) Generally large (5–100 mm)Genome DNA with nonhistone protein; DNA complexed with

genome in nucleoid, not histone and nonhistonesurrounded by membrane proteins in chromosomes;

chromosomes in nucleuswith membranous envelope

Cell division Fission or budding; no mitosis Mitosis including mitoticspindle; centrioles in many species

Membrane-bounded Absent Mitochondria, chloroplasts (inorganelles plants, some algae), endoplasmic

reticulum, Golgi complexes,lysosomes (in animals), etc.

Nutrition Absorption; some photosynthesis Absorption, ingestion;photosynthesis in some species

Energy metabolism No mitochondria; oxidative Oxidative enzymes packaged inenzymes bound to plasma mitochondria; more unifiedmembrane; great variation pattern of oxidativein metabolic pattern metabolism

Cytoskeleton None Complex, with microtubules,intermediate filaments, actinfilaments

Intracellular movement None Cytoplasmic streaming,endocytosis, phagocytosis,mitosis, vesicle transport

Source: Modified from Hickman, C.P., Roberts, L.S., & Hickman, F.M. (1990) Biology ofAnimals, 5th edn, p. 30, Mosby–Yearbook, Inc., St. Louis, MO.


figure 2–7Schematic illustrations of the two major types of eukary-otic cell: a representative animal cell (a) and a represen-tative plant cell (b). Plant cells are usually 10 to 100 mmin diameter—larger than animal cells, which typicallyrange from 5 to 30 mm. Structures labeled in red areunique to either animal or plant cells.

Ribosomes

Peroxisome

Lysosome

Transport vesicle

Golgi complex

Smoothendoplasmic reticulum

Nucleus

Ribosomes Cytoskeleton

Cytoskeleton

Golgicomplex

Nucleolus

Roughendoplasmic

reticulumMitochondrion

Plasmamembrane

Chloroplast

Starch granule

Thylakoids

Cell wall

Cell wall ofadjacent cell

Plasmodesma

Nuclearenvelope

Vacuole

(a)

(b)

The Plasma Membrane Contains Transporters and ReceptorsThe external surface of a cell is in contact with other cells, the extracellu-lar fluid, and the solutes, nutrient molecules, hormones, neurotransmitters,and antigens in that fluid. The plasma membranes of all cells contain manytransporters, proteins that span the membrane and carry nutrients intothe cell and various products out. Cells also have surface membrane pro-teins (signal receptors) with highly specific binding sites for extracellularsignaling molecules (receptor ligands). When an external ligand binds to itsspecific receptor, the receptor protein transduces the signal carried by thatligand into an intracellular message (Fig. 2–8). For example, some surfacereceptors are associated with ion channels that open when the receptor isoccupied, permitting entry of specific ions; others activate or inhibit cellu-lar enzymes on the inner membrane surface. Whatever the mode of signal

Chapter 2 Cells 31

Transporter

Ions, nutrients

Receptorenzyme

Gated ionchannel

Ligands Ions

IonsProductIons, nutrientsSubstrate

(Intracellular signals)

transduction, surface receptors characteristically act as signal amplifiers—a single ligand molecule bound to a single receptor may cause the flux of thousands of ions through an opened channel or the synthesis of thou-sands of molecules of an intracellular messenger molecule by an activatedenzyme.

Some surface receptors recognize ligands of low molecular weight, andothers recognize macromolecules. For example, binding of acetylcholine(Mr 146) to its receptor begins a cascade of cellular events that underlie thetransmission of signals for muscle contraction. Blood proteins (Mr �20,000)that carry lipids (lipoproteins) are recognized by specific cell surface re-ceptors, which mediate lipid entry into the cells. Antigens (proteins,viruses, or bacteria, recognized by the immune system as foreign) bind tospecific receptors and trigger the production of antibodies. During the development of multicellular organisms, neighboring cells influence eachother’s developmental paths, as signal molecules from one cell type reactwith receptors of other cells. Thus the surface membrane of a cell is a com-plex mosaic of different kinds of highly specific “molecular antennae”through which cells receive, amplify, and react to external signals.

Most cells of higher plants have a cell wall outside the plasma mem-brane (Fig. 2–7b), which serves as a rigid, protective shell. The cell wall,composed of cellulose and other carbohydrate polymers, is thick butporous. It allows water and small molecules to pass readily, but swelling ofthe cell due to the accumulation of water is resisted by the rigidity of thewall.

Endocytosis and Exocytosis Carry Traffic across the Plasma MembraneEndocytosis is a mechanism for transporting components of the sur-rounding medium deep into the cytoplasm. In this process (Fig. 2–9), a re-gion of the plasma membrane invaginates, enclosing a small volume of ex-tracellular fluid within a bud that pinches off inside the cell by membranefission. The resulting small vesicle (endosome) can move into the interiorof the cell, delivering its contents to another organelle bounded by a singlemembrane (a lysosome, for example; see p. 33) by fusion of the two mem-branes. The endosome thus serves as an intracellular extension of theplasma membrane, effectively allowing intimate contact between compo-nents of the extracellular medium and regions deep within the cytoplasm,which could not be reached by diffusion alone. Phagocytosis is a specialcase of endocytosis in which the material carried into the cell (within aphagosome) is particulate, such as a cell fragment or even another, smaller

figure 2–8Proteins in the plasma membrane serve as transporters,signal receptors, and ion channels. Transporters carrysubstances into and out of the cell; some transporters useenergy to pump ions and compounds against a concen-tration gradient. Extracellular signals are amplified byreceptors: binding of a single ligand molecule to thesurface receptor causes the formation of many moleculesof an intracellular messenger or the flow of many ionsthrough an opened channel.


figure 2–9The endomembrane system. This system includes thenuclear envelope, endoplasmic reticulum, Golgi complex,and several types of small vesicles. It encloses a compart-ment (lumen) distinct from the cytosol. Contents of thelumen move from one region of the endomembranesystem to another as small transport vesicles bud fromone component and fuse with another. High-magnificationelectron micrographs of a sectioned cell show rough endo-plasmic reticulum studded with ribosomes, smooth endo-plasmic reticulum, and the Golgi complex. (The size of theGolgi complex is exaggerated in the diagram for clarity.)

The endomembrane system is dynamic; newly syn-thesized proteins move into the lumen of the rough endo-

plasmic reticulum and thus to the smooth endoplasmicreticulum, then to the Golgi complex via transport vesi-cles. The cis portion of the Golgi complex faces thenucleus; the trans portion is that nearer the plasma mem-brane. In the Golgi complex, molecular “addresses” areadded to specific proteins to direct them to the cellsurface, lysosomes, or secretory granules. The contents ofsecretory granules are released from the cell by exocy-tosis. Endocytosis and phagocytosis bring extracellularmaterials into the cell. Fusion of endosomes (or phago-somes) with lysosomes, which contain digestive enzymes,results in degradation of the extracellular materials.

0.4 m�

�

�

0.4 m

0.4 m

cell. The inverse of endocytosis is exocytosis (Fig. 2–9), in which a vesi-cle in the cytoplasm moves to the inside surface of the plasma membrane,fuses with it, then releases the vesicular contents outside the membrane.Many proteins destined for secretion into the extracellular space are pack-aged into vesicles called secretory granules then released by exocytosis.

The Endoplasmic Reticulum Organizes the Synthesis of Proteins and LipidsThe small transport vesicles moving to and from the plasma membrane inexocytosis and endocytosis are parts of a dynamic system of intracellularmembranes that includes the endoplasmic reticulum, the Golgi complex,

Chapter 2 Cells 33

the nuclear envelope, and a variety of small vesicles such as lysosomes andperoxisomes (Fig. 2–9). Although generally represented as discrete andstatic elements, these structures are in fact in constant flux, with mem-brane vesicles continually budding off, moving through the cell, and merg-ing with membranous structures elsewhere.

The endoplasmic reticulum (ER) is a highly convoluted, three-dimensional network of membrane-enclosed spaces extending throughoutthe cytoplasm and enclosing a subcellular compartment (the lumen of theER) separate from the cytoplasm. The many flattened branches (cisternae)of this compartment are continuous with each other and with the nuclearenvelope. In cells specialized for the secretion of proteins, such as the pan-creatic cells that secrete the hormone insulin, the ER is particularly promi-nent. The ribosomes that synthesize proteins destined for export attach tothe outer (cytoplasmic) surface of the ER, and the secretory proteins arepassed through the membrane into the lumen as they are synthesized. Di-gestive enzymes that will be sequestered within lysosomes or proteins des-tined for insertion into the nuclear or plasma membranes are also synthe-sized on ribosomes attached to the ER. By contrast, proteins that willremain and function within the cytosol are synthesized on cytoplasmic ri-bosomes unassociated with the ER.

