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 amino acids in an order specified by messenger RNA, using transfer RNA molecules to carry amino acids and to read the mRNA three nucleotides at a time; the genetic code is similar among all organisms and can be expressed in a simple table with 64 entries. The code defines how sequences of nucleotide triplets, called codons, specify which amino acid will be added next during protein synthesis. With some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid; the vast majority of genes are encoded with a single scheme. That scheme is referred to as the canonical or standard genetic code, or the genetic code, though variant codes exist. While the "genetic code" determines a protein's amino acid sequence, other genomic regions determine when and where these proteins are produced according to various "gene regulatory codes".
Efforts to understand how proteins are encoded began after DNA's structure was discovered in 1953. George Gamow postulated that sets of three bases must be employed to encode the 20 standard amino acids used by living cells to build proteins, which would allow a maximum of 43 = 64 amino acids; the Crick, Brenner and Watts-Tobin experiment first demonstrated that codons consist of three DNA bases. Marshall Nirenberg and Heinrich J. Matthaei were the first to reveal the nature of a codon in 1961, they used a cell-free system to translate a poly-uracil RNA sequence and discovered that the polypeptide that they had synthesized consisted of only the amino acid phenylalanine. They thereby deduced; this was followed by experiments in Severo Ochoa's laboratory that demonstrated that the poly-adenine RNA sequence coded for the polypeptide poly-lysine and that the poly-cytosine RNA sequence coded for the polypeptide poly-proline. Therefore, the codon AAA specified the amino acid lysine, the codon CCC specified the amino acid proline.
Using various copolymers most of the remaining codons were determined. Subsequent work by Har Gobind Khorana identified the rest of the genetic code. Shortly thereafter, Robert W. Holley determined the structure of transfer RNA, the adapter molecule that facilitates the process of translating RNA into protein; this work was based upon Ochoa's earlier studies, yielding the latter the Nobel Prize in Physiology or Medicine in 1959 for work on the enzymology of RNA synthesis. Extending this work and Philip Leder revealed the code's triplet nature and deciphered its codons. In these experiments, various combinations of mRNA were passed through a filter that contained ribosomes, the components of cells that translate RNA into protein. Unique triplets promoted the binding of specific tRNAs to the ribosome. Leder and Nirenberg were able to determine the sequences of 54 out of 64 codons in their experiments. Khorana and Nirenberg received the 1968 Nobel for their work; the three stop codons were named by discoverers Richard Charles Steinberg.
"Amber" was named after their friend Harris Bernstein. The other two stop codons were named "ochre" and "opal". In a broad academic audience, the concept of the evolution of the genetic code from the original and ambiguous genetic code to a well-defined code with the repertoire of 20 canonical amino acids is accepted. However, there are different opinions, concepts and ideas, the best way to change it experimentally. Models are proposed that predict "entry points" for synthetic amino acid invasion of the genetic code. Since 2001, 40 non-natural amino acids have been added into protein by creating a unique codon and a corresponding transfer-RNA:aminoacyl – tRNA-synthetase pair to encode it with diverse physicochemical and biological properties in order to be used as a tool to exploring protein structure and function or to create novel or enhanced proteins. H. Murakami and M. Sisido extended some codons to have five bases. Steven A. Benner constructed a functional 65th codon. In 2015 N. Budisa, D. Söll and co-workers reported the full substitution of all 20,899 tryptophan residues with unnatural thienopyrrole-alanine in the genetic code of the bacterium Escherichia coli.
In 2016 the first stable semisynthetic organism was created. It was a bacterium with two synthetic bases; the bases survived cell division. In 2017, researchers in South Korea reported that they had engineered a mouse with an extended genetic code that can produce proteins with unnatural amino acids. A reading frame is defined by the initial triplet of nucleotides, it sets the frame for a run of successive, non-overlapping codons, known as an "open reading frame". For example, the string 5'-AAATGAACG-3', if read from the first position, contains the codons AAA, TGA, ACG; every sequence can, thus, be read in its 5' → 3' direction in three reading frames, each producing a distinct amino acid sequence: in the given example, Lys -Trp -Thr, Asn -Glu, or Met -Asn, respectively. When DNA is double-stranded, six possible reading frames are defined, three in the forward orientation on one strand
The ribosome is a complex molecular machine, found within all living cells, that serves as the site of biological protein synthesis. Ribosomes link amino acids together in the order specified by messenger RNA molecules. Ribosomes consist of two major components: the small ribosomal subunits, which read the RNA, the large subunits, which join amino acids to form a polypeptide chain; each subunit consists of a variety of ribosomal proteins. The ribosomes and associated molecules are known as the translational apparatus; the sequence of DNA, which encodes the sequence of the amino acids in a protein, is copied into a messenger RNA chain. It may be copied many times into RNA chains. Ribosomes can bind to a messenger RNA chain and use its sequence for determining the correct sequence of amino acids for generating a given protein. Amino acids are selected and carried to the ribosome by transfer RNA molecules, which enter one part of the ribosome and bind to the messenger RNA chain, it is during this binding that the correct translation of nucleic acid sequence to amino acid sequence occurs.
