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Cell_Biology_Alberts. H2S photosynthesis H2O photosynthesis green sulfur bacteria purple sulfur bacteria green flamentous bacteria ˜-proteobacteria (e.g., Bordetella) MITOCHONDRIACHLOROPLASTS EUKARYOTES PROKARYOTES OXIDIZING ATMOSPHERE REDUCING ATMOSPHERE cyanobacteria (e.g., Synechococcus) ancestral fermenting bacteria O2 respiration purple nonsulfur bacteria °-proteobacteria (e.g., Agrobacterium) ˛-proteobacteria (e.g., E. coli)


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Cell_Biology_Alberts. Figure 14–57 Evolutionary scheme showing the postulated origins of mitochondria and chloroplasts and their bacterial ancestors. the consumption of oxygen by respiration is thought to have first developed about 2 billion years ago. Nucleotide-sequence analyses suggest that an endosymbiotic oxygen-evolving cyanobacterium (cyan) gave rise to chloroplasts (dark green), while mitochondria arose from an α-proteobacterium. the nearest relatives of mitochondria (pink) are members of three closely related groups of α-proteobacteria—the rhizobacteria, agrobacteria, and rickettsias—known to form intimate associations with present-day eukaryotic cells. proteobacteria are pink, purple photosynthetic bacteria are purple, and other photosynthetic bacteria are light green.


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Cell_Biology_Alberts. Chloroplasts and photosynthetic bacteria have the unique ability to harness the energy of sunlight to produce energy-rich compounds. This is achieved by the photosystems, in which chlorophyll molecules attached to proteins are excited when hit by a photon. Photosystems are composed of an antenna complex that collects solar energy and a photochemical reaction center, in which the collected energy is funneled to a chlorophyll molecule held in a special position, enabling it to withdraw electrons from an electron donor. Chloroplasts and cyanobacteria contain two distinct photosystems. The two photosystems are normally linked in series in the Z scheme, and they transfer electrons from water to NADP+ to form NADPH, generating a transmembrane electrochemical potential. One of the two photosystems—photosystem II—can split water by removing electrons from this ubiquitous, low-energy compound. All the molecular oxygen (O2) in our atmosphere is a by-product of the water-splitting reaction in


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Cell_Biology_Alberts. II—can split water by removing electrons from this ubiquitous, low-energy compound. All the molecular oxygen (O2) in our atmosphere is a by-product of the water-splitting reaction in this photosystem. The three-dimensional structures of photosystems I and II are strikingly similar to the photosystems of purple photosynthetic bacteria, demonstrating a remarkable degree of conservation over billions of years of evolution.


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Cell_Biology_Alberts. The two photosystems and the cytochrome b6-f complex reside in the thylakoid membrane, a separate membrane system in the central stroma compartment of the chloroplast that is differentiated into stacked grana and unstacked stroma thylakoids. Electron-transport processes in the thylakoid membrane cause protons to be released into the thylakoid space. The backflow of protons through the chloroplast ATP synthase then generates ATP. This ATP is used in conjunction with the NADPH produced by photosynthesis to drive a large number of biosynthetic reactions in the chloroplast stroma, including the carbon-fixation cycle, which generates large amounts of carbohydrates from CO2.


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Cell_Biology_Alberts. In the early evolution of life, cyanobacteria overcame a major obstacle in devising a way to use solar energy to split water and fix carbon dioxide. Cyanobacteria produced both abundant organic nutrients and molecular oxygen, enabling the rise of a multitude of aerobic life-forms. The chloroplasts in plants have evolved from a cyanobacterium that was endocytosed long ago by an aerobic eukaryotic host organism. Figure 14–58 A comparison of three electron-transport chains discussed in this chapter.


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Cell_Biology_Alberts. Figure 14–58 A comparison of three electron-transport chains discussed in this chapter. Bacteria, chloroplasts, and mitochondria all contain a membrane-bound enzyme complex that resembles the cytochrome c reductase of mitochondria. these complexes all accept electrons from a quinone carrier (Q) and pump h+ across their respective membranes. Moreover, in reconstituted in vitro systems, the different complexes can substitute for one another, and the structures of their protein components reveal that they are evolutionarily related. Note that the purple nonsulfur bacteria use a cyclic flow of electrons to produce a large electrochemical proton gradient that drives a reverse electron flow through NaDh dehydrogenase to produce NaDh from NaD+ + h+ + e –.


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Cell_Biology_Alberts. As we discussed in Chapter 1, mitochondria and chloroplasts are thought to have evolved from endosymbiotic bacteria (see Figures 1–29 and 1–31). Both types of organelles still contain their own genomes (Figure 14–59). As we will discuss shortly, they also retain their own biosynthetic machinery for making RNA and organellar proteins.


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Cell_Biology_Alberts. Like bacteria, mitochondria and chloroplasts proliferate by growth and division of an existing organelle. In actively dividing cells, each type of organelle must double in mass in each cell generation and then be distributed into each daughter cell. In addition, nondividing cells must replenish organelles that are degraded as part of the continual process of organelle turnover, or produce additional organelles as the need arises. Organelle growth and proliferation are therefore carefully controlled. The process is complicated because mitochondrial and chloroplast proteins are encoded in two places: the nuclear genome and the separate genomes harbored in the organelles themselves. The biogenesis of mitochondria and chloroplasts thus requires contributions from two separate genetic systems, which must be closely coordinated.


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Cell_Biology_Alberts. Most organellar proteins are encoded by the nuclear DNA. The organelle imports these proteins from the cytosol, after they have been synthesized on cytosolic ribosomes, through the mitochondrial protein translocases of the outer and inner mitochondrial membrane—TOM and TIM. In Chapter 12, we discussed how this happens. Here, we describe the organelle genomes and genetic systems, and consider the consequences of separate organelle genomes for the cell and the organism as a whole. the Genetic Systems of Mitochondria and Chloroplasts resemble those of prokaryotes


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Cell_Biology_Alberts. the Genetic Systems of Mitochondria and Chloroplasts resemble those of prokaryotes As discussed in Chapter 12, it is thought that eukaryotic cells originated through a symbiotic relationship between an archaeon and an aerobic bacterium (a proteobacterium). The two organisms are postulated to have merged to form the ancestor of all nucleated cells, with the archeaon providing the nucleus and the proteobacterium serving as a respiring, ATP-producing endosymbiont—one that would eventually evolve into the mitochondrion (see Figure 12–3). This most likely occurred roughly 1.6 billion years ago, when oxygen had entered the atmosphere in substantial amounts (see Figure 14–56). The chloroplast was derived later, after the plant and animal lineages diverged, through endocytosis of an oxygen-producing cyanobacterium.


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Cell_Biology_Alberts. This endosymbiont hypothesis of organelle development receives strong support from the observation that the genetic systems of mitochondria and chloroplasts are similar to those of present-day bacteria. For example, chloroplast ribosomes are very similar to bacterial ribosomes, both in their structure and in their sensitivity to various antibiotics (such as chloramphenicol, streptomycin, erythromycin, and tetracyclin). In addition, protein synthesis in chloroplasts starts with N-formylmethionine, as in bacteria, and not with methionine as in the cytosol of eukaryotic cells. Although mitochondrial genetic systems are much less similar to those of present-day bacteria than are the genetic systems of chloroplasts, their ribosomes are also sensitive to antibacterial antibiotics, and protein synthesis in mitochondria also starts with N-formylmethionine.


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Cell_Biology_Alberts. Figure 14–59 Staining of nuclear and mitochondrial DNA. In this confocal micrograph of a human fibroblast, the nuclear DNa is stained with the dye DapI (blue) and mitochondrial DNa is visualized with fluorescent antibodies that bind DNa (green). the mitochondria are stained with fluorescent antibodies that recognize a specialized protein translocase specific to the outer mitochondrial membrane (red). Numerous copies of the mitochondrial genome are distributed in distinct nucleoids throughout the mitochondria that snake through the cytoplasm. (From C. Kukat et al., Proc. Natl Acad. Sci. USA 108:13534–13539, 2011. With permission from the National academy of Sciences.) 5 ˜m


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Cell_Biology_Alberts. The processes of organelle DNA transcription, protein synthesis, and DNA replication take place where the genome is located: in the matrix of mitochondria or the stroma of chloroplasts. Although the enzymes that mediate these genetic processes are unique to the organelle, and resemble those of bacteria (or even of bacterial viruses) rather than their eukaryotic analogs, the nuclear genome encodes the vast majority of these enzymes. Indeed, most present-day mitochondrial and chloroplast proteins are encoded by genes that reside in the cell nucleus. Over time, Mitochondria and Chloroplasts have Exported Most of their Genes to the Nucleus by Gene transfer


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Cell_Biology_Alberts. The nature of the organelle genes located in the nucleus of the cell demonstrates that an extensive transfer of genes from organelle to nuclear DNA has occurred in the course of eukaryotic evolution. Such successful gene transfer is expected to be rare, because any gene moved from the organelle needs to adapt to both nuclear transcription and cytoplasmic translation requirements. In addition, the protein needs to acquire a signal sequence that directs it to the correct organelle after its synthesis in the cytosol. By comparing the genes in the mitochondria from different organisms, we can infer that some of the gene transfers to the nucleus occurred relatively recently. The smallest and presumably most highly evolved mitochondrial genomes, for example, encode only a few hydrophobic inner-membrane proteins of the electron-transport chain, plus ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs). Other mitochondrial genomes that have remained more complex tend to contain this same subset


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Cell_Biology_Alberts. proteins of the electron-transport chain, plus ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs). Other mitochondrial genomes that have remained more complex tend to contain this same subset of genes along with others (Figure 14–60). The most complex mitochondrial genomes include genes that encode components of the mitochondrial genetic system, such as RNA polymerase subunits and ribosomal proteins; these same genes are found in the cell nucleus in yeast and all animal cells.


