PART INFORMATION PATHWAYS 24 Genes an 25 DNA Metabolism 948 26 RNA Metabolism 995 27 Protein Metabolism 1034 28 Regulation of Gene Ex 1 e of DNA in1953 The third and final part of this book explores the bio-of coding by chemical mechanisms underlying the apparently con-tic diffraction analysis. tradictory requirements for both genetic continuity and the evolution of living organisms. What is the molecular found impa k hypothesis arose from transmitted from one ge to the next with high wide range of opservations disciplines. fidelity? Hov ding of the struc- that are the raw How is ge-ture of DNA inevitably stimulated questions about its g- sequences of the astonishing variety of prot cules in a living cell? The fund t re rise to the tein, so much of the ma comprising the that a er DNA molecules with mational units form the focal points The second is tran- Part. Modern bi oded in DNA are copied precisely into RNA. function has ble to that stimulate Darwin's the- encoded in messenger RNA is translated on the ribo- ory on the origin of species nearly 150 years ago. un- somes into a polypeptide with a particular sequence of derstanding of ed in . 9 中
T he third and final part of this book explores the biochemical mechanisms underlying the apparently contradictory requirements for both genetic continuity and the evolution of living organisms. What is the molecular nature of genetic material? How is genetic information transmitted from one generation to the next with high fidelity? How do the rare changes in genetic material that are the raw material of evolution arise? How is genetic information ultimately expressed in the amino acid sequences of the astonishing variety of protein molecules in a living cell? The fundamental unit of information in living systems is the gene. A gene can be defined biochemically as a segment of DNA (or, in a few cases, RNA) that encodes the information required to produce a functional biological product. The final product is usually a protein, so much of the material in Part III concerns genes that encode proteins. A functional gene product might also be one of several classes of RNA molecules. The storage, maintenance, and metabolism of these informational units form the focal points of our discussion in Part III. Modern biochemical research on gene structure and function has brought to biology a revolution comparable to that stimulated by the publication of Darwin’s theory on the origin of species nearly 150 years ago. An understanding of how information is stored and used in cells has brought penetrating new insights to some of the most fundamental questions about cellular structure and function. A comprehensive conceptual framework for biochemistry is now unfolding. Today’s understanding of information pathways has arisen from the convergence of genetics, physics, and chemistry in modern biochemistry. This was epitomized by the discovery of the double-helical structure of DNA, postulated by James Watson and Francis Crick in 1953 (see Fig. 8–15). Genetic theory contributed the concept of coding by genes. Physics permitted the determination of molecular structure by x-ray diffraction analysis. Chemistry revealed the composition of DNA. The profound impact of the Watson-Crick hypothesis arose from its ability to account for a wide range of observations derived from studies in these diverse disciplines. This revolution in our understanding of the structure of DNA inevitably stimulated questions about its function. The double-helical structure itself clearly suggested how DNA might be copied so that the information it contains can be transmitted from one generation to the next. Clarification of how the information in DNA is converted into functional proteins came with the discovery of both messenger RNA and transfer RNA and with the deciphering of the genetic code. These and other major advances gave rise to the central dogma of molecular biology, comprising the three major processes in the cellular utilization of genetic information. The first is replication, the copying of parental DNA to form daughter DNA molecules with identical nucleotide sequences. The second is transcription, the process by which parts of the genetic message encoded in DNA are copied precisely into RNA. The third is translation, whereby the genetic message encoded in messenger RNA is translated on the ribosomes into a polypeptide with a particular sequence of amino acids. PART INFORMATION PATHWAYS III 24 Genes and Chromosomes 923 25 DNA Metabolism 948 26 RNA Metabolism 995 27 Protein Metabolism 1034 28 Regulation of Gene Expression 1081 921 8885d_c24_920-947 2/11/04 1:36 PM Page 921 mac76 mac76:385_reb:
885dc24_9222/11/043:11 PM Page922mac76mac76:385reb: Part Il Information Pathways upon which life itself is based. We might expect the for- DNA mation of phosphodiester bonds in DNA or peptide bonds in proteins to be a trivial feat for cells, given the arsenal of enzymatic and chemical tools described in Part Il. However, the framework of patterns and rules established in our examination of metabolic pathways RNA thus far must be enlarged considerably to take into account molecular information. Bonds must be formed Translation between particular subunits in informational biopoly- mers, avoiding either the occurrence or the persistence of sequence errors. This has an enormous impact on the thermodynamics, chemistry, and enzymology of the biosynthetic processes. Formation of a peptide bond re- The central dogma of molecular biology, showing the general path- quires an energy input of only about 21 kJ/mol of bonds tion. The term"dogma"is a misnomer. Introduced by Francis Crick at and can be catalyzed by relatively simple enzymes.But a time when little evidence supported these ideas, the dogma has be. to synthesize a bond between two specific amino acids come a well-established principle. at a particular point in a polypeptide, the cell invests about 125 kJ/mol while making use of more than 200 enzymes, RNA molecules, and specialized proteins. The chemistry involved in peptide bond formation does not change because of this requirement, but additional Part Ill explores these and related pi In processes are layered over the basic reaction to ensure pter 24 we examine the structure, topology, and that the peptide bond is formed between particular ackaging of chromosomes and genes. The processes amino acids. Information is expensive underlying the central dogma are elaborated in Chap- The dynamic interaction between nucleic acids and ters 25 through 27. Finally, we turn to regulation, ex- proteins is another central theme of Part Ill. with the amining how the expression of genetic information is important exception of a few catalytic RNA molecules controlled(Chapter 28) (discussed in Chapters 26 and 27), the processes that A major theme running through these chapters is make up the pathways of cellular information flow are the added complexity inherent in the biosynthesis of catalyzed and regulated by proteins. An understanding macromolecules that contain information. Assembling of these enzymes and other proteins can have practical nucleic acids and proteins with particular sequences of as well as intellectual rewards, because they form the nucleotides and amino acids represents nothing less basis of recombinant dna technology (introduced in than preserving the faithful expression of the template Chapter 9)
