Часть 1 (B. Alberts, A. Johnson, J. Lewis и др. - Molecular Biology of The Cell (5th edition)), страница 10

Not surprisingly, cells with complementary needs and capabilitieshave developed close associations. Some of these associations, as we see below,have evolved to the point where the partners have lost their separate identitiesaltogether: they have joined forces to form a single composite cell.The Greatest Biochemical Diversity Exists Among ProcaryoticCellsFrom simple microscopy, it has long been clear that living organisms can beclassified on the basis of cell structure into two groups: the eucaryotes and theprocaryotes.

Eucaryotes keep their DNA in a distinct membrane-enclosed intracellular compartment called the nucleus. (The name is from the Greek, meaning“truly nucleated,” from the words eu, “well” or “truly,” and karyon, “kernel” or“nucleus”.) Procaryotes have no distinct nuclear compartment to house theirDNA. Plants, fungi, and animals are eucaryotes; bacteria are procaryotes, as arearchaea—a separate class of procaryotic cells, discussed below.Most procaryotic cells are small and simple in outward appearance (Figure1–17), and they live mostly as independent individuals or in loosely organizedcommunities, rather than as multicellular organisms.

They are typically sphericalor rod-shaped and measure a few micrometers in linear dimension. They oftenhave a tough protective coat, called a cell wall, beneath which a plasma membrane encloses a single cytoplasmic compartment containing DNA, RNA, proteins, and the many small molecules needed for life. In the electron microscope,this cell interior appears as a matrix of varying texture without any discernibleorganized internal structure (Figure 1–18).Figure 1–18 The structure of a bacterium. (A) The bacterium Vibriocholerae, showing its simple internal organization.

Like many other species,Vibrio has a helical appendage at one end—a flagellum—that rotates as apropeller to drive the cell forward. (B) An electron micrograph of alongitudinal section through the widely studied bacterium Escherichia coli(E. coli). This is related to Vibrio but has many flagella (not visible in thissection) distributed over its surface. The cell’s DNA is concentrated in thelightly stained region. (B, courtesy of E. Kellenberger.)plasmamembraneDNAcell wallflagellum1 mmribosomes(A)(B)1 mmTHE DIVERSITY OF GENOMES AND THE TREE OF LIFEHS15V10 mmFigure 1–19 The phototrophicbacterium Anabaena cylindrica viewedin the light microscope. The cells of thisspecies form long, multicellular filaments.Most of the cells (labeled V) performphotosynthesis, while others becomespecialized for nitrogen fixation (labeledH), or develop into resistant spores(labeled S). (Courtesy of Dave G.

Adams.)Procaryotic cells live in an enormous variety of ecological niches, and theyare astonishingly varied in their biochemical capabilities—far more so thaneucaryotic cells. Organotrophic species can utilize virtually any type of organicmolecule as food, from sugars and amino acids to hydrocarbons and methanegas. Phototrophic species (Figure 1–19) harvest light energy in a variety of ways,some of them generating oxygen as a byproduct, others not.

Lithotrophic speciescan feed on a plain diet of inorganic nutrients, getting their carbon from CO2, andrelying on H2S to fuel their energy needs (Figure 1–20)—or on H2, or Fe2+, or elemental sulfur, or any of a host of other chemicals that occur in the environment.Many parts of this world of microscopic organisms are virtually unexplored.Traditional methods of bacteriology have given us an acquaintance with thosespecies that can be isolated and cultured in the laboratory. But DNA sequenceanalysis of the populations of bacteria in samples from natural habitats—suchas soil or ocean water, or even the human mouth—has opened our eyes to thefact that most species cannot be cultured by standard laboratory techniques.According to one estimate, at least 99% of procaryotic species remain to becharacterized.The Tree of Life Has Three Primary Branches: Bacteria, Archaea,and EucaryotesThe classification of living things has traditionally depended on comparisons oftheir outward appearances: we can see that a fish has eyes, jaws, backbone,brain, and so on, just as we do, and that a worm does not; that a rosebush iscousin to an apple tree, but less similar to a grass.

As Darwin showed, we canreadily interpret such close family resemblances in terms of evolution fromcommon ancestors, and we can find the remains of many of these ancestors preserved in the fossil record. In this way, it has been possible to begin to draw afamily tree of living organisms, showing the various lines of descent, as well asbranch points in the history, where the ancestors of one group of speciesbecame different from those of another.When the disparities between organisms become very great, however, thesemethods begin to fail.

