Chromosomes are thread-like structures located inside the nucleus of animal and plant cells. Each chromosome is made of protein and a single molecule of deoxyribonucleic acid (DNA). Passed from parents to offspring, DNA contains the specific instructions that make each type of living creature unique.

The term chromosome comes from the Greek words for color (chroma) and body (soma). Scientists gave this name to chromosomes because they are cell structures, or bodies, that are strongly stained by some colorful dyes used in research.

The unique structure of chromosomes keeps DNA tightly wrapped around spool-like proteins, called histones. Without such packaging, DNA molecules would be too long to fit inside cells. For example, if all of the DNA molecules in a single human cell were unwound from their histones and placed end-to-end, they would stretch 6 feet.

For an organism to grow and function properly, cells must constantly divide to produce new cells to replace old, worn-out cells. During cell division, it is essential that DNA remains intact and evenly distributed among cells. Chromosomes are a key part of the process that ensures DNA is accurately copied and distributed in the vast majority of cell divisions. Still, mistakes do occur on rare occasions.

Changes in the number or structure of chromosomes in new cells may lead to serious problems. For example, in humans, one type of leukemia and some other cancers are caused by defective chromosomes made up of joined pieces of broken chromosomes.

It is also crucial that reproductive cells, such as eggs and sperm, contain the right number of chromosomes and that those chromosomes have the correct structure. If not, the resulting offspring may fail to develop properly. For example, people with Down syndrome have three copies of chromosome 21, instead of the two copies found in other people.

Chromosomes vary in number and shape among living things. Most bacteria have one or two circular chromosomes. Humans, along with other animals and plants, have linear chromosomes that are arranged in pairs within the nucleus of the cell.

The only human cells that do not contain pairs of chromosomes are reproductive cells, or gametes, which carry just one copy of each chromosome. When two reproductive cells unite, they become a single cell that contains two copies of each chromosome. This cell then divides and its successors divide numerous times, eventually producing a mature individual with a full set of paired chromosomes in virtually all of its cells.

Besides the linear chromosomes found in the nucleus, the cells of humans and other complex organisms carry a much smaller type of chromosome similar to those seen in bacteria. This circular chromosome is found in mitochondria, which are structures located outside the nucleus that serve as the cell's powerhouses.

Scientists think that, in the past, mitochondria were free-living bacteria with the ability to convert oxygen into energy. When these bacteria invaded cells lacking the power to tap into oxygen's power, the cells retained them, and, over time, the bacteria evolved into modern-day mitochondria.

The constricted region of linear chromosomes is known as the centromere. Although this constriction is called the centromere, it usually is not located exactly in the center of the chromosome and, in some cases, is located almost at the chromosome's end. The regions on either side of the centromere are referred to as the chromosome's arms.

Centromeres help to keep chromosomes properly aligned during the complex process of cell division. As chromosomes are copied in preparation for production of a new cell, the centromere serves as an attachment site for the two halves of each replicated chromosome, known as sister chromatids.

Telomeres are repetitive stretches of DNA located at the ends of linear chromosomes. They protect the ends of chromosomes in a manner similar to the way the tips of shoelaces keep them from unraveling.

In many types of cells, telomeres lose a bit of their DNA every time a cell divides. Eventually, when all of the telomere DNA is gone, the cell cannot replicate and dies.

White blood cells and other cell types with the capacity to divide very frequently have a special enzyme that prevents their chromosomes from losing their telomeres. Because they retain their telomeres, such cells generally live longer than other cells.

Telomeres also play a role in cancer. The chromosomes of malignant cells usually do not lose their telomeres, helping to fuel the uncontrolled growth that makes cancer so devastating.

Humans have 23 pairs of chromosomes, for a total of 46 chromosomes.

In fact, each species of plants and animals has a set number of chromosomes. A fruit fly, for example, has four pairs of chromosomes, while a rice plant has 12 and a dog, 39.

In humans and most other complex organisms, one copy of each chromosome is inherited from the female parent and the other from the male parent. This explains why children inherit some of their traits from their mother and others from their father.

The pattern of inheritance is different for the small circular chromosome found in mitochondria. Only egg cells - and not sperm cells - keep their mitochondria during fertilization. So, mitochondrial DNA is always inherited from the female parent. In humans, a few conditions, including some forms of hearing impairment and diabetes, have been associated with DNA found in the mitochondria.

Yes, they differ in a pair of chromosomes known as the sex chromosomes. Females have two X chromosomes in their cells, while males have one X and one Y chromosome.

