chromosome

Compaction

Each nucleus in the cell of a human or other mammal contains some 6 billion base pairs of DNA which, if stretched out, would form a very thin thread about 6 ft (2 m) long. This DNA has to be packaged into the chromosome within a nucleus that is much smaller than a printed dot (Fig. 1). Each chromosome contains a single length of DNA comprising a specific portion of the genetic material of the organism. Tiny stretches of DNA, about 140 base pairs long and containing acidic phosphate groups, are individually wrapped around an octamer consisting of two molecules of each of the four basic histone proteins H2a, H2b, H3, and H4. This arrangement produces small structures called nucleosomes and results in a sevenfold compaction of the DNA strand. Further compaction is achieved by binding the histone protein H1 and several nonhistone proteins, resulting in a supercoiled structure in which the chromosome is shortened by about 1600-fold in the interphase nucleus and by about 8000-fold during metaphase and anaphase, where the genetic material must be fully compacted for transport to the two daughter cells. At the point of maximum compaction, human chromosomes range in size from about 2 to 10 micrometers in length, that is, less than 0.0004 in. See Nucleosome

Organization of DNA into chromosomes

Number and size

Each diploid (2n) organism has a characteristic number of chromosomes in each body (somatic) cell, which can vary from two in a nematode worm and one species of ant, to hundreds in some butterflies, crustaceans, and plants. The diploid number of chromosomes includes a haploid (n) set from each parent. Many one-celled organisms are haploid throughout most of their life cycle. The human diploid number is 46.

There is some relationship between the number of chromosomes and their size. Some of the chromosomes in certain classes of organisms with large numbers of chromosomes are very tiny, and have been called microchromosomes. In birds and some reptiles, there are about 30–40 pairs of microchromosomes in addition to 5–7 or so pairs of regular-sized macrochromosomes. The number of microchromosomes is constant in any species carrying them, and only their size distinguishes them from the widespread macrochromosomes. At least seven microchromosomes in birds have been shown to contain genes, and all are thought to.

In some species of insects, plants, flatworms, snails, and rarely vertebrates (such as the fox), the number of chromosomes can vary because of the presence of a variable number of accessory chromosomes, called B chromosomes. It is not clear what role, if any, B chromosomes play, but they appear to be made primarily of DNA that neither contains functional genes nor has much effect on the animal or plant even when present in multiple copies.

Structure

A telomere caps each end of every chromosome and binds specific proteins that protect it from being digested by enzymes (exonucleases) present in the same cell. Most important, the telomere permits DNA replication to continue to the very end of the chromosome, thus assuring its stability. The telomere is also involved in attachment of the chromosome ends to the nuclear membrane and in pairing of homologous chromosomes during meiosis. The structure of telomeric DNA is very similar in virtually all eukaryotic organisms except the fruit fly (Drosophila). One strand of the DNA is rich in guanine and is oriented toward the end of the chromosome, and the other strand is rich in cytosine and is oriented toward the centromere. In most organisms, the telomere consists of multiple copies of a very short DNA repeat.

The centromere is responsible for proper segregation of each chromosome pair during cell division. The chromatids in mitosis and each pair of homologous chromosomes in meiosis are held together at the centromere until anaphase, when they separate and move to the spindle poles, thus being distributed to the two daughter cells. The kinetochore, which is the attachment site for the microtubules that guide the movement of the chromosomes to the poles, is organized around the centromere. The molecular structures of centromeres in most species are still unclear. The repetitive DNA making up and surrounding the centromere is called heterochromatin because it remains condensed throughout the cell cycle and hence stains intensely.

One or more pairs of chromosomes in each species have a region called a secondary constriction which does not stain well. This region contains multiple copies of the genes that transcribe, within the nucleolus, the ribosomal RNA (rRNA). The number of active rRNA genes may be regulated, and an organism that has too few copies of the rRNA genes may develop abnormally or not survive. See Ribosomes

