Cell_Biology_Alberts

Cell_Biology_Alberts. Li P, Banjade S, Cheng H-C et al. (2012) Phase transitions in the assembly of multivalent signalling proteins. Nature 483, 336–340. Lindquist SL & Kelly JW (2011) Chemical and biological approaches for adapting proteostasis to ameliorate protein misfolding and aggregation diseases—progress and prognosis. Cold Spring Harb. Perspect. Biol. 3, a004507. Maji SK, Perrin MH, Sawaya MR et al. (2009) Functional amyloids as natural storage of peptide hormones in pituitary secretory granules. Science 325, 328–332. Nelson R, Sawaya MR, Balbirnie M et al. (2005) Structure of the cross-β spine of amyloid-like fibrils. Nature 435, 773–778. Nomura M (1973) Assembly of bacterial ribosomes. Science 179, 864–873. Oldfield CJ & Dunker AK (2014) Intrinsically disordered proteins and intrinsically disordered protein regions. Annu. Rev. Biochem. 83, 553–584. Orengo CA & Thornton JM (2005) Protein families and their evolution—a structural perspective. Annu. Rev. Biochem. 74, 867–900.


Cell_Biology_Alberts

Cell_Biology_Alberts. Orengo CA & Thornton JM (2005) Protein families and their evolution—a structural perspective. Annu. Rev. Biochem. 74, 867–900. Pauling L & Corey RB (1951) Configurations of polypeptide chains with favored orientations around single bonds: two new pleated sheets. Proc. Natl Acad. Sci. USA 37, 729–740. Pauling L, Corey RB & Branson HR (1951) The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain. Proc. Natl Acad. Sci. USA 37, 205–211. Prusiner SB (1998) Prions. Proc. Natl Acad. Sci. USA 95, 13363–13383. Toyama BH & Weissman JS (2011) Amyloid structure: conformational diversity and consequences. Annu. Rev. Biochem. 80, 557–585. Zhang C & Kim SH (2003) Overview of structural genomics: from structure to function. Curr. Opin. Chem. Biol. 7, 28–32. Alberts B (1998) The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92, 291–294.


Cell_Biology_Alberts

Cell_Biology_Alberts. Alberts B (1998) The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92, 291–294. Benkovic SJ (1992) Catalytic antibodies. Annu. Rev. Biochem. 61, 29–54. Berg OG & von Hippel PH (1985) Diffusion-controlled macromolecular interactions. Annu. Rev. Biophys. Biophys. Chem. 14, 131–160. Bourne HR (1995) GTPases: a family of molecular switches and clocks. Philos. Trans. R. Soc. Lond. B Biol. Sci. 349, 283–289. Costanzo M, Baryshnikova A, Bellay J et al. (2010) The genetic landscape of a cell. Science 327, 425–431. Deshaies RJ & Joazeiro CAP (2009) RING domain E3 ubiquitin ligases. Annu. Rev. Biochem. 78, 399–434. Dickerson RE & Geis I (1983) Hemoglobin: Structure, Function, Evolution, and Pathology. Menlo Park, CA: Benjamin Cummings. Fersht AR (1999) Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. New York: WH Freeman.


Cell_Biology_Alberts

Cell_Biology_Alberts. Fersht AR (1999) Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. New York: WH Freeman. Haucke V, Neher E & Sigrist SJ (2011) Protein scaffolds in the coupling of synaptic exocytosis and endocytosis. Nat. Rev. Neurosci. 12, 127–138. Hua Z & Vierstra RD (2011) The cullin-RING ubiquitin-protein ligases. Annu. Rev. Plant Biol. 62, 299–334. Hunter T (2012) Why nature chose phosphate to modify proteins. Philos. Trans. R. Soc. Lond. B Biol. Sci. 367, 2513–2516. Johnson LN & Lewis RJ (2001) Structural basis for control by phosphorylation. Chem. Rev. 101, 2209–2242. Kantrowitz ER & Lipscomb WN (1988) Escherichia coli aspartate transcarbamylase: the relation between structure and function. Science 241, 669–674. Kerscher O, Felberbaum R & Hochstrasser M (2006) Modification of proteins by ubiquitin and ubiquitin-like proteins. Annu. Rev. Cell Dev. Biol. 22, 159–180.


Cell_Biology_Alberts

Cell_Biology_Alberts. Kerscher O, Felberbaum R & Hochstrasser M (2006) Modification of proteins by ubiquitin and ubiquitin-like proteins. Annu. Rev. Cell Dev. Biol. 22, 159–180. Kim E & Sheng M (2004) PDZ domain proteins of synapses. Nat. Rev. Neurosci. 5, 771–781. Koshland DE Jr (1984) Control of enzyme activity and metabolic pathways. Trends Biochem. Sci. 9, 155–159. Krogan NJ, Cagney G, Yu H et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637–643. Lichtarge O, Bourne HR & Cohen FE (1996) An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol. 257, 342–358. Maier T, Leibundgut M & Ban N (2008) The crystal structure of a mammalian fatty acid synthase. Science 321, 1315–1322. Monod J, Changeux JP & Jacob F (1963) Allosteric proteins and cellular control systems. J. Mol. Biol. 6, 306–329.


Cell_Biology_Alberts

Cell_Biology_Alberts. Monod J, Changeux JP & Jacob F (1963) Allosteric proteins and cellular control systems. J. Mol. Biol. 6, 306–329. Perutz M (1990) Mechanisms of Cooperativity and Allosteric Regulation in Proteins. Cambridge: Cambridge University Press. Radzicka A & Wolfenden R (1995) A proficient enzyme. Science 267, 90–93. Schramm VL (2011) Enzymatic transition states, transition-state analogs, dynamics, thermodynamics, and lifetimes. Annu. Rev. Biochem. 80, 703–732. Scott JD & Pawson T (2009) Cell signaling in space and time: where proteins come together and when they’re apart. Science 326, 1220–1224. Taylor SS, Keshwani MM, Steichen JM & Kornev AP (2012) Evolution of the eukaryotic protein kinases as dynamic molecular switches. Philos. Trans. R. Soc. Lond. B Biol. Sci. 367, 2517–2528. Vale RD & Milligan RA (2000) The way things move: looking under the hood of molecular motor proteins. Science 288, 88–95.


Cell_Biology_Alberts

Cell_Biology_Alberts. Vale RD & Milligan RA (2000) The way things move: looking under the hood of molecular motor proteins. Science 288, 88–95. Wilson MZ & Gitai Z (2013) Beyond the cytoskeleton: mesoscale assemblies and their function in spatial organization. Curr. Opin. Microbiol. 16, 177–183. DNA, Chromosomes, and genomes Life depends on the ability of cells to store, retrieve, and translate the genetic instructions required to make and maintain a living organism. This hereditary information is passed on from a cell to its daughter cells at cell division, and from one generation of an organism to the next through the organism’s reproductive cells. The instructions are stored within every living cell as its genes, the information-containing elements that determine the characteristics of a species as a whole and of the individuals within it.


Cell_Biology_Alberts

Cell_Biology_Alberts. As soon as genetics emerged as a science at the beginning of the twentieth century, scientists became intrigued by the chemical structure of genes. The information in genes is copied and transmitted from cell to daughter cell millions of times during the life of a multicellular organism, and it survives the process essentially unchanged. What form of molecule could be capable of such accurate and almost unlimited replication and also be able to exert precise control, directing multicellular development as well as the daily life of every cell? What kind of instructions does the genetic information contain? And how can the enormous amount of information required for the development and maintenance of an organism fit within the tiny space of a cell?


Cell_Biology_Alberts

Cell_Biology_Alberts. The answers to several of these questions began to emerge in the 1940s. At this time researchers discovered, from studies in simple fungi, that genetic information consists largely of instructions for making proteins. Proteins are phenomenally versatile macromolecules that perform most cell functions. As we saw in Chapter 3, they serve as building blocks for cell structures and form the enzymes that catalyze most of the cell’s chemical reactions. They also regulate gene expression (Chapter 7), and they enable cells to communicate with each other (Chapter 15) and to move (Chapter 16). The properties and functions of cells and organisms are determined to a great extent by the proteins that they are able to make.


Cell_Biology_Alberts

Cell_Biology_Alberts. Painstaking observations of cells and embryos in the late nineteenth century had led to the recognition that the hereditary information is carried on chromosomes—threadlike structures in the nucleus of a eukaryotic cell that become visible by light microscopy as the cell begins to divide (Figure 4–1). Later, when biochemical analysis became possible, chromosomes were found to consist of deoxyribonucleic acid (DNA) and protein, with both being present in roughly the same amounts. For many decades, the DNA was thought to be merely a structural


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–1 Chromosomes in cells. (A) Two adjacent plant cells photographed through a light microscope. The DNA has been stained with a fluorescent dye (DAPI) that binds to it. The DNA is present in chromosomes, which become visible as distinct structures in the light microscope only when they become compact, sausage-shaped structures in preparation for cell division, as shown on the left. The cell on the right, which is not dividing, contains identical chromosomes, but they cannot be clearly distinguished at this phase in the cell’s life cycle, because they are in a more extended conformation. (b) Schematic diagram of the outlines of the two cells along with their chromosomes. (A, courtesy of Peter Shaw.) element. However, the other crucial advance made in the 1940s was the identification of DNA as the likely carrier of genetic information. This breakthrough in our understanding of cells came from studies of inheritance in bacteria (Figure 4–2). But still, as the 1950s began, both how


Cell_Biology_Alberts

Cell_Biology_Alberts. of DNA as the likely carrier of genetic information. This breakthrough in our understanding of cells came from studies of inheritance in bacteria (Figure 4–2). But still, as the 1950s began, both how proteins could be specified by instructions in the DNA and how this information might be copied for transmission from cell to cell seemed completely mysterious. The puzzle was suddenly solved in 1953, when James Watson and Francis Crick derived the mechanism from their model of DNA structure. As outlined in Chapter 1, the determination of the double-helical structure of DNA immediately solved the problem of how the information in this molecule might be copied, or replicated. It also provided the first clues as to how a molecule of DNA might use the sequence of its subunits to encode the instructions for making proteins. Today, the fact that DNA is the genetic material is so fundamental to biological thought that it is difficult to appreciate the enormous intellectual gap that was filled


Cell_Biology_Alberts

Cell_Biology_Alberts. for making proteins. Today, the fact that DNA is the genetic material is so fundamental to biological thought that it is difficult to appreciate the enormous intellectual gap that was filled by this breakthrough discovery.


