Gene

A gene (the term coined by Wilhelm Johannsen in 1909) is a unit of heredity. Employing a universal code that is recognized with only minor variations across all forms of life, including viruses, a gene conveys information as a sequence of nucleotides--especially a DNA sequence--which specifies in turn the amino-acid sequence of a protein. Johannsen's choice of terminology has turned out to be a good fit despite the fact that in 1909 he had no way of knowing the mechanism by which DNA determines the stuff of living beings: genes do literally generate the building blocks of organisms.

In the restrictive molecular biological sense of the word, some elaboration can be necessary to guarantee against confusion within the intricacies of the science. For example, two nucleotide sequences may differ, and yet they may be regarded as simply variants of one gene, either as alleles, alternative splicings or mutant forms of that gene. Conversely, identical sequences may be said to be different genes if duplicate copies fall under different regulation in the chromosomes, typically by virtue of position; or when they appear in different species. Independently of whether or not they are regarded as distinct genes, distinct sequences may nevertheless encode identical proteins, due to degeneracies in the genetic code, which relate nucleotides to amino acids via the cellular machinery of translation. Lastly, a single sequence on one DNA molecule may nevertheless contribute to several genes. This occurs predominantly in viruses, which often overlap their genes to achieve compactness.

These nuances cause conflicts with any definition of "gene" that refers to it as something concrete--like a piece of DNA composed of a particular sequence of nucleotides. But as molecular biologists use the word it connotes a sequence in the abstract, albeit often one with a defined role or context.

A broader but similarly abstract definition says that a gene need not encode a protein. In the chromosomes of all organisms there exist sequences, for example, which do not undergo translation but which through proximity or other factors influencing the chromosomal function affect the ability of a cell to "read" or transcribe other sequences that do. Molecular biologists typically refer to such sequences as regulatory elements--to distinguish them from genes--yet natural variations within these sequences also underlie many of the heritable characteristics seen in organisms. The impact of such sequence variations in the steering of evolution through natural selection may be as large as or larger than the so-called coding genes. Thus a definition that includes regulatory elements within the scope of the word "gene" accords better with its operational sense, which refers to the biological unit that conveys heritable traits ("phenotypic" characters) from one generation to the next. Breeders and geneticists often use "gene" in this sense in their technical communications, as do most people in everyday speech, and this indeed is the traditional meaning of the word.

An equally common use of "gene" to refer to a variant implicated in disease --as in "the gene for obesity"-- conflicts with the usage of biologists and many breeders. In this example, a biologist might refer to "the allele for obsesity" or the "mutation that causes obesity." This too would be a form of shorthand, however. Based on the incidence of obesity across parents and offspring, not to mention common sense, not just genes but factors such as upbringing, culture and the availability of food decide whether or not a person is obese. It also appears unlikely that variations within a single gene--or single genetic locus--determine one's genetic predisposition. With regard to many and perhaps most traits, these aspects of inheritance involve a complex interplay between multiple genes and an individual's environment.

Multicellular organisms possess a complete set of genes that (to a first approximation) is identical in every somatic cell of the body.

Their existence was posited by Gregor Mendel, who studied inheritance in pea plants and explained his results in terms of inherited characteristics. Mendel was also the first to hypothesize independent assortment, the distinction between dominant and recessive traits, the distinction between a heterozygote and homozygote, and the difference between what would later be described as genotype and phenotype.

Genes are said to be expressed when their trait is exhibited in the organism that contains them. Individuals may have more than one kind of gene that compete for expression or combine for traits; for example, a brown-eyed father and blue-eyed mother may each pass on different genes for eye color to the same child. Which trait is expressed is determined by the nature of the genes; sometimes one is said to dominate another (that is, a child with a mixed set will always show the dominant trait), and sometimes they combine to form a mixed trait.

Active genes generally are delimited by a "start" and a "stop" codon (a short DNA sequence which is recognized as a point either to start or to stop transcription of the gene), and contain any number of codons in between that code for amino acids according to the genetic code.

Different genes in the population that occupy the same chromosomal locus (and therefore compete or combine for similar traits) are called alleles.

Much of the chromosomal DNA in many organisms does not code for proteins, and is of no apparent function (sometimes referred to as "junk DNA"). In many cases, this probably represents genes which have become inactive due to DNA rearrangement or mutation at the delimiting codon sites. An interesting field of exploration is the attempt to "re-activate" such "lost" genes, producing such things as real hen's teeth, for instance.

Other junk DNA is thought to serve structural roles in the chromosome, such as the regions of heterochromatin near the chromosome's centromere or the telomeres at the ends. Some junk DNA may serve a regulatory role, providing binding sites for the many signal proteins that affect gene transcription.

Finally, as Richard Dawkins points out in The Selfish Gene, it is quite possible that much, or all, DNA exists literally for no reason other than to propagate itself, even at the expense of the host organism. The possibly disappointing answer to the question "what is the meaning of life?" may be "the survival and perpetuation of ribonucleic acids and their associated proteins".

Typical numbers of genes in an organism:

organism	# of genes	base pairs
Plants	<50000	<10¹¹
Humans	35000	3x10⁸
Flies	12000	1.6x10⁸
Fungi	6000	1.3x10⁷
Bacteria	500-6000	10⁷
Mycoplasma Genitalium	500	10⁶
DNA viruses	10-300	5000-200.000
RNA viruses	1-25	1000-23.000
Viroids	0-1	~500
Prions	0	;0

See also: genetics, gene therapy, Homeobox, Genomics, DNA, Protein