Amino Termination codons

An opening frame contains a series of codons (base triplets) coding for amino acids without any termination codons. There are six potential reading frames of an unidentified sequence. 

The terms first, second, and third nucleotide refer to the individual nucleotides of a triplet codon. U, uridine nucleotide C, cytosine nucleotide A, adenine nucleotide G, guanine nucleotide Term, chain terminator codon. AUG, which codes for Met, serves as the initiator codon in mammalian cells and encodes for internal methionines in a protein. (Abbreviations of amino acids are explained in Chapter 3.)... 

The charging of the tRNA molecule with the aminoacyl moiety requires the hydrolysis of an ATP to an AMP, equivalent to the hydrolysis of two ATPs to two ADPs and phosphates. The entry of the aminoacyl-tRNA into the A site results in the hydrolysis of one GTP to GDP. Translocation of the newly formed pep-tidyl-tRNA in the A site into the P site by EF2 similarly results in hydrolysis of GTP to GDP and phosphate. Thus, the energy requirements for the formation of one peptide bond include the equivalent of the hydrolysis of two ATP molecules to ADP and of two GTP molecules to GDP, or the hydrolysis of four high-energy phosphate bonds. A eukaryotic ribosome can incorporate as many as six amino acids per second prokaryotic ribosomes incorporate as many as 18 per second. Thus, the process of peptide synthesis occurs with great speed and accuracy until a termination codon is reached. 

Figure 38-10. Picornavimses disrupt the 4F complex. The 4E-4G complex (4F) directs the 40S ribosomal subunit to the typical capped mRNA (see text). 4G alone is sufficient for targeting the 40S subunit to the internal ribosomal entry site (IRES) of viral mRNAs. To gain selective advantage, certain viruses (eg, poliovirus) have a protease that cleaves the 4E binding site from the amino terminal end of 4G. This truncated 4G can direct the 40S ribosomal subunit to mRNAs that have an IRES but not to those that have a cap. The widths of the arrows indicate the rate of translation initiation from the AUG codon in each example.

Fig. 8.4 Outline of the main events in protein synthesis initiation, elongation, translocation and termination. AUG is an initiation codon on the mRNA it codes for Af-fomiylmelhionine and initiates the formation of the 70S rihosome. UAG is a termination codon it does not code for any amino acid and brings about termination of protein synthesis.

A gene encodes a protein with 150 amino adds. There is one intron of 1000 bps, a 5 -untranslated region of 100 bp and a 3 -nntranslated re on of 200 bp. In the final processed mRNA, how many bases lie between the start AUG codon and the final termination codon ... 

Fig.1. The in vitro site-directed suppression mutagenesis system. Utilizing site-directed mutagenesis a specific codon within a gene under the control of an inducible promoter is converted to an amber termination codon. The gene is added to a cell-free expression system and transcription is induced in the presence of an aminoacyl suppressor tRNA, yielding protein containing the noncoded amino acid at the site corresponding to the termination codon...

Building on earlier work of Osawa and co-workers [55], Oliver and Kowal [52] tested the feasibility of introducing a noncoded amino acid at an unassigned codon in M. luteus. DNA templates were prepared which coded for 19-mer polypeptides containing either the unassigned codon AGA(Arg) or the termination codon TAG at position 13 under the control of a T7 RNA polymerase promoter. The corresponding tRNAs, produced as described in Sect. 2, were based on tRNA and acylated with phenylalanine. The tRNA was modified to prevent recognition by the alanine aminoacyl-tRNA synthetase and to increase translational efficiency. 

While readthrough is usually a detrimental process, in some cases it can help to suppress problems, e.g. arising from premature stop codons present on the DNA level. This type of readthrough, also termed nonsense suppression, leads to the generation of a fraction of the full length protein in addition to the shortened version. Omnipotent suppressors cause nonsense suppression of all three termination codons. In this process, a near cognate tRNA successfully competes with the termination factors such that amino acid incorporation rather than premature termination of translation occurs. Omnipotent suppression can be caused by mutations in various factors involved in the process of translation termination. Nonsense suppression can also result from an aa-tRNA that decodes a termination codon (suppressor tRNA) in this case only one of the termination codons is efficiently suppressed (Hawthorne and Leupold 1974 Stansfield and Tuite 1994). 

The ribosome can carry two aminoacyl-tRNAs simultaneously. In the chain elongation stage, the growing polypeptide is carried on one of these tRNAs. The chain is transferred to the second tRNA, which adds its amino acid to the growing peptide, and displaces the first tRNA. The ribosome then moves one codon along the mRNA to allow the next to be read. Termination of protein synthesis involves the release of the completed polypeptide, expulsion of the last tRNA, and dissociation of the ribosome from the mRNA. This is signaled by specific termination codons (UAA, UAG, or UGA) in the mRNA and requires the participation of various release factors. 