Cell_Biology_Alberts

Cell_Biology_Alberts. We begin this chapter by describing the structure of DNA. We see how, despite its chemical simplicity, the structure and chemical properties of DNA make it ideally suited as the raw material of genes. We then consider how the many proteins in chromosomes arrange and package this DNA. The packing has to be done in an orderly fashion so that the chromosomes can be replicated and apportioned correctly between the two daughter cells at each cell division. And it must also allow access to chromosomal DNA, both for the enzymes that repair DNA damage and for the specialized proteins that direct the expression of its many genes. In the past two decades, there has been a revolution in our ability to determine the exact order of subunits in DNA molecules. As a result, we now know the RNA protein DNA lipid carbohydratelive R strain cells grown in presence of either heat-killed S strain cells or cell-free molecules tested for transformation of R strain cellsextract of S strain cells


Cell_Biology_Alberts

Cell_Biology_Alberts. CONCLUSION: Molecules that can CONCLUSION: The molecule that carry heritable information are carries the heritable information present in S strain cells. is DNA. Figure 4–2 The first experimental demonstration that DNA is the genetic material. These experiments, carried out in the 1920s (A) and 1940s (b), showed that adding purified DNA to a bacterium changed the bacterium’s properties and that this change was faithfully passed on to subsequent generations. Two closely related strains of the bacterium Streptococcus pneumoniae differ from each other in both their appearance under the microscope and their pathogenicity. One strain appears smooth (S) and causes death when injected into mice, and the other appears rough (R) and is nonlethal. An initial experiment shows that some substance present in the S strain can change (or transform) the R strain into the S strain and that this change is inherited by subsequent generations of bacteria.


Cell_Biology_Alberts

Cell_Biology_Alberts. This experiment, in which the R strain has been incubated with various classes of biological molecules purified from the S strain, identifies the active substance as DNA. sequence of the 3.2 billion nucleotide pairs that provide the information for producing a human adult from a fertilized egg, as well as having the DNA sequences for thousands of other organisms. Detailed analyses of these sequences are providing exciting insights into the process of evolution, and it is with this subject that the chapter ends.


Cell_Biology_Alberts

Cell_Biology_Alberts. This is the first of four chapters that deal with basic genetic mechanisms—the ways in which the cell maintains, replicates, and expresses the genetic information carried in its DNA. In the next chapter (Chapter 5), we shall discuss the mechanisms by which the cell accurately replicates and repairs DNA; we also describe how DNA sequences can be rearranged through the process of genetic recombination. Gene expression—the process through which the information encoded in DNA is interpreted by the cell to guide the synthesis of proteins—is the main topic of Chapter 6. In Chapter 7, we describe how this gene expression is controlled by the cell to ensure that each of the many thousands of proteins and RNA molecules encrypted in its DNA is manufactured only at the proper time and place in the life of a cell.


Cell_Biology_Alberts

Cell_Biology_Alberts. Biologists in the 1940s had difficulty in conceiving how DNA could be the genetic material. The molecule seemed too simple: a long polymer composed of only four types of nucleotide subunits, which resemble one another chemically. Early in the 1950s, DNA was examined by x-ray diffraction analysis, a technique for determining the three-dimensional atomic structure of a molecule (discussed in Chapter 8). The early x-ray diffraction results indicated that DNA was composed of two strands of the polymer wound into a helix. The observation that DNA was double-stranded provided one of the major clues that led to the Watson–Crick model for DNA structure that, as soon as it was proposed in 1953, made DNA’s potential for replication and information storage apparent. A DNA molecule Consists of Two Complementary Chains of Nucleotides


Cell_Biology_Alberts

Cell_Biology_Alberts. A deoxyribonucleic acid (DNA) molecule consists of two long polynucleotide chains composed of four types of nucleotide subunits. Each of these chains is known as a DNA chain, or a DNA strand. The chains run antiparallel to each other, and hydrogen bonds between the base portions of the nucleotides hold the two chains together (Figure 4–3). As we saw in Chapter 2 (Panel 2–6, pp. 100–101), nucleotides are composed of a five-carbon sugar to which are attached one or more phosphate groups and a nitrogen-containing base. In the case of the nucleotides in DNA, the sugar is deoxyribose attached to a single phosphate group (hence the name deoxyribonucleic acid), and the base may be either adenine (A), cytosine (C), guanine (G), or thymine (T). The nucleotides are covalently linked together in a chain through the sugars and phosphates, which thus form a “backbone” of alternating sugar–phosphate–sugar–phosphate. Because only the base differs in each of the four types of nucleotide subunit, each


Cell_Biology_Alberts

Cell_Biology_Alberts. through the sugars and phosphates, which thus form a “backbone” of alternating sugar–phosphate–sugar–phosphate. Because only the base differs in each of the four types of nucleotide subunit, each polynucleotide chain in DNA is analogous to a sugar-phosphate necklace (the backbone), from which hang the four types of beads (the bases A, C, G, and T). These same symbols (A, C, G, and T) are commonly used to denote either the four bases or the four entire nucleotides—that is, the bases with their attached sugar and phosphate groups.


Cell_Biology_Alberts

Cell_Biology_Alberts. The way in which the nucleotides are linked together gives a DNA strand a chemical polarity. If we think of each sugar as a block with a protruding knob (the 5ʹ phosphate) on one side and a hole (the 3ʹ hydroxyl) on the other (see Figure 4–3), each completed chain, formed by interlocking knobs with holes, will have all of its subunits lined up in the same orientation. Moreover, the two ends of the chain will be easily distinguishable, as one has a hole (the 3ʹ hydroxyl) and the other a knob (the 5ʹ phosphate) at its terminus. This polarity in a DNA chain is indicated by referring to one end as the 3ʹ end and the other as the 5ʹ end, names derived from the orientation of the deoxyribose sugar. With respect to DNA’s building blocks of DNA DNA strand information-carrying capacity, the chain of nucleotides in a DNA strand, being both directional and linear, can be read in much the same way as the letters on this page.


Cell_Biology_Alberts

Cell_Biology_Alberts. The three-dimensional structure of DNA—the DNA double helix—arises from the chemical and structural features of its two polynucleotide chains. Because these two chains are held together by hydrogen-bonding between the bases on the different strands, all the bases are on the inside of the double helix, and the sugar-phosphate backbones are on the outside (see Figure 4–3). In each case, a bulkier two-ring base (a purine; see Panel 2–6, pp. 100–101) is paired with a single-ring base (a pyrimidine): A always pairs with T, and G with C (Figure 4–4). This complementary base-pairing enables the base pairs to be packed in the energetically most favorable arrangement in the interior of the double helix. In this arrangement, each base pair is of similar width, thus holding the sugar-phosphate backbones a constant distance apart along the DNA molecule. To maximize the efficiency of base-pair packing, the two sugar-phosphate backbones wind around each other to form a right-handed double helix,


Cell_Biology_Alberts

Cell_Biology_Alberts. a constant distance apart along the DNA molecule. To maximize the efficiency of base-pair packing, the two sugar-phosphate backbones wind around each other to form a right-handed double helix, with one complete turn every ten base pairs (Figure 4–5).


Cell_Biology_Alberts

Cell_Biology_Alberts. The members of each base pair can fit together within the double helix only if the two strands of the helix are antiparallel—that is, only if the polarity of one strand is oriented opposite to that of the other strand (see Figures 4–3 and 4–4). A consequence of DNA’s structure and base-pairing requirements is that each strand of a DNA molecule contains a sequence of nucleotides that is exactly complementary to the nucleotide sequence of its partner strand. Figure 4–3 DNA and its building blocks.


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–3 DNA and its building blocks. DNA is made of four types of nucleotides, which are linked covalently into a polynucleotide chain (a DNA strand) with a sugar-phosphate backbone from which the bases (A, C, g, and T) extend. A DNA molecule is composed of two antiparallel DNA strands held together by hydrogen bonds between the paired bases. The arrowheads at the ends of the DNA strands indicate the polarities of the two strands. In the diagram at the bottom left of the figure, the DNA molecule is shown straightened out; in reality, it is twisted into a double helix, as shown on the right. For details, see Figure 4–5 and Movie 4.1. The Structure of DNA Provides a mechanism for Heredity


Cell_Biology_Alberts

Cell_Biology_Alberts. The Structure of DNA Provides a mechanism for Heredity The discovery of the structure of DNA immediately suggested answers to the two most fundamental questions about heredity. First, how could the information to specify an organism be carried in a chemical form? And second, how could this information be duplicated and copied from generation to generation? The answer to the first question came from the realization that DNA is a linear polymer of four different kinds of monomer, strung out in a defined sequence like the letters of a document written in an alphabetic script. The answer to the second question came from the double-stranded nature of the structure: because each strand of DNA contains a sequence of nucleotides that is exactly complementary to the nucleotide sequence of its partner strand, each strand can act as a template, or mold, for the synthesis of a new complementary strand. In other words, if we designate the two DNA strands as S and Sʹ, strand 0.34 nm


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–4 Complementary base pairs in the DNA double helix. The shapes and chemical structures of the bases allow hydrogen bonds to form efficiently only between A and T and between g and C, because atoms that are able to form hydrogen bonds (see Panel 2–3, pp. 94–95) can then be brought close together without distorting the double helix. As indicated, two hydrogen bonds form between A and T, while three form between g and C. The bases can pair in this way only if the two polynucleotide chains that contain them are antiparallel to each other. Figure 4–5 The DNA double helix. A space-filling model of 1.5 turns of the DNA double helix. Each turn of DNA is made up of 10.4 nucleotide pairs, and the center-to-center distance between adjacent nucleotide pairs is 0.34 nm. The coiling of the two strands around each other creates two grooves in the double helix: the wider groove is called the major groove, and the smaller the minor groove, as indicated.


Cell_Biology_Alberts

Cell_Biology_Alberts. A short section of the double helix viewed from its side, showing four base pairs. The nucleotides are linked together covalently by phosphodiester bonds that join the 3ʹ-hydroxyl (–OH) group of one sugar to the 5ʹ-hydroxyl group of the next sugar. Thus, each polynucleotide strand has a chemical polarity; that is, its two ends are chemically different. The 5ʹ end of the DNA polymer is by convention often illustrated carrying a phosphate group, while the 3ʹ end is shown with a hydroxyl. S can serve as a template for making a new strand Sʹ, while strand Sʹ can serve as a template for making a new strand S (Figure 4–6). Thus, the genetic information in DNA can be accurately copied by the beautifully simple process in which strand S separates from strand Sʹ, and each separated strand then serves as a template for the production of a new complementary partner strand that is identical to its former partner.


