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{{for|a non-technical introduction to the topic|Introduction to Genetics}}
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| [[Image:Gene.png|right|thumbnail|270px|This stylistic schematic diagram shows a gene in relation to the double helix structure of [[DNA]] and to a [[chromosome]] (right). [[Intron]]s are regions often found in [[eukaryote]] genes which are removed in the [[splicing (genetics)|splicing]] process (after the DNA is transcribed into RNA): only the [[exon]]s encode the [[protein]]. This diagram labels a region of only 40 or so bases as a gene. In reality most genes are hundreds of times larger, and the relationships between Introns and exons can be highly complex.]]
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{{Genetics glossary}}
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A '''gene''' is a locatable region of [[genomic sequence]], corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions.<ref name=Pearson_2006>{{cite journal |author=Pearson H |title=Genetics: what is a gene? |journal=Nature |volume=441 |issue=7092 |pages=398-401 |year=2006 |pmid=16724031}}</ref><ref name = "Rethink">{{cite journal |author=Elizabeth Pennisi|title=DNA Study Forces Rethink of What It Means to Be a Gene |journal=Science|volume=316|issue=5831|pages=1556-1557 |year=2007}}</ref> The physical [[developmental biology|development]] and [[phenotype]] of organisms can be thought of as a product of genes interacting with each other and with the environment<ref>see eg [[Martin Nowak]]'s ''Evolutionary Dynamics''</ref>, and genes can be considered as units of [[inheritance]]. A concise definition of gene taking into account complex patterns of regulation and transcription, genic conservation and non-coding RNA genes, has been proposed by Gerstein et al.<ref name=Gerstein_2007>{{cite journal |author=Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M |title=What is a gene, post-ENCODE? History and updated definition |journal=Genome Research |volume=17 |issue=6 |pages=669-681 |year=2007 |pmid=17567988}}</ref> "A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products".

In cells, genes consist of a long strand of [[DNA]] that contains a [[promoter]], which controls the activity of a gene, and a coding sequence, which determines what the gene produces. When a gene is active, the coding sequence is copied in a process called [[Transcription (genetics)|transcription]], producing an RNA copy of the gene's information. This RNA can then direct the synthesis of proteins via the [[genetic code]]. However, RNAs can also be used directly, for example as part of the [[ribosome]]. These molecules resulting from gene expression, whether [[RNA]] or [[protein]], are known as [[gene product]]s.

Most genes contain non-coding regions that do not code for the gene products, but [[gene regulation|regulate gene expression]]. The genes of [[eukaryote|eukaryotic]] organisms can contain non-coding regions called [[intron]]s that are removed from the messenger RNA in a process known as [[Splicing (genetics)|splicing]]. The regions that actually encode the gene product, which can be much smaller than the [[intron]]s, are known as [[exon]]s. One single gene can lead to the synthesis of multiple proteins through the different arrangements of exons produced by alternative splicings.

The total complement of genes in an organism or cell is known as its [[genome]]. The [[genome size]] of an organism is generally lower in [[prokaryote]]s such as [[bacteria]] and [[archaea]] have generally smaller genomes, both in number of [[base pair]]s and number of genes, than even single-celled [[eukaryote]]s, although there is no clear relationship between genome sizes and perceived complexity of eukaryotic organisms. One of the largest known genomes belongs to the single-celled [[amoeba]] ''Amoeba dubia'', with over 670 billion base pairs, some 200 times larger than the human genome.<ref name="Cavalier-Smith">Cavalier-Smith T. (1985). Eukaryotic gene numbers, non-coding DNA, and genome size. In Cavalier-Smith T, ed. ''The Evolution of Genome Size'' Chichester: John Wiley.</ref> The estimated number of genes in the [[human genome]] has been repeatedly revised downward since the completion of the [[Human Genome Project]]; current estimates place the human genome at just under 3 billion base pairs and about 20,000–25,000 genes.<ref name="IHSGC2004">{{cite journal | author = International Human Genome Sequencing Consortium | title = Finishing the euchromatic sequence of the human genome. | journal = Nature | volume = 431 | issue = 7011 | pages = 931-45 | year = 2004 | url = http://www.nature.com/nature/journal/v431/n7011/full/nature03001.html | id = PMID 15496913}}</ref>. A recent ''[[Science (journal)|Science]]'' article gives a final number of 20,488, with perhaps 100 more yet to be discovered .<ref name="gene_count2007">{{cite journal | author = Pennisi, Elizabeth | title = Working the (Gene Count) Numbers_ Finally, a Firm Answer | journal = Science | volume = 316 | issue = 5828 | pages = 1113 | year = 2007 | url = http://www.sciencemag.org/cgi/content/full/316/5828/1113a?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=gene+count&searchid=1&FIRSTINDEX=0&resourcetype=HWCIT}}</ref> The gene density of a genome is a measure of the number of genes per million base pairs (called a megabase, Mb); prokaryotic genomes have much higher gene densities than eukaryotes. The gene density of the human genome is roughly 12–15 genes/Mb.<ref name=Watson_2004>{{cite book | author = Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R | title = Molecular Biology of the Gene | edition = 5th ed. | publisher = Peason Benjamin Cummings (Cold Spring Harbor Laboratory Press) | year = 2004 | id = ISBN 080534635X }}</ref>

==History==
{{main|History of genetics}}

The existence of genes was first suggested by [[Gregor Mendel]] (1822-1884), who, in the [[1860s]], studied inheritance in [[pea]] plants and [[hypothesis|hypothesized]] a factor that conveys traits from parent to offspring. He spent over 10 years of his life on one experiment. 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 gene|dominant]] and [[recessive]] traits, the distinction between a [[heterozygote]] and [[homozygote]], and the difference between what would later be described as [[genotype]] and [[phenotype]]. Mendel's concept was given a name by [[Hugo de Vries]] in 1889, who, at that time probably unaware of Mendel's work, in his book ''Intracellular Pangenesis'' coined the term "pangen" for "the smallest particle <nowiki>[representing]</nowiki> one hereditary characteristic"<ref name=pangen />. [[Wilhelm Johannsen]] abbreviated this term to "gene" ("gen" in Danish and German) two decades later.