Consolidation of the results from many experiments permitted the assignment of 61 of the 64 possible codons. The other three were identified as termination codons, in part because they disrupted amino acid coding patterns when they occurred in a synthetic RNA polymer (Fig. 27-6). Meanings for all the triplet codons (tabulated in Fig. 27-7) were established by 1966 and have been verified in many different ways. The cracking of the genetic code is regarded as one of the most important scientific discoveries of the twentieth century. 

The codons are written in the 5 —>3 direction. The third base of each codon (in bold type) plays a lesser role in specifying an amino acid than the first two. The three termination codons are shaded in pink, the initiation codon AUG in green. All the amino acids except methionine and tryptophan have more than one codon. In most cases, codons that specify the same amino acid differ only at the third base. 

Protein synthesis begins at the amino-terminal end and proceeds by the stepwise addition of amino acids to the carboxyl-terminal end of the growing polypeptide, as determined by Howard Dintzis in 1961 (Fig. 27-19). The AUG initiation codon thus specifies an amino-terminal methionine residue. Although methionine has only one codon, (5 )AUG, all organisms have two tRNAs for methionine. One is used exclusively when (5 )AUG is the initiation codon for protein synthesis. The other is used to code for a Met residue in an internal position in a polypeptide. 

When a mutation introduces a termination codon in the interior of a gene, translation is prematurely halted and the incomplete polypeptide is usually inactive. These are called nonsense mutations. The gene can be restored to normal function if a second mutation either (1) converts the misplaced termination codon to a codon specifying an amino acid or (2) suppresses the effects of the termination codon. Such restorative mutations are called nonsense suppressors they generally involve mutations in tRNA genes to produce altered (suppressor) tRNAs that can recognize the termination codon and insert an amino acid at that position. Most known suppressor tRNAs have single base substitutions in their anticodons. 

Termination ("stop" or "nonsense ) codons Three of the codons, UAG, UGA, and UAA, do not code for amino acids, bit rather are termination codons. When one of these codons appears in an mRNA sequence, it signals that synthesis of the peptide chain coded for by that mRNA is completed. 

The pathway of protein synthesis translates the three-letter alphabet of nucleotide sequences on mRNA into the twenty-letter alphabet of amino acids that constitute proteins. The mRNA is translated from its 5 -end to its 3 -end, producing a protein synthesized from its amino-terminal end to its carboxyl-terminal end. Prokaryotic mRNAs often have several coding regions, that is, they are polycistronic (see p. 420). Each coding region has its own initiation codon and produces a separate species of polypeptide. In contrast, each eukaryotic mRNA codes for only one polypeptide chain, that is, it is monocistronic. The process of translation is divided into three separate steps initiation, elongation, and termination. The polypeptide chains produced may be modified by posttranslational modification. Eukaryotic protein synthesis resembles that of prokaryotes in most details. [Note Individual differences are mentioned in the text.]... 

Altering the nucleotide sequence in a codon can cause silent mutations (the altered codon also codes for the original amino acid), missense mutations (the altered codon codes for a different amino acid), or nonsense mutations (the altered codon is a termination codon). 

It has been shown that the code for specifying a particular amino acid in a protein is determined by a sequence of three nucleotides (a codon) in a DNA chain. There are four different kinds of nucleotide units in DNA. How many different codons exist Note that this is larger than the number of different amino acids (20) that are incorporated into proteins plus the three stop (termination) codons (see Tables 5-5 and 5-6 for a list of codons). 

In addition to those codons assigned to specific amino acids, three are designated as chain termination codons UAA, UAG, and UGA. These are frequently referred to as "nonsense" codons. The termination codons UAA and UAG are also known as ochre and amber, respectively, although these names have no scientific significance.41 The codons AUG (methionine)... 

Figure 29-16 Schematic diagram of the tmRNA structure and its function in the rescue of ribosomes stalled at the end of a messenger RNA that has been broken and has lost its inframe termination codon. After it binds into the ribosomal A site the tmRNA, which has been charged with alanine, undergoes the peptidyltransferase reaction and translocation to the P site. Then it lays down its mRNA-like coding sequence, which is used by the ribosome to add ten more amino acids to form the 11-residue C-terminal degradation signal A ANDENYALAA. This induces rapid degradation of the imperfect protein that has been formed.4363...

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