The attachment of thousands of ribosomes (usually in regions of largecisternae) gives the rough endoplasmic reticulum its granular appear-ance (Fig. 2–9) and thus its name. In other regions of the cell, the ER is freeof ribosomes. This smooth endoplasmic reticulum, which is physicallycontinuous with the rough ER, is the site of lipid biosynthesis and a varietyof other important processes, including the metabolism of certain drugs andtoxic compounds. Smooth ER is generally tubular, in contrast to the long,flattened cisternae typical of rough ER. In some tissues (skeletal muscle, forexample), the ER is specialized for the storage and rapid release of calciumions. Release of Ca2� is the trigger for many cellular events, including mus-cle contraction.

The Golgi Complex Processes and Sorts ProteinsNearly all eukaryotic cells have Golgi complexes, systems of membranoussacs, or cisternae, arranged as flattened stacks (Fig. 2–9). Named after itsdiscoverer, Camillo Golgi, the Golgi complex is asymmetric, structurally andfunctionally. The cis side faces the rough endoplasmic reticulum (and thenucleus), and the trans side faces the plasma membrane; between these arethe medial elements. Proteins, during their synthesis on ribosomes boundto the rough ER, are inserted into the interior (lumen) of the ER cisternae.Small membrane vesicles containing the newly synthesized proteins budfrom the ER and move to the Golgi complex, fusing with the cis side. As theproteins pass through the Golgi complex to the trans side, enzymes in thecomplex modify the protein molecules by adding sulfate, carbohydrate, orlipid moieties to side chains of certain amino acids. One of the functions ofthis modification of a newly synthesized protein is to “address” it to itsproper destination as it leaves the Golgi complex in a transport vesicle bud-ding from the trans side. Certain proteins are enclosed in secretory gran-ules, eventually to be released from the cell by exocytosis. Others are tar-geted for intracellular organelles such as lysosomes or for incorporationinto the plasma membrane during cell growth.

Lysosomes Are the Sites of Degradative ReactionsLysosomes, found only in animal cells, are spherical vesicles bounded by asingle membrane bilayer (Fig. 2–9). They are usually about 1 mm in diame-ter. Lysosomes contain enzymes capable of digesting proteins, polysaccha-rides, nucleic acids, and lipids. They function as cellular recycling centers,


breaking down complex molecules brought into the cell by endocytosis,fragments of foreign cells brought in by phagocytosis, or worn-out or-ganelles from the cell’s own cytoplasm. These materials selectively enterthe lysosome by fusion of the lysosomal membrane with endosomes, phago-somes, or defective organelles, and are then degraded to their simple com-ponents (amino acids, monosaccharides, fatty acids, etc.), which are re-leased into the cytosol to be recycled into new cellular components orfurther catabolized.

The degradative enzymes within a lysosome would be free to act on allcellular components were they not confined by the lysosomal membrane. Asecond line of defense against unwanted destruction of cytosolic macro-molecules by lysosomal enzymes is the difference in pH between the lyso-some and the cytosol, maintained by the action of an ATP-fueled protonpump in the lysosomal membrane. The lysosomal compartment is moreacidic (pH � 5) than the cytosol (pH � 7), and lysosomal enzymes aremuch less active at the higher pH of the cytosol.

Vacuoles of Plant Cells Play Several Important RolesPlant cells do not have lysosomes, but their vacuoles carry out similardegradative reactions as well as other functions not found in animal cells.Growing plant cells contain several small vacuoles, vesicles bounded by asingle membrane bilayer. As the cell matures, the vacuoles fuse and becomeone large central vacuole (Fig. 2–10; see also Fig. 2–7b). The vacuole mayrepresent as much as 90% of the total cell volume in a mature cell, pressingthe cytoplasm into a thin layer between the vacuole and the plasma mem-brane. The membrane surrounding the vacuole, called the tonoplast, reg-ulates the entry of ions, metabolites, and cellular structures destined fordegradation, and the liquid within the vacuole contains digestive enzymesthat degrade and recycle macromolecular components. As in the lysosome,the pH within the vacuole is generally lower than the pH of the surroundingcytosol. In some plant cells, the vacuole contains high concentrations of pig-ments (anthocyanins) that give flowers and fruits their deep purple and redcolors. In addition to its role in storage and degradation of cellular compo-nents, the vacuole also provides physical support to the plant cell. Becausethe concentration of solutes (salts, ions, degradation products) is greater inthe vacuole than in the cytosol, water passes osmotically into the vacuole,establishing, at equilibrium, an outward turgor pressure on the cytoplasmand the cell wall that stiffens the plant tissue (Fig. 2–10).

Peroxisomes Destroy Hydrogen Peroxide, and Glyoxysomes Convert Fats to CarbohydratesSome of the oxidative reactions in the breakdown of amino acids and fatsproduce free radicals and hydrogen peroxide (H2O2), very reactive chemi-cal species that could damage cellular machinery. To protect the cell fromthese destructive byproducts, such reactions are segregated within smallmembrane-bounded vesicles called peroxisomes. The hydrogen peroxideis degraded by catalase, an enzyme present at high concentration in perox-isomes; it catalyzes the reaction

2H2O2 88n 2H2O � O2.

Glyoxysomes are specialized peroxisomes found in certain plant cells.They contain high concentrations of the enzymes of the glyoxylate cycle,

a metabolic pathway unique to plants that converts stored fats to carbohy-drates during seed germination. Lysosomes, peroxisomes, and glyoxysomesare sometimes referred to collectively as microbodies.

figure 2–10The vacuole of a plant cell contains high concentrationsof Ca2� and a variety of stored compounds and wasteproducts. Water enters the vacuole, increasing the vac-uolar volume and pressing the cytoplasm against theplasma membrane, creating turgor pressure. The rigidityof the cell wall prevents expansion and rupture of theplasma membrane.

Chapter 2 Cells 35

The Nucleus Contains the GenomeThe eukaryotic nucleus is quite complex in structure and biological activitycompared with the relatively simple nucleoid of prokaryotes. The nucleuscontains nearly all of the cell’s DNA, which can be thousands of times morethan is present in a bacterial cell; a small amount of DNA is also present inmitochondria and chloroplasts. The nucleus is surrounded by a nuclear en-

velope, composed of two membrane bilayers separated by a narrow spaceand continuous with the rough endoplasmic reticulum (Fig. 2–11; see alsoFig. 2–9). At intervals the inner and outer nuclear membranes are pinchedtogether around openings (nuclear pores), which have a diameter ofabout 90 nm. Associated with the pores are protein structures called nu-clear pore complexes, specific transporters that allow certain macromole-cules to pass between the cytoplasm and the aqueous phase of the nucleus(the nucleoplasm). Traffic into the nucleus through the nuclear pore com-plexes includes enzymes and other proteins synthesized in the cytoplasmand required in the nucleoplasm for DNA replication and repair, transcrip-tion, and RNA processing. Passing out through the nuclear pores are mes-senger RNA precursors, with associated proteins, which will be translatedon ribosomes in the cytoplasm.

The nucleus of an interphase (nondividing) cell is filled with a diffusematerial called chromatin, so called because early microscopists foundthat it stained brightly with certain dyes. Chromatin consists of DNA andproteins bound tightly together and is the substance of the chromosomes,which do not condense and become individually visible until the cell isready to divide. The nucleolus is a specific region of the nucleus in whichthe DNA contains many copies of the genes encoding ribosomal RNA. Toproduce the large number of ribosomes needed by the cell, these genes arecontinually transcribed into RNA. The nucleolus appears dense in electronmicrographs (Fig. 2–11b) because of its high RNA content. Ribosomal RNAproduced in the nucleolus enters the cytoplasm through the nuclear pores.

Nuclear division (mitosis) occurs before cell division (cytokinesis).

The double-helical DNA of the chromatin is replicated, then in the first

figure 2–11The nucleus and nuclear envelope.

Ribosomes

Roughendoplasmicreticulum

Paired membranes of nuclear envelope

Chromatin–tight complex ofDNA and histoneproteins

Nucleolus–transcription ofribosomal RNA

Nuclear pores–specific transportof RNA and proteins

(a) Scanning electron micrograph of the surface of thenuclear envelope, showing numerous nuclear pores.

(b) Electron micrograph of the nucleus of the algaChlamydomonas. The dark body in the center is thenucleolus, and the granular material that fills the rest ofthe nucleus is chromatin. Two nuclear pores piercing thepaired membranes of the nuclear envelope are shown byarrows.

