Gene

:''For the band called Gene, see Gene (band)'' [[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). Introns are regions often found in eukaryote genes which are removed in the splicing (genetics) process: only the exons encode the protein. This diagram labels a region of only 40 or so bases as a gene. In reality many genes are much larger.]] Genes are entity that parenting pass to offspring during reproduction. These entities code information essential for the construction and regulation of proteins (such as enzymes) and other molecules that determine the growth and functioning of the organism. The word "gene" is shared by many disciplines, including classical genetics, molecular genetics, evolutionary biology and population genetics. Because each discipline models the biology of life differently, the usage of the word gene varies between disciplines. It may refer to either material or conceptual entities. Following the discovery that DNA is the genetic material, and with the growth of biotechnology and the project to sequencing the human genome, the common usage of the word "gene" has increasingly reflected its meaning in molecular biology. In the molecular-biological sense, genes are the segments of DNA which cell (biology) transcription into RNA and translation (biology), at least in part, into proteins. In common speech, "gene" is often used to refer to the heredity cause of a trait, disease or condition—as in "the gene for obesity." Speaking more precisely, a biologist might refer to an allele or a mutation that ''has been implicated in'' or ''is associated with'' obesity. This is because biologists know that many factors other than genes decide whether a person is obese or not: prenatal environment, upbringing, culture and the availability of food, for example. Moreover, it is very unlikely that variations within a single gene—or single genetic locus—fully determine one's genetic predisposition for obesity. These aspects of inheritance—the interplay between genes and environment, the influence of many genes—appear to be the norm with regard to many and perhaps most ("complex" or "multifactoral") traits. The term phenotype refers to the characteristics that result from this interplay (see genotype-phenotype distinction). ==Overview== ===Properties of genes=== In molecular biology, the DNA of a gene encodes the chemical structure of a protein. The genetic code determines the sequence of the amino acids that make up a protein. The coding of a three nucleotide DNA sequence to a specific amino acid is essentially the same for all known life, from bacterium to human. Through the proteins they encode, genes govern the cells in which they reside. In multicellular organism they control the morphogenesis of the individual from the fertilization Ovum and the day-to-day functions of the cells that make up biological tissues and organ (anatomy)s. The instrumental roles of their protein products range from mechanical support of the cell structure to the transportation and manufacture of other molecules and to the regulation of other proteins' activities. The genes that exist today are those that have reproduced successfully in the past. Often, many individual organisms share a gene; thus, the death of an individual need not mean the extinction of the gene. Indeed, if the sacrifice of one individual enhances the survivability of other individuals with the same gene, the death of an individual may enhance the overall survival of the gene. This is the basis of the selfish gene view, popularized by Richard Dawkins. He points out in his book, ''The Selfish Gene'', that to be successful genes need have no other "purpose" than to selfish DNA, even at the expense of their host organism's welfare. A human that behaved in such a way would be described as "selfish," although ironically a selfish gene may promote altruism behaviors. According to Dawkins, the possibly disappointing answer to the question "what is the meaning of life?" may be "the survival and perpetuation of ribonucleic acids and their associated proteins". ===Types of genes=== Due to rare, spontaneous errors (e.g. in DNA replication) mutations in the sequence of a gene may arise. Once propagated to the next generation, this mutation may lead to variations within a species' population. Variants of a single gene are known as alleles, and differences in alleles may give rise to differences in traits, for example eye color. A gene's most common allele is called the wild type allele, and rare alleles are called mutants. Normally, RNA is an intermediate product in the translation of a molecular gene into a protein. However, for some gene sequences, RNA molecules are actually the functional end products. For example, RNAs known as ribozyme are capable of enzyme, or siRNA have a regulatory role. The DNA sequences from which such RNAs are transcribed are known as non-coding RNA, or RNA genes. All living organisms carry their genes and transmit them to offspring as DNA, but some viruses carry only RNA. Because they use RNA, 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 AIDS, require the reverse transcription of their genome