What is the need for organic evolution

The building blocks of life

Amino acids are the building blocks of all proteins that are present in all of our living beings on our earth. We produce some of the amino acids ourselves, some we take in with our food. This wide variety of proteins in every living being is made from just twenty amino acids.

There are two additional amino acids, which are sometimes the building blocks of proteins. However, since their use is not often found in nature, we will not deal with them here, but only with the twenty basic amino acids, which are referred to as "natural amino acids", in contrast to the other amino acids, which we here "unnatural amino acids" “Will be called. Why are there no living things in which the proteins are made up of other amino acids? How did these amino acids crystallize in evolution? And were there other amino acids in the past that went extinct?

When we talk about evolution we usually mean changes in the genetic material (DNA) that distinguish one biological species from another biological species, or even a generation from another generation of the same species. The DNA sequence in turn determines the sequence of the amino acids that make up every protein in the body, so that different living beings carry different proteins, which even between the parents and their offspring mutations, i.e. mutations. H. Changes in the instructions for the arrangement of the amino acid chains.

This entire process takes place within a narrow framework of chemical rules. The elementary structure of DNA and proteins does not change between generations, nor does it change from one living being to another. However, these chemical structures probably did not initially exist, but evolved over the course of chemical evolution, in a process that occurred in a period known as the prebiotic era.

During this time, about four billion years ago, according to the theory of evolution, life began on earth. And what was before - hullabaloo? From our point of view as living beings, it is actually more or less what it was then. Researchers call this original environment the "primordial soup", a name that describes a watery environment rich in organic compounds and minerals. According to a currently accepted theory, this primordial soup contained extraterrestrial substances such as meteorites or interstellar dust. Under certain physical conditions, the ancestors of the amino acids and proteins that later enabled the development of life as we know it, spontaneously formed.

The original amino acids

Amic acids are small molecules made up of two parts: a carboxyl group and a group with a nitrogen atom called "amino". Between the two groups is a kind of tail that differs from amino acid to amino acid and is known as the "side chain".

Amino acid lysine: carboxyl residue (in red), amine (in blue) and the side chain (in green). Graph: Daniel Seidmann

A protein is a chain of amino acids that are linked together by a peptide bond. This connection is made on the ribosome - a system that makes the proteins in the cell - between the amino side of one amino acid and the carboxyl side of the other amino acid. Such a chain, before it folds into a protein, is called a peptide.

Peptide made up of the amino acids glycine, serine and valine (from left to right). The connections between the individual amino acids are marked in blue. Graph: Daniel Seidmann

Several studies have shown that the peptides had an ancestor that arose spontaneously under the conditions that prevailed in the primordial soup that was then on Earth. This original peptide is called the depsipeptide and differs from the peptides we know today in the bonds between two adjacent carboxyl ends, which are called ester bonds instead of amide bonds.

Depsipeptide blue: amide bond, green: ester bond. Graph: Daniel Seidmann

How were the amino acids chosen?

A 2019 study by Israeli researcher Moran Frenkel-Pinter focused on three amino acids that have a positive electrical charge on the side chain: lysine, arginine, and histidine. These amino acids were compared to three other positively charged amino acids, ornithine (Orn), Dab and Dpr, which are not basic building blocks of proteins but are used in nature. Ornithine e.g. B. has a role in the uric acid cycle found in humans and many other animals. These three amino acids are similar to lysine, but differ in at least one atom.

The three positively charged natural amino acids compared to the three unnatural amino acids. Graph: Daniel Seidmann

The study sought to reconstruct the prebiotic conditions for the formation of depsipeptides in order to explain why the three natural amino acids were chosen in the course of chemical evolution and the others were not. The researchers were able to show that in the spontaneous formation under these conditions, the natural amino acids were preferred over the unnatural and that the peptide bond was preferred to all other bonds. Since electrical charges play an important role in the binding of proteins to DNA and RNA molecules, the researchers hypothesized that the original peptides were important for the binding actions in connection with the original molecules of the genetic material.

"I believe that you can never say exactly how the amino acids developed and how they were selected, but it is definitely possible to clarify and understand the chemical principles," said Frenkel-Pinter in an interview with the Davidson Institute. According to her, there were probably more intermediate steps from the primordial molecules to the proteins of today. The transition from one phase to another is based on the formation of new chemical complexes, such as those shown here. "The gradual increase in complexity was important for the development of systems and processes during chemical evolution," she testified.

Frenkel-Pinter therefore intends to further explore the chemistry of primitive life and to increase the complexity. "In order to decipher the important things of the original life, we have to slowly but surely leave the comfort zone of simple systems and look at more complex systems, even if this comes at the expense of a deep understanding of every little detail in the system," she said.

A study from the laboratory of Dan Tawfik from the Weizmann Institute under the direction of Liam M. Longo, which was published this year, opens up the possibility that the amino acid ornithine itself could have been the ancestor of the amino acid arginine and also the first positively charged Amino acid. This process could have occurred in the prebiotic era because ornithine can turn into arginine in a spontaneous process without external intervention. This study admits the possibility that ornithine enabled the primordial proteins to bind to DNA and RNA molecules. To prove this hypothesis, the researchers made artificial proteins in the laboratory in which the only positively charged amino acid was ornithine, and showed that this protein could actually bind to RNA.

Amino acids of the future

Protein design is a relatively new area of ​​research with enormous potential for application. Artificial proteins made in the laboratory or factory can be used for a wide variety of applications such as making medicines, sugars, new substances, and much more. In contrast to the proteins that are produced in the body, we can control the sequence of the artificial proteins without the need for evolutionary selection processes.

In addition to selecting the sequence, researchers have developed methods of incorporating amino acids into proteins that are not part of the twenty amino acids that exist in living things. However, the methods are complex and have many limitations. This includes the need for a new system to be developed for every new amino acid that is to be incorporated into the protein. New research is trying to improve these methods so that they are likely to be easier to apply in the years to come. So it is possible that in the future we will be able to take drugs based on proteins made up of man-made amino acids that were not created through natural evolution.