Part III explores these and related processes. In Chapter 24 we examine the structure, topology, and packaging of chromosomes and genes. The processes underlying the central dogma are elaborated in Chapters 25 through 27. Finally, we turn to regulation, examining how the expression of genetic information is controlled (Chapter 28). A major theme running through these chapters is the added complexity inherent in the biosynthesis of macromolecules that contain information. Assembling nucleic acids and proteins with particular sequences of nucleotides and amino acids represents nothing less than preserving the faithful expression of the template upon which life itself is based. We might expect the formation of phosphodiester bonds in DNA or peptide bonds in proteins to be a trivial feat for cells, given the arsenal of enzymatic and chemical tools described in Part II. However, the framework of patterns and rules established in our examination of metabolic pathways thus far must be enlarged considerably to take into account molecular information. Bonds must be formed between particular subunits in informational biopolymers, avoiding either the occurrence or the persistence of sequence errors. This has an enormous impact on the thermodynamics, chemistry, and enzymology of the biosynthetic processes. Formation of a peptide bond requires an energy input of only about 21 kJ/mol of bonds and can be catalyzed by relatively simple enzymes. But to synthesize a bond between two specific amino acids at a particular point in a polypeptide, the cell invests about 125 kJ/mol while making use of more than 200 enzymes, RNA molecules, and specialized proteins. The chemistry involved in peptide bond formation does not change because of this requirement, but additional processes are layered over the basic reaction to ensure that the peptide bond is formed between particular amino acids. Information is expensive. The dynamic interaction between nucleic acids and proteins is another central theme of Part III. With the important exception of a few catalytic RNA molecules (discussed in Chapters 26 and 27), the processes that make up the pathways of cellular information flow are catalyzed and regulated by proteins. An understanding of these enzymes and other proteins can have practical as well as intellectual rewards, because they form the basis of recombinant DNA technology (introduced in Chapter 9). 922 Part III Information Pathways The central dogma of molecular biology, showing the general pathways of information flow via replication, transcription, and translation. The term “dogma” is a misnomer. Introduced by Francis Crick at a time when little evidence supported these ideas, the dogma has become a well-established principle. RNA Protein Transcription Translation Replication DNA 8885d_c24_922 2/11/04 3:11 PM Page 922 mac76 mac76:385_reb:
8885dc24920-9472/11/041:36 PM Page923mac76mac76:385 chapter GENES AND CHROMOSOMES 24.1 Chromosomal Elements 924 tain them (Fig. 24-1). In this chapter we shift our focus 24.2 DNA Supercoiling 930 from the secondary structure of DNA, considered in 24.3 The Structure of Chromosomes 938 Chapter 8, to the extraordinary degree of organization required for the tertiary packaging of DNA into chromo- somes. We first examine the elements within viral and cellular chromosomes, then assess their size and organi- DNA topoisomerases are the magicians of the DNA world. zation. We next consider DNA topology, providing a By allowing DNa strands or double helices to pass through each other, they can solve all of the topological blems of DNA in replication, transcription and other cellular transactions mes Wang, article in Nature Reviews in Molecular Cell Biology, 2002 Supercoiling, in fact, does more for DNa than act as an executive enhancer; it keeps the unruly, spreading DNA inside the cramped confines that the cell has provided Nicholas Cozzarelli, Harvey Lectures, 1993 Most every cell of a multicellular organism contains the same complement of genetic material--its genome. Just look at any human individual for a hint of the wealth of information contained in each human cell Chromosomes the nucleic acid molecules that are the repository of an organisms genetic information, the largest molecules in a cell and may contain thou- sands of genes as well as considerable tracts of inter- genic DNA. The 16 chromosomes in the relatively small genome of the yeast Saccharomyces cerevisiae have molecular masses ranging from1.5×10t1×10°dal- FIGURE 24-1 Bacteriophage T2 protein coat surrounded by its sin- gle, linear molecule of DNA. The DNA was released by lysing the tons, corresponding to DNA molecules with 230,000 to bacteriophage particle in distilled water and allowing the DNA to 1,532,000 contiguous base pairs(bp). Human chromo- spread on the water surface. An undamaged T2 bacteriophage parti somes range up to 279 million bp cle consists of a head structure that tapers to a tail by which the bac. The very size of DNA molecules presents an inter- teriophage attaches itself to the outer surface of a bacterial cell. All esting biological puzzle, given that they are generally the DNA shown in this electron micrograph is normally packaged in. much longer than the cells or viral packages that con- side the phage head
chapter Almost every cell of a multicellular organism contains the same complement of genetic material—its genome. Just look at any human individual for a hint of the wealth of information contained in each human cell. Chromosomes, the nucleic acid molecules that are the repository of an organism’s genetic information, are the largest molecules in a cell and may contain thousands of genes as well as considerable tracts of intergenic DNA. The 16 chromosomes in the relatively small genome of the yeast Saccharomyces cerevisiae have molecular masses ranging from 1.5 108 to 1 109 daltons, corresponding to DNA molecules with 230,000 to 1,532,000 contiguous base pairs (bp). Human chromosomes range up to 279 million bp. The very size of DNA molecules presents an interesting biological puzzle, given that they are generally much longer than the cells or viral packages that contain them (Fig. 24–1). In this chapter we shift our focus from the secondary structure of DNA, considered in Chapter 8, to the extraordinary degree of organization required for the tertiary packaging of DNA into chromosomes. We first examine the elements within viral and cellular chromosomes, then assess their size and organization. We next consider DNA topology, providing a GENES AND CHROMOSOMES 24.1 Chromosomal Elements 924 24.2 DNA Supercoiling 930 24.3 The Structure of Chromosomes 938 DNA topoisomerases are the magicians of the DNA world. By allowing DNA strands or double helices to pass through each other, they can solve all of the topological problems of DNA in replication, transcription and other cellular transactions. —James Wang, article in Nature Reviews in Molecular Cell Biology, 2002 Supercoiling, in fact, does more for DNA than act as an executive enhancer; it keeps the unruly, spreading DNA inside the cramped confines that the cell has provided for it. —Nicholas Cozzarelli, Harvey Lectures, 1993 24 923 0.5 m FIGURE 24–1 Bacteriophage T2 protein coat surrounded by its single, linear molecule of DNA. The DNA was released by lysing the bacteriophage particle in distilled water and allowing the DNA to spread on the water surface. An undamaged T2 bacteriophage particle consists of a head structure that tapers to a tail by which the bacteriophage attaches itself to the outer surface of a bacterial cell. All the DNA shown in this electron micrograph is normally packaged inside the phage head. 8885d_c24_920-947 2/11/04 1:36 PM Page 923 mac76 mac76:385_reb:
8885d_c24_920-9472/11/041:36 PM Page924mac76mac76:385 924 Chapter 24 Genes and Chromosomes description of the coiling of DNA molecules. Finally, we catalytic function. DNA also contains other segments or discuss the protein-DNA interactions that organize sequences that have a purely regulatory function. Reg hromosomes into compact structures ulatory sequences provide signals that may denote the beginning or the end of genes, or influence the tran scription of genes, or function as initiation points for 24.1 Chromosomal Elements replication or recombination(Chapter 28). Some genes can be expressed in different ways to generate multiple Cellular DNA contains genes and intergenic both of which may serve functions vital to the IS, gene products from one segment of DNA. The special le transcriptional and translational mechanisms that allow more complex genomes, such as those of C this are described in Chapters 26 through 28 cells, demand increased levels of chromosomal organi- We can make direct estimations of the minimum zation, and this is reflected in the chromosomes struc verall size of genes that encode proteins. As described tural features. We begin by considering the ditterent in detail in Chapter 27, each amino acid of a polypep- types of DNA sequences and structural elements within tide chain is coded for by a sequence of three consec- utive nucleotides in a single strand of DNA(Fig. 24-2) with these"codons"arranged in a sequence that corre- Genes Are Segments of DNA That Code sponds to the sequence of amino acids in the polypep- for Polypeptide Chains and RNAs tide that the gene encodes. a polypeptide chain of 350 amino acid residues(an average-size chain)corre- Our understanding of genes has evolved tremendot over the last century. Classically, a gene was defined as a portion of a chromosome that determines or affects a single character or phenotype(visible property), such DNA mRNA Polypeptide as eye color. George Beadle and Edward Tatum proposed a molecular definition of a gene in 1940. After exposing spores of the fungus Neurospora crassa to x rays and TIlIA other agents known to damage dNa and cause alterations in DNA sequence(mutations ), they detected mutant fungal strains that lacked one or another specific en- zyme, sometimes resulting in the failure of an entire TIIA metabolic pathway. Beadle and Tatum concluded that a gene is a segment of genetic material that determines or codes for one enzyme: the one gene-one enzym hypothesis. Later this concept was broadened to one TIIA gene-one polypeptide, because many genes code for proteins that are not enzymes or for one polypeptide of UACACUUUUG TIIA U a multisubunit protein. The modern biochemical definition of a gene is even more precise. a gene is all the dna that encodes the primary sequence of some final gene product, which can be either a polypeptide or an RNa with a structural or TIIA TIIA TIIA GCcGUUUCU CIlI TIIA termi Template strand FIGURE 24-2 Colinearity of the coding nucleotide sequences of DNA and mRNA and the amino acid sequence of a polypeptide chain. a protein through the intermediary mRNA. One of the DNA strands serves as a template for synthesis of mRNA, which has nucleotide triplets (codons)complementary to those of the DNA. In some bacte. orge W. Bead award L. Tatum al and many eukaryotic genes, coding sequences are interrupted at 1903-198 1909-1975 tervals by regions of noncoding sequences(called introns)
description of the coiling of DNA molecules. Finally, we discuss the protein-DNA interactions that organize chromosomes into compact structures. 24.1 Chromosomal Elements Cellular DNA contains genes and intergenic regions, both of which may serve functions vital to the cell. The more complex genomes, such as those of eukaryotic cells, demand increased levels of chromosomal organization, and this is reflected in the chromosome’s structural features. We begin by considering the different types of DNA sequences and structural elements within chromosomes. Genes Are Segments of DNA That Code for Polypeptide Chains and RNAs Our understanding of genes has evolved tremendously over the last century. Classically, a gene was defined as a portion of a chromosome that determines or affects a single character or phenotype (visible property), such as eye color. George Beadle and Edward Tatum proposed a molecular definition of a gene in 1940. After exposing spores of the fungus Neurospora crassa to x rays and other agents known to damage DNA and cause alterations in DNA sequence (mutations), they detected mutant fungal strains that lacked one or another specific enzyme, sometimes resulting in the failure of an entire metabolic pathway. Beadle and Tatum concluded that a gene is a segment of genetic material that determines or codes for one enzyme: the one gene–one enzyme hypothesis. Later this concept was broadened to one gene–one polypeptide, because many genes code for proteins that are not enzymes or for one polypeptide of a multisubunit protein. The modern biochemical definition of a gene is even more precise. A gene is all the DNA that encodes the primary sequence of some final gene product, which can be either a polypeptide or an RNA with a structural or catalytic function. DNA also contains other segments or sequences that have a purely regulatory function. Regulatory sequences provide signals that may denote the beginning or the end of genes, or influence the transcription of genes, or function as initiation points for replication or recombination (Chapter 28). Some genes can be expressed in different ways to generate multiple gene products from one segment of DNA. The special transcriptional and translational mechanisms that allow this are described in Chapters 26 through 28. We can make direct estimations of the minimum overall size of genes that encode proteins. As described in detail in Chapter 27, each amino acid of a polypeptide chain is coded for by a sequence of three consecutive nucleotides in a single strand of DNA (Fig. 24–2), with these “codons” arranged in a sequence that corresponds to the sequence of amino acids in the polypeptide that the gene encodes. A polypeptide chain of 350 amino acid residues (an average-size chain) corre- 924 Chapter 24 Genes and Chromosomes George W. Beadle, 1903–1989 Edward L. Tatum, 1909–1975 U C U A G A C G U G C A G G A C C T U A C A T G A C U T G A U U U A A A G C C C G G G U U C A A 5 3 3 5 DNA mRNA T C T C G T G G A T A C A C T T T T G C C G T T 3 5 Arg Gly Tyr Thr Phe Ala Val Ser Carboxyl terminus Amino terminus Polypeptide Template strand FIGURE 24–2 Colinearity of the coding nucleotide sequences of DNA and mRNA and the amino acid sequence of a polypeptide chain. The triplets of nucleotide units in DNA determine the amino acids in a protein through the intermediary mRNA. One of the DNA strands serves as a template for synthesis of mRNA, which has nucleotide triplets (codons) complementary to those of the DNA. In some bacterial and many eukaryotic genes, coding sequences are interrupted at intervals by regions of noncoding sequences (called introns). 8885d_c24_920-947 2/11/04 1:36 PM Page 924 mac76 mac76:385_reb:
885c249252/12/0411:21 AM Page925mac76mac76:385ebd 24.1 Chromosomal elements sponds to 1, 050 bp. Many genes in eukaryotes and a few double-stranded. a typical medium-sized DNA virus is in prokaryotes are interrupted by noncoding DNA seg- bacteriophage A (lambda), which infects E. coli. In its ments and are therefore considerably longer than this replicative form inside cells, A DNA is a circular double simple calculation would suggest helix. This double-stranded DNA contains 48, 502 bp and How many genes are in a single chromosome? The has a contour length of 17.5 um Bacteriophage x174 Escherichia coli chromosome, one of the prokaryotic is a much smaller DNa virus; the DNA in the viral par genomes that has been completely sequenced, is a cir- ticle is a single-stranded circle, and the double-stranded cular DNA molecule (in the sense of an endless loop replicative form contains 5, 386 bp. Although viral rather than a perfect circle) with 4, 639, 221 bp. These genomes are small, the contour lengths of their dNAs base pairs encode about 4, 300 genes for proteins and are much greater than the long dimensions of the viral another 115 genes for stable RNA molecules. Among eu- particles that contain them. The DNA of bacteriophage karyotes, the approximately 3.2 billion base pairs of the T4, for example, is about 290 times longer than the vi human genome include 30,000 to 35,000 genes on 24 ral particle itself (Table 24-1) different chromosomes Bacteria A single E coli cell contains almost 100 times DNA Molecules Are Much Longer Than the Cellular as much DNA as a bacteriophage A particle. The chro- Packages That contain Them mosome of an E. coli cell is a single double-stranded circular DNA molecule. Its 4, 639, 221 bp have a contour Chromosomal DNAs are often many orders of magni- length of about 1.7 mm, some 850 times the length of tude longer than the cells