How do we decide whether a fungus is closer kin to a plantor to an animal? When it comes to procaryotes, the task becomes harder still:one microscopic rod or sphere looks much like another. Microbiologists havetherefore sought to classify procaryotes in terms of their biochemistry and nutritional requirements. But this approach also has its pitfalls.

Amid the bewilderingvariety of biochemical behaviors, it is difficult to know which differences trulyreflect differences of evolutionary history.Genome analysis has given us a simpler, more direct, and more powerfulway to determine evolutionary relationships. The complete DNA sequence of anorganism defines its nature with almost perfect precision and in exhaustivedetail. Moreover, this specification is in a digital form—a string of letters—thatcan be entered straightforwardly into a computer and compared with the corresponding information for any other living thing. Because DNA is subject to random changes that accumulate over long periods of time (as we shall see shortly),the number of differences between the DNA sequences of two organisms canprovide a direct, objective, quantitative indication of the evolutionary distancebetween them.This approach has shown that the organisms that were traditionally classedtogether as “bacteria” can be as widely divergent in their evolutionary origins as6 mmFigure 1–20 A lithotrophic bacterium.Beggiatoa, which lives in sulfurousenvironments, gets its energy byoxidizing H2S and can fix carbon even inthe dark.

Note the yellow deposits ofsulfur inside the cells. (Courtesy of RalphW. Wolfe.)16Chapter 1: Cells and GenomesA R CH A EAEUARIBACTESulfolobushumanHaloferaxAeropyrumcyanobacteriamaizeMethanothermobacterBacillusMethanococcusyeastCARYOTEParameciumSDictyosteliumEuglenaE. coliThermotogaAquifexcommonancestorcellTrypanosomaGiardia1 change/10 nucleotidesTrichomonasFigure 1–21 The three major divisions (domains) of the living world. Note that traditionally the wordbacteria has been used to refer to procaryotes in general, but more recently has been redefined to refer toeubacteria specifically.

The tree shown here is based on comparisons of the nucleotide sequence of aribosomal RNA subunit in the different species, and the distances in the diagram represent estimates of thenumbers of evolutionary changes that have occurred in this molecule in each lineage (see Figure 1–22).The parts of the tree shrouded in gray cloud represent uncertainties about details of the true pattern ofspecies divergence in the course of evolution: comparisons of nucleotide or amino acid sequences ofmolecules other than rRNA, as well as other arguments, lead to somewhat different trees.

There is generalagreement, however, as to the early divergence of the three most basic domains—the bacteria, thearchaea, and the eucaryotes.is any procaryote from any eucaryote. It now appears that the procaryotes comprise two distinct groups that diverged early in the history of life on Earth, eitherbefore the ancestors of the eucaryotes diverged as a separate group or at aboutthe same time. The two groups of procaryotes are called the bacteria (or eubacteria) and the archaea (or archaebacteria). The living world therefore has threemajor divisions or domains: bacteria, archaea, and eucaryotes (Figure 1–21).Archaea are often found inhabiting environments that we humans avoid,such as bogs, sewage treatment plants, ocean depths, salt brines, and hot acidsprings, although they are also widespread in less extreme and more homelyenvironments, from soils and lakes to the stomachs of cattle.

In outward appearance they are not easily distinguished from bacteria. At a molecular level,archaea seem to resemble eucaryotes more closely in their machinery for handling genetic information (replication, transcription, and translation), but bacteria more closely in their apparatus for metabolism and energy conversion. Wediscuss below how this might be explained.Some Genes Evolve Rapidly; Others Are Highly ConservedBoth in the storage and in the copying of genetic information, random accidentsand errors occur, altering the nucleotide sequence—that is, creating mutations.Therefore, when a cell divides, its two daughters are often not quite identical toone another or to their parent.

On rare occasions, the error may represent achange for the better; more probably, it will cause no significant difference in thecell’s prospects; and in many cases, the error will cause serious damage—forexample, by disrupting the coding sequence for a key protein. Changes due tomistakes of the first type will tend to be perpetuated, because the altered cell hasan increased likelihood of reproducing itself.