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Proteins are organic macromolecules made up of thousands of atoms. Among the elements that make them up we can find, mainly, carbon, hydrogen, nitrogen, oxygen, sulfur, phosphorus, halogens and, in some cases, even some metallic cations.
The structure of a protein can be understood chemically as a natural heteropolymer made up of a combination of 20 amino acids (AA) such as glycine, methionine, glutamic acid and cysteine, to name a few. But what holds all these atoms together? In other words, what types of chemical bonds exist in proteins?
The bonds that are present in proteins can be classified in different ways. On the one hand, they can be classified in a general way, based on an exclusively structural criterion related to the behavior of electrons to keep atoms together. On the other hand, they can also be classified from a more functional point of view, more common in biology and biochemistry.
General classification of bonds present in proteins
From a chemical point of view, proteins contain most of the possible types of bonds known in chemistry. Let us remember that the main types of chemical bonds that hold the atoms together in the different substances that make up matter are:
- The pure covalent bond , characterized by the presence of two atoms that equally share one or more pairs of valence electrons.
- The polar covalent bond , characterized by the presence of two atoms that share valence electrons, but not equally due to a difference in electronegativities of both atoms.
- The ionic bond , which occurs between atoms whose electronegativities are very different, as when an alkali metal is bonded with a nonmetal.
- The metallic bond , which occurs mainly between neutral metallic atoms.
In addition to these types of bonds, there is also a special type of covalent bond that forms between Lewis acids and bases called a dative or coordinate covalent bond . This bond is formed between a Lewis base, which is an electron-rich species that has lone (unshared) pairs of electrons, and a Lewis acid, an electron-deficient species (which has the incomplete octet). In these cases, a covalent bond can be formed between both species, but with the particularity that both bond electrons come from the same species.
Proteins contain mainly covalent bonds
Being organic compounds, proteins are composed mainly of non-metallic elements, such as those mentioned at the beginning of the article. The electronegativity difference of these elements is not high enough for ionic bonds to form. For this reason, almost all the bonds that join the atoms of a protein are covalent bonds.
Some of these covalent bonds are pure covalent (such as when one carbon atom bonds with another) while many others are polar covalent bonds (such as CO, CN, NH, etc.).
Proteins also contain ionic bonds.
Many of the amino acids that make up proteins have functional groups that can be acidic or basic and, therefore, ionized or protonated in a medium with physiological pH. In fact, a protein can contain thousands of both positive and negative charges distributed throughout its structure, making it what is known as a “zwitterion.”
This means that proteins, in addition to having thousands of covalent bonds, also have ionic bonds. These links can occur between different parts of the same protein that have opposite charges, or between the electrical charges of its structure and other free ions, such as sodium cations or chloride anions, to name a few.
Some proteins have coordinate covalent bonds.
Many proteins, especially those that perform catalytic functions such as enzymes, contain metal centers such as iron (II) or (III), calcium (II), magnesium (II) cations, among others. What holds these cations in place is usually a set of coordinated covalent bonds, such as the four bonds that hold the ferrous (Fe 2+ ) cation in the center of the heme group in the proteins hemoglobin and myoglobin . , which is shown in the following figure.
The heme group is not, in itself, a protein, but proteins such as hemoglobin contain this group in their structure, as shown in the following image:
They do not have metallic bonds
The metallic bond is one of the few bond types that is not present in proteins.
hydrogen bonds
Formerly called “hydrogen bonds,” hydrogen bonds are a special type of chemical bond that involves three atoms, one of which is hydrogen, while the others may be oxygen, nitrogen, sulfur, or one of the halogens. These hydrogen bonds are formed between a highly polarized -OH, -NH, or -SH group, which acts as a donor of the hydrogen atom, and another group that contains an N, O, S atom, or a halogen that has a lone pair of electrons, which acts as an acceptor.
Hydrogen bonds are on the border between what are considered weak intermolecular interactions and covalent bonds. For a long time this type of interaction was called a hydrogen bond, but its particular characteristics make it more convenient to classify it as a separate type of bond.
Proteins can have thousands of hydrogen bonds throughout their structure. The importance of this type of link for life is enormous, mainly because they determine, to a large extent, the secondary structure of proteins. Thus, these links are responsible for the formation of alpha helices and beta sheets that structurally characterize the different domains or structures of a protein. In addition, they are also, in many cases, the most important type of interactions that occur between an enzyme and its substrate, facilitating the catalytic activity of the former on the latter.
