Charles Darwin faced a dilemma. In his great book On the Origin ofSpecies, published in 1859, he proposed the theory of natural selec-tion to explain the gradual appearance and disappearance of differ-ent forms of animals and plants over long periods of time. But he re-

alized that the fossil record, on which he based his theory, was incomplete, especiallyfor the beginning of life. The oldest fossils that had been found in Darwin’s time werecomplex organisms in rocks dated at about 550 million years ago (the Cambrian pe-riod). Where were the missing Precambrian fossils? These would surely provide alink to the origin of life.

As we saw in Chapter 3, conditions on Earth were probably suitable for the emer-gence of life by 4 billion years ago, about 600 million years after Earth began to form.But until recently there was no evidence for life older than the Cambrian. By the turnof the twentieth century, there was evidence for fossilized clumps of algae (simpleaquatic photosynthetic organisms) in rocks at the base of the Grand Canyon thatwere close to 1 billion years old.

It took nearly another century to push the clock of life back nearer to its origins.In 1993, geologist J. William Schopf found fossilized chains of cylindrical objects, quitesimilar in size and shape to contemporary cyanobacteria (“blue-green algae”), inrocks in Western Australia that he dated at an astonishing 3.5 billion years old. Hethen used a chemical analysis method called laser Raman spectroscopy to show thatthese objects apparently contain carbon deposits that are chemical signatures of life.

Rounded or cylindrical objects in Earth’s rocks or in a meteorite from Mars (seeChapter 3) get scientists excited because they realize that life is not just a bunch ofmacromolecules. Rather, life is macromole-cules that can perform unique functions be-cause they are enclosed in a structural com-partment that is separate from the externalenvironment. This separation allows livingthings to maintain a constant internal envi-ronment (homeostasis).

The “living compartment” is the cell, thesubject of this chapter. The water-insolublephospholipid structure (see Figure 3.21) thatdefines and contains cells is called theplasma membrane. It and its functions are soimportant that we will devote the entire nextchapter to membranes. Subsequent chapterswill be devoted to the chemical activities thattake place inside all cells.

Cells: The Basic Units of Life

The Earliest Trace of Life? This fossilfrom Western Australia is 3.5 billion yearsold and shows carbon traces that indicatelife. Its form is similar to that of modern filamentous cyanobacteria (inset).

4

The Cell: The Basic Unit of LifeJust as atoms are the units of chemistry, cells are the buildingblocks of life. Three statements constitute the cell theory:

� Cells are the fundamental units of life.� All organisms are composed of cells.� All cells come from preexisting cells.

Cells are composed of water molecules and the small andlarge molecules we examined in the previous two chapters.Each cell contains at least 10,000 different types of molecules,most of them present in many copies. Cells use these mole-cules to transform matter and energy, to respond to their en-vironment, and to reproduce themselves.

The cell theory has three important implications. First, itmeans that studying cell biology is in some sense the same asstudying life. The principles that underlie the functions of thesingle cell in a bacterium are similar to those governing the 60trillion cells of your body. Second, it means that life is contin-uous. All those cells in your body came from a single cell, thefertilized egg, which came from the fusion of two cells, asperm and an egg from your parents, whose cells came fromtheir fertilized eggs, and so on. Finally, it means that the ori-gin of life on Earth was marked by the origin of the first cells.

Cells may have come from stable bubblesIsolation from the general environment can be achieved inthe laboratory within aggregates produced from moleculesmade in prebiotic synthesis experiments. Called protobionts,these aggregates cannot reproduce, but they can maintain in-ternal chemical environments that differ from their sur-

roundings. Under the microscope, they look a lot like tinycells (Figure 4.1).

In the 1920s, Russian scientist Alexander Oparin mixed alarge protein and a polysaccharide in solution. When he ag-itated this mixture, bubbles formed. He could also do thiswith other polymers. The interiors of these bubbles hadmuch higher concentrations of the macromolecules than theirsurroundings. Moreover, they catalyzed chemical reactions,and they had some control over what left them and crossedthe boundary into the environment. In other words, theywere protobionts. Later, other researchers showed that iflipids are mixed in an aqueous environment, they sponta-neously arrange themselves into droplets surrounded by abilayer.

Taken together with the prebiotic chemistry models andRNA world hypothesis described in Chapter 3, these exper-iments suggest a bubble theory for the origin of cells.

Cell size is limited by the surface area-to-volume ratioMost cells are tiny. The volume of cells ranges from 1 to 1,000µm3 (Figure 4.2). The eggs of some birds are enormous ex-ceptions, to be sure, and individual cells of several types ofalgae and bacteria are large enough to be viewed with theunaided eye. And although neurons (nerve cells) have a vol-ume that is within the “normal” cell range, they often havefine projections that may extend for meters, carrying signalsfrom one part of a large animal to another. But by and large,cells are minuscule. The reason for this relates to the changein the surface area-to-volume ratio (SA/V) of any object asit increases in size.

As a cell increases in volume, its surface area also in-creases, but not to the same extent (Figure 4.3). This phe-nomenon has great biological significance for two reasons:

� The volume of a cell determines the amount of chemicalactivity it carries out per unit of time.

� The surface area of a cell determines the amount of sub-stances the cell can take in from the outside environmentand the amount of waste products it can release to theenvironment.

As a living cell grows larger, its rate of waste production andits need for resources increase faster than its surface area. Thisexplains why large organisms must consist of many smallcells: Cells are small in volume in order to maintain a largesurface area-to-volume ratio.

In a multicellular organism, the large surface area repre-sented by the multitude of small cells that make up the or-ganism enables it to carry out the multitude of functions re-quired for survival. Special structures transport food, oxygen,and waste materials to and from the small cells that are dis-tant from the external surface of the organism.

62 CHAPTER FOUR

90 nm

4.1 Protobionts These aggregates, made by agitating a solution ofmacromolecules, are chemical compartments, can perform somemetabolic reactions, and can exchange materials with their environ-ment. They are a model of how cells may have originated.

Microscopes are needed to visualize cells

Most cells are invisible to the human eye. The smallest objecta person can typically discern is about 0.2 mm (200 µm) insize. We refer to this measure as resolution, the distance aparttwo objects must be in order for them to be distinguished asseparate; if they are closer together, they appear as a singleblur. Many cells are much smaller than 200 µm. Microscopesare instruments used to improve resolution so that cells andtheir internal structures can be seen.

There are two basic types of microscopes: light micro-scopes and electron microscopes. The light microscope (LM)uses glass lenses and visible light to form a magnified imageof an object. It has a resolving power of about 0.2 µm, whichis 1,000 times that of the human eye. It allows visualizationof cell sizes and shapes and some internal cell structures. Thelatter are hard to see under ordinary light, so cells are oftenkilled and stained with various dyes to make certain struc-tures stand out.

An electron microscope (EM) uses magnets to focus anelectron beam, much as a light microscope uses glass lensesto focus a beam of light. Since we cannot see electrons, theelectron microscope directs them at a fluorescent screen orphotographic film to create a visible image. The resolvingpower of electron microscopes is about 0.5 nm, which is400,000 times that of the human eye. This resolving powerpermits the details of many subcellular structures to be dis-tinguished.

Many techniques have been developed to enhance theviews of cells we see under the light and electron micro-scopes (Figure 4.4).

CELLS: THE BASIC UNITS OF LIFE 63

0.1 nm 1 nm

Atoms

Small molecules

Lipids

Protein

T2 phage

Chloroplast

Most bacteria

Plantandanimalcells Fish

egg Hummingbird

Human

Bluewhale

Californiaredwood

10 nm 100 nm 1 µm 10 µm 100 µm 1 mm 1 cm 0.1 m 1 m 10 m 100 m 1 km

Electron microscope

Light microscope

Unaided eye

This scale is logarithmic. Each unit is ten times bigger than the previous unit.

Most cell diameters are in the range of 1–100 µm.

4.2 The Scale of Life This scale shows the relative sizes ofmolecules, cells, and multicellular organisms.

6 sides × 12

= 6 mm2

13 = 1 mm3

6/1

1-mm cube

6 sides × 22

= 24 mm2

23 = 8 mm3

3/1

2-mm cube

6 sides × 42

= 96 mm2

43 = 64 mm3

1.5/1

4-mm cube

Surface area

Volume

Surface area-to-volume ratio

There is a smaller surface area compared to volume.

There is a larger surface area compared to volume.

4.3 Why Cells Are Small As an object grows larger, its volumeincreases more rapidly than its surface area. Cells must maintain a large surface area-to-volume ratio in order to function, whichexplains why large organisms must be composed of many small cells rather than a few huge ones.

64 CHAPTER FOUR

4.4 Looking at Cells The top six panels show some techniques usedin light microscopy. The lower three images were created using electronmicroscopes.

RESEARCH METHOD

In bright-field microscopy, light passes directly through the cells. Unless natural pigments are present, there is little contrast and details are not distinguished.

In phase-contrast microscopy, contrast in the image is increased by emphasizing differences in refractive index (the capacity to bend light), thereby enhancing light and dark regions in the cell.

Differential interference-contrast microscopy uses two beams of polarized light. The combined images look as if the cell is casting a shadow on one side.

In fluorescence microscopy, a natural substance in the cell or a fluorescent dye that binds to a specific cell material is stimulated by a beam of light, and the longer-wavelength fluorescent light is observed coming directly from the dye.

Confocal microscopy uses fluorescent materials but adds a system of focusing both the stimulating and emitted light so that a single plane through the cell is seen. The result is a sharper two-dimentional image than with standard fluorescence microscopy.

