2-22 Transfer RNA is the ferry for amino acids

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• Transfer RNA has an L shape in its native three-dimensional form.
• There are unique tRNAs for each of the 20 common amino acids
• Aminoacyl-tRNA synthetases recognize their respective tRNA and add the appropriate amino acid.

Transfer RNA (tRNA) is the ferry that transports the amino acids to the ribosome. There are one or more different tRNA molecules for each of the 20 amino acids. Each consists of 70 to 80 nucleotides of single-stranded RNA that is extensively base-paired to form four short helical domains. These structures are commonly represented as a two-dimensional cloverleaf, but look more like an "L" in the native three-dimensional structure as shown in Figure 2-31. Now the tertiary structures of tRNAs are all rather similar, so the critical features that make each appropriate to a specific amino acid are largely found in the primary structure itself. Many bases in tRNA molecules are chemically modified by enzymes to help the molecule carry out its function.

The aminoacyl-tRNA synthetases are the enzymes that add the amino acid to the tRNAs. Figure 2-32 depicts a complex between an aminoacyl tRNA synthetase and tRNA. There is a single synthetase for each amino acid and it binds each of its appropriate tRNA molecules and charges it with its appropriate amino acid. The synthetases avoid both the wrong tRNAs as well as the wrong amino acids. However, the process is somewhat trickier than it first appears. First, one might expect that the synthetase might recognize the proper tRNAs by examining the anticodon loop, the part recognized by the ribosome to match the tRNA to the mRNA. After all, the anticodon certainly does define the amino acid in translation. This is not the case, however, perhaps because the anticodon is very far away from the end of the tRNA that is charged with the amino acid. In any event, it is clear that most of the basis for proper synthetase-tRNA recognition lies elsewhere in the tRNA. This then raises another problem: when one looks at the different tRNAs that all carry a given amino acid and are therefore all recognized by a single synthetase, no obvious pattern emerges. In other words, the important features that allow the alanine synthetase to recognize only alanine tRNAs are not completely clear, though great strides in understanding this process have been made.

One final thought before we move on. Think about the chicken-and-egg conundrum that translation brings up. This whole process has the express purpose of synthesizing proteins, yet it involves proteins at every step. How could these proteins have evolved to serve this function when they are needed for their own synthesis? In other words, how could you synthesize any protein until a complete set of translation proteins had evolved? Part of the answer is that primordial translation was probably much simpler, though less accurate and efficient. Perhaps only very few and somewhat general protein functions were actually required. Alternatively, perhaps early translation used no proteins at all: Some scientists believe that early life employed RNA molecules that were capable of both carrying out necessary enzymatic functions and storing hereditary information. They posit that it was only later that proteins came along and started to assist in their own synthesis. However, this hypothesis still does not explain how one simultaneously evolved functional proteins and a process for creating them.

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