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Cell_Biology_Alberts. The proteins that are encoded by genes in the organellar DNA are synthesized on ribosomes within the organelle, using organelle-produced messenger RNA (mRNA) to specify their amino acid sequence (Figure 14–61). The protein traffic between the cytosol and these organelles seems to be unidirectional: proteins are normally not exported from mitochondria or chloroplasts to the cytosol. An important exception occurs when a cell is about to undergo apoptosis. As will be


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Cell_Biology_Alberts. Figure 14–60 Comparison of mitochondrial genomes. Less complex mitochondrial genomes encode subsets of the proteins and ribosomal rNas that are encoded by larger mitochondrial genomes. In this comparison, there are only five genes that are shared by the six mitochondrial genomes; these encode ribosomal rNas (rns and rnl), cytochrome b (cob), and two cytochrome oxidase subunits (cox1 and cox3). Blue indicates ribosomal rNas; green, ribosomal proteins; and brown, components of the respiratory chain and other proteins. (adapted from M.W. Gray, G. Burger and B.F. Lang, Science 283:1476–1481, 1999.) discussed in detail in Chapter 18, during apoptosis the mitochondrion releases proteins (most notably cytochrome c) from the crista space through its outer mitochondrial membrane, as part of an elaborate signaling pathway that is triggered to cause cells to undergo programmed cell death. the Fission and Fusion of Mitochondria are topologically Complex processes


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Cell_Biology_Alberts. the Fission and Fusion of Mitochondria are topologically Complex processes In mammalian cells, mitochondrial DNA makes up less than 1% of the total cellular DNA. In other cells, however, such as the leaves of higher plants or the very large egg cells of amphibians, a much larger fraction of the cellular DNA may be present in mitochondria or chloroplasts (Table 14–2), and a large fraction of the total RNA and protein synthesis takes place in the organelles. Mitochondria and chloroplasts are large enough to be visible by light microscopy in living cells. For example, mitochondria can be visualized by expressing in cells a genetically engineered fusion of a mitochondrial protein linked to green


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Cell_Biology_Alberts. Figure 14–61 Biogenesis of the respiratory-chain proteins in human mitochondria. Most of the protein components of the mitochondrial respiratory chain are encoded by nuclear DNa, with only a small number encoded by mitochondrial DNa (mtDNa). transcription of mtDNa produces 13 mrNas, all of which encode subunits of the oxidative phosphorylation system, and the 24 rNas (22 transfer rNas and 2 ribosomal rNas) needed for translation of these mrNas on the mitochondrial ribosomes (brown).


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Cell_Biology_Alberts. the mrNas produced by transcription of nuclear genes are translated on cytoplasmic ribosomes (green), which are distinct from the mitochondrial ribosomes. the nuclear-encoded mitochondrial proteins (dark green) are imported into mitochondria through two protein translocases called tOM and tIM, and constitute the vast majority of the approximately 1000 different protein species present in mammalian mitochondria. the nuclear-encoded mitochondrial proteins in humans include the majority of the oxidative phosphorylation system subunits, all proteins needed for expression and maintenance of mtDNa, and all proteins of the mitochondrial ribosomes. the mtDNa-encoded subunits (orange) assemble together with the nuclear subunits to form a functional oxidative phosphorylation system. (adapted from N.G. Larsson, Annu. Rev. Biochem. 79:683–706, 2010.)


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Cell_Biology_Alberts. Figure 14–62 The mitochondrial reticulum is dynamic. (a) In yeast cells, mitochondria form a continuous reticulum on the cytoplasmic side of the plasma membrane (stereo pair). (B) a balance between fission and fusion determines the arrangement of the mitochondria in different cells. (C) time-lapse fluorescent microscopy shows the dynamic behavior of the mitochondrial network in a yeast cell. In addition to shape changes, fission and fusion constantly remodel the network (red arrows). these pictures were taken at 3-minute intervals. (a and C, from J. Nunnari et al., Mol. Biol. Cell 8:1233–1242, 1997. With permission from the american Society for Cell Biology.) fluorescent protein (GFP), or cells can be incubated with a fluorescent dye that is specifically taken up by mitochondria because of their membrane potential. Such images demonstrate that the mitochondria in living cells are dynamic— frequently dividing by fission, fusing, and changing shape (Figure 14–62 and Movie 14.12). The


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Cell_Biology_Alberts. of their membrane potential. Such images demonstrate that the mitochondria in living cells are dynamic— frequently dividing by fission, fusing, and changing shape (Figure 14–62 and Movie 14.12). The fission of mitochondria may be necessary so that small parts of the network can pinch off and reach remote regions of the cell—for example in the thin, extended axon and dendrites of a neuron.


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Cell_Biology_Alberts. The fission and fusion of mitochondria are topologically complex processes that must ensure the integrity of the separate mitochondrial compartments defined by the inner and outer membranes. These processes control the number and shape of mitochondria, which can vary dramatically in different cell types, ranging from multiple spherical or wormlike organelles to a highly branched, net-shaped single organelle called a reticulum. Each depends on its own special set of proteins. The mitochondrial fission machine works by assembling dynamin-related GTPases (discussed in Chapter 13) into helical oligomers that cause local constrictions in tubular mitochondria. GTP hydrolysis then generates the mechanical force that severs the inner and outer mitochondrial membranes in one step (Figure 14–63). Mitochondrial fusion requires two separate machineries, one each for the outer and the inner membrane (Figure 14–64). In addition to GTP hydrolysis for force generation, both mechanisms also depend on


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Cell_Biology_Alberts. fusion requires two separate machineries, one each for the outer and the inner membrane (Figure 14–64). In addition to GTP hydrolysis for force generation, both mechanisms also depend on the mitochondrial proton-motive force for reasons that are still unknown.


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Cell_Biology_Alberts. animal Mitochondria Contain the Simplest Genetic Systems Known Comparisons of DNA sequences in different organisms reveal that, in vertebrates (including ourselves), the mutation rate during evolution has been roughly 100 times greater in the mitochondrial genome than in the nuclear genome. This difference is likely to be due to lower fidelity of mitochondrial DNA replication,


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Cell_Biology_Alberts. Figure 14–63 A model for mitochondrial division. Dynamin-1 (yellow) exists as dimers in the cytosol, which form larger oligomeric structures in a process that requires Gtp hydrolysis. Dynamin assemblies interact with the outer mitochondrial membrane through special adaptor proteins, forming a spiral of Gtp-dynamin around the mitochondrion that causes a constriction. a concerted Gtp-hydrolysis event in the dynamin subunits is then thought to produce the conformational changes that result in fission. (adapted from S. hoppins, L. Lackner and J. Nunnari, Annu. Rev. Biochem. 76:751–780, 2007.) inefficient DNA repair, or both, given that the mechanisms that perform these processes in the organelle are relatively simple compared with those in the nucleus. As discussed in Chapter 4, the relatively high rate of evolution of animal mitochondrial genes makes a comparison of mitochondrial DNA sequences especially useful for estimating the dates of relatively recent evolutionary events, such as


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Cell_Biology_Alberts. high rate of evolution of animal mitochondrial genes makes a comparison of mitochondrial DNA sequences especially useful for estimating the dates of relatively recent evolutionary events, such as the steps in primate evolution.


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Cell_Biology_Alberts. There are 13 protein-encoding genes in human mitochondrial DNA (Figure 14–65). These code for hydrophobic components of the respiratory-chain complexes and of ATP synthase. In contrast, roughly 1000 mitochondrial proteins are encoded in the nucleus, produced on cytosolic ribosomes, and imported by the protein import machinery in the outer and inner membrane (discussed in Chapter 12). It has been suggested that the cytosolic production of hydrophobic membrane proteins and their import into the organelle may present a problem to the cell, and that this is the reason why their genes have remained in the mitochondrion. However, some of the most hydrophobic mitochondrial proteins, such as the c subunit of the ATP synthase rotor ring, are imported from the cytosol in some species (though they are mitochondrially encoded in others). And the parasites Plasmodium falciparum and Leishmania tarentolae, which spend most of their life cycles inside cells of their host organisms, have retained only


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Cell_Biology_Alberts. mitochondrially encoded in others). And the parasites Plasmodium falciparum and Leishmania tarentolae, which spend most of their life cycles inside cells of their host organisms, have retained only two or three mitochondrially encoded proteins.


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Cell_Biology_Alberts. The size range of mitochondrial DNAs is similar to that of viral DNAs. The mitochondrial DNA in Plasmodium falciparum (the human malaria parasite) has less than 6000 nucleotide pairs, whereas the mitochondrial DNAs of some land plants contain more than 300,000 nucleotide pairs (Figure 14–66). In animals, the mitochondrial genome is a simple DNA circle of about 16,600 nucleotide pairs (less than 0.001% of the nuclear genome), and it is nearly the same size in organisms as different from us as Drosophila and sea urchins. The human mitochondrial genome has several surprising features that distinguish it from nuclear, chloroplast, and bacterial genomes: 1.


Cell_Biology_Alberts

Cell_Biology_Alberts. The human mitochondrial genome has several surprising features that distinguish it from nuclear, chloroplast, and bacterial genomes: 1. Dense gene packing. Unlike other genomes, the human mitochondrial genome seems to contain almost no noncoding DNA: nearly every nucleotide seems to be part of a coding sequence, either for a protein or for one of the rRNAs or tRNAs. Since these coding sequences run directly into each other, there is very little room left for regulatory DNA sequences. 2. Relaxed codon usage. Whereas 30 or more tRNAs specify amino acids in the cytosol and in chloroplasts, only 22 tRNAs are required for mitochondrial protein synthesis. The normal codon–anticodon pairing rules are relaxed in mitochondria, so that many tRNA molecules recognize any one of the four nucleotides in the third (wobble) position. Such “2 out of 3” pairing human mtDNA16,569 bporigin ofreplication cytochrome bdehydrogenase dehydrogenasecytochrome oxidasesubunitsATP synthase subunits


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Cell_Biology_Alberts. Figure 14–64 A model for mitochondrial fusion. the fusions of the outer and inner mitochondrial membranes are coordinated sequential events, each of which requires a separate set of protein factors. Outer membrane fusion is brought about by an outer-membrane Gtpase (purple), which forms an oligomeric complex that includes subunits anchored in the two membranes to be fused. Fusion of outer membranes requires Gtp and an h+ gradient across the inner membrane. For fusion of the inner membrane, a dynamin-related protein forms an oligomeric tethering complex (blue) that includes subunits anchored in the two inner membranes to be fused. Fusion of the inner membranes requires Gtp and the electrical component of the potential across the inner membrane. (adapted from S. hoppins, L. Lackner and J. Nunnari, Annu. Rev. Biochem. 76:751–780, 2007.)


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Cell_Biology_Alberts. Figure 14–65 The organization of the human mitochondrial genome. the human mitochondrial genome of ≈16,600 nucleotide pairs contains 2 rrNa genes, 22 trNa genes, and 13 protein-coding sequences. there are two transcriptional promoters, one for each strand of the mitochondrial DNa (mtDNa). the DNas of many other animal mitochondrial genomes have been completely sequenced. Most of these animal mitochondrial DNas encode precisely the same genes as humans, with the gene order being identical for animals ranging from fish to mammals. allows one tRNA to pair with any one of four codons and permits protein synthesis with fewer tRNA molecules. 3. Variant genetic code. Perhaps most surprising, comparisons of mitochondrial gene sequences and the amino acid sequences of the corresponding proteins indicate that the genetic code is different: 4 of the 64 codons have different “meanings” from those of the same codons in other genomes (Table 14–3).


