Structure of the Amino Acid

10 facts about proteins and polypeptides

1: "Proteins are linear polymeric molecules consisting of a sequence of amino acid residues". Although in the wildlife there are dozens of different amino acids and many of them can be part of proteins, the main ones are twenty directly encoded in DNA. Each of the amino acids has the same chemical group that, during polymerization, forms a peptide bond (this is the kind of amide bond that is formed by the interaction of the -NH 2 group of one amino acid with the -COOH group another) with adjacent amino acids in the linear polypeptide chain, and the specific side a chain that distinguishes one amino acid from another.
                                         

2: A feature of proteins that distinguishes them from most other natural and synthetic polymers is that all molecules of the same protein are folded into the same strictly defined spatial structure (conformation). There are exceptions to this rule, but very few of them.

3: In a living cell, proteins are synthesized in a complex macromolecular complex called a ribosome. For the operation of the ribosome, separate amino acids dissolved in the cytoplasm of the cell and a ribonucleic acid molecule (RNA) are necessary, in the nucleotide sequence of which the amino acid sequence of a given protein is encoded (well, Elementary link in the linear chain of DNA and RNA). Each of the 20 amino acids corresponds to a combination of three adjacent nucleotides in RNA. Thus, the ribosome extends through itself a chain of RNA, "reads" its nucleotide sequence, depending on the combination of nucleotides, captures from one's surrounding amino acid, binds it with a peptide bond to the previous amino acid in the chain, and so on, until RNA ends a region encoding an amino acid sequence.

4: After leaving the ribosome, the polypeptide chain is added to its native spatial structure in a time of the order of one second. And this is very surprising. The point is that the polypeptide chain has a very large number of degrees of conformational freedom. If the native structure (which, according to the basic laws of physics, should have minimal energy), it is not necessary to search for any possible conformations by simple search of all possible conformations and at the same time to spend time on the order of one picosecond (i.e., 10 -12 s), then the search for the required confirmation enough even the time of life of the universe. Nature manages this process much faster.

5: The spatial structure of the protein is determined by its amino acid sequence. Despite intensive research, scientists have not yet developed a method that would in all cases accurately predict the structure of the protein from its amino acid sequence.
6: The length of the chain for different proteins can vary by orders of magnitude. The smallest proteins (to which the name oligopeptides are more applicable) consist of 15-20 amino acid residues, and the largest proteins have many thousands of residues. Proteins vary very much not only in size but also in their biological function. There are protein-enzymes, regulators, suppressors, transport proteins, receptors, structural proteins, etc. It should be noted that there are many proteins whose function in living organisms is still unknown.

7: Conditionally, proteins can be divided into three classes. First, they are globular proteins. They usually have a compact structure (globule), are soluble in water and function in a liquid medium. Secondly, they are membrane proteins that are located and operate on the surface and/or inside biological membranes. Thirdly, it is fibrillar proteins, insoluble in water, which form long fibers (fibrils ), serving as the basis for muscle and connective tissues, a typical example of such a protein is collagen.

8: Although most proteins have a strictly defined structure, this structure is not absolutely rigid; it has a certain degree of conformational mobility. This mobility is extremely important for the biological function of proteins. Nature designed the proteins in such a way that the chaotic thermal energy of the surrounding solution is converted into a protein in the targeted molecular movements of the polypeptide structure, without which in many cases the proteins would not work.

9: At present, there are only two experimental methods that allow determining the spatial structure of the protein, X-ray structural analysis, and nuclear magnetic resonance (NMR) method. In the XRD single crystal protein (not all, but many proteins can form crystals) is irradiated with X-rays, which after passing through the sample give a diffraction pattern. In this picture, using the complex calculation methods, the structure of the protein is restored. In the NMR experiment, the force of magnetic interactions between magnetic nuclei is measured, which depends on the distance between them. The structure of the macromolecule is also determined with the help of complex computer algorithms, according to the internuclear distances measured in this way.

10: Due to the development of genetic engineering for research, so-called recombinant proteins are often used today. To produce them, the genome (DNA) of bacteria is modified in order to synthesize protein in large quantities, which is necessary for researchers. The main advantage of this method in comparison with the isolation of natural proteins from living organisms is that it makes it possible to obtain mutant proteins (i.e., proteins with a modified amino acid sequence) relatively easily, as well as proteins with isotope enrichment. In the same way, many proteins widely used in medicine as drugs (insulin, erythropoietin, growth factors, etc.) are produced.