In the early 1900s, Mendel's work received renewed attention from scientists. In 1910, [[Thomas Hunt Morgan]] showed that genes reside on specific [[chromosome]]s. He later showed that genes occupy specific locations on the chromosome. With this knowledge, Morgan and his students began the first chromosomal map of the fruit fly ''[[Drosophila melanogaster|Drosophila]]''. In 1928, [[Frederick Griffith]] showed that genes could be transferred. In what is now known as [[Griffith's experiment]], injections into a mouse of a deadly strain of [[bacteria]] that had been heat-killed transferred genetic information to a safe strain of the same bacteria, killing the mouse.

In 1941, [[George Wells Beadle]] and [[Edward Lawrie Tatum]] showed that mutations in genes caused errors in certain steps in [[metabolic pathway]]s. This showed that specific genes code for specific proteins, leading to the "one gene, one enzyme" hypothesis. <ref name="Gerstein"/> [[Oswald Avery]], [[Collin Macleod]], and [[Maclyn McCarty]] showed in 1944 that DNA holds the gene's information. In 1953, [[James D. Watson]] and [[Francis Crick]] demonstrated the molecular structure of [[DNA]]. Together, these discoveries established the [[central dogma of molecular biology]], which states that proteins are translated from [[RNA]] which is transcribed from DNA. This dogma has since been shown to have exceptions, such as [[reverse transcription]] in [[retrovirus]]es.

In [[1972]], [[Walter Fiers]] and his team at the Laboratory of Molecular Biology of the [[University of Ghent]] ([[Ghent]], [[Belgium]]) were the first to determine the sequence of a gene: the gene for [[Bacteriophage MS2]] coat protein.<ref name=Min_1972>{{cite journal |author=Min Jou W, Haegeman G, Ysebaert M, Fiers W |title=Nucleotide sequence of the gene coding for the bacteriophage MS2 coat protein |journal=Nature |volume=237 |issue=5350 |pages=82-8 |year=1972 |pmid=4555447}}</ref> [[Richard J. Roberts]] and [[Phillip Sharp]] discovered in 1977 that genes can be split into segments. This leads to the idea that one gene can make several proteins. Recently (as of [[2003]]-[[2006]]), [[biology|biological]] results let the notion of gene appear more slippery. In particular, genes do not seem to sit side by side on [[DNA]] like discrete beads. Instead, [[region]]s of the DNA producing distinct proteins may overlap, so that the idea emerges that "genes are one long [[continuum]]".<ref name=Pearson_2006 />

==Mendelian inheritance and classical genetics==
{{main|Mendelian inheritance|Classical genetics}}
Darwin used the term [[Gemmule]] to describe a microscopic unit of inheritance, and what would later become known as [[Chromosome]]s had been observed separating out during cell division by [[Wilhelm Hofmeister]] as early as 1848. The idea that chromosomes were the carriers of inheritance was expressed in 1883 by [[Wilhelm Roux]]. The modern conception of the gene originated with work by [[Gregor Mendel]], a [[19th century]] [[Augustinian]] monk who systematically studied heredity in pea plants. Mendel's work was the first to illustrate [[particulate inheritance]], or the theory that inherited traits are passed from one generation to the next in discrete units that interact in well-defined ways. [[Denmark|Danish]] [[botanist]] [[Wilhelm Johannsen]] coined the word "gene" in 1909 to describe these fundamental physical and functional units of heredity,<ref name="genome">{{cite web | url=http://www.genome.gov/Pages/Education/Kit/main.cfm?pageid=24 | title=The Human Genome Project Timeline | accessdate=2006-09-13 }}</ref> while the related word [[genetics]] was first used by [[William Bateson]] in [[1905]].<ref name="Gerstein"/> The word was derived from [[Hugo De Vries]]' 1889 term ''pangen'' for the same concept <ref name="pangen">Vries, H. de (1889) ''Intracellular Pangenesis'' [http://www.esp.org/books/devries/pangenesis/facsimile/] ("pangen" definition on page 7 and 40 of this 1910 translation in English)</ref>, itself a derivative of the word ''[[pangenesis]]'' coined by [[Charles Darwin|Darwin]] (1868).<ref name="Darwin">Darwin C. (1868). Animals and Plants under Domestication (1868).</ref> The word pangenesis is made from the [[Greek language|Greek]] words ''pan'' (a prefix meaning "whole", "encompassing") and ''genesis'' ("birth") or ''genos'' ("origin").

According to the theory of Mendelian inheritance, variations in [[phenotype]] - the observable physical and behavioral characteristics of an organism - are due to variations in [[genotype]], or the organism's particular set of genes, each of which specifies a particular trait. Different genes for the same trait, which give rise to different phenotypes, are known as [[allele]]s. Organisms such as the pea plants Mendel worked on, along with many plants and animals, have two alleles for each trait, one inherited from each parent. Alleles may be [[dominant gene|dominant]] or [[recessive gene|recessive]]; dominant alleles give rise to their corresponding phenotypes when paired with any other allele for the same trait, while recessive alleles give rise to their corresponding phenotype only when paired with another copy of the same allele. For example, if the allele specifying tall stems in pea plants is dominant over the allele specifying short stems, then pea plants that inherit one tall allele from one parent and one short allele from the other parent will also have tall stems. Mendel's work found that alleles assort independently in the production of [[gamete]]s, or [[germ cell]]s, ensuring variation in the next generation.

