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Gene
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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: 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.
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: 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.
Genetics glossary
A-F[show]
Adenine[show]

One of the four nucleotide bases in DNA or RNA; pairs with thymine in DNA or uracil in RNA.
Allele[show]

One of multiple alternative forms of a single gene, each of which is a viable DNA sequence occupying a given position, or locus on a chromosome. For example, in humans, one allele of the eye-color gene produces blue eyes and another allele of the eye-color gene produces brown eyes.
Base pair[show]

A pair of nucleotide bases on complementary DNA or RNA strands organized in a double helix.
Chromosome[show]

A molecular "package" for carrying DNA in cells, organized as two double-helical DNA molecules that encode many genes. Some simple organisms have only one chromosome made of circular DNA, while most eukaryotes have multiple chromosomes made of linear DNA.
Cytosine[show]

One of the four nucleotide bases in DNA or RNA; pairs with guanine.
DNA[show]

A polymeric molecule made of deoxyribonucleotides, hence then name deoxyribonucleic acid. Most often has the form of a "double helix", which consists of two paired DNA molecules and resembles a ladder that has been twisted. The "rungs" of the ladder are made of base pairs, or nucleotides with complementary hydrogen bonding patterns.
G-Z[show]
Gene[show]

The unit of heredity in living organisms, typically encoded in a sequence of nucleotide monomers that make up a long strand of DNA, or deoxyribonucleic acid. A particular gene can have multiple different forms, or alleles, which are defined by different sequences of DNA.
Gene expression[show]

The process in which the infomation encoded in a gene is converted into a form useful for the cell. The first step is transcription, which produces a messenger RNA molecule complementary to the DNA molecule on which a gene is encoded. For protein-coding genes, the second step is translation, in which the messenger RNA is read by the ribosome to produce a protein.
Gene pool[show]

The sum of all the alleles shared by members of a single population.
Genetics[show]

The field of biology that studies genes and their inheritance.
Genome[show]

The total complement of genetic material contained in an organism or cell.
Genotype[show]

The complement of alleles present in a particular individual's genome that give rise to the individual's phenotype.
Guanine[show]

One of the four nucleotide bases in DNA or RNA; pairs with cytosine.
Locus[show]

A location on a chromosome where a particular gene resides.
Phenotype[show]

The observable physical or behavioral traits of an organism, largely determined by the organism's genotype.
Protein[show]

A linear polymeric molecule made of of amino acids linked by peptide bonds. Proteins carry out the majority of chemical reactions that occur inside the cell.
RNA[show]

A polymeric molecule made of ribonucleotides, hence the name ribonucleic acid, similar to but less stable than DNA. One type, messenger RNA, plays an important role in gene expression. Ribosomes are also made largely of RNA.
Thymine[show]

One of the four nucleotide bases in DNA; pairs with adenine. In RNA, thymine is replaced with uracil.
Transcription[show]

The first step in gene expression, in which a messenger RNA molecule complementary to particular gene encoded in DNA is synthesized by enzymes called RNA polymerases. To produce a functional protein, transcription is followed by translation.
translation[show]

The second step in gene expression, in which a messenger RNA molecule is read by the ribosome to produce a functional protein. Translation is always preceded by transcription.
Uracil[show]

One of the four nucleotide bases in RNA; pairs with adenine. In DNA, uracil is replaced with thymine.
For other meanings of this term, see gene (disambiguation).
For a non-technical introduction to the topic, please see Introduction to genetics.

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] Genes interact with each other to influence physical development and behavior. Genes consist of a long strand of DNA (RNA in some viruses) 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 loosely dependent on its complexity; 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. However, the largest known genome belongs to the single-celled amoeba Amoeba dubia, with over 6 billion base pairs.[2] 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.[3] 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.[4]
Contents
[hide]

    * 1 Mendelian inheritance and classical genetics
    * 2 Physical definitions
          o 2.1 RNA genes
          o 2.2 Functional structure of a gene
          o 2.3 Chromosomes
    * 3 Gene expression
          o 3.1 Genetic code
          o 3.2 Transcription
          o 3.3 Translation
    * 4 DNA replication and inheritance
          o 4.1 Molecular inheritance
          o 4.2 Mutation
    * 5 The genome
          o 5.1 Chromosomal organization
          o 5.2 Composition of the genome
          o 5.3 Genetic and genomic nomenclature
    * 6 Evolutionary concept of a gene
    * 7 History
    * 8 See also
    * 9 References
    * 10 Further reading
    * 11 External links
          o 11.1 Tutorial and news
          o 11.2 References and databases

[edit] Mendelian inheritance and classical genetics

    Main articles: Mendelian inheritance and Classical genetics

The modern conception of the gene originated with work by Gregor Mendel, a 19th century Austrian 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.[5] The word was derived from Hugo De Vries' term pangen, itself a derivative of the word pangenesis coined by Darwin (1868).[6] 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.

[edit] Physical definitions
The chemical structure of a four-base fragment of a DNA double helix.
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, cytosine, 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, cytidine, 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 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.

[edit] 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 researcher 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.[7] While RNA is common as genetic storage material in viruses, in mammals in particular RNA inheritance has been observed very rarely.

[edit] 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, 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.

[edit] 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.[8]

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.[3]

[edit] Gene expression

    Main article: 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 transcribed from DNA to messenger RNA (mRNA), and second, it must be 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.

[edit] Genetic code
Schematic diagram of a single-stranded RNA molecule illustrating the position of three-base codons.
Schematic diagram of a single-stranded RNA molecule illustrating the position of three-base codons.

    Main article: 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 codons, 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.

[edit] Transcription

The process of genetic transcription produces a single-stranded RNA molecule known as messenger RNA, whose nucleotide sequence is complementary to the DNA from which it was transcribed. The DNA strand whose sequence matches that of the RNA is known as the coding strand and the strand from which the RNA was synthesized is the template strand. Transcription is performed by an enzyme called an RNA polymerase, which reads the template strand in the 3' to 5' direction and synthesizes the RNA from 5' to 3'. To initiate transcription,the polymerase first recognizes and binds a promoter region of the gene. Thus a major mechanism of gene regulation is the blocking or sequestering of the promoter region, either by tight binding by repressor molecules that physically block the polymerase, or by organizing the DNA so that the promoter region is not accessible.

In prokaryotes, transcription occurs in the cytoplasm; for very long transcripts, translation may begin at the 5' end of the RNA while the 3' end is still being transcribed. In eukaryotes, transcription necessarily occurs in the nucleus, where the cell's DNA is sequestered; the RNA molecule produced by the polymerase is known as the primary transcript and must undergo post-transcriptional modifications before being exported to the cytoplasm for translation. The splicing of introns present within the transcribed region is a modification unique to eukaryotes; alternative splicing mechanisms can result in mature transcripts from the same gene having different sequences and thus coding for different proteins. This is a major form of regulation in eukaryotic cells.

[edit] Translation

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

[edit] DNA replication and inheritance

The growth, development, and reproduction of organisms relies on cell division, or the process by which a single cell divides into two usually identical daughter cells. This requires first making a duplicate copy of every gene in the genome in a process called DNA replication. The copies are made by specialized enzymes known as DNA polymerases, which "read" one strand of the double-helical DNA, known as the template strand, and synthesize a new complementary strand. Because the DNA double helix is held together by base pairing, the sequence of one strand completely specifies the sequence of its complement; hence only one strand needs to be read by the enzyme to produce a faithful copy. The process of DNA replication is semiconservative; that is, the copy of the genome inherited by each daughter cell contains one original and one newly synthesized strand of DNA.[4]

After DNA replication is complete, the cell must physically separate the two copies of the genome and divide into two distinct membrane-bound cells. In prokaryotes - bacteria and archaea - this usually occurs via a relatively simple process called binary fission, in which each circular genome attaches to the cell membrane and is separated into the daughter cells as the membrane invaginates to split the cytoplasm into two membrane-bound portions. Binary fission is extremely fast compared to the rates of cell division in eukaryotes. Eukaryotic cell division is a more complex process known as the cell cycle; DNA replication occurs during a phase of this cycle known as S phase, while the process of segregating chromosomes and splitting the cytoplasm occurs during M phase. In many single-celled eukaryotes such as yeast, reproduction by budding is common, which results in asymmetrical portions of cytoplasm in the two daughter cells.

[edit] 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 asexually reproducing organisms, the offspring will be a genetic copy or clone of the parent organism. In sexually reproducing organisms, a specialized form of cell division called meiosis produces cells called gametes or germ cells that are haploid, or contain only one copy of each gene. The gametes produced by females are called eggs or ova, and those produced by males are called sperm. Two gametes fuse to form a fertilized egg, a single cell that once again has a diploid number of genes - each with one copy from the mother and one copy from the father.

During the process of meiotic cell division, an event called genetic recombination or crossing-over can sometimes occur, in which a length of DNA on one chromatid is swapped with a length of DNA on the corresponding sister chromatid. This has no effect if the alleles on the chromatids are the same, but results in reassortment of otherwise linked alleles if they are different. The Mendelian principle of independent assortment asserts that each of a parent's two genes for each trait will sort independently into gametes; which allele an organism inherits for one trait is unrelated to which allele it inherits for another trait. This is in fact only true for genes that do not reside on the same chromosome, or are located very far from one another on the same chromosome. The closer two genes lie on the same chromosome, the more closely they will be associated in gametes and the more often they will appear together; genes that are very close are essentially never separated because it is extremely unlikely that a crossover point will occur between them. This is known as genetic linkage.

[edit] Mutation

    Main article: Mutation

DNA replication is for the most part extremely accurate, with an error rate per site of around 10-6 to 10-10 in eukaryotes.[4] 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 mutations. 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.

Mutations propagated to the next generation 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. 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 mutants. However, this does not imply that the wild-type allele is the ancestor from which the mutants are descended.

