Gene

A gene is a discrete structural unit of hereditary information that living organisms use to construct and regulate proteins and other molecules. The information contained in genes is in the form a "universal language" which biologists call the genetic code. This code is found with only minor variations across all forms of life, including viruses, and is "written" in "letters" called nucleotides, in "words" called triplets, which form "books" called genomes (a genome contains all the genetic information of an organism). A gene, therefore, can be thought of as an individual "paragraph" in that book that represents a specific product called a protein. In eukaryotic-based organisms, another level of organization, the chromosome is used. Chromosomes can be thought of as "sections" in a book.

Genes, along with environmental factors as well as random molecular and cellular movements, play a crucial role in the production of organisms (as well as in the reproduction of genes themselves).

The term was first coined by Wilhelm Johannsen in 1909 to refer to the unit of heredity suggested by Gregor Mendel in the previous century.

DNA vs RNA

There are two slightly different "alphabets" that are used to store and transfer this information: DNA and RNA. The great majority of organisms use DNA to store genetic information in the form of genes and RNA to transfer the stored information to the cellular machinery that translates the message contained in the gene into a polypeptide. This in turn is added to and modified to construct a protein. Viroids and some viruses, however, only use RNA.

Codons

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.

Alleles

The identification of a gene is not determined solely by the specific sequence of nucleotides. On the one hand, two nucleotide sequences may differ, and yet they may be regarded as simply variants of one gene -- for example, as alleles (different genes in the population that occupy the same chromosomal locus and therefore compete or combine for similar traits), or mutant forms of that gene. On the other hand, 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 if the proteins they encode play disparate physiological roles 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 relates 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). In short, a "gene" is not something concrete (for example, a piece of DNA composed of a particular sequence of nucleotides); it is a sequence in the abstract, albeit often one with defined role or context.

Regulation

According to a broader but similarly abstract definition, 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 too underlie many of the heritable characteristics seen in organisms. The impact of such sequence variations in the direction of evolution through natural selection may be as large or larger than those in the so-called coding genes. So 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.

Expression

Genes are said to be expressed when their trait is exhibited in the organism that contains them (for example, when the child does in fact have blue eyes). Individuals may have more than one kind of gene that compete 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.

Use of the term

Pace Mendel, in common parlance today one may speak of, for example, the "gene for blue eyes" being passed from a mother to her children. Similarly, many non-specialists use the term "gene" to refer to a variant implicated in disease -- as in "the gene for obesity." Specialists such as biogists and many breeders, however, would refer instead 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 many genes and an individual's environment (the degree to which a manifest physical feature is the produce of inherited traits is called "heritability.")

History

The existence of genes was first suggested by Gregor Mendel, who studied inheritance in pea plants; although he did not use the term "gene," he 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.

Since the discovery of DNA as the mechanism of heredity, the term is sometimes used to refer to a specific sequence of DNA at a specific locus on a chromosome that codes for a particular protein, whether or not that protein results in a single identifiable heritable trait.

Junk DNA

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.

"Selfish" gene

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	3x10⁹
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