Types of Bonds seen in biological molecules

• In biological systems, smaller molecules participate in metabolism while larger molecules are structural
or informational in nature.
• Major Biological molecules include water, and organic substances such as proteins, polysaccharides and
lipids as well as nucleic acids which are in turn made up of C, N, O and H.

• Proteins , polysaccharides and Nucleic acids are formed by monomers namely amino acids,
monosaccharides and nucleotides respectively

• Biological molecules are held together by strong and weak forces between their atoms facilitating
interactions in them

• Covalent bond is a strong interaction in which two atoms share one or multiple pairs of electrons

• Non covalent bonds are weak attractive forces but they determine the properties and functions of
biomolecules (ionic interactions, hydrogen bonds, van der Waal’s interactions and hydrophobic effects)
• 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
• 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.

• 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 bonds, Hydrophobic Interactions, disulfide bond, Ionic Interactions

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
Glycosidic Bond
• 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 (-NH 2) 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.
• 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.
• 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
• 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;
• One ester linkage attaches the phosphate group with the 5’ carbon of one nucleotide
• 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 Bonds

• Hydrophobic interactions

• Disulfide bond

• Ionic Interactions
• Hydrogen Bonds
• 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 (less
stronger than )

• A hydrogen bond is an intermolecular force (IMF) that forms a

special type of dipole-dipole attraction when a hydrogen atom
bonded to a strongly electronegative atom exists in the vicinity of
another electronegative atom with a lone pair of electrons.
Intermolecular forces (IMFs) occur between molecules. Other
examples include ordinary dipole-dipole interactions and
dispersion forces. Hydrogen bonds are are generally stronger
than ordinary dipole-dipole and dispersion forces, but weaker
than true covalent and ionic bonds.
Origin of Hydrogen Bonding
The molecules capable of hydrogen bonding include the following:

Figure 3: The lone pairs responsible for hydrogen bonding in NH3, H2O, and HF.
The solid line represents a bond in the plane of the screen or paper. Dotted bonds are going back into the
screen or paper away from you, and wedge-shaped ones are coming out towards you.

Notice that in each of these molecules:

•The hydrogen is attached directly to a highly electronegative atoms, causing the hydrogen to acquir
a highly positive charge.
•Each of the highly electronegative atoms attains a high negative charge and has at least one "active
lone pair.
• 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

ionic bond, also called electrovalent bond, type of
linkage formed from the electrostatic attraction
between oppositely charged ions in a chemical
compound.
Such a bond forms when the valence (outermost)
electrons of one atom are transferred permanently
to another atom.
• 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.
Van-der-Waals force
It is the relatively weak attractive forces that act on neutral
atoms and molecules and that arise because of the electric
polarization induced in each of the particles by the presence of
other particles.
They differ from covalent and ionic bonding in that they are caused
by correlations in the fluctuating polarizations of nearby particles (a
consequence of quantum dynamics)
Various interactions in biomolecule
 Water is a Biomolecule….

• Water has some unusual chemical properties that make it very good at
supporting life. These properties are important to biology on many different
levels, from cells to organisms to ecosystems. You can learn more about the
life-sustaining properties of water in the following articles:
• Solvent properties of water: Learn how and why water dissolves many polar
and charged molecules.
• Cohesion and adhesion of water: Water can stick to itself (cohesion) and
other molecules (adhesion).
• Specific heat, heat of vaporization, and density of water: Water has a high
heat capacity and heat of vaporization, and ice—solid water—is less dense
than liquid water.
• Water owes these unique properties to the polarity of its molecules and,
specifically, to their ability to form hydrogen bonds with each other and with
other molecules.