Hydrogen bonds

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A hydrogen bond is an attraction between a hydrogen atom and an electronegative atom, most common ones being nitrogen (N), oxygen (O) or fluorine (F). Hydrogen bonds appear frequently within biological molecules and it exists in polar compounds, a common example of this being water where the attractive interaction exists between the oxygen and hydrogen. Hydrogen bonding occurs as intermolecular attractions, where the Hydrogen bond is found between different molecules, or intramolecular, where the bond exists between different parts of the same molecule [1].

A hydrogen bond is a non-covalent bond; they have much stronger attractions than Van der Waals forces and permanent dipole-permanent dipole interactions, but are weaker than ionic bonding or covalent bonding. Evidence for hydrogen bonding can be found when comparing the boiling points of hydrogen molecules across groups 5, 6 and 7 of the periodic table. The compounds where hydrogen bonding is present produce a much higher boiling point as hydrogen bonds require more energy to be broken than Van der Waals forces [2].

The distance between two parts of the same molecule, or different molecule, can vary and this has an effect on the strength of the hydrogen bond. This why the hydrogen bonds are said to be "elastic," the greater the distance between the hydrogen atom and the electronegative atom the longer the hydrogen bond will be and this results in a weaker hydrogen bond.

A hydrogen bond can be defined as the polar interaction between an electronegative atom (Nitrogen, oxygen or fluorine) and a hydrogen atom which is covalently bonded to another electronegative atom that is wither on the same molecule, or on a different molecule. The bond is strongest when all three of these atoms are arranged in a way in which they can be linked along a straight line [3].

Hydrogen bonding is extremely prevalent throughout nature and can be found in water, DNA base-pair interactions, protein folding, protein structure and protein-ligand binding.



A water molecule consists of one oxygen atom attached to two hydrogen atoms. A hydrogen bond can be formed between two molecules of water due to the 'unequal distribution of electrons within a water molecule' [4]. The oxygen has a strong attraction for the electrons and has a negative charge, whereas the hydrogen only has a weak attraction and therefore has a slight positive charge. When these two oppositely-charged regions come close to each other, the result is a hydrogen bond [5].

Although water has a low molecular mass, it has an unusually high boiling point. This property can be attributed to the large amount of hydrogen bonds that exists within water. Since these bonds are difficult to break, water’s melting and boiling points are relatively high in comparison to other liquids that are similar but lack the hydrogen bonding.


In the DNA helix,the bases: adenine, cytosine, thymine and guanine are each linked with their complementary base by hydrogen bonding. Adenine pairs with thymine with 2 hydrogen bonds. Guanine pairs with cytosine with 3 hydrogen bonds.[6]


An alpha-helix contains hydrogen bonds between the N-H of one peptide bongs and the C=O of another peptide bond which is found 4 peptide bonds away on the same chain.

Also the individual, antiparallel strands of the beta-pleated-sheet have hydrogen bonds which connect the peptide bonds of different strands [7].


  1. http://www.chemguide.co.uk/atoms/bonding/hbond.html
  2. http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/H/HydrogenBonds.html
  3. Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. p57.
  4. Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. p55
  5. Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. p55
  6. J.M.Berg, J.L.Tymoczko, L.Stryer,(2007) Biochemistry, 6th edition, New York: W.H.Freeman and company p112
  7. Alberts, B et al. (2008). Molecular Biology of the Cell. 5th ed. US: Garland Science. 1268. p137

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