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The genetic code is the set of rules used by living cells to translate information encoded within genetic material into proteins. Translation is accomplished by the ribosome, which links proteinogenic amino acids in an order specified by messenger RNA (mRNA), using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries.
In molecular biology, a stop codon is a codon that signals the termination of the translation process of the current protein. Most codons in messenger RNA correspond to the addition of an amino acid to a growing polypeptide chain, which may ultimately become a protein; stop codons signal the termination of this process by binding release factors, which cause the ribosomal subunits to disassociate, releasing the amino acid chain.
Mitochondrial DNA is the DNA located in mitochondria, cellular organelles within eukaryotic cells that convert chemical energy from food into a form that cells can use, such as adenosine triphosphate (ATP). Mitochondrial DNA is only a small portion of the DNA in a eukaryotic cell; most of the DNA can be found in the cell nucleus and, in plants and algae, also in plastids such as chloroplasts.
Molecular evolution is the process of change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes. Major topics in molecular evolution concern the rates and impacts of single nucleotide changes, neutral evolution vs. natural selection, origins of new genes, the genetic nature of complex traits, the genetic basis of speciation, the evolution of development, and ways that evolutionary forces influence genomic and phenotypic changes.
In biology, translation is the process in living cells in which proteins are produced using RNA molecules as templates. The generated protein is a sequence of amino acids. This sequence is determined by the sequence of nucleotides in the RNA. The nucleotides are considered three at a time. Each such triple results in addition of one specific amino acid to the protein being generated. The matching from nucleotide triple to amino acid is called the genetic code. The translation is performed by a large complex of functional RNA and proteins called ribosomes. The entire process is called gene expression.
In molecular biology, a reading frame is a way of dividing the sequence of nucleotides in a nucleic acid molecule into a set of consecutive, non-overlapping triplets. Where these triplets equate to amino acids or stop signals during translation, they are called codons.
Transfer RNA is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length, that serves as the physical link between the mRNA and the amino acid sequence of proteins. Transfer RNA (tRNA) does this by carrying an amino acid to the protein synthesizing machinery of a cell called the ribosome. Complementation of a 3-nucleotide codon in a messenger RNA (mRNA) by a 3-nucleotide anticodon of the tRNA results in protein synthesis based on the mRNA code. As such, tRNAs are a necessary component of translation, the biological synthesis of new proteins in accordance with the genetic code.
A synonymous substitution is the evolutionary substitution of one base for another in an exon of a gene coding for a protein, such that the produced amino acid sequence is not modified. This is possible because the genetic code is "degenerate", meaning that some amino acids are coded for by more than one three-base-pair codon; since some of the codons for a given amino acid differ by just one base pair from others coding for the same amino acid, a mutation that replaces the "normal" base by one of the alternatives will result in incorporation of the same amino acid into the growing polypeptide chain when the gene is translated. Synonymous substitutions and mutations affecting noncoding DNA are often considered silent mutations; however, it is not always the case that the mutation is silent.
The start codon is the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon always codes for methionine in eukaryotes and archaea and a N-formylmethionine (fMet) in bacteria, mitochondria and plastids.
Pancrustacea is the clade that comprises all crustaceans, including hexapods. This grouping is contrary to the Atelocerata hypothesis, in which Hexapoda and Myriapoda are sister taxa, and Crustacea are only more distantly related. As of 2010, the Pancrustacea taxon was considered well accepted, with most studies recovering Hexapoda within Crustacea. The clade has also been called Tetraconata, referring to having four cone cells in the ommatidia. This name is preferred by some scientists as a means of avoiding confusion with the use of "pan-" to indicate a clade that includes a crown group and all of its stem group representatives.
MT-ND2 is a gene of the mitochondrial genome coding for the NADH dehydrogenase 2 (ND2) protein. The ND2 protein is a subunit of NADH dehydrogenase (ubiquinone), which is located in the mitochondrial inner membrane and is the largest of the five complexes of the electron transport chain. Variants of human MT-ND2 are associated with mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS), Leigh's syndrome (LS), Leber's hereditary optic neuropathy (LHON) and increases in adult BMI.