Prior to Mendel's work, the dominant theory of heredity was one of [[blending inheritance]], which proposes that the traits of the parents blend or mix in a smooth, continuous gradient in the offspring. Although Mendel's work was largely unrecognized after its first publication in 1866, it was rediscovered in 1900 by three European scientists, [[Hugo de Vries]], [[Carl Correns]], and [[Erich von Tschermak]], who had reached similar conclusions from their own research. However, these scientists were not yet aware of the identity of the 'discrete units' on which genetic material resides.

A series of subsequent discoveries led to the realization decades later that [[chromosome]]s within [[cell (biology)|cells]] are the carriers of genetic material, and that they are made of [[DNA]] (deoxyribonucleic acid), a [[polymer]]ic molecule found in all cells on which the 'discrete units' of Mendelian inheritance are encoded. The modern study of [[genetics]] at the level of DNA is known as [[molecular genetics]] and the synthesis of molecular genetics with traditional [[Charles Darwin|Darwinian]] [[evolution]] is known as the [[modern evolutionary synthesis]].

==Physical definitions==
[[Image:DNA chemical structure.svg|thumb|300px|The chemical structure of a four-base fragment of a DNA double helix.]]
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 [[Watson-Crick base pair|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 [[gene expression|expression]] of genes encoded in DNA begins by [[transcription (genetics)|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 [[protein]]s are composed of a series of three-[[nucleotide]] sequences called [[codon]]s, which serve as the "words" in the genetic "language". The [[genetic code]] specifies the correspondence during [[translation (genetics)|protein translation]] between codons and [[amino acid]]s. The genetic code is nearly the same for all known organisms.

===RNA genes===
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 [[ribozyme]]s are capable of [[enzyme|enzymatic function]], and [[microRNA|miRNAs]] have a regulatory role. The [[DNA]] sequences from which such RNAs are transcribed are known as [[non-coding DNA]], or [[RNA gene]]s.

Some [[virus]]es store their entire genomes in the form of RNA, and contain no DNA at all. Because they use RNA to store genes, their [[cell (biology)|cellular]] [[host (biology)|hosts]] may synthesize their proteins as soon as they are [[infection|infected]] and without the delay in waiting for transcription. On the other hand, RNA [[retrovirus]]es, such as [[HIV]], require the [[reverse transcription]] of their [[genome]] from RNA into DNA before their proteins can be synthesized.
<!-- this is such a specific little nit that I really doubt its usefulness so early in a very basic article -->
In 2006, French researchers came across a puzzling example of RNA-mediated inheritance in mouse. Mice with a [[Mutation#By effect on function|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.<ref name="rass">{{cite journal |author=Rassoulzadegan M, Grandjean V, Gounon P, Vincent S, Gillot I, Cuzin F |title=RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse |journal=Nature |volume=441 |issue=7092 |pages=469-74 |year=2006 |pmid=16724059}}</ref> While RNA is common as genetic storage material in viruses, in mammals in particular RNA inheritance has been observed very rarely.

===Functional structure of a gene===
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 [[enhancer (genetics)|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 [[operon]]s, or groups of genes whose products have related functions and which are transcribed as a unit. By contrast, [[Eukaryotic gene example|eukaryotic genes]] are transcribed only one at a time, but may include long stretches of DNA called [[intron]]s which are transcribed but never translated into protein (they are spliced out before translation).

===Chromosomes===
The total complement of genes in an organism or cell is known as its [[genome]], which may be stored on one or more [[chromosome]]s; the region of the chromosome at which a particular gene is located is called its [[locus (genetics)|locus]]. A chromosome consists of a single, very long DNA helix on which thousands of genes are encoded. [[Prokaryote]]s - [[bacteria]] and [[archaea]] - typically store their genomes on a single large, circular chromosome, sometimes supplemented by additional small circles of DNA called [[plasmid]]s, 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]].
<!-- this would be a good place for a table of % 'junk' or similar -->
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 [[cell nucleus|nucleus]] in complex with storage proteins called [[histone]]s. 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 [[telomere]]s, 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.<ref name="Braig">{{cite journal |author=Braig M, Schmitt C |title=Oncogene-induced senescence: putting the brakes on tumor development |journal=Cancer Res |volume=66 |issue=6 |pages=2881-4 |year=2006 |pmid=16540631}}</ref>

While the chromosomes of prokaryotes are relatively gene-dense, those of eukaryotes often contain so-called "[[junk DNA]]", or regions of DNA that serve no obvious function. Simple single-celled eukaryotes have relatively small amounts of such DNA, while the genomes of complex multicellular organisms, including humans, contain an absolute majority of DNA without an identified function.<ref name="IHSGC2004" /> However it now appears that, although protein-coding DNA makes up barely 2% of the human genome, about 80% of the bases in the genome may be being expressed, so the term "junk DNA" may be a misnomer.<ref name="Rethink">

==Gene expression==
{{main|Gene expression}}

In all organisms, there are two major steps separating a protein-coding gene from its protein: first, the DNA on which the gene resides must be ''[[transcription (genetics)|transcribed]]'' from DNA to [[messenger RNA]] (mRNA), and second, it must be ''[[translation (genetics)|translated]]'' from mRNA to protein. RNA-coding genes must still go through the first step, but are not translated into protein. The process of producing a biologically functional molecule of either RNA or protein is called [[gene expression]], and the resulting molecule itself is called a [[gene product]].