0.2 m�

0.5 m�


figure 2–12Chromosomes are visible microscopically during mitosis.Shown here is an electron micrograph of one of the 46human chromosomes in a diploid (somatic) cell. Everymitotic chromosome is composed of two chromatids,each consisting of tightly folded chromatin fibers. Eachchromatin fiber is in turn formed by the packaging of aDNA molecule wrapped about histone proteins to form aseries of nucleosomes. (Adapted from Becker, W.M. &Deamer, D.W. (1991) The World of the Cell, 2nd edn, Fig. 13–20, The Benjamin/Cummings PublishingCompany, Menlo Park, CA.)

Chromatid(~600 nmin diameter)

Mitoticchromosome

Chromatin fiber(30 nm indiameter)

Nucleosomes(10 nm indiameter)

Histones

DNA

phase of mitosis the chromatin fibers condense into discrete bodies, thechromosomes, each consisting of two identical chromatids (Fig. 2–12).The two sister chromatids separate, one moving to each pole of the cell,where they become part of the newly formed nucleus of each daughter cell.

Cells of each species have a characteristic number of chromosomes ofspecific sizes and shapes. For example, the protist Tetrahymena pyri-

formis has 5 pairs; cabbage has 9, humans have 23, and the fern Ophioglos-

sum reticulatum has about 630! The cells that make up most of the bodyof a multicellular organism, the somatic cells, have two copies of each chro-mosome and are said to be diploid (2n). Gametes (egg and sperm, for ex-ample), produced by meiosis (Chapter 25) and having only one copy ofeach chromosome, are haploid (n). During sexual reproduction, two hap-loid gametes combine to regenerate a diploid cell in which each chromo-some pair consists of a maternal and a paternal chromosome.

The DNA of chromatin and chromosomes is bound tightly to a family ofpositively charged proteins, the histones, which associate strongly withthe many negatively charged phosphate groups in DNA. About half themass of chromatin is DNA and half is histones. When DNA replicates priorto cell division, large quantities of histones are also synthesized to maintainthis 1�1 mass ratio. The histones and DNA associate in complexes callednucleosomes, in which the DNA strand winds around a core of histonemolecules (Fig. 2–12). The DNA of a single human chromosome formsabout a million nucleosomes; nucleosomes associate to form very regularand compact supramolecular complexes. The resulting chromatin fibers,about 30 nm in diameter, condense further by forming a series of looped re-gions, which cluster with adjacent looped regions to form the chromosomesvisible during cell division. This tight packing of DNA into nucleosomesachieves a remarkable condensation of the DNA molecules. The DNA in thechromosomes of a single diploid human cell would have a combined lengthof about 2 m if fully extended as a DNA double helix, but the combinedlength of all 46 chromosomes is only about 200 mm.

Mitochondria Are the Power Plants of Aerobic Eukaryotic CellsMitochondria (singular, mitochondrion) are very conspicuous in the cy-toplasm of most eukaryotic cells when viewed by electron microscopy (Fig.2–13). These membrane-bounded organelles vary in size, but typically havea diameter of about 1 mm, similar to that of bacterial cells. Mitochondria alsovary widely in shape, number, and location, depending on the cell type ortissue function. Most plant and animal cells contain several hundred to athousand mitochondria. Generally, cells in more metabolically active tissuesdevote a larger proportion of their volume to mitochondria.

Each mitochondrion has two membranes. The outer membrane is un-wrinkled and completely surrounds the organelle. The inner membrane has

Chapter 2 Cells 37

DNACrista

Matrix

Ribosomes

Inner membrane

Outer membrane

0.5 �m

infoldings called cristae, which give it a large surface area. Enclosed by theinner membrane is the matrix, a very concentrated aqueous solution of en-zymes and chemical intermediates involved in energy-yielding metabolism.Mitochondrial enzymes catalyze the oxidation of organic nutrients by mole-cular oxygen (O2); some of these enzymes are in the matrix and some areembedded in the inner membrane. The chemical energy released in mito-chondrial oxidations is used to generate ATP, the major energy-carryingmolecule of cells. In aerobic cells, mitochondria are the principal producersof ATP, which diffuses to all parts of the cell and provides the energy for cel-lular work.

Unlike other membranous structures such as lysosomes, Golgi com-plexes, and the nuclear envelope, mitochondria are produced only by divi-sion of previously existing mitochondria; each mitochondrion contains itsown DNA, RNA, and ribosomes. Mitochondrial DNA codes for certain pro-teins specific to the mitochondrial inner membrane. This and other evi-dence supports the theory (outlined below) that mitochondria are the de-scendants of aerobic bacteria that lived endosymbiotically with earlyeukaryotic cells.

Chloroplasts Convert Solar Energy into Chemical EnergyThe cytoplasm of plants contains plastids, specialized organelles sur-rounded by envelopes consisting of two membranes. Most conspicuous ofthe plastids and characteristically present in the photosynthetic cells ofplants and algae are the chloroplasts (Fig. 2–14). Like mitochondria, thechloroplasts may be considered power plants, with the important differencethat chloroplasts use solar energy, whereas mitochondria use the chemicalenergy of oxidizable compounds. Pigment molecules in chloroplasts absorbthe energy of light and use it to make ATP and, ultimately, to reduce carbondioxide to form carbohydrates such as starch and sucrose. Photosynthesisin eukaryotes and in cyanobacteria produces O2 as a byproduct of the light-capturing reactions. Photosynthetic plant cells contain both chloroplastsand mitochondria. Chloroplasts produce ATP only in the light; mitochondriafunction independently of light, oxidizing carbohydrates generated by pho-tosynthesis during daylight hours.

Chloroplasts are generally larger (diameter 5 mm) than mitochondriaand have various shapes. Because chloroplasts contain a high concentrationof the pigment chlorophyll, photosynthetic cells are usually green, buttheir color depends on the relative amounts of other pigments present.Chlorophyll and other pigment molecules, which together can absorb light

1 �m

Outer membrane

Inner membrane

DNA Ribosomes Thylakoids

figure 2–13Structure of a mitochondrion. The electron micrographshows the extensive infolding of the inner membrane; thefolds are called cristae. (Note the rough endoplasmicreticulum surrounding the mitochondrion.)

figure 2–14Structure of a chloroplast. The thylakoids are flattenedmembranous sacs that contain chlorophyll, the light-harvesting pigment.


energy over much of the visible spectrum, are localized in the internal mem-branes of the chloroplast; these membranes form stacks of closed cisternaeknown as thylakoids (Fig. 2–14). Like mitochondria, chloroplasts containDNA, RNA, and ribosomes.

Mitochondria and Chloroplasts Probably Evolved from Endosymbiotic BacteriaSeveral independent lines of evidence suggest that the mitochondria andchloroplasts of modern eukaryotes were derived during evolution from aer-obic bacteria and cyanobacteria that took up endosymbiotic residence inearly eukaryotic cells (Fig. 2–15; see also Fig. 2–6). Mitochondria are al-ways derived from preexisting mitochondria, and chloroplasts from chloro-plasts, by simple fission, just as bacteria multiply by fission. Mitochondriaand chloroplasts are in fact semiautonomous; they contain DNA, ribosomes,and the enzymatic machinery to synthesize proteins encoded in their DNA.Sequences in mitochondrial DNA are strikingly similar to sequences in cer-tain aerobic bacteria, and chloroplast DNA shows strong sequence similar-ity to the DNA of certain cyanobacteria. The ribosomes of mitochondria andchloroplasts are more similar in size, overall structure, and RNA sequencesto those of bacteria than to those in the cytoplasm of the eukaryotic cell.The enzymes that catalyze protein synthesis in these organelles also moreclosely resemble those of bacteria.

Despite their complement of DNA and protein-synthesizing machinery,mitochondria and chloroplasts are only semiautonomous. If these or-

figure 2–15A plausible theory for the evolutionary origin of mito-chondria and chloroplasts. It is based on a number ofstriking biochemical and genetic similarities betweencertain aerobic bacteria and mitochondria, and betweencertain cyanobacteria and chloroplasts. During the evolu-tion of eukaryotic cells, the bacteria became symbioticwithin the ancestral anaerobe. Ultimately the cytoplasmicbacteria became the mitochondria and chloroplasts ofmodern eukaryotes.

Anaerobicmetabolismis inefficientbecause fuel is notcompletely oxidized.

Ancestral anaerobiceukaryote

Nucleus

Aerobic metabolism isefficient because fuelis oxidized to CO2.

Aerobic bacterium

Bacterialgenome

Light energy is usedto synthesizebiomolecules from CO2.

