Each human individual is made up of several hundred million million microscopic cells (plus considerable noncellular material such as bone and water). Cells come in a variety of shapes and sizes. Some are rounded, some flat, some angular, some irregular, and some (e.g., nerve cells) have long projections (See Figure 1, the nucleus, containing the DNA is shown in blue). A typical cell, such as a white blood cell, is about 1/2,000 inch in diameter. The part of the cell of greatest genetic interest, the inner part or nucleus, is usually roughly spherical. All the cells in the body are descended from a single fertilized egg, which by successive divisions has produced the vast number and various cell types that comprise the human body. The nucleus contains a number of worm like or threadlike microscopic bodies, called chromosomes. Every species has a characteristic number of chromosomes—a typical human cell has 46.
The nucleus of a fertilized human egg starts out with 23 chromosomes from the mother’s egg and a corresponding set of 23 from the father’s sperm. A sperm or egg cell, containing a single set of chromosomes, is said to be haploid. A cell with two sets, a total of 23 pairs or 46 chromosomes, is diploid. The fertilized egg divides into two, these two into four, and so on throughout embryonic development, and for many kinds of cells, throughout life. This process of cell division, called mitosis, distributes these chromosomes precisely. Before the cell divides, each chromosome has split longitudinally in half, and each daughter cell receives on of the halves. Thus, after cell division, each of the daughter cells has identical chromosomes, the same as in the parent cell. This precise process assures that every cell in the body has an identical 46-chromosome makeup in its nucleus. Yet, as always in biology, there are exceptions. A red blood cell has no nucleus and therefore no chromosomes. Sometimes the chromosomes divide without a cell division, doubling the number. For example, liver cells, are usually polyploid, that is, having four or more sets of chromosomes. The great bulk of cells, however, play by the rules; they are nucleated and have 46 chromosomes. Sometimes, two embryos will develop from the same fertilized egg, either because the two cells separate after the first division or each develops separately or, more often, by the multicellular embryo dividing into two parts at a later stage. This leads to identical twins. They necessarily have identical chromosomes and resemble each other closely; the differences they possess are due to environmental factors and the vagaries of development.
In the formation of a sperm or egg, the chromosome number is halved (fortunately, or otherwise each generation would have twice as many chromosomes as the previous one). During the process of meiosis, the chromosomes are allocated so that each gamete (sperm or egg) has one representative of each pair, for a total of 23. The members of different pairs behave independently in meiosis. If the chromosome from the number 1 pair in a sperm is maternal, that is, derived from the mother, the chromosome from the number 2 pair is equally likely to be either maternal or paternal, and so on. For convenience, the human chromosomes are identified by a number, starting with the largest. Most chromosomes have a short and a long arm, designated by p and q respectively. Hence, 7p designates the short arm of the 7th largest chromosome.
The two members of a chromosome pair, as viewed through a microscope, are identical in shape and size, with an important exception – the sex chromosomes. In the human cell, the Y chromosome is much smaller than the X chromosome. A body cell from a female has two X chromosomes; a cell from a male has an X and a Y. Through the process of meiosis, an egg ends up with a single X chromosome (in addition to 22 other chromosomes, called autosomes, for a total of 23). A sperm has either an X or a Y plus 22 autosomes. At fertilization, chance determines, whether the successful sperm carries an X or Y chromosome, that is, determines whether the developing embryo will be female or male. The X and Y chromosomes are not numbered, so the chromosomes of a gamete are numbered 1 through 22, plus X or Y.
Each chromosome appears in the microscope as a three-dimensional object, a condensed sausage-shaped blob, at some stages of the cell division cycle, and as a long, often invisible thread at others. The core of the chromosome is a very long, extremely thin thread of deoxyribonucleic acid; henceforth we shall use its more familiar nickname, DNA. The DNA molecule in a chromosome is surprisingly long. A single human chromosome, as seen with an ordinary microscope, is about 1/5,000 inch long, yet the DNA molecule in this chromosome is an inch or more in length, compacted into the chromosome by successive coiling and supercoiling. The total DNA in a human cell, if the DNA molecules of each chromosome were lined up end to end, would be some 6 feet in length. The DNA molecule is a double thread, coiled into a helix. The genetically important constituents of DNA are four nucleotides (or bases), abbreviated A, T, G, and C. The double thread consists of two phosphate-sugar strands bridged by many pairs of nucleotides, AT, TA, GC, or CG. A always pairs with T and G with C. The DNA molecule can be thought of as a twisted rope ladder with four kinds of stair steps. Each chromosome has the base pairs in a specific order. The genetic difference between one gene and another, or one person and another, is not in the kinds of base pairs; always the same four are used. It is the sequence in which these occur that determines genetic individuality. With an enormous number of base pairs (stair steps), the number of orders (permutations) is astronomical. No wonder we are all different; yet at the DNA level we are remarkably alike, as the next paragraph will explain.
The chromosomes of a sperm or egg contain about 3 billion base pairs, so a body cell has 6 billion. The whole set of base pairs in a gamete is called the genome. The precise processes of DNA duplication and cell division ensure that each cell (with few exceptions, to be discussed later) contains the same sequence of DNA bases. Any two human genomes are alike for the overwhelming majority of their bases; DNA samples from two unrelated persons differ on the average at only about one base per thousand. Yet 1/1,000 of 6 billion is 6 million. These 6 million base differences are sufficient to produce all the genetic differences between those two persons. Although any two genomes differ at some 1/1,000 of their bases, these are not necessarily the same bases as those that are different in another pair of genomes. So the great diversity of shapes, sizes, color, behavior, disease susceptibility, and so on that characterize humanity is no surprise. Even though two persons share an overwhelming proportion of their DNA, there are still enough differences that no two are genetically alike, unless they are identical twins. If we had the complete sequence of the DNA from two persons, or even 1 percent of the DNA, we could (except for identical twins) be certain whether they came from one person or two. In practice, as will be dis cussed later, a much smaller fraction is analyzed, so that identification becomes probabilistic rather than certain.