Staining

Staining with quinacrine mustard produces consistent, bright and less bright fluorescence bands (Q bands) along the chromosome arms because of differences in the relative amounts of CG (cytosine-guanine) or AT (adenine-thymine) base pairs. The distinctive Q-band pattern of each chromosome makes it possible to identify every chromosome in the human genome. Quinacrine fluorescence can also reveal a difference in the amount or type of heterochromatin on the two members of a homologous pair of chromosomes, called heteromorphism or polymorphism. Such differences can be used to identify the parental origin of a specific chromosome, such as the extra chromosome in individuals who have trisomy 21. Two other methods involve treating chromosomes in various ways before staining with Giemsa. Giemsa or G-band patterns are essentially identical to Q-band patterns; reverse Giemsa or R-band patterns are the reverse, or reciprocal, of those seen with Q or G banding. In humans, most other mammals, and birds (macrochromosomes only), the Q-, G-, and R-banding patterns are so distinctive that each chromosome pair can be individually identified, making it possible to construct a karyotype, or organized array of the chromosome pairs from a single cell (Fig. 2). The chromosomes are identified on the basis of the banding patterns, and the pairs are arranged and numbered in some order, often based on length. In the human karyotype, the autosomes are numbered 1 through 22, and the sex chromosomes are called X and Y. The short arm of a chromosome is called the p arm, and the long arm is called the q arm; a number is assigned to each band on the arm. Thus, band 1q23 refers to band 23 on the long arm of human chromosome 1.

Imprinting

A chromosome carries the same complement of genes whether it is transmitted from the father or the mother, and most of these genes appear to be functionally the same. However, a small number of mammalian genes are functionally different depending on whether they were transmitted by the egg or by the sperm. This phenomenon is known as imprinting. It appears to be caused by the inactivation of certain genes in sperm or ova, probably by methylation of cytosine residues within the regulatory (promotor) region of the imprinted gene. As a result of imprinting, normal development of the mammalian embryo requires the presence of both a maternal and a paternal set of chromosomes. Parthenogenesis, the formation of a normal individual from two sets of maternal chromosomes, is therefore not possible in mammals.

Sex chromosomes

In most mammals, the sex of an individual is determined by whether or not a Y chromosome is present because the Y chromosome carries the male-determining SRY gene. Thus XX and the rare XO individuals are female, while XY and the uncommon XXY individuals are male. In contrast, sex in the fruit fly depends on the balance of autosomes (non-sex chromosomes) and X chromosomes. Thus, in diploids, XX and the rare XXY flies are female, while XY and the rare XO flies are male. In both mammals and fruit flies, males are the heterogametic sex, producing gametes that contain either an X or a Y chromosome; and females are the homogametic sex, producing only gametes containing an X. In birds and butterflies, however, females are the heterogametic sex and males the homogametic sex. Other sex-determining systems are used by some classes of organisms, while sex in some species is determined by a single gene or even by environmental factors such as temperature (some turtles and alligators) or the presence of a nearby female (Bonellia, a marine worm) rather than by a chromosome-mediated mechanism.

More than 900 gene loci have been mapped to the human X chromosome. If the genes on both X chromosomes were fully expressed in female mammalian cells, then male cells, which have only one X, would exhibit only half as much gene product as female cells. However, dosage compensation is achieved, because genes on only one X chromosome are expressed, and genes on any additional X chromosomes are inactivated. This X inactivation randomly occurs during an early stage in embryonic development, and is transmitted unchanged to each of the daughter cells. Mammalian females are therefore mosaics of two types of cells, those with an active maternally derived X and those with an active paternally derived X. Species other than mammals do not show this type of dosage compensation mechanism for sex-linked genes, and some show none at all.

The Y chromosome is one of the smallest chromosomes in the genome in most mammalian species. Usually the mammalian Y chromosome has a very high proportion of heterochromatin, as does the large Y chromosome in Drosophila. Very few genes are located on the Y chromosome in mammals or in Drosophila, and most of these genes are concerned with either sex determination or the production of sperm. In some species of insects and other invertebrates, no Y chromosome is present, and sex in these species is determined by the X:autosome balance (XX female, XO male). See Cell nucleus, Genetics, Human genetics, Sex determination, Sex-linked inheritance

an organoid in a cell nucleus. The aggregate of chromosomes determines the main hereditary characteristics of cells and organisms. The complete chromosome set of a given organism is called the karyotype. In most animals and plants, every chromosome in every cell is represented twice. One chromosome of each pair is received from the father and the other from the mother when the nuclei of sex cells fuse during fertilization. Such chromosomes are called homologous, and the set of homologous chromosomes is termed a diploid set. The chromosome set in the cells of dioecious organisms contains one or more pairs of sex chromosomes, which usually differ in morphological characters according to sex; the chromosomes other than sex chromosomes are called autosomes. In mammals the genes that determine sex are localized in the sex chromosomes, whereas in the fruit fly Drosophila sex is determined by the ratio of the sex chromosomes to the autosomes, a concept expressed by the balance theory of sex determination.

