Gene

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This article is about the heritable unit for transmission of biological traits. Gene_sentence_0

For other uses, see Gene (disambiguation). Gene_sentence_1

In biology, a gene is a sequence of nucleotides in DNA or RNA that encodes the synthesis of a gene product, either RNA or protein. Gene_sentence_2

During gene expression, the DNA is first copied into RNA. Gene_sentence_3

The RNA can be directly functional or be the intermediate template for a protein that performs a function. Gene_sentence_4

The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic traits. Gene_sentence_5

These genes make up different DNA sequences called genotypes. Gene_sentence_6

Genotypes along with environmental and developmental factors determine what the phenotypes will be. Gene_sentence_7

Most biological traits are under the influence of polygenes (many different genes) as well as gene–environment interactions. Gene_sentence_8

Some genetic traits are instantly visible, such as eye color or the number of limbs, and some are not, such as blood type, the risk for specific diseases, or the thousands of basic biochemical processes that constitute life. Gene_sentence_9

Genes can acquire mutations in their sequence, leading to different variants, known as alleles, in the population. Gene_sentence_10

These alleles encode slightly different versions of a protein, which cause different phenotypical traits. Gene_sentence_11

Usage of the term "having a gene" (e.g., "good genes," "hair colour gene") typically refers to containing a different allele of the same, shared gene. Gene_sentence_12

Genes evolve due to natural selection / survival of the fittest and genetic drift of the alleles. Gene_sentence_13

The concept of gene continues to be refined as new phenomena are discovered. Gene_sentence_14

For example, regulatory regions of a gene can be far removed from its coding regions, and coding regions can be split into several exons. Gene_sentence_15

Some viruses store their genome in RNA instead of DNA and some gene products are functional non-coding RNAs. Gene_sentence_16

Therefore, a broad, modern working definition of a gene is any discrete locus of heritable, genomic sequence which affect an organism's traits by being expressed as a functional product or by regulation of gene expression. Gene_sentence_17

The term gene was introduced by Danish botanist, plant physiologist and geneticist Wilhelm Johannsen in 1909. Gene_sentence_18

It is inspired by the ancient Greek: γόνος, gonos, that means offspring and procreation. Gene_sentence_19

History Gene_section_0

Main article: History of genetics Gene_sentence_20

Discovery of discrete inherited units Gene_section_1

The existence of discrete inheritable units was first suggested by Gregor Mendel (1822–1884). Gene_sentence_21

From 1857 to 1864, in Brno, Austrian Empire (today's Czech Republic), he studied inheritance patterns in 8000 common edible pea plants, tracking distinct traits from parent to offspring. Gene_sentence_22

He described these mathematically as 2 combinations where n is the number of differing characteristics in the original peas. Gene_sentence_23

Although he did not use the term gene, he explained his results in terms of discrete inherited units that give rise to observable physical characteristics. Gene_sentence_24

This description prefigured Wilhelm Johannsen's distinction between genotype (the genetic material of an organism) and phenotype (the observable traits of that organism). Gene_sentence_25

Mendel was also the first to demonstrate independent assortment, the distinction between dominant and recessive traits, the distinction between a heterozygote and homozygote, and the phenomenon of discontinuous inheritance. Gene_sentence_26

Prior to Mendel's work, the dominant theory of heredity was one of blending inheritance, which suggested that each parent contributed fluids to the fertilisation process and that the traits of the parents blended and mixed to produce the offspring. Gene_sentence_27

Charles Darwin developed a theory of inheritance he termed pangenesis, from Greek pan ("all, whole") and genesis ("birth") / genos ("origin"). Gene_sentence_28

Darwin used the term gemmule to describe hypothetical particles that would mix during reproduction. Gene_sentence_29

Mendel's work went largely unnoticed after its first publication in 1866, but was rediscovered in the late 19th century by Hugo de Vries, Carl Correns, and Erich von Tschermak, who (claimed to have) reached similar conclusions in their own research. Gene_sentence_30

Specifically, in 1889, Hugo de Vries published his book Intracellular Pangenesis, in which he postulated that different characters have individual hereditary carriers and that inheritance of specific traits in organisms comes in particles. Gene_sentence_31

De Vries called these units "pangenes" (Pangens in German), after Darwin's 1868 pangenesis theory. Gene_sentence_32

Sixteen years later, in 1905, Wilhelm Johannsen introduced the term 'gene' and William Bateson that of 'genetics' while Eduard Strasburger, amongst others, still used the term 'pangene' for the fundamental physical and functional unit of heredity. Gene_sentence_33