In addition to differences in individual nucleotides, there are also variations in their number. There are some DNA regions in which a small number of bases is repeated a variable number of times, so the total amount of DNA in different individuals is not exactly the same. Some of the regions that are of the greatest use forensically are such repeated sequences in which the number of repeats varies from person to person.
At present, the Human Genome Project is nearing completion. In June 2000 it was about 90 percent complete. The object is to determine the complete sequence of base pairs in a representative person or a composite of several persons. Soon we shall know the complete encoded genetic information in a genome. This contains the totality of the genetic instructions in an egg or sperm, which together with all of the environmental influences determine the developmental outcome. The chromosomal DNA is not quite the totality of the biological inheritance, for a tiny fraction of the genetic information transmitted from one generation to the next is in the maternally transmitted mitochondria.
A gene is a stretch of DNA from 1,000 to 100,000 or more base pairs in length that has a specific function; usually a gene is responsible for a particular protein. Alternative forms of the gene are called alleles. For example, a specific allele of a particular gene is responsible for the enzyme that converts the amino acid phenylalanine into tyrosine. When this enzyme is missing or abnormal, the child develops the disease, phenylketonuria, or PKU.
The result is severe mental retardation unless the child is treated; happily, with a specific diet the child develops normally. A child will develop PKU only if both representatives of the appropriate chromosome pair carry the abnormal allele. If there is only one PKU allele and the other is normal, the child will be normal; the amount of enzyme produced by a single normal allele is enough. Alleles that express their characteristic trait only when present in duplicate, like the PKU allele, are recessive. Those, like the normal allele, that are effective when present singly, are dominant. It is customary to designate genes by letter symbols, so we can designate the PKU allele by a and the normal alternative by A. An individual with two representatives of the same allele, aa or AA, is homozygous (noun: homozygote). If the two are different, Aa, the individual is heterozygous (noun:heterozygote). Finally, we need two more words. Genotype is the genetic makeup of the individual, such as AA or Aa. The genotypic designation may be extended to include several gene loci. Phenotype is the trait, such as mental retardation if observed externally or the metabolic defect if measured chemically. It may include several traits or it may be a quantitative measure such as height
The rules of inheritance can be deduced from the behavior of chromosomes in meiosis and fertilization. However, before the mechanism of inheritance was understood, the rules were inferred by the Austrian monk, Gregor Mendel, from his experiments breeding garden peas. Although his studies were reported in 1865, they remained unknown until the principles were rediscovered in 1900. It was immediately obvious that Mendel’s hereditary factors followed the same rules as chromosomes; hence the genes must be carried by chromosomes.
As stated earlier, the human chromosomes are numbered from 1 to 22, starting with the largest, plus the X and Y. Each gene occupies a specific position (or locus) on a specific chromosome. The gene causing PKU is at a locus on 12q, meaning that it is on the long arm of chromosome number 12. Typically, there are more than two different alleles at a locus in a population. There may be hundreds in some extreme cases, but of course any fertilized egg has at most two kinds. A locus with more than one allele in the population is said to be polymorphic. Highly polymorphic loci are particularly useful for forensic identification.
In the process of meiosis, one member of each chromosome pair is included in the gamete. Early in meiosis, the two homologous chromosomes pair up. While lined up side by side they often break at corresponding sites and exchange partners. Thus, two genes that were formerly on the same chromosome may end up on different chromosomes, if there has been an exchange between them. The tendency for two different genes on the same chromosome to be inherited together is called linkage. The closer together two genes are on the chromosome, the less probable it is that a break will occur between them and the more probable that they are to be inherited together. This property has been used in classical genetics to “map” the position of genes on the chromosome; the closer together two genes are, the more tightly linked they are in inheritance. This method, developed in experimental animals, also is used to locate genes on human chromosomes, although in recent times it is often supplemented by more direct physical means.
Genes are ordinarily transmitted from generation to generation unchanged. Sometimes, however, the gene is changed, a rare process called mutation. For example, the normal allele may change to the one causing PKU. When a gene mutates, the mutant form is as stable and as regularly transmitted as the original. Mutations come in all sizes. A mutation may be a substitution of one base for another, or one or more bases may be gained or lost, or the order of a group of bases may be changed, inverted for example.
Chromosomes are sometimes broken and reattached in new ways. Or a whole chromosome may be lost or duplicated. All of these come under the general name of mutation, although the term is more often restricted to those changes that are transmitted as a Mendelian unit.
The genes make up only a tiny fraction of the DNA. The rest, the great bulk—about 97 percent—has no known function. It is sometimes referred to as “junk DNA.” Nevertheless, these nongenic regions show the same genetic variability that genes do, in fact usually more. These differences are not overt, but can be detected by laboratory tests. Regions of DNA that are used for forensic analysis are usually not genes, but rather are located in those parts of the chromosomes without known functions, or if part of a gene, not in the part that produces a detectable effect. (One reason for this choice has been to protect individual privacy.) Nevertheless, the words commonly used for describing genes (e.g., allele, homozygous, polymorphic) are carried over to DNA regions used for identification. It is customary to call the genotype for the group of loci involved in a forensic analysis a profile.