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.


Introduction: Common Macromolecules- Nucleic Acids.

A nucleic acid is a polymer made up of many nucleotides. A nucleotide is generally made of;

Typical Nucleotide.

i. Nitrogen-containing base; a heterocyclic molecule, containing a closed ring of atoms of which at least one is not a carbon atom and replaced with a nitrogen atom.

ii. Pentose sugar; meaning contains five carbon atoms in the sugar molecule.

iii. Phosphate Group; usually a phosphorus atom surrounded by a double bonded oxygen atom, single bonded to two oxygen negative ions and an oxygen atom.

Since the least complicated molecule is the phosphate group, it can easily be distinguished. However, for now, the distinguishing features for the nitrogen containing base will be the nitrogen atom. If the phosphate group is absent, the sugar-base combination is called a nucleoside.

The most common two forms of nucleotides are Ribonucleotides which form the nucleic acid Ribonucleic acid (RNA) and Deoxyribonucleotides which form the polynucleotide or nucleic acid Deoxyribonucleic acid (DNA), the molecules responsible for coding the proteins in the cell. In ribonucleotides, the sugar is ribose. In deoxyribonucleotides, the sugar is deoxyribose.


The difference between the two is that the pentose sugar in DNA has one oxygen atom less in the hydroxyl group of Carbon atom 2. Also, since these two are the prime nucleic acids we shall be focusing on, their polymer structure is generally helical.

Another popular nucleotide is Adenosine Triphosphate (ATP) which is used as an energy currency in the cell. This will be clearer in later chapters.


Thus, nucleic acids are biopolymers composed of monomers called nucleotides. The term polynucleotide is a more accurate description of a single molecule of nucleic acid.

The nitrogenous bases of nucleotides belong to two families known as purines and pyrimidines.

In nucleotides, the base is joined to C-1 of the sugar and the phosphate group is attached to one of the other sugar carbons, usually C-5.

There are three phosphoryl groups; alpha(α), beta(β), and gama(γ) esterified to the C-5 hydroxyl group of the ribose. The linkage between ribose and the α-phosphoryl group is a phosphoester linkage because it includes a carbon and a phosphorus atom, whereas, the β- and γ-phosphoryl groups in ATP are connected by phosphoanhydride linkages that don’t involve carbon atoms. All Phosphoanhydride have considerable chemical potential energy, and ATP is no exception. This potential energy can be used directly in biochemical reactions.

The Phosphate Business

In polynucleotides, the phosphate group of one nucleotide is covalently linked to the C-5 oxygen atom of the sugar of another nucleotide creating a second phosphoester linkage. The entire linkage between carbons of adjacent nucleotides is called a phosphodiester linkage, because it contains two phosphoester linkages.

Nucleic acids contain many nucleotide residues and are characterized by a backbone consisting of alternating sugars and phosphates. In DNA, the bases of two different polynucleotide strands interact to form a helical structure.

DNA Back bone.

RNA contains ribose rather than deoxyribose, and is usually a single stranded polynucleotide. There are four kinds of RNA molecules: Messenger RNA (mRNA), transfer RNA (tRNA), Ribosomal RNA (rRNA), and a heterogeneous class of small RNAs that carry out a variety of different functions.