The first description of chromosomes was made in 1888 by the German geneticist W. von Waldeyer-Hartz, who described them as solid bodies that stain strongly with basic dyes. It later became apparent, however, that the external appearance of chromosomes changes substantially during the different stages of the cell cycle. As compact formations with a characteristic morphology, chromosomes may be clearly distinguished in a light microscope only during cell division—in the metaphase of mitosis and meiosis.

The basic elements of chromosomes at all stages of the cell cycle are chromonemata, that is, threadlike structures that are tightly coiled during cell division, causing spiralization of the chromosomes, but that remain uncoiled (despiralized) in nondividing cells. After cell division is completed, the chromosomes that moved to the cells’ poles disintegrate and become surrounded by a nuclear membrane. During the period between two cell divisions—the interphase—the despiralization of the chromosomes continues and the chromosomes are no longer visible in the light microscope.

The morphology of the chromosomes of eukaryotes differs substantially from that of prokaryotes and viruses. Prokaryotes and viruses generally contain a single linear or circular chromosome that does not have a supramolecular structure and that is not separated from the cytoplasm by a nuclear membrane. The concept of chromosomes may be applied to the genetic material of prokaryotes only provisionally: this concept, formulated during the study of eukaryotic chromosomes, assumes that chromosomes have a complex of biopolymers (nucleic acids and proteins) as well as a specific supramolecular structure. Consequently, only eukaryotic chromosomes are described below.

The changes in the external appearance of chromosomes during the cellular and life cycles are caused by the chromosomes’ functional characteristics. However, the principles underlying the chromosomes’ organization, individuality, and continuity over several generations of cells and in different organisms remain unaltered, as shown by biochemical, cytological, and genetic studies on the chromosomes of different organisms. These studies have served as the basis of the chromosomes theory of heredity.

Molecular basis of chromosome structure. The significance of chromosomes as cellular organoids capable of storing, reproducing, and effecting hereditary information results from the characteristics of their constituent biopolymers. The first molecular model of a chromosome was devised in 1928 by N. K. Kol’tsov, who hypothesized the principles of the chromosome’s organization. Hereditary information in chromosomes is recorded by the deoxyribonucleic acid (DNA) molecule and by its genetic code. Approximately 99 percent of all the DNA in a cell is concentrated in the chromosomes. The remaining DNA is located in other cellular organoids and determines cytoplasmic inheritance. The DNA in eukaryotic chromosomes is combined with basic proteins (histones) and with nonhistone proteins. The nonhistone proteins effect the complex assemblage of DNA in the chromosomes and regulate the DNA’s transcription, that is, the DNA’s ability to synthesize ribonucleic acid (RNA).

Chromosomes during the interphase. Since chromosomes perform their main functions—reproduction and transcription— during the interphase, their structure at this stage of the cell’s cycle is of particular interest. Chromosomes are barely discernible during the interphase since the euchromatin, which comprises many areas of the chromosomes, is completely uncoiled owing to the active synthesis of RNA. The heterochromatin in the chromosomes, however, is not involved in RNA synthesis and continues to retain its solid structure. The euchromatin contains elementary deoxyribonucleoprotein (DNP) threads, as well as ribonucleoprotein particles 200–500 angstroms in diameter that are called ribonucleoprotein (RNP) granules, intergranules, or perichromatin granules. These particles, which represent an assemblage of RNA synthesized on the chromosomes and combined with protein, aid in the development of messenger RNA and its transfer to the cytoplasm.

Interphasic chromosomes are studied by biochemical methods of isolating chromatin—the chromosomal material in a nucleus— and separating it into euchromatin and heterochromatin. These chromosomes are also studied by electron microscopy of intact nuclei and of isolated chromatin. Giant lampbrush chromosomes from the oocytes of animals, and multifilamentous (polytene) chromosomes of dipterous insects, are used as models of interphasic chromosomes. In lampbrush chromosomes, the inactive regions have the appearance of tightly coiled structures. These are the chromomeres, which are also found in the chromosomes of somatic cells, particularly during the prophase of mitosis. The chromomeres are believed to be morphological, and perhaps functional, units of chromosomes. In those regions of chromosomes that actively synthesize RNA, the chromomeres are uncoiled and form lateral loops. In these loops the RNA molecules combine with protein to form ribonucleoproteins (RNP). These are particles that represent an assemblage of gene products; some of their lateral loops differ in size and in morphological characters. Polytene chromosomes appear in the tissues of dipterous insects and of some plants owing to repeated replication (doubling) of the original chromosomes without subsequent disjunction of the daughter chromosomes. The inactive parts of these polytene chromosomes have a disklike shape, whereas the active parts form swellings called chromosome puffs. Like lampbrush chromosomes, chromosome puffs contain RNP particles 200–500 angstroms in diameter. Electron microscopy and biochemical studies have indicated that the main structural unit in chromatin isolated from cells, in intact nuclei, and in giant chromosomes is a DNP strand 100–200 angstroms in diameter.

