One of the four nucleotide bases in DNA or RNA; pairs with thymine in DNA or uracil in RNA.
One of multiple alternative forms of a single gene, each of which is a viable DNA sequence occupying a given position, or locus on a chromosome. For example, in humans, one allele of the eye-color gene produces blue eyes and another allele of the eye-color gene produces brown eyes.
A pair of nucleotide bases on complementary DNA or RNA strands organized in a double helix.
A molecular "package" for carrying DNA in cells, organized as two double-helical DNA molecules that encode many genes. Some simple organisms have only one chromosome made of circular DNA, while most eukaryotes have multiple chromosomes made of linear DNA.
One of the four nucleotide bases in DNA or RNA; pairs with guanine.
A polymeric molecule made of deoxyribonucleotides, hence then name deoxyribonucleic acid. Most often has the form of a "double helix", which consists of two paired DNA molecules and resembles a ladder that has been twisted. The "rungs" of the ladder are made of base pairs, or nucleotides with complementary hydrogen bonding patterns.
The unit of heredity in living organisms, typically encoded in a sequence of nucleotide monomers that make up a long strand of DNA, or deoxyribonucleic acid. A particular gene can have multiple different forms, or alleles, which are defined by different sequences of DNA.
The process in which the infomation encoded in a gene is converted into a form useful for the cell. The first step is transcription, which produces a messenger RNA molecule complementary to the DNA molecule on which a gene is encoded. For protein-coding genes, the second step is translation, in which the messenger RNA is read by the ribosome to produce a protein.
The sum of all the alleles shared by members of a single population.
The field of biology that studies genes and their inheritance.
The total complement of genetic material contained in an organism or cell.
The complement of alleles present in a particular individual's genome that give rise to the individual's phenotype.
One of the four nucleotide bases in DNA or RNA; pairs with cytosine.
A location on a chromosome where a particular gene resides.
The observable physical or behavioral traits of an organism, largely determined by the organism's genotype.
A linear polymeric molecule made of of amino acids linked by peptide bonds. Proteins carry out the majority of chemical reactions that occur inside the cell.
A polymeric molecule made of ribonucleotides, hence the name ribonucleic acid, similar to but less stable than DNA. One type, messenger RNA, plays an important role in gene expression. Ribosomes are also made largely of RNA.
One of the four nucleotide bases in DNA; pairs with adenine. In RNA, thymine is replaced with uracil.
The first step in gene expression, in which a messenger RNA molecule complementary to particular gene encoded in DNA is synthesized by enzymes called RNA polymerases. To produce a functional protein, transcription is followed by translation.
The second step in gene expression, in which a messenger RNA molecule is read by the ribosome to produce a functional protein. Translation is always preceded by transcription.
One of the four nucleotide bases in RNA; pairs with adenine. In DNA, uracil is replaced with thymine.
A gene is a set of segments of nucleic acid that contains the information necessary to produce a functional RNA product in a controlled manner. They contain regulatory regions dictating under what conditions this product is made, transcribed regions dictating the sequence of the RNA product, and/or other functional sequence regions.

Mendelian inheritance and classical genetics
The vast majority of living organisms encode their genes in long strands of DNA. DNA consists of a chain made from four types of nucleotide subunits: adenosine, cytidine, guanosine, and thymidine. Each nucleotide subunit consists of three components: a phosphate group, a deoxyribose sugar ring, and a nucleobase. Thus, nucleotides in DNA or RNA are typically called 'bases'; consequently they are commonly referred to simply by their purine or pyrimidine original base components adenine, cytosine, guanine, thymine. Adenine and guanine are purines and cytosine and thymine are pyrimidines. The most common form of DNA in a cell is in a double helix structure, in which two individual DNA strands twist around each other in a right-handed spiral. In this structure, the base pairing rules specify that guanine pairs with cytosine and adenine pairs with thymine (each pair contains one purine and one pyrimidine). The base pairing between guanine and cytosine forms three hydrogen bonds, while the base pairing between adenine and thymine forms two hydrogen bonds. The two strands in a double helix must therefore be complementary, that is, their bases must align such that the adenines of one strand are paired with the thymines of the other strand, and so on.
Due to the chemical composition of the pentose residues of the bases, DNA strands have directionality. One end of a DNA polymer contains an exposed hydroxyl group on the deoxyribose, this is known as the 3' end of the molecule. The other end contains an exposed phosphate group, this is the 5' end. The directionality of DNA is vitally important to many cellular processes, since double helices are necessarily directional (a strand running 5'-3' pairs with a complementary strand running 3'-5') and processes such as DNA replication occur in only one direction. All nucleic acid synthesis in a cell occurs in the 5'-3' direction, because new monomers are added via a dehydration reaction that uses the exposed 3' hydroxyl as a nucleophile.
The expression of genes encoded in DNA begins by transcribing the gene into RNA, a second type of nucleic acid that is very similar to DNA, but whose monomers contain the sugar ribose rather than deoxyribose. RNA also contains the base uracil in place of thymine. RNA molecules are less stable than DNA and are typically single-stranded. Genes that encode proteins are composed of a series of three-nucleotide sequences called codons, which serve as the "words" in the genetic "language". The genetic code specifies the correspondence during protein translation between codons and amino acids. The genetic code is nearly the same for all known organisms.

