Biochemistry I

Opposite charges attract. For example, Mg ²⁺ ions associate with the negatively charged phosphates of nucleotides and nucleic acids. Within proteins, salt bridges can form between nearby charged residues, for example, between a positively charged amino group and a negatively charged carboxylate ion. These electrostatic interactions make an especially large contribution to the folded structure of nucleic acids, because the monomers each carry a full negative charge.

Van der Waals interactions (see Figure  1) represent the attraction of the nuclei and electron clouds between different atoms. The nucleus is positively charged, while the electrons around it are negatively charged. When two atoms are brought close together, the nucleus of one atom attracts the electron cloud of the other, and vice versa. If the atoms are far apart (a few atomic radii away) from each other, the van der Waals force becomes insignificant, because the energy of the interaction varies with the 12 ^th power of distance. If the atoms come closer together (so that their electron clouds overlap) the van der Waals force becomes repulsive, because the like charges of the nucleus and electron cloud repel each other. Thus, each interaction has a characteristic optimal distance. For two identical atoms, the optimal distance is d=2r, where r is atom radius. Within a biomolecule, these interactions fix the final three‐dimensional shape. While van der Waals interactions individually are very weak, they become collectively important in determining biological structure and interactions.