Discovery of DNA Gene_section_2

Advances in understanding genes and inheritance continued throughout the 20th century. Gene_sentence_34

Deoxyribonucleic acid (DNA) was shown to be the molecular repository of genetic information by experiments in the 1940s to 1950s. Gene_sentence_35

The structure of DNA was studied by Rosalind Franklin and Maurice Wilkins using X-ray crystallography, which led James D. Watson and Francis Crick to publish a model of the double-stranded DNA molecule whose paired nucleotide bases indicated a compelling hypothesis for the mechanism of genetic replication. Gene_sentence_36

In the early 1950s the prevailing view was that the genes in a chromosome acted like discrete entities, indivisible by recombination and arranged like beads on a string. Gene_sentence_37

The experiments of Benzer using mutants defective in the rII region of bacteriophage T4 (1955–1959) showed that individual genes have a simple linear structure and are likely to be equivalent to a linear section of DNA. Gene_sentence_38

Collectively, this body of research established the central dogma of molecular biology, which states that proteins are translated from RNA, which is transcribed from DNA. Gene_sentence_39

This dogma has since been shown to have exceptions, such as reverse transcription in retroviruses. Gene_sentence_40

The modern study of genetics at the level of DNA is known as molecular genetics. Gene_sentence_41

In 1972, Walter Fiers and his team were the first to determine the sequence of a gene: that of Bacteriophage MS2 coat protein. Gene_sentence_42

The subsequent development of chain-termination DNA sequencing in 1977 by Frederick Sanger improved the efficiency of sequencing and turned it into a routine laboratory tool. Gene_sentence_43

An automated version of the Sanger method was used in early phases of the Human Genome Project. Gene_sentence_44

Modern synthesis and its successors Gene_section_3

Main article: Modern synthesis (20th century) Gene_sentence_45

The theories developed in the early 20th century to integrate Mendelian genetics with Darwinian evolution are called the modern synthesis, a term introduced by Julian Huxley. Gene_sentence_46

Evolutionary biologists have subsequently modified this concept, such as George C. Williams' gene-centric view of evolution. Gene_sentence_47

He proposed an evolutionary concept of the gene as a unit of natural selection with the definition: "that which segregates and recombines with appreciable frequency." Gene_sentence_48

In this view, the molecular gene transcribes as a unit, and the evolutionary gene inherits as a unit. Gene_sentence_49

Related ideas emphasizing the centrality of genes in evolution were popularized by Richard Dawkins. Gene_sentence_50

Molecular basis Gene_section_4

Main article: DNA Gene_sentence_51

DNA Gene_section_5

The vast majority of organisms encode their genes in long strands of DNA (deoxyribonucleic acid). Gene_sentence_52

DNA consists of a chain made from four types of nucleotide subunits, each composed of: a five-carbon sugar (2-deoxyribose), a phosphate group, and one of the four bases adenine, cytosine, guanine, and thymine. Gene_sentence_53

Two chains of DNA twist around each other to form a DNA double helix with the phosphate-sugar backbone spiraling around the outside, and the bases pointing inwards with adenine base pairing to thymine and guanine to cytosine. Gene_sentence_54

The specificity of base pairing occurs because adenine and thymine align to form two hydrogen bonds, whereas cytosine and guanine form three hydrogen bonds. Gene_sentence_55

The two strands in a double helix must, therefore, be complementary, with their sequence of bases matching such that the adenines of one strand are paired with the thymines of the other strand, and so on. Gene_sentence_56

Due to the chemical composition of the pentose residues of the bases, DNA strands have directionality. Gene_sentence_57

One end of a DNA polymer contains an exposed hydroxyl group on the deoxyribose; this is known as the 3' end of the molecule. Gene_sentence_58

The other end contains an exposed phosphate group; this is the 5' end. Gene_sentence_59

The two strands of a double-helix run in opposite directions. Gene_sentence_60

Nucleic acid synthesis, including DNA replication and transcription occurs in the 5'→3' direction, because new nucleotides are added via a dehydration reaction that uses the exposed 3' hydroxyl as a nucleophile. Gene_sentence_61

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. Gene_sentence_62

RNA also contains the base uracil in place of thymine. Gene_sentence_63

RNA molecules are less stable than DNA and are typically single-stranded. Gene_sentence_64