===Genetic code===
[[Image:Rna-codons-protein.png|thumb|200px|Schematic diagram of a single-stranded RNA molecule illustrating the position of three-base codons.]]

{{main|Genetic code}}

The genetic code is the set of rules by which a gene is translated into a functional protein. Each gene consists of a specific sequence of nucleotides encoded in a DNA (or sometimes RNA) strand; a correspondence between nucleotides, the basic building blocks of genetic material, and amino acids, the basic building blocks of proteins, must be established for genes to be successfully translated into functional proteins. Sets of three nucleotides, known as [[codon]]s, each correspond to a specific amino acid or to a signal; three codons are known as "stop codons" and, instead of specifying a new amino acid, alert the translation machinery that the end of the gene has been reached. There are 64 possible codons (four possible nucleotides at each of three positions, hence 4³ possible codons) and only 20 standard amino acids; hence the code is redundant and multiple codons can specify the same amino acid. The correspondence between codons and amino acids is nearly universal among all known living organisms.

===Transcription===
The process of genetic [[transcription (genetics)|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' end|3']] to [[5' end|5']] direction and synthesizes the RNA from [[5' end|5']] to [[3' end|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 [[prokaryote]]s, 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 [[eukaryote]]s, 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 modification]]s before being exported to the cytoplasm for translation. The [[splicing]] of [[intron]]s 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.

===Translation===
[[Translation (genetics)|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 [[ribosome]]s, large complexes of RNA and protein responsible for carrying out the chemical reactions to add new [[amino acid]]s to a growing [[polypeptide chain]] by the formation of [[peptide bond]]s. The genetic code is read three nucleotides at a time, in units called [[codon]]s, 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 [[covalent]]ly 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 [[N-terminus|amino terminus]] to [[C-terminus|carboxyl terminus]]. During and after its synthesis, the new protein must [[protein folding|fold]] to its active [[tertiary structure|three-dimensional structure]] before it can carry out its cellular function.

==DNA replication and inheritance==
The growth, development, and reproduction of organisms relies on [[cell division]], or the process by which a single [[cell (biology)|cell]] divides into two usually identical [[daughter cell]]s. 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 [[enzyme]]s known as [[DNA polymerase]]s, 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 pair]]ing, 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 replication|semiconservative]]; that is, the copy of the genome inherited by each daughter cell contains one original and one newly synthesized strand of DNA.<ref name=Watson_2004 />

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 [[prokaryote]]s - [[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 [[invaginate]]s to split the [[cytoplasm]] into two membrane-bound portions. Binary fission is extremely fast compared to the rates of cell division in [[eukaryote]]s. 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 [[chromosome]]s 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.

===Molecular 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 [[asexual reproduction|asexually reproducing]] organisms, the offspring will be a genetic copy or [[clone]] of the parent organism. In [[sexual reproduction|sexually reproducing]] organisms, a specialized form of cell division called [[meiosis]] produces cells called [[gamete]]s or [[germ cell]]s that are [[haploid]], or contain only one copy of each gene. The gametes produced by females are called [[egg (biology)|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 [[allele]]s 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===
{{main|Mutation}}

DNA replication is for the most part extremely accurate, with an error rate per site of around 10<sup>-6</sup> to 10<sup>-10</sup> in eukaryotes.<ref name=Watson_2004 /> Rare, spontaneous alterations in the base sequence of a particular gene arise from a number of sources, such as errors in [[DNA replication]] and the aftermath of [[DNA damage]]. These errors are called [[mutation]]s. The cell contains many [[DNA repair]] mechanisms for preventing mutations and maintaining the integrity of the genome; however, in some cases — such as breaks in both DNA strands of a chromosome — repairing the physical damage to the molecule is a higher priority than producing an exact copy. Due to the degeneracy of the genetic code, some mutations in protein-coding genes are ''silent'', or produce no change in the amino acid sequence of the protein for which they code; for example, the codons UCU and UUC both code for [[serine]], so the U↔C mutation has no effect on the protein. Mutations that do have phenotypic effects are most often neutral or deleterious to the organism, but sometimes they confer benefits to the organism's [[fitness (biology)|fitness]].

Mutations propagated to the next [[generation]] lead to variations within a species' population. Variants of a single gene are known as [[allele]]s, and differences in [[allele]]s may give rise to differences in traits. Although it is rare for the variants in a single gene to have clearly distinguishable phenotypic effects, certain well-defined traits are in fact controlled by single genetic loci. A gene's most common allele is called the [[wild type]] allele, and rare alleles are called [[mutant]]s. However, this does not imply that the wild-type allele is the [[ancestor]] from which the [[mutant]]s are descended.

==The genome==
===Chromosomal organization===
The total complement of genes in an organism or cell is known as its [[genome]]. In [[prokaryote]]s, the vast majority of genes are located on a single chromosome of circular DNA, while [[eukaryote]]s usually possess multiple individual linear DNA helices packed into dense DNA-protein complexes called [[chromosome]]s. [[Extrachromosomal DNA]] is present in many prokaryotes and some simple eukaryotes as small, circular pieces of DNA called [[plasmid]]s, 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 [[telomere]]s are not. The location (or [[locus (genetics)|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 [[mouse|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 [[Sex-determination system|Y chromosome]].

Many species carry more than one copy of their genome within each of their [[somatic cell]]s. 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.

