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30% Inefficiency by Design

By - April 1, 2001
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Cells use a highly wasteful process when producing proteins.

Roughly 30 percent of all newly synthesized proteins must be degraded (broken down) by the cell immediately after formation because they are improperly made.1 On the surface, this new discovery seems to challenge the notion that an Intelligent Designer is responsible for life’s chemistry, but closer examination reveals a specific purpose for the “inefficiency” of protein synthesis.2-4

Anyone with experience in manufacturing would agree that a production process with a 30 percent defect rate needs much improvement. Yet, the seemingly wasteful process of protein synthesis actually plays a critical role in the ability of the immune system to respond rapidly to viral infections. Without this 30 percent defect rate, viral infections like the common cold could be much more severe.

A quick review of basic biochemistry will help demonstrate how inefficient protein production benefits the immune response. 5 To begin the process of protein production, a messenger RNA molecule carries information from a gene on one of the DNA strands to a structure in the cell called a ribosome. These ribosomes help assemble protein chains by linking together small, subunit molecules, called amino acids. Each of the myriad proteins found inside the cell possesses a unique sequence pulled from a pool of twenty different amino acids. The physical and chemical properties of the amino acid sequence determine how the protein chain folds to form its three-dimensional structure. Protein molecules called chaperones often play a key role in assisting the folding of the protein chain. The three-dimensional architecture of a protein determines its functional or structural role inside the cell.

After proteins have outlived their usefulness to the cell or have become damaged in the process of carrying out their cellular function, they are degraded. Upon degradation, the protein’s amino acids are released, and hence, become available for use in the production of new proteins.

The degradation process of any protein (including those defectively made) uses small fragments of the protein to communicate to the body’s immune system what is happening inside the cell. The cell uses a complex assembly of molecules called the class I major histocompatibility complex (MHC) to transport the fragment to the cell’s surface, where it is presented to the immune system.6, 7

In the case of virally infected cells, viral DNA takes over the cellular machinery and produces viral proteins. Before recent studies, experts thought that only viral proteins that had resided in the cell for some time were degraded and presented to the immune system through the class I MHC. This understanding of the process created a dilemma for researchers, because if the cell waited until well into the viral infection to communicate with the immune system, the body could not respond to the infection before the viral invasion progressed too far.

Enter the new discoveries.8, 9 It turns out that 30 percent of the viral proteins are also produced improperly and degraded immediately with the rest of the cell’s defective proteins. Fragments of the viral protein are then incorporated into the class I MHC and the immune system is quickly alerted to the presence of viral particles inside the cell.

This new discovery reveals that the high level of defective proteins produced by the cell is necessary to allow for a highly efficient immune response to viral infection. There is elegant design in the inefficiency of protein synthesis. This finding teaches an important lesson about so-called imperfections in nature. Without exception, an improved understanding of a “poorly” designed system and a proper viewing of the system from a broader context invariably reveal perfection that points to an Intelligent Designer.

 


 

References:

 

  1. Ulrich Schubert et al., “Rapid Degradation of a Large Fraction of Newly Synthesized Proteins by Proteasomes,” Nature 404 (2000), 770-74.
  2. Hansjörg Schild and Hans-Georg Rammensee, “Perfect Use of Imperfection,” Nature 404 (2000), 709-10.
  3. J. Travis, “Trashed Proteins May Help Immune System,” Science News 157 (2000): 245.
  4. Eric A. J. Reits et al., “The Major Substrates for TAP in vivo are Derived from Newly Synthesized Proteins,” Nature 404 (2000), 774-78.
  5. Harvey Lodish et al., Molecular Cell Biology, 4th ed. (New York: Freeman, 2000), 51-63.
  6. Eric Palmer and Peter Cresswell, “Mechanisms of MHC Class-I Restricted Antigen Processing,” Annual Review of Immunology 16 (1998): 323-58.
  7. Kenneth L. Rock and Alfred L. Goldberg, “Degradation of Cell Proteins and the Generation of MHC Class-I Presented Peptides,” Annual Review of Immunology 17 (1999): 739-79.
  8. Schubert et al., 770-74.
  9. Reits et al., 774-78.

Category
  • Bad Designs
Tags
  • Biochemical Design
  • Bad Designs

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