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Cells As Experimental ModelsThe evolution of present-day cells from a common ancestor has important implications for cell and molecular

biology as an experimental science. Because the fundamental properties of all cells have been conserved during

evolution, the basic principles learned from experiments performed with one type of cell are generally applicable to

other cells. On the other hand, because of the diversity of present-day cells, many kinds of experiments can be more

readily undertaken with one type of cell than with another. Several different kinds of cells and organisms are

commonly used as experimental models to study various aspects of cell and molecular biology. The features of some

of these cells that make them particularly advantageous as experimental models are discussed in the sections that

follow.

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E. coli

Because of their comparative simplicity,prokaryotic cells(bacteria) are ideal models for studying many

fundamental aspects of biochemistry and molecular biology. The most thoroughly studied species of bacteria

isE. coli, which has long been the favored organism for investigation of the basic mechanisms of molecular

genetics. Most of our present concepts of molecular biologyincluding our understanding ofDNAreplication,

thegenetic code,geneexpression, and protein synthesis

derive from studies of this humble bacterium.E. coli has been especially useful to molecular biologists because of both its relative simplicity and the ease with

which it can be propagated and studied in the laboratory. The genome ofE. coli, for example, consists of

approximately 4.6 million base pairs and encodes about 4000 differentproteins. The human genome is nearly a

thousand times more complex (approximately 3 billion base pairs) and encodes about 100,000 different proteins

(seeTable 1.2). The small size of theE. coli genome provides obvious advantages for genetic analysis, and the

sequence of the entireE. coli genome has been determined.

Molecular genetic experiments are further facilitated by the rapid growth ofE. coli under well-defined laboratory

conditions. Depending on the culture conditions,E. coli divide every 20 to 60 minutes. Moreover, a clonal

population ofE. coli, in which all cells are derived by division of a single cell of origin, can be readily isolated as a

colony grown on semisolid agar-containing medium (Figure 1.14). Because bacterial colonies containing as many as

108 cells can develop overnight, selecting genetic variants of anE. coli strainfor example, mutants that are

resistant to an antibiotic, such as penicillin

is easy and rapid. The ease with which such mutants can be selectedand analyzed was critical to the success of experiments that defined the basic principles of molecular genetics,

discussed in Chapter 3.

Figure 1.14

Bacterial colonies. Photograph of colonies ofE. coli growing on the surface of agar-containing medium. (A. M.

Siegelman/Visuals Unlimited.)

The nutrient mixtures in whichE. coli divide most rapidly include glucose, salts, and various organic compounds,

such as amino acids, vitamins, and nucleic acid precursors. However,E. coli can also grow in much simpler media

consisting only of salts, a source of nitrogen (such as ammonia), and a source of carbon and energy (such as

glucose). In such a medium, the bacteria grow a little more slowly (with a division time of about 40 minutes)because they must synthesize all their own amino acids, nucleotides, and other organic compounds. The ability

ofE. coli to carry out these biosynthetic reactions in simple defined media has made them extremely useful in

elucidating the biochemical pathways involved. Thus, the rapid growth and simple nutritional requirements

ofE.coli have greatly facilitated fundamental experiments in both molecular biology and biochemistry.