Physical definitions
In most cases, RNA is an intermediate product in the process of manufacturing proteins from genes. However, for some gene sequences, the RNA molecules are the actual functional products. For example, RNAs known as ribozymes are capable of enzymatic function, and miRNAs have a regulatory role. The DNA sequences from which such RNAs are transcribed are known as non-coding DNA, or RNA genes.
Some viruses store their entire genomes in the form of RNA, and contain no DNA at all. Because they use RNA to store genes, their cellular hosts may synthesize their proteins as soon as they are infected and without the delay in waiting for transcription. On the other hand, RNA retroviruses, such as HIV, require the reverse transcription of their genome from RNA into DNA before their proteins can be synthesized. In 2006, French researchers came across a puzzling example of RNA-mediated inheritance in mouse. Mice with a loss-of-function mutation in the gene Kit have white tails. Offspring of these mutants can have white tails despite having only normal Kit genes. The research team traced this effect back to mutated Kit RNA. While RNA is common as genetic storage material in viruses, in mammals in particular RNA inheritance has been observed very rarely.

RNA genes
All genes have regulatory regions in addition to regions that explicitly code for a protein or RNA product. A universal regulatory region shared by all genes is known as the promoter, which provides a position that is recognized by the transcription machinery when a gene is about to be transcribed and expressed. Although promoter regions have a consensus sequence that is the most common sequence at this position, some genes have "strong" promoters that bind the transcription machinery well, and others have "weak" promoters that bind poorly. These weak promoters usually permit a lower rate of transcription than the strong promoters, because the transcription machinery binds to them and initiates transcription less frequently. Other possible regulatory regions include enhancers, which can compensate for a weak promoter. Most regulatory regions are "upstream"—that is, before or toward the 5' end of the transcription initiation site. Eukaryotic promoter regions are much more complex and difficult to identify than prokaryotic promoters.
Many prokaryotic genes are organized into operons, or groups of genes whose products have related functions and which are transcribed as a unit. By contrast, eukaryotic genes are transcribed only one at a time, but may include long stretches of DNA called introns which are transcribed but never translated into protein.

Functional structure of a gene
The total complement of genes in an organism or cell is known as its genome, which may be stored on one or more chromosomes; the region of the chromosome at which a particular gene is located is called its locus. A chromosome consists of a single, very long DNA helix on which thousands of genes are encoded. Prokaryotes - bacteria and archaea - typically store their genomes on a single large, circular chromosome, sometimes supplemented by additional small circles of DNA called plasmids, which usually encode only a few genes and are easily transferable between individuals. For example, the genes for antibiotic resistance are usually encoded on bacterial plasmids and can be passed between individual cells, even those of different species, via horizontal gene transfer. Although some simple eukaryotes also possess plasmids with small numbers of genes, the majority of eukaryotic genes are stored on multiple linear chromosomes, which are packed within the nucleus in complex with storage proteins called histones. The manner in which DNA is stored on the histone, as well as chemical modifications of the histone itself, are regulatory mechanisms governing whether a particular region of DNA is accessible for gene expression. The ends of eukaryotic chromosomes are capped by long stretches of repetitive sequences called telomeres, which do not code for any gene product but are present to prevent degradation of coding and regulatory regions during DNA replication. The length of the telomeres tends to decrease each time the genome is replicated in preparation for cell division; the loss of telomeres has been proposed as an explanation for cellular senescence, or the loss of the ability to divide, and by extension for the aging process in organisms.