Inheriting too many or not enough copies of sex chromosomes can lead to serious problems. For example, females who have extra copies of the X chromosome are usually taller than average and some have mental disability. Males with more than one X chromosome have Klinefelter syndrome, which is a condition characterized by tall stature and, often, impaired fertility. Another syndrome caused by imbalance in the number of sex chromosomes is Turner syndrome. Women with Turner have one X chromosome only. They are very short, usually do not undergo puberty and some may have kidney or heart problems.

Scientists looking at cells under the microscope first observed chromosomes in the late 1800s. However, at the time, the nature and function of these cell structures were unclear.

Researchers gained a much better understanding of chromosomes in the early 1900s through Thomas Hunt Morgan's pioneering studies. Morgan made the link between chromosomes and inherited traits by demonstrating that the X chromosome is related to gender and eye color in fruit flies.

The speculation that chromosomes might be the key to understanding heredity led several scientists to examine Mendel’s publications and reevaluate his model in terms of chromosome behavior during mitosis and meiosis. In 1902, Theodor Boveri observed that proper sea urchin embryonic development does not occur unless chromosomes are present. That same year, Walter Sutton observed chromosome separation into daughter cells during meiosis (Figure 13.2). Together, these observations led to the Chromosomal Theory of Inheritance , which identified chromosomes as the genetic material responsible for Mendelian inheritance.

The Chromosomal Theory of Inheritance was consistent with Mendel’s laws, which the following observations supported:

• During meiosis, homologous chromosome pairs migrate as discrete structures that are independent of other chromosome pairs.
• Chromosome sorting from each homologous pair into pre-gametes appears to be random.
• Each parent synthesizes gametes that contain only half their chromosomal complement.
• Even though male and female gametes (sperm and egg) differ in size and morphology, they have the same number of chromosomes, suggesting equal genetic contributions from each parent.
• The gametic chromosomes combine during fertilization to produce offspring with the same chromosome number as their parents.

Despite the lack of direct evidence that chromosomes carry traits, the compelling correlation between chromosome behavior during meiosis and Mendel's abstract laws led scientists to propose the Chromosomal Theory of Inheritance. Critics pointed out that individuals had far more independently segregating traits than they had chromosomes. About ten years after the theory was proposed, Eleanor Carothers was the first to discover physical evidence supporting it; she observed independent chromosome assortment in grasshoppers. Then, after several years of carrying out crosses with the fruit fly, Drosophila melanogaster, Thomas Hunt Morgan provided additional experimental evidence to support the Chromosomal Theory of Inheritance.

Genetic Linkage and Distances

Mendel’s work suggested that traits are inherited independently of each other. Morgan identified a 1:1 correspondence between a segregating trait and the X chromosome, suggesting that random chromosome segregation was the physical basis of Mendel’s model. This also demonstrated that linked genes disrupt Mendel’s predicted outcomes. That each chromosome can carry many linked genes explains how individuals can have many more traits than they have chromosomes. However, researchers in Morgan’s laboratory suggested that alleles positioned on the same chromosome were not always inherited together. During meiosis, linked genes somehow became unlinked.

Homologous Recombination

In 1909, Frans Janssen observed chiasmata—the point at which chromatids are in contact with each other and may exchange segments—prior to the first meiotic division. He suggested that alleles become unlinked and chromosomes physically exchange segments. As chromosomes condensed and paired with their homologs, they appeared to interact at distinct points. Janssen suggested that these points corresponded to regions in which chromosome segments exchanged. We now know that the pairing and interaction between homologous chromosomes, or synapsis, does more than simply organize the homologs for migration to separate daughter cells. When synapsed, homologous chromosomes undergo reciprocal physical exchanges at their arms in homologous recombination , or more simply, “crossing over.”

To better understand the type of experimental results that researchers were obtaining at this time, consider a heterozygous individual that inherited dominant maternal alleles for two genes on the same chromosome (such as A and B) and two recessive paternal alleles for those same genes (such as a and b). If the genes are linked, one would expect this individual to produce gametes that are either AB or ab with a 1:1 ratio. If the genes are unlinked, the individual should produce AB, Ab, aB, and ab gametes with equal frequencies, according to the Mendelian concept of independent assortment. Because they correspond to new allele combinations, the genotypes Ab and aB are nonparental types that result from homologous recombination during meiosis. Parental types are progeny that exhibit the same allelic combination as their parents. Morgan and his colleagues, however, found that when they test crossed such heterozygous individuals to a homozygous recessive parent (AaBb × aabb), both parental and nonparental cases occurred. For example, 950 offspring might be recovered that were either AaBb or aabb, but 50 offspring would also result that were either Aabb or aaBb. These results suggested that linkage occurred most often, but a significant minority of offspring were the products of recombination.