[edit] The genome

[edit] Chromosomal organization

The total complement of genes in an organism or cell is known as its genome. In prokaryotes, the vast majority of genes are located on a single chromosome of circular DNA, while eukaryotes usually possess multiple individual linear DNA helices packed into dense DNA-protein complexes called chromosomes. Extrachromosomal DNA is present in many prokaryotes and some simple eukaryotes as small, circular pieces of DNA called plasmids, which usually contain only a few genes each. Generally, regulatory regions and junk DNA are considered to be part of an organism's genome, but structural regions such as telomeres are not. The location (or locus) of a gene and the chromosome on which it is situated is in a sense arbitrary. Genes that appear together on the chromosomes of one species, such as humans, may appear on separate chromosomes in another species, such as mice. Two genes positioned near one another on a chromosome may encode proteins that figure in the same cellular process or in completely unrelated processes. As an example of the former, many of the genes involved in spermatogenesis reside together on the Y chromosome.

Many species carry more than one copy of their genome within each of their somatic cells. Cells or organisms with only one copy of each gene are called haploid; those with two copies are called diploid; and those with more than two copies are called polyploid. When more than one copy is present, the two copies are not necessarily identical; in sexually reproducing organisms, one copy is normally inherited from each parent. The copies may contain distinct DNA sequences encoding distinct alleles.

[edit] Composition of the genome
+Gene content and genome size of various organisms[4]
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
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 genomes vary widely among organisms, even those that are fairly closely evolutionarily related. Although it was believed before the completion of the Human Genome Project that the human genome would contain many more genes than simpler animals such as mice or fruit flies, the completion of the project has revealed that the human genome has an unexpectedly low gene density.[3] Estimates of the number of genes in a genome are difficult to compile because they depend on gene finding algorithms that search for patterns resembling those present in known genes, such as open reading frames, promoter regions with sequences resembling the consensus promoter sequence, and related regulatory regions such as TATA boxes in eukaryotes. Gene finding is less reliable in eukaryotic than in prokaryotic genomes due to the presence of non-coding DNA such as introns and pseudogenes.[9] 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.[4]

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.[10] 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.

[edit] Genetic and genomic 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 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.

[edit] 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 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.

[edit] History

    Main article: 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 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 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. 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. 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 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]

Xblade-3o5- wrote:

Gene
From Wikipedia, the free encyclopedia
(Redirected from Genes)
Jump to: navigation, search
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: 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.
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: 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.
Genetics glossary
A-F[show]
Adenine[show]

One of the four nucleotide bases in DNA or RNA; pairs with thymine in DNA or uracil in RNA.
Allele[show]

One of multiple alternative forms of a single gene, each of which is a viable DNA sequence occupying a given position, or locus on a chromosome. For example, in humans, one allele of the eye-color gene produces blue eyes and another allele of the eye-color gene produces brown eyes.
Base pair[show]

A pair of nucleotide bases on complementary DNA or RNA strands organized in a double helix.
Chromosome[show]

A molecular "package" for carrying DNA in cells, organized as two double-helical DNA molecules that encode many genes. Some simple organisms have only one chromosome made of circular DNA, while most eukaryotes have multiple chromosomes made of linear DNA.
Cytosine[show]

One of the four nucleotide bases in DNA or RNA; pairs with guanine.
DNA[show]

A polymeric molecule made of deoxyribonucleotides, hence then name deoxyribonucleic acid. Most often has the form of a "double helix", which consists of two paired DNA molecules and resembles a ladder that has been twisted. The "rungs" of the ladder are made of base pairs, or nucleotides with complementary hydrogen bonding patterns.
G-Z[show]
Gene[show]

The unit of heredity in living organisms, typically encoded in a sequence of nucleotide monomers that make up a long strand of DNA, or deoxyribonucleic acid. A particular gene can have multiple different forms, or alleles, which are defined by different sequences of DNA.
Gene expression[show]

The process in which the infomation encoded in a gene is converted into a form useful for the cell. The first step is transcription, which produces a messenger RNA molecule complementary to the DNA molecule on which a gene is encoded. For protein-coding genes, the second step is translation, in which the messenger RNA is read by the ribosome to produce a protein.
Gene pool[show]

The sum of all the alleles shared by members of a single population.
Genetics[show]

The field of biology that studies genes and their inheritance.
Genome[show]

The total complement of genetic material contained in an organism or cell.
Genotype[show]

The complement of alleles present in a particular individual's genome that give rise to the individual's phenotype.
Guanine[show]

One of the four nucleotide bases in DNA or RNA; pairs with cytosine.
Locus[show]

A location on a chromosome where a particular gene resides.
Phenotype[show]

The observable physical or behavioral traits of an organism, largely determined by the organism's genotype.
Protein[show]

A linear polymeric molecule made of of amino acids linked by peptide bonds. Proteins carry out the majority of chemical reactions that occur inside the cell.
RNA[show]

A polymeric molecule made of ribonucleotides, hence the name ribonucleic acid, similar to but less stable than DNA. One type, messenger RNA, plays an important role in gene expression. Ribosomes are also made largely of RNA.
Thymine[show]

One of the four nucleotide bases in DNA; pairs with adenine. In RNA, thymine is replaced with uracil.
Transcription[show]

The first step in gene expression, in which a messenger RNA molecule complementary to particular gene encoded in DNA is synthesized by enzymes called RNA polymerases. To produce a functional protein, transcription is followed by translation.
translation[show]

The second step in gene expression, in which a messenger RNA molecule is read by the ribosome to produce a functional protein. Translation is always preceded by transcription.
Uracil[show]

One of the four nucleotide bases in RNA; pairs with adenine. In DNA, uracil is replaced with thymine.
For other meanings of this term, see gene (disambiguation).
For a non-technical introduction to the topic, please see Introduction to genetics.

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] Genes interact with each other to influence physical development and behavior. Genes consist of a long strand of DNA (RNA in some viruses) 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 loosely dependent on its complexity; 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. However, the largest known genome belongs to the single-celled amoeba Amoeba dubia, with over 6 billion base pairs.[2] 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.[3] 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.[4]
Contents
[hide]

    * 1 Mendelian inheritance and classical genetics
    * 2 Physical definitions
          o 2.1 RNA genes
          o 2.2 Functional structure of a gene
          o 2.3 Chromosomes
    * 3 Gene expression
          o 3.1 Genetic code
          o 3.2 Transcription
          o 3.3 Translation
    * 4 DNA replication and inheritance
          o 4.1 Molecular inheritance
          o 4.2 Mutation
    * 5 The genome
          o 5.1 Chromosomal organization
          o 5.2 Composition of the genome
          o 5.3 Genetic and genomic nomenclature
    * 6 Evolutionary concept of a gene
    * 7 History
    * 8 See also
    * 9 References
    * 10 Further reading
    * 11 External links
          o 11.1 Tutorial and news
          o 11.2 References and databases

[edit] Mendelian inheritance and classical genetics

    Main articles: Mendelian inheritance and Classical genetics

The modern conception of the gene originated with work by Gregor Mendel, a 19th century Austrian 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.[5] The word was derived from Hugo De Vries' term pangen, itself a derivative of the word pangenesis coined by Darwin (1868).[6] 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.

[edit] Physical definitions
The chemical structure of a four-base fragment of a DNA double helix.
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, cytosine, 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, cytidine, 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 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.

[edit] 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 researcher 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.[7] While RNA is common as genetic storage material in viruses, in mammals in particular RNA inheritance has been observed very rarely.

[edit] 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, 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.

[edit] 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.[8]

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.[3]

[edit] Gene expression

    Main article: 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 transcribed from DNA to messenger RNA (mRNA), and second, it must be 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.

[edit] Genetic code
Schematic diagram of a single-stranded RNA molecule illustrating the position of three-base codons.
Schematic diagram of a single-stranded RNA molecule illustrating the position of three-base codons.

    Main article: 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 codons, 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.

[edit] Transcription

The process of genetic transcription produces a single-stranded RNA molecule known as messenger RNA, whose nucleotide sequence is complementary to the DNA from which it was transcribed. The DNA strand whose sequence matches that of the RNA is known as the coding strand and the strand from which the RNA was synthesized is the template strand. Transcription is performed by an enzyme called an RNA polymerase, which reads the template strand in the 3' to 5' direction and synthesizes the RNA from 5' to 3'. To initiate transcription,the polymerase first recognizes and binds a promoter region of the gene. Thus a major mechanism of gene regulation is the blocking or sequestering of the promoter region, either by tight binding by repressor molecules that physically block the polymerase, or by organizing the DNA so that the promoter region is not accessible.

In prokaryotes, transcription occurs in the cytoplasm; for very long transcripts, translation may begin at the 5' end of the RNA while the 3' end is still being transcribed. In eukaryotes, transcription necessarily occurs in the nucleus, where the cell's DNA is sequestered; the RNA molecule produced by the polymerase is known as the primary transcript and must undergo post-transcriptional modifications before being exported to the cytoplasm for translation. The splicing of introns present within the transcribed region is a modification unique to eukaryotes; alternative splicing mechanisms can result in mature transcripts from the same gene having different sequences and thus coding for different proteins. This is a major form of regulation in eukaryotic cells.

