Chapter 2 Nucleic Acids

Nucleotides are made up of a pentose sugar, a phosphate group and a nitrogen - containing organic base. They are joinged together by condensation reactions. The bond between two nucleotides is called a phosphpdiester bond which forms a dinucleotide. 

Ribonucleic Acid - short, single polynucleotide chain with ribose as its pentose sugar and uracil, adenine, guanine and cytosine as its organic bases. 

Deoxyribonucleic Acid - double stranded, adenine pairs with thymine, cytosine pairs with guanine. Bases are joined by hydrogen bonds. 2 bonds between AT and 3 bonds between CG. A+T = C+G. The double helix is  also anti-parallel. 

• DNA has a phoaphodiesster backbone which protects the more chemically reactive bases
• The higher the proportion of CG bonds, the more stable the DNA molecule is.

Functions of DNA

• pass gentic info - rarely mutates
• extremely large mol - carries immense genetic info
• strands joined only by hydrogen bonds - able to separate for replication and protein synthesis

Semi Conservative Replication

Both strands acts as a template strand. A new DNA molecule consists of a parent strand (from original) and a daughter strand.  

• The enzyme DNA helicase breaks the hydrogen bonds between the organic bases in the double helix. 
• The two strands separates and unwinds. 
• Each exposed polynucleotide strand acts as a template where free floating nucleotides bind by complimentary base pairing. AT and CG
• The nucleotides are then joined together through condensation reactions by the enzyme DNA polymerase, forming the polynucleotide daughter strand. 
• The new DNA molecule now consists of an original strand and a daughter strand.

NOTE: The DNA polymerase is only complimentary to the 3' to 5' direction. Therefore, it only works in the 5' to 3' direction. Since the double helix are anti - parallel, the DNA polymerase had to work on the lagging strand in opposite directions. As a result, DNA replication happens in sections in the lagging strand called Okazaki fragments. These sections are then joined by the enzyme DNA ligase. 

ATP contains adenine, ribose sugar and 3 inorganic phosphate groups. These phosphate groups have bonds which has low activation energy which makes them easily broken. 

ATP + water gives ADP + inorganic phosphate +energy. This is a hydrolysis reaction catalysed by ATP hydrolase to give out energy. This is also a reversible reaction which cpould synthesise back ATP. This reaction is catalysed by the ATP synthase. 

ATP could be synthesised by either photophosphorylation. oxidative phosphorylation or substrate - level phosphporylation

Roles of ATP - immediate energy source of a cell

• metabolic processes - provides energy for building up macromolecules. For example, production of glucose and polypeptides
• movement - proviides energy for muscle contraction
• active transport - provides energy for changing the shape of carrier proteins.
• Secretion - needed in formation of lysosomes.
• activation of molecules - hydrolysos of ATP gives out inorganic phosphate which could phosphorylate other compunds to make them more reactive. 

Water consists of two hydrogen atoms and one oxygen atom. The oxygen atom is describe to have a slightly negative charge whereas the hydrogen atoms have slightly negative charge. Therefore, a water molecule is said to be dipolar due to its different charges at opposite poles.

Due to being dipolar, hydrogen bonding occurs between water molecules. 

• specific heat capacity - water molecules stick together so it takes more energy to heat a given mass of water. This makes water act as a  buffer against sudden temperature changes. This is why the aquatic enironment is temperature stable which makes it a suitable habitiat for aquatic animals. 
• Latent heat of vaporisation - requires a lot of energy to evaporate one gram of water
• Cohesion  - water molecules have the tendency to stick together which allows them to be pulled up through a tube. This is very important in transpiration of water through xylem vessels. 
• Water in metabolism - it is a major component in photosynthesis (photolysis of water), involved in hydrolysis and condensation reactions. 
• Water as a solvent - readily dissolves gases (CO2, O2), wastes (NH2, urea) and inorganic ions