In stained bright-field microscopy, a stain added to preserve cells enhances contrast and reveals details not otherwise visible. Stains differ greatly in their chemistry and their capacity to bind to cell materials, so many choices are available.

In transmission electron microscopy (TEM), a beam of electrons is focused on the object by magnets. Objects appear darker if they absorb the electrons. If the electrons pass through they are detected on a fluorescent screen.

Scanning electron microscopy (SEM) directs electrons to the surface of the sample, where they cause other electrons to be emitted. These electrons are viewed on a screen. The three-dimentional surface of the object can be visualized.

Cryoelectron microscopy uses quickly frozen samples to reduce aberrations that are seen when samples are treated chemically. Computer analysis of thick sections can reconstruct a sample in three dimensions.

25 µm 25 µm 25 µm

75 µm40 µm40 µm

8.5 µm 8 µm 5 µm

CELLS: THE BASIC UNITS OF LIFE 65

Cells are surrounded by a plasma membrane

As we have noted, a plasma membrane separates each cellfrom its environment, creating a segregated (but not isolated)compartment. The plasma membrane is composed of a phos-pholipid bilayer, with the hydrophilic “heads” of the lipidsfacing the cell’s aqueous interior on one side of the mem-brane and the extracellular environment on the other (seeFigure 3.21). Proteins are embedded in the lipids. In manycases, these proteins protrude into the cytoplasm and into theextracellular environment. We will devote most of Chapter 5to detailing the structure and functions of the plasma mem-brane, but summarize its roles here.

� The plasma membrane allows the cell to maintain amore or less constant internal environment. A self-main-taining, constant internal environment is a key characteris-tic of life that will be discussed in detail in Chapter 41.

� The plasma membrane acts as a selectively permeable bar-rier, preventing some substances from crossing whilepermitting other substances to enter and leave the cell.

� As the cell’s boundary with the outside environment, theplasma membrane is important in communicating withadjacent cells and receiving extracellular signals. We willdescribe this function in Chapter 15.

� The plasma membrane often has molecules protrudingfrom it that are responsible for binding and adhering toadjacent cells.

Cells show two organizational patterns

Prokaryotic cell organization is characteristic of the domainsBacteria and Archaea. Organisms in these domains are calledprokaryotes. Their cells do not have membrane-enclosed in-ternal compartments. The first cells ever to form were un-doubtedly similar in organization to modern prokaryotes.

Eukaryotic cell organization is found in the domain Eu-karya, which includes the protists, plants, fungi, and animals.The genetic material (DNA) of eukaryotic cells is containedin a special membrane-enclosed compartment called the nu-cleus. Eukaryotic cells also contain other membrane-enclosedcompartments in which specific chemical reactions takeplace. Organisms with this type of cell organization areknown as eukaryotes.

Both prokaryotes and eukaryotes have prospered formany hundreds of millions of years of evolution, and bothare great success stories. Let’s look first at prokaryotic cells.

Prokaryotic Cells

Prokaryotes can live off more different and diverse energysources than any other living creatures, and they inhabit

greater environmental extremes, such as very hot springs andvery salty water. The vast diversity within the prokaryoticdomains is the subject of Chapter 27.

Prokaryotic cells are generally smaller than eukaryoticcells, ranging from 0.25 × 1.2 µm to 1.5 × 4 µm. Eachprokaryote is a single cell, but many types of prokaryotesare usually seen in chains, small clusters, or even clusterscontaining hundreds of individuals. In this section, we willfirst consider the features that cells in the domains Bacte-ria and Archaea have in common. Then we will examinestructural features that are found in some, but not all,prokaryotes.

Prokaryotic cells share certain featuresAll prokaryotic cells have the same basic structure:

� The plasma membrane encloses the cell, regulating thetraffic of materials into and out of the cell and separatingit from its environment.

� A region called the nucleoid contains the hereditarymaterial (DNA) of the cell.

The rest of the material enclosed in the plasma membrane iscalled the cytoplasm. The cytoplasm is composed of twoparts: the liquid cytosol, and insoluble suspended particles,including ribosomes.

� The cytosol consists mostly of water that contains dis-solved ions, small molecules, and soluble macromole-cules such as proteins.

� Ribosomes are granules about 25 nm in diameter thatare sites of protein synthesis.

The cytoplasm is not a static region. Rather, the substancesin this aqueous environment are in constant motion. For ex-ample, a typical protein moves around the entire cell withina minute, and encounters many molecules along the way.

Although structurally less complicated than eukaryoticcells, prokaryotic cells are functionally complex, carrying outthousands of biochemical transformations.

Some prokaryotic cells have specialized featuresAs they evolved, some prokaryotes developed specializedstructures that gave a selective advantage to those cells thathad them. These structures include a protective cell wall, aninternal membrane for compartmentalization of chemical reactions, and flagella for cell movement through the wateryenvironment. These features are shown in Figures 4.5 and4.6.

CELL WALLS. Most prokaryotes have a cell wall locatedoutside the plasma membrane. The rigidity of the cell wall

supports the cell and determines its shape. The cell walls ofmost bacteria, but not archaea, contain peptidoglycan, apolymer of amino sugars, cross-linked by covalent bonds toform a single giant molecule around the entire cell. In somebacteria, another layer—the outer membrane (a polysac-charide-rich phospholipid membrane)—encloses the pep-tidoglycan layer. Unlike the plasma membrane, this outermembrane is not a major permeability barrier, and some ofits polysaccharides are disease-causing toxins.

Enclosing the cell wall in some bacteria is a layer of slime,composed mostly of polysaccharides and referred to as acapsule. The capsules of some bacteria may protect themfrom attack by white blood cells in the animals they infect.The capsule helps keep the cell from drying out, and some-times it helps the bacterium attach to other cells. Many pro-karyotes produce no capsule, and those that do have cap-sules can survive even if they lose them, so the capsule is notessential to cell life.

As you will see later in this chapter, eukaryotic plant cellsalso have a cell wall, but it differs in composition and struc-ture from the cell walls of prokaryotes.

INTERNAL MEMBRANES. Some groups of bacteria—thecyanobacteria and some others—carry on photosynthesis.In these photosynthetic bacteria, the plasma membranefolds into the cytoplasm to form an internal membrane sys-tem that contains bacterial chlorophyll and other com-pounds needed for photosynthesis. The development ofphotosynthesis, probably by such internal membranes, was

an important event in the early evolution of life on Earth.Other prokaryotes have internal membrane folds thatremain attached to the plasma membrane. These mesosomesmay function in cell division or in various energy-releasingreactions.

FLAGELLA AND PILI. Some prokaryotes swim by usingappendages called flagella (Figure 4.6a,c). A single flagel-lum, made of a protein called flagellin, looks at times like atiny corkscrew. It spins on its axis like a propeller, drivingthe cell along. Ring structures anchor the flagellum to theplasma membrane and, in some bacteria, to the outer mem-brane of the cell wall (Figure 4.6c). We know that the fla-gella cause the motion of the cell because if they areremoved, the cell cannot move.

Pili project from the surfaces of some groups of bacteria(Figure 4.6b). Shorter than flagella, these threadlike structureshelp bacteria adhere to one another during mating, as wellas to animal cells for protection and food.

CYTOSKELETON. Recent evidence suggests that someprokaryotes, especially rod-shaped bacteria, have an inter-nal filamentous helical structure just below the plasmamembrane. The proteins that make up this structure aresimilar in amino acid sequence to actin in eukaryotic cells,and since actin is part of the cytoskeleton in those cells (seebelow), it has been suggested that the helical filaments inprokaryotes play a role in cell shape.

Eukaryotic Cells

Animals, plants, fungi, and protists have cells that are usu-ally larger and structurally more complex than those of theprokaryotes. To get a sense of the most prominent differ-

66 CHAPTER FOUR

Cytoplasm

Ribosomes

Nucleoid

Plasma membrane

Capsule

PeptidoglycanCellwall

Outer membrane

200 nm

4.5 A Prokaryotic Cell The bacterium Pseudomonas aerugi-nosa illustrates typical prokaryotic cell structures. Note theexistence of several protective structures external to the plas-ma membrane.

CELLS: THE BASIC UNITS OF LIFE 67

ences, compare the eukaryotic plant and animal cells shownin Figure 4.7 with the prokaryotic cell in Figure 4.5.

Eukaryotic cells generally have dimensions ten timesgreater than those of prokaryotes; for example, the sphericalyeast cell has a diameter of 8 µm. Like prokaryotic cells, eu-karyotic cells have a plasma membrane, cytoplasm, and ri-bosomes. But added on to this basic organization are com-partments in the cytoplasm whose interiors are separatedfrom the cytosol by a membrane.

Compartmentalization is the key to eukaryotic cell function

Some of the compartments in eukaryotic cells are like little fac-tories that make specific products. Others are like power plantsthat take in energy in one form and convert it to a more usefulform. These membranous compartments, as well as otherstructures (such as ribosomes) that lack membranes but pos-sess distinctive shapes and functions, are called organelles (seeFigure 4.7). Each of these organelles has specific roles in its par-ticular cell. These roles are defined by chemical reactions.

� The nucleus contains most of the cell’s genetic material(DNA). The duplication of the genetic material and thefirst steps in decoding genetic information take place inthe nucleus.

� The mitochondrion is a power plant and industrial park,where energy stored in the bonds of carbohydrates isconverted to a form more useful to the cell (ATP) andcertain essential biochemical conversions of amino acidsand fatty acids occur.