Cell_Biology_Alberts

Cell_Biology_Alberts. The ability of each strand of a DNA molecule to act as a template for producing a complementary strand enables a cell to copy, or replicate, its genome before passing it on to its descendants. We shall describe the elegant machinery that the cell uses to perform this task in Chapter 5. Organisms differ from one another because their respective DNA molecules have different nucleotide sequences and, consequently, carry different biological messages. But how is the nucleotide alphabet used to make messages, and what do they spell out?


Cell_Biology_Alberts

Cell_Biology_Alberts. As discussed above, it was known well before the structure of DNA was determined that genes contain the instructions for producing proteins. If genes are made of DNA, the DNA must therefore somehow encode proteins (Figure 4–7). As discussed in Chapter 3, the properties of a protein, which are responsible for its biological function, are determined by its three-dimensional structure. This structure is determined in turn by the linear sequence of the amino acids of which it is composed. The linear sequence of nucleotides in a gene must therefore somehow spell out the linear sequence of amino acids in a protein. The exact correspondence between the four-letter nucleotide alphabet of DNA and the twenty-letter amino acid alphabet of proteins—the genetic code—is not at all obvious from the DNA structure, and it took over a decade after the discovery of the double helix before it was worked out. In Chapter 6, we will describe this code in detail in the course of elaborating the process of


Cell_Biology_Alberts

Cell_Biology_Alberts. structure, and it took over a decade after the discovery of the double helix before it was worked out. In Chapter 6, we will describe this code in detail in the course of elaborating the process of gene expression, through which a cell converts the nucleotide sequence of a gene first into the nucleotide sequence of an RNA molecule, and then into the amino acid sequence of a protein.


Cell_Biology_Alberts

Cell_Biology_Alberts. The complete store of information in an organism’s DNA is called its genome, and it specifies all the RNA molecules and proteins that the organism will ever synthesize. (The term genome is also used to describe the DNA that carries this information.) The amount of information contained in genomes is staggering. The nucleotide sequence of a very small human gene, written out in the four-letter nucleotide alphabet, occupies a quarter of a page of text (Figure 4–8), while the complete sequence of nucleotides in the human genome would fill more than a thousand books the size of this one. In addition to other critical information, it includes roughly 21,000 protein-coding genes, which (through alternative splicing; see p. 415) give rise to a much greater number of distinct proteins. In Eukaryotes, DNA Is Enclosed in a Cell Nucleus


Cell_Biology_Alberts

Cell_Biology_Alberts. In Eukaryotes, DNA Is Enclosed in a Cell Nucleus As described in Chapter 1, nearly all the DNA in a eukaryotic cell is sequestered in a nucleus, which in many cells occupies about 10% of the total cell volume. This compartment is delimited by a nuclear envelope formed by two concentric lipid Figure 4–6 DNA as a template for its own duplication. because the nucleotide A successfully pairs only with T, and g pairs with C, each strand of DNA can act as a template to specify the sequence of nucleotides in its complementary strand. In this way, double-helical DNA can be copied precisely, with each parental DNA helix producing two identical daughter DNA helices. Figure 4–7 The relationship between genetic information carried in DNA and proteins. (Discussed in Chapter 1.)


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–7 The nucleotide sequence of the human β-globin gene. by convention, a nucleotide sequence is written from its 5ʹ end to its 3ʹ end, and it should be read from left to right in successive lines down the page as though it were normal English text. This gene carries the information for the amino acid sequence of one of the two types of subunits of the hemoglobin molecule; a different gene, the α-globin gene, carries the information for the other. (Hemoglobin, the protein that carries oxygen in the blood, has four subunits, two of each type.) Only one of the two strands of the DNA double helix containing the β-globin gene is shown; the other strand has the exact complementary sequence. The DNA sequences highlighted in yellow show the three regions of the gene that specify the amino acid sequence for the β-globin protein. we shall see in Chapter 6 how the cell splices these three sequences together at the level of messenger RNA in order to synthesize a full-length β-globin


Cell_Biology_Alberts

Cell_Biology_Alberts. amino acid sequence for the β-globin protein. we shall see in Chapter 6 how the cell splices these three sequences together at the level of messenger RNA in order to synthesize a full-length β-globin protein.


Cell_Biology_Alberts

Cell_Biology_Alberts. bilayer membranes (Figure 4–9). These membranes are punctured at intervals by large nuclear pores, through which molecules move between the nucleus and the cytosol. The nuclear envelope is directly connected to the extensive system of intracellular membranes called the endoplasmic reticulum, which extend out from it into the cytoplasm. And it is mechanically supported by a network of intermediate filaments called the nuclear lamina—a thin feltlike mesh just beneath the inner nuclear membrane (see Figure 4–9B). The nuclear envelope allows the many proteins that act on DNA to be concentrated where they are needed in the cell, and, as we see in subsequent chapters, it also keeps nuclear and cytosolic enzymes separate, a feature that is crucial for the proper functioning of eukaryotic cells.


Cell_Biology_Alberts

Cell_Biology_Alberts. Genetic information is carried in the linear sequence of nucleotides in DNA. Each molecule of DNA is a double helix formed from two complementary antiparallel strands of nucleotides held together by hydrogen bonds between G-C and A-T base pairs. Duplication of the genetic information occurs by the use of one DNA strand as a template for the formation of a complementary strand. The genetic information stored in an organism’s DNA contains the instructions for all the RNA molecules and proteins that the organism will ever synthesize and is said to comprise its genome. In eukaryotes, DNA is contained in the cell nucleus, a large membrane-bound compartment.


Cell_Biology_Alberts

Cell_Biology_Alberts. The most important function of DNA is to carry genes, the information that specifies all the RNA molecules and proteins that make up an organism—including information about when, in what types of cells, and in what quantity each RNA molecule and protein is to be made. The nuclear DNA of eukaryotes is divided up into chromosomes, and in this section we see how genes are typically arranged on each chromosome. In addition, we describe the specialized DNA sequences that are required for a chromosome to be accurately duplicated as a separate entity and passed on from one generation to the next.


Cell_Biology_Alberts

Cell_Biology_Alberts. We also confront the serious challenge of DNA packaging. If the double helices comprising all 46 chromosomes in a human cell could be laid end to end, they would reach approximately 2 meters; yet the nucleus, which contains the DNA, is only about 6 μm in diameter. This is geometrically equivalent to packing 40 km (24 miles) of extremely fine thread into a tennis ball. The complex task of packaging DNA is accomplished by specialized proteins that bind to the DNA and fold it, generating a series of organized coils and loops that provide increasingly higher levels of organization, and prevent the DNA from becoming an unmanageable tangle. Amazingly, although the DNA is very tightly compacted, it nevertheless remains accessible to the many enzymes in the cell that replicate it, repair it, and use its genes to produce RNA molecules and proteins.


Cell_Biology_Alberts

Cell_Biology_Alberts. endoplasmic reticulum nuclear pore outer nuclear membrane inner nuclear membrane nuclear envelope nuclear lamina microtubule centrosome nucleolus DNA and associated proteins (chromatin), plus many RNA and protein molecules 2 µm (A) (B) nucleolus nuclear envelope heterochromatinheterochromatin


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–9 A cross-sectional view of a typical cell nucleus. (A) Electron micrograph of a thin section through the nucleus of a human fibroblast. (b) Schematic drawing, showing that the nuclear envelope consists of two membranes, the outer one being continuous with the endoplasmic reticulum (ER) membrane (see also Figure 12–7). The space inside the endoplasmic reticulum (the ER lumen) is colored yellow; it is continuous with the space between the two nuclear membranes. The lipid bilayers of the inner and outer nuclear membranes are connected at each nuclear pore. A sheetlike network of intermediate filaments (brown) inside the nucleus forms the nuclear lamina (brown), providing mechanical support for the nuclear envelope (for details, see Chapter 12). The dark-staining heterochromatin contains specially condensed regions of DNA that will be discussed later. (A, courtesy of E.g. Jordan and J. mcgovern.) Eukaryotic DNA Is Packaged into a Set of Chromosomes


Cell_Biology_Alberts

Cell_Biology_Alberts. Eukaryotic DNA Is Packaged into a Set of Chromosomes Each chromosome in a eukaryotic cell consists of a single, enormously long linear DNA molecule along with the proteins that fold and pack the fine DNA thread into a more compact structure. In addition to the proteins involved in packaging, chromosomes are also associated with many other proteins (as well as numerous RNA molecules). These are required for the processes of gene expression, DNA replication, and DNA repair. The complex of DNA and tightly bound protein is called chromatin (from the Greek chroma, “color,” because of its staining properties).


Cell_Biology_Alberts

Cell_Biology_Alberts. Bacteria lack a special nuclear compartment, and they generally carry their genes on a single DNA molecule, which is often circular (see Figure 1–24). This DNA is also associated with proteins that package and condense it, but they are different from the proteins that perform these functions in eukaryotes. Although the bacterial DNA with its attendant proteins is often called the bacterial “chromosome,” it does not have the same structure as eukaryotic chromosomes, and less is known about how the bacterial DNA is packaged. Therefore, our discussion of chromosome structure will focus almost entirely on eukaryotic chromosomes.


Cell_Biology_Alberts

Cell_Biology_Alberts. With the exception of the gametes (eggs and sperm) and a few highly specialized cell types that cannot multiply and either lack DNA altogether (for example, red blood cells) or have replicated their DNA without completing cell division (for example, megakaryocytes), each human cell nucleus contains two copies of each chromosome, one inherited from the mother and one from the father. The maternal and paternal chromosomes of a pair are called homologous chromosomes (homologs). The only nonhomologous chromosome pairs are the sex chromosomes in males, where a Y chromosome is inherited from the father and an X chromosome from the mother. Thus, each human cell contains a total of 46 chromosomes—22 pairs common to both males and females, plus two so-called sex chromosomes (X and Y in males, two Xs in females). These human chromosomes can be readily distinguished by “painting” each one a different color using a technique based on DNA hybridization (Figure 4–10). In this method (described in


Cell_Biology_Alberts

Cell_Biology_Alberts. Xs in females). These human chromosomes can be readily distinguished by “painting” each one a different color using a technique based on DNA hybridization (Figure 4–10). In this method (described in detail in Chapter 8), a short strand of nucleic acid tagged with a fluorescent dye serves as a “probe” that picks out its complementary DNA sequence, lighting up the target chromosome at any site where it binds. Chromosome painting is most frequently done at the stage in the cell cycle called mitosis, when chromosomes are especially compacted and easy to visualize (see below).


