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.
   2. Increased hydrophobic interactions.

How pH Affects Protein Structure

1. The pH of a solution affects the ionization of amino acid R-groups.
2. Many R-groups contain carboxyl (-COOH) or amine (-NH₂) groups that can gain or lose protons depending on the pH, altering their charges.
3. This disrupts ionic and hydrogen bonds that stabilize the protein's structure.

What Happens?

1. At extreme pH levels, the charges on R-groups change.
2. Ionic bonds between oppositely charged R-groups may break, and new, incorrect bonds may form.
3. The protein's tertiary structure is disrupted, leading to denaturation.

Why Does This Matter?

1. Proteins are often optimized to function at specific pH levels.
   1. Example: Enzymes in the stomach work in acidic conditions, while those in the small intestine require a basic environment.
2. A change in pH can render these proteins inactive.

The Role of Buffers in Biological Systems

1. To protect proteins from pH-induced denaturation, organisms maintain a stable internal pH using buffers. For instance:
   1. The bicarbonate buffer system keeps blood pH around 7.4.
   2. Significant deviations from this pH can disrupt protein function, leading to severe physiological consequences.

Real-World Applications of Denaturation

1. Denaturation is not always harmful, it has practical applications in various fields:
2. Cooking: Heat-induced denaturation explains why egg whites solidify and meat becomes firmer during cooking.
3. Sterilization: Heat denatures proteins in bacteria and viruses, making autoclaving a reliable sterilization method.
4. Diagnostic Tests: Denatured proteins, such as albumin in urine, can indicate kidney disease and are measured using colorimetric methods.