For each coding triplet in the messenger RNA there is a distinct transfer RNA that matches and which carries the correct amino acid for that coding triplet. The attached amino acids are linked together by another part of the ribosome. Once the protein is produced, it can fold to produce a specific functional three-dimensional structure although during synthesis some proteins start folding into their correct form. A ribosome is therefore a ribonucleoprotein; each ribosome is divided into two subunits: a smaller subunit which binds to a larger subunit and the mRNA pattern, a larger subunit which binds to the tRNA, the amino acids, the smaller subunit. When a ribosome finishes reading an mRNA molecule, these two subunits split apart. Ribosomes are ribozymes, because the catalytic peptidyl transferase activity that links amino acids together is performed by the ribosomal RNA. Ribosomes are associated with the intracellular membranes that make up the rough endoplasmic reticulum. Ribosomes from bacteria and eukaryotes in the three-domain system, resemble each other to a remarkable degree, evidence of a common origin.
They differ in their size, sequence and the ratio of protein to RNA. The differences in structure allow some antibiotics to kill bacteria by inhibiting their ribosomes, while leaving human ribosomes unaffected. In bacteria and archaea, more than one ribosome may move along a single mRNA chain at one time, each "reading" its sequence and producing a corresponding protein molecule; the mitochondrial ribosomes of eukaryotic cells, are produced from mitochondrial genes, functionally resemble many features of those in bacteria, reflecting the evolutionary origin of mitochondria. Ribosomes were first observed in the mid-1950s by Romanian-American cell biologist George Emil Palade, using an electron microscope, as dense particles or granules; the term "ribosome" was proposed by scientist Richard B. Roberts in the end of 1950s: During the course of the symposium a semantic difficulty became apparent. To some of the participants, "microsomes" mean the ribonucleoprotein particles of the microsome fraction contaminated by other protein and lipid material.
The phrase "microsomal particles" does not seem adequate, "ribonucleoprotein particles of the microsome fraction" is much too awkward. During the meeting, the word "ribosome" was suggested, which has a satisfactory name and a pleasant sound; the present confusion would be eliminated if "ribosome" were adopted to designate ribonucleoprotein particles in sizes ranging from 35 to 100S. Albert Claude, Christian de Duve, George Emil Palade were jointly awarded the Nobel Prize in Physiology or Medicine, in 1974, for the discovery of the ribosome; the Nobel Prize in Chemistry 2009 was awarded to Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath for determining the detailed structure and mechanism of the ribosome; the ribosome is a complex cellular machine. It is made up of specialized RNA known as ribosomal RNA as well as dozens of distinct proteins; the ribosomal proteins and rRNAs are arranged into two distinct ribosomal pieces of different size, known as the large and small subunit of the ribosome.
Ribosomes consist of two subunits that fit together and work as one to translate the mRNA into a polypeptide chain during protein synthesis. Because they are formed from two subunits of non-equal size, they are longer in the axis than in diameter. Prokaryotic ribosomes are around 20 nm in diameter and are composed of 65% rRNA and 35% ribosomal proteins. Eukaryotic ribosomes are between 25 and 30 nm in diameter with an rRNA-to-protein ratio, close to 1. Crystallographic work has shown that there are no ribosomal proteins close to the reaction site for polypeptide synthesis; this suggests that the protein components of ribosomes do not directly participate in peptide bond formation catalysis, but rather that these proteins act as a scaffold that may enhance the ability of rRNA to synthesize protein. The ribosomal subunits of prokaryotes and eukaryotes are quite similar; the unit of measurement used to describe the ribosomal subunits and the rRNA fragments is the Svedberg unit, a measure of the rate of sedimentation in centrifugation rather than size.
