Genetic code stop codons

Section 28 11 Three RNAs are involved m gene expression In the transcription phase a strand of messenger RNA (mRNA) is synthesized from a DNA tern plate The four bases A G C and U taken three at a time generate 64 possible combinations called codons These 64 codons comprise the genetic code and code for the 20 ammo acids found m proteins plus start and stop signals The mRNA sequence is translated into a prescribed protein sequence at the ribosomes There small polynucleotides called... 

The genetic code is composed of four letters —two pyrimidine nitrogenous bases, thymine and cytosine, and two purine bases, guanine and adenine—which can be regarded functionally as arranged in codons (or triplets). Each codon consists of a combination of three letters therefore, 43 (64) different codons are possible. Sixty-one codons code for specific amino acids (three produce stop signals), and as only 20 different amino acids are used to make proteins, one amino acid can be specified by more than one codon. 

Figure 10 Alteration of the genetic code for incorporation of non-natural amino acids, (a) In nonsense suppression, the stop codon UAG is decoded by a non-natural tRNA with the anticodon CUA. In vivo decoding of the UAG codon by this tRNA is in competition with termination of protein synthesis by release factor 1 (RFl). Purified in vitro translation systems allow omission of RF1 from the reaction mixture, (b) A new codon-anticodon pair can be created using four-base codons such as GGGU. Crystal structures of these codon-anticodon complexes in the ribosomal decoding center revealed that the C in the third anticodon position interacts with both the third and fourth codon position (purple line) while the extra A in the anticodon loop does not contact the codon.(c) Non-natural base pairs also allow creation of new codon-anticodon pairs. Shown here is the interaction of the base Y with either base X or (hydrogen bonds are indicated by red dashes).

Genetic code Start AUG (also codes for Met) Stop UAG,UGA,UAA Unambiguous (1 codon = 1 amino acid) Redundant (1 amino acid >1 codon) often differ at base 3 ... 

Translation of the information encoded in DNA, expressed as a particular nucleotide sequence, into a protein, expressed as an amino acid sequence, depends on the genetic code. In this code, sequences of three nucleotides (termed a codon) represent one of the 20 amino acids that compose the protein molecule. Because there are 64 codons which can be constructed for the four different bases, and only 20 different amino acids that are coded for, several amino acids may be coded for by more than one codon. There are also three codons, called stop codons, that terminate the transfer of information. Furthermore, although all cells contain the same complement of genes, certain cells (for example, the neurons) have specialized genes that encode specific proteins for the synthesis of specific transmitters. The expression of such genes is under the control of regulatory proteins called transcription factors which control the transcription of mRNAs from the genes they control. 

As the genetic code provides 4 = 64 codons for the 20 amino acids, there are several synonymous codons for most amino acids— the code is degenerate. Three triplets do not code for amino acids, but instead signal the end of translation (stop codons). Another special codon, the start codon, marks the start of translation. The code shown here is almost universally applicable only the mitochondria (see p. 210) and a few microorganisms deviate from it slightly. 

The following table indicates the standard codons that serve as the basis of the genetic code. Note (a) Stop codons have no amino acids assigned to them (b) Met indicates the AUG start codon. 

The last stage of peptide chain synthesis is termination. The genetic code specifies three stop codons, indicating the termination of a coding sequence. When the ribosome encounters one of these stop codons on the mRNA, certain release factors... 

C, G or T. This is not sufficient to encode the 20 possible amino acids. In triplets of 3 positions, there are 64 possible combinations. Hence, the system uses triplets, called codons. The code for each protein starts with an ATG (start codon) and ends with a TAA, TAG or a TGA (stop codons). The code is almost universal only mitochondria and ciliated protozoa have a different genetic code. 

In the next step, translation, the sequence of nucleotides in the newly synthesized mRNA strand is used to determine the sequence of amino acids in the protein to be synthesized. This is done by way of a genetic code, which was fully deciphered by 1966 and is shown in Figure 13.34. According to the genetic code, it takes three mRNA nucleotides—each three-nucleotide unit is called a codon—to code for a single amino acid. The mRNA nucleotide sequence AGU, for example, codes for the amino acid serine, and AAG codes for lysine. (Note from Figure 13.34 that more than one codon can call for the same amino acid.) A few codons, such as AUG and UGA, are the signals for protein synthesis to either start or stop. 

DNA replication under low-fidelity conditions, typically error-prone PCR (Arkin, 1992 Zaccolo, 1999) the method is simple and convenient, but the conservative nature of the genetic code limits the available substitutions to only five to seven amino acid substitutions per codon and the incorporation of stop codons limits the acceptable mutation rate to around two amino acid substitutions per gene (Smith, 1993 Arnold, 2000) ... 

The genetic code involves sequences of three bases called codons, each of which translates to a specific amino acid. The code is degenerate (that is, there is more than one codon per amino acid), and some codons are "stop" signals that terminate synthesis. 

Table 1.9 The genetic code. The start codon is always AUG. Some codons act as start and stop signals in protein synthesis. Codons are always written left to right, 5 to 3 ...

The genetic code is the rules that specify how the nucleotide sequence of an mRNA is translated into the amino acid sequence of a polypeptide. The nucleotide sequence is read as triplets called codons. The codons UAG, UGA and UAA do not specify amino acids and are called termination codons or Stop codons. AUG codes for methionine and also acts as an initiation (Start) codon. 

Mean-field theory can be used to predict the effects of mutation rate and parent fitness on the moments of the mutant fitness distribution (Voigt et al, 2000a). In this analysis, only the portion of the mutant distribution that is not dead (zero fitness) or parent (unmutated) is considered. The mutant effects are averaged over the transition probabilities without the cases of mutations to stop codons or when no mutations are made on a sequence. In order to obtain the fitness distribution, two probabilities are required (1) the probability pi(a) that a particular amino-acid identity a exists at a residue i, and (2) the transition probability that one amino acid will mutate into another Q = 1 — (1 — pm)3. The probability vectors p a) can be determined through a mean-held approach (Lee, 1994 Koehl and Delarue, 1996 Saven and Wolynes, 1997). The amino acid transition probabilities Q are calculated based on the special connectivity of the genetic code and the per-nucleotide mutation rate. Removing transitions to stop codons and unmutated sequences only requires the proper normalization of the probabilities pi and the moments. For example, the first moment of the fitness improvement w of the uncoupled fitness function is written as... 

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