Cell_Biology_Alberts

Cell_Biology_Alberts. Another more traditional way to distinguish one chromosome from another is to stain them with dyes that reveal a striking and reproducible pattern of bands along each mitotic chromosome (Figure 4–11). These banding patterns presumably reflect variations in chromatin structure, but their basis is not well understood. Nevertheless, the pattern of bands on each type of chromosome is unique, and it provided the initial means to identify and number each human chromosome reliably.


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–10 The complete set of human chromosomes. These chromosomes, from a female, were isolated from a cell undergoing nuclear division (mitosis) and are therefore highly compacted. Each chromosome has been “painted” a different color to permit its unambiguous identification under the fluorescence microscope, using a technique called “spectral karyotyping.” Chromosome painting can be performed by exposing the chromosomes to a large collection of DNA molecules whose sequence matches known DNA sequences from the human genome. The set of sequences matching each chromosome is coupled to a different combination of fluorescent dyes. DNA molecules derived from chromosome 1 are labeled with one specific dye combination, those from chromosome 2 with another, and so on. because the labeled DNA can form base pairs, or hybridize, only to the chromosome from which it was derived, each chromosome becomes labeled with a different combination of dyes. For such experiments, the chromosomes are


Cell_Biology_Alberts

Cell_Biology_Alberts. can form base pairs, or hybridize, only to the chromosome from which it was derived, each chromosome becomes labeled with a different combination of dyes. For such experiments, the chromosomes are subjected to treatments that separate the two strands of double-helical DNA in a way that permits base-pairing with the single-stranded labeled DNA, but keeps the overall chromosome structure relatively intact. (A) The chromosomes visualized as they originally spilled from the lysed cell.


Cell_Biology_Alberts

Cell_Biology_Alberts. The same chromosomes artificially lined up in their numerical order. This arrangement of the full chromosome set is called a karyotype. (Adapted from N. mcNeil and T. Ried, Expert Rev. Mol. Med. 2:1–14, 2000. with permission from Cambridge University Press.)


Cell_Biology_Alberts

Cell_Biology_Alberts. N. mcNeil and T. Ried, Expert Rev. Mol. Med. 2:1–14, 2000. with permission from Cambridge University Press.) Figure 4–11 The banding patterns of human chromosomes. Chromosomes 1–22 are numbered in approximate order of size. A typical human cell contains two of each of these chromosomes, plus two sex chromosomes—two X chromosomes in a female, one X and one Y chromosome in a male. The chromosomes used to make these maps were stained at an early stage in mitosis, when the chromosomes are incompletely compacted. The horizontal red line represents the position of the centromere (see Figure 4–19), which appears as a constriction on mitotic chromosomes. The red knobs on chromosomes 13, 14, 15, 21, and 22 indicate the positions of genes that code for the large ribosomal RNAs (discussed in Chapter 6). These banding patterns are obtained by staining chromosomes with giemsa stain, and they can be observed under the light microscope. (Adapted from


Cell_Biology_Alberts

Cell_Biology_Alberts. U. Francke, Cytogenet. Cell Genet. 31:24– 32, 1981. with permission from the author.) Figure 4–12 Aberrant human chromosomes. (A) Two normal human chromosomes, 4 and 6. (b) In an individual carrying a balanced chromosomal translocation, the DNA double helix in one chromosome has crossed over with the DNA double helix in the other chromosome due to an abnormal recombination event. The chromosome painting technique used on the chromosomes in each of the sets allows the identification of even short pieces of chromosomes that have become translocated, a frequent event in cancer cells. (Courtesy of Zhenya Tang and the NIgmS Human genetic Cell Repository at the Coriell Institute for medical Research: gm21880.)


Cell_Biology_Alberts

Cell_Biology_Alberts. The display of the 46 human chromosomes at mitosis is called the human karyotype. If parts of chromosomes are lost or are switched between chromosomes, these changes can be detected either by changes in the banding patterns or—with greater sensitivity—by changes in the pattern of chromosome painting (Figure 4–12). Cytogeneticists use these alterations to detect inherited chromosome abnormalities and to reveal the chromosome rearrangements that occur in cancer cells as they progress to malignancy (discussed in Chapter 20). Chromosomes Contain long Strings of genes


Cell_Biology_Alberts

Cell_Biology_Alberts. Chromosomes Contain long Strings of genes Chromosomes carry genes—the functional units of heredity. A gene is often defined as a segment of DNA that contains the instructions for making a particular protein (or a set of closely related proteins), but this definition is too narrow. Genes that code for protein are indeed the majority, and most of the genes with clear-cut mutant phenotypes fall under this heading. In addition, however, there are many “RNA genes”—segments of DNA that generate a functionally significant RNA molecule, instead of a protein, as their final product. We shall say more about the RNA genes and their products later.


Cell_Biology_Alberts

Cell_Biology_Alberts. As might be expected, some correlation exists between the complexity of an organism and the number of genes in its genome (see Table 1–2, p. 29). For example, some simple bacteria have only 500 genes, compared to about 30,000 for humans. Bacteria, archaea, and some single-celled eukaryotes, such as yeast, have concise genomes, consisting of little more than strings of closely packed genes. However, the genomes of multicellular plants and animals, as well as many other eukaryotes, contain, in addition to genes, a large quantity of interspersed DNA whose function is poorly understood (Figure 4–13). Some of this additional DNA is crucial for the proper control of gene expression, and this may in part explain why there is so much of it in multicellular organisms, whose genes have to be switched on and off according to complicated rules during development (discussed in Chapters 7 and 21).


Cell_Biology_Alberts

Cell_Biology_Alberts. Differences in the amount of DNA interspersed between genes, far more than differences in numbers of genes, account for the astonishing variations in genome size that we see when we compare one species with another (see Figure 1–32). For example, the human genome is 200 times larger than that of the yeast Saccharomyces cerevisiae, but 30 times smaller than that of some plants and amphibians and 200 times smaller than that of a species of amoeba. Moreover, because of differences in the amount of noncoding DNA, the genomes of closely related organisms (bony fish, for example) can vary several hundredfold in their DNA content, even though they contain roughly the same number of genes. Whatever the excess


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–13 The arrangement of genes in the genome of S. cerevisiae compared to humans. (A) S. cerevisiae is a budding yeast widely used for brewing and baking. The genome of this single-celled eukaryote is distributed over 16 chromosomes. A small region of one chromosome has been arbitrarily selected to show its high density of genes. (b) A region of the human genome of equal length to the yeast segment in (A). The human genes are much less densely packed and the amount of interspersed DNA sequence is far greater. Not shown in this sample of human DNA is the fact that most human genes are much longer than yeast genes (see Figure 4–15). DNA may do, it seems clear that it is not a great handicap for a eukaryotic cell to carry a large amount of it.


Cell_Biology_Alberts

Cell_Biology_Alberts. DNA may do, it seems clear that it is not a great handicap for a eukaryotic cell to carry a large amount of it. How the genome is divided into chromosomes also differs from one eukaryotic species to the next. For example, while the cells of humans have 46 chromosomes, those of some small deer have only 6, while those of the common carp contain over 100. Even closely related species with similar genome sizes can have very different numbers and sizes of chromosomes (Figure 4–14). Thus, there is no simple relationship between chromosome number, complexity of the organism, and total genome size. Rather, the genomes and chromosomes of modern-day species have each been shaped by a unique history of seemingly random genetic events, acted on by poorly understood selection pressures over long evolutionary times. The Nucleotide Sequence of the Human genome Shows How Our genes Are Arranged


Cell_Biology_Alberts

Cell_Biology_Alberts. The Nucleotide Sequence of the Human genome Shows How Our genes Are Arranged With the publication of the full DNA sequence of the human genome in 2004, it became possible to see in detail how the genes are arranged along each of our chromosomes (Figure 4–15). It will be many decades before the information contained in the human genome sequence is fully analyzed, but it has already stimulated new experiments that have had major effects on the content of every chapter in this book. (A) human chromosome 22 in its mitotic conformation, composed of two double-stranded DNA molecules, each 48 ×106 nucleotide pairs long 10% of chromosome arm ~40 genes (B) ×10 1% of chromosome arm containing 4 genes (C) one gene of 3.4 ×104 nucleotide pairs (D) exon intron


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–14 Two closely related species of deer with very different chromosome numbers. In the evolution of the Indian muntjac, initially separate chromosomes fused, without having a major effect on the animal. These two species contain a similar number of genes. (Chinese muntjac photo courtesy of Deborah Carreno, Natural wonders Photography.)


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–15 The organization of genes on a human chromosome. (A) Chromosome 22, one of the smallest human chromosomes, contains 48 × 106 nucleotide pairs and makes up approximately 1.5% of the human genome. most of the left arm of chromosome 22 consists of short repeated sequences of DNA that are packaged in a particularly compact form of chromatin (heterochromatin) discussed later in this chapter. (b) A tenfold expansion of a portion of chromosome 22, with about 40 genes indicated. Those in dark brown are known genes and those in red are predicted genes. (C) An expanded portion of (b) showing four genes. (D) The intron–exon arrangement of a typical gene is shown after a further tenfold expansion. Each exon (red) codes for a portion of the protein, while the DNA sequence of the introns (gray) is relatively unimportant, as discussed in detail in Chapter 6.


Cell_Biology_Alberts

Cell_Biology_Alberts. The human genome (3.2 × 109 nucleotide pairs) is the totality of genetic information belonging to our species. Almost all of this genome is distributed over the 22 different autosomes and 2 sex chromosomes (see Figures 4–10 and 4–11) found within the nucleus. A minute fraction of the human genome (16,569 nucleotide pairs—in multiple copies per cell) is found in the mitochondria (introduced in Chapter 1, and discussed in detail in Chapter 14). The term human genome sequence refers to the complete nucleotide sequence of DNA in the 24 nuclear chromosomes and the mitochondria. being diploid, a human somatic cell nucleus contains roughly twice the haploid amount of DNA, or 6.4 × 109 nucleotide pairs, when not duplicating its chromosomes in preparation for division. (Adapted from International Human genome Sequencing Consortium, Nature 409:860–921, 2001. with permission from macmillan Publishers ltd.)


Cell_Biology_Alberts

Cell_Biology_Alberts. The first striking feature of the human genome is how little of it (only a few percent) codes for proteins (Table 4–1 and Figure 4–16). It is also notable that nearly half of the chromosomal DNA is made up of mobile pieces of DNA that have gradually inserted themselves in the chromosomes over evolutionary time, multiplying like parasites in the genome (see Figure 4–62). We discuss these transposable elements in detail in later chapters.