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Yeasts

http://www.ncbi.nlm.nih.gov/books/NBK9917/#ui-ncbiinpagenav-2http://www.ncbi.nlm.nih.gov/books/NBK9917/#ui-ncbiinpagenav-2http://www.ncbi.nlm.nih.gov/books/n/cooper/A2886/def-item/A3281/http://www.ncbi.nlm.nih.gov/books/n/cooper/A2886/def-item/A3281/http://www.ncbi.nlm.nih.gov/books/n/cooper/A2886/def-item/A3281/http://www.ncbi.nlm.nih.gov/books/n/cooper/A2886/def-item/A3010/http://www.ncbi.nlm.nih.gov/books/n/cooper/A2886/def-item/A3010/http://www.ncbi.nlm.nih.gov/books/n/cooper/A2886/def-item/A3010/http://www.ncbi.nlm.nih.gov/books/n/cooper/A2886/def-item/A3085/http://www.ncbi.nlm.nih.gov/books/n/cooper/A2886/def-item/A3085/http://www.ncbi.nlm.nih.gov/books/n/cooper/A2886/def-item/A3085/http://www.ncbi.nlm.nih.gov/books/n/cooper/A2886/def-item/A3080/http://www.ncbi.nlm.nih.gov/books/n/cooper/A2886/def-item/A3080/http://www.ncbi.nlm.nih.gov/books/n/cooper/A2886/def-item/A3080/http://www.ncbi.nlm.nih.gov/books/n/cooper/A2886/def-item/A3297/http://www.ncbi.nlm.nih.gov/books/n/cooper/A2886/def-item/A3297/http://www.ncbi.nlm.nih.gov/books/n/cooper/A2886/def-item/A3297/http://www.ncbi.nlm.nih.gov/books/n/cooper/A90/table/A106/?report=objectonlyhttp://www.ncbi.nlm.nih.gov/books/n/cooper/A90/table/A106/?report=objectonlyhttp://www.ncbi.nlm.nih.gov/books/n/cooper/A90/table/A106/?report=objectonlyhttp://www.ncbi.nlm.nih.gov/books/NBK9917/figure/A113/?report=objectonlyhttp://www.ncbi.nlm.nih.gov/books/NBK9917/figure/A113/?report=objectonlyhttp://www.ncbi.nlm.nih.gov/books/NBK9917/figure/A113/?report=objectonlyhttp://www.ncbi.nlm.nih.gov/books/NBK9917/figure/A113/?report=objectonlyhttp://www.ncbi.nlm.nih.gov/books/NBK9917/figure/A113/?report=objectonlyhttp://www.ncbi.nlm.nih.gov/books/NBK9917/#ui-ncbiinpagenav-2http://www.ncbi.nlm.nih.gov/books/NBK9917/#ui-ncbiinpagenav-2http://www.ncbi.nlm.nih.gov/books/NBK9917/figure/A113/?report=objectonlyhttp://www.ncbi.nlm.nih.gov/books/NBK9917/#ui-ncbiinpagenav-2http://www.ncbi.nlm.nih.gov/books/NBK9917/figure/A113/?report=objectonlyhttp://www.ncbi.nlm.nih.gov/books/NBK9917/figure/A113/?report=objectonlyhttp://www.ncbi.nlm.nih.gov/books/n/cooper/A90/table/A106/?report=objectonlyhttp://www.ncbi.nlm.nih.gov/books/n/cooper/A2886/def-item/A3297/http://www.ncbi.nlm.nih.gov/books/n/cooper/A2886/def-item/A3080/http://www.ncbi.nlm.nih.gov/books/n/cooper/A2886/def-item/A3085/http://www.ncbi.nlm.nih.gov/books/n/cooper/A2886/def-item/A3010/http://www.ncbi.nlm.nih.gov/books/n/cooper/A2886/def-item/A3281/http://www.ncbi.nlm.nih.gov/books/NBK9917/#ui-ncbiinpagenav-2

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Although bacteria have been an invaluable model for studies of many conserved properties of cells, they obviously

cannot be used to study aspects of cell structure and function that are unique to eukaryotes. Yeasts, the simplest

eukaryotes, have a number of experimental advantages similar to those ofE. coli. Consequently,yeastshave

provided a crucial model for studies of many fundamental aspects of eukaryotic cell biology.

The genome of the most frequently studied yeast, Saccharomyces cerevisiae, consists of 12 million base pairs

ofDNAand contains about 6000 genes. Although the yeast genome is approximately three times larger than that

ofE. coli, it is far more manageable than the genomes of more complex eukaryotes, such as humans. Yet even in its

simplicity, the yeast cell exhibits the typical features ofeukaryotic cells(Figure 1.15): It contains a

distinctnucleussurrounded by a nuclear membrane, its genomic DNA is organized as 16 linearchromosomes, and

its cytoplasm contains acytoskeletonand subcellular organelles.

Figure 1.15

Electron micrograph ofSaccharomyces cerevisiae. (David Scharf/Peter Arnold, Inc.)

Yeasts can be readily grown in the laboratory and can be studied by many of the same molecular genetic approaches

that have proved so successful withE. coli. Althoughyeastsdo not replicate as rapidly as bacteria, they still divide

as frequently as every 2 hours and can easily be grown as colonies from a single cell. Consequently, yeasts can be

used for a variety of genetic manipulations similar to those that can be performed using bacteria.

These features have made yeast cells the most approachableeukaryotic cellsfrom the standpoint of molecular

biology. Yeast mutants have been important in understanding many fundamental processes in eukaryotes,

includingDNAreplication,transcription,RNAprocessing, protein sorting, and the regulation of cell division, as will

be discussed in subsequent chapters. The unity of molecular cell biology is made abundantly clear by the fact that

the general principles of cell structure and function revealed by studies ofyeastsapply to all eukaryotic cells.

