Introduction

Chemical bonds are the linkages or associations between two or more atoms that together form molecules of compounds. For example, in a water molecule, two bonds connect the two hydrogen atoms to one oxygen atom, resulting in the formation of a water molecule. 

The biological molecules are divided into four major categories; carbohydrates, lipids, proteins, and nucleic acids. All these biological molecules are formed as a result of chemical associations or linkages between different atoms. These bonds not only form the biological molecule but are also responsible for the maintenance of their complex structures. 

The chemical bonds in case of biological molecules can be divided into two categories; 

• Primary Bonds
• Secondary Bonds

In this article, we will have a detailed discussion about various types of bonds found in biological molecules. 

Primary Bonds

These are the covalent bonds formed as a result of electron sharing among two or more atoms. They are formed as a result of a chemical reaction that may be reversible or irreversible. Primary bonds are the permanent attractions that are developed among the atoms by the sharing of electrons. The formation of a primary bond either consumes or releases energy and the same energy is needed to break the primary bond. 

Primary bonds usually form the primary structure of the biological molecules except the disulfide linkage that serves to maintain the secondary or tertiary structures. The following are the various type of primary bonds found in the biological molecules. 

Glycosidic Bond

It is a primary bond or a covalent bond that serves to connect carbohydrates to other groups or molecules. The partner or combining molecule may be carbohydrate or non-carbohydrate in nature.

This bond is formed as a result of a reaction between the carbonyl group of a carbohydrate or its derivate and a hydroxyl group of some other compound. The carbonyl group of carbohydrate may be a part of an aldehydic group or a ketonic group. A molecule of water is released in this process, making it an irreversible reaction. 

Classification

Based on the nature of the molecule linking with a carbohydrate, glycosidic bonds can be of the following types.

O-Glycosidic Bond

It is the most abundant glycosidic bond found in nature. In an O-glycosidic linkage, the carbonyl group of carbohydrates reacts with the hydroxyl group of another compound. This results in a compound in which the sugar or carbohydrate residue is attached to the oxygen of the other compound, thus the name O-glycosidic bond. 

The O-glycosidic linkage is found in all oligosaccharides like sucrose, maltose, maltotriose, etc. as well as polysaccharides like cellulose, starch, and glycogen. They are called O-glycosides. It is the primary bond in all types of carbohydrates above the level of monosaccharides. 

N-Glycosidic Bond

These are the glycosidic bonds in which a sugar moiety is attached to nitrogen of the non-carbohydrate compound. This bond is formed as a result of a chemical reaction between the carbonyl group of a carbohydrate molecule and amino group (-NH₂) of a non-carbohydrate molecule. 

This type of linkage is seen in amino sugars and glucosyl amines. Such compounds are called N-glycosides. An example of glucosyl amines is the nucleoside molecule in which the ribose sugar is attached to a nitrogenous base via an N-glycosidic bond. 

C-Glycosidic Bond

It is a strange type of glycosidic bond in which the sugar moiety is attached directly to the carbon atom of the other molecule. It is formed as a result of the reaction between the carbonyl group of a sugar molecule and an alkyl compound like methane etc. 

These compounds are known as C-glycosides. An example of C-glycosides is Aloin found in aloe vera species. It is a yellowish-brown compound having bitter taste which is formed by modification of the anthraquinone structure by adding a sugar molecule. 

S-Glycosidic Bond

In this type of glycosidic bond, the sugar residue is attached to the sulfur group of the non-carbohydrate compound. It is formed when the carbonyl group of sugar reacts with the thiol (-SH) group of the other compound. 

The compounds with S-glycosidic bonds are called S-glycosides for example Sinigrin. It is a toxic compound found in some plants like seed of black mustard etc.  

Orientation

Based on the stereochemistry of the anomeric carbon or its orientation in space, a glycosidic bond can either be an alpha-bond or a beta-bond. 

Alpha-Glycosidic bond

In an alpha-glycosidic bond, the atoms forming the bond are directed in the same plane i.e. they are identical in stereochemistry. The glycosidic bonds among the glucose molecules in starch are examples of the alpha-glycosidic bonds. 

Beta-Glycosidic bond

In beta-glycosidic bonds, the two bond-forming atoms are directed in opposite plane having different stereochemistry. The glycosidic bonds among the glucose residues in cellulose are beta-glycosidic. 

Degradation

Glycosidic bond undergoes degradation in a process called glycolysis. It is a hydrolytic process in which a water molecule is used to break the glycosidic bond and release the carbohydrate and other residues. 

Enzymes required to break different types of glycosidic bonds are present in different animals. For example, the enzyme to break the beta-O-glycosidic bond between the glucose molecules in cellulose is present in the GIT of herbivores but not present in humans. 

Peptide Bond

It is the second most abundant bond found in biological molecules. A peptide bond is the one that links amino acids to form polypeptide chains. 