===Composition of the genome===
{| class="wikitable" style="float:right; margin:0 0 1em 1em"
|+ Gene content and genome size of various organisms<ref name=Watson_2004 />
|-
! Species
! Genome size (Mb)
! Number of genes
|-
| ''[[Mycoplasma genitalium]]''
| 0.58
| 500
|-
| ''[[Streptococcus pneumoniae]]''
| 2.2
| 2300
|-
| ''[[Escherichia coli]]''
| 4.6
| 4400
|-
| ''[[Saccharomyces cerevisiae]]''
| 12
| 5800
|-
| ''[[Arabidopsis thaliana]]''
| 125
| 25,500
|-
| ''[[Caenorhabditis elegans]]''
| 97
| 19,000
|-
| ''[[Sea urchin]]''
| 814
| 23,300
|-
| ''[[Drosophila melanogaster]]''
| 180
| 13,700
|-
| ''[[Mus musculus]]''
| 2500
| 29,000
|-
| ''[[Homo sapiens]]''
| 2900
| 27,000
|-
| ''[[Oryza sativa]]''
| 466
| 45-55,000
|}

Typical numbers of genes and size of [[genome]]s vary widely among organisms, even those that are fairly closely [[evolution]]arily 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 [[mouse|mice]] or [[Drosophila|fruit flies]], the completion of the project has revealed that the human genome has an unexpectedly low gene density.<ref name="IHSGC2004" /> Estimates of the number of genes in a genome are difficult to compile because they depend on [[gene finding]] [[algorithm]]s that search for patterns resembling those present in known genes, such as [[open reading frame]]s, [[promoter]] regions with sequences resembling the [[consensus sequence|consensus]] promoter sequence, and related regulatory regions such as [[TATA box]]es in eukaryotes. Gene finding is less reliable in eukaryotic than in prokaryotic genomes due to the presence of non-coding DNA such as [[intron]]s and [[pseudogene]]s.<ref name=Mount_2004>{{cite book | last = Mount | first = DW | title = Bioinformatics: Sequence and genome analysis | edition = 2nd ed. | publisher = Cold Spring Harbor Laboratory Press: Cold Spring Harbor, New York | year = 2004 | id = ISBN 0879697121 }}</ref> Computational gene finding methods are still significantly more reliable than earlier techniques that required mapping the locations of specific mutations that gave rise to distinguishable alleles.<ref name=Watson_2004 />

In most [[Eukaryote|eukaryotic]] species, very little of the DNA in the genome encodes proteins, and the genes may be separated by vast regions of [[non-coding DNA]], much of which has been labeled "[[junk DNA]]" due to its apparent lack of function in the modern organism. A commonly studied type of "junk DNA" is the [[pseudogene]]s, or region of non-coding DNA that resembles expressed genes but usually lacks appropriate promoters and other control sequences; such regions are hypothesized to be the results of [[gene duplication]] events in a lineage's [[evolution]]ary past.<ref name="Lodish">Lodish, H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipursky SL, Darnell J. (2004). ''Molecular Cell Biology'', 5th, New York: WH Freeman.</ref> Moreover, the genes are often fragmented internally by non-coding sequences called [[intron]]s, which can be many times longer than the coding sequence but are [[splicing|spliced]] during [[post-transcriptional modification]] of pre-[[mRNA]].

===Genetic and genomic nomenclature===
[[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 [http://www.genenames.org/cgi-bin/hgnc_search.pl 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 [[electronics|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]].

==Evolutionary concept of a gene==
[[George C. Williams]] first explicitly advocated the [[gene-centered view of evolution|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 [[asexuality|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 machine]]s. A river of genes may fork into two branches representing two non-[[Hybrid|interbreeding]] [[species]] as a result of geographical separation.

==The ''gene'' concept is still changing==

The concept of the gene has changed considerably (see [[gene#history|history section]]). Originally considered a "unit of inheritance" 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]].<ref name="Gerstein"/>

And the definition of gene is still changing. The first cases of [[RNA]]-based [[biological inheritance|inheritance]] have been discovered in mammals.<ref name="rass">Rassoulzadegan and colleagues (2006) RNA-mediated non-mendelian inheritance of an [[epigenetic]] change in the mouse. PMID 16724059</ref> In plants, cases of traits reappearing after several generation of absence have lead researchers to hypothesise RNA-directed overwriting of genomic DNA.<ref>Lolle & colleagues (2005) Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis. PMID 15785770</ref> Evidence is also accumulating that the [[Enhancer (genetics)|control regions]] of a gene do not necessarily have to be close to the [[coding sequence]] on the linear molecule or even on the same chromosome. Spilianakis and colleagues discovered that the [[promoter region]] of the [[interferon-gamma]] gene on chromosome 10 and the regulatory regions of the T(H)2 [[cytokine]] locus on chromosome 11 come into close proximity in the [[cell nucleus|nucleus]] possibly to be jointly regulated.<ref>Spilianakis & colleagues (2005) Interchromosomal associations between alternatively expressed loci. PMID 15880101</ref>

The concept that genes are clearly limited is also being eroded. There is evidence for fused proteins stemming from two adjacent genes that can produce two separate protein products. While it is not clear whether these fusion proteins are functional, the phenomena is more frequent than previously thought.<ref>Parra & colleagues (2006) Tandem chimerism as a means to increase protein complexity in the human genome. PMID 16344564</ref> Even more ground-breaking than the discovery of fused genes is the observation that some proteins can be composed of [[exons]] from far away regions and even different chromosomes.<ref>Kapranov & colleagues (2005) Examples of the complex architecture of the human transcriptome revealed by [[RACE]] and high-density tiling arrays. PMID 15998911</ref><ref name="Rethink"/> This new data has led to an updated, and probably tentative, definition of a gene as "a union of genomic sequences encoding a coherent set of potentially overlapping functional products."<ref name="Gerstein">
Mark B. Gerstein ''et al.'', "What is a gene, post-ENCODE? History and updated definition," ''Genome Research'' 17(6) (2007): 669-681
</ref> This new definition categorizes genes by functional products, whether they be proteins or RNA, rather than specific DNA loci; all regulatory elements of DNA are therefore classified as ''gene-associated'' regions.<ref name="Gerstein"/>

