The amino acids synthesis pathways can be grouped into several logical units. These units reflect either common mechanisms or the use of common enzymes that synthesize more than one amino acid. These categories are: simple reactions, branch chain amino acids, aromatic amino acids, threonine/lysine, serine/glycine, and unique pathways. The aromatic amino acids, threonine/lysine and serine/glycine pathways have a common beginning and then diverge to form the amino acid of interest.
Notice that each pathway begins with a central metabolite or something derived from "central metabolism". Using common compounds instead of synthesizing them from scratch saves energy and conserves genes since fewer enzymes are needed to code for the pathways.
Threonine biosynthesis is completed in three steps. First a second reduction with NADPH + H+, yields homoserine. This is phosphorylated to homoserine phosphate by ATP and finally converted into threonine.
The synthesis of lysine has been found to consist of different reactions in different bacterial species. A somewhat generalize pathway is presented. Lysine synthesis involves the addition of pyruvate to aspartate semialdehyde, the use of a CoA intermediate (either acetyl CoA or succinyl-CoA) and the addition of an amino group from glutamate. The group added from CoA (either succinyl or acetyl) serves as a blocking group, protecting the amino group from attack during transamination by glutamate. NADPH + H+ is required for reduction in the second step of the pathway.
Synthesis of threonine and lysine begins by the conversion of oxaloacetate to aspartate semialdehyde. This shared pathway costs one ATP and two NADPH + H+
Alanine synthesisis is a bit of a mystery. Several reactions have been identified, but it has been impossible to generate an alanine and therefore positively identify a required pathway. There are several pathways and the most likely is formation of alanine by transamination from glutamate onto pyruvate. A transamination using valine instead of glutamate is also possible.
Figure 4 - Formation of asparagine. Notice the use of AMP instead of ADP in this reaction. This releases more energy which is needed to drive the synthesis.
The biosynthesis of serine and glycine constitute a major metabolic pathway that plays a central role in the formation of other amino acids, nucleic acids and phospholipids. When is grown on glucose, fully 15% of carbon assimilated passes through the serine pathway. Synthesis of serine and glycine starts with oxidation of 3-phosphoglycerate forming 3-phosphohydroxy pyruvate and NADH. A transamination reaction with glutamate forms 3-phosphoserine and removal of the phosphate yields serine. Glycine is generated by removal of the methyl group from serine. Energy is not required for this pathway, in fact it yields energy in the form of reduced NADH.
The rest of the simple reactions involve transfer of the amino group (transamination) from glutamate or glutamine to a central metabolite to make the required amino acid. Aspartate is synthesize by the transfer of a ammonia group from glutamate to oxaloacetate.
Leucine biosynthesis starts of with the last intermediate in the valine synthesis, -ketoisovalerate. In the first step Acetyl-CoA is used to add an acetyl group to the molecule. Electrons are transferred to NAD+ (note these can be used for other cellular processes) and one carbon is lost in the form of CO2 at the fourth step of the pathway. In the final step, the amine from glutamate is added to -ketoisocaproate to form leucine.
In most cases these amino acids can be synthesize by one step reactions from central metabolites. They are simple in structure and their synthesis is also straight forward.
Synthesis of the aromatic amino acids begins with the synthesis of chorismate - an important intermediate for many biosynthetic pathways. Phosphoenol pyruvate and erythrose 4-phosphate serve as beginning substrates for the pathway. A price of one NADPH + H+ and one ATP is exacted for every chorismate formed. In the sixth step of the synthesis another phosphoenol pyruvate molecule is added to the growing molecule.
In most cases bacteria would rather use amino acids in their environment than make them from scratch. It takes a considerable amount of energy to make the enzymes for the pathway as well as the energy required to drive some of the reactions of amino acid biosynthesis. The genes that code for amino acid synthesis enzymes and the enzymes themselves are under tight control and are only turned on when they are needed.
Chorismate is converted to phenylpyruvate in two steps and phenylalanine is synthesized by a transamination reaction with glutamate. No energy is require to run these reactions.