Genes that encode proteins are composed of a series of three-nucleotide sequences called codons, which serve as the "words" in the genetic "language". Gene_sentence_65

The genetic code specifies the correspondence during protein translation between codons and amino acids. Gene_sentence_66

The genetic code is nearly the same for all known organisms. Gene_sentence_67

Chromosomes Gene_section_6

The total complement of genes in an organism or cell is known as its genome, which may be stored on one or more chromosomes. Gene_sentence_68

A chromosome consists of a single, very long DNA helix on which thousands of genes are encoded. Gene_sentence_69

The region of the chromosome at which a particular gene is located is called its locus. Gene_sentence_70

Each locus contains one allele of a gene; however, members of a population may have different alleles at the locus, each with a slightly different gene sequence. Gene_sentence_71

The majority of eukaryotic genes are stored on a set of large, linear chromosomes. Gene_sentence_72

The chromosomes are packed within the nucleus in complex with storage proteins called histones to form a unit called a nucleosome. Gene_sentence_73

DNA packaged and condensed in this way is called chromatin. Gene_sentence_74

The manner in which DNA is stored on the histones, as well as chemical modifications of the histone itself, regulate whether a particular region of DNA is accessible for gene expression. Gene_sentence_75

In addition to genes, eukaryotic chromosomes contain sequences involved in ensuring that the DNA is copied without degradation of end regions and sorted into daughter cells during cell division: replication origins, telomeres and the centromere. Gene_sentence_76

Replication origins are the sequence regions where DNA replication is initiated to make two copies of the chromosome. Gene_sentence_77

Telomeres are long stretches of repetitive sequences that cap the ends of the linear chromosomes and prevent degradation of coding and regulatory regions during DNA replication. Gene_sentence_78

The length of the telomeres decreases each time the genome is replicated and has been implicated in the aging process. Gene_sentence_79

The centromere is required for binding spindle fibres to separate sister chromatids into daughter cells during cell division. Gene_sentence_80

Prokaryotes (bacteria and archaea) typically store their genomes on a single large, circular chromosome. Gene_sentence_81

Similarly, some eukaryotic organelles contain a remnant circular chromosome with a small number of genes. Gene_sentence_82

Prokaryotes sometimes supplement their chromosome with additional small circles of DNA called plasmids, which usually encode only a few genes and are transferable between individuals. Gene_sentence_83

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. Gene_sentence_84

Whereas the chromosomes of prokaryotes are relatively gene-dense, those of eukaryotes often contain regions of DNA that serve no obvious function. Gene_sentence_85

Simple single-celled eukaryotes have relatively small amounts of such DNA, whereas the genomes of complex multicellular organisms, including humans, contain an absolute majority of DNA without an identified function. Gene_sentence_86

This DNA has often been referred to as "junk DNA". Gene_sentence_87

However, more recent analyses suggest that, although protein-coding DNA makes up barely 2% of the human genome, about 80% of the bases in the genome may be expressed, so the term "junk DNA" may be a misnomer. Gene_sentence_88

Structure and function Gene_section_7

Structure Gene_section_8

The structure of a gene consists of many elements of which the actual protein coding sequence is often only a small part. Gene_sentence_89

These include DNA regions that are not transcribed as well as untranslated regions of the RNA. Gene_sentence_90

Flanking the open reading frame, genes contain a regulatory sequence that is required for their expression. Gene_sentence_91

First, genes require a promoter sequence. Gene_sentence_92

The promoter is recognized and bound by transcription factors that recruit and help RNA polymerase bind to the region to initiate transcription. Gene_sentence_93

The recognition typically occurs as a consensus sequence like the TATA box. Gene_sentence_94

A gene can have more than one promoter, resulting in messenger RNAs (mRNA) that differ in how far they extend in the 5' end. Gene_sentence_95

Highly transcribed genes have "strong" promoter sequences that form strong associations with transcription factors, thereby initiating transcription at a high rate. Gene_sentence_96

Others genes have "weak" promoters that form weak associations with transcription factors and initiate transcription less frequently. Gene_sentence_97

Eukaryotic promoter regions are much more complex and difficult to identify than prokaryotic promoters. Gene_sentence_98

Additionally, genes can have regulatory regions many kilobases upstream or downstream of the open reading frame that alter expression. Gene_sentence_99

These act by binding to transcription factors which then cause the DNA to loop so that the regulatory sequence (and bound transcription factor) become close to the RNA polymerase binding site. Gene_sentence_100

