IB Biology Topic B1.2.8: Pleating and Coiling of Secondary Structure of Proteins Notes

Secondary Structure: Regular Patterns from Backbone Hydrogen Bonds

How Secondary Structure Forms

1. After a polypeptide chain is synthesised, hydrogen bonds form between atoms in the backbone, not the R-groups.
2. These bonds create repeating structural patterns called secondary structure.
3. The two main types are the alpha helix and the beta-pleated sheet.
4. In both cases, hydrogen bonds form between the carbonyl group (C=O) of one amino acid and the amine group (N-H) of another.
   1. Because these bonds involve backbone atoms and not R-groups, secondary structure is set by the backbone geometry rather than the specific side chains.

The Alpha Helix: A Right-Handed Coil

1. In an alpha helix, the polypeptide backbone coils into a right-handed spiral.
2. Hydrogen bonds form between the C=O group of one amino acid and the N-H group of the amino acid four residues ahead in the sequence.
   1. These bonds run parallel to the axis of the helix, pulling it into a tight, stable coil.
3. The R-groups project outward from the helix, so they do not interfere with the backbone hydrogen bonding.
   1. This leaves them free to interact with the surrounding environment or with other parts of the protein.
4. Alpha helices are found in many proteins, including keratin (the structural protein in hair and nails) and haemoglobin.

The Beta-Pleated Sheet: Strands Held Side by Side

1. In a beta-pleated sheet, sections of the polypeptide chain lie side by side.
   1. They are connected by hydrogen bonds between the C=O group on one strand and the N-H group on the adjacent strand.
2. The backbone zigzags, giving the sheet a pleated appearance, like a folded paper fan.
3. The strands can run in the same direction (parallel) or in opposite directions (antiparallel).
   1. Antiparallel sheets are more stable because the hydrogen bonds are more linear and therefore stronger.
4. R-groups alternate above and below the plane of the sheet, available for interactions with other parts of the protein.

Hydrogen Bonds: Weak Individually, Strong Collectively

1. A single hydrogen bond is weak.
2. But proteins contain hundreds or thousands of them, and their collective effect provides significant structural stability.
3. Alpha helices and beta-pleated sheets are stable enough to hold their shape under physiological conditions.
   1. They stay flexible enough to allow the conformational changes many proteins need to function.
4. Secondary structure provides the scaffold on which tertiary and quaternary structures are built.
   1. Without stable helices and sheets, the higher levels of protein organisation could not form.