It is a covalent bond formed as a result of a chemical reaction between the amino group of one amino acid and the carboxylic group of another amino acid. 

Synthesis

As mentioned above, it is formed when the amino group and the carboxylic groups of amino acids react and release a water molecule. It is only formed when both the carboxylic group and the amino group are non-side chain groups. It means that in order to form a peptide bond, both the groups much be attached to the alpha carbon and must not be a component of the side chains of amino acids. 

In the process of making a peptide bond, the carboxylic group loses hydrogen and oxygen atoms while the amino group only loses its hydrogen. 

The resultant compound is called a dipeptide. This dipeptide can also form additional peptide bonds because of the presence of free amino group and carboxylic group at its N-terminal and C-terminal, respectively.  

Properties

The peptide bond is unique in its properties. 

• It has the characteristics of a partial dual bond. Although it is a single bond, it is shorter than the traditional single covalent bonds. Recall that shorter the bond length, the stronger is the bond. Thus, this short bond length imparts rigidity to the peptide bond making it rigid and planar to the extent that the groups attached to it cannot be rotated freely. However, it must be kept in mind that the groups attached to the a-carbon, a-amino and a-carboxylic groups of these amino acids can be rotated freely. 
• Peptide bond is a polar bond that participates in making hydrogen bonds when the polypeptide chains are organized into higher structural levels. However, the -C=O and the -NH groups in the peptide bond carry no charge and are electrically neutral. 

Examples

Peptide bond is found in proteins, peptones, polypeptides, and dipeptides, etc. Whenever the two amino acids are joined, the bond between them is called a polypeptide. 

Degradation

Peptide bonds are broken down during the process of protein degradation. It is also a hydrolytic process as a water molecule is utilized to break the bond between two amino acids. 

In living organisms, the hydrolysis of the peptide bond is catalyzed by enzymes during the digestion of proteins in GIT as well as the normal turnover of proteins within the cell.  

Ester Bond

It is a covalent bond that is essential in various types of lipids. An ester bond or ester linkage is formed between an acid and an alcohol. 

Synthesis

An ester bond is formed when a molecule having the carboxylic group reacts with another molecule having a hydroxyl group. The carboxylic group loses its hydrogen and oxygen while the alcohol loses hydrogen of its hydroxyl group. As a result, a water molecule is released, and the two carbons are linked via an oxygen bridge forming a -COC- linkage. 

Example

The bonds between the glycerol and the fatty acids in a triglyceride are the examples of ester bonds. 

Thioester bond

It is a modified form of ester linkage in which the oxygen bridge is used to connect a carbon atom with a sulfur atom. It is formed as a result of the reaction between the carboxylic group of one molecule and the thiol group (-SH) of another molecule. The carboxylic group loses the oxygen and hydrogen while the thiol group loses its hydrogen and a thioester bond is formed. 

An example of thioester linkage is the one between the thiol group of CoA and the carboxylic group of acetic acid in Acetyl CoA. 

Degradation

The ester linkage is a very high-energy bond releasing a tremendous amount of energy upon hydrolysis. Like the rest of the bonds discussed earlier, it is also broken down by incorporating a water molecule. The hydrolysis of the ester linkage yields 9 Kcal/g energy. 

Phosphodiester Bond

It is the primary covalent bond that joins different nucleotides in a polynucleotide or nucleic acids. It is also a type of ester bond but involves two ester linkages. 

Degradation

A phosphodiester bond is a double ester linkage formed when the phosphate group at the 5’ end of one nucleotide reacts with the free hydroxyl group at the 3’ end of another nucleotide. A molecule of water is released, and two ester linkages are formed. In these linkages, the oxygen bridge is used to connect a carbon atom with a phosphate group. The two ester linkages are as follows;

1. One ester linkage attaches the phosphate group with the 5’ carbon of one nucleotide
2. The second ester linkage attaches the same phosphate to the 3’ carbon of the other nucleotide

The compound thus formed is called a dinucleotide. It can form additional phosphodiester bonds at both ends because of having a free hydroxyl group at the 3’ end and a free phosphate group at the 5’ end. 

Examples

Phosphodiester bonds are used to attach nucleotides in DNA and RNA. They are also present in dinucleotides like NAD and NADP. Polynucleotide that don’t fall in the category of nucleic acids also have phosphodiester bond linking the individual nucleotides. 

Degradation

The degradation of phosphodiester bonds also requires the use of a water molecule and is thus a hydrolytic process. In living organisms, the degradation of the phosphodiester bond is catalyzed by specific enzymes called nucleases. They are of two types;

• Exonucleases, they break the phosphodiester bond beginning from one end of the chain. 
• Endonucleases, they can break the phosphodiester bond even from within the chain of nucleotides.

Both these enzymes are used in the living cells during the normal turn-over of nucleic acids. 

