Protein Structure Notes

General Biochemistry: Protein Structure

3D Structures of Proteins

  • Proteins are essential for virtually all biochemical activities under normal or pathological conditions.

  • A protein's activity and capability depend on its 3D shape, which is determined by its amino acid sequence.

  • Understanding biochemistry requires knowledge of the proteins involved and their 3D structures.

  • Determining the 3D position of every atom (H, C, O, N, S) in a protein is a significant challenge.

  • Specializing in protein science and determining the 3D shape of a single protein is presented as a major scientific challenge.

The Four Levels of Protein Structure

  • Primary structure: The sequence of amino acids from N-terminal to C-terminal, as discussed in Chapter 4.

  • Secondary structure: The 3D structure of a portion of the protein, such as an alpha-helix.

  • Tertiary structure: The 3D structure of the entire protein.

  • Quaternary structure: The combination of two or more tertiary structures into a single, large, multi-protein complex. Individual proteins are bound through non-covalent interactions.

Forces Determining Protein Structure

  • The primary structure is dictated by covalent bonds between amino acids.

  • Higher-order structural features (secondary, tertiary) are determined by weaker, non-covalent interactions:

    • Hydrophobic interactions:

      • Clustering of non-polar residues in the protein's interior.

      • Tendency of some amino acids to minimize contact with water.

      • The driving force for protein folding.

    • Hydrogen bonds:

      • Formed whenever possible within the protein structure.