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tailed kinetic models such as 38 or others taking into account stochastic aspects of translation and using computer simulations many chemical kinetics based models of protein synthesis have been developed and analyzed in the last four decades 39 40 beyond chemical kinetics various modeling formalisms such as totally asymmetric simple exclusion process 40 probabilistic boolean networks petri nets and max plus algebra have been applied to model the detailed kinetics of protein synthesis or some of its stages a basic model of protein synthesis that takes into account all eight elementary processes has been developed 37 following the paradigm that useful models are simple and extendable 41 the simplest model m0 is represented by the reaction kinetic mechanism figure m0 it was generalise to include 40s 60s and initiation factors if binding figure m1 it was extended further to include effect of microrna on protein synthesis 42 most of models in this hierarchy can be solved analytically these solutions were used to extract kinetic signatures of different specific mechanisms of synthesis regulation genetic code edit main article genetic code it is also possible to translate either by hand for short sequences or by computer after first programming one appropriately see section below this allows biologists and chemists to draw out the primary amino acid sequence of the encoded protein on paper first convert each template dna base to its rna complement note that the complement of a is now u as shown below note that the template strand of the dna is the one the rna is polymerized against the other dna strand would be the same as the rna but with thymine instead of uracil dna rna a u t a c g g c a t a u then split the rna into triplets groups of three bases note that there are 3 translation windows or reading frames depending on where you start reading the code finally use the table at genetic code to translate the above into a structural formula as used in chemistry this will give the primary structure of the protein however proteins tend to fold depending in part on hydrophilic and hydrophobic segments along the chain secondary structure can often still be guessed but the proper tertiary structure is often very hard to determine in order to determine the precise 3d structure and atomic interactions structural biology and several other biophysics methods are used whereas other aspects such as the 3d structure called tertiary structure of protein can only be predicted using sophisticated algorithms the amino acid sequence called primary structure can be determined solely from the nucleic acid sequence with the aid of a translation table this approach may not give the correct amino acid composition of the protein in particular if unconventional amino acids such as selenocysteine are incorporated into the protein which is coded for by a conventional stop codon in combination with a downstream hairpin selenocysteine insertion sequence or secis there are many computer programs capable of translating a dna rna sequence into a protein sequence normally this is performed using the standard genetic code however few programs can handle all the special cases such as the use of the alternative initiation codons which are biologically significant for instance the rare alternative start codon ctg codes for methionine when used as a start codon and for leucine in all other positions example condensed translation table for the standard genetic code from the ncbi taxonomy webpage 43 aas ffllssssyy cc wllllpppphhqqrrrriiimttttnnkkssrrvvvvaaaaddeegggg starts m m m base1 ttttttttttttttttccccccccccccccccaaaaaaaaaaaaaaaagggggggggggggggg base2 ttttccccaaaaggggttttccccaaaaggggttttccccaaaaggggttttccccaaaagggg base3 tcagtcagtcagtcagtcagtcagtcagtcagtcagtcagtcagtcagtcagtcagtcagtcag the starts row indicate three start codons uug cug and the very common aug it also indicates the first amino acid residue when interpreted as a start in this case it is all methionine translation tables edit main articles list of genetic codes and genetic code list of alternative codons even when working with ordinary eukaryotic sequences such as the yeast genome it is often desired to be able to use alternative translation tables namely for translation of the mitochondrial genes currently the following translation tables are defined by the ncbi taxonomy group for the translation of the sequences in genbank 43 the standard code the vertebrate mitochondrial code the yeast mitochondrial code the mold protozoan and coelenterate mitochondrial code and the mycoplasma spiroplasma code the invertebrate mitochondrial code the ciliate dasycladacean and hexamita nuclear code the kinetoplast code the echinoderm and flatworm mitochondrial code the euplotid nuclear code the bacterial archaeal and plant plastid code the alternative yeast nuclear code the ascidian mitochondrial code the alternative flatworm mitochondrial code the blepharisma nuclear code the chlorophycean mitochondrial code the trematode mitochondrial code the scenedesmus obliquus mitochondrial code the thraustochytrium mitochondrial code the pterobranchia mitochondrial code the candidate division sr1 and gracilibacteria code the pachysolen tannophilus nuclear code the karyorelict nuclear code the condylostoma nuclear code the mesodinium nuclear code the peritrich nuclear code the blastocrithidia nuclear code the cephalodiscidae mitochondrial code see also edit cell division dna codon table epigenetics expanded genetic code gene expression gene regulation gene life protein methods references edit liutkute marija maiti manisankar samatova ekaterina enderlein jörg rodnina marina v 2020 10 27 hegde ramanujan s wolberger cynthia eds gradual compaction of the nascent peptide during cotranslational folding on the ribosome elife 9 e60895 doi 10 7554 elife 60895 issn 2050 084x pmc 7593090 pmid 33112737 1 2 tirumalai mr rivas m tran q fox ge november 2021 the peptidyl transferase center a window 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signatures of microrna modes of action ...