Amino Acid Reactions

Amino acids are organic compounds that contain the functional groups amino (–NH₂) and carboxyl (–COOH), as well as a side chain (R group) unique to each amino acid. Carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) are the four essential elements of amino acid, while other elements can be present in the side chains of some amino acids. 

They are categorized as alpha, beta, gamma, or delta amino acids based on the position of the core structural functional groups; other categories include polarity, pH level, and side-chain group form (aliphatic, acyclic, aromatic, etc.).

Amino acid residues, in the form of proteins, are the second-largest component of human muscles and other tissues (water is the largest). Amino acids are involved in a variety of processes, including neurotransmitter transport and biosynthesis, in addition to their function as protein residues.

How Peptide Bond Formation Takes Place?

On a molecular level, a peptide bond is formed by a dehydration synthesis or reaction. Dehydration synthesis bonds two amino acids together to form a peptide bond, as seen in the diagram below. Each of the amino acids contributes a carboxyl group to the reaction while losing a hydroxyl group (hydrogen and oxygen).

The amine group (NH₂) of the other amino acid is depleted of hydrogen. A peptide bond is formed when the hydroxyl group is replaced by nitrogen. One of the main reasons why peptide bonds are referred to as substituted amide linkages is because of this. Covalent bonds exist between the two amino acids. A dipeptide is a compound made up of freshly produced amino acids. Let's take a look at a simplified illustration of the peptide bond formation.

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Some Common Amino Acid Reactions are:

Transamination Reaction- Transamination is a chemical reaction in which an amino group is transferred from an amino acid to a keto acid, resulting in the formation of new amino acids. The deamination of most amino acids occurs through this mechanism. This is a significant mechanism for the conversion of essential amino acids to non-essential amino acids (amino acids that can be synthesised by the organism body itself).

Transamination is carried out in biochemistry by enzymes such as transaminases or aminotransferases. As the predominant amino-group acceptor, -ketoglutarate produces glutamate as the new amino acid.

Aminoacid + α-ketoglutarate ↔️ α-keto acid + Glutamate

In a transamination of alanine the amino group of alanine is transferred to some other group. Transamination of alanine to pyruvate allows pyruvate to form glucose through the gluconeogenic pathway. The amino group of alanine is attached to α-ketoglutarate through transamination into glutamate. In a transamination reaction, the amino group of glutamate is transferred to oxaloacetate, yielding aspartate. Aminotransferase catalyses transamination in two steps.

The amino group of an amino acid is passed to the enzyme in the first step, resulting in the corresponding -keto acid and animated enzyme. The amino group is moved to the keto acid acceptor in the second step, forming the amino acid product while regenerating the enzyme. During transamination, an amino acid's chirality is calculated. Aminotransferases require the participation of an aldehyde-containing coenzyme, pyridoxal-5'-phosphate (PLP), a Pyridoxine derivative, to complete the reaction (Vitamin B6). Conversion of this coenzyme to pyridoxamine-5'-phosphate accommodates the amino group (PMP). The Schiff Base linkage formed by the condensation of PLP's aldehyde group with the -amino group of an enzymatic Lys residue covalently attaches PLP to the enzyme. 

The coenzyme activity is centred on the Schiff base, which is conjugated to the enzyme's pyridinium ring.

The availability of -keto acids affects the outcome of transamination reactions. Since their corresponding alpha-keto acids are formed by fuel metabolism, the products are usually alanine, aspartate, or glutamate. Lysine, proline, and threonine are the only three amino acids that do not always undergo transamination and instead use respective dehydrogenase as a degradative amino acid route.

Strecker Synthesis - The Strecker Synthesis is a method for producing -aminonitriles, which are useful intermediates in the synthesis of amino acids through nitrile hydrolysis.

Mechanism of the Strecker Synthesis

Acid promotes the reaction, and HCN must be supplied or manufactured in situ from cyanide salts; in the latter case, one equivalent of acid is consumed in the process.

NH₄Cl + NaCN ⇌ NH₃ + HCN +NaCl

The condensation of ammonia with the aldehyde to form an imine is most likely the first step:

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The cyanide acts as a nucleophile and reacts with the imine carbon to form -aminonitrile:

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This substance can be hydrolyzed to the corresponding amino acid if desired.:

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Deamination of Amino Acids - The removal of an amino group from a molecule is known as deamination. Deaminases are enzymes that catalyse this reaction. Deamination is a technique for converting amino acids into electricity. The amino group of the amino acid is separated and converted to ammonia. The amino acid's remaining components, mainly carbon and hydrogen, are recycled or oxidised for energy. Ammonia is harmful to the human body, so enzymes in the urea cycle, which also occurs in the liver, convert it to urea or uric acid by adding carbon dioxide molecules (which is not considered a deamination process). Urea and uric acid can be safely absorbed into the bloodstream and then excreted in the urine.

Decarboxylation of Amino Acids - Decarboxylation is a chemical reaction in which a carboxyl group is removed and carbon dioxide (CO₂) is released. Decarboxylation is usually described as a reaction between carboxylic acids that removes a carbon atom from a carbon chain. Carboxylation, or the addition of CO₂ to a compound, is the reverse process and is the first chemical step in photosynthesis. Decarboxylases, or carboxylases in the more formal language, are enzymes that catalyse decarboxylations.

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Amino Acid Ninhydrin Reaction - Ninhydrin (2,2-dihydroxybenzene-1,3-dione) is a compound that can be used to detect ammonia or primary and secondary amines. Ruhemann's purple is a deep blue or purple colour that results from interacting with these free amines. Since the terminal amines of lysine residues in peptides and proteins sloughed off in fingerprints react with ninhydrin, it is most widely used to detect fingerprints. At room temperature, it is a white solid that is soluble in ethanol and acetone. Indane-1,2,3-trione hydrate can be thought of as ninhydrin.