MT-ND4L is a gene of the mitochondrial genome coding for the NADH-ubiquinone oxidoreductase chain 4L (ND4L) protein. The ND4L protein is a subunit of NADH dehydrogenase (ubiquinone), which is located in the mitochondrial inner membrane and is the largest of the five complexes of the electron transport chain. Variants of human MT-ND4L are associated with increased BMI in adults and Leber's Hereditary Optic Neuropathy (LHON).
MT-ATP8 is a mitochondrial gene with the full name 'mitochondrially encoded ATP synthase membrane subunit 8' that encodes a subunit of mitochondrial ATP synthase, ATP synthase Fo subunit 8. This subunit belongs to the Fo complex of the large, transmembrane F-type ATP synthase. This enzyme, which is also known as complex V, is responsible for the final step of oxidative phosphorylation in the electron transport chain. Specifically, one segment of ATP synthase allows positively charged ions, called protons, to flow across a specialized membrane inside mitochondria. Another segment of the enzyme uses the energy created by this proton flow to convert a molecule called adenosine diphosphate (ADP) to ATP. Subunit 8 differs in sequence between Metazoa, plants and Fungi.
Cytochrome c oxidase II is a protein in eukaryotes that is encoded by the MT-CO2 gene. Cytochrome c oxidase subunit II, abbreviated COXII, COX2, COII, or MT-CO2, is the second subunit of cytochrome c oxidase. It is also one of the three mitochondrial DNA (mtDNA) encoded subunits of respiratory complex IV.
A codon table can be used to translate a genetic code into a sequence of amino acids. The standard genetic code is traditionally represented as an RNA codon table, because when proteins are made in a cell by ribosomes, it is messenger RNA (mRNA) that directs protein synthesis. The mRNA sequence is determined by the sequence of genomic DNA. In this context, the standard genetic code is referred to as translation table 1. It can also be represented in a DNA codon table. The DNA codons in such tables occur on the sense DNA strand and are arranged in a 5′-to-3′ direction. Different tables with alternate codons are used depending on the source of the genetic code, such as from a cell nucleus, mitochondrion, plastid, or hydrogenosome.
The pterobranchia mitochondrial code is a genetic code used by the mitochondrial genome of Rhabdopleura compacta (Pterobranchia). The Pterobranchia are one of the two groups in the Hemichordata which together with the Echinodermata and Chordata form the three major lineages of deuterostomes. AUA translates to isoleucine in Rhabdopleura as it does in the Echinodermata and Enteropneusta while AUA encodes methionine in the Chordata. The assignment of AGG to lysine is not found elsewhere in deuterostome mitochondria but it occurs in some taxa of Arthropoda. This code shares with many other mitochondrial codes the reassignment of the UGA STOP to tryptophan, and AGG and AGA to an amino acid other than arginine. The initiation codons in Rhabdopleura compacta are ATG and GTG.
The vertebrate mitochondrial code is the genetic code found in the mitochondria of all vertebrata.
The mold, protozoan, and coelenterate mitochondrial code and the mycoplasma/spiroplasma code is the genetic code used by various organisms, in some cases with slight variations, notably the use of UGA as a tryptophan codon rather than a stop codon.
The ambush hypothesis is a hypothesis in the field of molecular genetics that suggests that the prevalence of “hidden” or off-frame stop codons in DNA selectively deters off-frame translation of mRNA to save energy, molecular resources, and to reduce strain on biosynthetic machinery by truncating the production of non-functional, potentially cytotoxic protein products. Typical coding sequences of DNA lack in-frame internal stop codons to avoid the premature reduction of protein products when translation proceeds normally. The ambush hypothesis suggests that kinetic, cis-acting mechanisms are responsible for the productive frameshifting of translational units so that the degeneracy of the genetic code can be used to prevent deleterious translation. Ribosomal slippage is the most well described mechanism of translational frameshifting where the ribosome moves one codon position either forward (+1) or backward (-1) to translate the mRNA sequence in a different reading frame and thus produce different protein products.
The ascidian mitochondrial code is a genetic code found in the mitochondria of Ascidia.