� The endoplasmic reticulum and Golgi apparatus arecompartments in which proteins are packaged and sentto appropriate locations in the cell.

� Lysosomes and vacuoles are cellular digestive systemsin which large molecules are hydrolyzed into usablemonomers.

� Chloroplasts perform photosynthesis.

The membrane surrounding each organelle does two es-sential things: First, it keeps the organelle’s molecules awayfrom other molecules in the cell with which they might reactinappropriately. Second, it acts as a traffic regulator, lettingimportant raw materials into the organelle and releasing itsproducts to the cytoplasm. The evolution of compartmental-ization was an important development in the ability of eu-karyotic cells to specialize, forming the organs and tissues ofa complex body.

Organelles can be studied by microscopy or isolated for chemical analysisCell organelles were first detected by light and electron mi-croscopy. The use of stains targeted to specific macromole-cules has allowed cell biologists to determine the chemicalcompositions of organelles. (See Figure 4.21, in which a sin-gle cell is stained for three different proteins.)

Besides microscopy, another way to look at cells is to takethem apart. Cell fractionation begins with the destruction ofthe cell membrane. This allows the cytoplasmic components

Outside of cell

Inside of cell

Peptidoglycan

Outer membrane

Plasmamembrane

Bacterial flagellum

FilamentHook

(b) (c)(a)

The flagellum is rotated by a complex protein “motor” secured in the plasma membrane.

Bacterial flagella rotate for locomotion.

Hairlike pili help this bacterium adhere to other cells.

Flagellum

500 nm 100 nm

4.6 Prokaryotic Projections Surface projections such as bacterialflagella (a) and pili (b) contribute to the movement, adhesion, andcomplexity of prokaryotic cells. (c) Complex protein ring structuresanchored in the bacterial cell membranes form a motor unit thatrotates the flagellum and propels the cell.

68 CHAPTER FOUR

Cytoskeleton

Mitochondrion

Golgiapparatus

Mitochondria are the cell’s power plants.

Centrioles

Plasma membrane

Nucleus

Rough endoplasmicreticulum

Smooth endoplasmicreticulum

Peroxisome

Ribosomes(bound to RER)

NucleolusNucleolusNucleolus

AN ANIMAL CELL

Ribosomes

The rough endoplasmic reticulum is the site of much protein synthesis.

The plasma membrane separates the cell from its environment and regulates traffic of materials into and out of the cell.

Centrioles are associated with nuclear division.

Nucleolus

The nucleus is the site of most cellular DNA which, with associated proteins, comprises chromatin.

A cytoskeleton composed of microtubules and microfilaments supports the cell and is involved in cell and organelle movement.

Outside of cell

Inside of cell

1.5 µm 0.8 µm

25 nm

0.5 µm

30 nm0.1 µm

CELLS: THE BASIC UNITS OF LIFE 69

Vacuole

Ribosomes manufacture proteins.

Chloroplasts harvest the energy of sunlight to produce sugar.

ChloroplastPlasmamembrane

Smoothendoplasmicreticulum

Golgiapparatus

Mitochondrion

Nucleus

Nucleolus

Free ribosomes

Plasmodesmata

Roughendoplasmicreticulum

A PLANT CELL

Peroxisome Cell wall

The Golgi apparatus processes and packages proteins.

Peroxisomes break down toxic peroxides.

A cell wall supports the plant cell.

0.5 µm

25 nm

0.5 µm

0.75 µm 0.75 µm 1 µm

Proteins and other molecules are chemically modified in the smooth endoplasmic reticulum.

4.7 Eukaryotic Cells In electron micrographs, many plant cell organellesare nearly identical in form to those observed in animal cells. Cellular struc-tures unique to plant cells include the cell wall and the chloroplasts. Animalcells contain centrioles, which are not found in plant cells.

to flow out into a test tube. The various organelles can thenbe separated from one another on the basis of size or density(Figure 4.8). Biochemical analyses can then be done on theisolated organelles. Microscopy and cell fractionation havecomplemented each other, giving a complete picture of thestructure and function of each organelle.

Organelles that Process Information

Living things depend on accurate, appropriate information—internal signals, environmental cues, and stored instruc-tions—to respond appropriately to changing conditions andmaintain a constant internal environment. In the cell, infor-mation is stored in the sequence of nucleotides in DNA mol-

ecules. Most of the DNA in eukaryotic cells resides in the nu-cleus. Information is translated from the language of DNAinto the language of proteins at the ribosomes. This processis described in detail in Chapter 12.

The nucleus contains most of the cell’s DNAThe single nucleus is usually the largest organelle in a cell(Figure 4.9; see also Figure 4.7). The nucleus of most animalcells is approximately 5 µm in diameter—substantially largerthan most entire prokaryotic cells. The nucleus has severalroles in the cell:

� The nucleus is the site of DNA duplication.� The nucleus is the site of genetic control of the cell’s

activities.� A region within the nucleus, the nucleolus, begins the

assembly of ribosomes from specific proteins and RNA.

The nucleus is surrounded by two membranes, which to-gether form the nuclear envelope. The two membranes ofthe nuclear envelope are separated by 10–20 nm and are per-forated by nuclear pores approximately 9 nm in diameter,which connect the interior of the nucleus with the cytoplasm.At these pores, the outer membrane of the nuclear envelopeis continuous with the inner membrane. Each pore is sur-rounded by a pore complex made up of eight large proteingranules arranged in an octagon where the inner and outermembranes merge (see Figure 4.9). RNA and proteins passthrough these pores to enter or leave the nucleus.

At certain sites, the outer membrane of the nuclear enve-lope folds outward into the cytoplasm and is continuouswith the membrane of another organelle, the endoplasmicreticulum (discussed later in this chapter).

Inside the nucleus, DNA combines with proteins to forma fibrous complex called chromatin. Chromatin consists ofexceedingly long, thin, entangled threads. Prior to cell divi-sion, the chromatin aggregates to form discrete, readily visi-ble structures called chromosomes (Figure 4.10).

Surrounding the chromatin are water and dissolved sub-stances collectively referred to as the nucleoplasm. Withinthe nucleoplasm, a network of apparently structural proteinscalled the nuclear matrix organizes the chromatin. At the pe-riphery of the nucleus, the chromatin is attached to a proteinmeshwork, called the nuclear lamina, which is formed by thepolymerization of proteins called lamins into filaments. Thenuclear lamina maintains the shape of the nucleus by its at-tachment to both the chromatin and the nuclear envelope.

During most of a cell’s life cycle, the nuclear envelope is astable structure. When the cell divides, however, the nuclearenvelope fragments into pieces of membrane with attachedpore complexes. The envelope re-forms when distribution ofthe duplicated DNA to the daughter cells is completed.

70 CHAPTER FOUR

A piece of tissue is homogenized by physically grinding it.

1

The cell homogenate contains large and small organelles.

2

A centrifuge is used to separate the organelles based on size and density.

3

The heaviest organelles can be removed and the remaining suspension re-centrifuged until the next heaviest organelles reach the bottom of the tube.

4

RESEARCH METHOD

Golgi

Mitochondria

Nuclei

4.8 Cell Fractionation The organelles of cells can be separatedfrom one another after cells are broken open and centrifuged.

CELLS: THE BASIC UNITS OF LIFE 71

Inside of cell

Inside of nucleus

Outer membrane

Inner membrane

Nucleoplasm

Nucleolus

Nucleolus Chromatin

Nuclearlamina

Nuclearenvelope

Nuclearpore

The nuclear envelope is continuous with the endoplasmic reticulum.

1 µm

0.25 µm

Proteinfibrils

Nuclear“cage”

The nuclear lamina is a network of filaments just inside the nuclear envelope. It interacts with chromatin and helps support the envelope to which it is attached.

20 nm

Nuclear envelope

An octagon of protein complexes surrounds each nuclear pore. Protein fibrils on the nuclear side form a cagelike structure.

Dense chromatin near the nuclear envelope is attached to the nuclear lamina.

Diffuse chromatin is in the nucleoplasm.

(a) (b)

0.5 µm1 µm

4.9 The Nucleus Is Enclosed by a Double Membrane The double-membraned nuclearenvelope, nucleolus, nuclear lamina, and nuclear pores are common features of all cellnuclei. The pores are the gateways through which proteins from the cytoplasm enter thenucleus and genetic material (mRNA) from the nucleus enters the cytoplasm.

4.10 Chromatin and Chromosomes(a) When a cell is not dividing, the nuclearDNA is aggregated with proteins to formchromatin, which is dispersed throughoutthe nucleus. (b) The chromatin in a divid-ing cell is packed into dense bodies calledchromosomes.

Ribosomes are the sites of protein synthesisIn prokaryotic cells, ribosomes float freely in the cytoplasm.In eukaryotic cells they occur in two places: in the cytoplasm,where they may be free or attached to the surface of theendoplasmic reticulum (described in the next section); andinside the mitochondria and chloroplasts, where energy isprocessed. In each of these locations, the ribosomes are thesites where proteins are synthesized under the direction ofnucleic acids. Although they seem small in comparison to thecell in which they are contained, ribosomes are huge ma-chines made up of several dozen kinds of molecules.

The ribosomes of prokaryotes and eukaryotes are similarin that both consist of two different-sized subunits. Eukary-otic ribosomes are somewhat larger, but the structure ofprokaryotic ribosomes is better understood. Chemically, ri-bosomes consist of a special type of RNA, called ribosomalRNA (rRNA), to which more than 50 different protein mole-cules are noncovalently bound.

