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Amino acids are organic compounds that contain amino and carboxylate −CO−2 functional groups, along with a side chain specific to each amino acid. The elements present in every amino acid are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N); in addition sulfur (S) is present in the side chains of cysteine and methionine, and selenium (Se) in the less common amino acid selenocysteine. More than 500 naturally occurring amino acids are known to constitute monomer units of peptides, including proteins, as of 2020
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.
Selenocysteine is the 21st proteinogenic amino acid. Selenoproteins contain selenocysteine residues. Selenocysteine is an analogue of the more common cysteine with selenium in place of the sulfur.
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.
Pyrrolysine is an α-amino acid that is used in the biosynthesis of proteins in some methanogenic archaea and bacteria; it is not present in humans. It contains an α-amino group, a carboxylic acid group. Its pyrroline side-chain is similar to that of lysine in being basic and positively charged at neutral pH.
In molecular biology and genetics, translation is the process in which ribosomes in the cytoplasm or endoplasmic reticulum synthesize proteins after the process of transcription of DNA to RNA in the cell's nucleus. The entire process is called gene expression.
Proteinogenic amino acids are amino acids that are incorporated biosynthetically into proteins during translation. The word "proteinogenic" means "protein creating". Throughout known life, there are 22 genetically encoded (proteinogenic) amino acids, 20 in the standard genetic code and an additional 2 that can be incorporated by special translation mechanisms.
A frameshift mutation is a genetic mutation caused by indels of a number of nucleotides in a DNA sequence that is not divisible by three. Due to the triplet nature of gene expression by codons, the insertion or deletion can change the reading frame, resulting in a completely different translation from the original. The earlier in the sequence the deletion or insertion occurs, the more altered the protein. A frameshift mutation is not the same as a single-nucleotide polymorphism in which a nucleotide is replaced, rather than inserted or deleted. A frameshift mutation will in general cause the reading of the codons after the mutation to code for different amino acids. The frameshift mutation will also alter the first stop codon encountered in the sequence. The polypeptide being created could be abnormally short or abnormally long, and will most likely not be functional.
The Nirenberg and Matthaei experiment was a scientific experiment performed in May 1961 by Marshall W. Nirenberg and his post-doctoral fellow, J. Heinrich Matthaei, at the National Institutes of Health (NIH). The experiment deciphered the first of the 64 triplet codons in the genetic code by using nucleic acid homopolymers to translate specific amino acids.
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. The most common start codon is AUG.
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 yeast mitochondrial code is a genetic code used by the mitochondrial genome of yeasts, notably Saccharomyces cerevisiae, Candida glabrata, Hansenula saturnus, and Kluyveromyces thermotolerans.
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 euplotid nuclear code is the genetic code used by Euplotidae. The euplotid code is a socalled "symmetrical code", which results from the symmetrical distribution of the codons. This symmetry allows for arythmic exploration of the codon distribution. In 2013, shCherbak and Makukov, reported that "the patterns are shown to match the criteria of an intelligent signal."
The ascidian mitochondrial code is a genetic code found in the mitochondria of Ascidia.
The alternative flatworm mitochondrial code is a genetic code found in the mitochondria of Platyhelminthes and Nematodes.
Low complexity regions (LCRs) in protein sequences, also defined in some contexts as compositionally biased regions (CBRs), are regions in protein sequences that differ from the composition and complexity of most proteins that is normally associated with globular structure. LCRs have different properties from normal regions regarding structure, function and evolution.
The Cephalodiscidae mitochondrial code is a genetic code used by the mitochondrial genome of Cephalodiscidae (Pterobranchia). The Pterobranchia are one of the two groups in the Hemichordata which together with the Echinodermata and Chordata form the major clades of deuterostomes.
Gracilibacteria is a bacterial candidate phylum formerly known as GN02, BD1-5, or SN-2. It is part of the Candidate Phyla Radiation and the Patescibacteria group.
References
This article incorporates text from the United States National Library of Medicine, which is in the public domain. [3]
- ↑ Davis, James P.; Youssef, Noha H.; Elshahed, Mostafa S. (June 2009). "Assessment of the diversity, abundance, and ecological distribution of members of candidate division SR1 reveals a high level of phylogenetic diversity but limited morphotypic diversity". Applied and Environmental Microbiology. 75 (12): 4139–4148. Bibcode:2009ApEnM..75.4139D. doi:10.1128/AEM.00137-09. ISSN 1098-5336. PMC 2698373 . PMID 19395567.
- ↑ J. H. Campbell; O'P. Donoghue; A. G. Campbell; P. Schwientek; A. Sczyrba; T. Woyke; D. Söll; M. Podar (2 April 2013). "UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota". Proc Natl Acad Sci U S A. 110 (14): 5540–5. Bibcode:2013PNAS..110.5540C. doi: 10.1073/pnas.1303090110 . PMC 3619370 . PMID 23509275.
- ↑ 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 19 March 2016.