References
This article incorporates text from the United States National Library of Medicine, which is in the public domain. [15]
- ↑ Abascal, Federico; Posada, David; Knight, Robin D.; Zardoya, Rafael (25 April 2006). "Parallel Evolution of the Genetic Code in Arthropod Mitochondrial Genomes". PLOS Biology. 4 (5): e127. doi: 10.1371/journal.pbio.0040127 . ISSN 1545-7885. PMC 1440934 . PMID 16620150.
- ↑ Telford, Maximilian J.; Herniou, Elisabeth A.; Russell, Robert B.; Littlewood, D. Timothy J. (10 October 2000). "Changes in mitochondrial genetic codes as phylogenetic characters: Two examples from the flatworms". Proceedings of the National Academy of Sciences. 97 (21): 11359–11364. doi: 10.1073/pnas.97.21.11359 . ISSN 0027-8424. PMC 17205 . PMID 11027335.
- ↑ Sengupta S, Yang X, Higgs PG (June 2007). "The mechanisms of codon reassignments in mitochondrial genetic codes". Journal of Molecular Evolution. 64 (6): 662–88. arXiv: q-bio/0703066 . Bibcode:2007JMolE..64..662S. doi:10.1007/s00239-006-0284-7. PMC 1894752 . PMID 17541678.
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- 1 2 Hoffmann RJ, Boore JL, Brown WM (June 1992). "A novel mitochondrial genome organization for the blue mussel, Mytilus edulis". Genetics. 131 (2): 397–412. doi:10.1093/genetics/131.2.397. PMC 1205014 . PMID 1386586.
- ↑ Batuecas B, Garesse R, Calleja M, Valverde JR, Marco R (July 1988). "Genome organization of Artemia mitochondrial DNA". Nucleic Acids Research. 16 (14A): 6515–29. doi:10.1093/nar/16.14.6515. PMC 338311 . PMID 3135541.
- ↑ Abascal F, Posada D, Knight RD, Zardoya R (May 2006). "Parallel evolution of the genetic code in arthropod mitochondrial genomes". PLOS Biology. 4 (5): e127. doi: 10.1371/journal.pbio.0040127 . PMC 1440934 . PMID 16620150.
- ↑ Robinson, Richard (25 April 2006). "For Arthropod Mitochondria, Variety in the Genetic Code Is Standard". PLOS Biology. 4 (5): e175. doi: 10.1371/journal.pbio.0040175 . PMC 1440929 . PMID 20076581.
- ↑ Clary DO, Wolstenholme DR (1985). "The mitochondrial DNA molecular of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code". Journal of Molecular Evolution. 22 (3): 252–71. Bibcode:1985JMolE..22..252C. doi:10.1007/BF02099755. PMID 3001325. S2CID 12384495.
- ↑ Gadaleta G, Pepe G, De Candia G, Quagliariello C, Sbisà E, Saccone C (July 1988). "Nucleotide sequence of rat mitochondrial NADH dehydrogenase subunit 1. GTG, a new initiator codon in vertebrate mitochondrial genome". Nucleic Acids Research. 16 (13): 6233. doi:10.1093/nar/16.13.6233. PMC 336868 . PMID 3399396.
- ↑ de Bruijn MH (1983). "Drosophila melanogaster mitochondrial DNA, a novel organization and genetic code". Nature. 304 (5923): 234–41. Bibcode:1983Natur.304..234D. doi:10.1038/304234a0. PMID 6408489. S2CID 35948584.
- ↑ Clary DO, Wolstenholme DR (June 1983). "Nucleotide sequence of a segment of Drosophila mitochondrial DNA that contains the genes for cytochrome c oxidase subunits II and III and ATPase subunit 6". Nucleic Acids Research. 11 (12): 4211–27. doi:10.1093/nar/11.12.4211. PMC 326036 . PMID 6306579.
- ↑ Fox TD (1987). "Natural variation in the genetic code". Annual Review of Genetics. 21: 67–91. doi:10.1146/annurev.ge.21.120187.000435. PMID 3327473.
- ↑ Elzanowski A, Ostell J, Leipe D, Soussov V. "The Genetic Codes". Taxonomy browser. National Center for Biotechnology Information (NCBI), U.S. National Library of Medicine. Retrieved 26 August 2015.
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