This accounts for why fragment names do not add up: for example, prokaryotic 70S ribosomes are made of 50S and 30S subunits. Prokaryotes have 70
Five prime untranslated region
The 5′ untranslated region is the region of an mRNA, directly upstream from the initiation codon. This region is important for the regulation of translation of a transcript by differing mechanisms in viruses and eukaryotes. While called untranslated, the 5′ UTR or a portion of it is sometimes translated into a protein product; this product can regulate the translation of the main coding sequence of the mRNA. In many organisms, the 5′ UTR is untranslated, instead forming complex secondary structure to regulate translation; the 5′ UTR has been found to interact with proteins relating to metabolism. In addition, this region has been involved in transcription regulation, such as the sex-lethal gene in Drosophila. Regulatory elements within 5′ UTRs have been linked to mRNA export; the 5′ UTR begins at the transcription start site and ends one nucleotide before the initiation sequence of the coding region. In prokaryotes, the length of the 5′ UTR tends to be 3-10 nucleotides long, while in eukaryotes it tends to be anywhere from 100 to several thousand nucleotides long.
For example, the ste11 transcript in Schizosaccharomyces pombe has a 2273 nucleotide 5′ UTR while the lac operon in Escherichia coli only has 7 nucleotides in its 5′ UTR. The differing sizes are due to the complexity of the eukaryotic regulation which the 5′ UTR holds, as well as the larger preinitiation complex which must form to begin translation; the elements of a eukaryotic and prokaryotic 5′ UTR differ greatly. The prokaryotic 5′ UTR contains a ribosome binding site known as the Shine Dalgarno sequence, 3-10 base pairs upstream from the initiation codon. In contrast, the eukaryotic 5′ UTR contains the Kozak consensus sequence, which contains the initiation codon; the eukaryotic 5′ UTR contains cis-acting regulatory elements called upstream open reading frames and upstream AUGs and termination codons, which have a great impact on the regulation of translation. Unlike prokaryotes, 5′ UTRs can harbor introns in eukaryotes. In humans, ~35% of all genes harbor introns within the 5′ UTR; as the 5′ UTR has a high GC content, secondary structures occur within it.
Hairpin loops are one such secondary structure that can be located within the 5′ UTR. These secondary structures impact the regulation of translation. In prokaryotes, the initiation of translation occurs when IF-3, along with the 30S ribosomal subunit, bind to the Shine-Dalgarno sequence of the 5′ UTR; this recruits many other proteins, such as the 50S ribosomal subunit, which allows for translation to begin. Each of these steps regulates the initiation of translation; the regulation of translation in eukaryotes is more complex than in prokaryotes. The eIF4F complex is recruited to the 5′ cap, which in turn recruits the ribosomal complex to the 5′ UTR. Both eIF4E and eIF4G bind the 5′ UTR, which limit the rate at which translational initiation can occur. However, this is not the only regulatory step of translation that involves the 5′ UTR. RNA-binding proteins sometimes serve to prevent the pre-initiation complex from forming. An example is regulation of the msl2 gene; the protein SXL attaches to an intron segment located within the 5′ UTR segment of the primary transcript, which leads to the inclusion of the intron after processing.
This sequence allows the recruitment of proteins that bind to both the 5′ and 3′ UTR, not allowing translation proteins to assemble. However, it has been noted that SXL can repress translation of RNAs that do not contain a poly tail, or more 3′ UTR. Another important regulator of translation is the interaction between 3′ UTR and the 5′ UTR; the closed-loop structure inhibits translation. This has been observed in Xenopus laevis in which eIF4E bound to the 5′ cap interacts with Maskin bound to CPEB on the 3′ UTR creating translationally inactive transcripts; this translational inhibition is lifted once CPEB is phosphorylated, displacing the Maskin binding site, allowing for the polymerization of the PolyA tail, which can recruit the translational machinery by means of PABP. However, it is important to note. Iron levels in cells are maintained by translation regulation of many proteins involved in iron storage and metabolism; the 5′ UTR has the ability to form a hairpin loop secondary structure, recognized by iron-regulatory proteins.
In low levels of iron, the ORF of the target mRNA is blocked as a result of steric hindrance from the binding of IRP1 and IRP2 to the iron-response element. When iron is high the two iron-regulatory proteins do not bind as and allow proteins to be expressed that have a role in iron concentration control; this function has gained some interest after it was revealed that the translation of amyloid precursor protein may be disrupted due to a single-nucleotide polymorphism to the iron response element found in the 5′ UTR of its mRNA, leading to a spontaneous increased risk of Alzheimer's Disease. Another form of translational regulation in eukaryotes comes from unique elements on the 5′ UTR called Upstream Open Reading Frames; these elements are common, occurring in 35-49% of all human genes. A uORF is a coding sequence located in the 5′ UTR located upstream of the coding sequences initiation site; these uORFs contain their own initiation codon, known as an upstream AUG. This codon can be scanned for by ribosomes and translated to create a product, which can regulate the translation of the main protein coding sequence or other uO
Messenger RNA is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they specify the amino acid sequence of the protein products of gene expression. RNA polymerase transcribes primary transcript mRNA into processed, mature mRNA; this mature mRNA is translated into a polymer of amino acids: a protein, as summarized in the central dogma of molecular biology. As in DNA, mRNA genetic information is in the sequence of nucleotides, which are arranged into codons consisting of three base pairs each; each codon encodes for a specific amino acid, except the stop codons, which terminate protein synthesis. This process of translation of codons into amino acids requires two other types of RNA: Transfer RNA, that mediates recognition of the codon and provides the corresponding amino acid, ribosomal RNA, the central component of the ribosome's protein-manufacturing machinery; the existence of mRNA was first suggested by Jacques Monod and François Jacob, subsequently discovered by Jacob, Sydney Brenner and Matthew Meselson at the California Institute of Technology in 1961.