Secondary Bonds

Recall that bonds are the electrostatic attractions that are developed among the atoms. The secondary bonds in biological molecules are the temporary forces of attractions that are developed when certain atoms or groups come close together. These bonds are mainly involved in maintaining the secondary, tertiary or other higher structures of biological molecules. They are most important in proteins and nucleic acids. 

Some of the important secondary bonds in biological molecules are the following. 

Hydrogen bond

It is the most important secondary bond in biological molecules. Hydrogen bond is the strongest secondary bond having strength almost equal to that of covalent bonds. 

Synthesis

Hydrogen bond is formed as between a hydrogen atom and a highly electronegative atom like oxygen or nitrogen. When a hydrogen atom comes within the electron affinity of a highly electronegative atom like oxygen or nitrogen, electrostatic forces of attraction among the proton of hydrogen and the lone pair of electrons in oxygen or nitrogen. 

The number of hydrogen bonds formed by an electronegative atom depends on the number of free electrons present in its outermost shell. Oxygen has two free electrons and thus can form two hydrogen bonds while nitrogen forms only one hydrogen bond due to one free electron. 

Importance

Hydrogen bond is highly important in the biological molecules. Take a look at the following points.  

• Water molecules are held together via hydrogen bonding. 
• The secondary structure of proteins i.e. alpha-helix and beta-sheets are maintained via hydrogen bonding among the peptide bond components. 
• Hydrogen bond also maintains the tertiary structure of proteins. 
• The DNA double helix is held together via hydrogen bonding among the bases of its nucleotides. 
• The coiling of RNA chain onto itself takes place via hydrogen bonding. 

Hydrophobic Interactions

These are the interactions among the non-polar molecules. Such molecules cannot dissolve in water. However, they tend to clump together away from the polar or charged molecules. This clumping of hydrophobic molecules is called hydrophobic interaction.

Hydrophobic interactions are important in maintaining the tertiary and quaternary structure of proteins.

They are also involved in protein folding. 

Disulfide Bond

Although it is a covalent bond, it is discussed under the heading of secondary bonds because it is involved in maintaining the higher structures of biological molecules. 

A disulfide bond is formed between the thiol groups present in the side chains of two cysteine residues to form one cystine residue. This bond brings the two cysteine residues together that have been kept apart by the intervening amino acids. 

This bond is involved in stabilizing the tertiary structure of proteins and guiding the protein folding. 

Ionic Interactions

These are the secondary forces of attractions formed between the charged groups. 

The acidic and basic groups in the side chains of amino acids either have a positive or negative charge at the physiologic pH. Together they form strong attractions in the tertiary structure of proteins. They are also involved in the folding of proteins. 

Summary

Chemical bonds are forces of attraction that keep together different atoms to form molecules.

The biological molecules have two types of bonds, primary and secondary. 

Primary bonds are permanent forces of attraction are required for joining together of atoms or molecules to form larger biological molecules. The important primary bonds in biological molecules are;

• Glycosidic bonds, they link sugars to one another or non-carbohydrate compounds in complex carbohydrates, amino sugars and nucleotides
• Peptide bonds, they link the amino acids together in proteins, peptones and other polypeptides
• Ester bonds, they attach the alcohol with an acid. They are important in lipids such as triglycerides.
• Phosphodiester bonds, they attach the nucleotides together in nucleic acids and other polynucleotides

Secondary bonds are the temporary attractive forces among the molecules or atoms. They are essential for maintaining the complex structures of biological molecules. These include;

• Hydrogen bonds, they are important in proteins and nucleic acids
• Hydrophobic interactions, they maintain the tertiary and quaternary protein structure
• Disulfide bridges, these are the covalent bonds that are involved in tertiary protein structure and protein folding
• Ionic interaction, they are among the charged groups and are involved in tertiary protein structure and folding

Frequently Asked Questions

What are the primary bonds in biological molecules?

Primary bonds are the covalent bonds formed between atoms due to electron sharing. Examples of such bonds include glycosidic bonds, peptide bonds, ester bonds, etc.

What are the secondary bonds found in biological molecules?

Secondary bonds are the temporary forces of attraction between certain atoms or groups of atoms when they are brought together. Examples of such bonds include hydrogen bonds, disulphide bonds, hydrophobic interactions, etc.

What is a glycosidic bond?

A glycosidic bond is a primary bond that connects carbohydrates to other molecules, which may or may not be carbohydrates. They may be O-glycosidic bonds or N-glycosidic bonds, depending upon the nature of 2nd molecule.

How is a peptide bond formed?

A peptide bond is formed between 2 amino acids when the amino group of one amino acid reacts with the carboxylic group of the other, and a water molecule is released. Both reacting groups should be attached to alpha carbon to form a peptide bond.

References

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3. Marco Brito-Arias, “Synthesis and Characterization of Glycosides”, second edition, Editorial Springer 2016.
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