For example, enhancers increase transcription by binding an activator protein which then helps to recruit the RNA polymerase to the promoter; conversely silencers bind repressor proteins and make the DNA less available for RNA polymerase. Gene_sentence_101

The transcribed pre-mRNA contains untranslated regions at both ends which contain a ribosome binding site, terminator and start and stop codons. Gene_sentence_102

In addition, most eukaryotic open reading frames contain untranslated introns which are removed before the exons are translated. Gene_sentence_103

The sequences at the ends of the introns dictate the splice sites to generate the final mature mRNA which encodes the protein or RNA product. Gene_sentence_104

Many prokaryotic genes are organized into operons, with multiple protein-coding sequences that are transcribed as a unit. Gene_sentence_105

The genes in an operon are transcribed as a continuous messenger RNA, referred to as a polycistronic mRNA. Gene_sentence_106

The term cistron in this context is equivalent to gene. Gene_sentence_107

The transcription of an operon's mRNA is often controlled by a repressor that can occur in an active or inactive state depending on the presence of specific metabolites. Gene_sentence_108

When active, the repressor binds to a DNA sequence at the beginning of the operon, called the operator region, and represses transcription of the operon; when the repressor is inactive transcription of the operon can occur (see e.g. Lac operon). Gene_sentence_109

The products of operon genes typically have related functions and are involved in the same regulatory network. Gene_sentence_110

Functional definitions Gene_section_9

Defining exactly what section of a DNA sequence comprises a gene is difficult. Gene_sentence_111

Regulatory regions of a gene such as enhancers do not necessarily have to be close to the coding sequence on the linear molecule because the intervening DNA can be looped out to bring the gene and its regulatory region into proximity. Gene_sentence_112

Similarly, a gene's introns can be much larger than its exons. Gene_sentence_113

Regulatory regions can even be on entirely different chromosomes and operate in trans to allow regulatory regions on one chromosome to come in contact with target genes on another chromosome. Gene_sentence_114

Early work in molecular genetics suggested the concept that one gene makes one protein. Gene_sentence_115

This concept (originally called the one gene-one enzyme hypothesis) emerged from an influential 1941 paper by George Beadle and Edward Tatum on experiments with mutants of the fungus Neurospora crassa. Gene_sentence_116

Norman Horowitz, an early colleague on the Neurospora research, reminisced in 2004 that “these experiments founded the science of what Beadle and Tatum called biochemical genetics. Gene_sentence_117

In actuality they proved to be the opening gun in what became molecular genetics and all the developments that have followed from that.” The one gene-one protein concept has been refined since the discovery of genes that can encode multiple proteins by alternative splicing and coding sequences split in short section across the genome whose mRNAs are concatenated by trans-splicing. Gene_sentence_118

A broad operational definition is sometimes used to encompass the complexity of these diverse phenomena, where a gene is defined as a union of genomic sequences encoding a coherent set of potentially overlapping functional products. Gene_sentence_119

This definition categorizes genes by their functional products (proteins or RNA) rather than their specific DNA loci, with regulatory elements classified as gene-associated regions. Gene_sentence_120

Gene expression Gene_section_10

Main article: Gene expression Gene_sentence_121

In all organisms, two steps are required to read the information encoded in a gene's DNA and produce the protein it specifies. Gene_sentence_122

First, the gene's DNA is transcribed to messenger RNA (mRNA). Gene_sentence_123

Second, that mRNA is translated to protein. Gene_sentence_124

RNA-coding genes must still go through the first step, but are not translated into protein. Gene_sentence_125

The process of producing a biologically functional molecule of either RNA or protein is called gene expression, and the resulting molecule is called a gene product. Gene_sentence_126

Genetic code Gene_section_11

The nucleotide sequence of a gene's DNA specifies the amino acid sequence of a protein through the genetic code. Gene_sentence_127

Sets of three nucleotides, known as codons, each correspond to a specific amino acid. Gene_sentence_128

The principle that three sequential bases of DNA code for each amino acid was demonstrated in 1961 using frameshift mutations in the rIIB gene of bacteriophage T4 (see Crick, Brenner et al. Gene_sentence_129 experiment). Gene_sentence_130

Additionally, a "start codon", and three "stop codons" indicate the beginning and end of the protein coding region. Gene_sentence_131

There are 64 possible codons (four possible nucleotides at each of three positions, hence 4 possible codons) and only 20 standard amino acids; hence the code is redundant and multiple codons can specify the same amino acid. Gene_sentence_132

