Chapter 2: Water- Hydrogen Bonding.

All living cells depend absolutely on water for their existence. In most living cell, water is the most abundant molecule, accounting for 60% to 90% of the mass of the cell. The macromolecule components of cells-proteins, polysaccharides, nucleic acids, and membranes- get their characteristics shapes in response to interactions with water and much of the metabolic processes of cells has to operate in an aqueous environment because water is an essential solvent as well as a substrate for many cellular reactions.

A water molecule (H2O) is V-shaped, with an angle of 104.5° between the two covalent O-H bonds.

A water molecule. Click on image for credit.

An oxygen atom has six electrons in the outer shell, but the outer shell can potentially accommodate four pairs of electrons in four sp3 orbitals. This means that oxygen can form covalent bonds involving two different hydrogen atoms, each sharing a single electron with the oxygen atom.

An oxygen nucleus (because it contains more protons or positive charge) attracts electrons more strongly towards it than the single proton in the hydrogen nucleus. This attraction of electrons defines oxygen atoms as being more electronegative than hydrogen atoms. As a result, an uneven distribution of charge occurs within each O-H bond of the water molecule, with oxygen bearing a partial negative charge and hydrogen bearing a partial positive charge (+). This uneven distribution of charge within a bond is known as a dipole, and the bond is said to be polar.

Dipolarity of water bonds.

The polarity of a molecule depends on both the polarity of its covalent bonds and its geometry. The angled arrangement of the polar O-H bonds of water creates a permanent dipole for the molecule as a whole.

A molecule of ammonia also contains a permanent diploe. Thus, even though water and gaseous ammonia are electrically neutral, both molecules are polar. The high solubility of the polar ammonia molecules in water is facilitated by strong interactions with polar water molecules.

Ammonia in the form of ammonium ions. Click on image for credit.

The reason why there’s an extra proton (H+) with ammonia is because due to the fact that it is highly polar, it will attract a hydrogen atom of a water molecule (which it has dissolved in; aqueous solution) and form a fourth hydrogen bond with it. In water, the attraction between a slightly positive hydrogen atom of one water molecule and the slightly negative oxygen atom of another produces what is referred to as a hydrogen bond.

Water is not the only molecule capable of forming hydrogen bonds; these interactions can occur between any electronegative atom and a hydrogen atom attached to another electronegative atom. In the case of ammonia, the N (Nitrogen atom) is the slightly electronegative atom and the hydrogen atom of a water molecule forms a hydrogen bond with it, converting it to ammonium ions (NH4+).

The distance between this hydrogen atom and the other oxygen atom, is about twice the length of the covalent bond and hydrogen bonds are much weaker than typical covalent bonds. A single water molecule can form hydrogen bonds with up to four other water molecules.

Hydrogen Bonds in water molecules. Click on image for credit.

Orientation is important in hydrogen bonding and the bonding is most stable when a hydrogen atom and the two electronegative atoms associated with it (the two oxygen atoms in the case of water) are aligned or nearly in line.

Linear H-Bonds. Click on image for credit.

Introduction- Organic Compounds, Functional Groups and Linkages.

Much of biochemistry deals with biopolymers that are macromolecules created by joining many smaller organic molecules (monomers) via condensation (removal of element of water). Each monomer that makes a macromolecular chain is called a residue.

In some cases like carbohydrates (more on it later), a single monomer or residue is repeated many times, in other cases like proteins and nucleic acids, a variety of residues are connected in a specific order.

The residues are added and converted into a polymer by repeating the same enzyme catalyzed reaction. Thus all of the residues in a biopolymer are aligned in the same direction.

Biopolymers have properties that are very different from those of their constituent monomers. Example: Starch is not soluble in water and does not taste sweet although it is a polymer of the sugar Glucose, which has both those properties.  So we can conclude that each new level of organization results in properties that cannot be predicted just from those of the previous level.

The levels of complexity in increasing order are atoms, then molecules, then biopolymers, then organelles then cells, tissue, organ, and all organisms and systems.


The types of organic compounds, functional groups and linkages commonly seen in biochemistry are;

Organic Compounds, Functional Groups and Linkages.

PS: Under most biological conditions, carboxylic acids exist as carboxylate anions: COO and amines exist as ammonium ions: NH3+ .

Please make sure you memorize the names and structures of the functional groups.

Biochemical reactions involve specific chemical bonds or parts of molecules called functional groups which we will deal with several times.

  • Ester and Ether are common linkages found in fatty acids and lipids.
  • Amide linkages are found in proteins.
  • Phosphate ester and Phosphoanhydride linkages occur in nucleotides.