[edit] Translation

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

[edit] DNA replication and inheritance

The growth, development, and reproduction of organisms relies on cell division, or the process by which a single cell divides into two usually identical daughter cells. This requires first making a duplicate copy of every gene in the genome in a process called DNA replication. The copies are made by specialized enzymes known as DNA polymerases, which "read" one strand of the double-helical DNA, known as the template strand, and synthesize a new complementary strand. Because the DNA double helix is held together by base pairing, the sequence of one strand completely specifies the sequence of its complement; hence only one strand needs to be read by the enzyme to produce a faithful copy. The process of DNA replication is semiconservative; that is, the copy of the genome inherited by each daughter cell contains one original and one newly synthesized strand of DNA.[4]

After DNA replication is complete, the cell must physically separate the two copies of the genome and divide into two distinct membrane-bound cells. In prokaryotes - bacteria and archaea - this usually occurs via a relatively simple process called binary fission, in which each circular genome attaches to the cell membrane and is separated into the daughter cells as the membrane invaginates to split the cytoplasm into two membrane-bound portions. Binary fission is extremely fast compared to the rates of cell division in eukaryotes. Eukaryotic cell division is a more complex process known as the cell cycle; DNA replication occurs during a phase of this cycle known as S phase, while the process of segregating chromosomes and splitting the cytoplasm occurs during M phase. In many single-celled eukaryotes such as yeast, reproduction by budding is common, which results in asymmetrical portions of cytoplasm in the two daughter cells.

[edit] 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 asexually reproducing organisms, the offspring will be a genetic copy or clone of the parent organism. In sexually reproducing organisms, a specialized form of cell division called meiosis produces cells called gametes or germ cells that are haploid, or contain only one copy of each gene. The gametes produced by females are called eggs or ova, and those produced by males are called sperm. Two gametes fuse to form a fertilized egg, a single cell that once again has a diploid number of genes - each with one copy from the mother and one copy from the father.

During the process of meiotic cell division, an event called genetic recombination or crossing-over can sometimes occur, in which a length of DNA on one chromatid is swapped with a length of DNA on the corresponding sister chromatid. This has no effect if the alleles on the chromatids are the same, but results in reassortment of otherwise linked alleles if they are different. The Mendelian principle of independent assortment asserts that each of a parent's two genes for each trait will sort independently into gametes; which allele an organism inherits for one trait is unrelated to which allele it inherits for another trait. This is in fact only true for genes that do not reside on the same chromosome, or are located very far from one another on the same chromosome. The closer two genes lie on the same chromosome, the more closely they will be associated in gametes and the more often they will appear together; genes that are very close are essentially never separated because it is extremely unlikely that a crossover point will occur between them. This is known as genetic linkage.

[edit] Mutation

    Main article: Mutation

DNA replication is for the most part extremely accurate, with an error rate per site of around 10-6 to 10-10 in eukaryotes.[4] 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 mutations. 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.

Mutations propagated to the next generation 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. 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 mutants. However, this does not imply that the wild-type allele is the ancestor from which the mutants are descended.

[edit] The genome

[edit] Chromosomal organization

The total complement of genes in an organism or cell is known as its genome. In prokaryotes, the vast majority of genes are located on a single chromosome of circular DNA, while eukaryotes usually possess multiple individual linear DNA helices packed into dense DNA-protein complexes called chromosomes. Extrachromosomal DNA is present in many prokaryotes and some simple eukaryotes as small, circular pieces of DNA called plasmids, which usually contain only a few genes each. Generally, regulatory regions and junk DNA are considered to be part of an organism's genome, but structural regions such as telomeres are not. The location (or locus) of a gene and the chromosome on which it is situated is in a sense arbitrary. Genes that appear together on the chromosomes of one species, such as humans, may appear on separate chromosomes in another species, such as mice. Two genes positioned near one another on a chromosome may encode proteins that figure in the same cellular process or in completely unrelated processes. As an example of the former, many of the genes involved in spermatogenesis reside together on the Y chromosome.

Many species carry more than one copy of their genome within each of their somatic cells. Cells or organisms with only one copy of each gene are called haploid; those with two copies are called diploid; and those with more than two copies are called polyploid. When more than one copy is present, the two copies are not necessarily identical; in sexually reproducing organisms, one copy is normally inherited from each parent. The copies may contain distinct DNA sequences encoding distinct alleles.

[edit] Composition of the genome
+Gene content and genome size of various organisms[4]
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
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 genomes vary widely among organisms, even those that are fairly closely evolutionarily related. Although it was believed before the completion of the Human Genome Project that the human genome would contain many more genes than simpler animals such as mice or fruit flies, the completion of the project has revealed that the human genome has an unexpectedly low gene density.[3] Estimates of the number of genes in a genome are difficult to compile because they depend on gene finding algorithms that search for patterns resembling those present in known genes, such as open reading frames, promoter regions with sequences resembling the consensus promoter sequence, and related regulatory regions such as TATA boxes in eukaryotes. Gene finding is less reliable in eukaryotic than in prokaryotic genomes due to the presence of non-coding DNA such as introns and pseudogenes.[9] 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.[4]

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.[10] 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.

[edit] Genetic and genomic 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 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.

[edit] 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 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.

[edit] History

    Main article: 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 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 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. 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. 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 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]



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Jeans
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This article is about the type of clothing. For the 1997 released Indian film, see Jeans (film).

Blue JeansJeans are trousers traditionally made from denim, but may also be made from a variety of fabrics including corduroy. Originally work clothes, they became popular among teenagers starting in the 1950s. Historic brands include Levi's and Wrangler. Today jeans are a very popular form of casual dress around the world and come in many styles and colors.

History
The earliest known pre-cursor for jeans is the Indian export of a thick cotton cloth, in the 16th century, known as dungaree. Dyed in indigo, it was sold near the Dongarii Fort near Mumbai. Sailors cut it to suit them.

Jeans were first created in Genoa, Italy when the city was an independent republic and a naval power. The first were made for the Genoese Navy because it required all-purpose trousers for its sailors that could be worn wet or dry, and whose legs could easily be rolled up to wear while swabbing the deck. These jeans would be laundered by dragging them in large mesh nets behind the ship, and the sea water would bleach them white. The first denim came from Nîmes, France, hence de Nimes, the name of the fabric. The French bleu de Gênes, from the Italian blu di Genova, literally the "blue of Genoa" dye of their fabric, is the root of the names for these trousers, "jeans" and "blue jeans", today.


Riveted jeans
In the 1850s Levi Strauss, a Franconian dry goods merchant living in San Francisco, was selling blue jeans under the "Levi's" name to the mining communities of California. One of Levi's customers was Jacob Davis, a tailor who frequently purchased bolts of cloth from the Levi Strauss & Co wholesale house. After one of Jacob's customers kept purchasing cloth to reinforce torn trousers, he had an idea to use copper rivets to reinforce the points of strain, such as on the pocket corners and at the base of the button fly. Jacobs did not have the required money to purchase a patent, so he wrote to Levi suggesting that they both go into business together. After Strauss accepted Davis's offer, on May 20, 1873, the two men received patent #139,121, a patent for an "Improvement in Fastening Pocket-Openings", from the United States Patent and Trademark Office.


Jeans in popular culture

Blue jeans

Copper rivets for reinforcing pockets are a characteristic feature of blue jeans.Initially blue jeans were simply sturdy trousers worn by workers especially in the factories during World War II. During this period men's jeans had the zipper down the front whereas women's jeans had the zipper down the right side. By the 1960s both men's and women's jeans had the zipper down the front. In the United States during the 1950s, wearing of blue jeans by teenagers and young adults became symbolic of mild protest against conformity. This was considered by some adults as disruptive; for example, some movie theaters and restaurants refused to admit patrons who wore blue jeans. During the 1960s the wearing of blue jeans became more acceptable and by the 1970s had become a general fashion in the United States, at least for informal wear. Notably, in the mid-1950s the denim and textiles industry was revolutionized by the introduction of the stone-washing technique by GWG (Great Western Garment). Entrepreneur, importer and noted eccentric, Donald Freeland of Edmonton, Alberta pioneered the method which helped to bring denim to a larger and more versatile market. Denim suddenly became an attractive product for all age groups and Freeland became one of the most important innovators in the history of denim and denim products. It should be noted, also, that Freeland contributed to a variety of other denim textile developments throughout his career with Great Western Garments (GWG)[2] Acceptance of jeans continued through the 1980s and 1990s to the point where jeans are now a wardrobe staple, with the average North American owning seven pairs [citation needed].

Being imported American products, especially in the case of the Soviet Union which restricted hard currency imports, jeans were somewhat expensive. In Spain they are known as vaqueros or "cowboys" and in Chinese, jeans are known as niuzaiku (SC: 牛仔裤), literally, "cowboy pants" (trousers), indicating their association with the American West, cowboy culture, and outdoors work.

Jeans can be worn very loose in a manner that completely conceals the shape of the wearer's lower body, or they can be snugly fitting and accentuate the body. Historic photographs indicate that in the decades before they became a staple of fashion, jeans generally fit quite loosely, much like a pair of bib overalls without the bib. Indeed, until 1960, Levi Strauss denominated its flagship product "waist overalls" rather than "jeans".


Fits
Fits of jeans are determined by current styles, gender, and by the manufacturer. Here are some of the fits produced for jeans:

Jeans for men have a longer rise and zipper, where as women have a shorter rise and zipper.

Ankle jeans - mostly for
Loose jeans
Straight jeans
Boot cut
Baggy
Skinny jeans - mostly for women
Phat pants
Slim Fit
Overalls
Boy Cut or Boyfriend - women
Bell Bottom/Flares
Saggy
Carpenter jeans
Original jeans
Classic
Wide Leg
Rises in jeans (the distance from the crotch to the waistband) range from high-waisted to superlow-rise.


Types
Besides trousers, denim can also be made into:

Overalls
Shorts
Skorts
Dresses
Skirts
Shirts
Jackets
Bags
Capris
Cut offs
Daisy Dukes

Law
On 10 February 1999 the Italian Supreme Court of Appeal in Rome overturned a rape conviction, stating that jeans are unable to be removed without the wearer's consent. Therefore, they ruled, the supposed victim must have been an active participant in the act. This last verdict, however, was also overturned, on 28 November 2001 by the Italian Supreme Court of Cassation, which finally established that wearing jeans does not excuse rape.