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Cell_Biology_Alberts. The close similarity of the genetic code in all organisms provides strong evidence that they all have evolved from a common ancestor. How, then, do we explain the differences in the genetic code in many mitochondria? A hint comes from the finding that the mitochondrial genetic code in different organisms is not the same. In the mitochondrion with the largest number of genes in Figure 14–60, that of the protozoan Reclinomonas, the genetic code is unchanged from the standard genetic code of the cell nucleus. Yet UGA, which is a stop codon elsewhere, is read as tryptophan in the mitochondria of mammals, fungi, and invertebrates. Similarly, the codon AGG normally codes for arginine, but it codes for stop in the mitochondria of mammals and codes for serine in the mitochondria of Drosophila (see Table 14–3). Such variation suggests that a random drift can occur in the genetic code in mitochondria. Presumably, the unusually small number of proteins encoded by the mitochondrial genome makes


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Cell_Biology_Alberts. Table 14–3). Such variation suggests that a random drift can occur in the genetic code in mitochondria. Presumably, the unusually small number of proteins encoded by the mitochondrial genome makes an occasional change in the meaning of a rare codon tolerable, whereas such a change in a larger genome would alter the function of many proteins and thereby destroy the cell.


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Cell_Biology_Alberts. Interestingly, in many species, one or two tRNAs for mitochondrial protein synthesis are encoded in the nucleus. Some parasites, for example trypanosomes, have not retained any tRNA genes in their mitochondrial DNA. Instead, the required tRNAs are all produced in the cytosol and are thought to be imported into the mitochondrion by special tRNA translocases that are distinct from the mitochondrial protein import system.


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Cell_Biology_Alberts. Figure 14–66 Comparison of various sizes of mitochondrial genomes with the genome of bacterial ancestors. the complete DNa sequences for thousands of mitochondrial genomes have been determined. the lengths of a few of these mitochondrial DNas are shown to scale— as circles for those genomes thought to be circular and lines for linear genomes. the largest circle represents the genome of Rickettsia prowazekii, a small pathogenic bacterium whose genome most closely resembles that of mitochondria. the size of mitochondrial genomes does not correlate well with the number of proteins encoded in them: while human mitochondrial DNa encodes 13 proteins, the 22-fold larger mitochondrial DNa of Arabidopsis thaliana encodes only 32 proteins—that is, about 2.5-fold as many as human mitochondrial DNa. the extra DNa that is found in Arabidopsis, Marchantia, and other plant mitochondria may be “junk DNa”—that is, noncoding DNa with no apparent function. the mitochondrial DNa of the protozoan


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Cell_Biology_Alberts. DNa. the extra DNa that is found in Arabidopsis, Marchantia, and other plant mitochondria may be “junk DNa”—that is, noncoding DNa with no apparent function. the mitochondrial DNa of the protozoan Reclinomonas americana has 98 genes. (adapted from M.W. Gray, G. Burger and B.F. Lang, Science 283:1476–1481, 1999.)


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Cell_Biology_Alberts. The chloroplast genomes of land plants range in size from 70,000 to 200,000 nucleotide pairs. More than 300 chloroplast genomes have now been sequenced. Many are surprisingly similar, even in distantly related plants (such as tobacco and liverwort), and even those of green algae are closely related (Figure 14–67). Chloroplast genes are involved in three main processes: transcription, translation, and photosynthesis. Plant chloroplast genomes typically encode 80–90 proteins and around 45 RNAs, including 37 or more tRNAs. As in mitochondria, most of the organelle-encoded proteins are part of larger protein complexes that also contain one or more subunits encoded in the nucleus and imported from the cytosol.


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Cell_Biology_Alberts. The genomes of chloroplasts and bacteria have striking similarities. Basic regulatory sequences, such as transcription promoters and terminators, are virtually identical. The amino acid sequences of the proteins encoded in chloroplasts are clearly recognizable as bacterial, and several clusters of genes with related functions (such as those encoding ribosomal proteins) are organized in the same way in the genomes of chloroplasts, the bacterium E. coli, and cyanobacteria.


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Cell_Biology_Alberts. The mechanisms by which chloroplasts and bacteria divide are also similar. Both utilize FtsZ proteins, which are self-assembling GTPases related to tubulins (see Chapter 16). Bacterial FtsZ is a soluble protein that assembles into a dynamic ring of membrane-attached protofilaments beneath the plasma membrane in the middle of the dividing cell. The FtsZ ring acts as a scaffold for recruitment of other cell-division proteins and generates a contractile force that results in membrane constriction and eventually in cell division. Presumably, chloroplasts divide in very much the same way. Although both employ membrane-interacting GTPases, the mechanisms by which mitochondria and chloroplasts divide are fundamentally different. The machinery for chloroplast division acts from the inside, as in bacteria, while the dynamin-like GTPases divide mitochondria from the outside (see Figure 14–63). The chloroplasts have remained closer to their bacterial origins than have mitochondria, since the


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Cell_Biology_Alberts. in bacteria, while the dynamin-like GTPases divide mitochondria from the outside (see Figure 14–63). The chloroplasts have remained closer to their bacterial origins than have mitochondria, since the eukaryotic mechanisms of membrane constriction and vesicle formation have been adapted for mitochondrial fission.


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Cell_Biology_Alberts. The RNA editing and RNA processing that is prevalent in chloroplasts owes everything to their eukaryotic hosts. This RNA processing includes the generation of transcript 5ʹ and 3ʹ termini and the cleavage of polycistronic transcripts. In addition, an RNA editing process converts specific C residues to U and can change the amino acid specified by the edited codon. These and other RNA-based 23S 16S 23S 16S liverwort chloroplast DNA 121,024 bp KEY: Figure 14–67 The organization of the liverwort chloroplast genome. the chloroplast genome organization is similar in all higher plants, although the size varies from species to species—depending on how much of the DNa surrounding the genes encoding the chloroplast’s 16S and 23S ribosomal rNas is present in two copies.


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Cell_Biology_Alberts. processes are catalyzed by protein families that are not found in prokaryotes. One can ask why the expression of so few chloroplast genes needs to be so complex. One explanation is that the expression of chloroplast and nuclear genes must be closely coordinated. More generally, the bacterial concept of the operon as a co-regulated set of genes in a single transcription unit has been largely abandoned in chloroplasts. Polycistronic transcripts are cleaved into smaller fragments, which then require splicing or RNA editing to become functional. Organelle Genes are Maternally Inherited in animals and plants


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Cell_Biology_Alberts. Organelle Genes are Maternally Inherited in animals and plants In Saccharomyces cerevisiae (baker’s yeast), when two haploid cells mate, they are equal in size and contribute equal amounts of mitochondrial DNA to the diploid zygote. Mitochondrial inheritance in yeasts is therefore biparental: both parents contribute equally to the mitochondrial gene pool of the progeny. However, during the course of the subsequent asexual, vegetative growth, the mitochondria become distributed more or less randomly to daughter cells. After a few generations, the mitochondria of any given cell contain only the DNA from one or the other parent cell, because only a small sample of the mitochondrial DNA passes from the mother cell to the bud of the daughter cell. This process is known as mitotic segregation, and it gives rise to a distinct form of inheritance that is called non-Mendelian, or cytoplasmic inheritance, in contrast to the Mendelian inheritance of nuclear genes.


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Cell_Biology_Alberts. The inheritance of mitochondria in animals and plants is quite different. In these organisms, the egg cell contributes much more cytoplasm to the zygote than does the male gamete (sperm in animals, pollen in plants). For example, a typical human oocyte contains about 100,000 copies of maternal mitochondrial DNA, whereas a sperm cell contains only a few. In addition, an active process ensures that the sperm mitochondria do not compete with those in the egg. As sperm mature, the DNA is degraded in their mitochondria. Sperm mitochondria are also specifically recognized then eliminated from the fertilized egg cell by autophagy in very much the same way that damaged mitochondria are removed (by ubiquitylation followed by delivery to lysosomes, as discussed in Chapter 13). Because of these two processes, the mitochondrial inheritance in both animals and plants is uniparental. More precisely, the mitochondrial DNA passes from one generation to the next by maternal inheritance.


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Cell_Biology_Alberts. In about two-thirds of higher plants, the chloroplast precursors from the male parent (contained in pollen grains) fail to enter the zygote, so that chloroplast as well as mitochondrial DNA is maternally inherited. In other plants, the chloroplast precursors from the pollen grains enter the zygote, making chloroplast inheritance biparental. In such plants, defective chloroplasts are a cause of variegation: a mixture of normal and defective chloroplasts in a zygote may sort out by mitotic segregation during plant growth and development, thereby producing alternating green and white patches in leaves. Leaf cells in the green patches contain normal chloroplasts, while those in the white patches contain defective chloroplasts (Figure 14–68).


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Cell_Biology_Alberts. In humans, as we have explained, all the mitochondrial DNA in a fertilized egg cell is inherited from the mother. Some mothers carry a mixed population of both mutant and normal mitochondrial genomes. Their daughters and sons will inherit this mixture of normal and mutant mitochondrial DNAs and be healthy unless the process of mitotic segregation results in a majority of defective mitochondria in a particular tissue. Muscle and the nervous system are most at risk. Because they need particularly large amounts of ATP, muscle and nerve cells are particularly dependent on fully functional mitochondria.


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Cell_Biology_Alberts. Numerous diseases in humans are caused by mutations in mitochondrial DNA. These diseases are recognized by their passage from affected mothers to both their daughters and their sons, with the daughters but not the sons producing children with the disease. As expected from the random nature of mitotic segregation, the symptoms of these diseases vary greatly between different family members—including not only the severity and age of onset, but also which tissue is affected. There are also mitochondrial diseases that are caused by mutations in nuclear-encoded mitochondrial proteins; these diseases are inherited in the regular, Mendelian fashion. Figure 14–68 A variegated leaf. In the white patches, the plant cells have inherited a defective chloroplast. (Courtesy of John Innes Foundation.) the accumulation of Mitochondrial DNa Mutations Is a Contributor to aging


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Cell_Biology_Alberts. Mitochondria are marvels of efficiency in energy conversion, and they supply the cells of our body with a readily available source of energy in the form of ATP. But in highly developed, long-lived animals such as ourselves, the cells in our body age and eventually die. A factor in this inevitable process is the accumulation of deletions and point mutations in mitochondrial DNA. Oxidative damage to the cell by reactive oxygen species (ROS) such as H2O2, superoxide, or hydroxyl radicals also increases with age. The mitochondrial respiratory chain is the main source of ROS in animal cells, and animals in which mitochondrial superoxide dismutase—the main ROS scavenger—has been knocked out, die prematurely.