Cell_Biology_Alberts

Cell_Biology_Alberts. A second notable feature of the human genome is the large average gene size—about 27,000 nucleotide pairs. As discussed above, a typical gene carries in its linear sequence of nucleotides the information for the linear sequence of the amino acids of a protein. Only about 1300 nucleotide pairs are required to encode a protein of average size (about 430 amino acids in humans). Most of the remaining sequence in a gene consists of long stretches of noncoding DNA that interrupt the relatively short segments of DNA that code for protein. As will be discussed in detail in Chapter 6, the coding sequences are called exons; the intervening (noncoding) sequences in genes are called introns (see Figure 4–15 and Table 4–1). The majority of human genes thus consist of a long string of alternating exons and introns, with most of the gene consisting of introns. In contrast, the majority of genes from organisms with concise genomes lack introns. This accounts for the much smaller size of their genes


Cell_Biology_Alberts

Cell_Biology_Alberts. and introns, with most of the gene consisting of introns. In contrast, the majority of genes from organisms with concise genomes lack introns. This accounts for the much smaller size of their genes (about one-twentieth that of human genes), as well as for the much higher fraction of coding DNA in their chromosomes.


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–16 Scale of the human genome. If drawn with a 1 mm space between each nucleotide pair, as in (A), the human genome would extend 3200 km (approximately 2000 miles), far enough to stretch across the center of Africa, the site of our human origins (red line in b). At this scale, there would be, on average, a protein-coding gene every 150 m. An average gene would extend for 30 m, but the coding sequences in this gene would add up to only just over a meter.


Cell_Biology_Alberts

Cell_Biology_Alberts. In addition to introns and exons, each gene is associated with regulatory DNA sequences, which are responsible for ensuring that the gene is turned on or off at the proper time, expressed at the appropriate level, and only in the proper type of cell. In humans, the regulatory sequences for a typical gene are spread out over tens of thousands of nucleotide pairs. As would be expected, these regulatory sequences are much more compressed in organisms with concise genomes. We discuss how regulatory DNA sequences work in Chapter 7.


Cell_Biology_Alberts

Cell_Biology_Alberts. Research in the last decade has surprised biologists with the discovery that, in addition to 21,000 protein-coding genes, the human genome contains many thousands of genes that encode RNA molecules that do not produce proteins, but instead have a variety of other important functions. What is thus far known about these molecules will be presented in Chapters 6 and 7. Last, but not least, the nucleotide sequence of the human genome has revealed that the archive of information needed to produce a human seems to be in an alarming state of chaos. As one commentator described our genome, “In some ways it may resemble your garage/bedroom/refrigerator/life: highly individualistic, but unkempt; little evidence of organization; much accumulated clutter (referred to by the uninitiated as ‘junk’); virtually nothing ever discarded; and the few patently valuable items indiscriminately, apparently carelessly, scattered throughout.” We shall discuss how this is thought to have come about in the final


Cell_Biology_Alberts

Cell_Biology_Alberts. nothing ever discarded; and the few patently valuable items indiscriminately, apparently carelessly, scattered throughout.” We shall discuss how this is thought to have come about in the final sections of this chapter entitled “How Genomes Evolve.”


Cell_Biology_Alberts

Cell_Biology_Alberts. Each DNA molecule That Forms a linear Chromosome must Contain a Centromere, Two Telomeres, and Replication Origins


Cell_Biology_Alberts

Cell_Biology_Alberts. To form a functional chromosome, a DNA molecule must be able to do more than simply carry genes: it must be able to replicate, and the replicated copies must be separated and reliably partitioned into daughter cells at each cell division. This process occurs through an ordered series of stages, collectively known as the cell cycle, which provides for a temporal separation between the duplication of chromosomes and their segregation into two daughter cells. The cell cycle is briefly summarized in Figure 4–17, and it is discussed in detail in Chapter 17. Briefly, during a long interphase, genes are expressed and chromosomes are replicated, with the two replicas remaining together as a pair of sister chromatids. Throughout this time, the chromosomes are extended and much of their chromatin exists as long threads in the nucleus so that individual chromosomes cannot be easily distinguished. It is only during a much briefer period of mitosis that each chromosome condenses so that its two


Cell_Biology_Alberts

Cell_Biology_Alberts. exists as long threads in the nucleus so that individual chromosomes cannot be easily distinguished. It is only during a much briefer period of mitosis that each chromosome condenses so that its two sister chromatids can be separated and distributed to the two daughter nuclei. The highly condensed chromosomes in a dividing cell are known as mitotic chromosomes (Figure 4–18). This is the form in which chromosomes are most easily visualized; in fact, the images of chromosomes shown so far in the chapter are of chromosomes in mitosis.


Cell_Biology_Alberts

Cell_Biology_Alberts. Each chromosome operates as a distinct structural unit: for a copy to be passed on to each daughter cell at division, each chromosome must be able to replicate, and the newly replicated copies must subsequently be separated and partitioned


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–17 A simplified view of the eukaryotic cell cycle. During interphase, the cell is actively expressing its genes and is therefore synthesizing proteins. Also, during interphase and before cell division, the DNA is replicated and each chromosome is duplicated to produce two closely paired sister DNA molecules (called sister chromatids). A cell with only one type of chromosome, present in maternal and paternal copies, is illustrated here. Once DNA replication is complete, the cell can enter M phase, when mitosis occurs and the nucleus is divided into two daughter nuclei. During this stage, the chromosomes condense, the nuclear envelope breaks down, and the mitotic spindle forms from microtubules and other proteins. The condensed mitotic chromosomes are captured by the mitotic spindle, and one complete set of chromosomes is then pulled to each end of the cell by separating the members of each sister-chromatid pair. A nuclear envelope re-forms around each chromosome set, and in


Cell_Biology_Alberts

Cell_Biology_Alberts. and one complete set of chromosomes is then pulled to each end of the cell by separating the members of each sister-chromatid pair. A nuclear envelope re-forms around each chromosome set, and in the final step of m phase, the cell divides to produce two daughter cells. most of the time in the cell cycle is spent in interphase; m phase is brief in comparison, occupying only about an hour in many mammalian cells.


Cell_Biology_Alberts

Cell_Biology_Alberts. nuclear envelope surrounding the nucleus INTERPHASE M PHASE INTERPHASE correctly into the two daughter cells. These basic functions are controlled by three types of specialized nucleotide sequences in the DNA, each of which binds specific proteins that guide the machinery that replicates and segregates chromosomes (Figure 4–19). Experiments in yeasts, whose chromosomes are relatively small and easy to manipulate, have identified the minimal DNA sequence elements responsible for each of these functions. One type of nucleotide sequence acts as a DNA replication origin, the location at which duplication of the DNA begins. Eukaryotic chromosomes contain many origins of replication to ensure that the entire chromosome can be replicated rapidly, as discussed in detail in Chapter 5.


Cell_Biology_Alberts

Cell_Biology_Alberts. After DNA replication, the two sister chromatids that form each chromosome remain attached to one another and, as the cell cycle proceeds, are condensed further to produce mitotic chromosomes. The presence of a second specialized DNA sequence, called a centromere, allows one copy of each duplicated and condensed chromosome to be pulled into each daughter cell when a cell divides. A protein complex called a kinetochore forms at the centromere and attaches the duplicated chromosomes to the mitotic spindle, allowing them to be pulled apart (discussed in Chapter 17).


Cell_Biology_Alberts

Cell_Biology_Alberts. The third specialized DNA sequence forms telomeres, the ends of a chromosome. Telomeres contain repeated nucleotide sequences that enable the ends of chromosomes to be efficiently replicated. Telomeres also perform another function: the repeated telomere DNA sequences, together with the regions adjoining them, form structures that protect the end of the chromosome from being mistaken by the cell for a broken DNA molecule in need of repair. We discuss both this type of repair and the structure and function of telomeres in Chapter 5.


Cell_Biology_Alberts

Cell_Biology_Alberts. In yeast cells, the three types of sequences required to propagate a chromosome are relatively short (typically less than 1000 base pairs each) and therefore use only a tiny fraction of the information-carrying capacity of a chromosome. Although telomere sequences are fairly simple and short in all eukaryotes, the DNA sequences that form centromeres and replication origins in more complex organisms are much longer than their yeast counterparts. For example, experiments suggest that a human centromere can contain up to a million nucleotide pairs and that it may not require a stretch of DNA with a defined nucleotide sequence. Instead, as we shall discuss later in this chapter, a human centromere is thought to consist of a large, regularly repeating protein–nucleic acid structure that can be inherited when a chromosome replicates. Figure 4–18 A mitotic chromosome.


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–18 A mitotic chromosome. A mitotic chromosome is a condensed duplicated chromosome in which the two new chromosomes, called sister chromatids, are still linked together (see Figure 4–17). The constricted region indicates the position of the centromere. (Courtesy of Terry D. Allen.) Figure 4–19 The three DNA sequences required to produce a eukaryotic chromosome that can be replicated and then segregated accurately at mitosis.


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–19 The three DNA sequences required to produce a eukaryotic chromosome that can be replicated and then segregated accurately at mitosis. Each chromosome has multiple origins of replication, one centromere, and two telomeres. Shown here is the sequence of events that a typical chromosome follows during the cell cycle. The DNA replicates in interphase, beginning at the origins of replication and proceeding bidirectionally from the origins across the chromosome. In m phase, the centromere attaches the duplicated chromosomes to the mitotic spindle so that a copy of the entire genome is distributed to each daughter cell during mitosis; the special structure that attaches the centromere to the spindle is a protein complex called the kinetochore (dark green). The centromere also helps to hold the duplicated chromosomes together until they are ready to be moved apart. The telomeres form special caps at each chromosome end.


Cell_Biology_Alberts

Cell_Biology_Alberts. All eukaryotic organisms have special ways of packaging DNA into chromosomes. For example, if the 48 million nucleotide pairs of DNA in human chromosome 22 could be laid out as one long perfect double helix, the molecule would extend for about 1.5 cm if stretched out end to end. But chromosome 22 measures only about 2 μm in length in mitosis (see Figures 4–10 and 4–11), representing an endto-end compaction ratio of over 7000-fold. This remarkable feat of compression is performed by proteins that successively coil and fold the DNA into higher and higher levels of organization. Although much less condensed than mitotic chromosomes, the DNA of human interphase chromosomes is still tightly packed.


