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Much of thehighly repetitive DNA is associated with two important structures ineukaryotic chromosomes—centromeres and telomeres.Each chromosome has a single centromere, which functions as anattachment point for proteins that link the chromosome to the microtubules of the mitotic spindle (see Fig. 2-14). This attachment is essential for the ordered segregation of chromosomes to daughter cells during cell division. The centromeres of yeast chromosomes have beenisolated and studied (Fig. 23-7).
The sequences essential to centromere function are about 130 base pairs long and are very rich in A = Tpairs. The centromeres of higher eukaryotes are much larger. Inhigher eukaryotes (but not in yeast), satellite DNA is generally foundin the centromeric region and consists of thousands of tandem (side-byside and in the same orientation) copies of one or a few short sequences. Characterized satellite sequences are generally 5 to 10 basepairs long. The precise role of satellite DNA in centromere function isnot yet understood.TelomereCentromereUnique sequences (genes),dispersed repeats, andmultiple replication originsTelomereFigure 23-7 Important structural features of ayeast chromosome.Part IV Information Pathways798Telomeres are sequences located at the ends of the linear eukaryotic chromosomes, which help stabilize them.
The best-characterizedtelomeres are those of simpler eukaryotes. Yeast telomeres end withabout 100 base pairs of imprecisely repeated sequences of the form(5'XTxGy)nOvalbumingeneLCytochrome bgeneA2,000 bpDB1,900 bpC1,500 bpD750 bpwhere x and y generally fall in the range of 1 to 4. The ends of a linearDNA molecule cannot be replicated by the cellular replication machinery (which may be one reason why bacterial DNA molecules are circular). The repeated sequences in telomeres are added to chromosomeends by special enzymes, one of which is telomerase, which will bediscussed in more detail in Chapter 25. What controls the number ofrepeats in a telomere is not known. The telomere repeats are a veryunusual DNA structure.Efforts have begun to construct artificial chromosomes as a meansof better understanding the functional significance of many structuralfeatures of eukaryotic chromosomes.
A reasonably stable, artificial,linear chromosome requires only three components: a centromere, telomeres at the ends, and sequences that direct the initiation of DNAreplication.Most moderately repetitive DNA consists of 150 to 300 base-pairrepeats scattered throughout the genome of higher eukaryotes. Someof these repeats have been characterized. A number of them have someof the structural properties of transposable elements, sequences thatmove about the genome at very low frequency (Chapter 24).
In humans, one class of these repeats (about 300 base pairs long) is calledthe Alu family, so named because their sequence generally includesone copy of the recognition sequence for the restriction endonucleaseAlul. (Restriction endonucleases are described in Chapter 28.) Hundreds of thousands of Alu repeats occur in the human genome, comprising 1 to 3% of the total DNA. They apparently were derived from agene for 7SL RNA, a component of a complex called the signal-recognition particle (SRP, Chapter 26) that functions in protein synthesis. TheAlu repeats, however, lack parts of the 7SL RNA gene sequence and donot produce functional 7SL RNAs. When Alu repeats are grouped withother classes of repeats with similar sizes and sequence structures,they make up 5 to 10% of the DNA in the human genome.
No functionfor this DNA is known.The unique sequences in eukaryotic chromosomes include most ofthe genes. There are an estimated 100,000 different genes in thehuman genome.Many Eukaryotic Genes Contain InterveningNontranscribed Sequences (Introns)Figure 23-8 Intervening sequences, or introns, intwo eukaryotic genes. The gene for ovalbumin hasseven introns (A to G), splitting the coding sequences into eight exons (L, 1 to 7). The gene forcytochrome b has four introns and five exons. Inboth cases, more DNA is devoted to introns than toexons.
The number of base pairs (bp) in the intronsof the cytochrome b gene is shown.Many, if not most, eukaryotic genes have a distinctive and puzzlingstructural 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 precisely colinear relationship between thenucleotide sequence of the gene and the amino acid sequence of thepolypeptide it encodes (Fig.
