2 Nucleic acids

DNA is a stable molecule becuase:

- the phosphodiester backbone protects the more chemically reactive organic bases inside the double helix.

- hydrogen bonds link the organic base pairs forming rungs between the phosphodiester uprights. The higher the proportion of C-G pairings, the more stable the DNA molecule.

- base stacking.

The stability of DNA is enhanced due to the interactions that result from base stacking.

The surfaces of the bases have few polarised bonds; consequently, base surfaces are hydrophobic.

As a result, the most energetically favourable conformation is attained by reducing exposure of the base surfaces to the aqueous environment, which is achieved by moving the bases closer together. In this conformation, the backbone is 'tilted' by an angle of 30˚ from horizontal.

Tilting the backbone in this way brings the planar rings of adjacent base pairs to a position where they lie vertically above one another, an arrangement that maximises hydrophobic interactions and in addition, maximises van der Waals attractive forces between them.

- it is a very stable structure which passes from generation to generation without change, and only rarely mutates.

- its two separate strands are joined only by hydrogen bonds, which allows them to separate during DNA replication and protein synthesis.

- it is a large molecule and so carries a large amount of genetic information.

- by having base pairs inside the helix, the genetic information is protected from corruption by outside chemical and physcial forces.

- base pairing leads to DNA being able to replicate and to transfer information as mRNA.

- DNA helicase breaks the hydrogen bonds linking base pairs of DNA, causing the double helix to separate into its two strands and unwind. 

- each exposed polynucleotide chain then acts as a template to which complementary free nucleotides bind by the specific base pairing.

- nucleotides are joined together in a condensation reaction by DNA polymerase to form the 'missing' polynucleotide strand on each of the original polynucleotide strands of DNA.

- each of the DNA molecules contains one of the original DNA strands and one new strand.

- Each ATP molecule releases less energy than each glucose molecule. The energy for reactions is therefore released in smaller, more manageable quantities.

- The hydrolysis of ATP to ADP is a single reaction that releases immediate energy. The breakdown of glucose is a long series of reactions, and therefore the energy release takes longer.

A water molecule is said to be dipolar, becuase it has a positive and a negative pole as a result of the uneven distribution of electrons within it. 

This creates attractive forces called hydrogen bonds between the opposite poles of different water molecules, causing them to stick together.

The stickiness of water means that its molecules are pulled inwards at its surface. This force is called surface tension.

As a result of water molecules sticking together, it takes more energy to separate them than would be needed if they did not hydrogen bond to one another. For this reason the boiling point of water is higher than would be expected. For the same reason, it takes more energy to heat a given mass of water, that is water has a high specific heat capacity. Water therefore acts as a buffer against sudden temperature changes.

Water has a high latent heat of vaporisation (it needs a lot of energy to evaporate 1 gram of water).

The tendency of water to stick together is called cohesion. With its hydrogen bonding, water has large cohesive forces (cohesion tension) and these allow it to be pulled up through a tube.

- water is the main constituent of all organisms; mammals are typically 65% water.

Water in metabolism:

- hydrolysis, e.g. proteins to amino aicds.

Water as a solvent:

Water readily dissolves other substances.

- gases, e.g. oxygen and carbon dioxide.

- wastes, e.g. ammonia and urea.

- inorganic ions and small hydrophilic molecules, e.g. amino acids, monosaccharides and ATP.

- enzymes, whose reactions take place in solution.

Other important features:

- evaporation allows thermoregulation.

- not easily compressed and so provides support, e.g. hydrostatic skeletons of animals (earthworm) and turgor pressure in plants.

- transparent so aquatic plants can photosynthesise, and light rays can penetrate fluid that fills the eye and so reach the retina.