==See also==
<div style="-moz-column-count:3; column-count:3;">
* [[DNA]]
* [[Epigenetics]]
* [[Gene-centered view of evolution|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]]
* [[Genetic Pollution]]
* [[Genetic Erosion]]

</div>

==References==
<!-- ---------------------------------------------------------------
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discussion of different citation methods and how to generate
footnotes using the <ref> & </ref> tags and the {{Reflist}} template
-------------------------------------------------------------------- -->

{{Reflist|2}}

==Further reading==
* {{cite book | first = Richard | last = Dawkins | authorlink = Richard Dawkins | title = [[The Selfish Gene]] | publisher = Oxford University Press | year = 1990 | id = ISBN 0-19-286092-5 }} [http://print.google.com/print?id=WkHO9HI7koEC Google Book Search]; first published 1976.
* {{cite book | first = Richard | last = Dawkins | authorlink = Richard Dawkins | title = [[River Out of Eden]] | publisher = Basic Books | year = 1995 | id = ISBN 0-465-06990-8 }}

==External links==
* [http://www.dnalc.org/ The Dolan DNA Learning Center]
* [http://www.dnai.org/ DNA Interactive]
* [http://www.dnaftb.org/ DNA From The Beginning]

{{wikibooks|Genes, Technology and Policy}}

{{Spoken Wikipedia|Gene.ogg|2005-04-21}}

===Tutorial and news===
* [http://www.scienceaid.co.uk/biology/genetics Science aid: Genetics] for beginners
* [http://www.newscientist.com/news/news.jsp?id=ns99996561 Recount slashes number of human genes] (from [[New Scientist]] magazine)
* [http://www.genome.gov/12513430 National Human Genome Research Institute — News Release]
* {{cite journal |author= |title=Finishing the euchromatic sequence of the human genome |journal=Nature |volume=431 |issue=7011 |pages=931-45 |year=2004 |pmid=15496913}}

===References and databases===
* [http://www.gene.ucl.ac.uk/nomenclature HUGO Gene Nomenclature Committee, HGNC]
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM OMIM] NIH's National Library of Medicine NCBI website link to Online Mendelian Inheritance in Man.
* [http://www.hugo-international.org Human Genome Organisation, HUGO]
* [http://www.ihop-net.org/UniPub/iHOP/ iHOP - Information Hyperlinked over Proteins]
* [http://www.pir.uniprot.org/ UniProt]
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene Entrez Gene - A searchable database of genes]
* [http://idconverter.bioinfo.cnio.es IDconverter - Map your ids to other known public DBs]

[[Category:Cloning]]
[[Category:Genetics]]
[[Category:Molecular biology]]
[[Category:Units of morphological analysis]]

{{Link FA|hu}}

[[af:Geen]]
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[[zh:基因]]

Revision as of 10:02, 10 October 2007

This stylistic schematic diagram shows a gene in relation to the double helix structure of DNA and to a chromosome (right). Introns are regions often found in eukaryote genes which are removed in the splicing process (after the DNA is transcribed into RNA): only the exons encode the protein. This diagram labels a region of only 40 or so bases as a gene. In reality most genes are hundreds of times larger, and the relationships between Introns and exons can be highly complex.

Template:Genetics glossary

A gene is a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions.[1][2] The physical development and phenotype of organisms can be thought of as a product of genes interacting with each other and with the environment[3], and genes can be considered as units of inheritance. A concise definition of gene taking into account complex patterns of regulation and transcription, genic conservation and non-coding RNA genes, has been proposed by Gerstein et al.[4] "A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products".

In cells, genes consist of a long strand of DNA that contains a promoter, which controls the activity of a gene, and a coding sequence, which determines what the gene produces. When a gene is active, the coding sequence is copied in a process called transcription, producing an RNA copy of the gene's information. This RNA can then direct the synthesis of proteins via the genetic code. However, RNAs can also be used directly, for example as part of the ribosome. These molecules resulting from gene expression, whether RNA or protein, are known as gene products.

Most genes contain non-coding regions that do not code for the gene products, but regulate gene expression. The genes of eukaryotic organisms can contain non-coding regions called introns that are removed from the messenger RNA in a process known as splicing. The regions that actually encode the gene product, which can be much smaller than the introns, are known as exons. One single gene can lead to the synthesis of multiple proteins through the different arrangements of exons produced by alternative splicings.

The total complement of genes in an organism or cell is known as its genome. The genome size of an organism is generally lower in prokaryotes such as bacteria and archaea have generally smaller genomes, both in number of base pairs and number of genes, than even single-celled eukaryotes, although there is no clear relationship between genome sizes and perceived complexity of eukaryotic organisms. One of the largest known genomes belongs to the single-celled amoeba Amoeba dubia, with over 670 billion base pairs, some 200 times larger than the human genome.[5] The estimated number of genes in the human genome has been repeatedly revised downward since the completion of the Human Genome Project; current estimates place the human genome at just under 3 billion base pairs and about 20,000–25,000 genes.[6]. A recent Science article gives a final number of 20,488, with perhaps 100 more yet to be discovered .[7] The gene density of a genome is a measure of the number of genes per million base pairs (called a megabase, Mb); prokaryotic genomes have much higher gene densities than eukaryotes. The gene density of the human genome is roughly 12–15 genes/Mb.[8]

History

The existence of genes was first suggested by Gregor Mendel (1822-1884), who, in the 1860s, studied inheritance in pea plants and hypothesized a factor that conveys traits from parent to offspring. He spent over 10 years of his life on one experiment. 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. Mendel's concept was given a name by Hugo de Vries in 1889, who, at that time probably unaware of Mendel's work, in his book Intracellular Pangenesis coined the term "pangen" for "the smallest particle [representing] one hereditary characteristic"[9]. Wilhelm Johannsen abbreviated this term to "gene" ("gen" in Danish and German) two decades later.