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Cell_Biology_Alberts. The less complex DNA replication and repair systems in mitochondria mean that accidents are corrected less efficiently. This results in a 100-fold higher occurrence of deletions and point mutations than in nuclear DNA. Mathematical modeling suggests that most of these mutations and lesions are acquired in childhood or early adult life, and then proliferate by clonal expansion in later life. Due to mitotic segregation, some cells will accumulate higher levels of faulty mitochondrial DNA than others. Above some threshold, serious deficiencies in respiratory-chain function will develop, producing cells that are senescent. In many organs of the human body, senescent cells with high levels of mitochondrial DNA damage are intermingled with normal cells, resulting in a mosaic of cells with and without respiratory-chain deficiency.


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Cell_Biology_Alberts. The main role of mitochondrial fusion in cellular physiology is most likely to ensure an even distribution of mitochondrial DNA throughout the mitochondrial reticulum, and to prevent the accumulation of damaged DNA in one part of the network. When the fusion machinery is defective, DNA is lost from a subset of the mitochondria in the cell. Loss of mitochondrial DNA leads to a loss of respiratory-chain function, and it can cause disease. All of the considerations just discussed have suggested to some scientists that changes in our mitochondria are major contributors to human aging. However, there are many other processes that tend to go wrong as cells and tissues age, as one might expect given the incredible complexity of human cell biology. Despite intensive research, the issue remains unresolved. Why Do Mitochondria and Chloroplasts Maintain a Costly Separate System for DNa transcription and translation?


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Cell_Biology_Alberts. Why Do Mitochondria and Chloroplasts Maintain a Costly Separate System for DNa transcription and translation? Why do mitochondria and chloroplasts require their own separate genetic systems, when other organelles that share the same cytoplasm, such as peroxisomes and lysosomes, do not? The question is not trivial, because maintaining a separate genetic system is costly: more than 90 proteins—including many ribosomal proteins, aminoacyl-tRNA synthetases, DNA polymerase, RNA polymerase, and RNA-processing and RNA-modifying enzymes—must be encoded by nuclear genes specifically for this purpose. Moreover, as we have seen, the mitochondrial genetic system entails the risk of aging and disease.


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Cell_Biology_Alberts. A possible reason for maintaining this costly and potentially hazardous arrangement is the highly hydrophobic nature of the nonribosomal proteins encoded by organelle genes. This may make their production in and import from the cytoplasm simply too difficult and energy-consuming. It is also possible that the evolution (and eventual elimination) of the organellar genetic systems is still ongoing, but for now there is no alternative for the cell than to maintain separate genetic systems for its nuclear, mitochondrial, and chloroplast genes.


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Cell_Biology_Alberts. Mitochondria are organelles that allow eukaryotes to carry out oxidative phosphorylation, while chloroplasts are organelles that allow plants to carry out photosynthesis. Presumably as a result of their prokaryotic origins, each organelle maintains and reproduces itself in a highly coordinated process that requires the contribution of two separate genetic systems—one in the organelle and the other in the cell nucleus. The vast majority of the proteins in these organelles are encoded by nuclear DNA, synthesized in the cytosol, and then imported individually into the organelle. Other organelle proteins, as well as organelle ribosomal and transfer RNAs, are encoded by the organelle DNA; these are synthesized in the organelle itself.


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Cell_Biology_Alberts. The ribosomes of chloroplasts closely resemble bacterial ribosomes, while the origin of mitochondrial ribosomes is more difficult to trace. Extensive protein similarities, however, suggest that both organelles originated when a primitive eukaryotic cell entered into a stable endosymbiotic relationship with a bacterium. Although some of the genes of these former bacteria still function to make organelle proteins and RNA, most of them have been transferred into the nuclear genome, where they encode bacteria-like enzymes that are synthesized on cytosolic ribosomes and then imported into the organelle. The mitochondrial DNA replication and DNA repair processes are substantially less effective than the corresponding processes in the cell nucleus. Damage therefore accumulates in the genome of mitochondria over time; this damage may be a substantial contributor to the aging of cells and organisms, and it can cause serious diseases. Which statements are true? Explain why or why not.


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Cell_Biology_Alberts. Which statements are true? Explain why or why not. 14–1 The three respiratory enzyme complexes in the mitochondrial inner membrane tend to associate with each other in ways that facilitate the correct transfer of electrons between appropriate complexes. 14–2 The number of c subunits in the rotor ring of ATP synthase defines how many protons need to pass through the turbine to make each molecule of ATP. 14–3 Mutations that are inherited according to Mendelian rules affect nuclear genes; mutations whose inheritance violates Mendelian rules are likely to affect organelle genes. Discuss the following problems. 14–4 In the 1860s, Louis Pasteur noticed that when he added O2 to a culture of yeast growing anaerobically on glucose, the rate of glucose consumption declined dramatically. Explain the basis for this result, which is known as the Pasteur effect.


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Cell_Biology_Alberts. 14–5 Heart muscle gets most of the ATP needed to power its continual contractions through oxidative phosphorylation. When oxidizing glucose to CO2, heart muscle consumes O2 at a rate of 10 μmol/min per g of tissue, in order to replace the ATP used in contraction and give a steady-state ATP concentration of 5 μmol/g of tissue. At this rate, What structures are needed to form the barriers that separate and maintain the differentiated membrane domains in a single continuous membrane—as for the cristae and inner boundary membrane in mitochondria? how does a eukaryotic cell regulate the many functions of mitochondria, including atp production? What are the origins and evolutionary history of photosynthetic complexes? are there undiscovered types of photosynthesis present on Earth to help answer this question? Why is the mutation rate so much higher in mitochondria than in the nucleus (and chloroplasts)? Could this high rate have been useful to the cell?


Cell_Biology_Alberts

Cell_Biology_Alberts. Why is the mutation rate so much higher in mitochondria than in the nucleus (and chloroplasts)? Could this high rate have been useful to the cell? What mechanisms and pathways have been used during evolution to transfer genes from the mitochondrion to the nucleus? how many seconds would it take the heart to consume an amount of ATP equal to its steady-state levels? (Complete oxidation of one molecule of glucose to CO2 yields 30 ATP, 26 of which are derived by oxidative phosphorylation using the 12 pairs of electrons captured in the electron carriers NADH and FADH2.) 14–6 Both H+ and Ca2+ are ions that move through the cytosol. Why is the movement of H+ ions so much faster than that of Ca2+ ions? How do you suppose the speed of these two ions would be affected by freezing the solution? Would you expect them to move faster or slower? Explain your answer.


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Cell_Biology_Alberts. 14–7 If isolated mitochondria are incubated with a source of electrons such as succinate, but without oxygen, electrons enter the respiratory chain, reducing each of the electron carriers almost completely. When oxygen is then introduced, the carriers become oxidized at different rates (Figure Q14–1). How does this result allow you to order Figure Q14–1 rapid spectrophotometric analysis of the rates of oxidation of electron carriers in the respiratory chain (problem 14–7). Cytochromes a and a3 cannot be distinguished and thus are listed as cytochrome (a + a3). the electron carriers in the respiratory chain? What is their (A) direction of rotation order?


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Cell_Biology_Alberts. 14–8 Normally, the flow of electrons to O2 is tightly linked to the production of ATP via the electrochemical gradient. If ATP synthase is inhibited, for example, electrons do not flow down the electron-transport chain and respiration ceases. Since the 1940s, several substances— such as 2,4-dinitrophenol—have been known to uncouple electron flow from ATP synthesis. Dinitrophenol was once prescribed as a diet drug to aid in weight loss. How would an uncoupler of oxidative phosphorylation pro mote weight loss? Why do you suppose dinitrophenol is (B) no longer prescribed? 5 14–9 In actively respiring liver mitochondria, the pH in 4 the matrix is about half a pH unit higher than it is in the cytosol. Assuming that the cytosol is at pH 7 and the matrix is a sphere with a diameter of 1 μm [V = (4/3)πr3], calcu late the total number of protons in the matrix of a respiring liver mitochondrion. If the matrix began at pH 7 (equal to that in the cytosol), how many protons would have to be pumped


Cell_Biology_Alberts

Cell_Biology_Alberts. calcu late the total number of protons in the matrix of a respiring liver mitochondrion. If the matrix began at pH 7 (equal to that in the cytosol), how many protons would have to be pumped out to establish a matrix pH of 7.5 (a difference of 0.5 pH units)?


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Cell_Biology_Alberts. 14–10 ATP synthase is the world’s smallest rotary motor. Passage of H+ ions through the membrane-embedded portion of ATP synthase (the Fo component) causes rotation of the single, central, axle-like γ subunit inside the head group. The tripartite head is composed of the three αβ dimers, the β subunit of which is responsible for synthesis of ATP. The rotation of the γ subunit induces conformational changes in the αβ dimers that allow ADP and Pi to be converted into ATP. A variety of indirect evidence had suggested rotary catalysis by ATP synthase, but seeing is believing.


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Cell_Biology_Alberts. To demonstrate rotary motion, a modified form of the α3β3γ complex was used. The β subunits were modified so they could be firmly anchored to a solid support and the γ subunit was modified (on the end that normally inserts into the Fo component in the inner membrane) so that a fluorescently tagged, readily visible filament of actin could be attached (Figure Q14–2A). This arrangement allows rotations of the γ subunit to be visualized as revolutions of the long actin filament. In these experiments, ATP synthase was studied in the reverse of its normal mechanism by allowing it to hydrolyze ATP. At low ATP concentrations, the actin filament was observed to revolve in steps of 120° and then pause for variable lengths of time, as shown in Figure Q14–2B. A. Why does the actin filament revolve in steps with pauses in between? What does this rotation correspond to in terms of the structure of the α3β3γ complex?