The Endomembrane System

Much of the volume of some eukaryotic cells is taken up byan extensive endomembrane system. This system includestwo main components, the endoplasmic reticulum and theGolgi apparatus. Continuities between the nuclear envelopeand the endomembrane system are visible under the electron

microscope. Tiny, membrane-surrounded droplets calledvesicles appear to shuttle between the various componentsof the endomembrane system. This system has various struc-tures, but all of them are essentially compartments, closed offby their membranes from the cytoplasm.

In this section, we will examine the functional significanceof these compartments, and we will see how materials syn-thesized in one organelle, the endoplasmic reticulum, aretransferred to another organelle, the Golgi apparatus, for fur-ther processing, storage, or transport. We will also describethe role of the lysosome in cellular digestion.

The endoplasmic reticulum is a complex factoryElectron micrographs reveal a network of interconnectedmembranes branching throughout the cytoplasm of a eu-karyotic cell, forming tubes and flattened sacs. These mem-branes are collectively called the endoplasmic reticulum, orER. The interior compartment of the ER, referred to as the lu-men, is separate and distinct from the surrounding cytoplasm(Figure 4.11). The ER can enclose up to 10 percent of the in-terior volume of the cell, and its foldings result in a surfacearea many times greater than that of the plasma membrane.

Parts of the ER are studded with ribosomes, which aretemporarily attached to the outer faces of its flattened sacs.Because of their appearance under the electron microscope,

72 CHAPTER FOUR

Rough ER

Smooth ER

Rough ER

Smooth ER

Ribosomes of the rough endoplasmic reticulum are sites for protein synthesis. They produce its rough appearance.

Smooth endoplasmic reticulum is a site for lipid synthesis and chemical modification of proteins.

Lumen

0.5 µm

4.11 The Endoplasmic Reticulum The transmission electron micrograph on theleft shows a two-dimensional slice through the three-dimensional structures depict-ed in the drawing. In normal living cells, membranes never have open ends; theydefine closed compartments set off from the surrounding cytoplasm.

these regions are called rough endoplasmic reticulum, orRER. RER has two roles:

� As a compartment, it segregates certain newly synthesizedproteins away from the cytoplasm and transports them toother locations in the cell.

� While inside the RER, proteins can be chemically modifiedso as to alter their function and eventual destination.

The attached ribosomes are sites for the synthesis of proteinsthat function outside the cytosol—that is, proteins that are tobe exported from the cell, incorporated into membranes, ormoved into the organelles of the endomembrane system.These proteins enter the lumen of the ER as they are synthe-sized. Once in the lumen of the ER, these proteins undergoseveral changes, including the formation of disulfide bridgesand folding into their tertiary structures (see Figure 3.4).

Proteins gain carbohydrate groups in the RER, thus be-coming glycoproteins. In the case of proteins directed to thelysosomes, the carbohydrate groups are part of an “address-ing” system that ensures that the right proteins are directedto the organelle.

Smooth endoplasmic reticulum or SER is more tubular(less like flattened sacs) and lacks ribosomes (see Figure 4.11).Within the lumen of the SER, proteins that have been syn-thesized on the RER are chemically modified. In addition, theSER has three other important roles:

� It is responsible for chemically modifying small moleculestaken in by the cell. This is especially true for drugs andpesticides.

� It is the site for the hydrolysis of glycogen in animal cells.� It is the site for the synthesis of lipids and steroids.

Cells that synthesize a lot of protein for export are usuallypacked with endoplasmic reticulum. Examples include glan-dular cells that secrete digestive enzymes and plasma cellsthat secrete antibodies. In contrast, cells that carry out lessprotein synthesis (such as storage cells) contain less ER. Livercells, which modify molecules that enter the body from thedigestive system, have abundant smooth ER.

The Golgi apparatus stores, modifies,and packages proteinsThe exact appearance of the Golgi apparatus (named for itsdiscoverer, Camillo Golgi) varies from species to species, butit always consists of flattened membranous sacs called cis-ternae and small membrane-enclosed vesicles. The cisternaeappear to be lying together like a stack of saucers (Figure4.12). The entire apparatus is about 1 µm long.

The Golgi apparatus has several roles:

� It receives proteins from the ER and may further modifythem.

� It concentrates, packages, and sorts proteins before theyare sent to their cellular or extracellular destinations.

� It is where some polysaccharides for the plant cell wallare synthesized.

CELLS: THE BASIC UNITS OF LIFE 73

Protein-containing vesicles from the endoplasmic reticulum transfer substances to the cis region of the Golgi apparatus.

1

The Golgi chemically modifies proteins in its lumen…

2

…and “targets” them to the correct addresses.

3

Rough endoplasmicreticulum

Golgiapparatuscis region

trans region

Cisternae

Proteins for usewithin the cell Proteins for use

outside the cell

Plasmamembrane

Inside of cell

Outside of cell

Flow ofmaterial

4.12 The Golgi ApparatusThe Golgi apparatus modifies proteins from the ERand “targets” them to the correct addresses withinor outside the cell.

In the cells of plants, protists, fungi, and many invertebrate an-imals, the stacks of cisternae are individual units scatteredthroughout the cytoplasm. In vertebrate cells, a few such stacksusually form a larger, single, more complex Golgi apparatus.

The Golgi apparatus appears to have three functionally dis-tinct parts: a bottom, a middle, and a top. The bottom cisternae,constituting the cis region of the Golgi apparatus, lie nearest tothe nucleus or a patch of RER (see Figure 4.12). The top cister-nae, constituting the trans region, lie closest to the surface of thecell. The cisternae in the middle make up the medial region ofthe complex. These three parts of the Golgi apparatus containdifferent enzymes and perform different functions.

The Golgi apparatus receives proteins from the ER, pack-ages them, and sends them on their way. Since there is oftenno direct membrane continuity between ER and Golgi appa-ratus, how does a protein get from one organelle to the other?The protein could simply leave the ER, travel across thecytoplasm, and enter the Golgi apparatus. But that wouldexpose the protein to interactions with other molecules inthe cytoplasm. On the other hand, segregation from thecytoplasm could be maintained if a piece of the ER could“bud off,” forming a vesicle that contains the protein—and that is exactly what happens. The protein makes thepassage from ER to Golgi apparatus safely enclosed in thevesicle. Once it arrives, the vesicle fuses with the mem-brane of the Golgi apparatus, releasing its cargo.

Vesicles form from the rough ER, move through thecytoplasm, and fuse with the cis region of the Golgi ap-paratus, releasing their contents into the lumen. Thevesicles may not have far to go: If living cells are stainedspecifically for ER and Golgi apparatus, the Golgi ap-paratus can be seen moving rapidly along the ER, pos-sibly picking up vesicles as they go. Other small vesiclesmay move between the cisternae, transporting proteins,and it appears that some proteins move from one cis-terna to the next by tiny channels. Vesicles budding offfrom the trans region carry their contents away from thecomplex (see Figure 4.12).

Lysosomes contain digestive enzymesOriginating in part from the Golgi apparatus are or-ganelles called lysosomes. They contain digestive en-zymes, and they are the sites where macromolecules—proteins, polysaccharides, nucleic acids, and lipids—arehydrolyzed into their monomers (see Figure 3.3). Lyso-somes are about 1 µm in diameter, are surrounded by asingle membrane, and have a densely staining, feature-less interior (Figure 4.13). There may be dozens of lyso-somes in a cell, depending on its needs.

Lysosomes are sites for the breakdown of food andforeign objects taken up by the cell. These materials get

into the cell by a process called phagocytosis (phago-, “eat-ing”; cytosis, “cellular”), in which a pocket forms in theplasma membrane and eventually deepens and encloses ma-terial from outside the cell. This pocket becomes a small vesi-cle that breaks free of the plasma membrane to move into thecytoplasm as a phagosome containing food or other material(see Figure 4.13). The phagosome fuses with a primary lyso-some, forming a secondary lysosome where digestion occurs.

The effect of this fusion is rather like releasing hungryfoxes into a chicken coop: The enzymes in the secondarylysosome quickly hydrolyze the food particles. These reac-tions are enhanced by the mild acidity of the lysosome’s in-terior, where the pH is lower than in the surrounding cyto-plasm. The products of digestion exit through the membraneof the lysosome, providing fuel molecules and raw materialsfor other cell processes. The “used” secondary lysosome, now

74 CHAPTER FOUR

Golgiapparatus

Plasmamembrane

Inside of cell

Outside of cell

The lysosome fuses with a phagosome.

2

Small molecules generated by digestion diffuse into the cytoplasm.

3

Undigested materials are released when the digestion vesicle fuses with the plasma membrane.

4

The primary lysosome is generated by the Golgi.

1

Primarylysosome

Secondarylysosome

Phagosome

Products ofdigestion

Food particlestaken in byphagocytosis

4.13 Lysosomes Isolate Digestive Enzymes from the CytoplasmLysosomes are sites for the hydrolysis of material taken into the cellby phagocytosis.

containing undigested particles, then moves to the plasmamembrane, fuses with it, and releases the undigested con-tents to the environment.

Lysosomes are also where the cell digests its own materialin a process called autophagy. Autophagy is an ongoingprocess in which organelles such as mitochondria are en-gulfed by lysosomes and hydrolyzed to monomers, whichpass out of the lysosome through its membrane into the cy-toplasm for reuse.

