B1.2.5 Effect of pH and temperature on protein structure Notes

The Delicate Architecture of Protein Structure

1. Proteins are composed of amino acids linked in a specific sequence, but their functionality arises from the way this sequence folds into complex three-dimensional shapes.
2. These shapes are stabilized by several types of interactions:
   1. Hydrogen Bonds: Weak bonds formed between polar groups or backbone atoms.
   2. Ionic Bonds: Attractions between oppositely charged R-groups (side chains).
   3. Disulfide Bonds: Strong covalent bonds between sulfur atoms in cysteine residues.
   4. Hydrophobic Interactions: Non-polar R-groups clustering to avoid water.

Levels of Protein Structure

1. Primary Structure:
   1. Definition: The linear sequence of amino acids.
2. Secondary Structure:
   1. Definition: Regular patterns such as alpha-helices and beta-pleated sheets, stabilized by hydrogen bonds.
3. Tertiary Structure:
   1. Definition: The overall folding of a single polypeptide chain, maintained by a combination of all interaction types.
4. Quaternary Structure:
   1. Definition: The arrangement of multiple polypeptide chains in a multi-subunit protein.

How Temperature Affects Protein Structure

1. Proteins are stabilized by relatively weak forces, such as hydrogen bonds and hydrophobic interactions.
2. As temperature increases, the kinetic energy of protein molecules also increases, causing vibrations that can break these bonds.

What Happens?

1. The protein unfolds, losing its secondary, tertiary, or quaternary structure.
2. Hydrophobic R-groups, previously buried in the protein's interior, are exposed to water, often causing the protein to precipitate.
3. Example: Egg whites solidify during cooking due to protein denaturation.

Why Does This Matter?

1. Denatured proteins lose their specific shape, which is critical for their function.
2. Enzymes with denatured active sites can no longer catalyze reactions.

Heat Tolerance in Extremophiles

1. Proteins from thermophilic organisms, such as bacteria living in hot springs, are adapted to withstand high temperatures.
2. These proteins often have enhanced stability due to:
   1. A higher proportion of disulfide bonds.