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Cell_Biology_Alberts. A. Why does the actin filament revolve in steps with pauses in between? What does this rotation correspond to in terms of the structure of the α3β3γ complex? B. In its normal mode of operation inside the cell, how many ATP molecules do you suppose would be synthesized for each complete 360° rotation of the γ subunit? Explain your answer. 14–11 How much energy is available in visible light? How much energy does sunlight deliver to Earth? How efficient


Cell_Biology_Alberts

Cell_Biology_Alberts. 14–11 How much energy is available in visible light? How much energy does sunlight deliver to Earth? How efficient Figure Q14–2 Experimental set-up for observing rotation of the γ subunit of atp synthase (problem 14–10). (a) the immobilized α3β3γ complex. the β subunits are anchored to a solid support and a fluorescent actin filament is attached to the γ subunit. (B) Stepwise revolution of the actin filament. the indicated trace is a typical example from one experiment. the inset shows the positions in the revolution at which the actin filament pauses. (B, from r. yasuda et al., Cell 93:1117–1124, 1998. With permission from Elsevier.) are plants at converting light energy into chemical energy? The answers to these questions provide an important backdrop to the subject of photosynthesis.


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Cell_Biology_Alberts. Each quantum or photon of light has energy hv, where h is Planck’s constant (6.6 × 10–37 kJ sec/photon) and v is the frequency in sec–1. The frequency of light is equal to c/λ, where c is the speed of light (3.0 × 1017 nm/ sec) and λ is the wavelength in nm. Thus, the energy (E) of a photon is A. Calculate the energy of a mole of photons (6 × 1023 photons/mole) at 400 nm (violet light), at 680 nm (red light), and at 800 nm (near-infrared light). B. Bright sunlight strikes Earth at the rate of about 1.3 kJ/sec per square meter. Assuming for the sake of calculation that sunlight consists of monochromatic light of wavelength 680 nm, how many seconds would it take for a mole of photons to strike a square meter?


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Cell_Biology_Alberts. C. Assuming that it takes eight photons to fix one molecule of CO2 as carbohydrate under optimal conditions (8–10 photons is the currently accepted value), calculate how long it would take a tomato plant with a leaf area of 1 square meter to make a mole of glucose from CO2. Assume that photons strike the leaf at the rate calculated above and, furthermore, that all the photons are absorbed and used to fix CO2. D. If it takes 468 kJ/mole to fix a mole of CO2 into carbohydrate, what is the efficiency of conversion of light energy into chemical energy after photon capture? Assume again that eight photons of red light (680 nm) are required to fix one molecule of CO2.


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Cell_Biology_Alberts. 14–12 In chloroplasts, protons are pumped out of the stroma across the thylakoid membrane, whereas in mitochondria, they are pumped out of the matrix across the crista membrane. Explain how this arrangement allows chloroplasts to generate a larger proton gradient across the thylakoid membrane than mitochondria can generate across the inner membrane. 14–13 Examine the variegated leaf shown in Figure Q14–3. Yellow patches surrounded by green are common, but there are no green patches surrounded by yellow. Propose an explanation for this phenomenon. Figure Q14–3 a variegated leaf of Aucuba japonica with green and yellow patches (problem 14–13). Cramer Wa & Knaff DB (1990) Energy transduction in Biological Membranes: a textbook of Bioenergetics. New york: Springer-Verlag. Mathews CK, van holde KE & ahern K-G (2012) Biochemistry, 4th ed. San Francisco: Benjamin Cummings. Nicholls DG & Ferguson SJ (2013) Bioenergetics, 4th ed. New york: academic press.


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Cell_Biology_Alberts. Mathews CK, van holde KE & ahern K-G (2012) Biochemistry, 4th ed. San Francisco: Benjamin Cummings. Nicholls DG & Ferguson SJ (2013) Bioenergetics, 4th ed. New york: academic press. Schatz G (2012) the fires of life. Annu. Rev. of Biochem.81, 34–59. The Mitochondrion Ernster L & Schatz G (1981) Mitochondria: a historical review. J. Cell Biol. 91, 227s–255s. Friedman Jr & Nunnari J (2014) Mitochondrial form and function. Nature 505, 335–43. Mitchell p (1961) Coupling of phosphorylation to electron and hydrogen transfer by a chemi-osmotic type of mechanism. Nature 191, 144–148. pebay-peyroula E & Brandolin G (2004) Nucleotide exchange in mitochondria: insight at a molecular level. Curr. Opin. Struct. Biol. 14, 420–425. Scheffler IE (1999) Mitochondria. New york/Chichester: Wiley-Liss.


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Cell_Biology_Alberts. Scheffler IE (1999) Mitochondria. New york/Chichester: Wiley-Liss. The Proton Pumps of the Electron-Transport Chain althoff t, Mills DJ, popot J-L & Kühlbrandt W (2011) arrangement of electron transport chain components in bovine mitochondrial supercomplex I1III2IV1. EMBO J. 30, 4652–4664. Baradaran r, Berrisford JM, Minhas GS & Sazanov La (2013) Crystal structure of the entire respiratory complex I. Nature 494, 443–448. Beinert h, holm rh & Münck E (1997) Iron-sulfur clusters: nature’s modular, multipurpose structures. Science 277, 653–659. Berry Ea, Guergova-Kuras M, huang LS & Crofts ar (2000) Structure and function of cytochrome bc complexes. Annu. Rev. Biochem. 69, 1005–1075. Brandt U (2006) Energy converting NaDh:quinone oxidoreductase (complex I). Annu. Rev. Biochem. 75, 69–92. Chance B & Williams Gr (1955) a method for the localization of sites for oxidative phosphorylation. Nature 176, 250–254.


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Cell_Biology_Alberts. Chance B & Williams Gr (1955) a method for the localization of sites for oxidative phosphorylation. Nature 176, 250–254. Cooley JW (2013) protein conformational changes involved in the cytochrome bc1 complex catalytic cycle Biochim. Biophys. Acta. 1827, 1340–45. Gottschalk G (1997) Bacterial Metabolism, 2nd ed. New york: Springer. Gray hB & Winkler Jr (1996) Electron transfer in proteins. Annu. Rev. Biochem. 65, 537–561. hirst J (2013) Mitochondrial complex I. Ann. Rev. Biochem. 82, 551–75. hosler Jp, Ferguson-Miller S & Mills Da (2006) Energy transduction: proton transfer through the respiratory complexes. Annu. Rev. Biochem. 75, 165–187. hunte C, Zickermann V & Brandt U (2010) Functional modules and structural basis of conformational coupling in mitochondrial complex I. Science 329, 448–451. Keilin D (1966) the history of Cell respiration and Cytochromes. Cambridge, UK: Cambridge University press.


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Cell_Biology_Alberts. Keilin D (1966) the history of Cell respiration and Cytochromes. Cambridge, UK: Cambridge University press. rouault ta, tracey a & tong Wh (2008) Iron–sulfur cluster biogenesis and human disease. Trends Genet. 24, 398–407. trumpower BL (2002) a concerted, alternating sites mechanism of ubiquinol oxidation by the dimeric cytochrome bc1 complex. Biochim. Biophys. Acta. 1555, 166–173. tsukihara t, aoyama h, yamashita E et al. (1996) the whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 Å. Science 272, 1136–1144. abrahams Jp, Leslie aG, Lutter r & Walker JE (1994) Structure at 2.8 Å resolution of F1-atpase from bovine heart mitochondria. Nature 370, 621–628. Berg hC (2003) the rotary motor of bacterial flagella. Annu. Rev. Biochem. 72, 19–54. Boyer pD (1997) the atp synthase—a splendid molecular machine. Annu. Rev. Biochem. 66, 717–749.


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Cell_Biology_Alberts. Meier t, polzer p, Diederichs K et al. (2005) Structure of the rotor ring of F-type Na+-atpase from Ilyobacter tartaricus. Science 308, 659–662. Stock D, Gibbons C, arechaga I et al. (2000) the rotary mechanism of atp synthase. Curr. Opin. Struct. Biol. 10, 672–679. von Ballmoos C, Wiedenmann a & Dimroth p (2009) Essentials for atp synthesis by F1F0 atp synthases. Annu. Rev. Biochem. 78, 649–672. Barber J (2013) photosystem II: the water-splitting enzyme of photosynthesis. Cold Spring Harbor Symp. Quant. Biol. 77, 295–307. Bassham Ja (1962) the path of carbon in photosynthesis. Sci. Am. 206, 89–100. Blankenship rE (2002) Molecular Mechanisms of photosynthesis. Oxford, UK: Blackwell Scientific. Blankenship rE & Bauer CE (eds) (1995) anoxygenic photosynthetic Bacteria. Dordrecht: Kluwer. Deisenhofer J & Michel h (1989) Nobel lecture. the photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis. EMBO J. 8, 2149–2170.


Cell_Biology_Alberts

Cell_Biology_Alberts. Deisenhofer J & Michel h (1989) Nobel lecture. the photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis. EMBO J. 8, 2149–2170. De Las rivas J, Balsera M & Barber J (2004) Evolution of oxygenic photosynthesis: genome-wide analysis of the OEC extrinsic proteins. Trends Plant Sci. 9:18–25. hohmann-Marriott MF & Blankenship rE (2011) Evolution of photosynthesis. Annu. Rev. Plant Biol. 62, 515–548. Jordan p, Fromme p, Witt ht et al. (2001) three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution. Nature 411, 909–917. Kühlbrandt W, Wang DN & Fujiyoshi y (1994) atomic model of plant light-harvesting complex by electron crystallography. Nature 367, 614–621. Lane N & Martin WF (2012) the origin of membrane bioenergetics. Cell 151, 1406–1416. Lyons tW, reinhard Ct & planavsky NJ (2014) the rise of oxygen in earth’s early ocean and atmosphere. Nature 506, 307–15.


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Cell_Biology_Alberts. Lyons tW, reinhard Ct & planavsky NJ (2014) the rise of oxygen in earth’s early ocean and atmosphere. Nature 506, 307–15. Nelson N & Ben-Shem a (2004) the complex architecture of oxygenic photosynthesis. Nat. Rev. Mol. Cell Biol. 5, 971–982. Orgel LE (1998) the origin of life—a review of facts and speculations. Trends Biochem. Sci. 23, 491–495. tang K-h, tang yJ & Blankenship rE (2011) Carbon metabolic pathways in phototrophic bacteria and their broader evolutionary implications. Front. Microbiol. 2, 165. Umena y, Kawakami K, Shen J-r & Kamiya N (2011) Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å. Nature 473, 55–60. Vinyard DJ, ananyev GM & Dismukes GC (2013) photosystem II: the reaction center of oxygenic photosynthesis. Annu. Rev. Biochem. 82, 577–606. yano J, Kern J, Sauer K et al. (2006) Where water is oxidized to dioxygen: structure of the photosynthetic Mn4Ca cluster. Science 314, 821–25.