Chromosomes

Main article: Gene expression Gene expression

Main article: Genetic code Genetic code
The process of genetic transcription produces a single-stranded RNA molecule known as messenger RNA, whose nucleotide sequence is complementary to the DNA from which it was transcribed. The DNA strand whose sequence matches that of the RNA is known as the coding strand and the strand from which the RNA was synthesized is the template strand. Transcription is performed by an enzyme called an RNA polymerase, which reads the template strand in the 3' to 5' direction and synthesizes the RNA from 5' to 3'. To initiate transcription,the polymerase first recognizes and binds a promoter region of the gene. Thus a major mechanism of gene regulation is the blocking or sequestering of the promoter region, either by tight binding by repressor molecules that physically block the polymerase, or by organizing the DNA so that the promoter region is not accessible.
In prokaryotes, transcription occurs in the cytoplasm; for very long transcripts, translation may begin at the 5' end of the RNA while the 3' end is still being transcribed. In eukaryotes, transcription necessarily occurs in the nucleus, where the cell's DNA is sequestered; the RNA molecule produced by the polymerase is known as the primary transcript and must undergo post-transcriptional modifications before being exported to the cytoplasm for translation. The splicing of introns present within the transcribed region is a modification unique to eukaryotes; alternative splicing mechanisms can result in mature transcripts from the same gene having different sequences and thus coding for different proteins. This is a major form of regulation in eukaryotic cells.

Transcription
Translation is the process by which a mature mRNA molecule is used as a template for synthesizing a new protein. Translation is carried out by ribosomes, large complexes of RNA and protein responsible for carrying out the chemical reactions to add new amino acids to a growing polypeptide chain by the formation of peptide bonds. The genetic code is read three nucleotides at a time, in units called codons, via interactions with specialized RNA molecules called transfer RNA (tRNA). Each tRNA has three unpaired bases known as the anticodon that are complementary to the codon it reads; the tRNA is also covalently attached to the amino acid specified by the complementary codon. When the tRNA binds to its complementary codon in an mRNA strand, the ribosome ligates its amino acid cargo to the new polypeptide chain, which is synthesized from amino terminus to carboxyl terminus. During and after its synthesis, the new protein must fold to its active three-dimensional structure before it can carry out its cellular function.

Translation
The growth, development, and reproduction of organisms relies on cell division, or the process by which a single cell divides into two usually identical daughter cells. This requires first making a duplicate copy of every gene in the genome in a process called DNA replication. The copies are made by specialized enzymes known as DNA polymerases, which "read" one strand of the double-helical DNA, known as the template strand, and synthesize a new complementary strand. Because the DNA double helix is held together by base pairing, the sequence of one strand completely specifies the sequence of its complement; hence only one strand needs to be read by the enzyme to produce a faithful copy. The process of DNA replication is semiconservative; that is, the copy of the genome inherited by each daughter cell contains one original and one newly synthesized strand of DNA.
After DNA replication is complete, the cell must physically separate the two copies of the genome and divide into two distinct membrane-bound cells. In prokaryotes - bacteria and archaea - this usually occurs via a relatively simple process called binary fission, in which each circular genome attaches to the cell membrane and is separated into the daughter cells as the membrane invaginates to split the cytoplasm into two membrane-bound portions. Binary fission is extremely fast compared to the rates of cell division in eukaryotes. Eukaryotic cell division is a more complex process known as the cell cycle; DNA replication occurs during a phase of this cycle known as S phase, while the process of segregating chromosomes and splitting the cytoplasm occurs during M phase. In many single-celled eukaryotes such as yeast, reproduction by budding is common, which results in asymmetrical portions of cytoplasm in the two daughter cells.

DNA replication and inheritance
The duplication and transmission of genetic material from one generation of cells to the next is the basis for molecular inheritance, and the link between the classical and molecular pictures of genes. Organisms inherit the characteristics of their parents because the cells of the offspring contain copies of the genes in their parents' cells. In asexually reproducing organisms, the offspring will be a genetic copy or clone of the parent organism. In sexually reproducing organisms, a specialized form of cell division called meiosis produces cells called gametes or germ cells that are haploid, or contain only one copy of each gene. The gametes produced by females are called eggs or ova, and those produced by males are called sperm. Two gametes fuse to form a fertilized egg, a single cell that once again has a diploid number of genes - each with one copy from the mother and one copy from the father.
During the process of meiotic cell division, an event called genetic recombination or crossing-over can sometimes occur, in which a length of DNA on one chromatid is swapped with a length of DNA on the corresponding sister chromatid. This has no effect if the alleles on the chromatids are the same, but results in reassortment of otherwise linked alleles if they are different. The Mendelian principle of independent assortment asserts that each of a parent's two genes for each trait will sort independently into gametes; which allele an organism inherits for one trait is unrelated to which allele it inherits for another trait. This is in fact only true for genes that do not reside on the same chromosome, or are located very far from one another on the same chromosome. The closer two genes lie on the same chromosome, the more closely they will be associated in gametes and the more often they will appear together; genes that are very close are essentially never separated because it is extremely unlikely that a crossover point will occur between them. This is known as genetic linkage.

