Amino acid dictionary

Residue name - one of the standard amino acids (lliree-letler abbreviations are used), nucleic acids (one- or two-lctter abbreviations), or the non-standard group designation as dc ncd in lire HHT dictionary 23-26 Residue sequence nuniber,... 

There is one separate tRNA for each amino acid and one separate specific synthetase. The enzyme must bind not only the correct amino acid but also the correct tRNA, so that each synthetase has specific recognition sites for both. Transfer RNAs contain a three-base sequence that is an anticodon, which binds to its complementary codon on messenger RNA. The importance of the synthetase in relation to fidelity of translating the information in messenger RNA is indicated by the fact that, once an amino acid is bound to tRNA, its identity as an amino acid is dictated by the anticodon site on the transfer RNA and not by the amino acid itself. (The enzyme can be considered as a dictionary, since it provides a cross-reference between the nucleic acid and amino acid languages.)... 

Most of the genetic information stored in the genome codes for the amino acid sequences of proteins. For these proteins to be expressed, a text in nucleic acid language therefore has to be translated into protein language. This is the origin of the use of the term translation to describe protein biosynthesis. The dictionary used for the translation is the genetic code. 

FIGURE 27-7 "Dictionary" of amino acid code words in mRNAs. 

How to translate a codon This table (or "dictionary") can be used to translate any codon sequence and, thus, to determine which amino acids are coded for by an mRNA sequence. For example, the codon 5 -AUG-3 codes for methionine (see Figure 31.2). Sixty-one of the 64 codons code for the twenty common amino acids. 

Chapman and Hall Chemical Database Chapman and Hall, Ltd. Dialog Dictionary of Organic Compounds (5th ed.), Dictionary of OrganometalUc Compounds, Carbohydrates, Amino Acids, Peptides, Dictionary of Antibiotics and Related Compounds, and Dictionary of Organophosphorus Compounds... 

Question Is the dictionary of amino acid codons shown in Table 17.1 the same for all organisms ... 

When proteins are hydrolyzed with acid at high temperature, they are broken down to their constituent amino acids. Commonly, the amino acid cystine is found among them. But cystine is not included among the amino acids listed in the dictionary of codons. Why ... 

The structures shown in Figure 3.5 can give rise to 32, 2,048, and 512 different stereoisomers, respectively, and do not accurately represent the chemical names displayed below. It is very common that the representation of stereochemistry for both amino acids and steroids is not reported in publications. Caution must be used with the generation of the N2S engine structure dictionary from representations that omit stereo configurations, for example, from nonstereo SMILES notation. 

Various numbering methods have been used to indicate substitution or other modification in or of the residues of a peptide. The method now recommended by lUPAC and introduced into the Dictionary of Natural Products (see Section 1.2.1) uses numerical locants of the type 3, where 3 is the locant of the substituent in the amino acid residue and 2 is the amino acid position in the ring or chain, numbered from the N-terminal end, which is standard for all peptides). A/ -methyloxytocin would indicate a methyl substituent on N-5 of the glutamine residue at position 4 of oxytocin. 

Protein segments adopt only a finite number of conformations in folded proteins.This limited dictionary of templates may be due to the inherent steric constraints of the backbone and other packing and electrostatic interactions in protein folding. This was most graphically demonstrated by Jones and Thirup. They showed that the majority of the polypeptide backbone of a new structure can be built up from component pieces of other structures, whether or not they are related. Unger et al. showed, in fact, that 76% of the main chain structure of an 82 protein data set can be constructed using only 100 unique hexapeptide templates. Amino acid side chains are also found in a restricted set of conformers. Recent work in our laboratory has shown that a set of four tetrapeptide templates is sufficient to define almost all loop conformations. 

As a result of all this work, by 1967 the following system of relationships (dictionary) between amino acids and the nucleotide triplets (codons) coding them had been established and was universal for all living systems which had been studied. 

Database of interacting proteins http //dip.doe-mbi.ucla.edu also dictionary of interfaces in proteins http //drug-redesign.de/superposition.html 3-[A,/V-bis(2-hydroxyethyl)amino]-2-hydroxypropanesulfonic acid Dynamic light scattering... 

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