It should not be confused with mitochondrial DNA. The brief existence of an mRNA molecule begins with transcription, ends in degradation. During its life, an mRNA molecule may be processed and transported prior to translation. Eukaryotic mRNA molecules require extensive processing and transport, while prokaryotic mRNA molecules do not. A molecule of eukaryotic mRNA and the proteins surrounding it are together called a messenger RNP. Transcription is when RNA is made from DNA. During transcription, RNA polymerase makes a copy of a gene from the DNA to mRNA as needed; this process is similar in prokaryotes. One notable difference, however, is that eukaryotic RNA polymerase associates with mRNA-processing enzymes during transcription so that processing can proceed after the start of transcription; the short-lived, unprocessed or processed product is termed precursor mRNA, or pre-mRNA. Processing of mRNA differs among eukaryotes and archea. Non-eukaryotic mRNA is, in essence, mature upon transcription and requires no processing, except in rare cases.
Eukaryotic pre-mRNA, requires extensive processing. A 5' cap is a modified guanine nucleotide, added to the "front" or 5' end of a eukaryotic messenger RNA shortly after the start of transcription; the 5' cap consists of a terminal 7-methylguanosine residue, linked through a 5'-5'-triphosphate bond to the first transcribed nucleotide. Its presence is critical for recognition by the protection from RNases. Cap addition is coupled to transcription, occurs co-transcriptionally, such that each influences the other. Shortly after the start of transcription, the 5' end of the mRNA being synthesized is bound by a cap-synthesizing complex associated with RNA polymerase; this enzymatic complex catalyzes the chemical reactions. Synthesis proceeds as a multi-step biochemical reaction. In some instances, an mRNA will be edited, changing the nucleotide composition of that mRNA. An example in humans is the apolipoprotein B mRNA, edited in some tissues, but not others; the editing creates an early stop codon, upon translation, produces a shorter protein.
Polyadenylation is the covalent linkage of a polyadenylyl moiety to a messenger RNA molecule. In eukaryotic organisms most messenger RNA molecules are polyadenylated at the 3' end, but recent studies have shown that short stretches of uridine are common; the poly tail and the protein bound to it aid in protecting mRNA from degradation by exonucleases. Polyadenylation is important for transcription termination, export of the mRNA from the nucleus, translation. MRNA can be polyadenylated in prokaryotic organisms, where poly tails act to facilitate, rather than impede, exonucleolytic degradation. Polyadenylation occurs during and/or after transcription of DNA into RNA. After transcription has been terminated, the mRNA chain is cleaved through the action of an endonuclease complex associated with RNA polymerase. After the mRNA has been cleaved, around 250 adenosine residues are added to the free 3' end at the cleavage site; this reaction is catalyzed by polyadenylate polymerase. Just as in alternative splicing, there can be more than one polyadenylation variant of an mRNA.
Polyadenylation site mutations occur. The primary RNA transcript of a gene is cleaved at the poly-A addition site, 100–200 A's are added to the 3’ end of the RNA. If this site is altered, an abnormally long and unstable mRNA construct will be formed. Another difference between eukaryotes and prokaryotes is mRNA transport; because eukaryotic transcription and translation is compartmentally separated, eukaryotic mRNAs must be exported from the nucleus to the cytoplasm—a process that may be regulated by different signaling pathways. Mature mRNAs are recognized by their processed modifications and exported through the nuclear pore by binding to the cap-binding proteins CBP20 and CBP80, as well as the transcription/export complex. Multiple mRNA export pathways have been identified in eukaryotes. In spatially complex cells, some mRNAs are transported to particular subcellar destinations. In mature neurons, certain mRNA are transported from the soma to dendrites. One site of mRNA translation is at polyribosomes selectively localized beneath synapses.
The mRNA for Arc/Arg3.1 is induced by synaptic activity and localizes selectively near active synapses based on signals generated by NMDA receptor