One of the experiments in Morgan's lab involving the crosses of flies for two traits, body color (gray or black) and wing shape (normal and vestigial), demonstrated the recombination events that lead to the development of nonparental phenotypes (Figure 13.3).

Genetic Maps

Janssen did not have the technology to demonstrate crossing over so it remained an abstract idea that scientists did not widely believe. Scientists thought chiasmata were a variation on synapsis and could not understand how chromosomes could break and rejoin. Yet, the data were clear that linkage did not always occur. Ultimately, it took a young undergraduate student and an “all-nighter” to mathematically elucidate the linkage and recombination problem.

In 1913, Alfred Sturtevant, a student in Morgan’s laboratory, gathered results from researchers in the laboratory, and took them home one night to mull them over. By the next morning, he had created the first “chromosome map,” a linear representation of gene order and relative distance on a chromosome (Figure 13.4).

As Figure 13.4 shows, by using recombination frequency to predict genetic distance, we can infer the relative gene order on chromosome 2. The values represent map distances in centimorgans (cM), which correspond to recombination frequencies (in percent). Therefore, the genes for body color and wing size were 65.5 − 48.5 = 17 cM apart, indicating that the maternal and paternal alleles for these genes recombine in 17 percent of offspring, on average.

To construct a chromosome map, Sturtevant assumed that genes were ordered serially on threadlike chromosomes. He also assumed that the incidence of recombination between two homologous chromosomes could occur with equal likelihood anywhere along the chromosome's length. Operating under these assumptions, Sturtevant postulated that alleles that were far apart on a chromosome were more likely to dissociate during meiosis simply because there was a larger region over which recombination could occur. Conversely, alleles that were close to each other on the chromosome were likely to be inherited together. The average number of crossovers between two alleles—that is, their recombination frequency —correlated with their genetic distance from each other, relative to the locations of other genes on that chromosome. Considering the example cross between AaBb and aabb above, we could calculate the recombination's frequency as 50/1000 = 0.05. That is, the likelihood of a crossover between genes A/a and B/b was 0.05, or 5 percent. Such a result would indicate that the genes were definitively linked, but that they were far enough apart for crossovers to occasionally occur. Sturtevant divided his genetic map into map units, or centimorgans (cM) , in which a 0.01 recombination frequency corresponds to 1 cM.

By representing alleles in a linear map, Sturtevant suggested that genes can range from linking perfectly (recombination frequency = 0) to unlinking perfectly (recombination frequency = 0.5) when genes are on different chromosomes or genes separate very far apart on the same chromosome. Perfectly unlinked genes correspond to the frequencies Mendel predicted to assort independently in a dihybrid cross. A 0.5 recombination frequency indicates that 50 percent of offspring are recombinants and the other 50 percent are parental types. That is, every type of allele combination is represented with equal frequency. This representation allowed Sturtevant to additively calculate distances between several genes on the same chromosome. However, as the genetic distances approached 0.50, his predictions became less accurate because it was not clear whether the genes were very far apart on the same or on different chromosomes.

In 1931, Barbara McClintock and Harriet Creighton demonstrated the crossover of homologous chromosomes in corn plants. Weeks later, Curt Stern demonstrated microscopically homologous recombination in Drosophila. Stern observed several X-linked phenotypes that were associated with a structurally unusual and dissimilar X chromosome pair in which one X was missing a small terminal segment, and the other X was fused to a piece of the Y chromosome. By crossing flies, observing their offspring, and then visualizing the offspring’s chromosomes, Stern demonstrated that every time the offspring allele combination deviated from either of the parental combinations, there was a corresponding exchange of an X chromosome segment. Using mutant flies with structurally distinct X chromosomes was the key to observing the products of recombination because DNA sequencing and other molecular tools were not yet available. We now know that homologous chromosomes regularly exchange segments in meiosis by reciprocally breaking and rejoining their DNA at precise locations. Aurora Ruiz-Herrera, for example, studies the occurrence of genetic breakpoints at locations in the chromosomes known as fragile sites. By identifying chromosomal fragile sites that are shared between humans and other primates, Ruiz-Herrera has provided a deeper understanding of mammalian and specifically human evolution.