The correspondence between codons and amino acids is nearly universal among all known living organisms. Gene_sentence_133

Transcription Gene_section_12

Transcription produces a single-stranded RNA molecule known as messenger RNA, whose nucleotide sequence is complementary to the DNA from which it was transcribed. Gene_sentence_134

The mRNA acts as an intermediate between the DNA gene and its final protein product. Gene_sentence_135

The gene's DNA is used as a template to generate a complementary mRNA. Gene_sentence_136

The mRNA matches the sequence of the gene's DNA coding strand because it is synthesised as the complement of the template strand. Gene_sentence_137

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'. Gene_sentence_138

To initiate transcription, the polymerase first recognizes and binds a promoter region of the gene. Gene_sentence_139

Thus, a major mechanism of gene regulation is the blocking or sequestering 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. Gene_sentence_140

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. Gene_sentence_141

In eukaryotes, transcription occurs in the nucleus, where the cell's DNA is stored. Gene_sentence_142

The RNA molecule produced by the polymerase is known as the primary transcript and undergoes post-transcriptional modifications before being exported to the cytoplasm for translation. Gene_sentence_143

One of the modifications performed is the splicing of introns which are sequences in the transcribed region that do not encode a protein. Gene_sentence_144

Alternative splicing mechanisms can result in mature transcripts from the same gene having different sequences and thus coding for different proteins. Gene_sentence_145

This is a major form of regulation in eukaryotic cells and also occurs in some prokaryotes. Gene_sentence_146

Translation Gene_section_13

Translation is the process by which a mature mRNA molecule is used as a template for synthesizing a new protein. Gene_sentence_147

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. Gene_sentence_148

The genetic code is read three nucleotides at a time, in units called codons, via interactions with specialized RNA molecules called transfer RNA (tRNA). Gene_sentence_149

Each tRNA has three unpaired bases known as the anticodon that are complementary to the codon it reads on the mRNA. Gene_sentence_150

The tRNA is also covalently attached to the amino acid specified by the complementary codon. Gene_sentence_151

When the tRNA binds to its complementary codon in an mRNA strand, the ribosome attaches its amino acid cargo to the new polypeptide chain, which is synthesized from amino terminus to carboxyl terminus. Gene_sentence_152

During and after synthesis, most new proteins must fold to their active three-dimensional structure before they can carry out their cellular functions. Gene_sentence_153

Regulation Gene_section_14

Genes are regulated so that they are expressed only when the product is needed, since expression draws on limited resources. Gene_sentence_154

A cell regulates its gene expression depending on its external environment (e.g. available nutrients, temperature and other stresses), its internal environment (e.g. cell division cycle, metabolism, infection status), and its specific role if in a multicellular organism. Gene_sentence_155

Gene expression can be regulated at any step: from transcriptional initiation, to RNA processing, to post-translational modification of the protein. Gene_sentence_156

The regulation of lactose metabolism genes in E. Gene_sentence_157 coli (lac operon) was the first such mechanism to be described in 1961. Gene_sentence_158

RNA genes Gene_section_15

A typical protein-coding gene is first copied into RNA as an intermediate in the manufacture of the final protein product. Gene_sentence_159

In other cases, the RNA molecules are the actual functional products, as in the synthesis of ribosomal RNA and transfer RNA. Gene_sentence_160

Some RNAs known as ribozymes are capable of enzymatic function, and microRNA has a regulatory role. Gene_sentence_161

The DNA sequences from which such RNAs are transcribed are known as non-coding RNA genes. Gene_sentence_162

Some viruses store their entire genomes in the form of RNA, and contain no DNA at all. Gene_sentence_163

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. Gene_sentence_164

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. Gene_sentence_165

RNA-mediated epigenetic inheritance has also been observed in plants and very rarely in animals. Gene_sentence_166

Inheritance Gene_section_16

Main articles: Mendelian inheritance and Heredity Gene_sentence_167

Organisms inherit their genes from their parents. Gene_sentence_168

Asexual organisms simply inherit a complete copy of their parent's genome. Gene_sentence_169

Sexual organisms have two copies of each chromosome because they inherit one complete set from each parent. Gene_sentence_170

Mendelian inheritance Gene_section_17

According to Mendelian inheritance, variations in an organism's phenotype (observable physical and behavioral characteristics) are due in part to variations in its genotype (particular set of genes). Gene_sentence_171