The partial positive charge on a carbonyl's carbon atom is increased by adjacent electron-withdrawing groups like carbonyl itself. As a result, the central carbon of a 1,2,3-tricarbonyl compound is much more electrophilic than a ketone's central carbon. As a result, indane-1,2,3-trione readily reacts with nucleophiles, such as water. Because of the destabilising effect of the neighbouring carbonyl groups, ninhydrin forms a stable hydrate of the central carbon, while most carbonyl compounds have a carbonyl shape that is more stable than a result of water addition (hydrate).

(2-(1,3-dioxoindan-2-yl)iminoindane-1,3-dione), To make a Schiff base, the amine is condensed with a molecule of ninhydrin. As a result, only ammonia and primary amines can pass through this point. To form the Schiff base, there must be alpha hydrogen present at this stage. As a result, amines bound to tertiary carbons do not undergo further reactions and are therefore undetectable. As ninhydrin reacts with secondary amines, it produces an iminium salt, which is also coloured, which is usually yellow-orange in colour.

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Oxidation of Amino Acids - Amino acid is the final class of biomolecules whose oxidation contributes significantly to the production of metabolic energy. Amino acids are derived primarily from protein in the diet or from the degradation of intracellular proteins. The percentage of metabolic energy obtained from amino acids varies greatly depending on the type of organism and the metabolic situation in which it is found. Carnivores can get up to 90% of their energy needs from amino acid oxidation in the hours after a meal. Herbivores can only be able to get a small portion of their energy from this source. 

Plants that are photosynthetic seldomly oxidise amino acids for energy generation purposes. Instead, they transform carbon dioxide and water molecules into carbohydrates, which is almost exclusively used as a source of energy. Amino acid levels in plant tissues are closely monitored to ensure that they only meet the minimum requirements for protein, nucleic acid, and a few other molecules required for growth. Plants do have amino acid catabolism, but it is usually for the processing of metabolites for other biosynthetic pathways.

Amino acids can be degraded by oxidation in three different metabolic situations in animals. Any of the amino acids released during protein breakdown can undergo oxidative degradation if they are not required for new protein synthesis during normal cellular protein synthesis and degradation. When a high-protein diet is consumed in excess of the body's requirements for protein synthesis, the excess amino acids can be catabolized; amino acids cannot be retained. When carbohydrates are either inaccessible or improperly used, such as during malnutrition or diabetes mellitus, body proteins are used as a source of energy. Amino acids lose their amino groups under these conditions, and the a-keto acids that result can be oxidised to carbon dioxide and water molecules. The carbon skeletons of amino acids also include three- and four-carbon units that can be converted to glucose, which can then be used to power the functions of the brain, muscle, and other tissues.

In most species, the degradative pathways for amino acids are very similar. The vertebrates are the subject of this chapter because amino acid catabolism has gotten the most attention in these species. The mechanisms of amino acid degradation converge on the central catabolic pathways for carbon metabolism, just as they do for sugar and fatty acid catabolic pathways. Amino acid carbon skeletons typically make their way through the citric acid cycle, where they are either oxidised to generate chemical energy or funnelled into gluconeogenesis. In certain cases, the reaction pathways are very similar to fatty acid catabolism steps.

However, amino acid degradation differs from the catabolic processes outlined thus far in one important way: each amino acid comprises an amino group. As a result, any degradative pathway includes a key step in which the a-amino group is removed from the carbon skeleton and directed to specialized amino group metabolism pathways. This biochemical fork in the road serves as the focal point of this chapter. The fate of the carbon skeletons derived from amino acids is discussed first, followed by amino group metabolism and nitrogen excretion.

Metabolism Fate of Amino Acids

Nitrogen is the fourth most abundant element in living cells, after carbon, hydrogen, and oxygen. The plentiful nitrogen in the atmosphere is too inert to be used in most biochemical processes. Since only a few microorganisms can transform N₂ to biologically useful forms like NH₃ biological systems make extensive use of amino groups.

The majority of amino groups come from amino acids obtained from dietary proteins. The liver is where the majority of amino acids are broken down. The excess ammonia is either secreted directly or converted to uric acid or urea for excretion, depending on the organism. Excess ammonia produced in other tissues (extrahepatic) is transferred to the liver, where it is converted to the proper excreted form. The coenzyme pyridoxal phosphate, the functional form of vitamin B6 and a key coenzyme in nitrogen metabolism, is encountered in these reactions.

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In these pathways, the amino acids glutamate and glutamine are particularly important. In the cytosol of liver cells (hepatocytes), amino groups from amino acids are normally transferred to -ketoglutarate to form glutamate. Glutamate is then transported into the mitochondria, where the amino group is removed and ammonium ions are formed. Most other tissues' excess ammonia is converted to glutamine's amide nitrogen, which is then transferred to the liver mitochondria. One or both of these amino acids are present in higher concentrations in most tissues as compared to other amino acids.

Excess amino groups are typically transferred to pyruvate to form alanine in muscle. Another essential molecule in the transport of amino groups from muscle to the liver is alanine.

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Did You Know?

• If amino acids are present in the ecosystem, most microorganisms can scavenge them and use them as fuel when metabolic conditions demand them.

• As of 1983, there are approximately 500 naturally occurring amino acids (though only 20 exist in the genetic code) that can be categorised in a variety of ways.