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When it encounters a suitable prey,usually another type of protozoan, itreleases numerous small paralyzing dartsfrom its snout region. Then, the Didiniumattaches to and devours the other cell byphagocytosis, inverting like a hollow ballto engulf its victim, which is almost aslarge as itself. (Courtesy of D. Barlow.)(A)100 mm(B)receiving shelter and nourishment in return for the power generation they performed for their hosts (Figure 1–34). This partnership between a primitiveanaerobic eucaryotic predator cell and an aerobic bacterial cell is thought tohave been established about 1.5 billion years ago, when the Earth’s atmospherefirst became rich in oxygen.(B)(C)(A)100 nmFigure 1–33 A mitochondrion.
(A) A cross section, as seen in the electronmicroscope. (B) A drawing of a mitochondrion with part of it cut away toshow the three-dimensional structure. (C) A schematic eucaryotic cell, withthe interior space of a mitochondrion, containing the mitochondrial DNAand ribosomes, colored. Note the smooth outer membrane and theconvoluted inner membrane, which houses the proteins that generate ATPfrom the oxidation of food molecules. (A, courtesy of Daniel S. Friend.)GENETIC INFORMATION IN EUCARYOTES29ancestraleucaryotic cellinternalmembranesearlyeucaryotic cellnucleusFigure 1–34 The origin of mitochondria.An ancestral eucaryotic cell is thought tohave engulfed the bacterial ancestor ofmitochondria, initiating a symbioticrelationship.mitochondriawith doublemembranebacteriumMany eucaryotic cells—specifically, those of plants and algae—also containanother class of small membrane-enclosed organelles somewhat similar to mitochondria—the chloroplasts (Figure 1–35).
Chloroplasts perform photosynthesis,using the energy of sunlight to synthesize carbohydrates from atmosphericcarbon dioxide and water, and deliver the products to the host cell as food. Likemitochondria, chloroplasts have their own genome and almost certainly originated as symbiotic photosynthetic bacteria, acquired by cells that already possessed mitochondria (Figure 1–36).A eucaryotic cell equipped with chloroplasts has no need to chase afterother cells as prey; it is nourished by the captive chloroplasts it has inheritedfrom its ancestors. Correspondingly, plant cells, although they possess thecytoskeletal equipment for movement, have lost the ability to change shaperapidly and to engulf other cells by phagocytosis. Instead, they create aroundthemselves a tough, protective cell wall. If the ancestral eucaryote was indeed apredator on other organisms, we can view plant cells as eucaryotes that havemade the transition from hunting to farming.Fungi represent yet another eucaryotic way of life.
Fungal cells, like animalcells, possess mitochondria but not chloroplasts; but in contrast with animalcells and protozoa, they have a tough outer wall that limits their ability to movechloroplastschlorophyllcontainingmembranesinnermembraneoutermembrane(A)10 mm(B)Figure 1–35 Chloroplasts. These organellescapture the energy of sunlight in plant cellsand some single-celled eucaryotes.(A) A single cell isolated from a leaf of aflowering plant, seen in the lightmicroscope, showing the greenchloroplasts. (B) A drawing of one of thechloroplasts, showing the highly foldedsystem of internal membranes containingthe chlorophyll molecules by which light isabsorbed.
(A, courtesy of Preeti Dahiya.)30Chapter 1: Cells and Genomesearlyeucaryotic cellphotosyntheticbacteriumearlyeucaryotic cellcapable ofphotosynthesischloroplasts withdouble membranerapidly or to swallow up other cells. Fungi, it seems, have turned from huntersinto scavengers: other cells secrete nutrient molecules or release them upondeath, and fungi feed on these leavings—performing whatever digestion is necessary extracellularly, by secreting digestive enzymes to the exterior.Eucaryotes Have Hybrid GenomesThe genetic information of eucaryotic cells has a hybrid origin—from the ancestral anaerobic eucaryote, and from the bacteria that it adopted as symbionts.Most of this information is stored in the nucleus, but a small amount remainsinside the mitochondria and, for plant and algal cells, in the chloroplasts.
Themitochondrial DNA and the chloroplast DNA can be separated from the nuclearDNA and individually analyzed and sequenced. The mitochondrial and chloroplast genomes are found to be degenerate, cut-down versions of the corresponding bacterial genomes, lacking genes for many essential functions. In ahuman cell, for example, the mitochondrial genome consists of only 16,569nucleotide pairs, and codes for only 13 proteins, two ribosomal RNA components, and 22 transfer RNAs.The genes that are missing from the mitochondria and chloroplasts have notall been lost; instead, many of them have been somehow moved from the symbiont genome into the DNA of the host cell nucleus.
The nuclear DNA of humanscontains many genes coding for proteins that serve essential functions insidethe mitochondria; in plants, the nuclear DNA also contains many genes specifying proteins required in chloroplasts.Eucaryotic Genomes Are BigNatural selection has evidently favored mitochondria with small genomes, justas it has favored bacteria with small genomes. By contrast, the nuclear genomesof most eucaryotes seem to have been free to enlarge.