Cell_Biology_Alberts

Cell_Biology_Alberts. In reading these sections it is important to keep in mind that chromosome structure is dynamic. We have seen that each chromosome condenses to an extreme degree in the M phase of the cell cycle. Much less visible, but of enormous interest and importance, specific regions of interphase chromosomes decondense to allow access to specific DNA sequences for gene expression, DNA repair, and replication—and then recondense when these processes are completed. The packaging of chromosomes is therefore accomplished in a way that allows rapid localized, on-demand access to the DNA. In the next sections, we discuss the specialized proteins that make this type of packaging possible. Nucleosomes Are a basic Unit of Eukaryotic Chromosome Structure


Cell_Biology_Alberts

Cell_Biology_Alberts. Nucleosomes Are a basic Unit of Eukaryotic Chromosome Structure The proteins that bind to the DNA to form eukaryotic chromosomes are traditionally divided into two classes: the histones and the non-histone chromosomal proteins, each contributing about the same mass to a chromosome as the DNA. The complex of both classes of protein with the nuclear DNA of eukaryotic cells is known as chromatin (Figure 4–20).


Cell_Biology_Alberts

Cell_Biology_Alberts. Histones are responsible for the first and most basic level of chromosome packing, the nucleosome, a protein–DNA complex discovered in 1974. When interphase nuclei are broken open very gently and their contents examined under the electron microscope, most of the chromatin appears to be in the form of a fiber with a diameter of about 30 nm (Figure 4–21A). If this chromatin is subjected to treatments that cause it to unfold partially, it can be seen under the electron microscope as a series of “beads on a string” (Figure 4–21B). The string is DNA, and each bead is a “nucleosome core particle” that consists of DNA wound around a histone core (Movie 4.2).


Cell_Biology_Alberts

Cell_Biology_Alberts. The structural organization of nucleosomes was determined after first isolating them from unfolded chromatin by digestion with particular enzymes (called nucleases) that break down DNA by cutting between the nucleosomes. After digestion for a short period, the exposed DNA between the nucleosome core particles, the linker DNA, is degraded. Each individual nucleosome core particle consists of a complex of eight histone proteins—two molecules each of histones H2A, Figure 4–20 Chromatin. As illustrated, chromatin consists of DNA bound to both histone and non-histone proteins. The mass of histone protein present is about equal to the total mass of non-histone protein, but—as schematically indicated here—the latter class is composed of an enormous number of different species. In total, a chromosome is about one-third DNA and two-thirds protein by mass.


Cell_Biology_Alberts

Cell_Biology_Alberts. H2B, H3, and H4—and double-stranded DNA that is 147 nucleotide pairs long. The histone octamer forms a protein core around which the double-stranded DNA is wound (Figure 4–22). The region of linker DNA that separates each nucleosome core particle from the next can vary in length from a few nucleotide pairs up to about 80. (The term nucleosome technically refers to a nucleosome core particle plus one of its adjacent DNA linkers, but it is often used synonymously with nucleosome core particle.) On average, therefore, nucleosomes repeat at intervals of about 200 nucleotide pairs. For example, a diploid human cell with 6.4 × 109 nucleotide pairs contains approximately 30 million nucleosomes. The formation of nucleosomes converts a DNA molecule into a chromatin thread about one-third of its initial length. The Structure of the Nucleosome Core Particle Reveals How DNA Is Packaged


Cell_Biology_Alberts

Cell_Biology_Alberts. The Structure of the Nucleosome Core Particle Reveals How DNA Is Packaged The high-resolution structure of a nucleosome core particle, solved in 1997, revealed a disc-shaped histone core around which the DNA was tightly wrapped in a left-handed coil of 1.7 turns (Figure 4–23). All four of the histones that make up the core of the nucleosome are relatively small proteins (102–135 amino acids), and they share a structural motif, known as the histone fold, formed from three α helices connected by two loops (Figure 4–24). In assembling a nucleosome, the histone folds first bind to each other to form H3–H4 and H2A–H2B dimers, and the H3–H4 dimers combine to form tetramers. An H3–H4 tetramer then further combines with two H2A–H2B dimers to form the compact octamer core, around which the DNA is wound.


Cell_Biology_Alberts

Cell_Biology_Alberts. The interface between DNA and histone is extensive: 142 hydrogen bonds are formed between DNA and the histone core in each nucleosome. Nearly half of these bonds form between the amino acid backbone of the histones and the sugar-phosphate backbone of the DNA. Numerous hydrophobic interactions and salt linkages also hold DNA and protein together in the nucleosome. More than one-fifth of the amino acids in each of the core histones are either lysine or arginine (two amino acids with basic side chains), and their positive charges can effectively


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–22 Structural organization of the nucleosome. A nucleosome contains a protein core made of eight histone molecules. In biochemical experiments, the nucleosome core particle can be released from isolated chromatin by digestion of the linker DNA with a nuclease, an enzyme that breaks down DNA. (The nuclease can degrade the exposed linker DNA but cannot attack the DNA wound tightly around the nucleosome core.) After dissociation of the isolated nucleosome into its protein core and DNA, the length of the DNA that was wound around the core can be determined. This length of 147 nucleotide pairs is sufficient to wrap 1.7 times around the histone core.


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–21 Nucleosomes as seen in the electron microscope. (A) Chromatin isolated directly from an interphase nucleus appears in the electron microscope as a thread about 30 nm thick. (b) This electron micrograph shows a length of chromatin that has been experimentally unpacked, or decondensed, after isolation to show the nucleosomes. (A, courtesy of barbara Hamkalo; b, courtesy of victoria Foe.) core histones linker DNA of nucleosome “beads-on-a-string” nucleosome includes form of chromatin ~200 nucleotide pairs of DNA


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–23 The structure of a nucleosome core particle, as determined by x-ray diffraction analyses of crystals. Each histone is colored according to the scheme in Figure 4–22, with the DNA double helix in light gray. (Adapted from k. luger et al., Nature 389:251–260, 1997. with permission from macmillan Publishers ltd.) neutralize the negatively charged DNA backbone. These numerous interactions explain in part why DNA of virtually any sequence can be bound on a histone octamer core. The path of the DNA around the histone core is not smooth; rather, several kinks are seen in the DNA, as expected from the nonuniform surface of the


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–24 The overall structural organization of the core histones. (A) Each of the core histones contains an N-terminal tail, which is subject to several forms of covalent modification, and a histone fold region, as indicated. (b) The structure of the histone fold, which is formed by all four of the core histones. (C) Histones 2A and 2b form a dimer through an interaction known as the “handshake.” Histones H3 and H4 form a dimer through the same type of interaction. (D) The final histone octamer on DNA. Note that all eight N-terminal tails of the histones protrude from the disc-shaped core structure. Their conformations are highly flexible, and they serve as binding sites for sets of other proteins.


Cell_Biology_Alberts

Cell_Biology_Alberts. core. The bending requires a substantial compression of the minor groove of the DNA helix. Certain dinucleotides in the minor groove are especially easy to compress, and some nucleotide sequences bind the nucleosome more tightly than others (Figure 4–25). This probably explains some striking, but unusual, cases of very precise positioning of nucleosomes along a stretch of DNA. However, the sequence preference of nucleosomes must be weak enough to allow other factors to dominate, inasmuch as nucleosomes can occupy any one of a number of positions relative to the DNA sequence in most chromosomal regions. In addition to its histone fold, each of the core histones has an N-terminal amino acid “tail,” which extends out from the DNA–histone core (see Figure 4–24D). These histone tails are subject to several different types of covalent modifications that in turn control critical aspects of chromatin structure and function, as we shall discuss shortly.


Cell_Biology_Alberts

Cell_Biology_Alberts. As a reflection of their fundamental role in DNA function through controlling chromatin structure, the histones are among the most highly conserved eukaryotic proteins. For example, the amino acid sequence of histone H4 from a pea differs from that of a cow at only 2 of the 102 positions. This strong evolutionary conservation suggests that the functions of histones involve nearly all of their amino acids, so that a change in any position is deleterious to the cell. But in addition to this remarkable conservation, eukaryotic organisms also produce smaller amounts of specialized variant core histones that differ in amino acid sequence from the main ones. As discussed later, these variants, combined with the surprisingly large number of covalent modifications that can be added to the histones in nucleosomes, give rise to a variety of chromatin structures in cells.


Cell_Biology_Alberts

Cell_Biology_Alberts. Nucleosomes Have a Dynamic Structure, and Are Frequently Subjected to Changes Catalyzed by ATP-Dependent Chromatin Remodeling Complexes For many years biologists thought that, once formed in a particular position on DNA, a nucleosome would remain fixed in place because of the very tight association between its core histones and DNA. If true, this would pose problems for genetic readout mechanisms, which in principle require easy access to many specific DNA sequences. It would also hinder the rapid passage of the DNA transcription and replication machinery through chromatin. But kinetic experiments show that the DNA in an isolated nucleosome unwraps from each end at a rate of about four times per second, remaining exposed for 10 to 50 milliseconds before the partially unwrapped structure recloses. Thus, most of the DNA in an isolated nucleosome is in principle available for binding other proteins.


Cell_Biology_Alberts

Cell_Biology_Alberts. For the chromatin in a cell, a further loosening of DNA–histone contacts is clearly required, because eukaryotic cells contain a large variety of ATP-dependent chromatin remodeling complexes. These complexes include a subunit that hydrolyzes ATP (an ATPase evolutionarily related to the DNA helicases discussed in Chapter 5). This subunit binds both to the protein core of the nucleosome and to the double-stranded DNA that winds around it. By using the energy of ATP hydrolysis to move this DNA relative to the core, the protein complex changes the structure of a nucleosome temporarily, making the DNA less tightly bound to the histone core. Through repeated cycles of ATP hydrolysis that pull the nucleosome core along the DNA double helix, the remodeling complexes can catalyze nucleosome sliding. In this way, they can reposition nucleosomes to expose specific regions of DNA, thereby making them available to other proteins in the cell (Figure 4–26). In addition, by cooperating with a variety


Cell_Biology_Alberts

Cell_Biology_Alberts. In this way, they can reposition nucleosomes to expose specific regions of DNA, thereby making them available to other proteins in the cell (Figure 4–26). In addition, by cooperating with a variety of other proteins that bind to histones and serve as histone chaperones, some remodeling complexes are able to remove either all or part of the nucleosome core from a nucleosome—catalyzing either an exchange of its H2A–H2B histones, or the complete removal of the octameric core from the DNA (Figure 4–27). As a result of such processes, measurements reveal that a typical nucleosome is replaced on the DNA every one or two hours inside the cell.


Cell_Biology_Alberts

Cell_Biology_Alberts. DNA of nucleosome histone core of nucleosome (histone octamer) AA, TT, and TA dinucleotides preferred here (minor groove inside) (minor groove outside) Figure 4–25 The bending of DNA in a nucleosome. The DNA helix makes 1.7 tight turns around the histone octamer. This diagram illustrates how the minor groove is compressed on the inside of the turn. Owing to structural features of the DNA molecule, the indicated dinucleotides are preferentially accommodated in such a narrow minor groove, which helps to explain why certain DNA sequences will bind more tightly than others to the nucleosome core.


