Question

Distinguish between intermolecular and intramolecular hydrogen bonding between the backbone groups on polypeptide chains. In what type of secondary structure do you find intermolecular hydrogen bonds? In what type do you find intramolecular hydrogen bonding?

Short answer

Answer: In the secondary structure of polypeptide chains, beta-sheet structures contain intermolecular hydrogen bonds, while alpha-helix structures contain intramolecular hydrogen bonds.

Step-by-step solution

1. Definition of Intermolecular and Intramolecular Hydrogen Bonding

Intermolecular hydrogen bonding occurs when hydrogen atoms are bonded to highly electronegative atoms like oxygen or nitrogen, and this bond is formed between different molecules. Intramolecular hydrogen bonding occurs when hydrogen bonding takes place within the same molecule or within different parts of a large molecule.

2. Secondary structure of Polypeptide chains

In proteins, the secondary structure refers to the local folding of the polypeptide chain into specific conformations. The two main types of secondary structures in proteins are alpha-helices and beta-sheets.

3. Intermolecular Hydrogen Bonds in Polypeptide Chains

Intermolecular hydrogen bonds in polypeptide chains occur when hydrogen bonds form between the backbone groups of different polypeptide chains or different regions of the same chain that has folded onto itself. These intermolecular hydrogen bonds are found mainly in beta-sheets.

4. Intramolecular Hydrogen Bonds in Polypeptide Chains

Intramolecular hydrogen bonds in polypeptide chains occur when hydrogen bonds form between the backbone groups within the same polypeptide chain or within different regions of the same chain that has folded onto itself. These intramolecular hydrogen bonds are found mainly in alpha-helices. In summary, intermolecular hydrogen bonds are found in beta-sheet structures, whereas intramolecular hydrogen bonds are found in alpha-helix structures within the secondary structure of polypeptide chains.

Key concepts

Intermolecular Hydrogen Bonding

Intermolecular hydrogen bonding is a fascinating phenomenon essential for the structure of certain proteins. It occurs when hydrogen atoms, usually bonded to electronegative atoms like oxygen or nitrogen, form bonds with electronegative atoms in a different molecule. This type of bonding is crucial in stabilizing the structure of substances by connecting different molecules.
In the context of polypeptide chains, these bonds are predominantly found in beta-sheet structures. A beta-sheet is a form of the secondary structure in proteins where the polypeptide chains are arranged in parallel or anti-parallel strands. In this arrangement, intermolecular hydrogen bonds form between the backbone groups of different segments or chains. These bonds give beta-sheets their distinctive strength and stability, allowing them to maintain a rigid and flat structure.

• Occurs between different molecules or different regions of the same folded chain
• Commonly found in beta-sheets
• Contributes to the stability of the protein structure

Understanding these bonds is crucial for grasping how proteins achieve their functional forms and their role in biochemical processes.

Intramolecular Hydrogen Bonding

Intramolecular hydrogen bonding takes place when hydrogen bonds form within the same molecule. This type of bonding is important in stabilizing certain structures and shapes of large molecules, including polypeptide chains. Unlike intermolecular bonding, it occurs within different parts of the same molecule, providing internal cohesion.
In proteins, intramolecular hydrogen bonds are fundamental in forming alpha-helices, another key secondary structure. An alpha-helix is a coiled structure stabilized by hydrogen bonds between the backbone's amino hydrogen and carbonyl oxygen within the same chain. These bonds enable the polypeptide chain to coil and preserve its shape, which is critical for the protein's functionality and interaction with other molecules.

• Occurs within the same molecule
• Forms the coiled structure of alpha-helices
• Essential for protein stability and function

Intramolecular bonds help in folding the protein into its required shape, which is necessary for its biological activities.

Secondary Structure

The secondary structure of proteins refers to the specific local formations of the polypeptide chains. It is one of the first levels of folding that a protein undergoes and plays a significant role in determining the protein's overall shape and function. The two primary types of secondary structures are alpha-helices and beta-sheets, each stabilizing the protein differently.
Alpha-helices are formed primarily through intramolecular hydrogen bonds within the same chain, creating a spiral shape. This structure is flexible and common in many functional proteins. On the other hand, beta-sheets are formed by intermolecular hydrogen bonds between different polypeptide chains or within different regions of the same chain that has folded back on itself.

• Alpha-helix: formed by intramolecular hydrogen bonds
• Beta-sheet: formed by intermolecular hydrogen bonds
• Crucial in maintaining protein structure and function

Understanding the secondary structure of proteins helps in comprehending their diverse roles in biological systems and their biochemical activities, such as enzymatic functions and cellular communications.