Converting Shop Drawings to Cell Structure and Function
Protein synthesis takes place on a complex structure, the ribosome, composed of many protein molecules and a specialized set of three different RNA molecules. Each cell has thousands of individual ribosomes and each ribosome is able to translate any mRNA molecule and thus to synthesize any of the thousands of protein molecules required for cell function. And since each ribosome can function independently the synthesis of many different types of proteins, and many copies of any single protein, can occur simultaneously.
Each protein molecule has a precise molecular shape and a precise molecular surface, each protein being the molecular expression of a small portion of the information contained in our genetic material. Taken together, these shapes and the precise fit that they make with one another provide the structure of the cell. Many proteins work as enzymes or biological catalysts and their molecular surfaces provide the means through which our cellular factory carries out its business, guiding the complex web of chemical interactions needed to convert fuels to energy, to capture that energy, and to use this chemical energy in the operation, maintenance and repair, and the production of new cells as needed.
Here we can get a glimpse of how the cell achieves great flexibility and economy by using a few components and assembling them in different ways. First, we noted above that RNA is being used in two very different ways. In one set of processes, RNA is being used as a messenger molecule shuttling information from the nucleus to the cytoplasm. At the same time, some RNA molecules are serving as structural components of
the cell, in this instance as an important kind of scaffolding upon which the protein molecules of the ribosome are assembled. In addition, carbohydrate molecules can be used either as fuel (see Liver) or as structural elements.
In a similar manner, depending on the precise details of their structure, protein molecules can serve as either structural scaffolding or as enzymes (catalysts.) The information contained in our blueprints folds back on itself in very interesting ways in that the cell is actively using its processes to make more process capacity available. For example, the ribosome, the site of protein synthesis, is a composite molecule that is actively involved in the construction of not just "other" proteins, but of the proteins that make up new ribosomes. The protein synthesis machinery has built into it the ability to make more protein synthesis machinery. In the same way, information contained in the DNA is copied into mRNA instructions that guide the synthesis of the very proteins that are needed for making mRNA molecules.
More About Coding and the Translation of mRNA Molecules
The details of the coding process are complex, but the principles involved are quite simple. Recall that there are four possible letters, ATCG, at each position in a DNA strand. These letters code in two ways. One way is in the production of new copies of the DNA needed when cells divide or organisms reproduce themselves. The other is in the production of mRNA.
Also, we have seen that while we want to make shop drawings, disposable copies of the information in DNA, we do not want these drawings to be confused with DNA and we want to be able to use them for a short time and then discard them (break them down to individual
letters) when no longer needed. RNA is chemically different from DNA, a fact that assures that shop drawings are not confused in master blueprints. In addition, RNA contains a slightly different family of letters. RNA does not contain any TŐs. Every place a T occurs in DNA, the RNA copy uses a slightly different base known as uracil, abbreviated as U. Thus there are four letters in RNA, A, U, C, and G.
Recall also that proteins are composed of twenty different amino acids. During the synthesis of the protein molecule, the sequence of letters in the mRNA molecule codes for the sequence of amino acids in the protein.
Clearly we have a problem here since four different letters can only code for four amino acids. The solution is simple, just as our language contains words composed of more than one letter (otherwise our alphabet would only allow us to have 26 words!) the code for amino acid sequence contains more than one letter. Given four letters, a two letter code would permit a unique sequence for only 16 amino acids (four letters in each of two positions lets us have 4x4 = 16 possibilities.)
Three is the minimum number of letters required for 20 amino acids. In fact, three letters gives 64 different possibilities. It turns out that the extra 44 possible sequences are used in two ways. Most amino acids are coded my more than one sequence, with the variation frequently occuring in the third letter. In addition, some three letter sequences are used as punctuation and reading instructions. There are defined "start" sequences for beginning a protein (AUG, for example) and for "stop" where the synthesis process is terminated at the point that a complete protein sequence has been assembled.