See also:
Denim
Designer jeans
Jeans fetishism
Lowrise jeans

/stolen pic

In befo da lock straight ballin'

Smithereener wrote:

Masterstyle wrote:

Xblade-3o5- wrote:

Gene
From Wikipedia, the free encyclopedia
(Redirected from Genes)
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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: 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.
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: 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.
Genetics glossary
A-F[show]
Adenine[show]

One of the four nucleotide bases in DNA or RNA; pairs with thymine in DNA or uracil in RNA.
Allele[show]

One of multiple alternative forms of a single gene, each of which is a viable DNA sequence occupying a given position, or locus on a chromosome. For example, in humans, one allele of the eye-color gene produces blue eyes and another allele of the eye-color gene produces brown eyes.
Base pair[show]

A pair of nucleotide bases on complementary DNA or RNA strands organized in a double helix.
Chromosome[show]

A molecular "package" for carrying DNA in cells, organized as two double-helical DNA molecules that encode many genes. Some simple organisms have only one chromosome made of circular DNA, while most eukaryotes have multiple chromosomes made of linear DNA.
Cytosine[show]

One of the four nucleotide bases in DNA or RNA; pairs with guanine.
DNA[show]

A polymeric molecule made of deoxyribonucleotides, hence then name deoxyribonucleic acid. Most often has the form of a "double helix", which consists of two paired DNA molecules and resembles a ladder that has been twisted. The "rungs" of the ladder are made of base pairs, or nucleotides with complementary hydrogen bonding patterns.
G-Z[show]
Gene[show]

The unit of heredity in living organisms, typically encoded in a sequence of nucleotide monomers that make up a long strand of DNA, or deoxyribonucleic acid. A particular gene can have multiple different forms, or alleles, which are defined by different sequences of DNA.
Gene expression[show]

The process in which the infomation encoded in a gene is converted into a form useful for the cell. The first step is transcription, which produces a messenger RNA molecule complementary to the DNA molecule on which a gene is encoded. For protein-coding genes, the second step is translation, in which the messenger RNA is read by the ribosome to produce a protein.
Gene pool[show]

The sum of all the alleles shared by members of a single population.
Genetics[show]

The field of biology that studies genes and their inheritance.
Genome[show]

The total complement of genetic material contained in an organism or cell.
Genotype[show]

The complement of alleles present in a particular individual's genome that give rise to the individual's phenotype.
Guanine[show]

One of the four nucleotide bases in DNA or RNA; pairs with cytosine.
Locus[show]

A location on a chromosome where a particular gene resides.
Phenotype[show]

The observable physical or behavioral traits of an organism, largely determined by the organism's genotype.
Protein[show]

A linear polymeric molecule made of of amino acids linked by peptide bonds. Proteins carry out the majority of chemical reactions that occur inside the cell.
RNA[show]

A polymeric molecule made of ribonucleotides, hence the name ribonucleic acid, similar to but less stable than DNA. One type, messenger RNA, plays an important role in gene expression. Ribosomes are also made largely of RNA.
Thymine[show]

One of the four nucleotide bases in DNA; pairs with adenine. In RNA, thymine is replaced with uracil.
Transcription[show]

The first step in gene expression, in which a messenger RNA molecule complementary to particular gene encoded in DNA is synthesized by enzymes called RNA polymerases. To produce a functional protein, transcription is followed by translation.
translation[show]

The second step in gene expression, in which a messenger RNA molecule is read by the ribosome to produce a functional protein. Translation is always preceded by transcription.
Uracil[show]

One of the four nucleotide bases in RNA; pairs with adenine. In DNA, uracil is replaced with thymine.
For other meanings of this term, see gene (disambiguation).
For a non-technical introduction to the topic, please see Introduction to genetics.

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] Genes interact with each other to influence physical development and behavior. Genes consist of a long strand of DNA (RNA in some viruses) 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 loosely dependent on its complexity; 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. However, the largest known genome belongs to the single-celled amoeba Amoeba dubia, with over 6 billion base pairs.[2] 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.[3] 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.[4]
Contents
[hide]

    * 1 Mendelian inheritance and classical genetics
    * 2 Physical definitions
          o 2.1 RNA genes
          o 2.2 Functional structure of a gene
          o 2.3 Chromosomes
    * 3 Gene expression
          o 3.1 Genetic code
          o 3.2 Transcription
          o 3.3 Translation
    * 4 DNA replication and inheritance
          o 4.1 Molecular inheritance
          o 4.2 Mutation
    * 5 The genome
          o 5.1 Chromosomal organization
          o 5.2 Composition of the genome
          o 5.3 Genetic and genomic nomenclature
    * 6 Evolutionary concept of a gene
    * 7 History
    * 8 See also
    * 9 References
    * 10 Further reading
    * 11 External links
          o 11.1 Tutorial and news
          o 11.2 References and databases

[edit] Mendelian inheritance and classical genetics

    Main articles: Mendelian inheritance and Classical genetics

The modern conception of the gene originated with work by Gregor Mendel, a 19th century Austrian 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.[5] The word was derived from Hugo De Vries' term pangen, itself a derivative of the word pangenesis coined by Darwin (1868).[6] 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.

[edit] Physical definitions
The chemical structure of a four-base fragment of a DNA double helix.
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, cytosine, 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, cytidine, 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 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.

[edit] 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 researcher 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.[7] While RNA is common as genetic storage material in viruses, in mammals in particular RNA inheritance has been observed very rarely.

[edit] 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, 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.

[edit] 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.[8]

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.[3]

[edit] Gene expression

    Main article: 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 transcribed from DNA to messenger RNA (mRNA), and second, it must be 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.

[edit] Genetic code
Schematic diagram of a single-stranded RNA molecule illustrating the position of three-base codons.
Schematic diagram of a single-stranded RNA molecule illustrating the position of three-base codons.

    Main article: 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 codons, 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.

[edit] Transcription

The process of genetic transcription produces a single-stranded RNA molecule known as messenger RNA, whose nucleotide sequence is complementary to the DNA from which it was transcribed. The DNA strand whose sequence matches that of the RNA is known as the coding strand and the strand from which the RNA was synthesized is the template strand. Transcription is performed by an enzyme called an RNA polymerase, which reads the template strand in the 3' to 5' direction and synthesizes the RNA from 5' to 3'. To initiate transcription,the polymerase first recognizes and binds a promoter region of the gene. Thus a major mechanism of gene regulation is the blocking or sequestering of the promoter region, either by tight binding by repressor molecules that physically block the polymerase, or by organizing the DNA so that the promoter region is not accessible.

In prokaryotes, transcription occurs in the cytoplasm; for very long transcripts, translation may begin at the 5' end of the RNA while the 3' end is still being transcribed. In eukaryotes, transcription necessarily occurs in the nucleus, where the cell's DNA is sequestered; the RNA molecule produced by the polymerase is known as the primary transcript and must undergo post-transcriptional modifications before being exported to the cytoplasm for translation. The splicing of introns present within the transcribed region is a modification unique to eukaryotes; alternative splicing mechanisms can result in mature transcripts from the same gene having different sequences and thus coding for different proteins. This is a major form of regulation in eukaryotic cells.

[edit] Translation

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

[edit] DNA replication and inheritance

The growth, development, and reproduction of organisms relies on cell division, or the process by which a single cell divides into two usually identical daughter cells. This requires first making a duplicate copy of every gene in the genome in a process called DNA replication. The copies are made by specialized enzymes known as DNA polymerases, which "read" one strand of the double-helical DNA, known as the template strand, and synthesize a new complementary strand. Because the DNA double helix is held together by base pairing, the sequence of one strand completely specifies the sequence of its complement; hence only one strand needs to be read by the enzyme to produce a faithful copy. The process of DNA replication is semiconservative; that is, the copy of the genome inherited by each daughter cell contains one original and one newly synthesized strand of DNA.[4]

After DNA replication is complete, the cell must physically separate the two copies of the genome and divide into two distinct membrane-bound cells. In prokaryotes - bacteria and archaea - this usually occurs via a relatively simple process called binary fission, in which each circular genome attaches to the cell membrane and is separated into the daughter cells as the membrane invaginates to split the cytoplasm into two membrane-bound portions. Binary fission is extremely fast compared to the rates of cell division in eukaryotes. Eukaryotic cell division is a more complex process known as the cell cycle; DNA replication occurs during a phase of this cycle known as S phase, while the process of segregating chromosomes and splitting the cytoplasm occurs during M phase. In many single-celled eukaryotes such as yeast, reproduction by budding is common, which results in asymmetrical portions of cytoplasm in the two daughter cells.

[edit] 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 asexually reproducing organisms, the offspring will be a genetic copy or clone of the parent organism. In sexually reproducing organisms, a specialized form of cell division called meiosis produces cells called gametes or germ cells that are haploid, or contain only one copy of each gene. The gametes produced by females are called eggs or ova, and those produced by males are called sperm. Two gametes fuse to form a fertilized egg, a single cell that once again has a diploid number of genes - each with one copy from the mother and one copy from the father.

During the process of meiotic cell division, an event called genetic recombination or crossing-over can sometimes occur, in which a length of DNA on one chromatid is swapped with a length of DNA on the corresponding sister chromatid. This has no effect if the alleles on the chromatids are the same, but results in reassortment of otherwise linked alleles if they are different. The Mendelian principle of independent assortment asserts that each of a parent's two genes for each trait will sort independently into gametes; which allele an organism inherits for one trait is unrelated to which allele it inherits for another trait. This is in fact only true for genes that do not reside on the same chromosome, or are located very far from one another on the same chromosome. The closer two genes lie on the same chromosome, the more closely they will be associated in gametes and the more often they will appear together; genes that are very close are essentially never separated because it is extremely unlikely that a crossover point will occur between them. This is known as genetic linkage.

