IB Biology Topic B1.2.10: Effect of Polar and Non-polar Amino Acids on Tertiary Structure of Proteins Notes

Polar and Non-Polar Amino Acids: How Water Drives Protein Folding

1. Every amino acid in a protein has an R-group that is either polar (hydrophilic) or non-polar (hydrophobic).
2. This single property is the main factor determining how a protein folds into its tertiary structure.
3. Proteins fold in an aqueous (water-based) environment, so their R-groups sort themselves according to how they behave around water.
   1. Non-polar R-groups are pushed inward to avoid water.
   2. Polar R-groups stay on the surface, where they form hydrogen bonds with the surrounding solution.
4. This partitioning is the primary force that shapes the protein's three-dimensional conformation.

Example

• Haemoglobin shows how polar and non-polar amino acids determine protein structure.
• Its hydrophobic amino acids are buried inside the protein, stabilising the core.
• Its hydrophilic amino acids face outward and interact with the watery environment of the blood.

Polar Amino Acids Sit on the Surface

1. Polar amino acids have R-groups that carry partial or full electrical charges, which makes them hydrophilic.
2. In globular proteins, polar amino acids are typically found on the outer surface, where they form hydrogen bonds with water molecules.
3. This surface arrangement has two effects.
   1. It makes the protein soluble in the aqueous cytoplasm or blood plasma.
   2. It gives the protein interaction sites for other polar molecules, including substrates, signalling molecules, and other proteins.

Non-Polar Amino Acids Form the Hydrophobic Core

1. Non-polar amino acids have R-groups that carry no charge and do not form hydrogen bonds with water, which makes them hydrophobic.
2. In an aqueous environment they cluster together in the interior of the protein, forming a stable hydrophobic core.
3. This clustering minimises the protein's contact with water and reduces the system's free energy, making the folded state thermodynamically favourable.
4. The hydrophobic effect is the single largest driving force behind protein folding.
5. In membrane proteins, the rules reverse.
   1. Non-polar amino acids face outward in the region spanning the lipid bilayer, where they interact with the hydrophobic fatty acid tails of the phospholipids.
   2. This anchors the protein in the membrane.

Channel Proteins: Both Properties at Work

1. Channel proteins show how polar and non-polar amino acids work together in a single protein.
   1. The region embedded in the membrane has non-polar R-groups facing outward, anchoring it among the lipid tails.
   2. The interior of the channel is lined with polar amino acids, creating a hydrophilic passage for ions and polar molecules.
2. This arrangement is what makes facilitated diffusion possible.
   1. Without the hydrophilic channel interior, polar solutes could not pass through the hydrophobic core of the membrane.

Why the Water-Driven Rules Matter

1. In a water-soluble protein, non-polar residues hide in the core and polar residues face the water.
2. In a membrane protein, the same rules produce the opposite layout because the surroundings are hydrophobic lipid tails, not water.