Each gene specifies a particular trait with a different sequence of a gene (alleles) giving rise to different phenotypes. Gene_sentence_172

Most eukaryotic organisms (such as the pea plants Mendel worked on) have two alleles for each trait, one inherited from each parent. Gene_sentence_173

Alleles at a locus may be dominant or recessive; dominant alleles give rise to their corresponding phenotypes when paired with any other allele for the same trait, whereas recessive alleles give rise to their corresponding phenotype only when paired with another copy of the same allele. Gene_sentence_174

If you know the genotypes of the organisms, you can determine which alleles are dominant and which are recessive. Gene_sentence_175

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. Gene_sentence_176

Mendel's work demonstrated that alleles assort independently in the production of gametes, or germ cells, ensuring variation in the next generation. Gene_sentence_177

Although Mendelian inheritance remains a good model for many traits determined by single genes (including a number of well-known genetic disorders) it does not include the physical processes of DNA replication and cell division. Gene_sentence_178

DNA replication and cell division Gene_section_18

The growth, development, and reproduction of organisms relies on cell division; the process by which a single cell divides into two usually identical daughter cells. Gene_sentence_179

This requires first making a duplicate copy of every gene in the genome in a process called DNA replication. Gene_sentence_180

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. Gene_sentence_181

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. Gene_sentence_182

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. Gene_sentence_183

The rate of DNA replication in living cells was first measured as the rate of phage T4 DNA elongation in phage-infected E. coli and found to be impressively rapid. Gene_sentence_184

During the period of exponential DNA increase at 37 °C, the rate of elongation was 749 nucleotides per second. Gene_sentence_185

After DNA replication is complete, the cell must physically separate the two copies of the genome and divide into two distinct membrane-bound cells. Gene_sentence_186

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. Gene_sentence_187

Binary fission is extremely fast compared to the rates of cell division in eukaryotes. Gene_sentence_188

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, whereas the process of segregating chromosomes and splitting the cytoplasm occurs during M phase. Gene_sentence_189

Molecular inheritance Gene_section_19

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. Gene_sentence_190

Organisms inherit the characteristics of their parents because the cells of the offspring contain copies of the genes in their parents' cells. Gene_sentence_191

In asexually reproducing organisms, the offspring will be a genetic copy or clone of the parent organism. Gene_sentence_192

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. Gene_sentence_193

The gametes produced by females are called eggs or ova, and those produced by males are called sperm. Gene_sentence_194

Two gametes fuse to form a diploid fertilized egg, a single cell that has two sets of genes, with one copy of each gene from the mother and one from the father. Gene_sentence_195

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 homologous non-sister chromatid. Gene_sentence_196

This can result in reassortment of otherwise linked alleles. Gene_sentence_197

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. Gene_sentence_198

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. Gene_sentence_199

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 (known as genetic linkage). Gene_sentence_200

Genes that are very close are essentially never separated because it is extremely unlikely that a crossover point will occur between them. Gene_sentence_201

Molecular evolution Gene_section_20

Main article: Molecular evolution Gene_sentence_202

Mutation Gene_section_21

DNA replication is for the most part extremely accurate, however errors (mutations) do occur. Gene_sentence_203

The error rate in eukaryotic cells can be as low as 10 per nucleotide per replication, whereas for some RNA viruses it can be as high as 10. Gene_sentence_204

This means that each generation, each human genome accumulates 1–2 new mutations. Gene_sentence_205

Small mutations can be caused by DNA replication and the aftermath of DNA damage and include point mutations in which a single base is altered and frameshift mutations in which a single base is inserted or deleted. Gene_sentence_206

Either of these mutations can change the gene by missense (change a codon to encode a different amino acid) or nonsense (a premature stop codon). Gene_sentence_207

Larger mutations can be caused by errors in recombination to cause chromosomal abnormalities including the duplication, deletion, rearrangement or inversion of large sections of a chromosome. Gene_sentence_208

Additionally, DNA repair mechanisms can introduce mutational errors when repairing physical damage to the molecule. Gene_sentence_209

The repair, even with mutation, is more important to survival than restoring an exact copy, for example when repairing double-strand breaks. Gene_sentence_210

When multiple different alleles for a gene are present in a species's population it is called polymorphic. Gene_sentence_211

Most different alleles are functionally equivalent, however some alleles can give rise to different phenotypic traits. Gene_sentence_212

A gene's most common allele is called the wild type, and rare alleles are called mutants. Gene_sentence_213