Photosyntheticcyanobacterium

Cyanobacterialgenome

Aerobic eukaryote

Bacterium isengulfed by ancestraleukaryote, andmultiplies within it.

Symbiotic systemcan now carry outaerobic catabolism.Some bacterial genesmove to the nucleus,and the bacterialendosymbionts becomemitochondria.

Photosyntheticeukaryote

Nonphotosyntheticeukaryote

Mitochondrion

Chloroplast

In time, some cyanobacterial genes move to the nucleus, and endosymbionts become plastids (chloroplasts).

Engulfedcyanobacteriumbecomes an endosymbiontand multiplies; new cell can make ATP using energy from sunlight.

Chapter 2 Cells 39

ganelles are indeed the descendants of early bacterial endosymbionts, someof the genes present in the original free-living bacteria must have beentransferred into the nuclear DNA of the host eukaryote over the course ofevolution. Neither mitochondria nor chloroplasts contain all the genes nec-essary to specify all of their proteins. Most mitochondrial and chloroplastproteins are encoded in nuclear genes, translated on cytoplasmic ribo-somes, and subsequently imported into the organelles.

The Cytoskeleton Stabilizes Cell Shape, Organizes the Cytoplasm, and Produces MotionSeveral types of protein filaments visible with the electron microscopecrisscross the eukaryotic cell, forming an interlocking three-dimensionalmeshwork, the cytoskeleton, that extends throughout the cytoplasm.There are three general types of cytoplasmic filaments: actin filaments, mi-crotubules, and intermediate filaments (Fig. 2–16). They differ in width(from about 6 to 22 nm), composition, and specific function, but all appar-ently provide structure and organization to the cytoplasm and shape to thecell. Actin filaments and microtubules also help to produce the motion of or-ganelles or of the whole cell.

Each of the cytoskeletal components is composed of simple proteinsubunits that polymerize to form filaments of uniform thickness. These fila-ments are not permanent structures; they undergo constant disassemblyinto their monomeric subunits and reassembly into filaments. Their loca-tions in cells are not rigidly fixed, but may change dramatically with mito-sis, cytokinesis, amoeboid motion, or changes in cell shape. All types of fil-aments associate with other proteins that cross-link filaments to themselvesor to other filaments, influence assembly or disassembly, or move cytoplas-mic organelles along the filaments.

Actin stress fibers(a)

Microtubules(b)

Intermediate filaments(c)

figure 2–16The three types of cytoskeletal filaments. The upperpanels show epithelial cells photographed after treatmentwith antibodies that bind to and specifically stain (a) actinfilaments bundled together to form “stress fibers,” (b)microtubules radiating from the cell center, and (c) inter-mediate filaments extending throughout the cytoplasm.For these experiments, antibodies that specifically recog-nize actin, tubulin, or intermediate filament proteins arecovalently attached to a fluorescent compound. When thecell is viewed with a fluorescence microscope, only thestained structures are visible. The lower panels showeach type of filament as visualized by transmission (a, b)or scanning (c) electron microscopy.


figure 2–17Individual subunits of actin polymerize to form actin fila-ments. The protein filamin holds two filaments togetherwhere they cross at right angles. The protein fodrin formscross-links between filaments to create side-by-sideaggregates or bundles.

ATP

Filamin Fodrin

Actin (thin)filaments

Actinsubunits

6–7 nm

+ +

The protein actin, found in virtually all eukaryotic cells, assembles inthe presence of ATP into long, helical, noncovalent polymers, 6 to 7 nm indiameter, called actin filaments or microfilaments (Fig. 2–17). Cellscontain a variety of proteins that bind to actin monomers or filaments andinfluence their localization or state of aggregation. Filamin and fodrin cross-link actin filaments to each other, stabilizing the meshwork and greatly in-creasing the viscosity of the surrounding medium. Large numbers of actinfilaments bound to specific plasma membrane proteins lie just beneath andmore or less parallel to the plasma membrane, conferring shape and rigid-ity on the cell surface (Fig. 2–16a).

Actin filaments also bind to a family of proteins called myosins, molec-ular motors that convert the chemical energy of ATP into mechanical work,moving themselves along the actin filament. The simplest members of thisfamily, such as myosin I, have a globular head and a short tail. The headbinds to and moves along an actin filament, driven by the breakdown of ATP(Fig. 2–18). The tail region binds to the membrane of a cytoplasmic or-ganelle, dragging the organelle behind as the myosin head moves along theactin filament. This motion is readily seen in living cells such as the giant cells of the green alga Nitella, in which organelles and vesicles moveuniformly around the cell in a process called cytoplasmic streaming (Fig. 2–18).This motion has the effect of mixing the cytoplasmic contents of the enor-mous algal cell much more efficiently than would occur by diffusion alone.

A larger form of myosin occurs in the contractile systems of a wide va-riety of organisms, from slime molds to humans. This myosin also has a globular head that binds to and moves along actin filaments in an ATP-driven reaction, but it has a longer tail, which permits the myosin moleculesto associate side by side to form thick filaments (see Fig. 7–30). Actin-myosin complexes form the contractile ring that squeezes the cytoplasm intwo during cytokinesis in all eukaryotes. The muscle cells of multicellularanimals are filled with highly organized arrays of actin (thin) filaments andmyosin (thick) filaments, which produce a coordinated contractile force byATP-driven sliding of actin filaments past stationary myosin filaments.

Like actin filaments, microtubules form spontaneously from theirmonomeric subunits, but the polymeric structure of microtubules is slightlymore complex. Dimers of a- and b-tubulin, two similar proteins, form thehollow microtubule, which is about 22 nm in diameter. In cells, most micro-tubules undergo continual polymerization and depolymerization by additionof tubulin subunits primarily at one end and dissociation at the other. Micro-tubules are present throughout the cytoplasm, but are concentrated in spe-cific regions at certain times. For example, after sister chromatids separateand move to opposite poles of a cell during mitosis, a highly organized arrayof microtubules (the mitotic spindle) provides the framework and probablythe motive force for the separation of these daughter chromosomes.

Microtubules, like actin filaments, associate with a variety of proteinsthat move along them, form cross-bridges, or influence their state of poly-merization. Kinesin and cytoplasmic dynein, proteins found in the cyto-plasm of many cells, bind to and move along microtubules using the energy

Chapter 2 Cells 41

figure 2–18Organelle transport. Myosin molecules move along actinfilaments using energy from ATP. Cytoplasmic streamingis produced in the giant cells of the green alga Nitella asmyosin pulls organelles around a track of actin filaments.Endoplasmic reticulum, mitochondria, nucleus, and othermembrane-bounded organelles and vesicles move uni-formly around the cell at 50 to 75 mm/s. The chloroplastsare located in the layer of stationary cytoplasm that liesbetween the actin filaments and the plasma membrane.

Actin filament

Myosin

Cytoplasmicorganelle or

vesicleATP

ADP �PO3

4�

Actinfilaments

Streamingcytoplasm

withorganelles

and vesicles

Vacuole

Chloroplastsin stationary

cytoplasm

of ATP to drive their motion (Fig. 2–19). Each protein is capable of associ-ating with specific organelles and pulling them along the microtubule overlong distances at rates of about 1 mm/s. The beating motion of cilia and eu-karyotic flagella also involves dynein and microtubules.

The contraction of skeletal muscle, the propelling action of cilia and fla-gella, and the intracellular transport of organelles all rely on the same funda-mental mechanism: the splitting of ATP by proteins such as kinesin, myosin,and dynein drives sliding motion along microfilaments or microtubules.

Intermediate filaments are a family of structures with dimensions(diameter 8 to 10 nm) intermediate between actin filaments and micro-tubules. Several different types of monomeric protein subunits reversiblyform intermediate filaments. The cytoplasmic distribution of these struc-tures is subject to regulated changes.

One function of intermediate filaments is to provide internal mechani-cal support for the cell and to position its organelles. For example, vimentinis the monomeric subunit of the intermediate filaments found in the en-dothelial cells that line blood vessels and in adipocytes (fat cells). Vimentinfibers appear to anchor the nucleus and fat droplets in specific cellular lo-cations. The intermediate filaments composed of keratins, a family of struc-tural proteins, are particularly prominent in certain epidermal cells of vertebrates, forming covalently cross-linked meshworks that persist evenafter the cell dies. Hair, fingernails, and feathers are among the structurescomposed primarily of keratins.