Mendel’s Mapped Traits

Homologous recombination is a common genetic process, yet Mendel never observed it. Had he investigated both linked and unlinked genes, it would have been much more difficult for him to create a unified model of his data on the basis of probabilistic calculations. Researchers who have since mapped the seven traits that Mendel investigated onto a pea plant genome's seven chromosomes have confirmed that all the genes he examined are either on separate chromosomes or are sufficiently far apart as to be statistically unlinked. Some have suggested that Mendel was enormously lucky to select only unlinked genes; whereas, others question whether Mendel discarded any data suggesting linkage. In any case, Mendel consistently observed independent assortment because he examined genes that were effectively unlinked.

If the DNA from all 46 chromosomes in a human cell nucleus were laid out end-to-end, it would measure approximately two meters; however, its diameter would be only 2 nm! Considering that the size of a typical human cell is about 10 µm (100,000 cells lined up to equal one meter), DNA must be tightly packaged to fit in the cell’s nucleus. At the same time, it must also be readily accessible for the genes to be expressed. For this reason, the long strands of DNA are condensed into compact chromosomes during certain stages of the cell cycle. There are a number of ways that chromosomes are compacted.

In the first level of compaction, short stretches of the DNA double helix wrap around a core of eight histone proteins at regular intervals along the entire length of the chromosome (Figure 10.4). The DNA-histone complex is called chromatin. The beadlike, histone DNA complex is called a nucleosome , and DNA connecting the nucleosomes is called linker DNA. A DNA molecule in this form is about seven times shorter than the double helix without the histones, and the beads are about 10 nm in diameter, in contrast with the 2-nm diameter of a DNA double helix.

The second level of compaction occurs as the nucleosomes and the linker DNA between them coil into a 30-nm chromatin fiber. This coiling further condenses the chromosome so that it is now about 50 times shorter than the extended form.

In the third level of compaction, a variety of fibrous proteins is used to “pack the chromatin.” These fibrous proteins also ensure that each chromosome in a non-dividing cell occupies a particular area of the nucleus that does not overlap with that of any other chromosome (see the top image in Figure 10.3).

DNA replicates in the S phase of interphase, which technically is not a part of mitosis, but must always precede it. After replication, the chromosomes are composed of two linked sister chromatids . When fully compact, the pairs of identically packed chromosomes are bound to each other by cohesin proteins. The connection between the sister chromatids is closest in a region called the centromere . The conjoined sister chromatids, with a diameter of about 1 µm, are visible under a light microscope. The centromeric region is highly condensed and thus will appear as a constricted area.

Humans display dramatic deleterious effects with autosomal trisomies and monosomies. Therefore, it may seem counterintuitive that human females and males can function normally, despite carrying different numbers of the X chromosome. Rather than a gain or loss of autosomes, variations in the number of sex chromosomes occur with relatively mild effects. In part, this happens because of the molecular process X inactivation. Early in development, when female mammalian embryos consist of just a few thousand cells (relative to trillions in the newborn), one X chromosome in each cell inactivates by tightly condensing into a quiescent (dormant) structure, or a Barr body. The chance that an X chromosome (maternally or paternally derived) inactivates in each cell is random, but once this occurs, all cells derived from that one will have the same inactive X chromosome or Barr body. By this process, females compensate for their double genetic dose of X chromosome. In so-called “tortoiseshell” cats, we observe embryonic X inactivation as color variegation. Females that are heterozygous for an X-linked coat color gene will express one of two different coat colors over different regions of their body, corresponding to whichever X chromosome inactivates in that region's embryonic cell progenitor.

An individual carrying an abnormal number of X chromosomes will inactivate all but one X chromosome in each of her cells. However, even inactivated X chromosomes continue to express a few genes, and X chromosomes must reactivate for the proper maturation of female ovaries. As a result, X-chromosomal abnormalities typically occur with mild mental and physical defects, as well as sterility. If the X chromosome is absent altogether, the individual will not develop in utero.

Scientists have identified and characterized several errors in sex chromosome number. Individuals with three X chromosomes, triplo-X, are phenotypically female but express developmental delays and reduced fertility. The XXY genotype, corresponding to one type of Klinefelter syndrome, corresponds to phenotypically male individuals with small testes, enlarged breasts, and reduced body hair. More complex types of Klinefelter syndrome exist in which the individual has as many as five X chromosomes. In all types, every X chromosome except one undergoes inactivation to compensate for the excess genetic dosage. We see this as several Barr bodies in each cell nucleus. Turner syndrome, characterized as an X0 genotype (i.e., only a single sex chromosome), corresponds to a phenotypically female individual with short stature, webbed skin in the neck region, hearing and cardiac impairments, and sterility.

Chromosome isolation and microscopic observation forms the basis of cytogenetics and is the primary method by which clinicians detect chromosomal abnormalities in humans. A karyotype is the number and appearance of chromosomes, and includes their length, banding pattern, and centromere position. To obtain a view of an individual’s karyotype, cytologists photograph the chromosomes and then cut and paste each chromosome into a chart, or karyogram. Another name is an ideogram (Figure 13.5).

Figure 13.5 This karyotype is of a female human. Notice that homologous chromosomes are the same size, and have the same centromere positions and banding patterns. A human male would have an XY chromosome pair instead of the XX pair. (credit: Andreas Blozer et al)

In a given species, we can identify chromosomes by their number, size, centromere position, and banding pattern. In a human karyotype, autosomes or “body chromosomes” (all of the non–sex chromosomes) are generally organized in approximate order of size from largest (chromosome 1) to smallest (chromosome 22). The X and Y chromosomes are not autosomes. However, chromosome 21 is actually shorter than chromosome 22. Researchers discovered this after naming Down syndrome as trisomy 21, reflecting how this disorder results from possessing one extra chromosome 21 (three total). Not wanting to change the name of this important disorder, scientists retained the numbering of chromosome 21 despite describing it having the shortest set of chromosomes. We may designate the chromosome “arms” projecting from either end of the centromere as short or long, depending on their relative lengths. We abbreviate the short arm p (for “petite”); whereas, we abbreviate the long arm q (because it follows “p” alphabetically). Numbers further subdivide and denote each arm. Using this naming system, we can describe chromosome locations consistently in the scientific literature.

In addition to losing or gaining an entire chromosome, a chromosomal segment may duplicate or lose itself. Duplications and deletions often produce offspring that survive but exhibit physical and mental abnormalities. Duplicated chromosomal segments may fuse to existing chromosomes or may be free in the nucleus. Cri-du-chat (from the French for “cry of the cat”) is a syndrome that occurs with nervous system abnormalities and identifiable physical features that result from a deletion of most 5p (the small arm of chromosome 5) (Figure 13.10). Infants with this genotype emit a characteristic high-pitched cry on which the disorder’s name is based.

Figure 13.10 This figure shows an individual with cri-du-chat syndrome at two, four, nine, and 12 years of age. (credit: Paola Cerruti Mainardi)

Although we refer to Mendel as the “father of modern genetics,” he performed his experiments with none of the tools that the geneticists of today routinely employ. One such powerful cytological technique is karyotyping, a method in which geneticists can identify traits characterized by chromosomal abnormalities from a single cell. To observe an individual’s karyotype, a geneticist first collects a person’s cells (like white blood cells) from a blood sample or other tissue. In the laboratory, the geneticist stimulates the isolated cells to begin actively dividing. The geneticist then applies the chemical colchicine to cells to arrest condensed chromosomes in metaphase. The geneticist then induces swelling in the cells using a hypotonic solution so the chromosomes spread apart. Finally, the geneticist preserves the sample in a fixative and applies it to a slide.

The geneticist then stains chromosomes with one of several dyes to better visualize each chromosome pair's distinct and reproducible banding patterns. Following staining, the geneticist views the chromosomes using bright-field microscopy. A common stain choice is the Giemsa stain. Giemsa staining results in approximately 400–800 bands (of tightly coiled DNA and condensed proteins) arranged along all 23 chromosome pairs. An experienced geneticist can identify each band. In addition to the banding patterns, geneticists further identify chromosomes on the basis of size and centromere location. To obtain the classic depiction of the karyotype in which homologous chromosome pairs align in numerical order from longest to shortest, the geneticist obtains a digital image, identifies each chromosome, and manually arranges the chromosomes into this pattern.

At its most basic, the karyogram may reveal genetic abnormalities in which an individual has too many or too few chromosomes per cell. Examples of this are Down Syndrome, which one identifies by a third copy of chromosome 21, and Turner Syndrome, which is characterized by the presence of only one X chromosome in females instead of the normal two. Geneticists can also identify large DNA deletions or insertions. For instance, geneticists can identify Jacobsen Syndrome—which involves distinctive facial features as well as heart and bleeding defects—by a deletion on chromosome 11. Finally, the karyotype can pinpoint translocations, which occur when a segment of genetic material breaks from one chromosome and reattaches to another chromosome or to a different part of the same chromosome. Translocations are implicated in certain cancers, including chronic myelogenous leukemia.

During Mendel’s lifetime, inheritance was an abstract concept that one could only infer by performing crosses and observing the traits that offspring expressed. By observing a karyogram, today’s geneticists can actually visualize an individual's chromosomal composition to confirm or predict genetic abnormalities in offspring, even before birth.