[edit] Mutation

    Main article: Mutation

DNA replication is for the most part extremely accurate, with an error rate per site of around 10-6 to 10-10 in eukaryotes.[4] 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 mutations. 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.

Mutations propagated to the next generation 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. 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 mutants. However, this does not imply that the wild-type allele is the ancestor from which the mutants are descended.

[edit] The genome

[edit] Chromosomal organization

The total complement of genes in an organism or cell is known as its genome. In prokaryotes, the vast majority of genes are located on a single chromosome of circular DNA, while eukaryotes usually possess multiple individual linear DNA helices packed into dense DNA-protein complexes called chromosomes. Extrachromosomal DNA is present in many prokaryotes and some simple eukaryotes as small, circular pieces of DNA called plasmids, which usually contain only a few genes each. Generally, regulatory regions and junk DNA are considered to be part of an organism's genome, but structural regions such as telomeres are not. The location (or locus) of a gene and the chromosome on which it is situated is in a sense arbitrary. Genes that appear together on the chromosomes of one species, such as humans, may appear on separate chromosomes in another species, such as mice. Two genes positioned near one another on a chromosome may encode proteins that figure in the same cellular process or in completely unrelated processes. As an example of the former, many of the genes involved in spermatogenesis reside together on the Y chromosome.

Many species carry more than one copy of their genome within each of their somatic cells. Cells or organisms with only one copy of each gene are called haploid; those with two copies are called diploid; and those with more than two copies are called polyploid. When more than one copy is present, the two copies are not necessarily identical; in sexually reproducing organisms, one copy is normally inherited from each parent. The copies may contain distinct DNA sequences encoding distinct alleles.

[edit] Composition of the genome
+Gene content and genome size of various organisms[4]
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
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 genomes vary widely among organisms, even those that are fairly closely evolutionarily related. Although it was believed before the completion of the Human Genome Project that the human genome would contain many more genes than simpler animals such as mice or fruit flies, the completion of the project has revealed that the human genome has an unexpectedly low gene density.[3] Estimates of the number of genes in a genome are difficult to compile because they depend on gene finding algorithms that search for patterns resembling those present in known genes, such as open reading frames, promoter regions with sequences resembling the consensus promoter sequence, and related regulatory regions such as TATA boxes in eukaryotes. Gene finding is less reliable in eukaryotic than in prokaryotic genomes due to the presence of non-coding DNA such as introns and pseudogenes.[9] 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.[4]

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.[10] 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.

[edit] Genetic and genomic 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 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.

[edit] 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 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.

[edit] History

    Main article: 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 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 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. 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. 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 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]



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ATG wrote:

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Legend
Solid     Solid     Liquid     Liquid     Gas     Gas     Synthetic     Synthetic
Alkali metals     Alkali metals     Alkali earth metals     Alkali earth metals     Transition metals     Transition metals     Rare earth metals     Rare earth metals
Other metals     Other metals     Noble gases     Noble gases     Halogens     Halogens     Other nonmetals     Other nonmetals
     
Periodic Table first discovered in 1869 by Dmitry I. Mendeleyev is a way of presenting all the elements so as to show their similarities and differences. The elements are arranged in increasing order of atomic number(Z) as you go from left to right accross the table. The horizontal rows a called periods and the vertical rows, groups.
A noble gas is found at the right hand side of each period. There is a progression from metals to non-metals across each period. Elements found in groups (e.g. alkali, halogens) have a similar electronic configuration. The number of electrons in outer shell is the same as the number of the group (e.g. lithium 2·1).
The block of elements between groups II and III are called transition metals. These are similar in many ways; they produce colored compounds, have variable valency and are often used as catalysts. Elements 58 to 71 are known as lanthanide or rare earth elements. These elements are found on earth in only very small amounts.
Elements 90 to 103 are known as the actinide elements. They include most of the will known elements which are found in nuclear reactions. The elements with larger atomic numbers than 92 do not occur naturally. They have all been produced artificially by bombarding other elements with particles.

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Gene
From Wikipedia, the free encyclopedia
(Redirected from Genes)
Jump to: navigation, search
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: 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.
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: 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.
Genetics glossary
A-F[show]
Adenine[show]

One of the four nucleotide bases in DNA or RNA; pairs with thymine in DNA or uracil in RNA.
Allele[show]

One of multiple alternative forms of a single gene, each of which is a viable DNA sequence occupying a given position, or locus on a chromosome. For example, in humans, one allele of the eye-color gene produces blue eyes and another allele of the eye-color gene produces brown eyes.
Base pair[show]

A pair of nucleotide bases on complementary DNA or RNA strands organized in a double helix.
Chromosome[show]

A molecular "package" for carrying DNA in cells, organized as two double-helical DNA molecules that encode many genes. Some simple organisms have only one chromosome made of circular DNA, while most eukaryotes have multiple chromosomes made of linear DNA.
Cytosine[show]

One of the four nucleotide bases in DNA or RNA; pairs with guanine.
DNA[show]

A polymeric molecule made of deoxyribonucleotides, hence then name deoxyribonucleic acid. Most often has the form of a "double helix", which consists of two paired DNA molecules and resembles a ladder that has been twisted. The "rungs" of the ladder are made of base pairs, or nucleotides with complementary hydrogen bonding patterns.
G-Z[show]
Gene[show]

The unit of heredity in living organisms, typically encoded in a sequence of nucleotide monomers that make up a long strand of DNA, or deoxyribonucleic acid. A particular gene can have multiple different forms, or alleles, which are defined by different sequences of DNA.
Gene expression[show]

The process in which the infomation encoded in a gene is converted into a form useful for the cell. The first step is transcription, which produces a messenger RNA molecule complementary to the DNA molecule on which a gene is encoded. For protein-coding genes, the second step is translation, in which the messenger RNA is read by the ribosome to produce a protein.
Gene pool[show]

The sum of all the alleles shared by members of a single population.
Genetics[show]

The field of biology that studies genes and their inheritance.
Genome[show]

The total complement of genetic material contained in an organism or cell.
Genotype[show]

The complement of alleles present in a particular individual's genome that give rise to the individual's phenotype.
Guanine[show]

One of the four nucleotide bases in DNA or RNA; pairs with cytosine.
Locus[show]

A location on a chromosome where a particular gene resides.
Phenotype[show]

The observable physical or behavioral traits of an organism, largely determined by the organism's genotype.
Protein[show]

A linear polymeric molecule made of of amino acids linked by peptide bonds. Proteins carry out the majority of chemical reactions that occur inside the cell.
RNA[show]

A polymeric molecule made of ribonucleotides, hence the name ribonucleic acid, similar to but less stable than DNA. One type, messenger RNA, plays an important role in gene expression. Ribosomes are also made largely of RNA.
Thymine[show]

One of the four nucleotide bases in DNA; pairs with adenine. In RNA, thymine is replaced with uracil.
Transcription[show]

The first step in gene expression, in which a messenger RNA molecule complementary to particular gene encoded in DNA is synthesized by enzymes called RNA polymerases. To produce a functional protein, transcription is followed by translation.
translation[show]

The second step in gene expression, in which a messenger RNA molecule is read by the ribosome to produce a functional protein. Translation is always preceded by transcription.
Uracil[show]

One of the four nucleotide bases in RNA; pairs with adenine. In DNA, uracil is replaced with thymine.
For other meanings of this term, see gene (disambiguation).
For a non-technical introduction to the topic, please see Introduction to genetics.

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] Genes interact with each other to influence physical development and behavior. Genes consist of a long strand of DNA (RNA in some viruses) 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 loosely dependent on its complexity; 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. However, the largest known genome belongs to the single-celled amoeba Amoeba dubia, with over 6 billion base pairs.[2] 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.[3] 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.[4]
Contents
[hide]

    * 1 Mendelian inheritance and classical genetics
    * 2 Physical definitions
          o 2.1 RNA genes
          o 2.2 Functional structure of a gene
          o 2.3 Chromosomes
    * 3 Gene expression
          o 3.1 Genetic code
          o 3.2 Transcription
          o 3.3 Translation
    * 4 DNA replication and inheritance
          o 4.1 Molecular inheritance
          o 4.2 Mutation
    * 5 The genome
          o 5.1 Chromosomal organization
          o 5.2 Composition of the genome
          o 5.3 Genetic and genomic nomenclature
    * 6 Evolutionary concept of a gene
    * 7 History
    * 8 See also
    * 9 References
    * 10 Further reading
    * 11 External links
          o 11.1 Tutorial and news
          o 11.2 References and databases

[edit] Mendelian inheritance and classical genetics

    Main articles: Mendelian inheritance and Classical genetics

The modern conception of the gene originated with work by Gregor Mendel, a 19th century Austrian 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.[5] The word was derived from Hugo De Vries' term pangen, itself a derivative of the word pangenesis coined by Darwin (1868).[6] 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.

[edit] Physical definitions
The chemical structure of a four-base fragment of a DNA double helix.
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, cytosine, 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, cytidine, 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 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.

[edit] 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 researcher 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.[7] While RNA is common as genetic storage material in viruses, in mammals in particular RNA inheritance has been observed very rarely.

[edit] 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, 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.

[edit] 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.[8]

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.[3]

[edit] Gene expression

    Main article: 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 transcribed from DNA to messenger RNA (mRNA), and second, it must be 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.

[edit] Genetic code
Schematic diagram of a single-stranded RNA molecule illustrating the position of three-base codons.
Schematic diagram of a single-stranded RNA molecule illustrating the position of three-base codons.

    Main article: 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 codons, 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.