Studies on polytene chromosomes in different tissues and at different stages in the development of dipterous insects have demonstrated that the number and set of active chromosome puffs are individualized according to tissue and species. Consequently, although all the cells of a multicellular organism have an identical set of genes arranged linearly on each chromosome, the set of chromosome regions that are active and inactive in RNA synthesis differs in each type of cell and at each stage of development. That is, the same region is euchromatic in some tissues and heterochromatic in others. Certain chromosome regions are heterochromatic during the interphase of different types of cells and generally contain frequently repeating sequences of DNA. The nucleolus organizer—the region in the chromosome where the genes of ribosomal RNA are concentrated—functions constantly during the interphase of all types of cells. The nucleolus, long regarded as an independent cellular organoid, is formed in this region and is the site at which the precursors of the ribosomes are formed.

The chromosomes in the interphasic nucleus are separated from the cytoplasm by a nuclear membrane. The chromosomes are attached to this membrane in many places, mainly by means of telomeres and centromeres, and consequently each chromosome is believed to occupy a specific site in the nucleus. The chromosomes replicate at the time when the cells are preparing to divide during the interphase. Each chromosome creates its own copy on the basis of semiconservative replication of the DNA. The chromosomes of eukaryotes have many starting and ending points during replication, whereas prokaryotes have only a single starting point and a single ending point. This permits the nonsimultaneous replication of different chromosome regions during synthesis and also regulates the activity of the chromosomes.

Chromosomes during mitosis and meiosis. When cells begin to divide, the synthesis of DNA and RNA in the chromosomes ceases and the amount of material within the chromosomes increases. For example, in a single human chromosome a DNA chain 160 mm in length becomes contained within a volume of only 0.5 × 10 micrometers. The nuclear membrane disintegrates, and the chromosomes align themselves on the cell’s equator. They are most accessible for observation and morphological analysis at this time. The main structural unit of metaphasic chromosomes, like that of interphasic chromosomes, is a strand of DNP 100–200 angstroms in diameter coiled in a tight spiral. Several researchers have discovered that strands 100–200 angstroms in diameter form structures with a second level consisting of strands approximately 2,000 angstroms in diameter that also form the body of a metaphasic chromosome.

Every metaphasic chromosome consists of chromatids, which are produced by the replication of the original interphasic chromosome. The use of labeled and modified precursors of DNA facilitated the precise identification of differentially stained chromatids in chromosomes during the metaphase of mitosis. This led to the discovery that sister chromatids often exchange segments during replication—a phenomenon known as crossing over. In traditional cytology, the matrix of metaphasic chromosomes was considered to be of great importance and was regarded as an essential chromosomal component in which spiralized chromonemata were embedded. Modern cytologists believe that the matrix of metaphasic chromosomes is residual material from the disintegrating nucleolus. The matrix is often completely indiscernible.

The formation of sex cells in animals and plants is accompanied by a unique type of division, meiosis. Meiotic chromosomes differ from mitotic chromosomes in several ways. During meiosis, the daughter cells receive half the usual complement of chromosomes, owing to the conjugation of homologous chromosomes in the prophase of meiosis and as a result of two successive cell divisions during a single replication of DNA. During mitosis, on the other hand, the number of chromosomes remains the same. In addition, in meiotic chromosomes there is a temporary interruption during the prophase of meiosis. The meiotic chromosomes return to the interphasic state when the chromosomes begin actively synthesizing RNA. During this period most of the animals under analysis have lampbrush chromosomes. Finally, chromosomes in the metaphase of meiosis contain a larger amount of material.

Although extensive research has been devoted to chromosomes, the study of their structural and functional organization remains one of the most urgent tasks of modern biology. Chromosomes perform highly complex functions within the cell and have an intricate structure that has resisted complete elucidation. During the 1960’s and 1970’s, great progress has been achieved in understanding the molecular basis of chromosome structure owing to the development of molecular genetics. This progress has brilliantly confirmed and substantiated the principles of the chromosome theory of heredity.