The genetic variation in relative frequencies of different alleles in a population is due to both natural selection and genetic drift. Gene_sentence_214

The wild-type allele is not necessarily the ancestor of less common alleles, nor is it necessarily fitter. Gene_sentence_215

Most mutations within genes are neutral, having no effect on the organism's phenotype (silent mutations). Gene_sentence_216

Some mutations do not change the amino acid sequence because multiple codons encode the same amino acid (synonymous mutations). Gene_sentence_217

Other mutations can be neutral if they lead to amino acid sequence changes, but the protein still functions similarly with the new amino acid (e.g. conservative mutations). Gene_sentence_218

Many mutations, however, are deleterious or even lethal, and are removed from populations by natural selection. Gene_sentence_219

Genetic disorders are the result of deleterious mutations and can be due to spontaneous mutation in the affected individual, or can be inherited. Gene_sentence_220

Finally, a small fraction of mutations are beneficial, improving the organism's fitness and are extremely important for evolution, since their directional selection leads to adaptive evolution. Gene_sentence_221

Sequence homology Gene_section_22

Genes with a most recent common ancestor, and thus a shared evolutionary ancestry, are known as homologs. Gene_sentence_222

These genes appear either from gene duplication within an organism's genome, where they are known as paralogous genes, or are the result of divergence of the genes after a speciation event, where they are known as orthologous genes, and often perform the same or similar functions in related organisms. Gene_sentence_223

It is often assumed that the functions of orthologous genes are more similar than those of paralogous genes, although the difference is minimal. Gene_sentence_224

The relationship between genes can be measured by comparing the sequence alignment of their DNA. Gene_sentence_225

The degree of sequence similarity between homologous genes is called conserved sequence. Gene_sentence_226

Most changes to a gene's sequence do not affect its function and so genes accumulate mutations over time by neutral molecular evolution. Gene_sentence_227

Additionally, any selection on a gene will cause its sequence to diverge at a different rate. Gene_sentence_228

Genes under stabilizing selection are constrained and so change more slowly whereas genes under directional selection change sequence more rapidly. Gene_sentence_229

The sequence differences between genes can be used for phylogenetic analyses to study how those genes have evolved and how the organisms they come from are related. Gene_sentence_230

Origins of new genes Gene_section_23

The most common source of new genes in eukaryotic lineages is gene duplication, which creates copy number variation of an existing gene in the genome. Gene_sentence_231

The resulting genes (paralogs) may then diverge in sequence and in function. Gene_sentence_232

Sets of genes formed in this way compose a gene family. Gene_sentence_233

Gene duplications and losses within a family are common and represent a major source of evolutionary biodiversity. Gene_sentence_234

Sometimes, gene duplication may result in a nonfunctional copy of a gene, or a functional copy may be subject to mutations that result in loss of function; such nonfunctional genes are called pseudogenes. Gene_sentence_235

"Orphan" genes, whose sequence shows no similarity to existing genes, are less common than gene duplicates. Gene_sentence_236

The human genome contains an estimate 18 to 60 genes with no identifiable homologs outside humans. Gene_sentence_237

Orphan genes arise primarily from either de novo emergence from previously non-coding sequence, or gene duplication followed by such rapid sequence change that the original relationship becomes undetectable. Gene_sentence_238

De novo genes are typically shorter and simpler in structure than most eukaryotic genes, with few if any introns. Gene_sentence_239

Over long evolutionary time periods, de novo gene birth may be responsible for a significant fraction of taxonomically-restricted gene families. Gene_sentence_240

Horizontal gene transfer refers to the transfer of genetic material through a mechanism other than reproduction. Gene_sentence_241

This mechanism is a common source of new genes in prokaryotes, sometimes thought to contribute more to genetic variation than gene duplication. Gene_sentence_242

It is a common means of spreading antibiotic resistance, virulence, and adaptive metabolic functions. Gene_sentence_243

Although horizontal gene transfer is rare in eukaryotes, likely examples have been identified of protist and alga genomes containing genes of bacterial origin. Gene_sentence_244

Genome Gene_section_24

The genome is the total genetic material of an organism and includes both the genes and non-coding sequences. Gene_sentence_245

Number of genes Gene_section_25

The genome size, and the number of genes it encodes varies widely between organisms. Gene_sentence_246

The smallest genomes occur in viruses, and viroids (which act as a single non-coding RNA gene). Gene_sentence_247

Conversely, plants can have extremely large genomes, with rice containing >46,000 protein-coding genes. Gene_sentence_248

