All forms of life on earth use mRNA as the way to carry and amplify the informational "message" of nucleotide sequence from the genome to the site of protein synthesis. In the complex series of events we call translation, the information in the mRNA is used to synthesize a polypeptide (protein) of specific amino acid sequence, and it is this sequence which completely determines the functioning of that protein.


1. How does translation start at the correct AUG codon in the mRNA?

Figure 10.17 shows the basic process of how the "translation initiation complex" forms at the AUG translational start codon in eukaryotes. As shown in the figure,the small ribosomal subunit, several accessory proteins, and the initiator tRNA form a complex at the 5' methyl cap, the complex then scans along the mRNA until the first AUG is encountered (an average of several hundred nucleotides for human genes), the large ribosomal subunit joins the complex, and then translation is set to begin.

In bacteria, the process is somewhat different. The primary transcript itself serves as the mRNA even as it is being made. There are no introns to be removed, there is no 5' methyl-G cap added, and there is no poly A tail added to the 3' end. As the mRNA is being synthesized, bacterial ribosomes bind to an internal "ribosome binding sequence" in the mRNA, and the initiation AUG will be the one just downstream (3' side) of this sequence.

This difference between eukaryotes and prokaryotes explains the observation that bacterial mRNAs may code for more than one protein (the "lac operon" mRNA, for example, gets translated into three different proteins), but eukaryotic mRNAs code for just one protein each.


2. How does nucleotide sequence information actually get translated into amino acid sequence information, i.e., how does the genetic code get read?

Figure 10.18 shows the mechanics of the reading of individual codons and synthesis of the polypeptide chain. It is important to study this figure closely enough so you develop a "feel" for how translation proceeds.

All of this "works" only because a set of special enzymes, the aminoacyl-tRNA synthetases, have already hooked the "correct" amino acids onto the "correct" tRNAs. So, we see that it is really these enzymes that provide the link between nucleic acid sequence information and protein sequence information. The structure of tRNAs is shown in Figure 10.30. The three-dimensional structure of an aminoacyl-tRNA synthetase enzyme bound to its correct tRNA is shown in Figure 10.31.


3. What actually happens at the stop codons UAG, UAA, and UGA?

For human genes, the translation stop codon is typically several hundred nucleotides in from the 3' end of the mRNA.
When the ribosome arrives at any in-phase stop codon, there is no tRNA that can bind. Into this "open space" a small protein called release factor binds to the A site on the ribosome and causes the enzymatic cleavage of the newly made protein from the final tRNA, as well as the release of the ribosomal subunits from the mRNA. This process is shown in Figure 10.20.


4. How do newly made proteins fold into their correct three dimensional shape?

The subject of protein folding has been an active area of research for decades, and still is. Figure 10.22 provides a broad overview. Most proteins fold correctly on their own. Some proteins require the help of other (specialized "chaperone" or "chaperonin") proteins to fold correctly.