Cell_Biology_Alberts

Cell_Biology_Alberts. yano J, Kern J, Sauer K et al. (2006) Where water is oxidized to dioxygen: structure of the photosynthetic Mn4Ca cluster. Science 314, 821–25. yoon hS (2004) a molecular timeline for the origin of photosynthetic eukaryotes. Mol. Biol. Evol. 21, 809–18. The Genetic Systems of Mitochondria and Chloroplasts anderson S, Bankier at, Barrell BG et al. (1981) Sequence and organization of the human mitochondrial genome. Nature 290, 457–465. Bendich aJ (2004) Circular chloroplast chromosomes: the grand illusion. Plant Cell 16, 1661–1666. Birky CW Jr (1995) Uniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolution. Proc. Natl Acad. Sci. USA 92, 11331–11338. Bullerwell CE & Gray MW (2004) Evolution of the mitochondrial genome: protist connections to animals, fungi and plants. Curr. Opin. Microbiol. 7, 528–534. Chen XJ & Butow ra (2005) the organization and inheritance of the mitochondrial genome. Nat. Rev. Genet. 6, 815–825.


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Cell_Biology_Alberts. Chen XJ & Butow ra (2005) the organization and inheritance of the mitochondrial genome. Nat. Rev. Genet. 6, 815–825. Clayton Da (2000) Vertebrate mitochondrial DNa—a circle of surprises. Exp. Cell Res. 255, 4–9. Daley DO & Whelan J (2005) Why genes persist in organelle genomes. Genome Biol. 6, 110. de Duve C (2007) the origin of eukaryotes: a reappraisal. Nat. Rev. Genet. 8, 395–403. Dyall SD, Brown Mt & Johnson pJ (2004) ancient invasions: from endosymbionts to organelles. Science 304, 253–257. Falkenberg M, Larsson NG & Gustafsson CM (2007) DNa replication and transcription in mammalian mitochondria. Annu. Rev. Biochem. 76, 679–699. harel a, Bromberg y, Falkowski pG & Bhattacharya D (2014) Evolutionary history of redox metal-binding domains across the tree of life. Proc. Natl Acad. Sci. USA 111, 7042–47. hoppins S, Lackner L & Nunnari J (2007) the machines that divide and fuse mitochondria. Annu. Rev. Biochem. 76, 751–780.


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Cell_Biology_Alberts. hoppins S, Lackner L & Nunnari J (2007) the machines that divide and fuse mitochondria. Annu. Rev. Biochem. 76, 751–780. Larsson NG (2010) Somatic mitochondrial DNa mutations in mammalian aging. Annu. Rev. Biochem. 79, 683–706. Ma h, Xu h & O’Farrell ph (2014) transmission of mitochondrial mutations and action of purifying selection in Drosophila melanogaster. Nat. Genet. 46, 393–97. Neupert W & herrmann JM (2007) translocation of proteins into mitochondria. Annu. Rev. Biochem. 76, 723–749. rawi a, Louvet-Vallee SS, Djeddi D et al. (2011) postfertilization autophagy of sperm organelles prevents paternal mitochondrial DNa transmission. Science 334, 1144–47. taylor rW, Barron MJ, Borthwick GM et al. (2003) Mitochondrial DNa mutations in human colonic crypt stem cells. J. Clin. Invest. 112, 1351–60. Wallace DC (1999) Mitochondrial diseases in man and mouse. Science 283, 1482–1488.


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Cell_Biology_Alberts. Wallace DC (1999) Mitochondrial diseases in man and mouse. Science 283, 1482–1488. Williams ta, Foster pG, Cox CJ & Embley tM (2014) an archaeal origin of eukaryotes supports only two primary domains of life. Nature 504, 231–36.


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Cell_Biology_Alberts. When things change, cells respond. Every cell, from the humble bacterium to the most sophisticated eukaryotic cell, monitors its intracellular and extracellular environment, processes the information it gathers, and responds accordingly. Unicellular organisms, for example, modify their behavior in response to changes in environmental nutrients or toxins. The cells of multicellular organisms detect and respond to countless internal and extracellular signals that control their growth, division, and differentiation during development, as well as their behavior in adult tissues. At the heart of all these communication systems are regulatory proteins that produce chemical signals, which are sent from one place to another in the body or within a cell, usually being processed along the way and integrated with other signals to provide clear and effective communication.


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Cell_Biology_Alberts. The study of cell signaling has traditionally focused on the mechanisms by which eukaryotic cells communicate with each other using extracellular signal molecules such as hormones and growth factors. In this chapter, we describe the features of some of these cell–cell communication systems, and we use them to illustrate the general principles by which any regulatory system, inside or outside the cell, is able to generate, process, and respond to signals. Our main focus is on animal cells, but we end by considering the special features of cell signaling in plants.


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Cell_Biology_Alberts. Long before multicellular creatures roamed the Earth, unicellular organisms had developed mechanisms for responding to physical and chemical changes in their environment. These almost certainly included mechanisms for responding to the presence of other cells. Evidence comes from studies of present-day unicellular organisms such as bacteria and yeasts. Although these cells lead mostly independent lives, they can communicate and influence one another’s behavior. Many bacteria, for example, respond to chemical signals that are secreted by their neighbors and accumulate at higher population density. This process, called quorum sensing, allows bacteria to coordinate their behavior, including their motility, antibiotic production, spore formation, and sexual conjugation. Similarly, yeast cells communicate with one another in preparation for mating. The budding yeast Saccharomyces cerevisiae provides a well-studied example: when a haploid individual is ready to mate, it secretes a peptide


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Cell_Biology_Alberts. communicate with one another in preparation for mating. The budding yeast Saccharomyces cerevisiae provides a well-studied example: when a haploid individual is ready to mate, it secretes a peptide mating factor that signals cells of the opposite mating type to stop proliferating and prepare to mate. The subsequent fusion of two haploid cells of opposite mating type produces a diploid zygote.


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Cell_Biology_Alberts. Intercellular communication achieved an astonishing level of complexity during the evolution of multicellular organisms. These organisms are tight-knit societies of cells, in which the well-being of the individual cell is often set aside for the benefit of the organism as a whole. Complex systems of intercellular communication have evolved to allow the collaboration and coordination of different tissues and cell types. Bewildering arrays of signaling systems govern every conceivable feature of cell and tissue function during development and in the adult. Communication between cells in multicellular organisms is mediated mainly by extracellular signal molecules. Some of these operate over long distances, plasma membrane of target cellCYTOSOL


Cell_Biology_Alberts

Cell_Biology_Alberts. Communication between cells in multicellular organisms is mediated mainly by extracellular signal molecules. Some of these operate over long distances, plasma membrane of target cellCYTOSOL Figure 15–1 A simple intracellular signaling pathway activated by an extracellular signal molecule. The signal molecule usually binds to a receptor protein that is embedded in the plasma membrane of the target cell. The receptor activates one or more intracellular signaling pathways, involving a series of signaling proteins. Finally, one or more of the intracellular signaling proteins alters the activity of effector proteins and thereby the behavior of the cell.


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Cell_Biology_Alberts. signaling to cells far away; others signal only to immediate neighbors. Most cells in multicellular organisms both emit and receive signals. Reception of the signals depends on receptor proteins, usually (but not always) at the cell surface, which bind the signal molecule. The binding activates the receptor, which in turn activates one or more intracellular signaling pathways or systems. These systems depend on intracellular signaling proteins, which process the signal inside the receiving cell and distribute it to the appropriate intracellular targets. The targets that lie at the end of signaling pathways are generally called effector proteins, which are altered in some way by the incoming signal and implement the appropriate change in cell behavior. Depending on the signal and the type and state of the receiving cell, these effectors can be transcription regulators, ion channels, components of a metabolic pathway, or parts of the cytoskeleton (Figure 15–1).


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Cell_Biology_Alberts. The fundamental features of cell signaling have been conserved throughout the evolution of the eukaryotes. In budding yeast, for example, the response to mating factor depends on cell-surface receptor proteins, intracellular GTP-binding proteins, and protein kinases that are clearly related to functionally similar proteins in animal cells. Through gene duplication and divergence, however, the signaling systems in animals have become much more elaborate than those in yeasts; the human genome, for example, contains more than 1500 genes that encode receptor proteins, and the number of different receptor proteins is further increased by alternative RNA splicing and post-translational modifications.


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Cell_Biology_Alberts. Many extracellular signal molecules remain bound to the surface of the signaling cell and influence only cells that contact it (Figure 15–2A). Such contact-dependent signaling is especially important during development and in immune responses. Contact-dependent signaling during development can sometimes operate over relatively large distances if the communicating cells extend long thin processes to make contact with one another. Figure 15–2 Four forms of intercellular signaling. (A) Contact-dependent signaling requires cells to be in direct membrane– membrane contact. (B) Paracrine signaling depends on local mediators that are released into the extracellular space and act on neighboring cells. (C) Synaptic signaling is performed by neurons that transmit signals electrically along their axons and release neurotransmitters at synapses, which are often located far away from the neuronal cell body.


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Cell_Biology_Alberts. (D) Endocrine signaling depends on endocrine cells, which secrete hormones into the bloodstream for distribution throughout the body. Many of the same types of signaling molecules are used in paracrine, synaptic, and endocrine signaling; the crucial differences lie in the speed and selectivity with which the signals are delivered to their targets. In most cases, however, signaling cells secrete signal molecules into the extracellular fluid. Often, the secreted molecules are local mediators, which act only on cells in the local environment of the signaling cell. This is called paracrine signaling (Figure 15–2B). Usually, the signaling and target cells in paracrine signaling are of different cell types, but cells may also produce signals that they themselves respond to: this is referred to as autocrine signaling. Cancer cells, for example, often produce extracellular signals that stimulate their own survival and proliferation.


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Cell_Biology_Alberts. Large multicellular organisms like us need long-range signaling mechanisms to coordinate the behavior of cells in remote parts of the body. Thus, they have evolved cell types specialized for intercellular communication over large distances. The most sophisticated of these are nerve cells, or neurons, which typically extend long, branching processes (axons) that enable them to contact target cells far away, where the processes terminate at the specialized sites of signal transmission known as chemical synapses. When a neuron is activated by stimuli from other nerve cells, it sends electrical impulses (action potentials) rapidly along its axon; when the impulse reaches the synapse at the end of the axon, it triggers secretion of a chemical signal that acts as a neurotransmitter. The tightly organized structure of the synapse ensures that the neurotransmitter is delivered specifically to receptors on the postsynaptic target cell (Figure 15–2C). The details of this synaptic signaling


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Cell_Biology_Alberts. organized structure of the synapse ensures that the neurotransmitter is delivered specifically to receptors on the postsynaptic target cell (Figure 15–2C). The details of this synaptic signaling process are discussed in Chapter 11.


