What Is A Secondary Structure
Definition
Secondary structure of a protein
The secondary structure of a protein refers to the regular, repeating patterns that form when a polypeptide chain folds. These patterns arise from interactions between the amino acids in the backbone of the protein.
- Proteins start as simple linear chains of amino acids, known as polypeptides.
- Due to interactions between the atoms in the polypeptide backbone, the chain folds into specific, stable patterns.
- These patterns are stabilized by hydrogen bonds between atoms in the backbone.
Hint
Hydrogen bonds form between the carbonyl group (C=O) of one amino acid and the amine group (N-H) of another.
Two Main Types of Secondary Structure
The Alpha Helix: A Coiled Spring
The alpha helix is a right-handed coil, like a spring.
- How it works:
- The polypeptide backbone coils into a spiral.
- Hydrogen bonds form between the C=O of one amino acid and the N-H of the amino acid four residues ahead in the sequence.
- These bonds run parallel to the axis of the helix.
- Key Features
- Compact and Stable: Hydrogen bonds hold the helix tightly together.
- R-Groups Project Outward: Side chains extend from the helix, allowing interactions with the environment or other molecules.
- Versatility: Found in many proteins, including enzymes and structural proteins like keratin in hair.
Example
- Hemoglobin, the protein that carries oxygen in your blood, contains alpha helices.
- These helices help form the compact, globular shape of the molecule, which is essential for binding oxygen efficiently.
Hint
To identify an alpha helix in a protein structure, look for a coiled pattern with hydrogen bonds running parallel to the coil’s axis.
The Beta-Pleated Sheet: A Folded Landscape
The beta-pleated sheet is a sheet-like structure formed by aligned polypeptide strands.
- Formation Process
- Polypeptide strands align side-by-side to form a sheet-like structure.
- Hydrogen bonds stabilize the alignment, forming between C=O groups of one strand and N-H groups of an adjacent strand.
- Chain Orientations
- Parallel: Both chains run in the same direction (N-terminus to C-terminus).
- Antiparallel: Chains run in opposite directions, which is more stable due to optimal hydrogen bonding.
- Key Features
- Pleated Structure: Appears pleated due to the tetrahedral bond angles in the backbone.
- Stability: Hydrogen bonds between adjacent chains stabilize the structure.
- R-Groups Alternate: Side chains project alternately above and below the sheet, allowing interactions with other molecules.
Hint
Antiparallel beta sheets are more stable than parallel sheets due to optimal hydrogen bonding geometry
Common Mistake
- Students often confuse the directionality of beta sheets.
- Remember that antiparallel sheets are more stable because the hydrogen bonds are more linear, while parallel sheets have slightly angled hydrogen bonds.
The Importance Of Hydrogen Bonds
- Stability: Hydrogen bonds, though individually weak, collectively provide significant stability to the protein’s secondary structure.
- Maintaining Shape: Allow proteins to maintain their specific shapes under physiological conditions.
- Framework for Higher Structures: Provide a foundation for the formation of tertiary and quaternary structures.
Note
The cumulative effect of hydrogen bonds ensures that proteins retain their functional conformations necessary for biological activity.
Self review
- What is secondary structure?
- What type of bond stabilizes secondary structures?
- Between which atoms do these bonds form?
- What are the two main types of secondary structure?
- Describe the structure of an alpha helix.
- In an alpha helix, which amino acids form hydrogen bonds with each other?
- Describe the structure of a beta-pleated sheet.
- What is the difference between parallel and antiparallel beta sheets?
