Proteins Made by Design, Part 2 (of 3)

Proteins Made by Design, Part 2 (of 3)

New Discoveries about Ribosomes Add to the Case for Intelligent Design

As I mentioned last week, several years ago I worked in research and development for a Fortune 500 company. As part of the job, I occasionally visited our manufacturing operations. I always enjoyed getting a chance to see firsthand how our products were made. Through these visits I came to appreciate how quality control checks are some of the most critical and sophisticated steps in any manufacturing procedure. These tasks are deliberately incorporated into the manufacturing operation to remove defective materials from the assembly sequence and ensure that no substandard finished product reaches the consumer’s hands.

Quality control measures intervene throughout a manufacturing process. Procedures that simply evaluate and reject out-of-specification finished products at the production process’ end are costly and inefficient. The best quality assurance checks step in at points where mistakes are most likely to occur or are the most costly.

Placing quality control checks at critical points in the production process yields manufacturing efficiency by removing a defective product near the point it occurs in the manufacturing sequence. This prevents the waste of resources and time. If not for immediate intervention, faulty materials accidentally generated in the midst of the manufacturing process will be carried through to the assembly line’s end, only to be discarded.

Similarly, quality control operations take place in the cell. These activities help ensure that biochemical products like proteins are manufactured properly. As I discuss in The Cell’s Design, the quality control operations of the cell suggest that life’s chemistry stems from the work of an Intelligent Agent.

Proteins are large complex molecules assembled from amino acids. The ribosome links amino acids together in a head-to-tail fashion to form a chain-like molecule. To a first approximation, the cell uses 20 different amino acids to build protein chains. The specific sequence of amino acids in the protein chains determines the structure and function of the protein. Once assembled, the amino acid chains fold into complex three-dimensional shapes. The shapes of proteins critically dictate their functions.

As I described last week proteins are made when the ribosome works in conjunction with messenger RNA (mRNA) and transfer RNA (tRNA). mRNA molecules contain the instructions needed to assemble the protein. tRNA molecules serve as couriers, ferrying amino acids to the ribosome per the directions housed in mRNA. Some of the most important quality control checks in protein synthesis take place during the processes that attach amino acids to the tRNA molecules and transport them to the ribosome. If the wrong amino acids are presented to the ribosome during the generation of the protein chain, an incorrect sequence will result.

New work by researchers from Johns Hopkins University School of Medicine identifies another quality control operation. Instead of focusing on the amino acid-tRNA complex this checkpoint takes place at the ribosome after the amino acids arrive.

It turns out that if the wrong amino acid is presented to the ribosome and accidently incorporated into the growing protein chain, the subsequent amino acid additions to the chain become more error prone. In other words, one mistake begets multiple mistakes. When this happens, it very quickly forces a premature termination of protein production, preventing the generation of faulty proteins. The Johns Hopkins scientists estimate that this one step improves the fidelity of protein synthesis by an order of magnitude (factor of ten). Interrupting protein production once an error has occurred makes sense since it prevents cellular resources from being wasted.

Effective and efficient quality control procedures don’t just happen. Implementing these kinds of control systems requires careful planning, a detailed understanding of the manufacturing process and of the product, and the way the consumer will use the product. In other words, quality control procedures reflect intelligence and ingenuity and serve as indicators of a well-designed process. The quality assurance operation that takes place at ribosomes indicates that life’s chemistry stems from the work of a mind.

Next week I will describe another new discovery having to do with the quality control operations that take place after protein synthesis and that further advances the case for biochemical intelligent design.

Part 1 | Part 2 | Part 3