Amino Acids—Synthesis and Degradation | Plant Physiology

In this article we will discuss about the synthesis and degradation of amino acids.

When a protein is hydrolyzed as many as 20 amino acids of different kinds are produced. These are protein amino acids. In addition non-protein amino acids are also present but they do not form structural components of proteins. The details of chemical name, molecular weight and structural formulae are given in Table 4-4.

Nothing definite is known regarding the function of non-protein amino acids. Their number and concentration vary with species and the organs. Seeds of some species have predominantly homoarginine. Storage organs of some species also contain derivatives of cysteine.

In general, non- protein amino acids have more of nitrogen than the protein amino acids and possibly they act as storage nitrogen in the seeds which can be easily mobilized for various synthetic processes. Other non-protein amino acids are homoserine and diaminopimelic acid. The latter is an intermediate substance in the lysine biosynthesis whereas homoserine is the intermediate substance between methionine and threonine.

Apparently non-protein amino acids form protein amino acids or constitute a group of secondary metabolites. However, much remains to be understood about their metabolism. In general, all the amino acids forming proteins have their amino groups inserted at the α -carbon to which its carboxylic group is also attached. The α-amino acid contains R as the side chain (Fig. 4-13).

Based on the structure of the side chain, protein amino acids are divided into seven groups. An amino acid comprises a carbon skeleton and NH3 (Table 4-4). Using radiotracers it has been shown that most of the amino acids have similar carbon-skeleton. Thus oxaloacetate is the source of aspartic acid which can further give rise to lysine, methionine, threonine, and isoleucine.

In general, there are four amino acid families and these are pyruvate, aspartate, glutamic acid and glyoxylate family as follows:

Glyoxylate has been shown to arise from glycolate in photosynthesis or from the glyoxylate cycle in the glyoxysomes. On the contrary pyruvate, oxaloacetate and α -ketoglutarate are the intermediates in the TCA cycle.

Plant may take nitrogen in any form but it is the ammonia which enters into amino acids. In C4 plants it is the aspartic acid which is synthesized first. In the plants with photorespiration ammonia is incorporated into glyoxylate yielding glycine, serine and cystenine.

On the other hand C3 plants form alanine, aspartic acid, glutamic acid from ammonia. It is also reported that pyruvate and oxaloacetate could also undergo reductive amination and the reactions are mediated by their respective dehydrogenases. Accordingly alanine and aspartic acid amino acids are produced, respectively. If glyoxylate is there then glycine may be obtained.

Glutamine and asparagine are the amides of glutamic acid and aspartic acid, respectively. Ammonia can be assimilated by other mechanisms as well e.g., aspartase reaction and carbamyl phosphate synthetase reaction.

In the former reaction fumarate and ammonia react to constitute aspartic acid while in the latter CO₂, ATP and ammonia react to produce carbamyl phosphate. The latter product is utilized in the formation of citrulline from ornithine. Glutamic acid and aspartic acid are termed as primary amino acids and other amino acids arise from them.

Various reactions to liberate ammonia from amino acids are of prime importance to the living organisms e.g. ammonia liberated from one amino acid may be utilized to produce another one, secondly, amino acids which have been deaminated may be oxidized to water and CO₂ through TCA cycle or even form glucose through reversal of glycolysis.

Further ammonia is toxic even in low concentrations and cell has evolved different systems to check this cellular toxicity. In plants high amount of ammonia may also be stored as glutamine and asparagine. The amides represent a storage form of nitrogen reserve.

Functions of Different Amino Acids (Table 4-4):

Glycine:

This amino acid can be formed by the transamination of several amino acids like glutamine, asparagine, aspartate, glutamate and even glyoxylate.

On deamination glycine can enter glyoxylate and through glyoxylate cycle it is oxidized to form glucose.

It is a component of purine, porphyrin ring of chlorophylls, cytochromes and even proteins. It is precursor of serine.

Alanine:

Through transamination it can give rise to other amino acids and even forms pyruvate by deamination. It is a part of protein.

Serine:

Glycine can give rise to serine or when alanine combines with phosphohydroxypyruvate through transamination. It also takes part in purine and pyrimidine synthesis and can enter the amphibolic pathways.

Threonine:

It is an important part of protein and through deamination forms α -ketobutyrate. Through intramolecular conversion it is formed from phosphohomoserine.

Valine, leucine, and isoleucine:

Through threonine deaminase, threonine is deaminated to produce α -ketobutyrate from which isoleucine can arise through series of steps.

The formation of valine and leucine is not well understood. The three amino acids constitute active components of enzymic proteins.

Lysine:

This amino acid can develop from alpha aminoadipic acid or aspartic β -semialdehyde by conversion into diaminopimelic acid through several steps.

Aspartic acid:

It gives rise to several amino acids e.g., lysine, threonine and forms part of proteins. It can also give rise to non-protein forming amino acid like homoserine.

It can also be converted to oxaloacetate and α -ketoglutarate through several degradation reactions. These may form glucose or fatty acids or even give rise to ATP when completely oxidized.

Ornithine, citrulline, arginine and proline:

They belong to glutamic acid family. Arginine, proline and hydroxy proline are protein amino acids whereas citrulline, ornithine and alpha aminobutyric acid are non-protein amino acids.