Mutation

The genome
The total complement of genes in an organism or cell is known as its genome. In prokaryotes, the vast majority of genes are located on a single chromosome of circular DNA, while eukaryotes usually possess multiple individual linear DNA helices packed into dense DNA-protein complexes called chromosomes. Extrachromosomal DNA is present in many prokaryotes and some simple eukaryotes as small, circular pieces of DNA called plasmids, which usually contain only a few genes each. Generally, regulatory regions and junk DNA are considered to be part of an organism's genome, but structural regions such as telomeres are not. The location (or locus) of a gene and the chromosome on which it is situated is in a sense arbitrary. Genes that appear together on the chromosomes of one species, such as humans, may appear on separate chromosomes in another species, such as mice. Two genes positioned near one another on a chromosome may encode proteins that figure in the same cellular process or in completely unrelated processes. As an example of the former, many of the genes involved in spermatogenesis reside together on the Y chromosome.
Many species carry more than one copy of their genome within each of their somatic cells. Cells or organisms with only one copy of each gene are called haploid; those with two copies are called diploid; and those with more than two copies are called polyploid. When more than one copy is present, the two copies are not necessarily identical; in sexually reproducing organisms, one copy is normally inherited from each parent. The copies may contain distinct DNA sequences encoding distinct alleles.

Chromosomal organization
Typical numbers of genes and size of genomes vary widely among organisms, even those that are fairly closely evolutionarily related. Although it was believed before the completion of the Human Genome Project that the human genome would contain many more genes than simpler animals such as mice or fruit flies, the completion of the project has revealed that the human genome has an unexpectedly low gene density. Moreover, the genes are often fragmented internally by non-coding sequences called introns, which can be many times longer than the coding sequence but are spliced during post-transcriptional modification of pre-mRNA.

Composition of the genome
Gene nomenclature has been established by the HUGO Gene Nomenclature Committee (HGNC) for each known human gene in the form of an approved gene name and symbol (short-form abbreviation). All approved symbols are stored in the HGNC Database. Each symbol is unique and each gene is only given one approved gene symbol. It is necessary to provide a unique symbol for each gene so that people can talk about them. This also facilitates electronic data retrieval from publications. In preference each symbol maintains parallel construction in different members of a gene family and can be used in other species, especially the mouse.

Genetic and genomic nomenclature
George C. Williams first explicitly advocated the gene-centric view of evolution in his 1966 book Adaptation and Natural Selection. He proposed an evolutionary concept of gene to be used when we are talking about natural selection favoring some genes. The definition is: "that which segregates and recombines with appreciable frequency." According to this definition, even an asexual genome could be considered a gene, insofar it have an appreciable permanency through many generations.
The difference is: the molecular gene transcribes as a unit, and the evolutionary gene inherits as a unit.
Richard Dawkins' The Selfish Gene and The Extended Phenotype defended the idea that the gene is the only replicator in living systems. This means that only genes transmit their structure largely intact and are potentially immortal in the form of copies. So, genes should be the unit of selection. In The Selfish Gene Dawkins attempts to redefine the word 'gene' to mean "an inheritable unit" instead of the generally accepted definition of "a section of DNA coding for a particular protein". In River Out of Eden, Dawkins further refined the idea of gene-centric selection by describing life as a river of compatible genes flowing through geological time. Scoop up a bucket of genes from the river of genes, and we have an organism serving as temporary bodies or survival machines. A river of genes may fork into two branches representing two non-interbreeding species as a result of geographical separation.

Evolutionary concept of a gene

Main article: History of genetics History
When trying to understand the concept of a gene, keep in mind that it is not static. It has evolved considerably from a scarcely explained "unit of inheritance" without a physical basis (see history section) to a usually DNA-based unit that can exert its effects on the organism through RNA or protein products. It was also previously believed that one gene makes one protein; this concept has been overthrown by the discovery of alternative splicing and trans-splicing.

The gene concept is still changing

DNA
Epigenetics
Gene-centric view of evolution
Gene expression
Gene family
Gene pool
Gene therapy
Genetic algorithm
Genetic programming
Gene regulatory network
Genetics
Genomes
Genomics
Homeobox
Human Genome Project
List of notable genes
Meme
Memetics
Protein
Pseudogene
Regulation of gene expression
RNA
Smart gene Further reading

The Dolan DNA Learning Center
DNA Interactive
DNA From The Beginning