or viruses in which they are the E coli cell (Fig. 24-3). In addition to the very large found(Fig. 24-1; Table 24-1). This is true of every class circular DNA chromosome in their nucleoid, many bac of organism or parasite teria contain one or more small circular DNa molecules that are free in the cytosol. These extrachromosomal Viruses Viruses are not free-living organisms; rather, elements are called plasmids(Fig. 244; see also they are infectious parasites that use the resources of a p. 311). Most plasmids are only a few thousand base host cell to carry out many of the processes they re- pairs long, but some contain more than 10,000 bp. They quire to propagate. Many viral particles consist of no carry genetic information and undergo replication to more than a genome(usually a single RNA or DNA mol- yield daughter plasmids, which pass into the daughter ecule) surrounded by a protein coat cells at cell division. Plasmids have been found in yeast Almost all plant viruses and some bacterial and an- and other fungi as well as in bacteria. imal viruses have rNa genomes. These genomes tend In many cases plasmids confer no obvious advan to be particularly small. For example, the genomes of tage on their host, and their sole function appears to b mammalian retroviruses such as HIv are about 9, 000 nu- self-propagation. However, some plasmids carry genes cleotides long, and that of the bacteriophage QB has that are useful to the host bacterium. For example 4, 220 nucleotides. Both types of viruses have single- some plasmid genes make a host bacterium resistant stranded RNA genomes to antibacterial agents. Plasmids carrying the gene for The genomes of DNA viruses vary greatly in size the enzyme B-lactamase confer resistance to B-lactam (Table 24-1). Many viral DNAs are circular for at least antibiotics such as penicillin and amoxicillin(see Box part of their life cycle. During viral replication within a 20-1). These and similar plasmids may pass from an host cell, specific types of viral DNA called replicative antibiotic-resistant cell to an antibiotic-sensitive cell of the forms may appear; for example, many linear DNAs be- same or another bacterial species, making the recipient lar and all single-stranded DNAs become cell antibiotic resistant. The extensive use of antibiotics TABLE 24-1 The Sizes of DNA and Viral Particles for Some Bacterial Viruses(Bacteriophages) Size of viral Length of DNA (bp) viral DNA (nm) viral particle(nm) dX174 5,386 1939 39936 14,377 A(lambda) 17.460 14 168889 60800 210 Note: Data on size of DNA are for the replicate form(double- stranded ). The contour length is calculated assuming that
sponds to 1,050 bp. Many genes in eukaryotes and a few in prokaryotes are interrupted by noncoding DNA segments and are therefore considerably longer than this simple calculation would suggest. How many genes are in a single chromosome? The Escherichia coli chromosome, one of the prokaryotic genomes that has been completely sequenced, is a circular DNA molecule (in the sense of an endless loop rather than a perfect circle) with 4,639,221 bp. These base pairs encode about 4,300 genes for proteins and another 115 genes for stable RNA molecules. Among eukaryotes, the approximately 3.2 billion base pairs of the human genome include 30,000 to 35,000 genes on 24 different chromosomes. DNA Molecules Are Much Longer Than the Cellular Packages That Contain Them Chromosomal DNAs are often many orders of magnitude longer than the cells or viruses in which they are found (Fig. 24–1; Table 24–1). This is true of every class of organism or parasite. Viruses Viruses are not free-living organisms; rather, they are infectious parasites that use the resources of a host cell to carry out many of the processes they require to propagate. Many viral particles consist of no more than a genome (usually a single RNA or DNA molecule) surrounded by a protein coat. Almost all plant viruses and some bacterial and animal viruses have RNA genomes. These genomes tend to be particularly small. For example, the genomes of mammalian retroviruses such as HIV are about 9,000 nucleotides long, and that of the bacteriophage Q has 4,220 nucleotides. Both types of viruses have singlestranded RNA genomes. The genomes of DNA viruses vary greatly in size (Table 24–1). Many viral DNAs are circular for at least part of their life cycle. During viral replication within a host cell, specific types of viral DNA called replicative forms may appear; for example, many linear DNAs become circular and all single-stranded DNAs become double-stranded. A typical medium-sized DNA virus is bacteriophage (lambda), which infects E. coli. In its replicative form inside cells, DNA is a circular double helix. This double-stranded DNA contains 48,502 bp and has a contour length of 17.5 m. Bacteriophage X174 is a much smaller DNA virus; the DNA in the viral particle is a single-stranded circle, and the double-stranded replicative form contains 5,386 bp. Although viral genomes are small, the contour lengths of their DNAs are much greater than the long dimensions of the viral particles that contain them. The DNA of bacteriophage T4, for example, is about 290 times longer than the viral particle itself (Table 24–1). Bacteria A single E. coli cell contains almost 100 times as much DNA as a bacteriophage particle. The chromosome of an E. coli cell is a single double-stranded circular DNA molecule. Its 4,639,221 bp have a contour length of about 1.7 mm, some 850 times the length of the E. coli cell (Fig. 24–3). In addition to the very large, circular DNA chromosome in their nucleoid, many bacteria contain one or more small circular DNA molecules that are free in the cytosol. These extrachromosomal elements are called plasmids (Fig. 24–4; see also p. 311). Most plasmids are only a few thousand base pairs long, but some contain more than 10,000 bp. They carry genetic information and undergo replication to yield daughter plasmids, which pass into the daughter cells at cell division. Plasmids have been found in yeast and other fungi as well as in bacteria. In many cases plasmids confer no obvious advantage on their host, and their sole function appears to be self-propagation. However, some plasmids carry genes that are useful to the host bacterium. For example, some plasmid genes make a host bacterium resistant to antibacterial agents. Plasmids carrying the gene for the enzyme -lactamase confer resistance to -lactam antibiotics such as penicillin and amoxicillin (see Box 20–1). These and similar plasmids may pass from an antibiotic-resistant cell to an antibiotic-sensitive cell of the same or another bacterial species, making the recipient cell antibiotic resistant. The extensive use of antibiotics 24.1 Chromosomal Elements 925 TABLE 24–1 The Sizes of DNA and Viral Particles for Some Bacterial Viruses (Bacteriophages) Size of viral Length of Long dimension of Virus DNA (bp) viral DNA (nm) viral particle (nm) X174 5,386 1,939 25 T7 39,936 14,377 78 (lambda) 48,502 17,460 190 T4 168,889 60,800 210 Note: Data on size of DNA are for the replicative form (double-stranded). The contour length is calculated assuming that each base pair occupies a length of 3.4 Å (see Fig. 8–15). 8885d_c24_925 2/12/04 11:21 AM Page 925 mac76 mac76:385_reb:
8885dc24920-9472/11/041:36 PM Page926mac76mac76:385 926 Chapter 24 Genes and Chromosomes FIGURE 24-3 The length of the E coli chromosome(1.7 mm) depicted in linear form relative to the length of a typical E. coli cell (2 um) E. coli FIGURE 24-4 DNA from a lysed E coli cell. In this electron micrograph several small, circu- lar plasmid DNAs are indicated by white arrows. The black spots and white specks are artifacts of the preparation in some human populations has served as a strong mosomes(Fig. 24-5). Each chromosome of a eukary- elective force, encouraging the spread of antibiotic otic cell, such as that shown in Figure 24-5a, contains resistance-coding plasmids(as well as transposable el- a single, very large, duplex DNA molecule. The DNA ements, described below, that harbor similar genes)in molecules in the 24 different types of human chromo- disease-causing bacteria and creating bacterial strains somes(22 matching pairs plus the X and Y sex chro- that are resistant to several antibiotics. Physicians are mosomes) vary in length over a 25-fold range. Each type becoming increasingly reluctant to prescribe antibiotics of chromosome in eukaryotes carries a characteristic set unless a clear clinical need is confirmed. For similar rea- of genes. Interestingly, the number of genes does not sons, the widespread use of antibiotics in animal feeds vary nearly as much as does genome size( see Chapter 9 for a discussion of the types of sequences, besides genes, that contribute to genome size) Eukaryotes A yeast cell, one of the simplest eukary The dNa of one human genome(22 chromosomes otes, has 2.6 times more dNA in its genome than an E. plus X and Y or two X chromosomes), placed end to coli cell ( Table 24-2). Cells of Drosophila, the fruit fly end, would extend for about a meter. Most human cells used in classical genetic studies, contain more than 35 are diploid and each cell contains a total of 2 m of dNA. times as much dna as e els, and human cells An adult human body contains approximately 10 cells have almost 700 times as much. The cells of many plants and thus a total dNa length of 2X 10 km. Compare and amphibians contain even more. The geneticmaterial this with the circumference of the earth(4 X 10"km) of eukaryotic cells is apportioned into chromosomes, the or the distance between the earth and the sun diploid(2n) number depending on the species (Table (1.5 X 10 km)-a dramatic illustration of the extraor- 24-2). A human somatic cell, for example, has 46 chro- dinary degree of DNA compaction in our cells
E. coli E. coli DNA mosomes (Fig. 24–5). Each chromosome of a eukaryotic cell, such as that shown in Figure 24–5a, contains a single, very large, duplex DNA molecule. The DNA molecules in the 24 different types of human chromosomes (22 matching pairs plus the X and Y sex chromosomes) vary in length over a 25-fold range. Each type of chromosome in eukaryotes carries a characteristic set of genes. Interestingly, the number of genes does not vary nearly as much as does genome size (see Chapter 9 for a discussion of the types of sequences, besides genes, that contribute to genome size). The DNA of one human genome (22 chromosomes plus X and Y or two X chromosomes), placed end to end, would extend for about a meter. Most human cells are diploid and each cell contains a total of 2 m of DNA. An adult human body contains approximately 1014 cells and thus a total DNA length of 2 1011 km. Compare this with the circumference of the earth (4 104 km) or the distance between the earth and the sun (1.5 108 km)—a dramatic illustration of the extraordinary degree of DNA compaction in our cells. in some human populations has served as a strong selective force, encouraging the spread of antibiotic resistance–coding plasmids (as well as transposable elements, described below, that harbor similar genes) in disease-causing bacteria and creating bacterial strains that are resistant to several antibiotics. Physicians are becoming increasingly reluctant to prescribe antibiotics unless a clear clinical need is confirmed. For similar reasons, the widespread use of antibiotics in animal feeds is being curbed. Eukaryotes A yeast cell, one of the simplest eukaryotes, has 2.6 times more DNA in its genome than an E. coli cell (Table 24–2). Cells of Drosophila, the fruit fly used in classical genetic studies, contain more than 35 times as much DNA as E. coli cells, and human cells have almost 700 times as much. The cells of many plants and amphibians contain even more. The genetic material of eukaryotic cells is apportioned into chromosomes, the diploid (2n) number depending on the species (Table 24–2). A human somatic cell, for example, has 46 chro- 926 Chapter 24 Genes and Chromosomes FIGURE 24–3 The length of the E. coli chromosome (1.7 mm) depicted in linear form relative to the length of a typical E. coli cell (2 m). FIGURE 24–4 DNA from a lysed E. coli cell. In this electron micrograph several small, circular plasmid DNAs are indicated by white arrows. The black spots and white specks are artifacts of the preparation. 8885d_c24_920-947 2/11/04 1:36 PM Page 926 mac76 mac76:385_reb:
8885d_c24_920-9472/11/041:36 PM Page927mac76mac76:385 24.1 Chromosomal Elements ∥中 °p FIGURE 24-5 Eukaryotic chromosomes. (a) A pair of linked and condensed sister chromatids from a human chromosome. Eukaryotic chromosomes an in this state after replication and at metaphase during mitosis. (b)A complete set of chromosomes from a leukocyte from one of the authors. There are 46 chromosomes in every normal human somatic cell. Eukaryotic cells also have organelles, mitochondria (Fig. 24-6)and chloroplasts, that contain DNA. Mito- chondrial DNA (mtDNA) molecules are much smaller than the nuclear chromosomes In animal cells. mtdNA contains fewer than 20,000 bp(16, 569 bp in human mtDNA) and is a circular duplex. Each mitochondrion typically has two to ten copies of this mtDNA molecule and the number can rise to hundreds in certain cells when an embryo is undergoing cell differentiation. In a few organisms(trypanosomes, for example) each mito- chondron contains thousands of copies of mtDNA, or- ganized into a complex and interlinked matrix known as a kinetoplast. Plant cell mtDNA ranges in size from 200,000 to 2,500,000 bp Chloroplast DNA (CpDNA)als exists as circular duplexes and ranges in size from 120,000 to 160,000 bp. The evolutionary origin of mito- chondrial and chloroplast dnAs has been the subject of much speculation. A widely accepted view is that they FIGURE 24-6 A dividing mitochondrion. Some mitochondrial are vestiges of the chromosomes of ancient bacteria that proteins and RNAs are encoded by one of the copies of the mito- gained access to the cytoplasm of host cells and became chondrial DNA (none of which are visible here). The DNA(mtDNA) the precursors of these organelles(see is replicated each time the mitochondrion divides, before cell division
Eukaryotic cells also have organelles, mitochondria (Fig. 24–6) and chloroplasts, that contain DNA. Mitochondrial DNA (mtDNA) molecules are much smaller than the nuclear chromosomes. In animal cells, mtDNA contains fewer than 20,000 bp (16,569 bp in human mtDNA) and is a circular duplex. Each mitochondrion typically has two to ten copies of this mtDNA molecule, and the number can rise to hundreds in certain cells when an embryo is undergoing cell differentiation. In a few organisms (trypanosomes, for example) each mitochondrion contains thousands of copies of mtDNA, organized into a complex and interlinked matrix known as a kinetoplast. Plant cell mtDNA ranges in size from 200,000 to 2,500,000 bp. Chloroplast DNA (cpDNA) also exists as circular duplexes and ranges in size from 120,000 to 160,000 bp. The evolutionary origin of mitochondrial and chloroplast DNAs has been the subject of much speculation. A widely accepted view is that they are vestiges of the chromosomes of ancient bacteria that gained access to the cytoplasm of host cells and became the precursors of these organelles (see Fig. 1–36). 24.1 Chromosomal Elements 927 (a) (b) FIGURE 24–6 A dividing mitochondrion. Some mitochondrial proteins and RNAs are encoded by one of the copies of the mitochondrial DNA (none of which are visible here). The DNA (mtDNA) is replicated each time the mitochondrion divides, before cell division. FIGURE 24–5 Eukaryotic chromosomes. (a) A pair of linked and condensed sister chromatids from a human chromosome. Eukaryotic chromosomes are in this state after replication and at metaphase during mitosis. (b) A complete set of chromosomes from a leukocyte from one of the authors. There are 46 chromosomes in every normal human somatic cell. 8885d_c24_920-947 2/11/04 1:36 PM Page 927 mac76 mac76:385_reb:
8885dc24920-9472/11/041:36 PM Page928mac76mac76:385 928 Chapter 24 Genes and Chromosomes TABLE 24-2 DNA Gene, and Chromosome Content in Some Genomes lotal DNA (bp) Number of chromosomes number of genes Bacterium(Escherichia coll) 4,639221 4.405 Yeast(Saccharomyces cerevisiae Nematode(Caenorhabditis elegans) 97.000000 19.000 Plant(Arabidopsis thaliana) 125,00000 25,500 Fruit fly(Drosophila melanogaster) 180,000.000 13,600 Plant(Oryza sativa; rice) 480.000000 24 57 Mouse(Mus musculus) 2500,00000 30,000-35,000 Human(Homo sapiens) 3.200000000 30000-35,000 Note: This information is constantly being refined. For the most current information, consult the websites for the individual genome project. The diploid chomosome number is ghen for all eukaryotes ecept yeast. Haploid chromosome number. Wild yeast strains generally have eight (octoploid)or more sets of these chromosomes INumber for females, with bo x chromosomes. Males have an x but no y thus 11 chromosomes in all. Mitochondrial dna codes for the mitochondrial trnas In higher eukaryotes, the typical gene has much and rRNAs and for a few mitochondrial proteins. More more intron sequence than sequences devoted to ex- than 95% of mitochondrial proteins are encoded by nu- ons. For example, in the gene coding for the single clear DNA Mitochondria and chloroplasts divide when polypeptide chain of the avian egg protein ovalbumin the cell divides. Their DNA is replicated before and dur-(Fig. 24-7), the introns are much longer than the ex- ng division, and the daughter dNa molecules pass into ons; altogether, seven introns make up 85% of the gene's he daughter organelles DNA. In the gene for the B subunit of hemoglobin, a sin- gle intron contains more than half of the genes dNA. Eukaryotic Genes and Chromosomes The gene for the muscle protein titin is the intron cham- Are Very Complex pion, with 178 introns. Genes for histones appear to have no introns. In most cases the function of introns is not Many bacterial species have only one chromosome per clear. In total, only about 1.5% of human dNa is"cod- cell and, in nearly all cases, each chromosome contains ing or exon DNA, carrying information for protein or only one copy of each gene. A very few genes, such as RNA products. However, when the much larger introns those for rRNAS, are repeated several times. Genes and are included in the count, as much as 30% of the hu- regulatory sequences account for almost all the dna in man genome consists of genes prokaryotes. Moreover, almost every gene is precisely The relative paucity of genes in the human genome colinear with the amino acid sequence (or RNA se- leaves a lot of DNa unaccounted for. Figure 24-8 quence) for which it codes(Fig. 24-2) provides a summary of sequence types. Much of the The organization of genes in eukaryotic DNA is nongene DNA is in the form of repeated sequences of tructurally and functionally much more complex. The several kinds. Perhaps most surprising, about half the study of eukaryotic chromosome structure, and more human genome is made up of moderately repeated se- recently the sequencing of entire eukaryotic genomes, quences that are derived from transposable elements- has yielded many surprises. Many, if not most, eukary- segments of DNA, ranging from a few hundred to sev- otic genes have a distinctive and puzzling structural eral thousand base pairs long, that can move from one feature: their nucleotide sequences contain one or more location to another in the genome. Transposable ele intervening segments of DNa that do not code for the ments(transposons) are a kind of molecular parasite, amino acid sequence of the polypeptide product. These efficiently making a home within the host genome. Many nontranslated inserts interrupt the otherwise colinear have genes encoding proteins that catalyze the trans- relationship between the nucleotide sequence of the position process, described in more detail in Chapters gene and the amino acid sequence of the polypeptide it 25 and 26. Some transposons in the human genome are encodes. Such nontranslated DNA segments in genes active, moving at a low frequency, but most are inactive re called intervening sequences or introns, and the relics, evolutionarily altered by mutations. Although coding segments are called exons. Few prokaryotic these elements generally do not encode proteins or genes contain introns. RNAs that are used in human cells, they have played a
Mitochondrial DNA codes for the mitochondrial tRNAs and rRNAs and for a few mitochondrial proteins. More than 95% of mitochondrial proteins are encoded by nuclear DNA. Mitochondria and chloroplasts divide when the cell divides. Their DNA is replicated before and during division, and the daughter DNA molecules pass into the daughter organelles. Eukaryotic Genes and Chromosomes Are Very Complex Many bacterial species have only one chromosome per cell and, in nearly all cases, each chromosome contains only one copy of each gene. A very few genes, such as those for rRNAs, are repeated several times. Genes and regulatory sequences account for almost all the DNA in prokaryotes. Moreover, almost every gene is precisely colinear with the amino acid sequence (or RNA sequence) for which it codes (Fig. 24–2). The organization of genes in eukaryotic DNA is structurally and functionally much more complex. The study of eukaryotic chromosome structure, and more recently the sequencing of entire eukaryotic genomes, has yielded many surprises. Many, if not most, eukaryotic genes have a distinctive and puzzling structural feature: their nucleotide sequences contain one or more intervening segments of DNA that do not code for the amino acid sequence of the polypeptide product. These nontranslated inserts interrupt the otherwise colinear relationship between the nucleotide sequence of the gene and the amino acid sequence of the polypeptide it encodes. Such nontranslated DNA segments in genes are called intervening sequences or introns, and the coding segments are called exons. Few prokaryotic genes contain introns. In higher eukaryotes, the typical gene has much more intron sequence than sequences devoted to exons. For example, in the gene coding for the single polypeptide chain of the avian egg protein ovalbumin (Fig. 24–7), the introns are much longer than the exons; altogether, seven introns make up 85% of the gene’s DNA. In the gene for the subunit of hemoglobin, a single intron contains more than half of the gene’s DNA. The gene for the muscle protein titin is the intron champion, with 178 introns. Genes for histones appear to have no introns. In most cases the function of introns is not clear. In total, only about 1.5% of human DNA is “coding” or exon DNA, carrying information for protein or RNA products. However, when the much larger introns are included in the count, as much as 30% of the human genome consists of genes. The relative paucity of genes in the human genome leaves a lot of DNA unaccounted for. Figure 24–8 provides a summary of sequence types. Much of the nongene DNA is in the form of repeated sequences of several kinds. Perhaps most surprising, about half the human genome is made up of moderately repeated sequences that are derived from transposable elements— segments of DNA, ranging from a few hundred to several thousand base pairs long, that can move from one location to another in the genome. Transposable elements (transposons) are a kind of molecular parasite, efficiently making a home within the host genome. Many have genes encoding proteins that catalyze the transposition process, described in more detail in Chapters 25 and 26. Some transposons in the human genome are active, moving at a low frequency, but most are inactive relics, evolutionarily altered by mutations. Although these elements generally do not encode proteins or RNAs that are used in human cells, they have played a 928 Chapter 24 Genes and Chromosomes TABLE 24–2 DNA, Gene, and Chromosome Content in Some Genomes Total DNA (bp) Number of Approximate chromosomes* number of genes Bacterium (Escherichia coli) 4,639,221 1 4,405 Yeast (Saccharomyces cerevisiae) 12,068,000 16† 6,200 Nematode (Caenorhabditis elegans) 97,000,000 12‡ 19,000 Plant (Arabidopsis thaliana) 125,000,000 10 25,500 Fruit fly (Drosophila melanogaster) 180,000,000 18 13,600 Plant (Oryza sativa; rice) 480,000,000 24 57,000 Mouse (Mus musculus) 2,500,000,000 40 30,000–35,000 Human (Homo sapiens) 3,200,000,000 46 30,000–35,000 Note: This information is constantly being refined. For the most current information, consult the websites for the individual genome projects. * The diploid chromosome number is given for all eukaryotes except yeast. † Haploid chromosome number. Wild yeast strains generally have eight (octoploid) or more sets of these chromosomes. ‡ Number for females, with two X chromosomes. Males have an X but no Y, thus 11 chromosomes in all. 8885d_c24_920-947 2/11/04 1:36 PM Page 928 mac76 mac76:385_reb:
8885dc24920-9472/11/041:36 PM Page929mac76mac76:385 24.1 Chromosomal Elements 929 Ovalbumin Exon 222bp 126bp 24-7 Introns in two eukaryotic genes. The gene for ovalbu- has two introns and three exons, including one intron that alone con- seven introns (A to G), splitting the coding sequences into tains more than half the base pairs of the gene. ight exons(L, and 1 to 7). The gene for the B subunit of hemoglobin role in human evolution: movement of trans- position often causes it to migrate as"satellite" bands can lead to the redistribution of other genomic (separated from the rest of the DNa) when fragmented sequences cellular DNa samples are centrifuged in a cesium chlo- Another 3%or so of the human genome consists of ride density gradient. Studies suggest that simple highly repetitive sequences, also referred to as sequence dna does not encode proteins or RNAs. Un- simple-sequence DNa or simple sequence repeats like the transposable elements, the highly repetitive (SSR). These short sequences, generally less than DNA can have identifiable functional importance in 10 bp long, are sometimes repeated millions of times per human cellular metabolism, because much of it is asso- cell. The simple-sequence DNA has also been called ciated with two defining features of eukaryotic chro- satellite DNA. so named because its unusual base com- mosomes: centromeres and telome FIGURE 24-8 Types of in the human genome. This pie chart divides the genome into transposons(transposable elements), genes, and miscellaneous sequences. There are four main classes of transposons. Long interspersed elements(LINEs), 6 to 8 kbp long(1 kbp 1,000 bp), typically include a few genes encoding proteins that cat- alyze transposition. The genome has about 850,000 LINEs. Short inter- spersed elements(SINEs)are about 100 to 300 bp long. Of the 1.5 million in the human genome more than 1 million are Alu elements, o called because they generally include one copy of the recognition LINE sequence for Alul, a restriction endonuclease (see Fig. 9-3).The also contains 450,000 copies of retroviruslike t Retroviruslike 1.5 to 11 kbp long. Although these are"trapped"in the genome and cannot move from one cell to another, they are evolutionarily related 15%Ex 3%6 SSR to the retroviruses( Chapter 26), which include HIV. A final class of transposons(making up <1% and not shown here) consists of a vari- 5% SD ety of transposon remnants that differ greatly in length 28.5% About 30% of the genome consists of sequences included in genes but only a small fraction of this DNA is in exons(codi quences). Miscellaneous sequences include simple-sequence re- peats(SSR) and large segmental duplications(SD), the latter being seg. ments that appear more than once in different locations. Among the encoding RNAs(which can be harder to identify than genes for pro- teins) and remnants of transposons that have been evolutionarily al. tered so that they are now hard to identify
major role in human evolution: movement of transposons can lead to the redistribution of other genomic sequences. Another 3% or so of the human genome consists of highly repetitive sequences, also referred to as simple-sequence DNA or simple sequence repeats (SSR). These short sequences, generally less than 10 bp long, are sometimes repeated millions of times per cell. The simple-sequence DNA has also been called satellite DNA, so named because its unusual base composition often causes it to migrate as “satellite” bands (separated from the rest of the DNA) when fragmented cellular DNA samples are centrifuged in a cesium chloride density gradient. Studies suggest that simplesequence DNA does not encode proteins or RNAs. Unlike the transposable elements, the highly repetitive DNA can have identifiable functional importance in human cellular metabolism, because much of it is associated with two defining features of eukaryotic chromosomes: centromeres and telomeres. 24.1 Chromosomal Elements 929 A BC D E F G 12 3 4 5 6 7 Ovalbumin gene A 131 bp B 851 bp 1 90 bp 2 222 bp 3 126 bp L Hemoglobin subunit Exon Intron FIGURE 24–7 Introns in two eukaryotic genes. The gene for ovalbumin has seven introns (A to G), splitting the coding sequences into eight exons (L, and 1 to 7). The gene for the subunit of hemoglobin has two introns and three exons, including one intron that alone contains more than half the base pairs of the gene. Genes 30% Miscellaneous 25% Transposons 45% 13% SINEs 8% Retroviruslike 3% SSR 5% SD 17% ? 28.5% Introns and noncoding segments 21% LINEs 1.5% Exons FIGURE 24–8 Types of sequences in the human genome. This pie chart divides the genome into transposons (transposable elements), genes, and miscellaneous sequences. There are four main classes of transposons. Long interspersed elements (LINEs), 6 to 8 kbp long (1 kbp 1,000 bp), typically include a few genes encoding proteins that catalyze transposition. The genome has about 850,000 LINEs. Short interspersed elements (SINEs) are about 100 to 300 bp long. Of the 1.5 million in the human genome more than 1 million are Alu elements, so called because they generally include one copy of the recognition sequence for AluI, a restriction endonuclease (see Fig. 9–3). The genome also contains 450,000 copies of retroviruslike transposons, 1.5 to 11 kbp long. Although these are “trapped” in the genome and cannot move from one cell to another, they are evolutionarily related to the retroviruses (Chapter 26), which include HIV. A final class of transposons (making up 1% and not shown here) consists of a variety of transposon remnants that differ greatly in length. About 30% of the genome consists of sequences included in genes for proteins, but only a small fraction of this DNA is in exons (coding sequences). Miscellaneous sequences include simple-sequence repeats (SSR) and large segmental duplications (SD), the latter being segments that appear more than once in different locations. Among the unlisted sequence elements (denoted by a question mark) are genes encoding RNAs (which can be harder to identify than genes for proteins) and remnants of transposons that have been evolutionarily altered so that they are now hard to identify. 8885d_c24_920-947 2/11/04 1:36 PM Page 929 mac76 mac76:385_reb:
885024-920-9472/11041:36age930nac76ma76:385律 930 Chapter 24 Genes and Chromosomes Telomere SUMMARY 24.1 Chromosomal elements Genes are segments of a chromosome that contain the information for a functional polypeptide or RNA molecule. In addition to and multiple replication origins genes, chromosomes contain a variety of regulatory sequences involved in replication, FIGURE 24-9 Important structural elements of a yeast chromosome. transcription, and other processes Genomic dna and rna molecules are generally orders of magnitude longer than the The centromere(Fig. 24-9)is a sequence of dNA viral particles or cells that contain them. that functions during cell division as an attachment point for proteins that link the chromosome to the mi- a Many genes in eukaryotic cells, and a few in totic spindle. This attachment is essential for the equal bacteria, are interrupted by noncoding and orderly distribution of chromosome sets to daugh- sequences called introns. The coding segments ter cells. The centromeres of Saccharomyces cere- separated by introns are called exons visiae have been isolated and studied. The sequences I Less than one-third of human genomic dNA essential to centromere function are about 130 bp long consists of genes. Much of the remainder and are very rich in A=T pairs. The centromeric se- consists of repeated sequences of various quences of higher eukaryotes are much longer and, un types. Nucleic acid parasites known as like those of yeast, generally contain simple-sequence transposons account for about half of the DNA, which consists of thousands of tandem copies of human genome. one or a few short sequences of 5 to 10 bp, in the same I Eukaryotic chromosomes have two important orientation. The precise role of simple-sequence dNA pecial- function repetitive DNA sequences in centromere function is not yet understood. centromeres, which are attachment points for Telomeres(Greek telos, "end) are sequences at the mitotic spindle, and telomeres, located at the ends of eukaryotic chromosomes that help stabilize the ends of chromosomes the chromosome. The best-characterized telomeres are those of the simpler eukaryotes. Yeast telomeres end with about 100 bp of imprecisely repeated sequences of the form 24.2 DNA Supercoiling (5)(T Cellular DNA, as we have seen, is extremely compacted, (3)(A2 plying a high degree of structural organization. The folding mechanism must not only pack the dna but also where a and y are generally between l and 4. The num- permit access to the information in the DNA. Before ber of telomere repeats, n, is in the range of 20 to 100 considering how this is accomplished in processes such for most single-celled eukaryotes and generally more as replication and transcription, we need to examine an than 1, 500 in mammals. The ends of a linear DNA mol- important property of DNa structure known as super cule cannot be routinely replicated by the cellular repli- coiling. cation machinery(which may be one reason why bac- Supercoiling means the coiling of a coil. a telephone erial DNA molecules are circular). Repeated telomeric cord, for example, is typically a coiled wire. The path sequences are added to eukaryotic chromosome ends taken by the wire between the base of the phone and 26-35). the receiver often includes one or more supercoils(Fig Artificial chromosomes(Chapter 9)have been con- 24-10). DNA is coiled in the form of a double helix, with structed as a means of better understanding the func- both strands of the dna coiling around an axis. The tional significance of many structural features of eukar- further coiling of that axis upon itself (Fig. 24-11)pro- yotic chromosomes A reasonably stable artificial linear duces DNA supercoiling. As detailed below, DNA chromosome requires only three components: a centro- supercoiling is generally a manifestation of structural mere, telomeres at each end, and sequences that allow strain. When there is no net bending of the dNa axis the initiation of DNAreplication. Yeast artificial chromo- upon itself, the DNA is said to be in a relaxed state somes (YACs; see Fig 9-8) have been developed as a We might have predicted that DNa compaction in- research tool in biotechnology. Similarly, human artificial volved some form of supercoiling. Perhaps less pre- chromosomes(HACs) are being developed for the treat- dictable is that replication and transcription of dNa al ment of genetic diseases by somatic gene therapy affect and are affected by supercoiling. Both processes
The centromere (Fig. 24–9) is a sequence of DNA that functions during cell division as an attachment point for proteins that link the chromosome to the mitotic spindle. This attachment is essential for the equal and orderly distribution of chromosome sets to daughter cells. The centromeres of Saccharomyces cerevisiae have been isolated and studied. The sequences essential to centromere function are about 130 bp long and are very rich in AUT pairs. The centromeric sequences of higher eukaryotes are much longer and, unlike those of yeast, generally contain simple-sequence DNA, which consists of thousands of tandem copies of one or a few short sequences of 5 to 10 bp, in the same orientation. The precise role of simple-sequence DNA in centromere function is not yet understood. Telomeres (Greek telos, “end”) are sequences at the ends of eukaryotic chromosomes that help stabilize the chromosome. The best-characterized telomeres are those of the simpler eukaryotes. Yeast telomeres end with about 100 bp of imprecisely repeated sequences of the form (5)(TxGy)n (3)(AxCy)n where x and y are generally between 1 and 4. The number of telomere repeats, n, is in the range of 20 to 100 for most single-celled eukaryotes and generally more than 1,500 in mammals. The ends of a linear DNA molecule cannot be routinely replicated by the cellular replication machinery (which may be one reason why bacterial DNA molecules are circular). Repeated telomeric sequences are added to eukaryotic chromosome ends primarily by the enzyme telomerase (see Fig. 26–35). Artificial chromosomes (Chapter 9) have been constructed as a means of better understanding the functional significance of many structural features of eukaryotic chromosomes. A reasonably stable artificial linear chromosome requires only three components: a centromere, telomeres at each end, and sequences that allow the initiation of DNA replication. Yeast artificial chromosomes (YACs; see Fig. 9–8) have been developed as a research tool in biotechnology. Similarly, human artificial chromosomes (HACs) are being developed for the treatment of genetic diseases by somatic gene therapy. SUMMARY 24.1 Chromosomal Elements ■ Genes are segments of a chromosome that contain the information for a functional polypeptide or RNA molecule. In addition to genes, chromosomes contain a variety of regulatory sequences involved in replication, transcription, and other processes. ■ Genomic DNA and RNA molecules are generally orders of magnitude longer than the viral particles or cells that contain them. ■ Many genes in eukaryotic cells, and a few in bacteria, are interrupted by noncoding sequences called introns. The coding segments separated by introns are called exons. ■ Less than one-third of human genomic DNA consists of genes. Much of the remainder consists of repeated sequences of various types. Nucleic acid parasites known as transposons account for about half of the human genome. ■ Eukaryotic chromosomes have two important special-function repetitive DNA sequences: centromeres, which are attachment points for the mitotic spindle, and telomeres, located at the ends of chromosomes. 24.2 DNA Supercoiling Cellular DNA, as we have seen, is extremely compacted, implying a high degree of structural organization. The folding mechanism must not only pack the DNA but also permit access to the information in the DNA. Before considering how this is accomplished in processes such as replication and transcription, we need to examine an important property of DNA structure known as supercoiling. Supercoiling means the coiling of a coil. A telephone cord, for example, is typically a coiled wire. The path taken by the wire between the base of the phone and the receiver often includes one or more supercoils (Fig. 24–10). DNA is coiled in the form of a double helix, with both strands of the DNA coiling around an axis. The further coiling of that axis upon itself (Fig. 24–11) produces DNA supercoiling. As detailed below, DNA supercoiling is generally a manifestation of structural strain. When there is no net bending of the DNA axis upon itself, the DNA is said to be in a relaxed state. We might have predicted that DNA compaction involved some form of supercoiling. Perhaps less predictable is that replication and transcription of DNA also affect and are affected by supercoiling. Both processes 930 Chapter 24 Genes and Chromosomes Unique sequences (genes), dispersed repeats, and multiple replication origins Telomere Centromere Telomere FIGURE 24–9 Important structural elements of a yeast chromosome. 8885d_c24_920-947 2/11/04 1:36 PM Page 930 mac76 mac76:385_reb:
