Each chromosome in a eukaryotic cell is composed of a single molecule of DNA that is unusually long and linear, as well as the proteins that are responsible for folding and packing the delicate DNA thread into a more compact form. In addition to the proteins that are involved in the packing process, chromosomes are also connected with a huge number of additional proteins (as well as a large number of RNA molecules). These are essential components for the processes of replicating DNA, repairing DNA, and expressing genes in cells. The complex of DNA and proteins that are closely bonded to one another is referred to as chromatin because of its ability to be stained (from the Greek chroma, "color").

Bacteria do not have a distinct nuclear compartment, so they typically carry all of their genes on a single molecule of DNA that is commonly circular in shape. This DNA is also coupled to the proteins that package and compress it, but these proteins are separate from the proteins that carry out these same jobs in eukaryotes and are therefore unique. This is not right; bacterial DNA does not have the same structure as eukaryotic chromosomes, and less is known about how this DNA is packaged. Although bacterial DNA and the proteins that go with it are commonly referred to as the bacterial "chromosome," this is erroneous. As a consequence of this, eukaryotic chromosomes will be the focus of virtually all of the debate that we have regarding the structure of chromosomes.

Except for gametes (eggs and sperm) and a few highly specialized cell types that cannot multiply and either lack DNA entirely (such as red blood cells) or have replicated their DNA without concluding cell division, the nucleus of every human cell contains two copies of each chromosome. One copy of each chromosome is inherited from the mother, and the other copy is inherited from the father (such as megakaryocytes). Homologous chromosomes are those that are identical in both the mother's and the father's copies (homologs). The only chromosomal pairs that are not homologous are those that make up a person's sex chromosomes. In men, a Y chromosome is inherited from the father, and an X chromosome is inherited from the mother. Therefore, each human cell contains a total of 46 chromosomes, including 22 pairs of chromosomes that are shared by both sexes as well as two chromosomes that are referred to as sex chromosomes (X and Y in males, two Xs in females). By "painting" each human chromosome a different color using a technique that is based on DNA hybridization, these human chromosomes may be easily identified and distinguished from one another. In this method, a short strand of nucleic acid that has been fluorescently tagged serves as a "probe" that picks the corresponding DNA sequence, illuminating the target chromosome wherever it binds. This allows the researcher to determine the location of a gene of interest. It is during the mitotic phase of the cell cycle that chromosome painting is most commonly performed because this is the phase of the cell cycle in which the chromosomes are in their most compact and visible state.

The chromosomes can also be stained with dyes that reveal a unique and repeatable pattern of bands along the length of each mitotic chromosome. This method is considered to be one of the more conventional approaches to distinguishing one chromosome from another. It is believed that these banding patterns are a reflection of changes in the structure of the chromatin, despite the fact that the explanation for these banding patterns is unknown. However, each type of chromosome has a unique arrangement of bands, and this pattern was the first solid method for distinguishing and identifying each human chromosome.

The human karyotype refers to the arrangement of the 46 chromosomes in a human cell that may be seen during mitosis. Alterations in the banding patterns or, at a higher level of sensitivity, alterations in the pattern of chromosomal painting can both be used to identify chromosome portions that are absent or have been exchanged amongst one another. Cytogeneticists make use of these alterations to detect chromosome abnormalities that are inherited and to demonstrate how chromosome rearrangements evolve in cancer cells as the cells progress toward a more malignant state.

Chromosomes are what carry genes, which are the functional building blocks of heredity. Although this definition of a gene is overly restricted, it is sometimes used to represent a region of DNA that supplies the instructions for generating a particular protein (or a collection of proteins that are closely linked to one another). The vast majority of genes are, in point of fact, those that code for proteins, and the majority of genes that have evident mutant defects fall into this category. On the other hand, there are also some "RNA genes," which are pieces of DNA that, rather than producing proteins as their end product, generate functionally significant RNA molecules. In a later section, we will go into further depth regarding the RNA genes and the products that they generate.

It stands to reason that there would be some kind of connection between the level of complexity of an organism and the number of genes contained in its genome. In contrast to humans, which have somewhere in the neighborhood of 30,000 genes, many types of bacteria have as little as 500 genes. The genomes of single-celled eukaryotes like yeast, bacteria, and archaea are small and only consist of densely packed strings of genes. Bacteria and archaea genomes are also short. However, in addition to genes, a wide variety of other eukaryotic organisms, such as multicellular plants and animals, include enormous amounts of DNA that is interspersed throughout their genomes. The function of this DNA is not well understood. Since a portion of this extra DNA is required for the accurate regulation of gene expression, the presence of such a large amount of this DNA in multicellular organisms may help to explain why they have such a large amount of it. During development, the genes in multicellular organisms must be turned on and off in accordance with a complex set of rules.

It is more likely that changes in the quantity of DNA interspersed between genes are to blame for the remarkable differences in genome size that we detect when comparing one species to another. Variations in gene counts are also a possible explanation of these differences. For example, the human genome is 200 times larger than the genome of the yeast Saccharomyces cerevisiae, but it is also 200 times smaller than the genome of a species of amoeba, and it is 30 times smaller than the genomes of many plants and amphibians. In addition, even while organisms that are closely related to one another, like bony fish, have almost the same number of genes, the amount of DNA that is contained in their genomes can vary by as much as several hundredfold due to differences in the amount of DNA that is noncoding. Regardless of the potential function of the additional DNA, it is abundantly clear that the presence of a large amount of this material within a eukaryotic cell does not result in a substantial detriment.

In addition, the configuration of the chromosomes contained inside the genome differs from one eukaryotic species to the next. For example, human cells have 46 chromosomes, whereas the cells of certain small deer have only six and the cells of common carp have over one hundred. Even for species that are closely related and have genomes of comparable proportions, the number of chromosomes and their sizes can differ substantially from one another. As a result, there is no direct relationship between the total number of chromosomes in an organism, the complexity of the organism, and the size of its genome as a whole. Instead, the genomes and chromosomes of living species have each been formed through a unique history of genetic events that looked to be unrelated to one another and were influenced by selection forces over a considerable amount of time that are not well understood.