from RNA into DNA before their proteins can be synthesized. ===Human gene nomenclature === For each known human gene the HUGO Gene Nomenclature Committee (HGNC) approve a gene name and symbol (short-form abbreviation). All approved symbols are stored in [http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl Genew], the Human Gene Nomenclature 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 data retrieval from publications. In preference each symbol maintains parallel construction in different members of a gene family and can also be used in other species, especially the mouse. ===Typical numbers of genes in an organism=== The following table gives typical numbers of genes and genome size for some organisms. Estimates of the number of genes in an organism are somewhat controversial, because it is only possible to discover a gene, and no techniques currently exist to prove that a DNA sequence contains no gene. Nonetheless, estimates are made based on current knowledge. {| border="1" cellpadding="2" |- ! organism ! genes ! base pairs |- | Plant | <50,000 | <10¹¹ |- | Human | 25,000 | 3×10⁹ |- | Fly | 12,000 | 1.6×10⁸ |- | Honey bee | 15,000 | 3×10⁸ |- | Caenorhabditis elegans | 19,000 | 9.7×10⁷ |- | Fungus | 6,000 | 1.3×10⁷ |- | Bacterium | 500–6,000 | 5×10⁵–10⁷ |- | Mycoplasma genitalium | 500 | 580,000 |- | DNA virus | 10–900 | 5,000–800,000 |- | RNA virus | 1–25 | 1,000–23,000 |- | Viroid | 0–1 | ~500 |- |} ==Chemistry and function of genes== ===Chemical structure of a gene=== Four kinds of sequentially linked nucleotides compose a DNA molecule or strand (more at DNA). These four nucleotides constitute the genetic alphabet. A sequence of three consecutive nucleotides, called a codon, is the protein-coding vocabulary. The sequence of codons in a gene specifies the amino acid sequence of the protein it encodes. In most Eukaryote species, very little of the DNA in the genome encodes proteins, and the genes may be separated by vast sequences of so-called junk DNA. Moreover, the genes are often fragmented internally by non-coding sequences called introns, which can be many times longer than the genes themselves. Introns are removed on the heels of transcription (genetics) by splicing. In the primary molecular sense they represent parts of a gene, however. All the genes and intervening DNA together make up the genome of an organism, which in many species is divided among several chromosomes and typically present in two or more copies. 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 Sex-determination system. Many species carry more than one copy of their genome within each of their somatic cells. These organisms are called diploid if they have two copies, or polyploid if they have more than two copies. In such organisms, the copies are practically never identical. With respect to each gene, the copies that an individual possesses are liable to be distinct alleles, which may act synergistically or antagonistically to generate a trait or phenotype. The ways that gene copies interact are explained by chemical dominance relationships (more at genetics, allele). === Expression of molecular genes=== For various reasons, the relationship between DNA strand and a phenotype trait is not direct. The same DNA strand in 2 different individuals may result in different traits because of the effect of other DNA strands or the environment. * The DNA strand is expressed into a trait only if it is Transcription (genetics) to RNA. Because the transcription starts from a specific base-pair sequence (a promoter) and stops at another (a Terminator_%28genetics%29), our DNA strand needs to be correctly placed between the two. If not, it is considered as junk DNA, and is not expressed. * Cells regulate the activity of genes in part by increasing or decreasing their rate of transcription. Over the short term, this regulation occurs through the binding or unbinding of proteins, known as transcription factors, to specific non-coding DNA sequences called regulatory sequence. So, to be expressed, our DNA strand needs to be properly regulated by other DNA strands. * The DNA strand may also be Gene silencing through DNA methylation or by chemical changes to the protein components of chromosomes (see histone). This is a permanent form of regulation of the transcription. * The RNA is often edited before its translation into a protein. Eukaryotic cells splicing the transcripts of a gene, by keeping the exons and removing the introns. So, the DNA strand needs to be in an exon to be expressed. Because of the complexity of the splicing process, one transcribed RNA may be spliced in alternate ways to produce not one but a variety of proteins (alternative splicing) from one pre-mRNA. Prokaryotes produce a similar effect by shifting reading frames during translation. * The translation (genetics) of RNA into a protein also starts with a specific start and stop sequence. * Once produced, the protein interacts with the many other proteins in the cell, according to the cell metabolism. This interaction finally produces the trait. This complex process helps explain the different meanings of "gene": * a nucleotide