ADP + PO4

Microtubule

ATP ATP

ADP + PO4

Kinesin

Dynein

Cytoplasmic organelleor vesicle

3– 3–

22 nm

a, b-Tubulin dimera b

figure 2–19Kinesin and cytoplasmic dynein are ATP-driven molecularmotors that can attach to cytoplasmic organelles or vesi-cles and drag them along microtubular “rails” at a rate ofabout 1 mm/s.


The Cytoplasm Is Crowded, Highly Ordered, and DynamicThe picture that emerges from this brief survey is of a eukaryotic cell witha cytoplasm crisscrossed by a meshwork of structural fibers, throughoutwhich extends a complex system of membrane-bounded compartments(Fig. 2–7). Both the filaments and the organelles are dynamic: the filamentsdisassemble and then reassemble elsewhere; membranous vesicles budfrom one organelle and fuse with another. Organelles move through the cy-toplasm along protein filaments, drawn by kinesin, cytoplasmic dynein,myosin, and perhaps other similar proteins. The endomembrane systemsegregates specific metabolic processes and provides surfaces on whichcertain enzyme-catalyzed reactions occur. Exocytosis and endocytosis pro-vide paths between the cell interior and the surrounding medium, allowingfor the secretion of proteins and other components produced within the celland the uptake of extracellular substances.

Although complex, this organization of the cytoplasm is far from ran-dom. The motion and positioning of organelles and cytoskeletal elementsare under tight regulation, and at certain stages in a eukaryotic cell’s life,dramatic, finely orchestrated reorganizations occur, such as the events ofmitosis. The interactions between the cytoskeleton and organelles are non-covalent, reversible, and subject to regulation in response to various intra-cellular and extracellular signals.

Study of Cellular ComponentsOrganelles Can Be Isolated by CentrifugationA major advance in the biochemical study of cells was the development ofmethods for separating organelles from the cytosol and from each other. Ina typical cellular fractionation, cells or tissues are disrupted by gentle ho-mogenization in a medium containing sucrose (about 0.2 M). This treatmentruptures the plasma membrane but leaves most of the organelles intact.(The sucrose creates a medium with an osmotic pressure similar to thatwithin organelles; this prevents diffusion of water into the organelles, whichwould cause them to swell, burst, and spill their contents.)

Organelles such as nuclei, mitochondria, and lysosomes differ in sizeand therefore sediment at different rates during centrifugation. They alsodiffer in specific gravity, and they “float” at different levels in a density gra-dient (Fig. 2–20). Differential centrifugation results in a rough fractionationof the cytoplasmic contents, which may be further purified by isopycnic(“same density”) centrifugation. In this procedure, organelles of differentbuoyant densities (the result of different ratios of lipid and protein in eachtype of organelle) are separated on a density gradient. By carefully remov-ing material from each region of the gradient and observing it with a micro-scope, the biochemist can establish the sedimentation position of each or-ganelle and obtain purified organelles for further study. In this way it was established, for example, that lysosomes contain degradative enzymes,mitochondria contain oxidative enzymes, and chloroplasts contain photo-synthetic pigments. The isolation of an organelle enriched in a certain en-zyme is often the first step in the purification of that enzyme.

In Vitro Studies May Overlook Important Interactions among MoleculesOne of the most effective approaches to understanding a biological processis to study purified individual molecules such as enzymes, nucleic acids, orstructural proteins. The purified components are amenable to detailedcharacterization in vitro; their physical properties and catalytic activitiescan be studied without “interference” from other molecules present in the

Chapter 2 Cells 43

❚

��

�

� ��

�

�

�

�

��

�

� �

�

�

�

�

�

❚

❚

❚❚

❚

❚

❚

❚

❚

❚

❚❚

❚

�

Low-speed centrifugation(1,000 g, 10 min)

Supernatant subjected tomedium-speed centrifugation(20,000 g, 20 min)

Supernatant subjected to high-speed centrifugation(80,000 g, 1 h)

Supernatant subjected tovery high-speed centrifugation(150,000 g, 3 h)

Differentialcentrifugation

Tissuehomogenization

Tissuehomogenate

Pelletcontains

mitochondria,lysosomes,

peroxisomes

Pelletcontains

microsomes(fragments of ER),

small vesicles

Pellet containsribosomes, largemacromolecules

Pelletcontains

whole cells,nuclei,

cytoskeletons,plasma

membranes

Centrifugation

Fractionation

Isopycnic(sucrose-density)centrifugation

Sample

Less densecomponent

More dense component

Sucrosegradient

Supernatantcontainssolubleproteins

8 7 6 5 34 2 1

❚❚

❚

❚

❚❚

❚

❚

❚

❚

❚

❚

❚

❚

❚

❚

�

❚

❚

❚

(a) (b)

��

��

��

�

��

��

��

�

�

❚

❚❚

❚ ❚

❚

❚

❚

❚

❚

❚

��

��

��

❚

❚❚ ❚ ❚❚

❚❚

❚

❚❚ ❚

❚❚ ❚ ❚❚

❚❚

❚

❚❚

figure 2–20Subcellular fractionation of tissue. A tissue such asliver is mechanically homogenized to break cells and dis-perse their contents in an aqueous buffer. The large andsmall particles in this suspension can be separated bycentrifugation at different speeds (a), or particles of dif-ferent density can be separated by isopycnic centrifuga-tion (b). In isopycnic centrifugation, a centrifuge tube isfilled with a solution, the density of which increases fromtop to bottom; a solute such as sucrose is dissolved at dif-ferent concentrations to produce the density gradient.When a mixture of organelles is layered on top of thedensity gradient and the tube is centrifuged at highspeed, individual organelles sediment until their buoyantdensity exactly matches that in the gradient. Each layercan be collected separately.

intact cell. Although this approach has been remarkably revealing, we mustkeep in mind that the inside of a cell is quite different from the inside of a test tube. The “interfering” components eliminated by purification may be critical to the biological function or regulation of the molecule purified.In vitro studies of pure enzymes are commonly done at very low enzymeconcentrations in thoroughly stirred aqueous solutions. In the cell, an en-zyme is dissolved or suspended in a gel-like cytosol with thousands of otherproteins, some of which bind to that enzyme and influence its activity. Someenzymes in cells are parts of multienzyme complexes in which reactants arechanneled from one enzyme to another without ever entering the bulk sol-vent. Diffusion is hindered in the gel-like cytosol, and the cytosolic compo-sition varies in different regions of the cell. In short, a given molecule mayfunction somewhat differently within the cell than it does in vitro. A centralchallenge of biochemistry is to understand the influences of cellular orga-nization and macromolecular associations on the function of individual enzymes—to understand function in vivo as well as in vitro.


Evolution of Multicellular Organisms and Cellular DifferentiationAll modern unicellular eukaryotes—the protists—contain the organellesand mechanisms that we have described, indicating that these organellesand mechanisms must have evolved relatively early. The protists are extra-ordinarily versatile. The ciliated protist Paramecium, for example, movesrapidly through its aqueous surroundings by beating its cilia; senses me-chanical, chemical, and thermal stimuli from its environment, and respondsby changing its path; finds, engulfs, and digests a variety of food organisms,and excretes the indigestible fragments; eliminates excess water that leaksin through its membrane; and finds and mates with sexual partners.Nonetheless, being unicellular has its limitations. Paramecia probably liveout their lives in a very small region of the pond in which they began life,because their motility is limited by the small thrust of their microscopiccilia, and their ability to detect a better environment at a distance is limitedby the short range of their sensory apparatus.

At some later stage of evolution, unicellular organisms found it advan-tageous to cluster together, thereby acquiring greater motility, efficiency, orreproductive success than their free-living single-celled competitors. Fur-ther evolution of such clustered organisms led to permanent associationsamong individual cells and eventually to specialization within the colony—to cellular differentiation.

The advantages of cellular specialization led to the evolution of evermore complex and highly differentiated organisms, in which some cells carried out the sensory functions, others the digestive, photosynthetic, orreproductive functions. Many modern multicellular organisms contain hundreds of different cell types, each specialized for some function thatsupports the entire organism. Fundamental mechanisms that evolved

0.5 �m

(a) (b)

45

figure 2–21A gallery of structurally and functionally differentiatedcells. (a) Secretory cell of the pancreas. Its extensiveendoplasmic reticulum is the site of synthesis of thesecreted protein(s). (b) Portion of a skeletal muscle cell(artificial color). The highly organized actin and myosin fil-aments slide relative to each other in the ATP-dependentprocess that produces macroscopic muscle contraction.(c) Collenchyma cells of a plant stem. These cells, lackinga rigid cell wall, provide flexible support for the growingstem. (d) Human sperm cells (artificial color). The longflagella propel the sperm through the female reproductivetract toward the egg. (e) Mature human erythrocytes (arti-ficial color). These cells have no nucleus or endomem-brane system; each cell is filled with the soluble oxygen-binding protein hemoglobin and is flexible enough to fitthrough capillaries of small diameter. (f) Human embryoat the two-celled stage. The egg cell from which it wasderived was packed with stored fuel and messenger RNA to support the rapid protein synthesis that followsfertilization.