Cell_Biology_Alberts

Cell_Biology_Alberts. Cells contain dozens of different ATP-dependent chromatin remodeling complexes that are specialized for different roles. Most are large protein complexes that can contain 10 or more subunits, some of which bind to specific modifications on histones (see Figure 4–26C). The activity of these complexes is carefully controlled by the cell. As genes are turned on and off, chromatin remodeling complexes are brought to specific regions of DNA where they act locally to influence chromatin structure (discussed in Chapter 7; see also Figure 4–40, below).


Cell_Biology_Alberts

Cell_Biology_Alberts. Although some DNA sequences bind more tightly than others to the nucleosome core (see Figure 4–25), the most important influence on nucleosome positioning appears to be the presence of other tightly bound proteins on the DNA. Some bound proteins favor the formation of a nucleosome adjacent to them. Others create obstacles that force the nucleosomes to move elsewhere. The exact positions of nucleosomes along a stretch of DNA therefore depend mainly on the presence and nature of other proteins bound to the DNA. And due to the presence of ATP-dependent chromatin remodeling complexes, the arrangement of nucleosomes on DNA can be highly dynamic, changing rapidly according to the needs of the cell.


Cell_Biology_Alberts

Cell_Biology_Alberts. Although enormously long strings of nucleosomes form on the chromosomal DNA, chromatin in a living cell probably rarely adopts the extended “beads-on-astring” form. Instead, the nucleosomes are packed on top of one another, generating arrays in which the DNA is even more highly condensed. Thus, when nuclei are very gently lysed onto an electron microscope grid, much of the chromatin is seen to be in the form of a fiber with a diameter of about 30 nm, which is considerably wider than chromatin in the “beads-on-a-string” form (see Figure 4–21).


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–26 The nucleosome sliding catalyzed by ATP-dependent chromatin remodeling complexes. (A) Using the energy of ATP hydrolysis, the remodeling complex is thought to push on the DNA of its bound nucleosome and loosen its attachment to the nucleosome core. Each cycle of ATP binding, ATP hydrolysis, and release of the ADP and Pi products thereby moves the DNA with respect to the histone octamer in the direction of the arrow in this diagram. It requires many such cycles to produce the nucleosome sliding shown.


Cell_Biology_Alberts

Cell_Biology_Alberts. (b) The structure of a nucleosome-bound dimer of the two identical ATPase subunits (green) that slide nucleosomes back and forth in the ISw1 family of chromatin remodeling complexes. (C) The structure of a large chromatin remodeling complex, showing how it is thought to wrap around a nucleosome. modeled in green is the yeast RSC complex, which contains 15 subunits— including an ATPase and at least four subunits with domains that recognize specific covalently modified histones. (b, from l.R. Racki et al., Nature 462:1016–1021, 2009. with permission from macmillan Publishers ltd; C, adapted from A.E. leschziner et al., Proc. Natl Acad. Sci. USA 104:4913–4918, 2007.) 192 Chapter 4: DNA, Chromosomes, and genomes


Cell_Biology_Alberts

Cell_Biology_Alberts. A.E. leschziner et al., Proc. Natl Acad. Sci. USA 104:4913–4918, 2007.) 192 Chapter 4: DNA, Chromosomes, and genomes How nucleosomes are organized into condensed arrays is unclear. The structure of a tetranucleosome (a complex of four nucleosomes) obtained by x-ray crystallography and high-resolution electron microscopy of reconstituted chromatin have been used to support a zigzag model for the stacking of nucleosomes in a 30-nm fiber (Figure 4–28). But cryoelectron microscopy of carefully prepared nuclei suggests that most regions of chromatin are less regularly structured.


Cell_Biology_Alberts

Cell_Biology_Alberts. What causes nucleosomes to stack so tightly on each other? Nucleosome-tonucleosome linkages that involve histone tails, most notably the H4 tail, constitute one important factor (Figure 4–29). Another important factor is an additional histone that is often present in a 1-to-1 ratio with nucleosome cores, known as Figure 4–28 A zigzag model for the 30histone H1. This so-called linker histone is larger than the individual core histones nm chromatin fiber. (A) The conformation of two of the four nucleosomes in a and it has been considerably less well conserved during evolution. A single his tetranucleosome, from a structure tone H1 molecule binds to each nucleosome, contacting both DNA and protein, determined by x-ray crystallography. and changing the path of the DNA as it exits from the nucleosome. This change in (b) Schematic of the entire tetranucleosome; the exit path of DNA is thought to help compact nucleosomal DNA (Figure 4–30). the fourth nucleosome is not visible, being stacked


Cell_Biology_Alberts

Cell_Biology_Alberts. This change in (b) Schematic of the entire tetranucleosome; the exit path of DNA is thought to help compact nucleosomal DNA (Figure 4–30). the fourth nucleosome is not visible, being stacked on the bottom nucleosome and behind it in this diagram. (C) Diagrammatic illustration of a possible zigzag structure that could account for the 30-nm chromatin fiber. (A, PDb code: 1Zbb; C, adapted from C.l. woodcock, Nat. Struct. Mol. Biol. 12:639–640, 2005. with permission from macmillan Publishers ltd.)


Cell_Biology_Alberts

Cell_Biology_Alberts. Most eukaryotic organisms make several histone H1 proteins of related but quite distinct amino acid sequences. The presence of many other DNA-binding proteins, as well as proteins that bind directly to histones, is certain to add important additional features to any array of nucleosomes.


Cell_Biology_Alberts

Cell_Biology_Alberts. A gene is a nucleotide sequence in a DNA molecule that acts as a functional unit for the production of a protein, a structural RNA, or a catalytic or regulatory RNA molecule. In eukaryotes, protein-coding genes are usually composed of a string of alternating introns and exons associated with regulatory regions of DNA. A chromosome is formed from a single, enormously long DNA molecule that contains a linear array of many genes, bound to a large set of proteins. The human genome contains 3.2 × 109 DNA nucleotide pairs, divided between 22 different autosomes (present in two copies each) and 2 sex chromosomes. Only a small percentage of this DNA codes for proteins or functional RNA molecules. A chromosomal DNA molecule also contains three other types of important nucleotide sequences: replication origins and telomeres allow the DNA molecule to be efficiently replicated, while a centromere attaches the sister DNA molecules to the mitotic spindle, ensuring their accurate segregation to


Cell_Biology_Alberts

Cell_Biology_Alberts. origins and telomeres allow the DNA molecule to be efficiently replicated, while a centromere attaches the sister DNA molecules to the mitotic spindle, ensuring their accurate segregation to daughter cells during the M phase of the cell cycle.


Cell_Biology_Alberts

Cell_Biology_Alberts. The DNA in eukaryotes is tightly bound to an equal mass of histones, which form repeated arrays of DNA–protein particles called nucleosomes. The nucleosome is composed of an octameric core of histone proteins around which the DNA double helix is wrapped. Nucleosomes are spaced at intervals of about 200 nucleotide pairs, and they are usually packed together (with the aid of histone H1 molecules) into quasi-regular arrays to form a 30-nm chromatin fiber. Even though compact, the structure of chromatin must be highly dynamic to allow access to the DNA. There is some spontaneous DNA unwrapping and rewrapping in the nucleosome itself; however, the general strategy for reversibly changing local chromatin structure features ATP-driven chromatin remodeling complexes. Cells contain a large set of such complexes, which are targeted to specific regions of chromatin at appropriate times. The remodeling complexes collaborate with histone chaperones to allow nucleosome cores to be repositioned,


Cell_Biology_Alberts

Cell_Biology_Alberts. of such complexes, which are targeted to specific regions of chromatin at appropriate times. The remodeling complexes collaborate with histone chaperones to allow nucleosome cores to be repositioned, reconstituted with different histones, or completely removed to expose the underlying DNA.


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–29 A model for the role played by histone tails in the compaction of chromatin. (A) A schematic diagram shows the approximate exit points of the eight histone tails, one from each histone protein, that extend from each nucleosome. The actual structure is shown to its right. In the high-resolution structure of the nucleosome, the tails are largely unstructured, suggesting that they are highly flexible. (b) As indicated, the histone tails are thought to be involved in interactions between nucleosomes that help to pack them together. (A, PDb code: 1k X5.)


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–30 How the linker histone binds to the nucleosome. The position and structure of histone H1 is shown. The H1 core region constrains an additional 20 nucleotide pairs of DNA where it exits from the nucleosome core and is important for compacting chromatin. (A) Schematic, and (b) structure inferred for a single nucleosome from a structure determined by high-resolution electron microscopy of a reconstituted chromatin fiber (C). (b and C, adapted from F. Song et al., Science 344:376–380, 2014.)


Cell_Biology_Alberts

Cell_Biology_Alberts. Having described how DNA is packaged into nucleosomes to create a chromatin fiber, we now turn to the mechanisms that create different chromatin structures in different regions of a cell’s genome. Mechanisms of this type have a variety of important functions in cells. Most strikingly, certain types of chromatin structure can be inherited; that is, the structure can be directly passed down from a cell to its descendants. Because the cell memory that results is based on an inherited chromatin structure rather than on a change in DNA sequence, this is a form of epigenetic inheritance. The prefix epi is Greek for “on”; this is appropriate, because epigenetics represents a form of inheritance that is superimposed on the genetic inheritance based on DNA.


Cell_Biology_Alberts

Cell_Biology_Alberts. In Chapter 7, we shall introduce the many different ways in which the expression of genes is regulated. There we discuss epigenetic inheritance in detail and present several different mechanisms that can produce it. Here, we are concerned with only one, that based on chromatin structure. We begin this section by reviewing the observations that first demonstrated that chromatin structures can be inherited. We then describe some of the chemistry that makes this possible— the covalent modification of histones in nucleosomes. These modifications have many functions, inasmuch as they serve as recognition sites for protein domains that link specific protein complexes to different regions of chromatin. Histones thereby have effects on gene expression, as well as on many other DNA-linked processes. Through such mechanisms, chromatin structure plays an important role in the development, growth, and maintenance of all eukaryotic organisms, including ourselves.


Cell_Biology_Alberts

Cell_Biology_Alberts. Light-microscope studies in the 1930s distinguished two types of chromatin in the interphase nuclei of many higher eukaryotic cells: a highly condensed form, called heterochromatin, and all the rest, which is less condensed, called euchromatin. Heterochromatin represents an especially compact form of chromatin (see Figure 4–9), and we are finally beginning to understand its molecular properties. It is highly concentrated in certain specialized regions, most notably at the centromeres and telomeres introduced previously (see Figure 4–19), but it is also present at many other locations along chromosomes—locations that can vary according to the physiological state of the cell. In a typical mammalian cell, more than 10% of the genome is packaged in this way.


