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Themutant gene therefore has a function inthe control of cell shape. But how, inmolecular terms, does the gene productperform that function? That is a harderquestion, and needs biochemical analysisto answer it. (Courtesy of Kenneth Sawinand Paul Nurse.)THE DIVERSITY OF GENOMES AND THE TREE OF LIFE25Figure 1–29 The genome of E. coli.(A) A cluster of E. coli cells. (B) A diagramof the genome of E. coli strain K-12. Thediagram is circular because the DNA ofE.
coli, like that of other procaryotes,forms a single, closed loop. Proteincoding genes are shown as yellow ororange bars, depending on the DNAstrand from which they are transcribed;genes encoding only RNA molecules areindicated by green arrows. Some genesare transcribed from one strand of theDNA double helix (in a clockwisedirection in this diagram), others from theother strand (counterclockwise).(A, courtesy of Dr. Tony Brain and DavidParker/Photo Researchers; B, adaptedfrom F.R. Blattner et al., Science277:1453–1462, 1997. With permissionfrom AAAS.)origin ofreplication(A)Escherichia coli K-124,639,221 nucleotide pairsterminus ofreplication(B)discovery raises new questions and provides new tools with which to tacklegeneral questions in the context of the chosen organism. For this reason, largecommunities of biologists have become dedicated to studying different aspectsof the same model organism.In the enormously varied world of bacteria, the spotlight of molecularbiology has for a long time focused intensely on just one species: Escherichiacoli, or E.
coli (see Figures 1–17 and 1–18). This small, rod-shaped bacterial cellnormally lives in the gut of humans and other vertebrates, but it can be growneasily in a simple nutrient broth in a culture bottle. It adapts to variable chemical conditions and reproduces rapidly, and it can evolve by mutation andselection at a remarkable speed. As with other bacteria, different strains of E.coli, though classified as members of a single species, differ genetically to amuch greater degree than do different varieties of a sexually reproducingorganism such as a plant or animal.
One E. coli strain may possess many hundreds of genes that are absent from another, and the two strains could have aslittle as 50% of their genes in common. The standard laboratory strain E. coliK-12 has a genome of approximately 4.6 million nucleotide pairs, contained ina single circular molecule of DNA, coding for about 4300 different kinds of proteins (Figure 1–29).In molecular terms, we know more about E. coli than about any other livingorganism. Most of our understanding of the fundamental mechanisms of life—for example, how cells replicate their DNA, or how they decode the instructionsrepresented in the DNA to direct the synthesis of specific proteins—has comefrom studies of E. coli. The basic genetic mechanisms have turned out to behighly conserved throughout evolution: these mechanisms are therefore essentially the same in our own cells as in E.
coli.26Chapter 1: Cells and GenomesSummaryProcaryotes (cells without a distinct nucleus) are biochemically the most diverseorganisms and include species that can obtain all their energy and nutrients frominorganic chemical sources, such as the reactive mixtures of minerals released athydrothermal vents on the ocean floor—the sort of diet that may have nourished thefirst living cells 3.5 billion years ago. DNA sequence comparisons reveal the familyrelationships of living organisms and show that the procaryotes fall into two groupsthat diverged early in the course of evolution: the bacteria (or eubacteria) and thearchaea.
Together with the eucaryotes (cells with a membrane-enclosed nucleus), theseconstitute the three primary branches of the tree of life. Most bacteria and archaea aresmall unicellular organisms with compact genomes comprising 1000–6000 genes.Many of the genes within a single organism show strong family resemblances in theirDNA sequences, implying that they originated from the same ancestral gene throughgene duplication and divergence. Family resemblances (homologies) are also clearwhen gene sequences are compared between different species, and more than 200 genefamilies have been so highly conserved that they can be recognized as common to mostspecies from all three domains of the living world.
Thus, given the DNA sequence of anewly discovered gene, it is often possible to deduce the gene’s function from the knownfunction of a homologous gene in an intensively studied model organism, such as thebacterium E. coli.GENETIC INFORMATION IN EUCARYOTESEucaryotic cells, in general, are bigger and more elaborate than procaryotic cells,and their genomes are bigger and more elaborate, too. The greater size is accompanied by radical differences in cell structure and function.