(c)0.1 �m

(d)2.5 �m

(e)7.5 �m

(f)0.75 �m

early have been further refined and embellished through evolution. Thesimple mechanism responsible for the motion of myosin along actin fila-ments in slime molds has been conserved and elaborated in vertebrate muscle cells. The same basic structure and mechanism that underlie thebeating motion of cilia in Paramecium and flagella in Chlamydomonas areemployed by the highly differentiated vertebrate sperm cell. Figure 2–21 illustrates some of the cellular specializations encountered in multicellularorganisms.


figure 2–22Cellular connections. Animal cells can be joined by threetypes of junctions. (a) Tight junctions produce a water-tight seal between adjacent epithelial cells. (b) Desmo-somes weld adjacent epithelial cells together and arereinforced by various cytoskeletal elements. (c) Gap junc-tions allow ions and electric currents to flow betweenadjacent cells. (d) In plants, plasmodesmata connectadjacent cells, providing a path through the cell wall forthe passage of small metabolites and proteins.

(a) Tight junction

(b) Desmosome

(c) Gap junction

(d) Plasmodesmata

Cell 1 Cell 2

Plasmamembrane

Cytoplasm

Cytoskeletalfilaments

Glycoproteinfilaments

Extracellularspace

Cell wall

Endoplasmicreticulum

Cytosol

Plasma membranesof two adjacent cells

The individual cells of a multicellular organism remain delimited bytheir plasma membranes, but they have developed specialized surfacestructures for attachment to and communication with each other (Fig. 2–22).Each type of intercellular junction is reinforced by membrane proteins orcytoskeletal filaments. Animals have three types of junctions that serve dif-ferent purposes. At tight junctions, the plasma membranes of adjacentepithelial cells are closely apposed, with no extracellular fluid separatingthem. Tight junctions form a belt around the cell, providing a barrier be-tween the tissue and the outside environment. Desmosomes are fibrousplaques that weld epithelial cells together; the small extracellular space be-tween the cells is filled with fibrous and adhesive proteins. Desmosomesmechanically strengthen the physical connections between cells, but do notprevent the passage of materials through the extracellular space betweenthe cells they connect. Gap junctions provide small, reinforced openingsbetween adjacent cells, through which electric currents, ions, and smallmolecules can pass. They serve as channels of communication between adjacent cells. Higher plants have plasmodesmata (singular, plasmo-

desma), channels functionally similar to gap junctions but structurallyquite different, in part because of the presence of the cell wall in plants.Plasmodesmata provide a path through the cell wall and plasma membranefor the movement of metabolites—even some small proteins—between ad-jacent cells.

Viruses: Parasites of CellsViruses are supramolecular complexes that can replicate themselves in ap-propriate host cells. They consist of a nucleic acid (DNA or RNA) moleculesurrounded by a protective shell, or capsid, made up of protein moleculesand, in some cases, a membranous envelope. Viruses exist in two states.Outside the host cells that formed them, viruses are simply nonliving parti-cles called virions, which can be crystallized. Once a virus or its nucleicacid component gains entry into a specific host cell, it becomes an intracel-lular parasite. The viral nucleic acid carries the genetic message specifyingthe structure of the intact virion. It diverts the host cell’s enzymes and ri-bosomes from their normal cellular roles to the manufacture of many newdaughter viral particles. As a result, hundreds of progeny viruses may arisefrom the single virion that infected the host cell. In some host-virus sys-tems, the progeny virions escape through the host cell’s plasma membrane.Other viruses cause cell lysis (membrane breakdown and host cell death)as they are released. Much of the pathology associated with viral diseasesresults from this lysis of the host cell.

A different type of response results from some viral infections, in whichviral DNA becomes integrated into a host chromosome and is replicatedwith the host’s own genes. Integrated viral genes may have little or no effecton the host’s survival, but, in rare cases, they cause profound changes in thehost cell’s appearance and activity.

Chapter 2 Cells 47

Many hundreds of different viruses are known (Fig. 2–23), each moreor less specific for a host cell, which may be an animal, plant, or bacterialcell. Viruses specific for bacteria are known as bacteriophages, or simplyphages (Greek phagein, “to eat”). Some viruses contain only one kind ofprotein in their capsid—the tobacco mosaic virus, for example, a simpleplant virus and the first to be crystallized. Other viruses contain as many asa hundred different kinds of proteins. Even some of these large and com-plex viruses have been crystallized, and their detailed molecular structuresare known. Viruses differ greatly in size. Bacteriophage øX174, one of thesmallest, has a diameter of 18 nm. Vaccinia virus is one of the largest; itsvirions are almost as large as the smallest bacteria. Viruses also differ inshape and complexity of structure. The human immunodeficiency virus(HIV) is relatively simple in structure, but devastating in effect; it causesAIDS by destroying cells central to the human immune response. The out-breaks of Hantavirus in the southwestern United States in 1993 and of theEbola virus in central Africa in 1995 illustrate the extreme pathogenicity ofsome viruses. Both viruses produce diseases with rapid courses and highmortality. Other viruses that are highly pathogenic in humans cause po-liomyelitis, influenza, herpes, hepatitis, the common cold, infectious mono-nucleosis, shingles, and certain types of cancer.

Biochemistry has profited enormously from the study of viruses, whichhas provided new information about the structure of the genome, the enzy-matic mechanisms of nucleic acid and protein synthesis, and the regulationof the flow of genetic information.

50 nm(a)

(d) (e) (f )

100 nm(b)

(c)

figure 2–23A gallery of viruses. (a) Electron micrograph showingturnip yellow mosaic virus (small spherical particles),tobacco mosaic virus (long cylinders), and bacteriophageT4 (shaped like a hand mirror with spidery legs). (b) Elec-tron micrograph (artificial color) showing human immuno-deficiency viruses (HIV), the causative agent of AIDS,leaving an infected T lymphocyte of the immune system.(c) Molecular surface model of filamentous phage fd. (d) Molecular surface model of the canine parvovirus, aserious health hazard to unvaccinated dogs. (e) Molecularsurface model of human poliovirus (type 2), a picor-navirus. Widespread vaccination has nearly eliminatedpoliovirus as a health hazard in humans. (f) Molecularsurface model of the bacteriophage fX174.


Cells, the structural and functional units of livingorganisms, are of microscopic dimensions. Theirsmall size, combined with convolutions of theirsurfaces, results in high surface-to-volume ra-tios, facilitating the diffusion of fuels, nutrients,and waste products between the cell and its sur-roundings. All cells share certain features: DNAcontaining the genetic information, ribosomes,and a plasma membrane that surrounds the cy-toplasm. In eukaryotes the genetic material issurrounded by a nuclear envelope; prokaryoteshave no such membrane.

The plasma membrane is a tough, flexible per-meability barrier, which contains numeroustransporters as well as receptors for a variety ofextracellular signals. The cytoplasm of eukary-otic cells consists of the cytosol and organelles.The cytosol is a concentrated solution of pro-teins, RNA, metabolic intermediates and cofac-tors, and inorganic ions. Ribosomes are supra-molecular complexes on which protein synthesisoccurs; bacterial ribosomes are slightly smallerthan those of eukaryotic cells, but are similar instructure and function.

Certain organisms, tissues, and cells offer ad-vantages for biochemical studies. E. coli andyeast can be cultured in large quantities, haveshort generation times, and are especiallyamenable to genetic manipulation. The special-ized functions of liver, muscle, and fat tissue, andof erythrocytes, make them attractive for thestudy of specific processes.

The first living cells were prokaryotic andanaerobic; they arose about 3.5 billion years ago,when the atmosphere was devoid of oxygen.With the passage of time, biological evolution ledto cells capable of photosynthesis, with O2 as abyproduct. As O2 accumulated, prokaryotic cellscapable of the aerobic oxidation of fuels evolved.The two major groups of prokaryotes, eubacteriaand archaebacteria, diverged early in evolution.The cell envelope of some types of bacteria in-cludes layers outside the plasma membrane thatprovide rigidity or protection. Some bacteriahave flagella for propulsion. The cytoplasm ofbacteria has no membrane-bounded organellesbut does contain ribosomes and granules ofstored fuels, as well as a nucleoid that containsthe cell’s DNA. Some photosynthetic bacteriahave extensive intracellular membranes that con-tain light-capturing pigments.