[edit] Transcription

The process of genetic transcription produces a single-stranded RNA molecule known as messenger RNA, whose nucleotide sequence is complementary to the DNA from which it was transcribed. The DNA strand whose sequence matches that of the RNA is known as the coding strand and the strand from which the RNA was synthesized is the template strand. Transcription is performed by an enzyme called an RNA polymerase, which reads the template strand in the 3' to 5' direction and synthesizes the RNA from 5' to 3'. To initiate transcription,the polymerase first recognizes and binds a promoter region of the gene. Thus a major mechanism of gene regulation is the blocking or sequestering of the promoter region, either by tight binding by repressor molecules that physically block the polymerase, or by organizing the DNA so that the promoter region is not accessible.

In prokaryotes, transcription occurs in the cytoplasm; for very long transcripts, translation may begin at the 5' end of the RNA while the 3' end is still being transcribed. In eukaryotes, transcription necessarily occurs in the nucleus, where the cell's DNA is sequestered; the RNA molecule produced by the polymerase is known as the primary transcript and must undergo post-transcriptional modifications before being exported to the cytoplasm for translation. The splicing of introns present within the transcribed region is a modification unique to eukaryotes; alternative splicing mechanisms can result in mature transcripts from the same gene having different sequences and thus coding for different proteins. This is a major form of regulation in eukaryotic cells.

[edit] Translation

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

[edit] DNA replication and inheritance

The growth, development, and reproduction of organisms relies on cell division, or the process by which a single cell divides into two usually identical daughter cells. This requires first making a duplicate copy of every gene in the genome in a process called DNA replication. The copies are made by specialized enzymes known as DNA polymerases, which "read" one strand of the double-helical DNA, known as the template strand, and synthesize a new complementary strand. Because the DNA double helix is held together by base pairing, the sequence of one strand completely specifies the sequence of its complement; hence only one strand needs to be read by the enzyme to produce a faithful copy. The process of DNA replication is semiconservative; that is, the copy of the genome inherited by each daughter cell contains one original and one newly synthesized strand of DNA.[4]

After DNA replication is complete, the cell must physically separate the two copies of the genome and divide into two distinct membrane-bound cells. In prokaryotes - bacteria and archaea - this usually occurs via a relatively simple process called binary fission, in which each circular genome attaches to the cell membrane and is separated into the daughter cells as the membrane invaginates to split the cytoplasm into two membrane-bound portions. Binary fission is extremely fast compared to the rates of cell division in eukaryotes. Eukaryotic cell division is a more complex process known as the cell cycle; DNA replication occurs during a phase of this cycle known as S phase, while the process of segregating chromosomes and splitting the cytoplasm occurs during M phase. In many single-celled eukaryotes such as yeast, reproduction by budding is common, which results in asymmetrical portions of cytoplasm in the two daughter cells.

[edit] 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 asexually reproducing organisms, the offspring will be a genetic copy or clone of the parent organism. In sexually reproducing organisms, a specialized form of cell division called meiosis produces cells called gametes or germ cells that are haploid, or contain only one copy of each gene. The gametes produced by females are called eggs or ova, and those produced by males are called sperm. Two gametes fuse to form a fertilized egg, a single cell that once again has a diploid number of genes - each with one copy from the mother and one copy from the father.

During the process of meiotic cell division, an event called genetic recombination or crossing-over can sometimes occur, in which a length of DNA on one chromatid is swapped with a length of DNA on the corresponding sister chromatid. This has no effect if the alleles on the chromatids are the same, but results in reassortment of otherwise linked alleles if they are different. The Mendelian principle of independent assortment asserts that each of a parent's two genes for each trait will sort independently into gametes; which allele an organism inherits for one trait is unrelated to which allele it inherits for another trait. This is in fact only true for genes that do not reside on the same chromosome, or are located very far from one another on the same chromosome. The closer two genes lie on the same chromosome, the more closely they will be associated in gametes and the more often they will appear together; genes that are very close are essentially never separated because it is extremely unlikely that a crossover point will occur between them. This is known as genetic linkage.

[edit] Mutation

    Main article: Mutation

DNA replication is for the most part extremely accurate, with an error rate per site of around 10-6 to 10-10 in eukaryotes.[4] 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 mutations. 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.

Mutations propagated to the next generation 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. 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 mutants. However, this does not imply that the wild-type allele is the ancestor from which the mutants are descended.

[edit] The genome

[edit] Chromosomal organization

The total complement of genes in an organism or cell is known as its genome. In prokaryotes, the vast majority of genes are located on a single chromosome of circular DNA, while eukaryotes usually possess multiple individual linear DNA helices packed into dense DNA-protein complexes called chromosomes. Extrachromosomal DNA is present in many prokaryotes and some simple eukaryotes as small, circular pieces of DNA called plasmids, which usually contain only a few genes each. Generally, regulatory regions and junk DNA are considered to be part of an organism's genome, but structural regions such as telomeres are not. The location (or locus) of a gene and the chromosome on which it is situated is in a sense arbitrary. Genes that appear together on the chromosomes of one species, such as humans, may appear on separate chromosomes in another species, such as mice. Two genes positioned near one another on a chromosome may encode proteins that figure in the same cellular process or in completely unrelated processes. As an example of the former, many of the genes involved in spermatogenesis reside together on the Y chromosome.

Many species carry more than one copy of their genome within each of their somatic cells. Cells or organisms with only one copy of each gene are called haploid; those with two copies are called diploid; and those with more than two copies are called polyploid. When more than one copy is present, the two copies are not necessarily identical; in sexually reproducing organisms, one copy is normally inherited from each parent. The copies may contain distinct DNA sequences encoding distinct alleles.

[edit] Composition of the genome
+Gene content and genome size of various organisms[4]
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
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 genomes vary widely among organisms, even those that are fairly closely evolutionarily related. Although it was believed before the completion of the Human Genome Project that the human genome would contain many more genes than simpler animals such as mice or fruit flies, the completion of the project has revealed that the human genome has an unexpectedly low gene density.[3] Estimates of the number of genes in a genome are difficult to compile because they depend on gene finding algorithms that search for patterns resembling those present in known genes, such as open reading frames, promoter regions with sequences resembling the consensus promoter sequence, and related regulatory regions such as TATA boxes in eukaryotes. Gene finding is less reliable in eukaryotic than in prokaryotic genomes due to the presence of non-coding DNA such as introns and pseudogenes.[9] 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.[4]

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.[10] 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.

[edit] Genetic and genomic 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 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.

[edit] 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 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.

[edit] History

    Main article: 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 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 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. 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. 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 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]



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Jeans
From Wikipedia, the free encyclopedia
Jump to: navigation, search
This article is about the type of clothing. For the 1997 released Indian film, see Jeans (film).

Blue JeansJeans are trousers traditionally made from denim, but may also be made from a variety of fabrics including corduroy. Originally work clothes, they became popular among teenagers starting in the 1950s. Historic brands include Levi's and Wrangler. Today jeans are a very popular form of casual dress around the world and come in many styles and colors.

History
The earliest known pre-cursor for jeans is the Indian export of a thick cotton cloth, in the 16th century, known as dungaree. Dyed in indigo, it was sold near the Dongarii Fort near Mumbai. Sailors cut it to suit them.

Jeans were first created in Genoa, Italy when the city was an independent republic and a naval power. The first were made for the Genoese Navy because it required all-purpose trousers for its sailors that could be worn wet or dry, and whose legs could easily be rolled up to wear while swabbing the deck. These jeans would be laundered by dragging them in large mesh nets behind the ship, and the sea water would bleach them white. The first denim came from Nîmes, France, hence de Nimes, the name of the fabric. The French bleu de Gênes, from the Italian blu di Genova, literally the "blue of Genoa" dye of their fabric, is the root of the names for these trousers, "jeans" and "blue jeans", today.


Riveted jeans
In the 1850s Levi Strauss, a Franconian dry goods merchant living in San Francisco, was selling blue jeans under the "Levi's" name to the mining communities of California. One of Levi's customers was Jacob Davis, a tailor who frequently purchased bolts of cloth from the Levi Strauss & Co wholesale house. After one of Jacob's customers kept purchasing cloth to reinforce torn trousers, he had an idea to use copper rivets to reinforce the points of strain, such as on the pocket corners and at the base of the button fly. Jacobs did not have the required money to purchase a patent, so he wrote to Levi suggesting that they both go into business together. After Strauss accepted Davis's offer, on May 20, 1873, the two men received patent #139,121, a patent for an "Improvement in Fastening Pocket-Openings", from the United States Patent and Trademark Office.


Jeans in popular culture

Blue jeans

Copper rivets for reinforcing pockets are a characteristic feature of blue jeans.Initially blue jeans were simply sturdy trousers worn by workers especially in the factories during World War II. During this period men's jeans had the zipper down the front whereas women's jeans had the zipper down the right side. By the 1960s both men's and women's jeans had the zipper down the front. In the United States during the 1950s, wearing of blue jeans by teenagers and young adults became symbolic of mild protest against conformity. This was considered by some adults as disruptive; for example, some movie theaters and restaurants refused to admit patrons who wore blue jeans. During the 1960s the wearing of blue jeans became more acceptable and by the 1970s had become a general fashion in the United States, at least for informal wear. Notably, in the mid-1950s the denim and textiles industry was revolutionized by the introduction of the stone-washing technique by GWG (Great Western Garment). Entrepreneur, importer and noted eccentric, Donald Freeland of Edmonton, Alberta pioneered the method which helped to bring denim to a larger and more versatile market. Denim suddenly became an attractive product for all age groups and Freeland became one of the most important innovators in the history of denim and denim products. It should be noted, also, that Freeland contributed to a variety of other denim textile developments throughout his career with Great Western Garments (GWG)[2] Acceptance of jeans continued through the 1980s and 1990s to the point where jeans are now a wardrobe staple, with the average North American owning seven pairs [citation needed].

Being imported American products, especially in the case of the Soviet Union which restricted hard currency imports, jeans were somewhat expensive. In Spain they are known as vaqueros or "cowboys" and in Chinese, jeans are known as niuzaiku (SC: 牛仔裤), literally, "cowboy pants" (trousers), indicating their association with the American West, cowboy culture, and outdoors work.