Moreover, manyclasses of eucaryotic cells form multicellular organisms that attain levels of complexity unmatched by any procaryote.Because they are so complex, eucaryotes confront molecular biologists witha special set of challenges, which will concern us in the rest of this book. Increasingly, biologists meet these challenges through the analysis and manipulation ofthe genetic information within cells and organisms. It is therefore important atthe outset to know something of the special features of the eucaryotic genome.We begin by briefly discussing how eucaryotic cells are organized, how thisreflects their way of life, and how their genomes differ from those of procaryotes.This leads us to an outline of the strategy by which molecular biologists, byexploiting genetic information, are attempting to discover how eucaryoticorganisms work.Eucaryotic Cells May Have Originated as PredatorsBy definition, eucaryotic cells keep their DNA in an internal compartmentcalled the nucleus.
The nuclear envelope, a double layer of membrane, surrounds the nucleus and separates the DNA from the cytoplasm. Eucaryotes alsohave other features that set them apart from procaryotes (Figure 1–30). Theircells are, typically, 10 times bigger in linear dimension, and 1000 times larger involume. They have a cytoskeleton—a system of protein filaments crisscrossingthe cytoplasm and forming, together with the many proteins that attach tothem, a system of girders, ropes, and motors that gives the cell mechanicalstrength, controls its shape, and drives and guides its movements.
<GTTA><ATGG> <TCGC> The nuclear envelope is only one part of a set of internalmembranes, each structurally similar to the plasma membrane and enclosingdifferent types of spaces inside the cell, many of them involved in digestion andsecretion. Lacking the tough cell wall of most bacteria, animal cells and thefree-living eucaryotic cells called protozoa can change their shape rapidly andengulf other cells and small objects by phagocytosis (Figure 1–31).It is still a mystery how all these properties evolved, and in what sequence.One plausible view, however, is that they are all reflections of the way of life of aGENETIC INFORMATION IN EUCARYOTES27microtubulecentrosome withpair of centrioles5 mmextracellular matrixchromatin (DNA)nuclear porenuclear envelopevesicleslysosomeactinfilamentsnucleolusperoxisomeribosomesin cytosolGolgi apparatusintermediatefilamentsplasma membranenucleusprimordial eucaryotic cell that was a predator, living by capturing other cells andeating them (Figure 1–32).
Such a way of life requires a large cell with a flexibleplasma membrane, as well as an elaborate cytoskeleton to support and movethis membrane. It may also require that the cell’s long, fragile DNA molecules besequestered in a separate nuclear compartment, to protect the genome fromdamage by the movements of the cytoskeleton.Modern Eucaryotic Cells Evolved from a SymbiosisendoplasmicreticulummitochondrionFigure 1–30 The major features ofeucaryotic cells. The drawing depicts atypical animal cell, but almost all thesame components are found in plantsand fungi and in single-celled eucaryotessuch as yeasts and protozoa. Plant cellscontain chloroplasts in addition to thecomponents shown here, and theirplasma membrane is surrounded by atough external wall formed of cellulose.A predatory way of life helps to explain another feature of eucaryotic cells.Almost all such cells contain mitochondria (Figure 1–33).
These small bodies inthe cytoplasm, enclosed by a double layer of membrane, take up oxygen andharness energy from the oxidation of food molecules—such as sugars—to produce most of the ATP that powers the cell’s activities. Mitochondria are similarin size to small bacteria, and, like bacteria, they have their own genome in theform of a circular DNA molecule, their own ribosomes that differ from thoseelsewhere in the eucaryotic cell, and their own transfer RNAs. It is now generallyaccepted that mitochondria originated from free-living oxygen-metabolizing(aerobic) bacteria that were engulfed by an ancestral eucaryotic cell that couldotherwise make no such use of oxygen (that is, was anaerobic).
Escaping digestion, these bacteria evolved in symbiosis with the engulfing cell and its progeny,10 mmFigure 1–31 Phagocytosis. This series ofstills from a movie shows a human whiteblood cell (a neutrophil) engulfing a redblood cell (artificially colored red) thathas been treated with antibody.(Courtesy of Stephen E. Malawista andAnne de Boisfleury Chevance.)28Chapter 1: Cells and GenomesFigure 1–32 A single-celled eucaryotethat eats other cells. (A) Didinium is acarnivorous protozoan, belonging to thegroup known as ciliates. It has a globularbody, about 150 mm in diameter,encircled by two fringes of cilia—sinuous,whiplike appendages that beatcontinually; its front end is flattenedexcept for a single protrusion, rather likea snout. (B) Didinium normally swimsaround in the water at high speed bymeans of the synchronous beating of itscilia.
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