The importance of lysosome function is indicated by agroup of human diseases called lysosomal storage diseases. If acell lacks the ability to hydrolyze one or more macromole-cules, these substances pile up in lysosomes, with harmfulconsequences. An example is Tay-Sachs disease, in which alipid accumulates in the lysosomes of brain cells, resulting indeath in early childhood.

Plant cells do not appear to contain lysosomes, but thecentral vacuole of a plant cell (which we will describe below)may function in an equivalent capacity because it, like lyso-somes, contains many digestive enzymes.

Organelles that Process Energy

A cell uses energy to synthesize cell-specific materials that itcan use for activities such as growth, reproduction, andmovement. Energy is transformed from one form to anotherin mitochondria (found in all eukaryotic cells) and in chloro-plasts (found in eukaryotic cells that harvest energy fromsunlight). In contrast, energy transformations in prokaryoticcells are associated with enzymes attached to the inner sur-face of the plasma membrane or extensions of the plasmamembrane that protrude into the cytoplasm.

Mitochondria are energy transformersIn eukaryotic cells, the breakdown of fuel molecules such asglucose begins in the cytosol. The molecules that result fromthis partial degradation enter the mitochondria (singular, mi-tochondrion), whose primary function is to convert the po-tential chemical energy of those fuel molecules into a formthat the cell can use: the energy-rich molecule ATP (adeno-sine triphosphate). The production of ATP in the mitochon-dria using fuel molecules and molecular oxygen (O2) is calledcellular respiration.

Typical mitochondria are small—somewhat less than 1.5µm in diameter and 2–8 µm in length—about the size ofmany bacteria. The number of mitochondria per cell rangesfrom one contorted giant in some unicellular protists to a fewhundred thousand in large egg cells. An average human livercell contains more than a thousand mitochondria. Cells thatrequire the most chemical energy tend to have the most mi-tochondria per unit of volume.

Mitochondria have two membranes. The outer membraneis smooth and protective, and it offers little resistance to themovement of substances into and out of the mitochondrion.Immediately inside the outer membrane is an inner membrane,which folds inward in many places, giving it a much greatersurface area than that of the outer membrane (Figure 4.14).These folds tend to be quite regular, giving rise to shelflikestructures called cristae.

The inner mitochondrial membrane contains many largeprotein molecules that participate in cellular respiration. Theinner membrane exerts much more control over what entersand leaves the mitochondrion than does the outer mem-brane. The region enclosed by the inner membrane is referredto as the mitochondrial matrix. In addition to many proteins,the matrix contains some ribosomes and DNA that are usedto make some of the proteins needed for cellular respiration.

CELLS: THE BASIC UNITS OF LIFE 75

The inner membrane is the primary barrier between the cytosol and mitochondrial enzymes.

The matrix contains ribosomes, DNA, and several of the enzymes used for cellular respiration.

The cristae contain key molecules for the generation of ATP from fuel molecules.

Matrix Cristae Innermembrane

Outermembrane

0.6 µm

4.14 A Mitochondrion Converts Energy from Fuel Molecules intoATP The electron micrograph is a two-dimensional slice through athree-dimensional organelle. As the drawing emphasizes, the cristaeare extensions of the inner mitochondrial membrane.

In Chapter 7 we will see how the different parts of the mi-tochondrion work together in cellular respiration.

Plastids photosynthesize or store materialsOne class of organelles—the plastids—is produced only inplants and certain protists. There are several types of plas-tids, with different functions.

CHLOROPLASTS. Chloroplasts contain the green pigmentchlorophyll and are the sites of photosynthesis (Figure4.15). In photosynthesis, light energy is converted into thechemical energy of bonds between atoms. The moleculesformed in photosynthesis provide food for the photosyn-thetic organisms, as well as for other organisms that eatthem. Directly or indirectly, photosynthesis is the energysource for most of the living world.

Chloroplasts are variable in size and shape (Figure 4.16).Like a mitochondrion, a chloroplast is surrounded by twomembranes. In addition, there is a series of internal mem-branes whose structure and arrangement vary from onegroup of photosynthetic organisms to another. Here we con-centrate on the chloroplasts of the flowering plants. Eventhese chloroplasts show some variation, but the patternshown in Figure 4.15 is typical.

The internal membranes of chloroplasts look like stacksof flat, hollow pita bread. These stacks, called grana (singu-lar, granum), consist of a series of flat, closely packed, circu-lar compartments called thylakoids. In addition to phos-pholipids and proteins, the membranes of the thylakoids

contain chlorophyll and other pigments that harvest light forphotosynthesis. The thylakoids of one granum may be con-nected to those of other grana, making the interior of thechloroplast a highly developed network of membranes,much like the ER.

The fluid in which the grana are suspended is thestroma. Like the mitochondrial matrix, the chloroplaststroma contains ribosomes and DNA, which are used tosynthesize some, but not all, of the proteins that make upthe chloroplast.

Animal cells do not produce chloroplasts, but some docontain functional chloroplasts. These are either taken upas free chloroplasts derived from the partial digestion ofgreen plants or contained within unicellular algae that livewithin the animal’s tissues. The green color of some coralsand sea anemones results from the chloroplasts in algaethat live within those animals (Figure 4.16c). The animalsderive some of their nutrition from the photosynthesis thattheir chloroplast-containing “guests” carry out. Such an in-timate relationship between two different organisms iscalled symbiosis.

OTHER TYPES OF PLASTIDS. Other types of plastids also storepigments or polysaccharides:

� Chromoplasts contain red, orange, and/or yellow pigmentsand give color to plant organs such as flowers (Figure4.17a). The chromoplasts have no known chemical func-

76 CHAPTER FOUR

Stroma

Thylakoid

Double membrane

Innermembrane

Outermembrane

Granum(stack ofthylakoids)

Thylakoid membranes are siteswhere light energy is harvested by the green pigment chlorophylland converted into ATP.

ATP is used in converting CO2 to glucose in the stroma, the area outside the thylakoid membranes.

0.7 µm

4.15 The Chloroplast: The Organelle That Feeds the World Theelectron micrograph shows a chloroplast from a leaf of corn.Chloroplasts are large compared with mitochondria and contain anextensive network of photosynthetic thylakoid membranes.

CELLS: THE BASIC UNITS OF LIFE 77

5 µm 1 µm

Starch grains

Leucoplast

(a) (b)

tion in the cell, but the colors they give to some petals andfruits probably encourage animals to visit flowers andthus aid in pollination, or to eat fruits and thus aid in seeddispersal. (On the other hand, carrot roots gain no appar-ent advantage from being orange.)

� Leucoplasts are storage depots for starch and fats (Figure4.17b).

Endosymbiosis may explain the origin of mitochondria and chloroplastsAlthough chloroplasts and mitochondria are about the sizeof prokaryotic cells and have the genetic material and pro-tein synthesis machinery needed to make some of their owncomponents, they are not independent of control by the nu-cleus. The vast majority of their proteins are encoded by nu-clear DNA, made in the cytoplasm, and imported into the or-ganelle. Observations of these organelles have led to theproposal that they originated by endosymbiosis—that is, thatthey were once independent prokaryotic organisms.

(a) (b) (c)

The chloroplasts in these single-celled green algae have assembled into spirals.

Chloroplasts Leaf cell

75 µm 250 µmChloroplast-filled green algae live in the tissues of this sea anemone.

4.16 Being Green (a) In green plants, chloroplasts are concentrat-ed in the leaf cells. (b) Green algae are photosynthetic and filled withchloroplasts. (c) No animal species produces its own chloroplasts, butin this symbiotic arrangement, unicellular green algae nourish a seaanemone.

4.17 Chromoplasts and Leucoplasts (a) Colorful pig-ments stored in the chromoplasts of flowers like this bego-nia may help attract pollinating insects. (b) Leucoplasts inthe cells of a potato are filled with white starch grains.

About 2 billion years ago, only prokaryotes inhabitedEarth. Some of them absorbed their food directly from theenvironment. Others were photosynthetic. Still others fed onsmaller prokaryotes by engulfing them (Figure 4.18).

Suppose that a small, photosynthetic prokaryote was in-gested by a larger one, but was not digested. Instead, itsomehow survived, trapped within a vesicle in the cyto-plasm of the larger cell. The smaller, ingested prokaryote di-vided at about the same rate as the larger one, so successivegenerations of the larger cell also contained the offspring ofthe smaller one. This phenomenon, called endosymbiosis(endo-, “within”; symbiosis, “living together”), exists today,as in the case of the algae that live within sea anemones (seeFigure 4.16c).

According to this scenario, endosymbiosis provided ben-efits for both partners: The larger cell obtained the photo-synthetic products from the smaller cell, and the smaller cellwas protected by the larger one. Over evolutionary time, thesmaller cell gradually lost much of its DNA to the nucleus ofthe larger cell, resulting in the modern chloroplast.

Much circumstantial evidence favors the endosymbiosistheory:

� On an evolutionary time scale of millions of years, there isevidence for DNA moving between organelles in the cell.

� There are many biochemical similarities between chloro-plasts and modern photosynthetic bacteria.

� DNA sequencing shows strong similarities betweenmodern chloroplast DNA and that of a photosyntheticprokaryote.

� The double membrane that encloses mitochondria andchloroplasts could have arisen through endosymbiosis.The outer membrane may have come from the engulfingcell’s plasma membrane and the inner membrane fromthe engulfed cell’s plasma membrane.

Similar evidence and arguments also support the propositionthat mitochondria are the descendants of respiring prokary-

otes engulfed by larger prokaryotes. The benefit of this en-dosymbiotic relationship might have been the capacity of theengulfed prokaryote to detoxify molecular oxygen (O2),which was increasing in Earth’s atmosphere as a result ofphotosynthesis.

