How Do Peptide Bonds and Other Bonds Shape Biomolecules?
Before we proceed with peptide linkage definition and different kinds of bonds that exist in biomolecules, let us take a look at a few relevant concepts.
All living organisms have biomolecules that are primarily constituted of polymers. Polymerisation is the formation resulting from multiple monomers. Monomers are the smaller units that are held together by various kinds of bonds.
The formation of these bonds is dependent on the monomer's chemical nature. It is these different kinds of bonds that are discussed.
Peptide Bond
If you are considering what is peptide linkage, it is another term for a peptide bond. When two molecules form a chemical bond in which the carboxyl group of one molecule undergoes reaction with the amino acid of another molecule, a peptide bond is formed.
Peptide bond formation steps are also called a dehydration synthesis reaction where one molecule of water is released in the process. As in the case of proteins, peptides are also made up of amino acids that are linked amongst itself in a chain-like formation.
Did You Know?
Nucleic acids are essentially such molecules that engage in coding genetic information of organisms. Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are the two types of nucleic acids that are instrumental in reproduction, repair and protein synthesis. RNA and DNA are the polymers that are made up of monomers known as nucleotides.
Glycosidic Bond
The covalent bond which joins a carbohydrate with another molecule or group is called a glycosidic bond. The constituting element of this bond is a glycoside. For instance, within adenosine molecule, adenine and ribose are connected by an N-glycosidic bond.
Glycosidic bonds are of two types – 1, 4 beta and 1, 4 alpha glycosidic bonds. When water reacts with glycosidic bonds, it hydrolyses forming two monosaccharides.
Phosphodiester Bond
The covalent bonds which join 5 carbon of one deoxyribose with that of 3 carbon of the next deoxyribose of the adjacent nucleotide, within phosphate groups, are called phosphodiester bonds.
It is one of the most critical components for structuring DNA and RNA to maintain genetic code integrity. The phosphodiester bond helps in linking phosphate molecules to sugar molecules.
Base Pairing in DNA
Base pair in DNA primarily relates to the bonding of two chemical bases with the formation of “rung of the DNA ladder”. There are two strands in the molecule that twist around each other, and the strands are made up of phosphate groups and alternating sugar or deoxyribose. The base pairing in DNA imparts its helical structure and allows replication.
Test Your Knowledge
i. Which of the following joins amino acids?
(a) Glycosidic bond
(b) Ionic bond
(c) Hydrogen bond
(d) Peptide bond
ii. Which of the following constitute a dipeptide?
(a) 2 amino acids and 3 peptide bonds
(b) 2 amino acids and 1 peptide bond
(c) 2 amino acids and 4 peptide bonds
(d) 2 amino acids and 2 peptide bonds
Solutions: i. (d) Peptide bond, ii. (b) 2 amino acids and 1 peptide bond
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FAQs on Peptide Bonds and Essential Biomolecular Connections
1. What is a peptide bond and how is it formed in proteins?
A peptide bond is a covalent chemical bond that links two consecutive amino acids in a protein. It is essentially an amide bond. The formation occurs through a dehydration synthesis reaction, where the carboxyl group (-COOH) of one amino acid reacts with the amino group (-NH₂) of another. This reaction releases one molecule of water (H₂O) and forms the strong peptide bond (-CO-NH-). A chain of amino acids linked by these bonds is called a polypeptide. For more details, you can explore the topic of peptides.
2. What are the main types of covalent bonds that join monomers in major biomolecules?
The three primary covalent bonds responsible for creating polymers from monomers in biomolecules are:
- Peptide Bonds: Link amino acids together to form polypeptides and proteins.
- Glycosidic Bonds: Link monosaccharides (simple sugars) together to form disaccharides and polysaccharides like starch and cellulose.
- Phosphodiester Bonds: Link nucleotides together to form the backbone of nucleic acids, such as DNA and RNA.
Each of these bonds is formed through a dehydration reaction. You can learn more in this overview of Biomolecules.
3. What is a glycosidic bond and in which biomolecules is it found?
A glycosidic bond is a type of covalent bond that joins a carbohydrate (sugar) molecule to another group, which can be another carbohydrate or a different molecule. In the context of building larger biomolecules, it specifically links monosaccharides to form polysaccharides. For example, glycosidic bonds hold glucose units together to create complex carbohydrates like starch in plants and glycogen in animals. These bonds are crucial for energy storage and structural support in organisms.
4. What is a phosphodiester bond and what is its role in nucleic acids?
A phosphodiester bond is a strong covalent bond that forms the backbone of DNA and RNA molecules. It connects the 3' carbon atom of one sugar molecule to the 5' carbon atom of another through a phosphate group. This repeated linkage creates the sugar-phosphate backbone, giving the nucleic acid its structural integrity and directionality (the 5' to 3' ends). This backbone is essential for storing and transmitting genetic information. You can read more about their structure in this guide on Nucleic Acids.
5. How do peptide, glycosidic, and phosphodiester bonds differ from each other?
While all three are formed by dehydration synthesis, they differ in the monomers they connect and the polymers they form:
- Monomers Linked: Peptide bonds link amino acids, glycosidic bonds link monosaccharides, and phosphodiester bonds link nucleotides.
- Resulting Polymer: Peptide bonds create proteins, glycosidic bonds create polysaccharides, and phosphodiester bonds create nucleic acids.
- Atoms Involved: A peptide bond forms between a carboxyl group and an amino group. A glycosidic bond forms between two hydroxyl groups of sugars. A phosphodiester bond links a phosphate group to the sugar molecules.
6. Why is the rigid and planar nature of the peptide bond crucial for protein structure?
The peptide bond has a partial double-bond character due to resonance, which makes it rigid and planar. This means there is no free rotation around the C-N bond axis. This rigidity is fundamental to protein architecture because it limits the possible conformations of the polypeptide backbone. This constraint forces the chain to fold into predictable, stable secondary structures like the alpha-helix and beta-pleated sheet, which are the building blocks of a protein's functional three-dimensional shape. Learn more about these structures in the explanation of the Alpha Helix and Beta-Pleated Sheet.
7. Besides covalent bonds, what other bonds are important for the final structure of a protein?
While covalent peptide bonds form the primary structure (the amino acid sequence), the correct three-dimensional folding of a protein (its tertiary structure) is stabilised by several weaker, non-covalent bonds and interactions. These include:
- Hydrogen Bonds: Form between different parts of the polypeptide chain, crucial for forming secondary structures.
- Hydrophobic Interactions: Nonpolar amino acid side chains cluster together in the protein's interior to avoid water.
- Ionic Bonds (Salt Bridges): Form between oppositely charged R-groups of amino acids.
- Disulfide Bonds: A strong covalent bond that can form between the side chains of two cysteine amino acids, providing significant stability.
These interactions collectively determine the precise protein structure required for its biological function.
8. Can hydrogen bonds be considered as important as peptide bonds in biomolecules?
Yes, but for different reasons. Peptide bonds are crucial for forming the primary structure—the fundamental, linear sequence of monomers. They are strong, covalent bonds that are not easily broken. Hydrogen bonds, while much weaker individually, are vital for creating the functional, three-dimensional shapes. Their importance lies in their vast numbers. For example, they hold the two strands of DNA together and are responsible for the alpha-helix and beta-sheet structures in proteins. In essence, peptide bonds provide permanence, while hydrogen bonds provide the specific shape and allow for dynamic changes.