Jeans can be worn very loose in a manner that completely conceals the shape of the wearer's lower body, or they can be snugly fitting and accentuate the body. Historic photographs indicate that in the decades before they became a staple of fashion, jeans generally fit quite loosely, much like a pair of bib overalls without the bib. Indeed, until 1960, Levi Strauss denominated its flagship product "waist overalls" rather than "jeans".


Fits
Fits of jeans are determined by current styles, gender, and by the manufacturer. Here are some of the fits produced for jeans:

Jeans for men have a longer rise and zipper, where as women have a shorter rise and zipper.

Ankle jeans - mostly for
Loose jeans
Straight jeans
Boot cut
Baggy
Skinny jeans - mostly for women
Phat pants
Slim Fit
Overalls
Boy Cut or Boyfriend - women
Bell Bottom/Flares
Saggy
Carpenter jeans
Original jeans
Classic
Wide Leg
Rises in jeans (the distance from the crotch to the waistband) range from high-waisted to superlow-rise.


Types
Besides trousers, denim can also be made into:

Overalls
Shorts
Skorts
Dresses
Skirts
Shirts
Jackets
Bags
Capris
Cut offs
Daisy Dukes

Law
On 10 February 1999 the Italian Supreme Court of Appeal in Rome overturned a rape conviction, stating that jeans are unable to be removed without the wearer's consent. Therefore, they ruled, the supposed victim must have been an active participant in the act. This last verdict, however, was also overturned, on 28 November 2001 by the Italian Supreme Court of Cassation, which finally established that wearing jeans does not excuse rape.


See also:
Denim
Designer jeans
Jeans fetishism
Lowrise jeans

/stolen pic
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History of the world
From Wikipedia, the free encyclopedia
Jump to: navigation, search
For the history of Earth which includes the time before Human existence, see History of Earth. For other uses, see History of the world (disambiguation).
Contents
[hide]

    * 1 Paleolithic Period
    * 2 Mesolithic Period
    * 3 Neolithic Period
          o 3.1 Development of agriculture
          o 3.2 Development of religion
    * 4 Rise of civilization
          o 4.1 State
          o 4.2 City and trade
          o 4.3 Religion and philosophy
    * 5 Major civilizations and regions
    * 6 Rise of Europe
          o 6.1 Background to European advance
          o 6.2 Europe's mercantile dominance
    * 7 Twentieth Century onward
    * 8 See also
          o 8.1 History topics
          o 8.2 History by period
          o 8.3 History by region
    * 9 Footnotes
    * 10 References
    * 11 Further reading
    * 12 External links

The history of the world, by convention, is human history, from the first appearance of Homo sapiens to the present. Human history is marked both by a gradual accretion of discoveries and inventions, as well as by quantum leaps — revolutions — that comprise epochs in the material and spiritual evolution of humankind.

Human history, as opposed to prehistory, has in the past been said to begin with the invention, independently at several sites on Earth, of writing, which created the infrastructure for lasting, accurately transmitted memories and thus for the diffusion and growth of knowledge.[citation needed] Writing, in its turn, had been made necessary in the wake of the Agricultural Revolution, which had given rise to civilization, i.e., to permanent settled communities, which fostered a growing diversity of trades.

Such scattered habitations, centered about life-sustaining bodies of water — rivers and lakes — coalesced over time into ever larger units, in parallel with the evolution of ever more efficient means of transport. These processes of coalescence, spurred by rivalries and conflicts between adjacent communities, gave rise over millenia to ever larger states, and then to superstates (empires). The fall of the Roman Empire in Europe at the end of antiquity signalled the beginning of the Middle Ages.

In the mid-15th century, Johannes Gutenberg's invention of modern printing, employing movable type, revolutionized communication, helping end the Middle Ages and usher in modern times, the European Renaissance and the Scientific Revolution.

By the 18th century, the accumulation of knowledge and technology, especially in Europe, had reached a critical mass that sparked into existence the Industrial Revolution. Over the quarter-millennium since, knowledge, technology, commerce, and — concomitantly with these — war have accelerated at a geometric rate, creating the opportunities and perils that now confront the human communities that together inhabit a finite planet.

[edit] Paleolithic Period

    Main article: Paleolithic

Map of early human migrations, according to mitochondrial population genetics. Numbers are millennia before the present.
Map of early human migrations, according to mitochondrial population genetics. Numbers are millennia before the present.

"Paleolithic" means "Old Stone Age." This was the earliest period of the Stone Age.

Scientific evidence based on genetics and the study of fossils, places the origin of modern Homo sapiens in Africa [1]. This occurred about 200,000 BP during the Palaeolithic period, after a long period of evolution. Ancestors of humans, such as Homo erectus, had been using simple tools for over a thousand millennia, but as time progressed, tools became far more refined and complex. Humans also developed language sometime during the Paleolithic period, as well as a conceptual repertoire that included systematic burial of the dead. The latter suggests a development of foresight after consistent exposure to rotting bodies.

Humans of this age also decorated themselves with objects to improve their appearance. During this period, all humans lived as hunter-gatherers, who were generally nomadic.

Some 75,000 years ago, a huge population bottleneck occurred after the Lake Toba supereruption, which may have killed off as many as 59 million people.

Modern humans spread rapidly over the globe from Africa and the frost-free zones of Europe and Asia. The rapid expansion of humankind to North America and Oceania took place at the climax of the most recent Ice Age, when today's temperate regions were extremely inhospitable. Yet, by the end of the Ice Age some 12,000 BP, humans had colonised nearly all the ice-free parts of the globe.

Hunter-gatherer societies have tended to be very small, though in some cases they have developed social stratification; and long-distance contacts may be possible, as in the case of Indigenous Australian "highways."

Eventually most hunter-gatherer societies have either developed into, or have been absorbed into, larger agricultural states. Those that have not, have either been exterminated or have remained in isolation, as is the case with the small hunter-gatherer societies that are still present in remote regions today.

[edit] Mesolithic Period

    Main article: Mesolithic

The "Mesolithic," or "Middle Stone Age" (from the Greek "mesos," "middle," and "lithos," "stone") was a period in the development of human technology between the Paleolithic and Neolithic periods of the Stone Age.

The Mesolithic period began at the end of the Pleistocene epoch, some 10,000 BP, and ended with the introduction of agriculture, the date of which varied by geographic region. In some areas, such as the Near East, agriculture was already underway by the end of the Pleistocene, and there the Mesolithic is short and poorly defined. In areas with limited glacial impact, the term "Epipaleolithic" is sometimes preferred.

Regions that experienced greater environmental effects as the last ice age ended have a much more evident Mesolithic era, lasting millennia. In Northern Europe, societies were able to live well on rich food supplies from the marshlands fostered by the warmer climate. Such conditions produced distinctive human behaviours which are preserved in the material record, such as the Maglemosian and Azilian cultures. These conditions also delayed the coming of the Neolithic until as late as 4000 BCE in northern Europe.

Remains from this period are few and far between, often limited to middens. In forested areas, the first signs of deforestation have been found, although this would only begin in earnest during the Neolithic, when more space was needed for agriculture.

The Mesolithic is characterized in most areas by small composite flint tools — microliths and microburins. Fishing tackle, stone adzes and wooden objects, e.g. canoes and bows, have been found at some sites. These technologies first occur in Africa, associated with the Azilian cultures, before spreading to Europe through the Ibero-Maurusian culture of Spain and Portugal, and the Kebaran culture of Palestine. Independent discovery is not always ruled out.

[edit] Neolithic Period

    Main article: Neolithic Period

"Neolithic" means "New Stone Age." This was a period of primitive technological and social development, toward the end of the "Stone Age." Beginning in the 10th millennium BCE, the Neolithic period saw the development of early villages, agriculture, animal domestication and tools.

[edit] Development of agriculture

    Main article: Agriculture

A major change, described by prehistorian Vere Gordon Childe as the "Agricultural Revolution," occurred about the 10th millennium BCE with the adoption of agriculture. The Sumerians first began farming ca. 9500 BCE. By 7000 BCE, agriculture had spread to the Indus Valley; by 6000 BCE, to Egypt; by 5000 BCE, to China. About 2700 BCE, agriculture had come to Mesoamerica.

Although attention has tended to concentrate on the Middle East's Fertile Crescent, archaeology in the Americas, East Asia and Southeast Asia indicates that agricultural systems, using different crops and animals, may in some cases have developed there nearly as early.

A further advance in Middle Eastern agriculture occurred with the development of organised irrigation, and the use of a specialised workforce, by the Sumerians, beginning about 5500 BCE. Stone was supplanted by bronze and iron in implements of agriculture and warfare. Agricultural settlements had until then been almost completely dependent on stone tools. In Eurasia, copper and bronze tools, decorations and weapons began to be commonplace about 3000 BCE. After bronze, the Eastern Mediterranean region, Middle East and China saw the introduction of iron tools and weapons.

The Americas may not have had metal tools until the Chavín horizon (900 BCE). The Moche did have metal armor, knives and tableware. Even the metal-poor Inca had metal-tipped plows, at least after the conquest of Chimor. However, little archaeological research has so far been done in Peru, and nearly all the khipus (recording devices, in the form of knots, used by the Incas) were burned in the Spanish conquest of Peru. As late as 2004, entire cities were still being unearthed. Some digs suggest that steel may have been produced there before it was developed in Europe.

The cradles of early civilizations were river valleys , such as the Yellow River valley in China, the Nile valley in Egypt, and the Indus Valley in the Indian subcontinent. Some nomadic peoples, such as the Indigenous Australians and the Bushmen of southern Africa, did not practice agriculture until relatively recent times.