About 1.5 billion years ago, eukaryotic cellsemerged. They were larger than prokaryotes andtheir genetic material was more complex. Theseearly cells established symbiotic relationshipswith prokaryotes that lived in their cytoplasm;modern mitochondria and chloroplasts are de-rived from these early endosymbionts. Mitochon-dria and chloroplasts are intracellular organellessurrounded by a double membrane. They are theprincipal sites of ATP synthesis in eukaryotic,aerobic cells. Chloroplasts are found only in pho-tosynthetic organisms, but mitochondria are ubiq-uitous among eukaryotes.

Modern eukaryotic cells have a complex sys-tem of intracellular membranes. This endomem-brane system consists of the nuclear envelope,rough and smooth endoplasmic reticulum, theGolgi complex, transport vesicles, lysosomes,and endosomes. Proteins synthesized on ribo-somes bound to the rough endoplasmic reticu-lum pass into the endomembrane system, travel-ing through the Golgi complex on their way toorganelles or to the cell surface, where they aresecreted by exocytosis. Endocytosis brings ex-tracellular materials into the cell, where they canbe digested by degradative enzymes in the lyso-somes. In plants, the central vacuole is the site ofdegradative processes; it also serves as a storagedepot for pigments and other metabolic productsand maintains cell turgor.

The genetic material in eukaryotic cells is or-ganized into chromosomes, highly ordered com-plexes of DNA and histone proteins. Before celldivision (cytokinesis), each chromosome is repli-cated and the duplicate chromosomes are sepa-rated by the process of mitosis.

The cytoskeleton is an intracellular meshworkof actin filaments, microtubules, and intermedi-ate filaments of several types. The cytoskeletonconfers shape on the cell, and reorganization ofcytoskeletal filaments results in the shapechanges accompanying amoeboid movement andcell division. Intracellular organelles move alongfilaments of the cytoskeleton, propelled by pro-teins such as kinesin, cytoplasmic dynein, andmyosin, using the energy of ATP. Biochemistsuse differential centrifugation and isopycnic cen-trifugation to isolate subcellular components forstudy.

In multicellular organisms, there is a division oflabor among different types of cells. The individual

summary

Chapter 2 Cells 49

further readingGeneralAlberts, B., Bray, D., Lewis, J., Raff, M.,

Roberts, K., & Watson, J.D. (1994) Molecular

Biology of the Cell, 3rd edn, Garland Publishing,Inc., New York.

A superb textbook on cell structure and function,covering the topics considered in this chapter, and auseful reference for many of the following chapters.

Becker, W.M., Reece, J.M., & Peonie, M.F. (1995)The World of the Cell, 3rd edn, The Benjamin/Cummings Publishing Company, Redwood City, CA.

An excellent introductory textbook of cell biology.

Lodish, H., Baltimore, D., Berk, A., Zipursky,

S.L., Matsudaira, P., & Darnell, J. (1995) Molecu-

lar Cell Biology, 3rd edn, Scientific American Books,Inc., New York.

Like the book by Alberts and coauthors, a superbtext useful for this and later chapters.

Margulis, L. (1996) Archaeal-eubacterial mergers inthe origin of Eukarya: phylogenetic classification oflife. Proc. Natl. Acad. Sci. USA 93, 1071–1076.

The arguments for dividing all living creatures intofive kingdoms: Monera, Protoctista, Fungi, Animalia,Plantae.

Margulis, L., Gould, S.J., Schwartz, K.V., & Mar-

gulis, A.R. (1998) Five Kingdoms: An Illustrated

Guide to the Phyla of Life on Earth, 3rd edn, W.H.Freeman and Company, New York.

Description of all major groups of organisms, beau-tifully illustrated with electron micrographs anddrawings.

Purves, W.K., Orians, G.H., Heller, H.C., &

Sadava, D. (1998) Life: The Science of Biology,

5th edn, Sinauer Associates, Inc., and W.H. Freemanand Company, New York.

A well-written, well-illustrated, up-to-date general biology textbook.

Structure of Cells, Organelles, and CytoskeletonBlock, S.M. (1998) Leading the procession: new insights into kinesin motors. J. Cell Biol. 140,

1281–1284.

Fawcett, D.W. & Jensh, R.O. (eds) (1997) Bloom

and Fawcett: Concise Histology, Chapman & Hall,London.

A well-illustrated textbook of cell structure at the microscopic level.

Frontiers in Cell Biology: The Cytoskeleton. (1998)Science 279, 509–533.

This special issue includes the following papers:

Hall, A., Rho GTPases and the actin cytoskeleton(pp. 509–514); Fuchs, E. & Cleveland, D.W., Astructural scaffolding of intermediate filaments inhealth and disease (pp. 514–519); Hirokawa, N.,

Kinesin and dynein superfamily proteins and themechanism of organelle transport (pp. 519–526);Mermall, V., Post, P.L., & Mooseker, M.S., Un-conventional myosins in cell movement, membranetraffic, and signal transduction (pp. 527–533).

Gelfand, V. & Bershadsky, A.D. (1991) Micro-tubule dynamics: mechanism, regulation, and func-tion. Annu. Rev. Cell Biol. 7, 93–116.

Organization of the Cytoplasm. (1981) Cold Spring

Harb. Symp. Quant. Biol. 46.

More than 90 excellent papers on microtubules, mi-crofilaments, and intermediate filaments and their biological roles.

Rothman, J.E. & Orci, L. (1996) Budding vesiclesin living cells. Sci. Am. 274 (March), 70–75.

A clear description of the dynamics of the endo-membrane system.

Schroer, T.A. & Sheetz, M.P. (1991) Functions ofmicrotubule-based motors. Annu. Rev. Physiol. 53,

629–652.

Spudich, J.A. (1996) Structure-function analysis ofthe motor domain of myosin. Annu. Rev. Cell Dev.

Biol. 12, 543–573.

Takai, Y., Sasaki, T., Tanaka, K., & Nakanishi, H.

(1995) Rho as a regulator of the cytoskeleton.Trends Biochem. Sci. 20, 227–231.

Short review of the evidence that the small GTP-binding protein Rho controls the assembly and struc-ture of actin filaments.

epithelial cells in animals can be joined to eachother mechanically by tight junctions and desmo-somes; communication channels are provided bygap junctions (in animals) and plasmodesmata(in plants). Viruses are parasites of living cells,

capable of subverting the cellular machinery fortheir own replication. They infect animal, plant,and bacterial cells and are responsible for a vari-ety of serious human diseases.


Vale, R.D. & Fletterick, R.J. (1997) The designplan of kinesin motors. Annu. Rev. Cell Dev. Biol.

13, 745–777.Detailed review of the structure and mechanism ofthe molecular motors in the kinesin superfamily.

Evolution of Cellsde Duve, C. (1995) The beginnings of life on earth.Am. Sci. 83, 428–437.

One scenario for the succession of chemical stepsthat led to the first living organism.

de Duve, C. (1996) The birth of complex cells. Sci.

Am. 274 (April), 50–57.

Dyer, B.D. & Obar, R.A. (1994) Tracing the His-

tory of Eukaryotic Cells: The Enigmatic Smile,

Columbia University Press, New York.

Fenchel, T. & Finlay, B.J. (1994) The evolution oflife without oxygen. Am. Sci. 82, 22–29.

Discussion of the endosymbiotic hypothesis in the light of modern endosymbiotic anaerobic organisms.

Knoll, A.H. (1991) End of the proterozoic eon. Sci.

Am. 265 (October), 64–73.Discussion of the evidence that an increase in atmos-pheric oxygen led to the development of multicellularorganisms, including large animals.

Lazcano, A. & Miller, S.L. (1994) How long did ittake for life to begin and evolve to cyanobacteria? J. Mol. Evol. 39, 546–554.

Lazcano, A. & Miller, S.L. (1996) The origin andearly evolution of life: prebiotic chemistry, the pre-RNA world, and time. Cell 85, 793–798.

Brief review of recent developments in studies of theorigin of life: primitive atmospheres, submarinevents, autotrophic versus heterotrophic origin, theRNA and pre-RNA worlds, and the time required forlife to arise.

Margulis, L. (1992) Symbiosis in Cell Evolution:

Microbial Evolution in the Archean and Protero-

zoic Eons, 2nd edn, W.H. Freeman and Company,New York.

Clear discussion of the hypothesis that mitochondriaand chloroplasts are descendants of bacteria; alleukaryotic cells evolved from microbial symbioses.