Other types of bonds present in proteins
In addition to the types of links already mentioned, in biology and biochemistry, certain functional organic groups that frequently appear as links between the different structural blocks that make up the large biomolecules that make life possible are also called “links”. Examples are glycosidic bonds in carbohydrates and phosphodiester bonds in nucleic acids. The most important ones that can be found in proteins are described below.
in peptide bond
As mentioned at the beginning, proteins are polymers made up of amino acids, which make up their structural blocks. The primary structure of a protein is made up of the amino acid sequence that forms its main chain, and the residues that stick out on the sides of it.
The link between each amino acid and the next is an amide group that is formed by condensation between the carboxyl group of one amino acid and the amino group of the next. This amido group is called, in the case of proteins, peptide bond, and is responsible for linking the alpha carbon of one amino acid (along with its particular side chain) with the alpha carbon of the next, as shown in the following figure.
As you can see, the group of atoms highlighted in each yellow rectangle serves as a link between the different alpha carbons of the protein structure, and corresponds to what is known as the peptide bond. This is the reason why proteins are also called polypeptides.
disulfide bridges
If the sequence of AA linked by peptide bonds determines the primary structure of a protein and hydrogen bonds determine its secondary structure, disulfide bonds are one of the most important forces that determine and maintain the tertiary structure, also known as folding. of a protein or its absolute conformation.
The disulfide bridge is a type of “link” that laterally joins two different polypeptide chains, or two sections of the same chain. Like the peptide bond, it is a covalent bond, but in this case, it occurs between two sulfur atoms. The disulfide bridge is formed through the oxidation of sulfhydryl (-SH) groups present on two amino acid residues, usually cysteine.
O-Glycosidic Bond
After the biosynthesis of the protein in the ribosomes, these are subjected to a series of post-translational modifications, among which are the addition of oligosaccharide chains to different residues of certain amino acids. In the event that the oligosaccharide is attached to a threonine or serine residue, the attachment is made by condensation between the OH group of these amino acids and an OH of the sugar in question, with the respective release of a water molecule. This type of bond between an amino acid and a carbohydrate mediated by an oxygen atom is called O-glycosidic bond.
N-Glycosidic Bond
The N-glycosidic bond is equivalent to the O-glycosidic bond described above, but with the difference that it is mediated by a nitrogen atom from the amino group of an asparagine residue.
Other classes of interactions
Finally, in addition to the chemical bonds mentioned so far, which are mostly comparatively strong interactions, there are other types of interactions in proteins that, although they are much weaker on their own, are so numerous that they also manage to contribute considerably. to the structure and function of a protein.
Specifically, we refer to weak van der Waals interactions. These types of interactions occur among all chemical substances, but they are so weak that they can only be clearly observed either when there is no other type of stronger interaction that opaques them, or when they are very numerous and add to each other to give observable effects.
In the case of proteins, van der Waals-type interactions occur between nonpolar amino acid residues such as alanine, leucine, and valine, among others. These amino acids are characterized by having apolar aliphatic side chains, which is why they present eminently hydrophobic interactions, such as London dispersion forces.
These types of interactions usually occur within proteins, in those parts of the structure that are hidden from the surrounding water. In addition, they are also responsible for the existence of domains or sections of a polypeptide chain that are inserted into or that cross the cell membrane, since the latter consists of a phospholipid bilayer that is completely hydrophobic inside.
References
Clark, MA, Douglas, M., & Choi, J. (2018, March 28). 3.4 Proteins – Biology 2e | OpenStax . Openstax.Org. https://openstax.org/books/biology-2e/pages/3-4-proteins
Protein structure, basic forces that stabilize the three-dimensional structure of proteins. (nd). UNAM. http://depa.fquim.unam.mx/proteinas/estructura/EPpran2.html
González M., JM (nd). proteins. Structure. Primary Structure. University of the Basque Country. http://www.ehu.eus/biomoleculas/proteinas/prot41.htm
Lehninger, AL (1997). Biochemistry (2nd ed.). OMEGA.
OLIGOSACCHARIDES (nd). http://www.ehu.eus/biomoleculas/hc/sugar33b.htm
