The explanation for the smaller number lies in the capability of a single tRNA anticodon to recognize more than one, but not necessarily every, codon corresponding to a given amino acid. Although the first and second bases of a codon form standard Watson-Crick base pairs with the third and second bases of the corresponding anticodon, four nonstandard interactions can occur between bases in the wobble position. Thus, a given anticodon in tRNA with G in the first wobble position can base-pair with the two corresponding codons that have either pyrimidine C or U in the third position Figure However, the base in the third or wobble position of an mRNA codon often forms a nonstandard base pair with more Although adenine rarely is found in the anticodon wobble position, many tRNAs in plants and animals contain inosine I , a deaminated product of adenine, at this position.
Inosine can form nonstandard base pairs with A, C, and U Figure For this reason, inosine-containing tRNAs are heavily employed in translation of the synonymous codons that specify a single amino acid. Recognition of the codon or codons specifying a given amino acid by a particular tRNA is actually the second step in decoding the genetic message. The first step, attachment of the appropriate amino acid to a tRNA, is catalyzed by a specific aminoacyl-tRNA synthetase see Figure Each of the 20 different synthetases recognizes one amino acid and all its compatible, or cognate, tRNAs.
In this reaction, the amino acid is linked to the tRNA by a high-energy bond and thus is said to be activated. The energy of this bond subsequently drives the formation of peptide bonds between adjacent amino acids in a growing polypeptide chain. The equilibrium of the aminoacylation reaction is driven further toward activation of the amino acid by hydrolysis of the high-energy phosphoanhydride bond in pyrophosphate.
The overall reaction is. Aminoacylation of tRNA. Each of these enzymes recognizes one kind of amino acid and all the cognate tRNAs that recognize codons for that amino acid. The two-step aminoacylation more The amino acid sequences of the aminoacyl-tRNA synthetases ARSs from many organisms are now known, and the three-dimensional structures of over a dozen enzymes of both classes have been solved.
The binding surfaces of class I enzymes tend to be somewhat complementary to those of class II enzymes. These different binding surfaces and the consequent alignment of bound tRNAs probably account in part for the difference in the hydroxyl group to which the aminoacyl group is transferred Figure Because some amino acids are so similar structurally, aminoacyl-tRNA synthetases sometimes make mistakes.
These are corrected, however, by the enzymes themselves, which check the fit in the binding pockets and facilitate deacylation of any misacylated tRNAs. This crucial function helps guarantee that a tRNA delivers the correct amino acid to the protein -synthesizing machinery. Recognition of a tRNA by aminoacyl synthetases. Shown here are the outlines of the three-dimensional structures of the two synthetases.
The more The ability of aminoacyl-tRNA synthetases to recognize their correct cognate tRNAs is just as important to the accurate translation of the genetic code as codon - anticodon pairing. Once a tRNA is loaded with an amino acid , codon-anticodon pairing directs the tRNA into the proper ribosome site; if the wrong amino acid is attached to the tRNA, an error in protein synthesis results. As noted already, each aminoacyl-tRNA synthetase can aminoacylate all the different tRNAs whose anticodons correspond to the same amino acid. One approach for studying the identity elements in tRNAs that are recognized by aminoacyl-tRNA synthetases is to produce synthetic genes that encode tRNAs with normal and various mutant sequences by techniques discussed in Chapter 7.
The normal and mutant tRNAs produced from such synthetic genes then can be tested for their ability to bind purified synthetases. Very probably no single structure or sequence completely determines a specific tRNA identity. However, some important structural features of several E. Perhaps the most logical identity element in a tRNA molecule is the anticodon itself.
Thus this synthetase specifically recognizes the correct anticodon. However, the anticodon may not be the principal identity element in other tRNAs see Figure Figure shows the extent of base sequence conservation in E. Identity elements are found in several regions, particularly the end of the acceptor arm.
Solution of the three-dimensional structure of additional complexes between aminoacyl-tRNA synthetases and their cognate tRNAs should provide a clear understanding of the rules governing the recognition of tRNAs by specific synthetases. Identity elements in tRNA involved in recognition by aminoacyl-tRNA synthetases, as demonstrated by both conservation and experimentation. The 67 known tRNA sequences in E. The conserved nucleotides in different more If the many components that participate in translating mRNA had to interact in free solution, the likelihood of simultaneous collisions occurring would be so low that the rate of amino acid polymerization would be very slow.
This two-part machine directs the elongation of a polypeptide at a rate of three to five amino acids added per second. On the other hand, it takes 2 to 3 hours to make the largest known protein, titin, which is found in muscle and contains 30, amino acid residues. The machine that accomplishes this task must be precise and persistent. With the aid of the electron microscope, ribosomes were first discovered as discrete, rounded structures prominent in animal tissues secreting large amounts of protein ; initially, however, they were not known to play a role in protein synthesis.