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Dictyostelium discoideum

Dictyostelium discoideumis a cellular slime mold, which, like yeast, is a comparatively simple unicellular

eukaryote. The genome ofDictyostelium is approximately ten times larger than that ofE. colimore complex than

the yeast genome but considerably simpler than the genomes of higher eukaryotes. Moreover, Dictyostelium can bereadily grown in the laboratory and is amenable to a variety of genetic manipulations.

Under conditions of plentiful food,Dictyostelium lives as a single-celled amoeba, feeding on bacteria andyeasts. It

is a highly mobile cell, and this property has madeDictyostelium an important model for studying the molecular

mechanisms responsible for animal cell movements (Figure 1.16). For example, introducing the appropriate

mutations intoDictyostelium has revealed the roles of several genes in cell motility.

Figure 1.16

Dictyostelium discoideum. These photographs show the movement of two amoebas over the course of about 40

seconds. (Courtesy of David Knecht, University of Connecticut.)

An additional interesting feature ofDictyostelium is the ability of single cells to aggregate into multicellular

structures. If an adequate supply of food is not available, the cells associate to form wormlike structures called slugs,

each consisting of up to 100,000 cells that function as a unit. Dictyostelium thus appears to straddle the border

between unicellular and multicellular organisms, providing an important model for studies of cell signaling and cell-

cell interactions.

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Caenorhabditis elegans

The unicellular eukaryotes Saccharomyces andDictyostelium are important models for studies ofeukaryotic cells,

but understanding the development of multicellular organisms requires the experimental analysis of plants and

animals, organisms that are more complex. The nematodeCaenorhabditis elegans(Figure 1.17) possesses several

notable features that make it one of the most widely used models for studies of animal development and cell

differentiation.

Figure 1.17

Caenorhabditis elegans. (From J. E. Sulston and H. R. Horvitz, 1977. Dev. Biol. 56: 110.)

Although the genome ofC. elegans (approximately 100 million base pairs) is larger than those of unicellular

eukaryotes, it is simpler and more manageable than the genomes of most animals. Its complete sequence has been

determined, revealing that the genome ofC. elegans contains approximately 19,000 genesabout three times the

number of genes in yeast, and one-fifth the number of genes predicted in humans. Biologically, C. elegans is also a

relatively simple multicellular organism: Adult worms consist of only 959 somatic cells, plus 1000 to 2000 germ

cells. In addition, C. elegans can be easily grown and subjected to genetic manipulations in the laboratory.

The simplicity ofC. elegans has enabled the course of its development to be studied in detail by microscopic

observation. Such analyses have successfully traced the embryonic origin and lineage of all the cells in the adult

worm. Genetic studies have also identified some of the mutations responsible for developmental abnormalities,

leading to the isolation and characterization of critical genes that control nematode development and differentiation.

Importantly, similar genes have also been found to function in complex animals (including humans),

making C. elegans an important model for studies of animal development.

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Drosophila melanogaster

Like C. elegans, the fruit flyDrosophila melanogaster(Figure 1.18) has been a crucial model organism in

developmental biology. The genome ofDrosophila is similar in size to that ofC. elegans, andDrosophila can beeasily maintained and bred in the laboratory. Furthermore, the short reproductive cycle ofDrosophila (about 2

weeks) makes it a very useful organism for genetic experiments. Many fundamental concepts of geneticssuch as

the relationship between genes andchromosomeswere derived from studies ofDrosophila early in the twentieth

century (see Chapter 3).

Figure 1.18

Drosophila melanogaster. (Darwin Dale/Photo Researchers, Inc.)

Extensive genetic analysis ofDrosophila has uncovered many genes that control development and differentiation,

and current methods of molecular biology have allowed the functions of these genes to be analyzed in detail.

Consequently, studies ofDrosophilahave led to striking advances in understanding the molecular mechanisms that

govern animal development, particularly with respect to formation of the body plan of complex multicellular

organisms. As with C. elegans, similar genes and mechanisms exist in vertebrates, validating the use

ofDrosophila as a major experimental model in contemporary developmental biology.

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Arabidopsis thaliana

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The study of plant molecular biology and development is an active and expanding field of considerable economic

importance as well as intellectual interest. Since the genomes of plants cover a range of complexity comparable to

that of animal genomes (seeTable 1.2), an optimal model for studies of plant development would be a relatively

simple organism with some of the advantageous properties ofC. elegans andDrosophila. The small flowering

plantArabidopsis thaliana(Figure 1.19) meets these criteria and is therefore widely used as a model to study the

molecular biology of plants.

Figure 1.19

Arabidopsis thaliana. (Jeremy Burgess/Photo Researchers, Inc.)