In the early 1900s, Mendel's work received renewed attention from scientists. In 1910, Thomas Hunt Morgan showed that genes reside on specific chromosomes. He later showed that genes occupy specific locations on the chromosome. With this knowledge, Morgan and his students began the first chromosomal map of the fruit fly Drosophila. In 1928, Frederick Griffith showed that genes could be transferred. In what is now known as Griffith's experiment, injections into a mouse of a deadly strain of bacteria that had been heat-killed transferred genetic information to a safe strain of the same bacteria, killing the mouse.

In 1941, George Wells Beadle and Edward Lawrie Tatum showed that mutations in genes caused errors in certain steps in metabolic pathways. This showed that specific genes code for specific proteins, leading to the "one gene, one enzyme" hypothesis. [10] Oswald Avery, Collin Macleod, and Maclyn McCarty showed in 1944 that DNA holds the gene's information. In 1953, James D. Watson and Francis Crick demonstrated the molecular structure of DNA. Together, these discoveries established the central dogma of molecular biology, which states that proteins are translated from RNA which is transcribed from DNA. This dogma has since been shown to have exceptions, such as reverse transcription in retroviruses.

In 1972, Walter Fiers and his team at the Laboratory of Molecular Biology of the University of Ghent (Ghent, Belgium) were the first to determine the sequence of a gene: the gene for Bacteriophage MS2 coat protein.[11] Richard J. Roberts and Phillip Sharp discovered in 1977 that genes can be split into segments. This leads to the idea that one gene can make several proteins. Recently (as of 2003-2006), biological results let the notion of gene appear more slippery. In particular, genes do not seem to sit side by side on DNA like discrete beads. Instead, regions of the DNA producing distinct proteins may overlap, so that the idea emerges that "genes are one long continuum".[1]

Mendelian inheritance and classical genetics

Darwin used the term Gemmule to describe a microscopic unit of inheritance, and what would later become known as Chromosomes had been observed separating out during cell division by Wilhelm Hofmeister as early as 1848. The idea that chromosomes were the carriers of inheritance was expressed in 1883 by Wilhelm Roux. The modern conception of the gene originated with work by Gregor Mendel, a 19th century Augustinian monk who systematically studied heredity in pea plants. Mendel's work was the first to illustrate particulate inheritance, or the theory that inherited traits are passed from one generation to the next in discrete units that interact in well-defined ways. Danish botanist Wilhelm Johannsen coined the word "gene" in 1909 to describe these fundamental physical and functional units of heredity,[12] while the related word genetics was first used by William Bateson in 1905.[10] The word was derived from Hugo De Vries' 1889 term pangen for the same concept [9], itself a derivative of the word pangenesis coined by Darwin (1868).[13] The word pangenesis is made from the Greek words pan (a prefix meaning "whole", "encompassing") and genesis ("birth") or genos ("origin").

According to the theory of Mendelian inheritance, variations in phenotype - the observable physical and behavioral characteristics of an organism - are due to variations in genotype, or the organism's particular set of genes, each of which specifies a particular trait. Different genes for the same trait, which give rise to different phenotypes, are known as alleles. Organisms such as the pea plants Mendel worked on, along with many plants and animals, have two alleles for each trait, one inherited from each parent. Alleles may be dominant or recessive; dominant alleles give rise to their corresponding phenotypes when paired with any other allele for the same trait, while recessive alleles give rise to their corresponding phenotype only when paired with another copy of the same allele. For example, if the allele specifying tall stems in pea plants is dominant over the allele specifying short stems, then pea plants that inherit one tall allele from one parent and one short allele from the other parent will also have tall stems. Mendel's work found that alleles assort independently in the production of gametes, or germ cells, ensuring variation in the next generation.

Prior to Mendel's work, the dominant theory of heredity was one of blending inheritance, which proposes that the traits of the parents blend or mix in a smooth, continuous gradient in the offspring. Although Mendel's work was largely unrecognized after its first publication in 1866, it was rediscovered in 1900 by three European scientists, Hugo de Vries, Carl Correns, and Erich von Tschermak, who had reached similar conclusions from their own research. However, these scientists were not yet aware of the identity of the 'discrete units' on which genetic material resides.

A series of subsequent discoveries led to the realization decades later that chromosomes within cells are the carriers of genetic material, and that they are made of DNA (deoxyribonucleic acid), a polymeric molecule found in all cells on which the 'discrete units' of Mendelian inheritance are encoded. The modern study of genetics at the level of DNA is known as molecular genetics and the synthesis of molecular genetics with traditional Darwinian evolution is known as the modern evolutionary synthesis.

Physical definitions

The chemical structure of a four-base fragment of a DNA double helix.

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.

RNA genes

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.[14] While RNA is common as genetic storage material in viruses, in mammals in particular RNA inheritance has been observed very rarely.

Functional structure of a gene

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 (they are spliced out before translation).