sequence in a DNA strand; * or the transcribed RNA, prior to splicing; * or the transcribed RNA after splicing, i.e. without the introns The latter meaning of gene is the result of more "material entity" than the first one. === Mutations and evolution === Just as there are many factors influencing the expression of a particular DNA strand, there are many ways to have genetic mutations. For example, natural variations within ''regulatory sequences'' appear to underlie many of the heritable characteristics seen in organisms. The influence of such variations on the trajectory of evolution through natural selection may be as large as or larger than variation in sequences that encode proteins. Thus, though regulatory elements are often distinguished from genes in molecular biology, in effect they satisfy the shared and historical sense of the word. Indeed, a breeder or geneticist, in following the inheritance pattern of a trait, has no immediate way to know whether this pattern arises from coding sequences or regulatory sequences. Typically, he or she will simply attribute it to variations within a gene. Errors during DNA replication may lead to the gene duplication of a gene, which may diverge over time. Though the two sequences may remain the same or be only slightly altered, they are typically regarded as separate genes (i.e. not as alleles of the same gene). The same is true when duplicate sequences appear in different species. Yet, though the alleles of a gene differ in sequence, nevertheless they are regarded as a single gene (occupying a single locus). == History == The existence of genes was first suggested by Gregor Mendel, who studied inheritance in pea plants and hypothesized a factor that conveys traits from parent to offspring. 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 finally named when Wilhelm Johannsen coined the word ''gene'' in 1909. 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 melanogaster''. 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 a 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. 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 transcribed from RNA which is translated from DNA. This dogma has since been shown to have exceptions, such as reverse transcription in retroviruses. ==See also== *Genetics, Gene expression, Gene therapy, Homeobox, Human Genome Project, Genomics, DNA, Protein, Gene family *Genetic programming, Genetic algorithm *Genomes, Genomes#Minimal genomes *Meme, Memetics *List of notable genes == References == [http://print.google.com/print?id=W0V9bya1ieUC&q=%22The+Selfish+Gene%22 Google print] ==External links== *[http://www.gene.ucl.ac.uk/hugo/ Human Genome Organisation, HUGO] *[http://www.gene.ucl.ac.uk/nomenclature HUGO Gene Nomenclature Committee, HGNC] *[http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl Genew the Human Gene Nomenclature Database] *[http://plato.stanford.edu/entries/gene/ Stanford Encyclopedia of Philosophy entry] *[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] **[http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v431/n7011/full/nature03001_fs.html Nature - 21 October 2004 - Finishing the euchromatic sequence of the human genome] Cloning Genetics Molecular biology simple:Gene th:หน่วยพันธุกรรม vi:Gene

Gene

---- *For earlier material, please go to: Talk:Gene(archive 1) */Archive 2 - up to March 2004 == Gene exactly? == The article states that "in molecular biology, a gene encodes the chemical structure of a protein". Is that one and only one protein or peptide per gene? Is a gene the amino acid code between and including start codon AUG, GUG and stop codon UAG, UGA, UAA? Thanks - User:Jerryseinfeld 08:16, 2 Oct 2004 (UTC) :In eukaryotes, the matter is far more complicated. There's alternative splicing, in which the RNA transcript can be modified post-transcriptionally into any of several different mRNAs. The issue of what a eukaryotic gene ''is'' is also somewhat more complicated as a result. Prokaryotes don't do splicing, as a general rule, so they're pretty much one-gene-one-protein beasties. Also, the regulatory sequences in noncoding regions around a gene are often very important to its function, so they might be included in the definition of a gene. User:Bryan Derksen 18:44, 2 Oct 2004 (UTC) *"genes" were for a long time theoretical entities. Chromosomes can be observed under a light microscope, so they seem to qualify as "physical entities". Molecules (including DNA), once theoretic entities, now would seem to be indirectly observable via electron-microscopes. In the scheme of things, genes would seem to be intermediate between atoms & chromosomes. I see usage of the term ''genetic material'' within a DNA molecule, but is it too early yet to say that genes can be identified as being particular pieces or strands on DNA molecules (as a string of atoms)?