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Cell_Biology_Alberts. A quite different strategy for signaling over long distances makes use of endocrine cells, which secrete their signal molecules, called hormones, into the bloodstream. The blood carries the molecules far and wide, allowing them to act on target cells that may lie anywhere in the body (Figure 15–2D). Extracellular Signal Molecules Bind to Specific Receptors


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Cell_Biology_Alberts. Extracellular Signal Molecules Bind to Specific Receptors Cells in multicellular animals communicate by means of hundreds of kinds of extracellular signal molecules. These include proteins, small peptides, amino acids, nucleotides, steroids, retinoids, fatty acid derivatives, and even dissolved gases such as nitric oxide and carbon monoxide. Most of these signal molecules are released into the extracellular space by exocytosis from the signaling cell, as discussed in Chapter 13. Some, however, are emitted by diffusion through the signaling cell’s plasma membrane, whereas others are displayed on the external surface of the cell and remain attached to it, providing a signal to other cells only when they make contact. Transmembrane signal proteins may operate in this way, or their extracellular domains may be released from the signaling cell’s surface by proteolytic cleavage and then act at a distance.


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Cell_Biology_Alberts. Regardless of the nature of the signal, the target cell responds by means of a receptor, which binds the signal molecule and then initiates a response in the target cell. The binding site of the receptor has a complex structure that is shaped to recognize the signal molecule with high specificity, helping to ensure that the receptor responds only to the appropriate signal and not to the many other signaling molecules surrounding the cell. Many signal molecules act at very low concentrations (typically ≤ 10–8 M), and their receptors usually bind them with high affinity (dissociation constant Kd ≤ 10–8 M; see Figure 3–44).


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Cell_Biology_Alberts. In most cases, receptors are transmembrane proteins on the target-cell surface. When these proteins bind an extracellular signal molecule (a ligand), they become activated and generate various intracellular signals that alter the behavior of the cell. In other cases, the receptor proteins are inside the target cell, and the signal molecule has to enter the cell to bind to them: this requires that the signal molecule be sufficiently small and hydrophobic to diffuse across the target cell’s plasma membrane (Figure 15–3). This chapter focuses primarily on signaling through cell-surface receptors, but we will briefly describe signaling through intracellular receptors later in the chapter. Each Cell Is Programmed to Respond to Specific Combinations of Extracellular Signals


Cell_Biology_Alberts

Cell_Biology_Alberts. Each Cell Is Programmed to Respond to Specific Combinations of Extracellular Signals A typical cell in a multicellular organism is exposed to hundreds of different signal molecules in its environment. The molecules can be soluble, bound to the extracellular matrix, or bound to the surface of a neighboring cell; they can be stimulatory or inhibitory; they can act in innumerable different combinations; and they can influence almost any aspect of cell behavior. The cell responds to this blizzard of signals selectively, in large part by expressing only those receptors and intracellular signaling systems that respond to the signals that are required for the regulation of that cell.


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Cell_Biology_Alberts. Most cells respond to many different signals in the environment, and some of these signals may influence the response to other signals. One of the key challenges in cell biology is to determine how a cell integrates all of this signaling information in order to make decisions—to divide, to move, to differentiate, and so on. Many cells, for example, require a specific combination of extracellular survival factors to allow the cell to continue living; when deprived of these signals, the cell activates a suicide program and kills itself—usually by apoptosis, a form of programmed cell death, as discussed in Chapter 18. Cell proliferation often depends on a combination of signals that promote both cell division and survival, as well as signals that stimulate cell growth (Figure 15–4). On the other hand, differentiation into a nondividing state (called terminal differentiation) frequently requires a different combination of survival and differentiation signals that must override any signal


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Cell_Biology_Alberts. hand, differentiation into a nondividing state (called terminal differentiation) frequently requires a different combination of survival and differentiation signals that must override any signal to divide.


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Cell_Biology_Alberts. In principle, the hundreds of signal molecules that an animal makes can be used in an almost unlimited number of combinations to control the diverse behaviors of its cells in highly specific ways. Relatively small numbers of types of signal molecules and receptors are sufficient. The complexity lies in the ways in which cells respond to the combinations of signals that they receive. A signal molecule often has different effects on different types of target cells. The neurotransmitter acetylcholine (Figure 15–5A), for example, decreases the small, hydrophobic signal molecule


Cell_Biology_Alberts

Cell_Biology_Alberts. A signal molecule often has different effects on different types of target cells. The neurotransmitter acetylcholine (Figure 15–5A), for example, decreases the small, hydrophobic signal molecule Figure 15–3 The binding of extracellular signal molecules to either cell-surface or intracellular receptors. (A) Most signal molecules are hydrophilic and are therefore unable to cross the target cell’s plasma membrane directly; instead, they bind to cell-surface receptors, which in turn generate signals inside the target cell (see Figure 15–1). (B) Some small signal molecules, by contrast, diffuse across the plasma membrane and bind to receptor proteins inside the target cell—either in the cytosol or in the nucleus (as shown here). Many of these small signal molecules are hydrophobic and poorly soluble in aqueous solutions; they are therefore transported in the bloodstream and other extracellular fluids bound to carrier proteins, from which they dissociate before entering the target cell.


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Cell_Biology_Alberts. rate of action potential firing in heart pacemaker cells (Figure 15–5B) and stimulates the production of saliva by salivary gland cells (Figure 15–5C), even though the receptors are the same on both cell types. In skeletal muscle, acetylcholine causes the cells to contract by binding to a different receptor protein (Figure 15–5D). The different effects of acetylcholine in these cell types result from differences in the intracellular signaling proteins, effector proteins, and genes that are activated. Thus, an extracellular signal itself has little information content; it simply induces the cell to respond according to its predetermined state, which depends on the cell’s developmental history and the specific genes it expresses.


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Cell_Biology_Alberts. Figure 15–4 An animal cell’s dependence on multiple extracellular signal molecules. Each cell type displays a set of receptors that enables it to respond to a corresponding set of signal molecules produced by other cells. These signal molecules work in various combinations to regulate the behavior of the cell. As shown here, an individual cell often requires multiple signals to survive (blue arrows) and additional signals to grow and divide (red arrows) or differentiate (green arrows). If deprived of appropriate survival signals, a cell will undergo a form of cell suicide known as apoptosis. The actual situation is even more complex. Although not shown, some extracellular signal molecules act to inhibit these and other cell behaviors, or even to induce apoptosis.


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Cell_Biology_Alberts. Figure 15–5 Various responses induced by the neurotransmitter acetylcholine. (A) The chemical structure of acetylcholine. (B–D) Different cell types are specialized to respond to acetylcholine in different ways. In some cases (B and C), acetylcholine binds to similar receptor proteins (G-protein-coupled receptors; see Figure 15–6), but the intracellular signals produced are interpreted differently in cells specialized for different functions. In other cases (D), the receptor protein is also different (here, an ion-channel-coupled receptor; see Figure 15–6). There Are Three Major Classes of Cell-Surface Receptor Proteins Most extracellular signal molecules bind to specific receptor proteins on the surface of the target cells they influence and do not enter the cytosol or nucleus. These cell-surface receptors act as signal transducers by converting an extracellular ligand-binding event into intracellular signals that alter the behavior of the target cell.


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Cell_Biology_Alberts. Most cell-surface receptor proteins belong to one of three classes, defined by their transduction mechanism. Ion-channel-coupled receptors, also known as transmitter-gated ion channels or ionotropic receptors, are involved in rapid synaptic signaling between nerve cells and other electrically excitable target cells such as nerve and muscle cells (Figure 15–6A). This type of signaling is mediated by a small number of neurotransmitters that transiently open or close an ion channel formed by the protein to which they bind, briefly changing the ion permeability of the plasma membrane and thereby changing the excitability of the postsynaptic target cell. Most ion-channel-coupled receptors belong to a large family of homologous, multipass transmembrane proteins. Because they are discussed in detail in Chapter 11, we will not consider them further here.


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Cell_Biology_Alberts. G-protein-coupled receptors act by indirectly regulating the activity of a separate plasma-membrane-bound target protein, which is generally either an enzyme or an ion channel. A trimeric GTP-binding protein (G protein) mediates the interaction between the activated receptor and this target protein (Figure 15–6B). The activation of the target protein can change the concentration of one or more small intracellular signaling molecules (if the target protein is an enzyme), or it can change the ion permeability of the plasma membrane (if the target protein is an ion channel). The small intracellular signaling molecules act in turn to alter the behavior of yet other signaling proteins in the cell.


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Cell_Biology_Alberts. Enzyme-coupled receptors either function as enzymes or associate directly with enzymes that they activate (Figure 15–6C). They are usually single-pass transmembrane proteins that have their ligand-binding site outside the cell and their catalytic or enzyme-binding site inside. Enzyme-coupled receptors are heterogeneous in structure compared with the other two classes; the great majority, however, are either protein kinases or associate with protein kinases, which phosphorylate specific sets of proteins in the target cell when activated.


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Cell_Biology_Alberts. There are also some types of cell-surface receptors that do not fit easily into any of these classes but have important functions in controlling the specialization of different cell types during development and in tissue renewal and repair in adults. We discuss these in a later section, after we explain how G-protein-coupled receptors and enzyme-coupled receptors operate. First, we continue our general discussion of the principles of signaling via cell-surface receptors. Numerous intracellular signaling molecules relay signals received by cell-surface receptors into the cell interior. The resulting chain of intracellular signaling events ultimately alters effector proteins that are responsible for modifying the behavior of the cell (see Figure 15–1).


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Cell_Biology_Alberts. Some intracellular signaling molecules are small chemicals, which are often called second messengers (the “first messengers” being the extracellular signals). They are generated in large amounts in response to receptor activation and diffuse away from their source, spreading the signal to other parts of the cell. Some, such as cyclic AMP and Ca2+, are water-soluble and diffuse in the cytosol, while others, such as diacylglycerol, are lipid-soluble and diffuse in the plane of the plasma membrane. In either case, they pass the signal on by binding to and altering the behavior of selected signaling or effector proteins.


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Cell_Biology_Alberts. Most intracellular signaling molecules are proteins, which help relay the signal into the cell by either generating second messengers or activating the next signaling or effector protein in the pathway. Many of these proteins behave like molecular switches. When they receive a signal, they switch from an inactive to an active state, until another process switches them off, returning them to their inactive state. The switching off is just as important as the switching on. If a signaling pathway is to recover after transmitting a signal so that it can be ready to transmit another, every activated molecule in the pathway must return to its original, unactivated state.


