Second genetic code

Importance of the Second Genetic Code Some aminoacyl-tRNA synthetases do not recognize and bind the anticodon of their cognate tRNAs but instead use other structural features of the tRNAs to impart binding specificity. The tRNAs for alanine apparently fall into this category. 

What then is an individual If not the molecules themselves, then how about the patterns in which they are assembled A glance at a set of identical twins tells you the answer to this second question is no. The molecular patterns in any organism are determined by the organism s genetic code, and identical twins have identical genetic codes. Each member in a set of identical twins has its own unique personality, however, despite the fact that the two persons have identical molecular patterns. 

The relationship between tRNAs and their synthases is sometimes called the second genetic code. Explain. 

Transfer RNA (tRNA) molecules mediate translation of the nucleic acid genetic code into the amino acid building blocks of proteins, thus ensuring the survivability of cells. The dynamic properties of tRNA molecules are crucial to their functions in both activity and specificity. This chapter summarizes two methods that have been recently developed or improved upon previous protocols to introduce fluorophores to site-specific positions in tRNA. One method enables incorporation of fluorophores carrying a primary amine (such as proflavin or rhodamine) to dihydrouridine (D) residues in the tRNA tertiary core, and a second method enables incorporation of pyrroloC and 2-aminopurine to positions 75 and 76, respectively, of the CCA sequence at the 3 end. These site-specific fluorophore labeling methods utilize tRNA transcripts as the... 

TRANSLATION The process by which a particular messenger RNA (mRNA) nucleotide sequence determines a specific amino acid sequence of a polypeptide chain occurs as the polypeptide is synthesized and is therefore the second step in the readout of the information in the genetic code (the first is transcription). 

Aminoacylation is a two-step process, catalyzed by a set of enzymes known as aminoacyl-tRNA synthetases. Twenty aminoacyl-tRNA synthetases reside in each cell, one per amino acid in the genetic code. In the first step of aminoacyl-tRNA synthesis, ATP and the appropriate amino acid form an aminoacyl adenylate intermediate. Inorganic pyrophosphate is released and subsequently broken down to free phosphate by the enzyme inorganic pyrophosphatase. The aminoacyl adenylate is a high-energy intermediate, and in the second step, the transfer of amino acids to the acceptor end of tRNA occurs without any further input of ATP, as shown in Figure 11-2. 

Codon positions Selective weighting of first, second, and third codon positions in translated genes, because of redundancy of genetic code. A general rule is that third-codon positions are under less selective constraint than first and second and, as such, are more... 

The EDITSEQ application allows you to manually enter DNA or protein sequence information into your computer. This application has several features that make it useful to the research scientist. First, it can identify open reading frames (possible gene sequences) within a DNA sequence. Second, it can provide the percent base composition (A,G,C,T), the percent GC, the percent AT, and the melting temperature of the entire sequence or a small subset of that sequence. Third, EDITSEQ can translate a nucleotide sequence into a protein sequence. Finally, the application is capable of translating or reverse translating a nucleotide sequence of interest using codes other than the standard genetic code. 

Gierasch, L. M. King, J. (1990). Protein Folding Deciphering the Second Half of the Genetic Code. American Association for the Advancement of Science, Washington, D. C. 

Polypeptides would have played only a limited role early in the evolution of life because their structures are not suited to self-replication in the way that nucleic acid structures are. However, polypeptides could have been included in evolutionary processes indirectly. For example, if the properties of a particular polypeptide favored the survival and replication of a class of RNA molecules, then these RNA molecules could have evolved ribozyme activities that promoted the synthesis of that polypeptide. This method of producing polypeptides with specific amino acid sequences has several limitations. First, it seems likely that only relatively short specific polypeptides could have been produced in this manner. Second, it would have been difficult to accurately link the particular amino acids in the polypeptide in a reproducible manner. Finally, a different ribozyme would have been required for each polypeptide. A critical point in evolution was reached when an apparatus for polypeptide synthesis developed that allowed the sequence of bases in an RNA molecule to directly dictate the sequence of amino acids in a polypeptide. A code evolved that established a relation between a specific sequence of three bases in RNA and an amino acid. We now call this set of three-base combinations, each encoding an amino acid, the genetic code. A decoding, or translation, system exists today as the ribosome and associated factors that are responsible for essentially all polypeptide synthesis from RNA templates in modem organisms. The essence of this mode of polypeptide synthesis is illustrated in Figure 2.8. 

The linkage of an amino acid to a tRNA is crucial for two reasons. First, the attachment of a given amino acid to a particular tRNA establishes the genetic code. When an amino acid has been linked to a tRNA, it will be incorporated into a growing polypeptide chain at a position dictated by the anticodon of the tRNA. Second, the formation of a peptide bond between free amino acids is not thermodynamically favorable. The amino acid must first be activated for protein synthesis to proceed. The activated intermediates in protein synthesis are amino acid esters, in which the carboxyl group... 

Second, microbial chemical transformations are accomplished by means of enzymes, proteins that act as catalysts. Catalysts bind with reactants and hold them in such an orientation that they more readily react. The products of the reaction are then released, leaving the catalyst ready to facilitate another transformation. (It is possible for an enzyme to be destroyed if a chemical mimics the proper substrate sufficiently to bind, but fails to react and subsequently release from the enzyme.) Because each enzyme is produced in response to a section of the genetic code (DNA) in the organism and many enzymes are extremely specific, it is possible that some strains of a species of bacteria may accomplish a certain chemical transformation while other individuals cannot. By using modern techniques of molecular biology, scientists can insert specific biotransformation capabilities into bacteria by means of genetic transfer. This procedure is easiest if the genetic material is associated with plasmids, which are small circular molecules of DNA that can exist independently within a bacterial cell. 

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