Protein Synthesis

I have approached the topic of information flow through the ecosystem in a rather unconventional format. This is partly to stir up your mind, if you are bored with the mantra. It is also because I believe the logic of the ecosystem is better expressed in this way. It’s easy enough to float you a metaphor or to oversimplify the complexity of the biological system in an effort to clearly present the overall beautify of its organization. Or to become poetic instead of scientific when trying to express that beauty. But I think this implies that you can not think for yourself. Of course, you can. If you know the facts.

Science is about facts. Science is not necessarily about details, but it often happens that people need the details in order to make a clear picture of the logic. I am trying to weave a pathway between the factual details and their relationship to the beautiful system(s) that maintains life on earth. So, for information that is commonly available and accurately presented by reliable sources on the web I assume you will go to the web if you want more detail. The first and second laws of thermodynamics, for example, that we discussed in chapter one. The chemistry of the molecular interactions. The details of DNA replication. All of those you can find on the web. What may not be on the web are the well established relationship between these details and the survival of life on earth. Speculation abounds, in spite of the facts that are so well established. Similarly, with protein synthesis, you can go to the web for the details, which are elegant, complex, and well established. But I will try to overview the process.

The process of information flow in individual cells and/or organisms branches from the genetic code in two directions. The first serves the important role of maintaining the code and passing it on to the next generation of cells or organisms. This function is served by the process of DNA replication followed by cell division. We have talked about mitosis and cell division to make genetically identical daughter cells. Later we will talk about the manner in which DNA replication is followed by meiosis and fertilization in eukaryotic organisms to make fertilized eggs. Either way, and also in prokaryotic organisms, DNA replication preserves the genome (the genome is all the genes in one individual) so the cell can make more cells that are genetically the same as itself. Sometimes we refer to these as clones. Your body is a clone of cells that were produced in this manner.

To stay alive — to do its processes, the cell must make many different kinds of proteins, when and where they are required. To do this, the cell uses structural genes, that carry the code of the protein, and regulatory genes that determine when and where the protein will be produced. We don’t need to talk about regulatory genes. Now – very, very briefly, protein synthesis.

We have already said that the chromosomes are double stranded. They are in the nucleus (if it’s a eukaryotic cell) and they stay there, well protected. On one strand of the DNA is the genetic code and on the other strand is the copy of the code. The two strands remain bonded together with weak bonds unless they are needed to do DNA replication or protein synthesis. Because all the nucleotides are bonded end to end with strong covalent bonds, the sequence of the code does not shift around. Because the two strands are held together with weak bonds, these can come apart when the chromosome needs to replicate or a gene is needed to code for a protein. When the strands are together, the code is kept safe, it cannot replicate until the correct time, and it cannot make proteins in the wrong times/places. When it is time for the chromosome to copy itself, and all the genes of which it is composed, the two sides come apart and DNA replication occurs in a very controlled fashion. This happens just before cell division.

During the remainder of the cell’s life, it needs to use the genes at various times to do protein synthesis. Protein synthesis is the production of a protein, within the cell, using the code of a structural gene. Then the two strands of the DNA double helix open up only at the location of the gene that is needed to make a protein.

Remember the two strands of DNA that preserve the genetic code are composed of four nucleotide molecules that are arranged in the sequence of the code. The four nucleotides are adenine, thymine, guanine and cytosine. When a protein is required, the gene opens up and a different sort of copy is made of the gene. The code is the same, the covalent bonds never come apart, but the weak bonds between the two strands open up and the code is copied as RNA rather than DNA. DNA and RNA are both nucleic acids and they are both large molecules composed of smaller nucleotide molecules.

RNA is a nucleic acid molecule made of small nucleotide molecules that are bonded end to end by strong covalent bonds, to preserve the code. But instead of thymine, RNA uses a different nucleotide named uracil.

So for example if the DNA code is:

AATACGGC

A DNA copy would be TTATGCCG

And an RNA copy would be UUAUGCCG

This means very little to you and me, but to the cell, it is the code for a protein.
Except that it is not a code for a protein. For one thing I just made it up and it probably has an invalid code. For another, proteins are very big molecules with dozens or hundreds of subunits. Proteins are large organic molecules made of smaller amino acid molecules that are fastened together end to end by strong covalent bonds. There are more or less 20 amino acids involved with this process. The RNA code identifies one amino acid with every three of its nucleotides. Therefore if a protein is small, only 100 amino acids, the RNA that carries the code would have to be 300 nucleotides in length (at least, but actually more because there are also signal sequences in the DNA and the RNA).

Next comes a very complicated, and almost incredible sequence of processes the cell uses, first to take the RNA copy of the gene out of the nucleus and into the cytoplasm, and then to use that code to make a protein. The energy for this large job will come from ATP molecules, and they got the energy — basically it comes from photosynthesis as we described earlier.

Besides energy, the cell requires many enzymes and different sorts of RNA molecules to grab hold of the message (the messenger RNA) and carry it out of the nucleus and match it up with the right amino acids and then make the covalent bonds between the amino acids to create the primary structure of that specific kind of protein that is encoded on that specific gene. The gene meanwhile can keep making more, or it can curl back up inside the nucleus and rest while the protein is doing its job somewhere else in the cell.

There are at least three kinds of genes involved in this process:

A structural gene is a gene that codes for the sequence of amino acids in a protein;
A regulatory gene is involved somehow in turning genes on and off;
And there are genes that encode the many kinds of molecules that are used to do all the processes that are required to do protein synthesis.

Stripped to its bare bones, a protein is produce inside a cell as follows:

DNA code → RNA code → Protein primary structure → then the protein folds up as we described earlier and is able to do its job
because of its shape (physical shape and distribution of energy charges).

If a genetic defect occurs so that there is no protein produced then one of the jobs of staying alive does not get done. For an example we used earlier, if there is no tyrosinase, then no pigment will form in the pigment cells and the result will be an albino animal. If the defective gene encoded a cell surface receptor, then if the receptor is not produced the cell can not respond to whatever signal the receptor was designed to detect.

And I am glad we are finished trying to overview the details of why this works the way it does. As incredible and marvelous as these facts are, the really most interesting part of this story is the way the information that is coded in the genes keeps the entire ecosystem alive and able to respond to changing circumstances.