Martin, W. & Mueller, M. (1998) The hydrogen hy-pothesis for the first eukaryote. Nature 392, 37–41.

An interesting new hypothesis for the origin of eu-karyotic cells, based on the comparative biochemistryof energy metabolism. It postulates that eukaryoticcells arose from fusion of an H2-producing eubac-terium with a strictly H2-dependent archaebacterium.

Schopf, J.W. (1992) Major Events in the History of

Life, Jones and Bartlett Publishers, Boston.

Vidal, G. (1984) The oldest eukaryotic cell. Sci. Am.

250 (February), 48–57.

Relationship of Archaea and EubacteriaBrow, J.R. & Doolittle, W.F. (1997) Archaea andthe prokaryote-to-eukaryote transition. Microbiol.

Mol. Biol. Rev. 61, 456–502.A very thorough discussion of the arguments forplacing the Archaea on the phylogenetic branch thatled to multicellular organisms.

Keeling, P.J. & Doolittle, W.F. (1995) Archaea:narrowing the gap between prokaryotes and eukary-otes. Proc. Natl. Acad. Sci. USA 92, 5761–5764.

Madigan, T. & Marris, B.L. (1997) Extremophiles.Sci. Am. 276 (April), 82–87.

A biochemical assessment of archaebacteria that livewhere it is hottest, coldest, saltiest, most acid, andmost alkaline.

Reviews of Archaea. (1997) Cell 89.

This issue contains five reviews of the biochemistryand genomics of the Archaea and their relationshipto the eukaryotes:

Olsen, G.J. & Woese, C.R., Archaeal genomics:an overview (pp. 991–994); Edgell, D.R. &

Doolittle, W.F., Archaea and the origin(s) of DNAreplication proteins (pp. 995–998); Reeve, J.N.,

Sandman, K., & Daniels, C.J., Archaeal histones,nucleosomes, and transcription initiation (pp. 999–1002); Belfort, M. & Weiner, A., Another bridgebetween kingdoms: tRNA splicing in Archaea andEukaryotes (pp. 1003–1006); Dennis, P.P., Ancientciphers: translation in Archaea (pp. 1007–1010).

problems

Some problems related to the contents of the chapterfollow. They involve simple geometrical and numericalrelationships concerning cell structure and activities.(In solving end-of-chapter problems, you may wish torefer to the tables printed on the inside of the backcover.) Each problem has a title for easy reference anddiscussion.

1. The Size of Cells and Their Components

(a) If you were to magnify a cell 10,000 fold(which is typical of the magnification that is achievedusing a microscope), how big would it appear? Assumeyou are viewing a “typical” eukaryotic cell with a cel-lular diameter of 50 microns.

Chapter 2 Cells 51

(b) If this cell were a muscle cell, how many mole-cules of actin could it hold assuming there were noother cellular components present? (Actin moleculesare spherical with a diameter of 3.6 nm; assume themuscle cell is spherical. The volume of a sphere is 4/3 pr3.)

(c) If this were a liver cell of the same dimensions,how many mitochondria could it hold assuming therewere no other cellular components present? (Assumemitochondria are spherical with a diameter of 1.5 mm;assume the liver cell is spherical. The volume of asphere is 4/3 pr3.)

(d) Glucose is the major energy-yielding nutrientfor most cells. Assuming it is present at a concentra-tion of 1 mM, calculate how many molecules of glucosewould be present in our hypothetical (and spherical)eukaryotic cell? (Avogadro’s number, the number ofmolecules in 1 mol of a nonionized substance is 6.02 � 1023.)

(e) Hexokinase is an important enzyme in the me-tabolism of glucose by cells (see Chapter 15). If themolar concentration of hexokinase in our eukaryoticcell is 20 mM, how many glucose molecules are avail-able for each hexokinase enzyme molecule to metab-olize?

2. Components of E. coli E. coli cells are rod-shaped, about 2 mm long and 0.8 mm in diameter. Thevolume of a cylinder is pr2h, where h is the height ofthe cylinder.

(a) If the average density of E. coli (mostly water)is 1.1 � 103 g/L, what is the mass of a single cell?

(b) The protective cell wall of E. coli is 10 nmthick. What percentage of the total volume of the bac-terium does the wall occupy?

(c) E. coli is capable of growing and multiplyingrapidly because of the inclusion in each cell of some15,000 spherical ribosomes (diameter 18 nm), whichcarry out protein synthesis. What percentage of the to-tal cell volume do the ribosomes occupy?

3. Genetic Information in E. coli DNA The ge-netic information contained in DNA consists of a linearsequence of successive coding units, known as codons.Each codon is a specific sequence of three nucleotides(three nucleotide pairs in double-stranded DNA), andeach codon codes for a single amino acid unit in a pro-tein. The molecular weight of an E. coli DNA moleculeis about 3.1 � 109. The average molecular weight of anucleotide pair is 660, and each nucleotide pair con-tributes 0.34 nm to the length of DNA.

(a) Calculate the length of an E. coli DNA mole-cule. Compare the length of the DNA molecule withthe cell dimensions (see Problem 2). How does theDNA molecule fit into the cell?

(b) Assume that the average protein in E. coli

consists of a chain of 400 amino acids. What is themaximum number of proteins that can be coded by anE. coli DNA molecule?

4. The High Rate of Bacterial Metabolism Bac-terial cells have a much higher rate of metabolism thananimal cells. Under ideal conditions some bacteria willdouble in size and divide in 20 min, whereas most an-imal cells under rapid growth conditions require 24 h.The high rate of bacterial metabolism requires a highratio of surface area to cell volume.

(a) Why would the surface-to-volume ratio havean effect on the maximum rate of metabolism?

(b) Calculate the surface-to-volume ratio for thespherical bacterium Neisseria gonorrhoeae (diame-ter 0.5 mm), responsible for the disease gonorrhea.Compare it with the surface-to-volume ratio for a glob-ular amoeba, a large eukaryotic cell (diameter 150 mm).The surface area of a sphere is 4pr2.

5. A Strategy to Increase the Surface Area of

Cells Certain cells whose function is to absorb nutri-ents, such as the cells lining the small intestine or theroot hair cells of a plant, are optimally adapted to theirrole because their exposed surface area is increasedby microvilli. Consider a spherical epithelial cell (di-ameter 20 mm) in the lining of the small intestine.Given that only a part of the cell surface faces the in-terior of the intestine, assume that a “patch” corre-sponding to 25% of the cell area is covered with mi-crovilli. Furthermore, assume that the microvilli arecylinders 0.1 mm in diameter, 1.0 mm long, and spacedin a regular grid 0.2 mm on center.

(a) Calculate the number of microvilli on thepatch.

(b) Calculate the surface area of the patch, as-suming it has no microvilli.

(c) Calculate the surface area of the patch, as-suming it does have microvilli.

(d) What percentage improvement in absorptivecapacity (reflected by the surface-to-volume ratio)does the presence of microvilli provide?

0.2 �m

0.1 �m

Arrangement of microvilli on the “patch”

(e) What other organelles and organ systems uti-lize this strategy to improve absorptive capacity?

6. Fast Axonal Transport Neurons possess long,thin processes called axons, which are structures spe-cialized for conducting signals throughout an organ-ism. Some axonal processes can be as long as 2 m—forexample, the axons that originate in the spinal cord andterminate in the muscles of your toes. Small membrane-enclosed vesicles carrying materials essential to ax-onal function move along microtubules from the cellbody to the tips of axons by kinesin-dependent “fastaxonal transport.”

(a) If the average velocity of a vesicle is 1 mm/sec,how long does it take a vesicle to move from a cellbody in the spinal cord to the axonal tip in the toes?

(b) Movement of large molecules in cells by diffu-sion occurs relatively slowly in cells. (For example, he-


moglobin diffuses at a rate of approximately 5 mm/s.)However, the diffusion of sucrose in an aqueous solu-tion occurs at a rate approaching that of fast transportmechanisms (about 4 mm/s). What are some advan-tages to a cell or an organism of fast, directed trans-port mechanisms, compared to what a cell could do re-lying on diffusion alone?

(c) Some of the studies that originally determinedthe velocity of vesicular movement were performed onmicrotubules in vitro (in a dish). In order to isolate themicrotubules for these studies, intact neurons wereinitially homogenized (broken) in the presence of 0.2 M sucrose to prevent osmotic swelling and burstingof intracellular organelles. Why is this an importantconsideration in studies involving cell fractionation?

cells - labs.icb.ufmg.brlabs.icb.ufmg.br/lbcd/prodabi3/integrantes/cibele/lehn02.pdf · the human...

Documents