Before 1800, many populations did not belong to states. Scientists disagree as to whether the term "tribe" should be applied to the kinds of societies that these people lived in. Large parts of the world were "tribal" territories before Europeans began colonizing them[citation needed]. Many tribal societies, in Europe and elsewhere, transformed into states when they were threatened, or otherwise impinged on, by existing states. Examples are the Marcomanni, Poland and Lithuania. Some "tribes," such as the Kassites and the Manchus, conquered states and were absorbed by them.

Agriculture made possible complex societies — civilizations. States and markets emerged. Technologies enhanced people's ability to control nature and to develop transport and communication.

[edit] Development of religion

It is to the Neolithic that most historians trace the beginnings of complex religion. Religious belief in this period commonly consisted in the worship of a Mother Goddess, a Sky Father, and of the Sun and Moon as deities. (see also Sun worship). Shrines developed, which over time evolved into temple establishments, complete with a complex hierarchy of priests and priestesses and other functionaries. Typical of the Neolithic was a tendency to worship anthropomorphic deities.

The earliest surviving religious scriptures are the Pyramid Texts, produced by the Egyptians (dating back to 3100 B.C.E).

[edit] Rise of civilization

[edit] State

    Main articles: State and Civilization

The Agricultural Revolution led to several major changes. It permitted far denser populations, which in time organised into states. There are several definitions for the term, "state." Max Weber and Norbert Elias defined a state as an organization of people that has a monopoly on the legitimate use of force in a particular geographic area.
Borders delineate states — a prominent example is the Great Wall of China, which stretches over 6,700 km, and was first erected in the 3rd century BCE to protect the north from nomadic invaders. It has since been rebuilt and augmented several times.
Borders delineate states — a prominent example is the Great Wall of China, which stretches over 6,700 km, and was first erected in the 3rd century BCE to protect the north from nomadic invaders. It has since been rebuilt and augmented several times.

The first states appeared in Mesopotamia, ancient Egypt and the Indus Valley, in the late 4th and early 3rd millennia BCE. In Mesopotamia, there were several city-states. Ancient Egypt began as a state without cities, but soon developed them.

A state ordinarily needs an army for the legitimate exercise of force. An army needs a bureaucracy to maintain it. The only exception to this appears to have been the Indus Valley civilization, for which there is no evidence of the existence of a military force.

States appeared in China in the late 3rd and early 2nd millennia BCE.

Major wars were waged among states in the Middle East. About 1275 BCE, the Hittites and Egyptians concluded the treaty of Kadesh, the world's oldest recorded peace treaty.

Empires came into being, with conquered areas ruled by central tribes, as in Persia (6th century BCE), the Mauryan Empire (4th century BCE), China (3rd century BCE), and the Roman Empire (1st century BCE).

Clashes among empires included those that took place in the 8th century, when the Islamic Caliphate of Arabia (ruling from Spain to Iran) and China's Tang dynasty (ruling from Xinjiang to Korea) fought for decades for control of Central Asia.

The largest continguous land empire was the 13th-century Mongolian Empire. By then, most people in Europe, Asia and North Africa belonged to states. There were states as well in Mexico and western South America. States controlled more and more of the world's territory and population; the last "empty" territories, with the exception of uninhabitated Antarctica, would be divided up among states by the Treaty of Berlin (1878).

[edit] City and trade

    Main articles: City and Trade

Vasco da Gama sailed to India to bring back spices in the late 15th and early 16th centuries.
Vasco da Gama sailed to India to bring back spices in the late 15th and early 16th centuries.

Agriculture also created, and allowed for the storage of, food surpluses that could support people not directly engaged in food production. The development of agriculture permitted the creation of the first cities. These were centers of trade, manufacture and political power with nearly no agricultural production of their own. Cities established a symbiosis with their surrounding countrysides, absorbing agricultural products and providing, in return, manufactures and varying degrees of military protection.

The development of cities equated, both etymologically and in fact, with the rise of civilization itself: first Sumerian civilization, in lower Mesopotamia (3500 BCE), followed by Egyptian civilization along the Nile (3300 BCE) and Harappan civilization in the Indus Valley (3300 BCE). Elaborate cities grew up, with high levels of social and economic complexity. Each of these civilizations was so different from the others that they almost certainly originated independently. It was at this time, and due to the needs of cities, that writing and extensive trade were introduced.

In China, proto-urban societies may have developed from 2500 BCE, but the first dynasty to be identified by archeology is the Shang Dynasty.

The 2nd millennium BCE saw the emergence of civilization in Crete, mainland Greece and central Turkey.

In the Americas, civilizations such as the Maya, Moche and Nazca emerged in Mesoamerica and Peru at the end of the 1st millennium BCE.

The world's first coinage was introduced around 625 BC in Lydia (western Anatolia, in modern Turkey).[1]

Trade routes appeared in the eastern Mediterranean in the 4th millennium BCE. Long-range trade routes first appeared in the 3rd millennium BCE, when Sumerians in Mesopotamia traded with the Harappan civilization of the Indus Valley. The Silk Road between China and Syria began in the 2nd millennium BCE. Cities in Central Asia and Persia were major crossroads of these trade routes. The Phoenician and Greek civilizations founded trade-based empires in the Mediterranean basin in the 1st millennium BCE.

In the late 1st millennium CE and early 2nd millennium CE, the Arabs dominated the trade routes in the Indian Ocean, East Asia, and the Sahara. In the late 1st millennium, Arabs and Jews dominated trade in the Mediterranean. In the early 2nd millennium, Italians took over this role, and Flemish and German cities were at the center of trade routes in northern Europe. In all areas, major cities developed at crossroads along trade routes.

[edit] Religion and philosophy

    Main articles: History of philosophy and Development of religion

New philosophies and religions arose in both east and west, particularly about the 6th century BCE. Over time, a great variety of religions developed around the world, with some of the earliest major ones being Hinduism and Buddhism in India, and Zoroastrianism in Persia. The Abrahamic religions trace their origin to Judaism, around 1800 BCE.

In the east, three schools of thought were to dominate Chinese thinking until the modern day. These were Taoism, Legalism and Confucianism. The Confucian tradition, which would attain dominance, looked for political morality not to the force of law but to the power and example of tradition.

In the west, the Greek philosophical tradition, represented by Plato and Aristotle, was diffused throughout Europe and the Middle East in the 4th century BCE by the conquests of Alexander of Macedon.

[edit] Major civilizations and regions

    Main article: Civilization

By the last centuries BCE, the Mediterranean, the Ganges River and the Yellow River had become seats of empires which future rulers would seek to emulate. In India, the Mauryan Empire ruled most of southern Asia, while the Pandyas ruled southern India. In China, the Qin and Han dynasties extended their imperial governance through political unity, improved communications and Emperor Wu's establishment of state monopolies.

In the west, the ancient Greeks established a civilization that is considered by most historians to be the foundational culture of modern western civilization. Some centuries later, in the 3rd century BCE, the Romans began expanding their territory through conquest and colonisation. By the reign of Emperor Augustus (late 1st century BCE), Rome controlled all the lands surrounding the Mediterranean.

The great empires depended on military annexation of territory and on the formation of defended settlements to become agricultural centres. The relative peace that the empires brought, encouraged international trade, most notably the massive trade routes in the Mediterranean that had been developed by the time of the Hellenistic Age, and the Silk Road.

The empires faced common problems associated with maintaining huge armies and supporting a central bureaucracy. These costs fell most heavily on the peasantry, while land-owning magnates were increasingly able to evade centralised control and its costs. The pressure of barbarians on the frontiers hastened the process of internal dissolution. China's Han Empire fell into civil war in 220 CE, while its Roman counterpart became increasingly decentralised and divided about the same time.

Throughout the temperate zones of Eurasia, America and North Africa, empires continued to rise and fall.

The gradual break-up of the Roman Empire, spanning several centuries after the 2nd century CE, coincided with the spread of Christianity westward from the Middle East. The western Roman Empire fell under the domination of Germanic tribes in the 5th century, and these polities gradually developed into a number of warring states, all associated in one way or another with the Roman Catholic Church. The remaining part of the Roman Empire, in the eastern Mediterranean, would henceforth be the Byzantine Empire. Centuries later, a limited unity would be restored to western Europe through the establishment of the Holy Roman Empire, comprising a number of states in what is now Germany and Italy.

In China, dynasties would similarly rise and fall. Nomads from the north began to invade in the 4th century CE, eventually conquering nearly all of northern China and setting up many small kingdoms. The Sui Dynasty reunified China in 581, and under the Tang Dynasty (618-907) China entered a second golden age. The Tang Dynasty also splintered, however, and after half a century of turmoil the Northern Song Dynasty reunified China in 982. Yet pressure from nomadic empires to the north became increasingly urgent. North China was lost to the Jurchen in 1141, and the Mongol Empire conquered all of China in 1279, as well as almost all of Eurasia's landmass, missing only central and western Europe and Japan.

In these times, northern India was ruled by the Guptas. In southern India, three prominent Dravidian kingdoms emerged: Cheras, Cholas and Pandyas. The ensuing stability contributed to heralding in the golden age of Hindu culture in the 4th and 5th centuries CE.
Machu Picchu, "the Lost City of the Incas," has become the most recognizable symbol of Inca civilization.

Edit: Too bad I couldn't fit the rest of the history of the world on here, you all really need to know this stuff.

Last edited by MorbiD.ShoT (2007-02-25 16:38:55)

wow this thread has been derailed. *tries to put /closed tape up, but gets hit by a train*

Smithereener wrote:

11sog_raider wrote:

wow this thread has been derailed. *tries to put /closed tape up, but gets hit by a train*

I dunno, I always thought the point of this thread was to make enormous quote pyramids. And we've been doing that.

This thread hasn't been derailed, but is more like... riding on the edge.

/win

How immature is this going to get?

New mods! I have a problem here, help me!