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Cell_Biology_Alberts. The largest class of molecular switches consists of proteins that are activated or inactivated by phosphorylation (discussed in Chapter 3). For these proteins, the switch is thrown in one direction by a protein kinase, which covalently adds one or more phosphate groups to specific amino acids on the signaling protein, and in the other direction by a protein phosphatase, which removes the phosphate groups (Figure 15–7A). The activity of any protein regulated by phosphorylation depends on the balance between the activities of the kinases that phosphorylate it and of the phosphatases that dephosphorylate it. About 30–50% of human proteins contain covalently attached phosphate, and the human genome encodes about 520 protein kinases and about 150 protein phosphatases. A typical mammalian cell makes use of hundreds of distinct types of protein kinases at any moment.


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Cell_Biology_Alberts. Protein kinases attach phosphate to the hydroxyl group of specific amino acids on the target protein. There are two main types of protein kinase. The great majority are serine/threonine kinases, which phosphorylate the hydroxyl groups of serines and threonines in their targets. Others are tyrosine kinases, which phosphorylate proteins on tyrosines. The two types of protein kinase are closely related members of a large family, differing primarily in the structure of their protein substrate binding sites. Many intracellular signaling proteins controlled by phosphorylation are themselves protein kinases, and these are often organized into kinase cascades. In such a cascade, one protein kinase, activated by phosphorylation, phosphorylates the next protein kinase in the sequence, and so on, relaying the signal onward and, in some cases, amplifying it or spreading it to other signaling pathways.


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Cell_Biology_Alberts. The other important class of molecular switches consists of GTP-binding proteins (discussed in Chapter 3). These proteins switch between an “on” (actively signaling) state when GTP is bound and an “off” state when GDP is bound. In the “on” state, they usually have intrinsic GTPase activity and shut themselves off by hydrolyzing their bound GTP to GDP (Figure 15–7B). There are two major types of GTP-binding proteins. Large, trimeric GTP-binding proteins (also called G proteins) help relay signals from G-protein-coupled receptors that activate them (see Figure 15–6B). Small monomeric GTPases (also called monomeric GTP-binding proteins) help relay signals from many classes of cell-surface receptors.


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Cell_Biology_Alberts. Specific regulatory proteins control both types of GTP-binding proteins. GTPase-activating proteins (GAPs) drive the proteins into an “off” state by increasing the rate of hydrolysis of bound GTP. Conversely, guanine nucleotide exchange factors (GEFs) activate GTP-binding proteins by promoting the release of bound GDP, which allows a new GTP to bind. In the case of trimeric G proteins, the activated receptor serves as the GEF. Figure 15–8 illustrates the regulation of monomeric GTPases. Not all molecular switches in signaling systems depend on phosphorylation or GTP binding. We see later that some signaling proteins are switched on or off by the binding of another signaling protein or a second messenger such as cyclic AMP or Ca2+, or by covalent modifications other than phosphorylation or dephosphorylation, such as ubiquitylation (discussed in Chapter 3).


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Cell_Biology_Alberts. For simplicity, we often portray a signaling pathway as a series of activation steps (see Figure 15–1). It is important to note, however, that most signaling pathways contain inhibitory steps, and a sequence of two inhibitory steps can have the same effect as one activating step (Figure 15–9). This double-negative activation is very common in signaling systems, as we will see when we describe specific pathways later in this chapter. Ideally, an activated intracellular signaling molecule should interact only with the appropriate downstream targets, and, likewise, the targets should only be activated by the appropriate upstream signal. In reality, however, intracellular


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Cell_Biology_Alberts. Figure 15–7 Two types of intracellular signaling proteins that act as molecular switches. (A) A protein kinase covalently adds a phosphate from ATP to the signaling protein, and a protein phosphatase removes the phosphate. Although not shown, many signaling proteins are activated by dephosphorylation rather than by phosphorylation. (B) A GTP-binding protein is induced to exchange its bound GDP for GTP, which activates the protein; the protein then inactivates itself by hydrolyzing its bound GTP to GDP. signaling molecules share the cytoplasm with a crowd of closely related signaling molecules that control a diverse array of cellular processes. It is inevitable that an occasional signaling molecule will bind or modify the wrong partner, potentially creating unwanted cross-talk and interference between signaling systems. How does a signal remain strong, precise, and specific under these noisy conditions?


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Cell_Biology_Alberts. The first line of defense comes from the high affinity and specificity of the interactions between signaling molecules and their correct partners compared to the relatively low affinity of the interactions between inappropriate partners. The binding of a signaling molecule to the correct target is determined by precise and complex interactions between complementary surfaces on the two molecules. Protein kinases, for example, contain active sites that recognize a specific amino acid sequence around the phosphorylation site on the correct target protein, and they often contain additional docking sites that promote a specific, high-affinity interaction with the target. These and related mechanisms help provide a strong and persistent interaction between the correct partners, reducing the likelihood of inappropriate interactions with other proteins.


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Cell_Biology_Alberts. Another important way that cells avoid responses to unwanted background signals depends on the ability of many downstream target proteins to simply ignore such signals. These proteins respond only when the upstream signal reaches a high concentration or activity level. Consider a signaling pathway in which a protein kinase activates some downstream target protein by phosphorylation. If a response is triggered only when more than half of the target proteins are phosphorylated, then there will be little harm done if a small number of them are occasionally phosphorylated by some inappropriate protein kinase. Furthermore, constitutively active protein phosphatases will further reduce the impact of background phosphorylation by rapidly removing much of it. In these and other ways, intracellular signaling systems filter out noise, generating little or no response to low levels of stimuli.


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Cell_Biology_Alberts. Figure 15–8 The regulation of a monomeric GTPase. GTPase-activating proteins (GAPs) inactivate the protein by stimulating it to hydrolyze its bound GTP to GDP, which remains tightly bound to the inactivated GTPase. Guanine nucleotide exchange factors (GEFs) activate the inactive protein by stimulating it to release its GDP; because the concentration of GTP in the cytosol is 10 times greater than the concentration of GDP, the protein rapidly binds GTP and is thereby activated. Figure 15–9 A sequence of two inhibitory signals produces a positive signal. In this simple signaling system, a transcription regulator is kept in an inactive state by a bound inhibitor protein. In response to some upstream signal, a protein kinase is activated and phosphorylates the inhibitor, causing its dissociation from the transcription regulator and thereby activating gene expression.


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Cell_Biology_Alberts. This signaling pathway can be diagrammed as a sequence of four steps, including two sequential inhibitory steps that are equivalent to a single activating step. Cells in a population often exhibit random variation in the concentration or activity of their intracellular signaling molecules. Similarly, individual molecules in a large population of molecules vary in their activity or interactions with other molecules. This signal variability introduces another form of noise that can interfere with the precision and efficiency of signaling. Most signaling systems, however, are built to generate remarkably robust and precise responses even when upstream signals are variable or even when some components of the system are disabled. In many cases, this robustness depends on the presence of backup mechanisms: for example, a signal might employ two parallel pathways to activate a single common downstream target protein, allowing the response to occur even if one pathway is crippled.


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Cell_Biology_Alberts. One simple and effective strategy for enhancing the specificity of interactions between signaling molecules is to localize them in the same part of the cell or even within large protein complexes, thereby ensuring that they interact only with each other and not with inappropriate partners. Such mechanisms often involve scaffold proteins, which bring together groups of interacting signaling proteins into signaling complexes, often before a signal has been received (Figure 15–10A). Because the scaffold holds the proteins in close proximity, they can interact at high local concentrations and be sequentially activated rapidly, efficiently, and selectively in response to an appropriate extracellular signal, avoiding unwanted cross-talk with other signaling pathways.


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Cell_Biology_Alberts. In other cases, such signaling complexes form only transiently in response to an extracellular signal and rapidly disassemble when the signal is gone. They often assemble around a receptor after an extracellular signal molecule has activated it. In many of these cases, the cytoplasmic tail of the activated receptor is phosphorylated during the activation process, and the phosphorylated amino acids then serve as docking sites for the assembly of other signaling proteins (Figure 15–10B). In yet other cases, receptor activation leads to the production of modified phospholipid molecules (called phosphoinositides) in the adjacent plasma membrane, which then recruit specific intracellular signaling proteins to this region of membrane, where they are activated (Figure 15–10C).


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Cell_Biology_Alberts. Simply bringing intracellular signaling proteins together into close proximity is sometimes sufficient to activate them. Thus, induced proximity, where a signal triggers assembly of a signaling complex, is commonly used to relay signals from protein to protein along a signaling pathway. The assembly of such signaling complexes depends on various highly conserved, small interaction domains, which are found in many intracellular signaling proteins. Each of these compact protein modules binds to a particular structural motif in another protein or lipid. The recognized motif in the interacting protein can be a short peptide sequence, a covalent modification (such as a phosphorylated amino acid), or another protein domain. The use of modular interaction domains presumably facilitated the evolution of new signaling pathways; because it can be inserted at many locations in a protein without disturbing the protein’s folding or function, a new interaction domain added to an existing signaling


Cell_Biology_Alberts

Cell_Biology_Alberts. of new signaling pathways; because it can be inserted at many locations in a protein without disturbing the protein’s folding or function, a new interaction domain added to an existing signaling protein could connect the protein to additional signaling pathways.


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Cell_Biology_Alberts. There are many types of interaction domains in signaling proteins. Src homology 2 (SH2) domains and phosphotyrosine-binding (PTB) domains, for example, bind to phosphorylated tyrosines in a particular peptide sequence on activated receptors or intracellular signaling proteins. Src homology 3 (SH3) domains bind to short, proline-rich amino acid sequences. Some pleckstrin homology (PH) domains bind to the charged head groups of specific phosphoinositides that are produced in the plasma membrane in response to an extracellular signal; they Figure 15–10 Three types of intracellular signaling complexes. (A) A receptor and some of the intracellular signaling proteins it activates in sequence are preassembled into a signaling complex on the inactive receptor by a large scaffold protein.


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Cell_Biology_Alberts. A signaling complex assembles transiently on a receptor only after the binding of an extracellular signal molecule has activated the receptor; here, the activated receptor phosphorylates itself at multiple sites, which then act as docking sites for intracellular signaling proteins. Activation of a receptor leads to the increased phosphorylation of specific phospholipids (phosphoinositides) in the adjacent plasma membrane; these then serve as docking sites for specific intracellular signaling proteins, which can now interact with each other. enable the protein they are part of to dock on the membrane and interact with other similarly recruited signaling proteins (see Figure 15–10C). Some signaling proteins consist solely of two or more interaction domains and function only as adaptors to link two other proteins together in a signaling pathway.