Chapter 2: Water- Non Covalent Bonds; Hydrogen Bonds & Hydrophobic interactions.

As we’ve already discussed these two before, here is a brief overview again.

3. Hydrogen bonds are among the strongest noncovalent forces in biological systems.

They are paradoxically strong enough to provide structural stability but weak enough to be readily broken.

In general, a hydrogen bond can form when a hydrogen atom covalently bonded to a strongly electronegative atom, such as nitrogenoxygen, or, in rare cases, sulfur.

Examples of hydrogen bonds that can form between molecules. Click on image for credit.

Hydrogen lies approximately 0.2 nm from another strongly electronegative atom that has an unshared electron pair. The total distance between the two electronegative atoms participating in a hydrogen bond is typically 0.27 to 0.30 nm. Some common examples of hydrogen bonds are shown.

All the functional groups are also capable of forming hydrogen bonds with water molecules. In order for hydrogen bonds to form between or within biological macromolecules, the donor and acceptor groups have to be shielded from water. In most cases this shielding occurs because the groups are buried in the hydrophobic interior of the macromolecule, where water can’t penetrate.

In DNA, for example, the hydrogen bonds between complementary base pairs are in the middle of the double helix as you can see.

Hydrogen bonds in DNA double helix. Click on image for credit.

4. Hydrophobic interactions: When relatively nonpolar molecule or group in aqueous solution associate with other nonpolar molecules rather than with water, it is termed a hydrophobic interaction.

Although hydrophobic interactions are sometimes called hydrophobic “bonds”, this description is incorrect. Nonpolar molecules or groups tend to group-up not because of mutual attraction but because the polar water molecules around them tend to pressure and entrap them close to each other as the water molecules form hydrogen bonds.

Hydrophobic interactions, like hydrogen bonds, are much weaker than covalent bonds. For example, the energy required to transfer a -CH2–  group from a hydrophobic to an aqueous environment is about 3kJ mole-1.

Again, all of the interactions covered here are individually weak compared to covalent bonds, but the combined effect of many such weak interactions can be significant.


Chapter 2: Water- Non Covalent Bonds; Van Der Waals Forces.

2. Van der Waals is another weak force involving the interaction between the permanent diploes of two uncharged polarized bonds (dipole-dipole) or the interactions between a permanent dipole and a transient dipole induced in a neighboring molecule (instantaneous dipole-induced dipole).


Dipole-Dipole interaction between two Hydrochloric Acids (HCl). Click on image for credit.

In dipole-dipole interactions, both the molecules are uncharged yet polarized, meaning they are not ions with an extra or missing electron (anion or cation), rather, they are molecules with one end being more electropositive and another more electronegative. Such as Hydrochloric acid (HCl). When two HCl come close, they immediately configure in such a way as to have their opposite poles face each other.


Instantaneous Dipole- Induced Dipole 1. Click on image for credit.

Instantaneous Dipole-Induced Dipole interactions 2. Click on image for credit.

In instantaneous dipole-induced dipole, the atom’s or molecules’ electrons are in spontaneous presence around the electron orbital causing fluctuations in their polarity structure. Once a dipole is spontaneously created, the incident will induce a polarity in another neighboring molecule.

These forces are of short range and small magnitude.

The attractive forces, also known as London dispersion forces, originate from the infinitesimal dipole generated in atoms by the random movement of the negatively charged electrons around the positively charged nucleus.

Although they operate over similar distances, van der Waals forces are much weaker then hydrogen bonds.

Van der Waals forces also have a repulsive component. When two nuclei are squeezed together, the electrons in their orbitals repel each other. This repulsion increases exponentially as the atoms are pressed together, and at very close distances it becomes prohibitive.

The sum of the attractive and repulsive components of van der Waals forces, are said to be in Van der Waals contact, and the attractive force between them is maximal.

Although individual Van der Waals forces are weak, the clustering of atoms within a protein, nucleic acid, or biological membrane permits the formation of a larger number of these weak interactions.

Once formed, these cumulative weak forces play important roles in maintaining the structure of the molecules.

For example, the heterocyclic bases of nucleic acids are stacked one above another in a double-stranded DNA. This arrangement is stabilized by a variety of noncovalent interactions, especially Van der Waals forces. These forces are collectively known as stacking interactions.

Chapter 2: Water- Non covalent bonds; Charge-Charge interactions.

Four major types of noncovalent bonds or forces are involved in the structure and function of biomolecules. In addition to hydrogen bonds and hydrophobicity, there are; charge-charge interactions and van der Waals forces.

Let us discuss each.

1. Charge-charge interactions, hydrogen bonds, and van der Waals forces are variations of a more general type of force called electrostatic interactions.

Charge-charge interactions are electrostatic interactions between two charged particles. These interactions are potentially the strongest noncovalent forces and can extend over greater distances than other noncovalent interactions.

The stabilization of sodium chloride or table salt (NaCl) crystals by interionic attraction is an example of a charge-charge interaction. Water, greatly weakens these interactions as we saw earlier.

Consequently, the stability of biological polymers in an aqueous environment is not strongly dependent on charge-charge interactions, but such interactions do play a role in the recognition of one molecule by another.

For example, most enzymes have either anionic or cationic sites that bind oppositely charged reactants. Attractions between oppositely charged functional groups of proteins are sometimes called salt bridges.

Salt bridges (hydrogen & charge-charge) between Glutamic acid and Lysine. Click on image for credit.

A salt bridge buried in the hydrophobic interior of a protein is stronger than one on the surface because it can’t be disrupted by water molecules. The most accurate term for such interactions is ion-pairing.

Charge-charge interactions are also responsible for the mutual repulsion of similarly charged ionic groups. And these charge repulsions can influence the structures of individual biomolecules as they interact with other, like-charged molecules (similar to the hydrophobic effect).

Chapter 2: Water- Detergents & Chaotropes.

Detergents, sometimes called surfactants, are molecules that are both hydrophilic and hydrophobic; they usually have a hydrophobic chain at least 12 carbon atoms long and an ionic or polar end. Such molecules are said to be amphipathic.

One of the synthetic detergents most commonly used in biochemistry is sodium dodecyl sulfate (SDS), which contains a 12-carbon tail and a polar sulfate group.

Sodium Dodecyl Sulfate. Click on image for credit.

Some ions such as thiocyanate (SCN) and perchlorate (CIO4) are called chaotropes, meaning they are structures that disrupt the structure of water, so as to promote activities inhibited by the water molecules. These ions are poorly solvated compared to ions such as ammonium (NH4+), sulfate (SO42-) and dihydrogen phosphate (H2PO4).



Dihydrogen phosphate

Chaotropes enhance the solubility of nonpolar compounds in water by disordering the water molecules (there is no general agreement on how chaotropes do this). Enzymes are usually amphipathic chaotropes.