Perhaps the eucaryoticway of life has made large size an advantage: predators typically need to be bigger than their prey, and cell size generally increases in proportion to genomesize. Perhaps enlargement of the genome has been driven by the accumulationof parasitic transposable elements (discussed in Chapter 5)—“selfish” segmentsof DNA that can insert copies of themselves at multiple sites in the genome.Whatever the explanation, the genomes of most eucaryotes are orders of magnitude larger than those of bacteria and archaea (Figure 1–37). And the freedom tobe extravagant with DNA has had profound implications.Eucaryotes not only have more genes than procaryotes; they also have vastlymore DNA that does not code for protein or for any other functional productmolecule.
The human genome contains 1000 times as many nucleotide pairs asthe genome of a typical bacterium, 20 times as many genes, and about 10,000Figure 1–36 The origin of chloroplasts.An early eucaryotic cell, alreadypossessing mitochondria, engulfed aphotosynthetic bacterium(a cyanobacterium) and retained it insymbiosis.
All present-day chloroplastsare thought to trace their ancestry backto a single species of cyanobacteriumthat was adopted as an internalsymbiont (an endosymbiont) over abillion years ago.GENETIC INFORMATION IN EUCARYOTESMycoplasmaBACTERIAAND ARCHAEA31Figure 1–37 Genome sizes compared.Genome size is measured in nucleotidepairs of DNA per haploid genome, that is,per single copy of the genome. (The cellsof sexually reproducing organisms such asourselves are generally diploid: theycontain two copies of the genome, oneinherited from the mother, the other fromthe father.) Closely related organisms canvary widely in the quantity of DNA in theirgenomes, even though they containsimilar numbers of functionally distinctgenes.
(Data from W.H. Li, MolecularEvolution, pp. 380–383. Sunderland,MA: Sinauer, 1997.)E. coliyeastFUNGIAmoebaPROTISTSArabidopsisPLANTSDrosophilaINSECTSbeanlilyfernMOLLUSKSsharkCARTILAGINOUS FISHFugu zebrafishBONY FISHnewtAMPHIBIANSREPTILESBIRDShumanMAMMALS1051061071081091010number of nucleotide pairs per haploid genome10111012times as much noncoding DNA (~98.5% of the genome for a human is noncoding, as opposed to 11% of the genome for the bacterium E. coli).Eucaryotic Genomes Are Rich in Regulatory DNAMuch of our noncoding DNA is almost certainly dispensable junk, retained likea mass of old papers because, when there is little pressure to keep an archivesmall, it is easier to retain everything than to sort out the valuable informationand discard the rest.
Certain exceptional eucaryotic species, such as the pufferfish (Figure 1–38), bear witness to the profligacy of their relatives; they havesomehow managed to rid themselves of large quantities of noncoding DNA. Yetthey appear similar in structure, behavior, and fitness to related species thathave vastly more such DNA.Even in compact eucaryotic genomes such as that of puffer fish, there ismore noncoding DNA than coding DNA, and at least some of the noncodingDNA certainly has important functions. In particular, it regulates the expressionof adjacent genes.
With this regulatory DNA, eucaryotes have evolved distinctiveways of controlling when and where a gene is brought into play. This sophisticated gene regulation is crucial for the formation of complex multicellularorganisms.The Genome Defines the Program of Multicellular DevelopmentThe cells in an individual animal or plant are extraordinarily varied. Fat cells,skin cells, bone cells, nerve cells—they seem as dissimilar as any cells could be.Yet all these cell types are the descendants of a single fertilized egg cell, and all(with minor exceptions) contain identical copies of the genome of the species.The differences result from the way in which the cells make selective use oftheir genetic instructions according to the cues they get from their surroundingsin the developing embryo.
The DNA is not just a shopping list specifying themolecules that every cell must have, and the cell is not an assembly of all theitems on the list. Rather, the cell behaves as a multipurpose machine, with sensors to receive environmental signals and with highly developed abilities to calldifferent sets of genes into action according to the sequences of signals to whichthe cell has been exposed. The genome in each cell is big enough to accommodate the information that specifies an entire multicellular organism, but in anyindividual cell only part of that information is used.A large fraction of the genes in the eucaryotic genome code for proteins thatregulate the activities of other genes.
Most of these gene regulatory proteins act byFigure 1–38 The puffer fish (Fugurubripes). This organism has a genomesize of 400 million nucleotide pairs—about one-quarter as much as azebrafish, for example, even though thetwo species of fish have similar numbersof genes. (From a woodcut by Hiroshige,courtesy of Arts and Designs of Japan.)32Chapter 1: Cells and Genomesreceptor protein in cell membranedetects environmental signalgene-regulatory proteinis activated......and binds to regulatory DNA......provoking activation of a geneto produce another protein...Figure 1–39 Controlling gene readoutby environmental signals.
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