Introduction to organic material

Functional group
These groups are linked to the carbon skeleton of the organic compound and conveniently divided into aliphatic and aromatic groups

Aromatic functional group

Benezene Phenol purine Imidazole

Pyrrole
Indole Pyrimidine

Cholesterol

Haemoglobin

Water
Water is the most abundant substance in living systems, making up 70% or more of the weight of most organisms. The first living organisms doubtless arose in aqueous environment, and the course of evolution has been shaped by the properties of the aqueous medium in which life began Water is the essential solvent of life and the main chemical constituent of all cells. One of the unusual characteristics of water is that despite of its low molecular weight, it is a liquid at most environmental temperature. Other molecules having similar molecular weights (e.g. ammonia, methane and H2S) are gases. Water has a higher melting point, boiling point and heat of vaporization than most other common solvents. These unusual properties are a consequence of attractions between adjacent water molecules that give liquid water great internal cohesion. A look at the electron structure of the H2O molecule reveals their intermolecular attraction.

Structure of water
In water, two hydrogen atoms are each covalently bonded to a single oxygen atom. Each hydrogen atom of a water molecule shares an electron pair with the oxygen atom. The geometry of the molecule is dictated by the shapes of the outer electron orbitals of the oxygen atom, which are similar to the bonding orbitals of carbon. There orbitals describe a rough tetrahedron, a hydrogen atom at each of two corners and unshared electron pairs at the other two corners. The H-O-H bond angle is 104.5 slightly less than the 109.5 of a perfect tetrahedron because of crowding by the nonbonding orbitals of the oxygen atom.

The oxygen nucleus attracts electrons more strongly than does the hydrogen nucleus (a proton); oxygen is more electronegative.
The sharing of electrons between H and O is therefore unequal; the electrons are more often in the vicinity of the oxygen atom than of the hydrogen. The result of this unequal electron sharing is two electric dipoles in the water molecule, one along each of the H-O bonds; the oxygen atom bears a partial negative charge (2-), and each hydrogen a partial positive charge (+)

 As a result, there is an electrostatic attraction between the oxygen atom of one water molecule and the hydrogen of another, called a Hydrogen bond represented by 3 horizontal lines

Structure of the water molecule. The dipolar nature of the H2O molecule is shown by (a) ball-and-stick and (b) space-filling models. The dashed lines in (a) represent the nonbonding orbitals. There is a nearly tetrahedral arrangement of the outer-shell electron pairs around the oxygen atom; the two hydrogen atoms have localized partial positive charges (+) and the oxygen atom has a partial negative charge (2 -). (c) Two H2O molecules joined by a hydrogen bond between the oxygen atom of the upper molecule and a hydrogen atom of the lower one. Hydrogen bonds are longer and weaker than covalent O-H bond.

 Thus, by means of two covalent bonds and two hydrogen bonds each oxygen atom may bond to as many as four hydrogen; the hydrogens form a tetrahedron about the oxygen. When the temperature of water is lowered, the concomitant decrease in kinetic energy allows the water to become denser until at 4C maximum density occurs. A continued decrease in kinetic energy allows more extensive and less transient formation of hydrogen bonds among the water molecules.

This promotes the development of a lattice structure.

In liquid water at room temperature and atmospheric pressure, however, water molecules are disorganized and in continuous motion, so that each molecule forms hydrogen bond with an average of only 3.4 other molecules. In ice, on the other hand, each water molecule is fixed in space and forms hydrogen bonds with a full complement of four other water molecules to yield a regular lattice structure As the freezing point of water is approached, more space is developed between the molecules of water and the density decreases; thus, freezing water and ice rice to the surface of the liquid.

 When water is heated, the increase in temperature reflects the faster motion of individual water molecules. During evaporation, more highly ordered arrays in liquid water relax into the less orderly hydrogen-bonded arrays. Ultimately reaching the wholly disordered gaseous state.

Properties and Physiological significance

Although water is often called the "Universal Solvent", not all substances dissolve in water. However, water does dissolve most salts and other ionic compounds, as well as non ionic polar compounds Water is a polar solvent. It readily dissolves most biomolecules, which are generally charged or polar compounds; compounds that dissolve easily in water are hydrophilic (Greek, water-loving). In contrast, nonpolar solvents such as chloroform and benzene are poor solvents for polar biomolecules but easily dissolve those that are hydrophobicnonpolar molecules such as lipids and waxes Many substances that contain both polar and non-polar groups (amphipathic compounds)(such as soaps, fatty acids and glycerophosphatides) do not dissolve in the water but they do form Micelles. A micellar arrangement is not a true solution but is a suspension or dispension. The behaviour of soap molecules in water is a good and also common example of micelle formation. Soap molecules, formed by the saponification of fatty acids consists of a long, nonpolar hydrocarbon chain terminating in a polar carboxyl group that is ionically bonded to a metal ion such as K+ or Na+. When dispersed in water, the soap molecules aggregate to form spherical clusters, called micelles, in which the polar carboxyl groups of the soap molecules are arranged at the surface of the sphere, where they form weak bonds with the surrounding water, and the non-polar hydrocarbon chains project inward.

Long-chain fatty acids have very hydrophobic alkyl chains, each of which is surrounded by a layer of highly ordered water molecules. (b) By clustering together in micelles, the fatty acid molecules expose the smallest possible hydrophobic surface area to the water, and fewer water molecules are required in the shell of ordered water. The energy gained by freeing immobilized water molecules stabilizes the micelle

Water dissolves many crystalline salts by hydrating their component ions. The NaCl crystal lattice is disrupted as water molecules cluster about the Cl- and Na+ ions. The ionic charges are partially neutralized, and the electrostatic attractions necessary for lattice formation are weakened

Osmosis: Osmosis, is the water movement across a semi-permeable membrane driven by difference in osmotic pressure, is an important factor in the life of most cells. Plasma membranes are more permeable to water than to most other small molecules, ions and macromolecules. This permeability is partly due to simple diffusion of water through the lipid bilayer and partly due to protein channels (aqua protiens) in the membrane that selectively permit the passage of water.

Solutions of equal osmolarity are set to be isotonic. Surrounded by an isotonic solution, a cell neither gains nor loses water as there is no net water movement
In case of an hypertonic solution water moves out and cell shrinks whereas in case of an hypotonic solution water moves in swelling the cell and eventually bursting it

In a hypertonic solution, one with higher osmolarity than the cytosol the cell shrinks as water flows out. In a hypotonic solution (of lower osmolarity), the cell swells and if unsupported by a cell wall, eventually bursts.
Cells generally contain higher concentration of bimolecules and ions than their surroundings, so osmotic pressure tends to drive water into the cells. Of not somehow counterbalanced, this inward movement of water would distend the plasma membrane and eventually cause explosion of cells (osmotic lysis).

Expands on freezing:when temperature of water is raised above 0C its volume decreases upto 4C and thereafter increases. Water has the minimum vol and hence the maximium density of 1.00 at 4C. the volume of water at 4C increases either on heating or cooling it. Uniquely high surface tension:like a strected membrane, the surface of a liquid tends to contract as much as possible. This phenomenon is called surface tension. Water has the highest surface tension of any known liquid.. And this is the reason why water rises to unusally high levels in a narrow capillary tubes and has great significance in physiology. Uniquely high heat capacity;Smaller temperature rise in water as compared to most other substances, when heat is applied it acts as a temp buffer. Water maintains its temp successfully than most other substances thus water has a high heat capacity.

 High solvent power:Water is a solvent for a great number of molecule which form ionised solution in water. It is called as universal solvent which facilitates chemical reaction both outside of and within biological systems.