Biochemistry

• An amino acid is a compound with an amine group and a carboxylic acid group. The amine group is always on the second carbon in the chain.
• The second carbon atom in amino acids is often chiral, meaning they exist as optical isomers. However, most amino acids in nature exist as a single negative enantiomer so they fit into the correct cells.
• The two functional groups in an amino acid means they can react as both acids and bases depending on the conditions of the reaction.
• In acidic conditions, amino acids exist in cationic form where a hydrogen bonds to the lone pair on the nitrogen, and so the molecule becomes positive.
• In basic conditions, amino acids exist in anionic form where a hydrogen is lost from the oxygen, and so the molecule becomes negative.
• An amino acid can have an acid base reaction with itself in a solid state, forming a zwitterion where one side of the molecule is positive and the other end is negative.
• Thin layer chromatography can be used to identify unknown amino acids using UV light and ninhydrin to view the traces on the silica plate.
• Proteins are amino acids joined together by peptide links.
• Proteins can be broken down into their constituent amino acids by hydrolysis with harsh conditions of boiling in concentrated hydrochloric acid for 24 hours, or by enzymes.
• The primary structure of a protein is a single polypeptide chain of amino acids.
• The secondary structure of a protein is an alpha helix or beta pleated sheet held together by hydrogen bonds.
• The tertiary structure of a protein is chains folded into a coil with hydrogen and disulfide bonding.
• Disulfide bonding in a protein is known as a sulfur bridge and keeps the protein structure stable by the two sulfurs losing a hydrogen and bonding together.
• Enzymes are proteins with a tertiary structure that acts as biological catalysts.
• Enzymes contain active sites that are specific to the substrate they break down and are also stereospecific, and so only break down one enantiomer and have no effect on the other optical isomer.
• DNA is a condensation polymer formed from a sugar, a phosphate and a base, which join together to form a nucleotide.
• Sugar - phosphate bonds hold together multiple nucleotides into a polynucleotide strand, and are known as a sugar - phosphate backbone.
• There are four bases that could be present in a nucleotide: adenine, cytosine, thymine, and guanine.
• The bases in DNA pair up in specific complimentary pairs: adenine and thymine bond with two hydrogen bonds and cytosine and guanine bond with three hydrogen bonds.
• The bases in DNA pair up to allow a single strand of DNA to join with another via hydrogen bonding to form a double helix structure.
• Cisplatin is the cis isomer of a square planar complex of platinum, and is an anticancer drug.
• Cells are chiral and so only the cis (Z) isomer of cisplatin is effective and will be in the correct orientation to fit the cells.
• Cisplatin bonds to mutated DNA with two adjacent guanine bases to prevent it from replicating via ligand replacement with guanine.
• Cisplatin can also bond to heated DNA strands causing side effects such as hair loss, and so must be administered in small doses and only when necessary.
• A peptide bond is between an N and C = O.