The Wisdom of Biochemical Systems

amino-acid-6New Year’s Day will soon be upon us. That means it’s time to come up with a few resolutions. Any commitment to lose weight won’t last long. Maybe, I’ll read through the book of Proverbs in 2015. More wisdom would be good.

The advice Solomon imparts stemmed from his experience and time spent in careful reflection. Divine insight also undergirds Proverbs. In fact, Solomon thought the wisdom reflected in Proverbs is the same wisdom the LORD exercised when He created the heavens and the earth (Proverbs 8:22–30).

Based on Proverbs 8 (and other passages), I would expect God’s wisdom to be manifested in the created order. The Creator’s fingerprints—so evident in nature—should not only reflect the work of intelligent agency, but also display undeniable wisdom. Without question, biochemical systems bear the hallmarks of both.1

When I began studying biochemistry as a graduate student, one of the things that most impressed me was the cleverness of the cell’s chemical systems. I could cite countless examples of biochemical sagacity, but for now I will focus on two recent studies (see here and here). Each relates to the amino acid composition of proteins.2

Cost Effective Amino Acid Sequences

Biochemists have long had interest in the relationship between amino acid sequence and protein structure and function. Proteins exhibit a great diversity of amino acid compositions and sequences. Biochemists believe this assortment is necessary to support the wide range of operations requisite for life.

And yet making proteins costs the cell energy and chemical resources. Some of the expense stems from the process of assembling protein chains. Cellular machinery links together amino acids to produce proteins. Each linkage requires energy. So does the production of the amino acids themselves. The cell synthesizes each of the twenty different amino acids used to assemble proteins via its own series of chemical reactions, which biochemists call a metabolic pathway. Some amino acids are easy to make, requiring minimal energy and chemical resources. Others are more expensive.

Ideally, cells need to minimize the cost of making proteins. There are thousands of proteins found in the cell at any one moment in time. If too many of these proteins are comprised of expensive amino acids, the cell won’t be able to harvest enough energy to generate the proteins needed to carry out all of its activities. This is bad news for the cell’s survival. Think of a business that sells its products for a loss. Eventually, the business will have to shut down if it can’t make a profit on what it produces. However, least-costly proteins lack the chemical diversity needed to carry out life’s necessary operations. To continue with the business analogy, think of a merchant who manufactures useless products that no one wants to buy.

Researchers from Argentina recently discovered how cells work around this conundrum. Based on modeling studies, the scientists showed that proteins found in nature are comprised of least-costly amino acids that simultaneously allow for maximal sequence diversity (and hence, function).3 In other words, proteins are optimized to balance competing interests of functionality and metabolic costs.

Optimization reflects the work of intelligent agency, evincing the Creator’s handiwork. Yet, as a biochemist, I am even more impressed with the elegant molecular logic that underlies the amino acid compositions of proteins. In principle, many different amino acid sequences can be used to achieve the same protein function. Yet the ones the cell employs are the most cost effective.

Making Proteins to Make Amino Acids to Make More Proteins

The availability of amino acids poses another biochemical conundrum, particularly for single-celled organisms such as bacteria. Proteins mediate each of the chemical reactions comprising the biosynthetic pathways used to produce amino acids. To put it another way, proteins make the amino acids that the cell’s machinery, in turn, uses to make proteins.

So what happens when cells face a shortage of a particular amino acid? Usually, the cells will ramp up production of the specific proteins needed to replenish the amino acid in short supply. But if that amino acid is required to make the proteins that make it, things come to a standstill.

By way of analogy, it is the same problem a manufacturing facility would face if it used an assembly line to manufacture widgets and the machines on the assembly line required widgets for their operation. If there were a worldwide shortage of widgets (and demand for the widgets kept increasing), there would be no way to ramp up production of widgets by adding more assembly lines because widgets would be needed to build the machines that make widgets. The only way around this stalemate would be to design manufacturing hardware that didn’t require widgets to make widgets—and this is exactly what cells do.

Investigators from UC Berkeley have discovered that the proteins that take part in the biosynthetic route that manufacture a specific amino acid make limited use of that amino acid in their compositional make up.4 In this way, when a particular amino acid is in short supply, the cell’s machinery can still make the proteins that synthesize the amino acid in demand. Again, as a biochemist, I can’t help but to marvel at the elegance and wisdom of this design.

In my experience, most biochemists (whether believers or skeptics) are taken with the elegant molecular wisdom that defines the architecture and operation of biochemical systems. The cleverness of the cell’s chemical systems convinced me that a Creator must be responsible for life. To think otherwise would be folly.

 

Endnotes

  1. For a few examples, check out the articles below.
  1. Teresa Krick et al., “Amino Acid Metabolism Conflicts with Protein Diversity,” Molecular Biology and Evolution 31 (November 2014): 2905–12; Rick A. Fasani and Michael A. Savageau, “Evolution of a Genome-Encoded Bias in Amino Acid Biosynthetic Pathways Is a Potential Indicator of Amino Acid Dynamics in the Environment,” Molecular Biology and Evolution 31 (November 2014): 2865–78.
  2. Krick et al., “Amino Acid Metabolism,” 2905–12.
  3. Fasani and Savageau, “Evolution of a Genome-Encoded Bias,” 2865–78.

 

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