--User:JimWae 04:25, 2005 Mar 27 (UTC) ::It goes without saying that life breaks boundaries and defies its own conventions all the time. So our shorthand definitions, our abstractions, are going to be wrong sometimes. I don't think hard-and-fast definitions are that important, really, just delivering the broad strokes. That's pretty much how biology works - learn the broad strokes, and fill in lots and lots of nuance. We can work on filling in some of the nuance - e.g. the original query highlights the fact that RNA genes are ignored by the given definition. User:Graft 04:45, 27 Mar 2005 (UTC) I noticed some bias on the table on genes. It shows humans having the most genes and most base pairs among all the examples given. One could conclude that we are the most "advanced" specie, or that the number of genes is a sign of intelligence maturity, name it.. I'm no specialist in this field but I recall reading that there are organisms that have a higher number of genes than humans... I think that would be a good addition to the table to dismiss the notion that humans ar at the top of the scale.... 08:46, 5 Oct 2004 (UTC) == Overhaul table of gene number and genome size? == I think the table listing the gene count of different organisms is slightly misleading, and overly simplistic. Categories such as 'Plants' or 'Flies' are too wide. I think the range of genome size and gene count in plants will be substantial. Maybe the table should only show examples from specific species and actually list the species name to avoid further confusion. E.g. Arabidopsis thaliana (thale cress) 120 Mb ~25,000 Saccharoymces cerevisiae (yeast) 14 Mb, ~6,000 Drosophila melanogaster (fruit fly) .... etc. I don't mind doing this if there are no objections. Keith == kudos == A year or two ago I was active in this article and involved in various edit wars. Today is the first time I have read over it in a long, long, time -- and I want to congratulate all the people who have been working on it. While I am sure it can still be improved, I think you have really turned out a well-written, clear, comprehensive article. It restores my faith in Wikipedia, User:Slrubenstein 21:51, 7 Dec 2004 (UTC) :Regarding the Dawkins - I haven't read him, but characterizations of his description seem far too anthropomorphic. That is, DNA does not exist to selfishly propagate itself. DNA is a stupid molecule that, left to itself, would slowly degenerate into nucleic acids. But genes that are good at propagating themselves, even at the expense of their organism, will thrive and become prevalent. This isn't as succinct an idea as the "selfish gene" sentence, but it is more accurate. The question is, is this Dawkins' charcterization? User:Graft 23:00, 7 Dec 2004 (UTC) Well, I am pretty sure you are referring to the text that was there before I made my additions. I too have problems with the anthropomorphizing, but my sense is, it is in Dawkins (and anthropologists and other social critics who object to this aspect of Dawkins' work usually use this as a jumping off point, that this kind of sociobiology is just the theory of evolution refracted through contemporary bourgeoise ideology). Note there is a problem even in your phrasing, "genes that are good at propegating themselves" because of course it is not the gene that propegates itself but the organism, which involves that gene and many more and environmental and random factors. In any event, IF you want to keep in the Dawkins paragraph, the task is to represent hs views accurately, not to represent our own views. I myself am pretty critical of him, I just wanted his view to be presented more fairly. User:Slrubenstein :How ironic... hard to escape the urge to attribute intent to everything, I guess. Um, but, okay, this is all I wanted to clarify: that Dawkins actually does anthropomorphize that way. User:Graft 21:07, 8 Dec 2004 (UTC) ::It's been many years since I read The Selfish Gene, but I don't recall that Dawkins was particularly anthropomophic in his descriptions; not more than most biologists who talk about the "purpose" of some aspect of biology. I've rewritten that section to better conform to my memory. I'll try to double check a copy of the text. --User:Rikurzhen 22:03, Dec 8, 2004 (UTC) The very word "selfish" anthropomorphizes. User:Slrubenstein | User talk:Slrubenstein 20:09, 27 Mar 2005 (UTC) :"anthropomorphizes" isn't quite accurate, since non-human animals could righly be said to be selfish. Dawkins could be charged with the pathetic fallacy, but from my reading of The Selfish Gene, the term selfish isn't meant literally, but rather just to describe--by analogy to an easy to understand term--the equilibrium outcome of gene evolution. --User:Rikurzhen 22:29, Mar 27, 2005 (UTC) ::Isn't it awesome how time has almost no meaning on Wikipedia? 06:01, 28 Mar 2005 (UTC) ==Request for references== Hi, I am working to encourage implementation of the goals of the Wikipedia:Verifiability policy. Part of that is to make sure articles Wikipedia:Cite sources. This is particularly important for featured articles, since they are a prominent part of Wikipedia. The Wikipedia:WikiProject Fact and Reference Check has more information. Thank you, and please [http://en.wikipedia.org/w/wiki.phtml?title=User_talk:Taxman&action=edit§ion=new leave me a message] when you have added a few references to the article. - User:Taxman 18:55, Apr 21, 2005 (UTC)

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