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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.
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.
Indel (insertion-deletion) is a molecular biology term for an insertion or deletion of bases in the genome of an organism. Indels ≥ 50 bases in length are classified as structural variants.
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.
In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protein-coding genes and non-coding genes.
The Kozak consensus sequence is a nucleic acid motif that functions as the protein translation initiation site in most eukaryotic mRNA transcripts. Regarded as the optimum sequence for initiating translation in eukaryotes, the sequence is an integral aspect of protein regulation and overall cellular health as well as having implications in human disease. It ensures that a protein is correctly translated from the genetic message, mediating ribosome assembly and translation initiation. A wrong start site can result in non-functional proteins. As it has become more studied, expansions of the nucleotide sequence, bases of importance, and notable exceptions have arisen. The sequence was named after the scientist who discovered it, Marilyn Kozak. Kozak discovered the sequence through a detailed analysis of DNA genomic sequences.
Pancrustacea is the clade that comprises all crustaceans, and all 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. The term "Tetraconata" is preferred by some scientists in order to avoid confusion with the use of "pan-" to indicate a clade that includes a crown group and all of its stem group representatives.
Neutral mutations are changes in DNA sequence that are neither beneficial nor detrimental to the ability of an organism to survive and reproduce. In population genetics, mutations in which natural selection does not affect the spread of the mutation in a species are termed neutral mutations. Neutral mutations that are inheritable and not linked to any genes under selection will be lost or will replace all other alleles of the gene. That loss or fixation of the gene proceeds based on random sampling known as genetic drift. A neutral mutation that is in linkage disequilibrium with other alleles that are under selection may proceed to loss or fixation via genetic hitchhiking and/or background selection.
A ribosome binding site, or ribosomal binding site (RBS), is a sequence of nucleotides upstream of the start codon of an mRNA transcript that is responsible for the recruitment of a ribosome during the initiation of translation. Mostly, RBS refers to bacterial sequences, although internal ribosome entry sites (IRES) have been described in mRNAs of eukaryotic cells or viruses that infect eukaryotes. Ribosome recruitment in eukaryotes is generally mediated by the 5' cap present on eukaryotic mRNAs.
MT-ATP6 is a mitochondrial gene with the full name 'mitochondrially encoded ATP synthase membrane subunit 6' that encodes the ATP synthase Fo subunit 6. 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. Mutations in the MT-ATP6 gene have been found in approximately 10 to 20 percent of people with Leigh syndrome.
Ribosomal frameshifting, also known as translational frameshifting or translational recoding, is a biological phenomenon that occurs during translation that results in the production of multiple, unique proteins from a single mRNA. The process can be programmed by the nucleotide sequence of the mRNA and is sometimes affected by the secondary, 3-dimensional mRNA structure. It has been described mainly in viruses, retrotransposons and bacterial insertion elements, and also in some cellular genes.
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.
An expanded genetic code is an artificially modified genetic code in which one or more specific codons have been re-allocated to encode an amino acid that is not among the 22 common naturally-encoded proteinogenic amino acids.
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 vertebrate mitochondrial code is the genetic code found in the mitochondria of all vertebrata.
The bacterial, archaeal and plant plastid code is the DNA code used by bacteria, archaea, prokaryotic viruses and chloroplast proteins. It is essentially the same as the standard code, however there are some variations in alternative start codons.
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 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.
- ↑ Crozier RH, Crozier YC (January 1993). "The mitochondrial genome of the honeybee Apis mellifera: complete sequence and genome organization". Genetics. 133 (1): 97–117. doi:10.1093/genetics/133.1.97. PMC 1205303 . PMID 8417993.
- 1 2 Boore JL, Brown WM (October 1994). "Complete DNA sequence of the mitochondrial genome of the black chiton, Katharina tunicata". Genetics. 138 (2): 423–43. doi:10.1093/genetics/138.2.423. PMC 1206160 . PMID 7828825.
- 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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