The total number of protein-coding genes (the Earth's proteome) is estimated to be 5 million sequences. Gene_sentence_249

Although the number of base-pairs of DNA in the human genome has been known since the 1960s, the estimated number of genes has changed over time as definitions of genes, and methods of detecting them have been refined. Gene_sentence_250

Initial theoretical predictions of the number of human genes were as high as 2,000,000. Gene_sentence_251

Early experimental measures indicated there to be 50,000–100,000 transcribed genes (expressed sequence tags). Gene_sentence_252

Subsequently, the sequencing in the Human Genome Project indicated that many of these transcripts were alternative variants of the same genes, and the total number of protein-coding genes was revised down to ~20,000 with 13 genes encoded on the mitochondrial genome. Gene_sentence_253

With the GENCODE annotation project, that estimate has continued to fall to 19,000. Gene_sentence_254

Of the human genome, only 1–2% consists of protein-coding sequences, with the remainder being 'noncoding' DNA such as introns, retrotransposons, and noncoding RNAs. Gene_sentence_255

Every multicellular organism has all its genes in each cell of its body but not every gene functions in every cell . Gene_sentence_256

Essential genes Gene_section_26

Main article: Essential gene Gene_sentence_257

Essential genes are the set of genes thought to be critical for an organism's survival. Gene_sentence_258

This definition assumes the abundant availability of all relevant nutrients and the absence of environmental stress. Gene_sentence_259

Only a small portion of an organism's genes are essential. Gene_sentence_260

In bacteria, an estimated 250–400 genes are essential for Escherichia coli and Bacillus subtilis, which is less than 10% of their genes. Gene_sentence_261

Half of these genes are orthologs in both organisms and are largely involved in protein synthesis. Gene_sentence_262

In the budding yeast Saccharomyces cerevisiae the number of essential genes is slightly higher, at 1000 genes (~20% of their genes). Gene_sentence_263

Although the number is more difficult to measure in higher eukaryotes, mice and humans are estimated to have around 2000 essential genes (~10% of their genes). Gene_sentence_264

The synthetic organism, Syn 3, has a minimal genome of 473 essential genes and quasi-essential genes (necessary for fast growth), although 149 have unknown function. Gene_sentence_265

Essential genes include housekeeping genes (critical for basic cell functions) as well as genes that are expressed at different times in the organisms development or life cycle. Gene_sentence_266

Housekeeping genes are used as experimental controls when analysing gene expression, since they are constitutively expressed at a relatively constant level. Gene_sentence_267

Genetic and genomic nomenclature Gene_section_27

Gene nomenclature has been established by the HUGO Gene Nomenclature Committee (HGNC), a committee of the Human Genome Organisation, for each known human gene in the form of an approved gene name and symbol (short-form abbreviation), which can be accessed through a database maintained by HGNC. Gene_sentence_268

Symbols are chosen to be unique, and each gene has only one symbol (although approved symbols sometimes change). Gene_sentence_269

Symbols are preferably kept consistent with other members of a gene family and with homologs in other species, particularly the mouse due to its role as a common model organism. Gene_sentence_270

Genetic engineering Gene_section_28

Main article: Genetic engineering Gene_sentence_271

Genetic engineering is the modification of an organism's genome through biotechnology. Gene_sentence_272

Since the 1970s, a variety of techniques have been developed to specifically add, remove and edit genes in an organism. Gene_sentence_273

Recently developed genome engineering techniques use engineered nuclease enzymes to create targeted DNA repair in a chromosome to either disrupt or edit a gene when the break is repaired. Gene_sentence_274

The related term synthetic biology is sometimes used to refer to extensive genetic engineering of an organism. Gene_sentence_275

Genetic engineering is now a routine research tool with model organisms. Gene_sentence_276

For example, genes are easily added to bacteria and lineages of knockout mice with a specific gene's function disrupted are used to investigate that gene's function. Gene_sentence_277

Many organisms have been genetically modified for applications in agriculture, industrial biotechnology, and medicine. Gene_sentence_278

For multicellular organisms, typically the embryo is engineered which grows into the adult genetically modified organism. Gene_sentence_279

However, the genomes of cells in an adult organism can be edited using gene therapy techniques to treat genetic diseases. Gene_sentence_280

See also Gene_section_29

Credits to the contents of this page go to the authors of the corresponding Wikipedia page: en.wikipedia.org/wiki/Gene.