Cell_Biology_Alberts

Cell_Biology_Alberts. The DNA in heterochromatin typically contains few genes, and when euchromatic regions are converted to a heterochromatic state, their genes are generally switched off as a result. However, we know now that the term heterochromatin encompasses several distinct modes of chromatin compaction that have different implications for gene expression. Thus, heterochromatin should not be thought of as simply encapsulating “dead” DNA, but rather as a descriptor for compact chromatin domains that share the common feature of being unusually resistant to gene expression. The Heterochromatic State Is Self-Propagating


Cell_Biology_Alberts

Cell_Biology_Alberts. The Heterochromatic State Is Self-Propagating Through chromosome breakage and rejoining, whether brought about by a natural genetic accident or by experimental artifice, a piece of chromosome that is normally euchromatic can be translocated into the neighborhood of heterochromatin. Remarkably, this often causes silencing—inactivation—of the normally active genes. This phenomenon is referred to as a position effect. It reflects a spreading of the heterochromatic state into the originally euchromatic region, and it has provided important clues to the mechanisms that create and maintain heterochromatin. First recognized in Drosophila, position effects have now been observed in many eukaryotes, including yeasts, plants, and humans. early in the developing embryo, heterochromatin forms and spreads into neighboring euchromatin to different extents in different cells clone of cells with clone of cells with clone of cells with gene 1 inactive genes 1, 2, and 3 inactive no genes inactivated


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–31 The cause of position effect variegation in Drosophila. (A) Heterochromatin (green) is normally prevented from spreading into adjacent regions of euchromatin (red) by barrier DNA sequences, which we shall discuss shortly. In flies that inherit certain chromosomal rearrangements, however, this barrier is no longer present. (b) During the early development of such flies, heterochromatin can spread into neighboring chromosomal DNA, proceeding for different distances in different cells. This spreading soon stops, but the established pattern of heterochromatin is subsequently inherited, so that large clones of progeny cells are produced that have the same neighboring genes condensed into heterochromatin and thereby inactivated (hence the “variegated” appearance of some of these flies; see Figure 4–32). Although “spreading” is used to describe the formation of new heterochromatin close to previously existing heterochromatin, the term may not be wholly accurate. There is evidence


Cell_Biology_Alberts

Cell_Biology_Alberts. see Figure 4–32). Although “spreading” is used to describe the formation of new heterochromatin close to previously existing heterochromatin, the term may not be wholly accurate. There is evidence that during expansion, the condensation of DNA into heterochromatin can “skip over” some regions of chromatin, sparing the genes that lie within them from repressive effects.


Cell_Biology_Alberts

Cell_Biology_Alberts. In chromosome breakage-and-rejoining events of the sort just described, the zone of silencing, where euchromatin is converted to a heterochromatic state, spreads for different distances in different early cells in the fly embryo. Remarkably, these differences then are perpetuated for the rest of the animal’s life: in each cell, once the heterochromatic condition is established on a piece of chromatin, it tends to be stably inherited by all of that cell’s progeny (Figure 4–31). This remarkable phenomenon, called position effect variegation, was first recognized through a detailed genetic analysis of the mottled loss of red pigment in the fly eye (Figure 4–32). It shares features with the extensive spread of heterochromatin that inactivates one of the two X chromosomes in female mammals. There too, a random process acts in each cell of the early embryo to dictate which X chromosome will be inactivated, and that same X chromosome then remains inactive in all the cell’s progeny, creating


Cell_Biology_Alberts

Cell_Biology_Alberts. too, a random process acts in each cell of the early embryo to dictate which X chromosome will be inactivated, and that same X chromosome then remains inactive in all the cell’s progeny, creating a mosaic of different clones of cells in the adult body (see Figure 7–50).


Cell_Biology_Alberts

Cell_Biology_Alberts. These observations, taken together, point to a fundamental strategy of heterochromatin formation: heterochromatin begets more heterochromatin. This positive feedback can operate both in space, causing the heterochromatic state to spread along the chromosome, and in time, across cell generations, propagating the heterochromatic state of the parent cell to its daughters. The challenge is to explain the molecular mechanisms that underlie this remarkable behavior.


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–32 The discovery of position effects on gene expression. The White gene in the fruit fly Drosophila controls eye pigment production and is named after the mutation that first identified it. wild-type flies with a normal White gene (White+) have normal pigment production, which gives them red eyes, but if the White gene is mutated and inactivated, the mutant flies (White–) make no pigment and have white eyes. In flies in which a normal White gene has been moved near a region of heterochromatin, the eyes are mottled, with both red and white patches. The white patches represent cell lineages in which the White gene has been silenced by the effects of the heterochromatin. In contrast, the red patches represent cell lineages in which the White gene is expressed. Early in development, when the heterochromatin is first formed, it spreads into neighboring euchromatin to different extents in different embryonic cells (see Figure 4–31). The presence of large patches of red and white


Cell_Biology_Alberts

Cell_Biology_Alberts. when the heterochromatin is first formed, it spreads into neighboring euchromatin to different extents in different embryonic cells (see Figure 4–31). The presence of large patches of red and white cells reveals that the state of transcriptional activity, as determined by the packaging of this gene into chromatin in those ancestor cells, is inherited by all daughter cells.


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–33 Some prominent types of covalent amino acid side-chain (B) SERINE PHOSPHORYLATION modifications found on nucleosomal histones. (A) Three different levels of lysine methylation are shown; each can be recognized by a different binding protein and thus each can have a different significance for the cell. Note that acetylation removes the plus charge on lysine, and that, most importantly, an acetylated lysine cannot be methylated, and vice versa. (b) Serine phosphorylation adds a negative charge to a histone. modifications of histones not shown here include the monoor dimethylation of an arginine, the phosphorylation of a threonine, the addition of ADP-ribose to a glutamic acid, and the addition of a ubiquityl, sumoyl, or biotin group to a lysine. OPO As a first step, one can carry out a search for the molecules that are involved.


Cell_Biology_Alberts

Cell_Biology_Alberts. As a first step, one can carry out a search for the molecules that are involved. This has been done by means of genetic screens, in which large numbers of mutants are generated, after which one picks out those that show an abnormality of the process in question. Extensive genetic screens in Drosophila, fungi, and mice have identified more than 100 genes whose products either enhance or suppress the spread of heterochromatin and its stable inheritance—in other words, genes that serve as either enhancers or suppressors of position effect variegation. Many of these genes turn out to code for non-histone chromosomal proteins that interact with histones and are involved in modifying or maintaining chromatin structure. We shall discuss how they work in the sections that follow. The Core Histones Are Covalently modified at many Different Sites


Cell_Biology_Alberts

Cell_Biology_Alberts. The Core Histones Are Covalently modified at many Different Sites The amino acid side chains of the four histones in the nucleosome core are subjected to a remarkable variety of covalent modifications, including the acetylation of lysines, the mono-, di-, and trimethylation of lysines, and the phosphorylation of serines (Figure 4–33). A large number of these side-chain modifications occur on the eight relatively unstructured N-terminal “histone tails” that protrude from the nucleosome (Figure 4–34). However, there are also more than 20 specific side-chain modifications on the nucleosome’s globular core.


Cell_Biology_Alberts

Cell_Biology_Alberts. All of the above types of modifications are reversible, with one enzyme serving to create a particular type of modification, and another to remove it. These enzymes are highly specific. Thus, for example, acetyl groups are added to specific lysines by a set of different histone acetyl transferases (HATs) and removed by a set of histone deacetylase complexes (HDACs). Likewise, methyl groups are added to lysine side chains by a set of different histone methyl transferases and removed by a set of histone demethylases. Each enzyme is recruited to specific sites on the chromatin at defined times in each cell’s life history. For the most part, the initial recruitment depends on transcription regulator proteins (sometimes called “transcription factors”). As we shall explain in Chapter 7, these proteins recognize and bind to specific DNA sequences in the chromosomes. They are produced at KEY:


Cell_Biology_Alberts

Cell_Biology_Alberts. Figure 4–34 The covalent modification of core histone tails. (A) The structure of the nucleosome highlighting the location of the first 30 amino acids in each of its eight N-terminal histone tails (green). These tails are unstructured and highly mobile, and thus will change their conformation depending on other bound proteins. (b) well-documented modifications of the four histone core proteins are indicated. Although only a single symbol is used here for methylation (m), each lysine (k) or arginine (R) can be methylated in several different ways. Note also that some positions (e.g., lysine 9 of H3) can be modified either by methylation or by acetylation, but not both. most of the modifications shown add a relatively small molecule onto the histone tails; the exception is ubiquitin, a 76-amino-acid protein also used for other cell processes (see Figure 3–69). Not shown are more than 20 possible modifications located in the globular core of the histones. (A, PDb: 1kX5; b, adapted from


Cell_Biology_Alberts

Cell_Biology_Alberts. protein also used for other cell processes (see Figure 3–69). Not shown are more than 20 possible modifications located in the globular core of the histones. (A, PDb: 1kX5; b, adapted from H. Santos-Rosa and


Cell_Biology_Alberts

Cell_Biology_Alberts. C. Caldas, Eur. J. Cancer 41:2381–2402, 2005. with permission from Elsevier.) different times and places in the life of an organism, thereby determining where and when the chromatin-modifying enzymes will act. In this way, the DNA sequence ultimately determines how histones are modified. But in at least some cases, the covalent modifications on nucleosomes can persist long after the transcription regulator proteins that first induced them have disappeared, thereby providing the cell with a memory of its developmental history. Most remarkably, as in the related phenomenon of position effect variegation discussed above, this memory can be transmitted from one cell generation to the next.


Cell_Biology_Alberts

Cell_Biology_Alberts. Very different patterns of covalent modification are found on different groups of nucleosomes, depending both on their exact position in the genome and on the history of the cell. The modifications of the histones are carefully controlled, and they have important consequences. The acetylation of lysines on the N-terminal tails loosens chromatin structure, in part because adding an acetyl group to lysine removes its positive charge, thereby reducing the affinity of the tails for adjacent nucleosomes. However, the most profound effects of the histone modifications lie in their ability to recruit specific other proteins to the modified stretch of chromatin. Trimethylation of one specific lysine on the histone H3 tail, for instance, attracts the heterochromatin-specific protein HP1 and contributes to the establishment and spread of heterochromatin. More generally, the recruited proteins act with the modified histones to determine how and when genes will be expressed, as well as other