Chromosomes

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.[15]

While the chromosomes of prokaryotes are relatively gene-dense, those of eukaryotes often contain so-called "junk DNA", or regions of DNA that serve no obvious function. Simple single-celled eukaryotes have relatively small amounts of such DNA, while the genomes of complex multicellular organisms, including humans, contain an absolute majority of DNA without an identified function.[6] However it now appears that, although protein-coding DNA makes up barely 2% of the human genome, about 80% of the bases in the genome may be being expressed, so the term "junk DNA" may be a misnomer.Cite error: A <ref> tag is missing the closing </ref> (see the help page). Computational gene finding methods are still significantly more reliable than earlier techniques that required mapping the locations of specific mutations that gave rise to distinguishable alleles.[8]

In most eukaryotic species, very little of the DNA in the genome encodes proteins, and the genes may be separated by vast regions of non-coding DNA, much of which has been labeled "junk DNA" due to its apparent lack of function in the modern organism. A commonly studied type of "junk DNA" is the pseudogenes, or region of non-coding DNA that resembles expressed genes but usually lacks appropriate promoters and other control sequences; such regions are hypothesized to be the results of gene duplication events in a lineage's evolutionary past.[16] 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.

Genetic and genomic nomenclature

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.

Evolutionary concept of a gene

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.

The gene concept is still changing

The concept of the gene has changed considerably (see history section). Originally considered a "unit of inheritance" 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.[10]

And the definition of gene is still changing. The first cases of RNA-based inheritance have been discovered in mammals.[14] In plants, cases of traits reappearing after several generation of absence have lead researchers to hypothesise RNA-directed overwriting of genomic DNA.[17] Evidence is also accumulating that the control regions of a gene do not necessarily have to be close to the coding sequence on the linear molecule or even on the same chromosome. Spilianakis and colleagues discovered that the promoter region of the interferon-gamma gene on chromosome 10 and the regulatory regions of the T(H)2 cytokine locus on chromosome 11 come into close proximity in the nucleus possibly to be jointly regulated.[18]

The concept that genes are clearly limited is also being eroded. There is evidence for fused proteins stemming from two adjacent genes that can produce two separate protein products. While it is not clear whether these fusion proteins are functional, the phenomena is more frequent than previously thought.[19] Even more ground-breaking than the discovery of fused genes is the observation that some proteins can be composed of exons from far away regions and even different chromosomes.[20][2] This new data has led to an updated, and probably tentative, definition of a gene as "a union of genomic sequences encoding a coherent set of potentially overlapping functional products."[10] This new definition categorizes genes by functional products, whether they be proteins or RNA, rather than specific DNA loci; all regulatory elements of DNA are therefore classified as gene-associated regions.[10]

See also

References

  1. ^ a b Pearson H (2006). "Genetics: what is a gene?". Nature. 441 (7092): 398–401. PMID 16724031.
  2. ^ a b Elizabeth Pennisi (2007). "DNA Study Forces Rethink of What It Means to Be a Gene". Science. 316 (5831): 1556–1557.
  3. ^ see eg Martin Nowak's Evolutionary Dynamics
  4. ^ Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M (2007). "What is a gene, post-ENCODE? History and updated definition". Genome Research. 17 (6): 669–681. PMID 17567988.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  5. ^ Cavalier-Smith T. (1985). Eukaryotic gene numbers, non-coding DNA, and genome size. In Cavalier-Smith T, ed. The Evolution of Genome Size Chichester: John Wiley.
  6. ^ a b International Human Genome Sequencing Consortium (2004). "Finishing the euchromatic sequence of the human genome". Nature. 431 (7011): 931–45. PMID 15496913.
  7. ^ Pennisi, Elizabeth (2007). "Working the (Gene Count) Numbers_ Finally, a Firm Answer". Science. 316 (5828): 1113.
  8. ^ a b Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R (2004). Molecular Biology of the Gene (5th ed. ed.). Peason Benjamin Cummings (Cold Spring Harbor Laboratory Press). ISBN 080534635X. {{cite book}}: |edition= has extra text (help)CS1 maint: multiple names: authors list (link)
  9. ^ a b Vries, H. de (1889) Intracellular Pangenesis [1] ("pangen" definition on page 7 and 40 of this 1910 translation in English)
  10. ^ a b c d e Mark B. Gerstein et al., "What is a gene, post-ENCODE? History and updated definition," Genome Research 17(6) (2007): 669-681
  11. ^ Min Jou W, Haegeman G, Ysebaert M, Fiers W (1972). "Nucleotide sequence of the gene coding for the bacteriophage MS2 coat protein". Nature. 237 (5350): 82–8. PMID 4555447.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  12. ^ "The Human Genome Project Timeline". Retrieved 2006-09-13.
  13. ^ Darwin C. (1868). Animals and Plants under Domestication (1868).
  14. ^ a b Rassoulzadegan M, Grandjean V, Gounon P, Vincent S, Gillot I, Cuzin F (2006). "RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse". Nature. 441 (7092): 469–74. PMID 16724059.{{cite journal}}: CS1 maint: multiple names: authors list (link) Cite error: The named reference "rass" was defined multiple times with different content (see the help page).
  15. ^ Braig M, Schmitt C (2006). "Oncogene-induced senescence: putting the brakes on tumor development". Cancer Res. 66 (6): 2881–4. PMID 16540631.
  16. ^ Lodish, H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipursky SL, Darnell J. (2004). Molecular Cell Biology, 5th, New York: WH Freeman.
  17. ^ Lolle & colleagues (2005) Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis. PMID 15785770
  18. ^ Spilianakis & colleagues (2005) Interchromosomal associations between alternatively expressed loci. PMID 15880101
  19. ^ Parra & colleagues (2006) Tandem chimerism as a means to increase protein complexity in the human genome. PMID 16344564
  20. ^ Kapranov & colleagues (2005) Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. PMID 15998911

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