Once reasonably pure ribosome preparations were obtained, radiolabeling experiments showed that radioactive amino acids first were incorporated into growing polypeptide chains associated with ribosomes before appearing in finished chains. A ribosome is composed of several different ribosomal RNA rRNA molecules and more than 50 proteins, organized into a large subunit and a small subunit. The proteins in the two subunits differ, as do the molecules of rRNA. The ribosomal subunits and the rRNA molecules are commonly designated in svedbergs S , a measure of the sedimentation rate of suspended particles centrifuged under standard conditions Chapter 3.
The lengths of the rRNA molecules, the quantity of proteins in each subunit, and consequently the sizes of the subunits differ in prokaryotic and eukaryotic cells. The small and large rRNAs are about and nucleotides long in bacteria and about and nucleotides long in humans.
Perhaps of more interest than these differences are the great structural and functional similarities among ribosomes from all species. This consistency is another reflection of the common evolutionary origin of the most basic constituents of living cells. The general structure of ribosomes in prokaryotes and eukaryotes. In all cells, each ribosome consists of a large and a small subunit. The two subunits contain rRNAs of different lengths, as well as a different set of proteins.
All ribosomes contain two more The sequences of the small and large rRNAs from several thousand organisms are now known. Although the primary nucleotide sequences of these rRNAs vary considerably, the same parts of each type of rRNA theoretically can form base -paired stem-loops, generating a similar threedimensional structure for each rRNA in all organisms. Evidence that such stem-loops occur in rRNA was obtained by treating rRNA with chemical agents that cross-link paired bases; the samples then were digested with enzymes that destroy single-stranded rRNA, but not any cross-linked base-paired regions.
Finally, the intact, cross-linked rRNA that remained was collected and sequenced, thus identifying the stem-loops in the original rRNA. Experiments of this type have located about 45 stem-loops at similar positions in small rRNAs from many different prokaryotes and eukaryotes Figure An even larger number of regularly positioned stem-loops have been demonstrated in large rRNAs.
All the ribosomal proteins have been identified and their sequences determined, and many have been shown to bind specific regions of rRNA. It seems clear that the fundamental protein -synthesizing machinery in all present-day cells arose only once and has been modified about a common plan during evolution. Two-dimensional map of the secondary structure of the small 16S rRNA from bacteria, showing the location of base-paired stems and loops.
In general, the length and position of the stem-loops are very similar in all species, although the exact sequence more During protein synthesis, a ribosome moves along an mRNA chain, interacting with various protein factors and tRNA and very likely even undergoes shape changes. Despite the complexity of the ribosome, great progress has been made in determining both the overall structure of bacterial ribosomes and in identifying reactive sites that bind specific proteins, mRNA, and tRNA and that participate in important steps in protein synthesis.
Quite detailed models of the large and small ribosomal subunits from E.
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These studies not only have determined the dimensions and overall shape of the ribosomal subunits, but also have localized the positions of tRNAs bound to the ribosome during protein chain elongation. Powerful chemical experiments have also helped unravel the complex interactions between proteins and RNAs.
In a technique called footprinting , for example, ribosomes are treated with chemical reagents that modify single-stranded RNA unprotected by binding either to protein or to another RNA. If the total sequence of the RNA is known, then the location of the modified nucleotides can be located within the molecule.
This technique, which is also useful for locating protein-binding sites in DNA , is described in Chapter Thus the overall structure and function of ribosomes during protein synthesis is finally, after 40 years, yielding to successful experiments. How these results aid in understanding the specific steps in protein synthesis is described in the next section.
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Nucleic Acids and Protein Synthesis, Part E, Volume 29 - 1st Edition
Figure Breaking the entire genetic code by use of chemically synthesized trinucleotides. Figure Translation of nucleic acid sequences in mRNA into amino acid sequences in proteins requires a two-step decoding process. Figure Structure of tRNAs. Nonstandard Base Pairing Often Occurs between Codons and Anticodons If perfect Watson-Crick base pairing were demanded between codons and anticodons, cells would have to contain exactly 61 different tRNA species, one for each codon that specifies an amino acid.
Figure Aminoacylation of tRNA. Figure Recognition of a tRNA by aminoacyl synthetases. Figure Identity elements in tRNA involved in recognition by aminoacyl-tRNA synthetases, as demonstrated by both conservation and experimentation. Ribosomes Are Protein-Synthesizing Machines If the many components that participate in translating mRNA had to interact in free solution, the likelihood of simultaneous collisions occurring would be so low that the rate of amino acid polymerization would be very slow.
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