Other Organelles

Eukaryotic cells have several other organelles that are sur-rounded by a single membrane.

Peroxisomes house specialized chemical reactionsPeroxisomes are organelles that collect the toxic peroxides(such as hydrogen peroxide, H2O2) that are the unavoidableby-products of chemical reactions. These peroxides can besafely broken down inside the peroxisomes without mixingwith other parts of the cell. Peroxisomes are small organelles,about 0.2 to 1.7 µm in diameter. They have a single mem-brane and a granular interior containing specialized enzymes(Figure 4.19). Peroxisomes are found at one time or anotherin at least some of the cells of almost every eukaryoticspecies.

A structurally similar organelle, the glyoxysome, is foundonly in plants. Glyoxysomes, which are most prominent inyoung plants, are the sites where stored lipids are convertedinto carbohydrates for transport to growing cells.

78 CHAPTER FOUR

Membrane ofsmaller cell

Doublemembrane

Membrane oflarger cell Double membranes may have originated when

one cell engulfed another.

4.18 The Endosymbiosis Theory Chloroplasts and mitochondriamay be descended from a small prokaryote that was engulfed byanother, larger prokaryote.

0.25 µm

Peroxisome

EnzymeEnzyme

4.19 A Peroxisome A diamond-shaped crystal, composed of anenzyme, almost entirely fills this rounded peroxisome in a leaf cell.The enzyme catalyzes one of the reactions that breaks down toxicperoxides in the peroxisome.

CELLS: THE BASIC UNITS OF LIFE 79

Vacuoles are filled with water and soluble substancesMany eukaryotic cells, but particularly those of plants andprotists, contain membrane-enclosed vacuoles filled withaqueous solutions containing many dissolved substances(Figure 4.20). Plant vacuoles have several functions:

� Storage: Plant cells produce a number of toxic by-prod-ucts and waste materials, many of which are simplystored within vacuoles. And since they are poisonous ordistasteful, these stored materials deter some animalsfrom eating the plants. Thus these stored wastes maycontribute to plant survival.

� Structure: In many plant cells, enormous vacuoles takeup more than 90 percent of the cell volume and grow asthe cell grows. The dissolved substances in the vacuole,working together with the vacuolar membrane, providethe turgor, or stiffness, of the cell, which in turn providessupport for the structure of nonwoody plants. The pres-ence of the dissolved substances causes water to enterthe vacuole, making it swell like a balloon. Plant cellshave a rigid cell wall, which resists the swelling of thevacuole, providing strength in the process.

� Reproduction: Some pigments (especially blue and pinkones) in petals and fruits are contained in vacuoles.These pigments—the anthocyanins—are visual cues thathelp attract the animals that assist in pollination or seeddispersal.

� Digestion: In some plants, the vacuoles contain enzymesthat hydrolyze seed proteins into monomers that a devel-oping plant embryo can use as food.

Food vacuoles are found in some simple and evolutionarilyancient groups of organisms—single-celled protists and sim-ple multicellular organisms such as sponges, for example. Inthese organisms, the cells engulf food particles by phagocyto-sis, generating a food vacuole. Fusion of this vacuole with alysosome results in digestion, and small molecules leave thevacuole and enter the cytoplasm for use or distribution toother organelles.

Contractile vacuoles are found in many freshwater protists.Their function is to get rid of the excess water that rushes intothe cell because of the imbalance in salt concentration be-tween the relatively salty interior of the cell and its freshwa-ter environment. The contractile vacuole enlarges as waterenters, then abruptly contracts, forcing the water out of thecell through a special pore structure.

The Cytoskeleton

In addition to its many membrane-enclosed organelles, theeukaryotic cytoplasm contains a set of long, thin fibers calledthe cytoskeleton. The cytoskeleton fills at least three impor-tant roles:

� It maintains cell shape and support.� It provides for various types of cellular movement.� Some of its fibers act as tracks or supports for motor

proteins, which help move things within the cell.

In the discussion that follows, we’ll look at three componentsof the cytoskeleton: microfilaments, intermediate filaments,and microtubules (Figure 4.21).

Microfilaments function in support and movementMicrofilaments can exist as single filaments, in bundles, orin networks. They are about 7 nm in diameter and severalmicrometers long. They are assembled from actin, a proteinthat exists in several forms and has many functions amongmembers of the animal phyla. The actin found in microfila-ments (which are also known as actin filaments) is extensivelyfolded and has distinct “head” and “tail” sites. These sites in-teract with other actin molecules to form long, double heli-cal chains (see Figure 4.21). The polymerization of actin intomicrofilaments is reversible, and they can disappear fromcells, breaking down into units of free actin.

Microfilaments have two major roles:

� They help the entire cell or parts of the cell to move.� They stabilize cell shape.

In muscle cells, actin fibers are associated with another pro-tein, myosin, and the interactions of these two proteins ac-count for the contraction of muscles. In non-muscle cells, actinfibers are associated with localized changes of shape in the cell.

Vacuole

2 µm

4.20 Vacuoles in Plant Cells Are Usually Large The large centralvacuole in this cell is typical of mature plant cells. Smaller vacuolesare visible toward each end of the cell.

For example, microfilaments are involved in a flowing move-ment of the cytoplasm called cytoplasmic streaming and in the“pinching” contractions that divide an animal cell into twodaughter cells. Microfilaments are also involved in the forma-tion of cellular extensions called pseudopodia (pseudo-, “false;”podia, “feet”) that enable some cells to move.

In some cell types, microfilaments form a meshwork justinside the plasma membrane. Actin-binding proteins thencross-link the microtubules to form a rigid structure that sup-ports the cell. For example, microfilaments support the tinymicrovilli that line the intestine, giving it a larger surface areathrough which to absorb nutrients (Figure 4.22).

Intermediate filaments are tough supporting elements

Intermediate filaments (see Figure 4.21) are found only inmulticellular organisms. In contrast to the other componentsof the cytoskeleton, there are at least 50 different kinds of in-termediate filaments, often specific to a few cell types. Theygenerally fall into six molecular classes, based on amino acidsequence, and share the same general structure, being com-posed of fibrous proteins of the keratin family, similar to theprotein that makes up hair and fingernails. In cells, these pro-teins are organized into tough, ropelike assemblages 8 to 12nm in diameter.

80 CHAPTER FOUR

25 nm

Tubulindimer

Fibrous subunit β-Tubulinmonomer

β α

7 nm

α-Tubulinmonomer

Actin monomer

Plasma membrane

Mitochondrion

Plasmamembrane

Ribosomes

Intermediate filament

Microfilaments

Microtubule

Rough endoplasmicreticulum

8–12 nm

Microfilaments are made up of strands of the protein actin and often interact with strands of other proteins. They change cell shape and drive cellular motion, including contraction, cytoplasmic streaming, and the “pinched“ shape changes that occur during cell division. Microfilaments and myosin strands together drive muscle action.

Intermediate filaments are made up of fibrous proteins organized into tough,ropelike assemblages that stabilize a cell'sstructure and help maintain its shape.Some intermediate filaments help to holdneighboring cells together. Others make up the nuclear lamina.

Microtubules are long, hollow cylindersmade up of many molecules of the proteintubulin. Tubulin consists of two subunits,α-tubulin and β-tubulin. Microtubuleslengthen or shorten by adding or sub-tracting tubulin dimers. Microtubuleshortening moves chromosomes. Inter-actions between microtubules drive the movement of cells. Microtubules serveas “tracks“ for the movement of vesicles.

20 µm 10 µm 10 µm

End+– End

4.21 The Cytoskeleton Three highlyvisible and important structural compo-nents of the cytoskeleton are shown herein detail. These structures maintain andreinforce cell shape and contribute to cellmovement.

CELLS: THE BASIC UNITS OF LIFE 81

Intermediate filaments have two major structural functions:

� They stabilize cell structure.� They resist tension.

In some cells, intermediate filaments radiate from the nuclearenvelope and may maintain the positions of the nucleus andother organelles in the cell. The lamins of the nuclear laminaare intermediate filaments. Other kinds of intermediate fila-ments help hold a complex apparatus of microfilaments inplace in muscle cells. Still other kinds stabilize and help main-tain rigidity in surface tissues by connecting “spot welds”called desmosomes between adjacent cells (see Figure 5.6).

Microtubules are long and hollowMicrotubules are long, hollow, unbranched cylinders about25 nm in diameter and up to several micrometers long. Mi-crotubules have two roles in the cell:

� They form a rigid internal skeleton for some cells.� They act as a framework along which motor proteins can

move structures in the cell.

Microtubules are assembled from molecules of the proteintubulin. Tubulin is a dimer—a molecule made up of twomonomers. The polypeptide monomers that make up thisprotein are known as a-tubulin and b-tubulin. Thirteen chainsof tubulin dimers surround the central cavity of the micro-tubule (see Figure 4.21). The two ends of a microtubule aredifferent. One end is designated the plus (+) end, the otherthe minus (–) end.

Tubulin dimers can be added or subtracted, mainly at theplus end, lengthening or shortening the microtubule. This ca-

pacity to change length rapidly makes mi-crotubules dynamic structures. This dynamicproperty of microtubules is seen in animalcells, where they are often found in parts ofthe cell that are changing shape.

Many microtubules radiate from a re-gion of the cell called the microtubule organ-izing center. Tubule polymerization resultsin rigidity, and tubule depolymerizationleads to a collapse of this rigid structure.