Arabidopsis is notable for its genome of only about 130 million base pairsa complexity similar to that

ofC. elegans andDrosophila. In addition,Arabidopsis is relatively easy to grow in the laboratory, and methods for

molecular genetic manipulations of this plant have been developed. These studies have led to the identification of

genes involved in various aspects of plant development, such as the development of flowers. Analysis of these genes

points to clear similarities between the mechanisms that control the development of plants and animals, further

emphasizing the fundamental unity of cell and molecular biology.

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Vertebrates

The most complex animals are the vertebrates, including humans and other mammals. The human genome is

approximately 3 billion base pairsabout 30 times larger than the genomes ofC. elegans,Drosophila,

orArabidopsis. Moreover, the human body is composed of more than 200 different kinds of specialized cell types.

This complexity makes the vertebrates difficult to study from the standpoint of cell and molecular biology, but much

of the interest in biological sciences nonetheless stems from the desire to understand the human organism.

Moreover, an understanding of many questions of immediate practical importance (e.g., in medicine) must be based

directly on studies of human (or closely related) cell types.

One important approach to studying human and other mammalian cells is to grow isolated cells in culture, where

they can be manipulated under controlled laboratory conditions. The use of cultured cells has allowed studies of

many aspects of mammalian cell biology, including experiments that have elucidated the mechanisms

ofDNAreplication,geneexpression, protein synthesis and processing, and cell division. Moreover, the ability to

culture cells in chemically defined media has allowed studies of the signaling mechanisms that normally control cell

growth and differentiation within the intact organism.

The specialized properties of some highly differentiated cell types have made them important models for studies of

particular aspects of cell biology. Muscle cells, for example, are highly specialized to undergo contraction,

producing force and movement. Because of this specialization, muscle cells are a crucial model for studying cell

movement at the molecular level. Another example is provided by nerve cells (neurons), which are specialized to

conduct electrochemical signals over long distances. In humans, nerve cell axons may be more than a meter long,

and some invertebrates, such as the squid, have giant neurons with axons as large as 1 mm in diameter. Because of

their highly specialized structure and function, these giant neurons have provided important models for studies of

ion transport across theplasma membrane, and of the role of thecytoskeletonin the transport of cytoplasmic

organelles.

The frogXenopus laevisis an important model for studies of early vertebrate development. Xenopus eggs are

unusually large cells, with a diameter of approximately 1 mm (Figure 1.20). Because those eggs develop outside of

the mother, all stages of development from egg to tadpole can be readily studied in the laboratory. In

addition,Xenopus eggs can be obtained in large numbers, facilitating biochemical analysis. Because of these

technical advantages,Xenopus has been widely used in studies of developmental biology and has provided

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important insights into the molecular mechanisms that control development, differentiation, and embryonic cell

division.

Figure 1.20

Eggs of the frogXenopus laevis. (Courtesy of Michael Danilchik and Kimberly Ray.)

Thezebrafish(Figure 1.21) possesses a number of advantages for genetic studies of vertebrate development. These

small fish are easy to maintain in the laboratory and they reproduce rapidly. In addition, the embryos develop

outside of the mother and are transparent, so that early stages of development can be easily observed. Powerful

methods have been developed to facilitate the isolation of mutations affectingzebrafishdevelopment, and several

thousand such mutations have now been identified. Because the zebrafish is an easily studied vertebrate, it promises

to bridge the gap between humans and the simpler invertebrate systems, such as C. elegans andDrosophila.

Figure 1.21

Zebrafish. (A) A 24-hour-old embryo. (B) An adult fish. (A, courtesy of Charles Kimmel, University of Oregon; B,

courtesy of S. Kondo)

Among mammals, the mouse is the most suitable for genetic analysis. Although the technical difficulties in studying

mouse genetics (compared, for example, to the genetics ofyeastsorDrosophila) are formidable, several mutations

affecting mouse development have been identified. Most important, recent advances in molecular biology have

enabled the production oftransgenic mice, in which specific mutant genes have been introduced into the mouse

germ line, so that their effects on development or other aspects of cell function can be studied in the context of the

whole animal. The suitability of the mouse as a model for human development is illustrated by the fact that

mutations in homologous genes result in similar developmental defects in both species; piebaldism is a striking

example (Figure 1.22).

Figure 1.22

The mouse as a model for human development. A child and a mouse show similar defects in pigmentation(piebaldism) as a result of mutations in a gene required for normal migration of melanocytes (the cells responsible

for skin pigmentation) during embryonic(more...)

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