As we saw in the previous session, once an RNA is synthesized, it detaches from the DNA. In organisms with cells that have nuclei (eukaryotes), the RNA comes out of the nucleus into the cytoplasm. There the information contained in its sequence of nucleotides is utilized to produce a protein with a specific sequence of amino acids. This process is called "translation", a very apt term, because represents the act of taking one sequence in one language and using it produce another sequence in another language -- going from the language of nucleotides into the language of amino acids.
Translation is a complicated process, requiring a multitude of molecular machines, all working together in an elaborate dance. Many of the subtle details of the choreography still remain to be investigated, although the overall picture seems to be well understood. We'll only cover the highlights of the process.
There are four major participants in the protein synthesis dance: the ribosome, mRNA (messenger RNA), a set of tRNA 's (transfer RNA), and a group of enzymes called amino acyl-tRNA synthetases (we'll call them synthetases for short). I'm going to begin with a discussion of the last two: the tRNA's and the synthetases.
The essence of translation is that the information contained in the sequence of nucleotides is somehow transformed into a sequence of amino acids. When you just beginning to learn a foreign language and you need to translate a word or phrase from English, you need a dictionary. It may come as a surprise to you that organisms carry around a dictionary that they use when translating RNA sequences into protein sequences. This dictionary, a rather short one, exists in the form of a series of molecules called tRNA's.
There are multiple tRNA's. In fact, there are fifty to seventy different tRNA's (depending on the organism), each with its own sequence and each transcribed by a different gene. Of course, they all share certain characteristics. All are small -- on the order of 65 to 95 nucleotides in length. All have a distinctive, highly convoluted structure (as shown in the figure below) which results from a single strand of RNA bending back on itself, forming loops and double stranded regions (the yellow line traces the molecule from beginning to end). The fact that there are so many different tRNA's is vitally important to the process of protein synthesis: Each one represents an entry in the dictionary.
There are two business ends to every tRNA (Click here!). One is a single stranded region at the 3' end of the molecule that is capable of forming a strong, covalent bond with an amino acid. The other part of the tRNA that is critical to its function is a loop of nucleotides.
Now we can begin to see why it is important that there are multiple tRNA's. Every different tRNA is dedicated to carrying one and only one specific amino acid. For instance, there is a tRNA that always forms a covalent bond with phenylalanine (actually, that's the one pictured above). Another tRNA -- one with a different sequence -- always carries a leucine. (Actually there are several tRNA's that are specific for alanine and leucine, but that is a detail that need not concern us).
In addition, each tRNA has a loop that "reads" a set of nucleotides in the mRNA. That is, each loop region carries several nucleotides that are complementary to specific ones in the mRNA. Now you should be able to see why the set of tRNA's act like a dictionary. They match a specific sequence of RNA with their loop (the are "looking up" the RNA sequence), and use their other end -- the one carrying the amino acid -- to assign it to a specific amino acid.
How is the dictionary set up? How are specific amino acids attached to specific tRNA's? As you might have guessed, this step is carried out by an enzyme. In fact, there are twenty such enzymes (called amino acyl-tRNA synthetases) each one of which recognizes a specific amino acid and an appropriate tRNA. These combinations of amino acids and specific tRNA's are the entries in the dictionary that translates mRNA sequences into protein sequences. They are present in abundance within the cytoplasm, awaiting their turn to carry out their function.
Ribosomes are enormous molecular structures, massive assemblages of 80-odd proteins and four RNA's.
The stereograms above shows some of the most detailed views that are now available. They come from a paper by H. Stark and coworkers, in the journal Structure (Volume 3, pg. 815, Fig 2). I found them on the WWW at this site. If you stare at the picture cross-eyed for a while, you may be able to visualize the structure of a ribosome in three dimensions. The small subunit is at the right of each pair, and the large subunit at the left. Note the intricate shape of these structures.
Another image of the ribosome, at a similar resolution, is shown below. Here, the small subunit is drawn in yellow and the large one in blue. This image comes from the laboratory of Joachim Frank and is copyright (1995) the Research Council of Canada.
As emphasized in the figures above, ribosomes consist of two unequally sized subunits, termed small and large. In turn, each of the subunits is comprised of many different proteins (on the order of four dozen for the large subunit, and about two dozen for the small) and several RNA's (three RNA's in the large subunit and 1 RNA in the small). Because these ribosomal RNA's are not translated into proteins, they fulfill a different role than the mRNA's that we've discussed previously. To distinguish ribosomal RNA's from RNA's destined to specify proteins, the ribosomal RNA's are called rRNA's and the protein-specifying ones are called mRNA's (for messenger RNA). We've already encountered a second structural RNA, tRNA, above.
The synthesis of a protein begins with the attachment of a specific tRNA to the small subunit of a ribosome (as shown in the animation). This tRNA is the initiator tRNA and it carries the amino acid methionine. The second step in protein synthesis if the attachment of a specific mRNA to the small subunit of the ribosome. Once bound, the mRNA initiates a remarkable series of events that results in the synthesis of a specific protein whose sequence is dictated by the sequence of that specific mRNA. It should be stressed that the ribosome has no specificity as to what protein its going to make. It is a molecular machine that can be used by any mRNA And it is the sequence of the mRNA, not the ribosome or rRNA, that dictates which protein is to be manufactured.
We left the mRNA attached to the small subunit of the ribosome, awaiting the next step in protein synthesis. As we have seen, also attached to the ribosome is a specific tRNA carrying the amino acid methionine. (This tRNA had methionine added by an amino acid synthetase as described above.) What happens next is remarkable. The ribosome and the ribosome and mRNA move with respect to one another. The mRNA bound near one end &emdash;its 5' end&emdash; and it moves, toward the other end. The methionine tRNA is positioned so that its second business end, its anticodon loop region, is close to the mRNA. When the single stranded loop region of the methionine tRNA complements a region in the mRNA (marked in purple and designated "Begin translation (AUG)), movement stops (from Frank et al. 1995).
At this point, the large ribosomal subunit joins the company. Shortly thereafter, a second tRNA, joined to a specific amino acid comes along. At this point, the situation looks like the figure below.
In this figure, the large subunit is shown in blue and in back of the small one (the figure at the left has the small subunit cut away so that the tRNA's and mRNA can be easily seen. The figure at the right is not cut away). The initiator tRNA is shown in green. Enter another tRNA (shown in purple). It has an amino acid bound, and its anticodon loop recognizes an adjacent region of the mRNA. It nestles next to the methionine tRNA. The two amino acids then form a peptide bond (catalyzed by some polymer on the large subunit). The second tRNA now has two amino acids bound to it, the methionine tRNA has none. It is released, and the second tRNA moves over into its the position on the ribosome occupied previously by the methionine tRNA. The mRNA slides over too. Another tRNA carrying the next amino acid to be joined attaches and the process repeats.
All of this is more easily visualized by virtue of an animation than a static description in the text. I've enlarged the region around where the tRNA's are attached to the ribosome. Notice that the mRNA moves as well as the tRNA's. The next tRNA is shown in red.
And here's another view with the mRNA and tRNA's enlarged.
