MoBio Hydrogen Bond Chapter 2

A hydrogen bond is formed by three atoms: one hydrogen atom and two electronegative atoms (often N or O). The hydrogen atom is covalently bonded to one of electronegative atoms, called the hydrogen bond donor. The other electronegative atom is named the hydrogen bond acceptor. The two electronegative atoms may take up some electron density from the hydrogen atom. As a result, each electronegative atom carries partial negative charge and the hydrogen atom carries partial positive charge. The hydrogen atom and the hydrogen bond acceptor can then have attractive interactions.

The strength of the hydrogen bond depends on the donor and acceptor as well as their environment. The bond energy usually ranges from 1 kcal/mol to 5 kcal/mol. This energy is smaller than covalent bond energy, but greater than thermal energy (0.6 kcal/mol at room temperature). Therefore, the hydrogen bond can provide a significant stabilizing force in macromolecules such as proteins and nucleic acids.

When a hydrogen bond is formed, the distance between the donor and the acceptor is about 0.28 nm (1 nm = 10-9 meter). The hydrogen atom is still covalently bonded to the donor and their distance is shorter than that between the hydrogen atom and the acceptor.

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Figure 2-C-3. Hydrogen bonds. (a) The general form. D: donor; A: acceptor. (b) The hydrogen bond between two water molecules. (c) The hydrogen bond in a polypeptide, e.g., in an α helix or between two β strands. (d) The hydrogen bond between residue 45 (a threonine) of RNase A and its substrate thymine.