In plants, microtubules help control thearrangement of the cellulose fibers of thecell wall. Electron micrographs of plantsfrequently show microtubules lying just in-side the plasma membrane of cells that are

forming or extending their cell walls. Experimental alterationof the orientation of these microtubules leads to a similarchange in the cell wall and a new shape for the cell.

In many cells, microtubules serve as tracks for motor pro-teins, specialized molecules that use energy to change theirshape and move. Motor proteins bond to and move along themicrotubules, carrying materials from one part of the cell toanother. Microtubules are also essential in distributing chro-mosomes to daughter cells during cell division. And they areintimately associated with movable cell appendages: the flagella and cilia.

Microtubules power cilia and flagellaMany eukaryotic cells possess flagella* or cilia, or both. Thesewhiplike organelles may push or pull the cell through itsaqueous environment, or they may move surrounding liquidover the surface of the cell (Figure 4.23a). Cilia and eukary-otic (but not prokaryotic) flagella are both assembled fromspecialized microtubules and have identical internal struc-tures, but they differ in their relative lengths and their pat-terns of beating:

� Flagella are longer than cilia and are usually foundsingly or in pairs. Waves of bending propagate from oneend of a flagellum to the other in snakelike undulation.

� Cilia are shorter than flagella and are usually present ingreat numbers. They beat stiffly in one direction andrecover flexibly in the other direction (like a swimmer’sarm), so that the recovery stroke does not undo the workof the power stroke.

Intermediate filaments

Plasmamembrane

A cap of proteins is attached to the end of microfilaments.

Actin microfilaments run the entire length and support each microvillus.

Cross-linking actin-binding proteins link microfilaments to each other and to the plasma membrane.

0.25 µm

4.22 Microfilaments for Support Microfilaments form the back-bone of the microvilli that increase the surface area of some cells,such as intestinal cells that absorb nutrients.

*Some prokaryotes have flagella, as we saw earlier, but prokaryotic fla-gella lack microtubules and dynein. The flagella of prokaryotes are nei-ther structurally nor evolutionarily related to those of eukaryotes. Theprokaryotic flagellum is assembled from a protein called flagellin, and ithas a much simpler structure and a smaller diameter than a singleeukaryotic microtubule. And whereas eukaryotic flagella beat in awavelike motion, prokaryotic flagella rotate (see Figure 4.6).

In cross section, a typical cilium or eukaryotic flagellum issurrounded by the plasma membrane and contains a “9 + 2”array of microtubules. As Figure 4.23c shows, nine fusedpairs of microtubules—called doublets—form an outer cylin-der, and one pair of unfused microtubules runs up the cen-ter. A spoke radiates from one microtubule of each doubletand connects the doublet to the center of the structure.

In the cytoplasm at the base of every eukaryotic flagellumor cilium is an organelle called a basal body. The nine mi-crotubule doublets extend into the basal body. In the basalbody, each doublet is accompanied by another microtubule,making nine sets of three microtubules. The central, unfusedmicrotubules do not extend into the basal body.

Centrioles are almost identical to the basal bodies of ciliaand flagella. Centrioles are found in all eukaryotes except theflowering plants, pine trees and their relatives, and some pro-tists. Under the light microscope, a centriole looks like asmall, featureless particle, but the electron microscope revealsthat it is made up of a precise bundle of microtubulesarranged as nine sets of three fused microtubules each. Cen-trioles lie in the microtubule organizing center in cells thatare about to divide. As you will see in Chapter 9, they are in-volved in the formation of the mitotic spindle, to which thechromosomes attach (see Figure 9.8).

Motor proteins move along microtubulesThe nine microtubule doublets of cilia and flagella are linkedby proteins. The motion of cilia and flagella results from the

sliding of the microtubules past each other. This sliding isdriven by a motor protein called dynein, which can undergochanges in its shape.

All motor proteins work by undergoing reversible shapechanges powered by energy from ATP. Dynein molecules at-tached to one microtubule doublet bind to a neighboringdoublet. As the dynein molecules change shape, they movethe microtubule past its neighbor (Figure 4.24a).

Dynein and another motor protein, kinesin, are responsi-ble for carrying protein-laden vesicles from one part of thecell to another. These motor proteins bind to a vesicle or otherorganelle, then “walk” it along a microtubule by changingtheir shape. Recall that microtubules have a plus end and aminus end. Dynein moves attached organelles toward theminus end, while kinesin moves them toward the plus end(Figure 4.24b).

Extracellular Structures

Although the plasma membrane is the functional barrier be-tween the inside and the outside of a cell, many structuresare produced by cells and secreted to the outside of theplasma membrane, where they play essential roles in pro-tecting, supporting, or attaching cells. Because they are out-side the plasma membrane, these structures are said to be ex-tracellular. The peptidoglycan cell wall of bacteria is such anextracellular structure. In eukaryotes, other extracellularstructures—the cell walls of plants and the extracellular ma-trices found between the cells of multicellular animals—playsimilar roles. Both of these structures are made up of a promi-nent fibrous macromolecule embedded in a jellylike medium.

82 CHAPTER FOUR

Motor protein(dynein)

Plasma membrane

”Linker“ protein(nexin)

CiliumThree cilia

Basal body

Radial spoke

Cross-section reveals the “9+2” pattern of microtubles, including nine pairs of fused microtubles…The beating of the cilia covering the

surface of this unicellular protist propels it through the water of its environment.

1

…and two unfused inner microtubules.

2

(b)(a) (c)

The basal body has nine fused microtuble triplets but no inner microtubles.

3

15 µm

0.25 µm4.23 Cilia are Made up of Microtubules (a) A ciliated protist.(b) Three cilia on a protist cell. (c) Cross section of a single cilium.

The plant cell wall consists largely of cellulose

The cell wall of plant cells is a semirigid structure outside theplasma membrane (Figure 4.25). It consists of cellulose fibersembedded in other complex polysaccharides and proteins.The cell wall has three major roles in plants:

� It provides support for the cell and limits its volume byremaining rigid.

� It acts as a barrier to infections by fungi and other organ-isms that can cause plant diseases.

� It contributes to plant form by growing as plant cellsexpand.

Because of their thick cell walls, plant cells viewed undera light microscope appear to be entirely isolated from eachother. But electron microscopy reveals that this is not the case.The cytoplasm of adjacent plant cells is connected by nu-merous plasma membrane-lined channels, called plasmodes-mata, that are about 20 to 40 nm in diameter and extendthrough the walls of adjoining cells (see Figure 15.19). Plas-modesmata permit the diffusion of water, ions, small mole-cules, and RNA and proteins between connected cells. Suchdiffusion ensures that the cells of a plant have uniform con-centrations of these substances.

Animal cells have elaborate extracellular matricesThe cells of multicellular animals lack the semirigid cell wallthat is characteristic of plant cells, but many animal cells aresurrounded by, or are in contact with, an extracellular ma-trix. This matrix is composed of fibrous proteins such as col-lagen (the most abundant protein in mammals) and glyco-

CELLS: THE BASIC UNITS OF LIFE 83

(a) Dynein

(b) Kinesin

(c)

Kinesin

Microtubuledoublet

Microtubuleof cytoskeleton

Vesicle or organelle

Direction of movement

End

End

Direction of movement

The motor protein kinesin attaches to organelles or vesicles and “walks” them along the microtubules of the cytoskeleton. The vesicle moves, while the microtubule is stationary.

–

–

+

+

End+

Dynein

Dynein is permanently attached to one microtubule and moves it with respect to a neighboring one.

– End

End

End

20 nm

Cell wallof cell 2

Interiorof cell 2

Interiorof cell 1

Cell wallof cell 1

1.5 µm

4.24 Motor Proteins Use Energy from ATP to Move Things(a) Dynein is responsible for flagellar movement. (b) Kinesin, likedynein, delivers vesicles to various parts of the cell. (c) This SEMshows a vesicle attached to a microtubule by a motor protein.

4.25 The Plant Cell Wall The semirigid cell wall provides supportfor plant cells.

proteins (Figure 4.26). These proteins, along with other sub-stances that are specific to certain body tissues, are secretedby cells that are present in or near the matrix. The functionsof the extracellular matrix are many:

� It holds cells together in tissues.� It contributes to the physical properties of cartilage, skin,

and other tissues.� It helps filter materials passing between different tissues.� It helps orient cell movements during embryonic devel-

opment and during tissue repair.� It plays a role in chemical signaling from one cell to

another.

In the human body, some tissues, such as those in thebrain, have very little extracellular matrix; other tissues, suchas bone and cartilage, have large amounts. Bone cells are em-bedded in an extracellular matrix that consists primarily ofcollagen and calcium phosphate. This matrix gives bone itsfamiliar rigidity. Epithelial cells, which line body cavities, lietogether as a sheet spread over a basal lamina, or basementmembrane, a form of extracellular matrix (see Figure 4.26).

Some extracellular matrices are made up, in part, of anenormous proteoglycan. A single molecule of this proteogly-can consists of many hundreds of polysaccharides covalentlyattached to about a hundred proteins, all of which are at-tached to one enormous polysaccharide. The molecularweight of this proteoglycan can exceed 100 million; the mol-ecule takes up as much space as an entire prokaryotic cell.

Chapter Summary

The Cell: The Basic Unit of Life� All cells come from preexisting cells and have certainprocesses, types of molecules, and structures in common.� The first cells may have arisen from aggregates of macro-molecules in bubbles. Review Figure 4.1� To maintain adequate exchanges with its environment, acell’s surface area must be large compared with its volume.Review Figures 4.2, 4.3. See Web/CD Activity 4.1� Cells can be visualized by various methods using micro-scopes. Review Figure 4.4. See Web/CD Activity 4.2� All cells are surrounded by a plasma membrane.