Sulphur amino acids:

This group includes methionine and cysteine. While the former is formed from aspartic acid the latter is produced from methionine through some reactions. The methyl group plays significant role in the biosynthesis of several substances like choline and methionine is the common donor of the methyl group in such reactions.

Cysteine is a key amino acid concerned with the tertiary structure of proteins and in forming the functional group of several enzymes. It is involved in the initiation of protein synthesis. When methionine is absent protein synthesis cannot take place in the cells.

Aromatic amino acids:

This category includes tryptophan, tyrosine, histidine and phenylalanine. The precursor of tryosine and phenylalanine amino acid is shikimic acid.

Nothing specific is known about the histidine pathway in plants. Not much information exists on the metabolism of aromatic amino acids.

However, some of the structural and enzymic proteins in plants do contain them. Shikmate dehydrogenase is reported to be associated with plastids of different plant tissues.

Transamination:

A transamination reaction is characterized by the transfer of an amino group. To be more specific, an amino group is transferred from a donor amino acid to an acceptor α -keto acid yielding the α -keto acid of the donor amino acid and the amino acid of the original α -keto acid acceptor.

The transamination reaction requires a metal ion and pyridoxal phosphate activity as shown below (Fig. 4-13 A, B):

Carbon Transformations:

In some amino acids the basic carbon skeleton is modified or substituted by various groups on their carbon chain. Thus new amino acids are formed.

In general specific metabolic relationships exist between different amino acids. In the following major families along with other compounds and amino acids are given (Fig.4-15).

The chief function of amino acids in a cell is the transformation and metabolism of energy. However, some pathways involve amino acids e.g., the glycolate pathway of sugar synthesis involving glycine and serine. Similarly, malate, aspartate and OAA may act as the carboxyl transporting C4 acids.

Methionine is involved in the synthesis of methylated compounds via transmethylation reactions. Tryptophan is a precursor of indole acetic acid. Hydroxyproline is a component of wall extension.

Amides:

A great deal of evidence indicates that amides are key detoxification products when plants are exposed to ammonia from the external sources. Either glutamine or asparagine may be the major form of assimilated nitrogen accumulating under these conditions. Amide accumulation appears to provide the primary means of combating ammonia toxicity during leaf senescence.

Glutamine and asparagine are two amides which contribute significantly in plant nitrogen metabolism. Amino and amido groups of these amides are involved in several transamination and deamination reactions. Amides constitute chief storage and transport compounds of nitrogen in plants. The two amides are homologues which differ in chain length by one carbon.

However, their behaviour is different biochemically and physiologically. For instance, glutamine is highly soluble in water whereas asparagine is insoluble. On the other hand, asparagine is stable and needs heating in strong acid to hydrolyse it. Glutamine is more unstable and hydrolyses to glutamic acid in boiling water. Ninhydrin reaction for the two is variable. For instance, glutamine releases CO₂ and forms purple colour while asparagine gives a brown colour.

Glutamine is synthesized from glutamic acid and ammonia as below:

As shown above energy is provided by the hydrolysis of ATP. There is also a requirement for Mg⁺², Mn⁺² and Co⁺².

The enzymic conversion of glutamine to glutamic acid needs ADP and Pi. Likewise the enzyme which converts aspartic acid to asparagine has not been well characterized.

However, the following reaction gives some idea on the combination of aspartic acid with ammonia.

There are many other pathways also in plants through which asparagine are produced. Much of these data have come from the isotope experiments.

Some of the plants have high level of cyanide (CN) metabolism and the content of cyanoglycoside is high here. HCN is incorporated into asparagine as below:

There is also a suggestion that asparagine is formed via condensation of C₁ + C₂. In the germinating seeds of some plants asparagine may be obtained from the protein or from the amination of aspartic acid obtained from hydrolysis of protein.

Asparagine is also obtained from aspartic acid produced from citric acid cycle. It may also be derived from the metabolic products of endogenous sugars. Most of the asparagine comes from the hydrolysis of proteins. Glutamine may be derived from glutamic acid released during protein breakdown or it may also be produced directly from photosynthesis.

When nitrogen is given in the form of ammonia or nitrate, glutamine formation is stimulated.

Glutamine is a potent donor of nitrogen in several synthetic processes and supplies nitrogen atoms at 3 and 9 positions of the purine ring and the amide nitrogen of NAD and NADP. Amide nitrogen is also utilized in supplying monomers of chitins. Glutamine also provides cyclic nitrogen to histidine and tryptophan.

Plants also contain compounds related to glutamine and some of these are not easily metabolized. The two amides perform specific functions and some of these functions overlap. Much remains to be understood regarding their metabolism. In any case, amides accumulate due to heavy nitrogen and are concerned with nitrogen translocation.

Asparagine is stored as protein in the seeds of some legume species whereas glutamine is the predominant translocatory substance in the rapidly growing plants. Further glutamine is involved in nitrogen translocation to be used for protein synthesis, whereas asparagine accumulation is linked with protein hydrolysis.

There is also a view that asparagine indicates unhealthy state of a plant, while reverse is true of glutamine. Some workers have shown domination of glutamine in plants grown in warm, dry long day conditions. The chief role of the two amides may be summarized as nitrogen, ammonia detoxification and storage mobilization of nitrogen for synthesis.