Часть 1 (B. Alberts, A. Johnson, J. Lewis и др. - Molecular Biology of The Cell (5th edition)), страница 9

Because the genetic information for every organism is written inthe universal language of DNA sequences, and the DNA sequence of any givenorganism can be obtained by standard biochemical techniques, it is now possible to characterize, catalogue, and compare any set of living organisms with reference to these sequences. From such comparisons we can estimate the place ofeach organism in the family tree of living species—the ‘tree of life’. But beforedescribing what this approach reveals, we need first to consider the routes bywhich cells in different environments obtain the matter and energy they requireto survive and proliferate, and the ways in which some classes of organismsdepend on others for their basic chemical needs.Cells Can Be Powered by a Variety of Free Energy SourcesLiving organisms obtain their free energy in different ways. Some, such as animals, fungi, and the bacteria that live in the human gut, get it by feeding onother living things or the organic chemicals they produce; such organisms arecalled organotrophic (from the Greek word trophe, meaning “food”).

Othersderive their energy directly from the nonliving world. These fall into twoclasses: those that harvest the energy of sunlight, and those that capture theirenergy from energy-rich systems of inorganic chemicals in the environment(chemical systems that are far from chemical equilibrium). Organisms of theformer class are called phototrophic (feeding on sunlight); those of the latterare called lithotrophic (feeding on rock). Organotrophic organisms could notexist without these primary energy converters, which are the most plentifulform of life.Phototrophic organisms include many types of bacteria, as well as algae andplants, on which we—and virtually all the living things that we ordinarily seearound us—depend. Phototrophic organisms have changed the whole chemistry of our environment: the oxygen in the Earth’s atmosphere is a by-productof their biosynthetic activities.Lithotrophic organisms are not such an obvious feature of our world,because they are microscopic and mostly live in habitats that humans do notfrequent—deep in the ocean, buried in the Earth’s crust, or in various otherinhospitable environments.

But they are a major part of the living world, and areespecially important in any consideration of the history of life on Earth.Some lithotrophs get energy from aerobic reactions, which use molecularoxygen from the environment; since atmospheric O2 is ultimately the product ofliving organisms, these aerobic lithotrophs are, in a sense, feeding on the products of past life. There are, however, other lithotrophs that live anaerobically, inplaces where little or no molecular oxygen is present, in circumstances similar tothose that must have existed in the early days of life on Earth, before oxygen hadaccumulated.The most dramatic of these sites are the hot hydrothermal vents found deepdown on the floor of the Pacific and Atlantic Oceans, in regions where the oceanfloor is spreading as new portions of the Earth’s crust form by a gradualupwelling of material from the Earth’s interior (Figure 1–15). Downward-percolating seawater is heated and driven back upward as a submarine geyser, carrying with it a current of chemicals from the hot rocks below.

A typical cocktailmight include H2S, H2, CO, Mn2+, Fe2+, Ni2+, CH2, NH4+, and phosphorus-containing compounds. A dense population of microbes lives in the neighborhoodof the vent, thriving on this austere diet and harvesting free energy from reactions between the available chemicals. Other organisms—clams, mussels, andgiant marine worms—in turn live off the microbes at the vent, forming an entireecosystem analogous to the system of plants and animals that we belong to, butpowered by geochemical energy instead of light (Figure 1–16).THE DIVERSITY OF GENOMES AND THE TREE OF LIFE13SEAdark cloud ofhot mineral-richwaterhydrothermalventanaerobic lithotrophicbacteriainvertebrateanimal communitychimney made fromprecipitated metalsulfides2–3°Csea floorFigure 1–15 The geology of a hothydrothermal vent in the ocean floor.Water percolates down toward the hotmolten rock upwelling from the Earth’sinterior and is heated and driven backupward, carrying minerals leached fromthe hot rock.

A temperature gradient isset up, from more than 350°C near thecore of the vent, down to 2–3°C in thesurrounding ocean. Minerals precipitatefrom the water as it cools, forming achimney. Different classes of organisms,thriving at different temperatures, live indifferent neighborhoods of the chimney.A typical chimney might be a few meterstall, with a flow rate of 1–2 m/sec.350°Ccontourpercolationof seawaterhot mineral solutionhot basaltSome Cells Fix Nitrogen and Carbon Dioxide for OthersTo make a living cell requires matter, as well as free energy.

DNA, RNA, and proteinare composed of just six elements: hydrogen, carbon, nitrogen, oxygen, sulfur, andphosphorus. These are all plentiful in the nonliving environment, in the Earth’srocks, water, and atmosphere, but not in chemical forms that allow easy incorporation into biological molecules. Atmospheric N2 and CO2, in particular, areextremely unreactive, and a large amount of free energy is required to drive thereactions that use these inorganic molecules to make the organic compoundsneeded for further biosynthesis—that is, to fix nitrogen and carbon dioxide, soas to make N and C available to living organisms. Many types of living cells lackthe biochemical machinery to achieve this fixation, and rely on other classes ofcells to do the job for them. We animals depend on plants for our supplies ofgeochemical energy andinorganic raw materialsbacteriamulticellular animals e.g., tubeworms1mFigure 1–16 Living organisms at a hothydrothermal vent.

Close to the vent, attemperatures up to about 120°C, variouslithotrophic species of bacteria andarchaea (archaebacteria) live, directlyfuelled by geochemical energy. A littlefurther away, where the temperature islower, various invertebrate animals liveby feeding on these microorganisms.Most remarkable are the giant (2-meter)tube worms, which, rather than feed onthe lithotrophic cells, live in symbiosiswith them: specialized organs in theworms harbor huge numbers ofsymbiotic sulfur-oxidizing bacteria. Thesebacteria harness geochemical energy andsupply nourishment to their hosts, whichhave no mouth, gut, or anus. Thedependence of the tube worms on thebacteria for the harnessing of geothermalenergy is analogous to the dependenceof plants on chloroplasts for theharnessing of solar energy, discussedlater in this chapter.

The tube worms,however, are thought to have evolvedfrom more conventional animals, and tohave become secondarily adapted to lifeat hydrothermal vents. (Courtesy ofDudley Foster, Woods HoleOceanographic Institution.)14Chapter 1: Cells and GenomesFigure 1–17 Shapes and sizes ofsome bacteria. Although most aresmall, as shown, measuring a fewmicrometers in linear dimension,there are also some giant species.An extreme example (not shown)is the cigar-shaped bacteriumEpulopiscium fishelsoni, which livesin the gut of a surgeonfish andcan be up to 600 mm long.2 mmspherical cellse.g., Streptococcusrod-shaped cellse.g., Escherichia coli,Vibrio choleraethe smallest cellse.g., Mycoplasma,Spiroplasmaspiral cellse.g., Treponema pallidumorganic carbon and nitrogen compounds.

Plants in turn, although they can fixcarbon dioxide from the atmosphere, lack the ability to fix atmospheric nitrogen, and they depend in part on nitrogen-fixing bacteria to supply their need fornitrogen compounds. Plants of the pea family, for example, harbor symbioticnitrogen-fixing bacteria in nodules in their roots.Living cells therefore differ widely in some of the most basic aspects of theirbiochemistry.