Prokaryotic Cells� All prokaryotic cells have a plasma membrane, a nucleoidregion with DNA, and a cytoplasm that contains ribosomes,water, and dissolved proteins and small molecules. ReviewFigure 4.5� Some prokaryotes have additional protective structures: cellwall, outer membrane, and capsule. Some prokaryotes containphotosynthetic membranes or mesosomes, and some have fla-gella or pili. Review Figure 4.6

Eukaryotic Cells� Like prokaryotic cells, eukaryotic cells have a plasma mem-brane, cytoplasm, and ribosomes. However, eukaryotic cells arelarger and contain many membrane-enclosed organelles.Review Figure 4.7. See Web/CD Tutorial 4.1� The membranes that envelop organelles in the eukaryotic cellare partial barriers, ensuring that the chemical composition ofthe interior of the organelle differs from that of the surroundingcytoplasm.� Organelles can be isolated by cell fractionation. ReviewFigure 4.8

84 CHAPTER FOUR

The fibrous protein collagen provides strength to the matrix.

The basal lamina is an extracellular matrix (ECM). Here it separates kidney cells from the blood vessel.

Proteoglycan

Collagen

The ECM is composed of a tangled complex of enormous molecules made of proteins and long polysaccharide chains.

Proteoglycans have long polysaccharide chains that provide a viscous medium for filtering.

Kidneycell

Bloodvessel

Kidneycell

Bloodvessel

20 nm

100 nm

4.26 An Extracellular Matrix Endothelial cells in the kidney secrete a basallamina, an extracellular matrix (ECM) that separates them from a nearby bloodvessel, and is also involved in filtering materials that pass between the kidneyand the blood.

CELLS: THE BASIC UNITS OF LIFE 85

Organelles that Process Information� The nucleus is usually the largest organelle in a cell. It is sur-rounded by a double membrane, the nuclear envelope, whichdisassembles during cell division. Within the nucleus, the nucle-olus is the source of the ribosomes found in the cytoplasm.Nuclear pores have a complex structure. Review Figure 4.9� The nucleus contains most of the cell’s DNA, which associ-ates with protein to form chromatin. Chromatin is diffusethroughout the nucleus until just before cell division, when itcondenses to form chromosomes. Review Figure 4.10

The Endomembrane System� The endomembrane system is made up of a series of inter-related compartments enclosed by membranes.� The rough endoplasmic reticulum has attached ribosomesthat synthesize proteins. The smooth endoplasmic reticulumlacks ribosomes and is associated with the synthesis of lipids.Review Figures 4.7, 4.11� The Golgi apparatus receives materials from the rough ER bymeans of vesicles that fuse with its cis region. Vesicles originat-ing from the trans region of the Golgi contain proteins targetedto different cellular locations. Some of these vesicles fuse withthe plasma membrane and release their contents outside thecell. Review Figures 4.7, 4.12. See Web/CD Tutorial 4.2� Lysosomes contain many digestive enzymes. Lysosomes fusewith the phagosomes produced by phagocytosis to form sec-ondary lysosomes, in which engulfed materials are digested.Undigested materials are secreted from the cell when the sec-ondary lysosome fuses with the plasma membrane. ReviewFigure 4.13. See Web/CD Activity 4.3

Organelles that Process Energy� Mitochondria are enclosed by an outer membrane and an innermembrane that folds inward to form cristae. Mitochondria containthe proteins needed for cellular respiration. Review Figure 4.14� The cells of photosynthetic eukaryotes contain chloroplasts.These organelles are enclosed by double membranes and con-tain an internal system of thylakoids organized as grana.Review Figures 4.7, 4.15� Thylakoids within chloroplasts contain the chlorophyll andproteins that harvest light energy for photosynthesis. � Both mitochondria and chloroplasts contain their own DNAand ribosomes and are capable of making some of their ownproteins.� The endosymbiosis theory of the evolutionary origin of mito-chondria and chloroplasts states that these organelles originatedwhen larger prokaryotes engulfed, but did not digest, smallerprokaryotes. Mutual benefits permitted this symbiotic relation-ship to be maintained, allowing the smaller cells to evolve intothe eukaryotic organelles observed today. Review Figure 4.18

Other Organelles � Peroxisomes and glyoxysomes contain special enzymes andcarry out specialized chemical reactions inside the cell. ReviewFigure 4.19� Vacuoles are prominent in many plant cells and consist of amembrane-enclosed compartment full of water and dissolvedsubstances. By taking in water, vacuoles enlarge and providethe pressure needed to stretch the cell wall and provide struc-tural support for the plant. Review Figure 4.20

The Cytoskeleton� The cytoskeleton within the cytoplasm of eukaryotic cellsprovides shape, strength, and movement. It consists of threeinteracting types of protein fibers. Review Figure 4.21

� Microfilaments consist of two chains of actin units thattogether form a double helix. Microfilaments strengthen cellu-lar structures and provide the movement in animal cell divi-sion, cytoplasmic streaming, and pseudopod extension. Micro-filaments may be found as individual fibers, bundles of fibers,or networks of fibers joined by linking proteins. ReviewFigures 4.21, 4.22� Intermediate filaments are formed of keratins and are organ-ized into tough, ropelike structures that hold organelles in placewithin the celland add strength to cell attachments in multicel-lular organisms. Review Figure 4.21� Microtubules are composed of dimers of the protein tubulin.They can lengthen and shorten by adding and losing tubulindimers. They are involved in the structure and function of ciliaand flagella, both of which have a characteristic “9 + 2” patternof microtubules. Review Figures 4.21, 4.23� The movements of cilia and flagella result from the bindingof the motor protein dynein to the microtubules. Dynein andanother motor protein, kinesin, also bind to microtubules tomove organelles through the cell. Review Figure 4.24� Centrioles, made up of triplets of microtubules, are involvedin the distribution of chromosomes during cell division.

Extracellular Structures� Materials external to the plasma membrane provide protec-tion, support, and attachment for cells in multicellular systems.� The cell walls of plants consist principally of cellulose. Theyare pierced by plasmodesmata that join the cytoplasm of adja-cent cells. Review Figure 4.25� In multicellular animals, the extracellular matrix consists ofdifferent kinds of proteins, including proteoglycans. In bone andcartilage, the protein collagen predominates. Review Figure 4.26

Self-Quiz1. Which is present in both prokaryotic cells and in eukaryotic

plant cells?a. Chloroplastsb. Cell wallsc. Nucleusd. Mitochondriae. Microtubules

2. The major factor limiting cell size is thea. concentration of water in the cytoplasm.b. need for energy.c. presence of membranous organelles.d. ratio of surface area to volume.e. composition of the plasma membrane.

3. Which statement about mitochondria is not true?a. Their inner membrane folds to form cristae.b. They are usually 1 µm or smaller in diameter.c. They are green because they contain chlorophyll.d. Energy-rich substances from the cytosol are oxidized in

them.e. Much ATP is synthesized in them.

4. Which statement about plastids is true?a. They are found in prokaryotes.b. They are surrounded by a single membrane.c. They are the sites of cellular respiration.d. They are found in fungi.e. They are of several types, with different functions.

5. If all the lysosomes within a cell suddenly ruptured, whatwould be the most likely result?a. The macromolecules in the cytosol would begin to break

down.b. More proteins would be made.c. The DNA within mitochondria would break down.d. The mitochondria and chloroplasts would divide.e. There would be no change in cell function.

6. The Golgi apparatusa. is found only in animals.b. is found in prokaryotes.c. is the appendage that moves a cell around in its

environment.d. is a site of rapid ATP production.e. packages and modifies proteins.

7. Which organelle is not surrounded by one or more membranes?a. Ribosomeb. Chloroplastc. Mitochondriond. Peroxisomee. Vacuole

8. The cytoskeleton consists ofa. cilia, flagella, and microfilaments.b. cilia, microtubules, and microfilaments.c. internal cell walls.d. microtubules, intermediate filaments, and microfilaments.e. calcified microtubules.

9. Microfilamentsa. are composed of polysaccharides.b. are composed of actin.

c. provide the motive force for cilia and flagella.d. make up the spindle that aids the movement of

chromosomes.e. maintain the position of the chloroplast in the cell.

10. Which statement about the plant cell wall is not true?a. Its principal chemical components are polysaccharides.b. It lies outside the plasma membrane.c. It provides support for the cell.d. It completely isolates adjacent cells from one another.e. It is semirigid.

For Discussion1. Which organelles and other structures are found in both plant

and animal cells? Which are found in plant but not animalcells? In animal but not plant cells? Discuss these differencesin relation to the activities of plants and animals.

2. Through how many membranes would a molecule have topass in going from the interior of a chloroplast to the interiorof a mitochondrion? From the interior of a lysosome to theoutside of a cell? From one ribosome to another?

3. How does the possession of double membranes by chloro-plasts and mitochondria relate to the endosymbiosis theory ofthe origins of these organelles? What other evidence supportsthe theory?

4. Compare the extracellular matrix of the animal cell with theplant cell wall with respect to composition of the fibrous andnonfibrous components, rigidity, and presence of cytoplasmic“bridges.”

5. Plastids and mitochondria may have arisen via endosymbio-sis. Propose a hypothesis for the origin of the cell nucleus.

86 CHAPTER FOUR