What Makes Me Tick - Part 3

Part 3 - Proteins in the Human Body

Proteins are complex molecules that are required for our body's structure, function, and regulation. Each type of protein is constructed from a sequence of amino acids. The human body uses 20 different amino acids to construct proteins, and proteins are an average length of 300 amino acids each. Some of these amino acids the body acquires from breaking down ingested proteins and others are synthesized during the body's Krebs cycle.

The proteins are defined by their sequence of amino acids. The amino acid sequence of a protein results in a unique fold of the structure which is integral to the protein's function. The human body's systems depend on at least 86,771 different proteins. The National Library of Medicine article at https://www.ncbi.nlm.nih.gov/books/NBK26830/ explains more about biological proteins.

Each of the proteins in the human body has a stable shape that "has its chemical properties finely tuned to enable the protein to perform a particular catalytic or structural function in the cell. Proteins are so precisely built that the change of even a few atoms in one amino acid can sometimes disrupt the structure of the whole molecule so severely that all function is lost." (Molecular Biology of the Cell, 4th edition, cited at https://www.ncbi.nlm.nih.gov/books/NBK26830/)

To begin to grasp an idea of how many different proteins could possibly be made, consider the number of distinct proteins that could be made the length of 300 amino acids (the average length of a protein). Each of the 300 amino acid positions can be filled by one of 20 different amino acids. Therefore, 20300 unique protein polypeptide chains could be made. To grasp an idea of how many this is, consider the following: The number of atoms required to produce just one molecule of each kind of this 300-length amino acid protein would require many more atoms than exist in the universe (Molecular Biology of the Cell. 4th edition, cited at https://www.ncbi.nlm.nih.gov/books/NBK26830/).

It is estimated that very few of the possible amino acid sequence chains actually result in a protein with a stable fold. Without a stable fold, the amino acid sequence is not usable in a cell. Scientists report that a very small fraction (some estimates say less than one in a billion) of the random generated amino acid chains result in a stable fold. This makes potentially usable proteins in a living cell rare in comparison to randomly generated amino acid sequences (Molecular Biology of the Cell. 4th edition, cited at https://www.ncbi.nlm.nih.gov/books/NBK26830/).

Functional proteins require stable folds. Studies have shown that sometimes one amino acid in a protein can be replaced and the resulting structure is still similar enough to allow its function to continue. However, when two amino acids are changed, almost always the structure is changed to the point where the protein is no longer able to serve its function.


Proteins in Chemical Cascades

The probability that all of the functional and coordinated proteins and enzymes involved in the photoreceptor cells of the retina simultaneously generated in one mutational event, is infinitesimally small. (Enzymes are a type of protein that regulate biochemical reactions.) Therefore, we must assume a simpler visual system once existed. In order for the simpler system to have been replaced by a system with more complex steps, each stepwise change towards the new system must have resulted in sufficiently significant beneficial changes to the organism.

A chemical cascade requires inputs and outputs that perfectly fit in sequence. If a new molecule (or sequential set of molecules) is added to a sequence, it must chemically react with the molecular component it follows. The result of its interaction must then be the perfect input for the next reaction in the sequence. A new molecule cannot start interacting with a preexisting chemical sequence unless the result also becomes a perfect molecular fit for the rest of the sequence that follows after it or for the initiation of the next process in the biological system.

In addition, the newly mutated or generated protein fold structures must also not interfere with any of the other input or output protein fold structures involved in the sequence. The quantity of the newly introduced molecule matters as well. Chemical regulators must be simultaneously present because if too much or too little of a molecule is present, the chemical cascade will come to its end.

Considering the chemical cascade initialized by a photon interacting with 11-sisretinal, more than just protein inputs and outputs are required. Enzyme catalysts are needed which increase the rate of the chemical reaction. Molecules are needed to bend and cut proteins to enable them to combine with other inputs. Inputs must have enzymes which restore them back to their original states after they are acted upon. The membrane composition for ion channels has to match the ions that were present.

In the system we have today, the absence of any one of the chemicals in this process leads to malfunction in the system. The evolution from a simpler chemical pathway to the more complicated pathway of today could not have been stepwise functional if a new chemical was introduced one protein at a time. Changes would necessarily have occurred in complex groups consisting of at least a coordination of proteins and enzymes for catalysts, shaping, regulation, and restoration.

If a simpler chemical pathway was once in existence, then to generate code for more steps, the new proteins and accompanying regulatory enzymes would have to be generated either by copy error, splicing and recombining, duplication, gene absorption, or some similar means. Their coordinated generation in groups would either have to fit with existing inputs and outputs and together add some advantage, or replace inputs and outputs without causing damage or overall dysfunction.  

The probability of a protein and its regulator simultaneously entering a system is much less likely than the appearance of just the new protein. To build up a more complex system, every step requires the generation of minimally dependent groups of molecules plus new functionality, or at a minimum, a neutral presence with no damage or interference to existing systems.

These chemical cascades in the retinal cells are just part of what is required for human vision of today. In Part 4, we will take a look at the anatomical structures that contribute to human sight.

What Makes Me Tick - Part 4

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