A2 - Biochemistry

We start with amino acids. These were first met in GCSE biology but now we can identify them as chemicals with two specific functional groups. Each molecule must have an amine group (-NH₂) at one side and a carboxylic acid at the other (-COOH). We know that these are the building blocks for more complicated molecules (polymers) and structures like proteins and enzymes. During a condensation reaction, a hydrogen from the amine group and the OH from the carboxylic acid break away (condensation polymerisation) and the two monomers join. As with any polymer, the monomers change the properties of the polymer. Here, the specific amino acids in a specific order make a specific chain/protein.

The amino acids behave very differently at different pH levels because the amine acts as a base so will accept a proton when the pH is low and the carboxylic acid will release its proton when the pH is high. At a neutral pH, a zwitter ion is formed, this is when the proton has left the carboxylic acid and is now attached to the lone pair or electrons on the nitrogen. This is a very special ion as it is both positive and negative at this specific pH.

A dipeptide is two amino acids joined with a peptide linkage. A polypeptide is many amino acids joined. A protein is a long sequence of specific amino acids joined in a very specific order.

When analysing amino acids using thin layer chromatography (TLC), the amino acids do not show in visible light. The two methods used to see them is either under UV light or staining them with Ninhydrin

Because of the forces between the polymer chains, the chains are not simple straight lines.

• Primary structure is the sequence of amino acids held together by strong covalent bonds

• Secondary structures are an alpha-helix or a beta-sheet, these are caused by hydrogen bonds between the different amino acids in the chain.

• Tertiary structures and 3-dimensional and are caused by hydrogen bonds, disulfide bonds and even ionic attractions.

Enzymes are biological catalysts and their shape/structure is essential to their function. Their shape is caused by these forces between chains/other parts of the chain which generates the active site. This makes them very specific and the active site is stereospecific and will only bond to a specific enantiomer of a substrate. Drugs that have been made to bond to these active sites to block enzyme action also have to be the correct enantiomer.

The backbone of DNA is a polymer with the repeating unit of phosphate-sugar-phosphate-sugar. On each sugar, a base is bonded to it. The 4 bases are adenine (2 hydrogen bonds), thymine (2 hydrogen bonds), guanine (3 hydrogen bonds) and cytosine (3 hydrogen bonds). These bases will only pair up with the corresponding pair (G-C or A-T) because they have to have the corresponding structure to form hydrogen bonds.

During DNA replication, bases are able to form hydrogen bonds to their opposite number so that a replica strand may be formed. If we want to prevent DNA replication in cells, such as in cancer cells, we can use a complex that will bind to the base Guanine and prevent replication. Cis-platin does this through a ligand exchange reaction and can be used to treat certain cancers such as testicular cancer (localised tumour) by preventing the production of RNA so that the cell can copy itself . Although a life saving drug, it can cause kidney damage and other issues as it does not discriminate between healthy cells and cancerous ones. This is why it is so important that you look into the risks and benefits of any treatment.