23-8). Such nontranslated DNA segmentsin genes are called intervening sequences, or introns, and the coding segments are called exons. A well-known example is the gene coding for the single polypeptide chain of the avian egg protein ovalbumin./799Figure 23—9 Supercoils. A typical phone cord is acoil. A phone cord twisted as shown is a supercoil.The illustration is especially appropriate, becausean examination of the twisting of phone cordshelped lead Jerome Vinograd and colleagues tothe insight that many properties of small, circularDNAs could be explained by supercoiling. They firstdetected DNA supercoiling in small, circular viralDNAs in 1965.Coil —<&*-> i?As can be seen in Figure 23-8, the introns of this particular gene aremuch longer than the exons; altogether the introns make up 85% of theDNA of this gene.
Most eukaryotic genes examined thus far appear tocontain introns that vary in number, position, and the fraction of thetotal length of the gene they occupy. For example, the serum albumingene contains 6 introns, the gene for the protein conalbumin of thechicken egg contains 17 introns, and a collagen gene has been found tohave over 50 introns. Genes for histones provide an example of a familyof genes that appear to have no introns. Only a few prokaryotic genescontain introns. In most cases the function of introns is not clear.DNA SupercoilingFrom the examples given above, it is clear that cellular DNA must bevery tightly compacted just to fit into the cell. This implies a highdegree of structural organization.
It is not enough just to fold the DNAinto a small space, however. The packaging must permit access to theinformation in the DNA for processes such as replication and transcription. Before considering how this is accomplished, we must examine an important property of DNA structure that we have not yet considered—DNA supercoiling.The term "supercoiling" means literally the coiling of a coil. A telephone cord for example, is typically a coiled wire. The twisted pathoften taken by that wire as it goes from the base of the phone to thereceiver generally describes a supercoil (Fig. 23-9).
DNA is coiled inthe form of a double helix. Let us define an axis about which bothstrands of the DNA coil. A bending or twisting of that axis upon itself(Fig. 23-10) is referred to as DNA supercoiling. As detailed below,DNA supercoiling is generally a manifestation of structural strain.Conversely, if there is no net bending of the DNA axis upon itself, theDNA is said to be in a relaxed state.It is probably apparent that DNA compaction must involve someform of supercoiling.
Perhaps less apparent is the fact that replicatingor transcribing DNA also must induce some degree of supercoiling.Figure 23-10 Supercoiling of DNA. Supercoiling isthe twisting of the DNA axis upon itself.khv*«—Supercoil/AxisDNA double helix(coil)AxisDNA supercoilChapter 23 Genes and ChromosomesThe DNA molecules in chromosomes are the largest macromolecules in cells.
Many smaller DNAsalso occur in cells, in the form of viral DNAs, plasmids, and (in eukaryotes) mitochondrial or chloroplast DNAs. Many DNAs, especially those in bacteria, mitochondria, and chloroplasts, are circular.Viral and chromosomal DNAs have one major feature in common: they are generally much longerthan the viral particles or cells in which they arepackaged. The total DNA content of a eukaryoticcell is much greater than that of a bacterial cell.Genes are segments of a chromosome that contain the information for a functional polypeptide orRNA molecule. In addition to these structuralgenes, chromosomes contain a variety of regulatory sequences involved in replication, transcription, and other processes. In eukaryotic chromosomes, there are two important special-functionrepetitive DNA sequences: centromeres, which areattachment points for the mitotic spindle, and telomeres, which occur at the ends of the linear chromosomes.
Many genes in eukaryotic cells, andoccasionally in bacteria, are interrupted by noncoding sequences called introns. The coding segments separated by introns are called exons.Most cellular DNAs are supercoiled. Supercoiling is a manifestation of structural strain impartedby the underwinding of the DNA molecule. Underwinding is a decrease in the total number of helicalturns in the DNA relative to the relaxed or B form.To maintain an underwound state, DNA must be aclosed circle or be bound with protein.
Supercoilsresulting from underwinding are defined as negative supercoils. Underwinding is quantified by atopological parameter called linking number, Lk.The linking number of a relaxed, closed-circularDNA is used as a reference {Lk0) and is equal to thenumber of base pairs divided by 10.5. Underwinding is measured in terms of the specific linking difference or cr, which equals (Lk - Lko)/Lko. For cellular DNAs, a typically equals -0.05 to -0.07,which means that approximately 5 to 7% of thehelical turns in the DNA have been removed.
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