To talk about the twenty amino acids that make up protein and modified structures, at least twelve specialized metabolic pathways should be described.
But why do cells use so many metabolic pathways that require energy (for example to regenerate the catalytic sites of enzymes), each with an enzymatic heritage, to catabolize amino acids? Almost all the amino acids can be obtained, through specialized routes, metabolites which in a small part are used to produce energy (for example, through gluconeogenesis and the path of ketone bodies) but which, above all, lead to the formation of complex molecules, with a high number of carbon atoms (for example from phenylalanine and tyrosine, hormones are produced in the adrenal glands that are specialized for this purpose); if on the one hand it would be easy to produce energy from amino acids, on the other it would be complicated to build complex molecules starting from small molecules: the catabolism of amino acids allows us to exploit their skeleton to obtain larger species.
Two or three ounces of amino acids are degraded daily by a healthy individual: 60-100 g of them, derive from the proteins introduced by the diet but over 2 ounces are obtained from the normal turnover of proteins that are an integral part of the body (amino acids of these proteins, which are damaged by redox processes, are replaced by others and catabolized).
The amino acids give an energy contribution in terms of ATP: after removing the α-amino group, the remaining carbon skeleton of the amino acids, following appropriate transformations, can enter the krebs cycle. Furthermore, when the supply of nutrients is lacking and the quantity of glucose decreases, gluconeogenesis is activated: gluconeogenetic amino acids are called those that, after appropriate modifications, can be introduced into gluconeogenesis; gluconeogenetic amino acids are those that can be converted into pyruvate or fumarate (the fumarate can be converted into a sick that comes out of the mitochondria and, in the cytoplasm, is transformed into oxaloacetate from which phosphoenol can be obtained). Instead, those that can be converted into acetyl coenzyme A and vinegar-acetate are said to be ketogenic amino acids.
The one just described is a very important aspect because amino acids can remedy a lack of sugar in the event of immediate fasting; if fasting persists, lipid metabolism intervenes after two days (because protein structures cannot be attacked much), it is in this phase that, since gluconeogenesis is very limited, fatty acids are converted into acetyl coenzyme A and ketone bodies . From further fasting, the brain also adapts to using ketone bodies.
The transfer of the α-amino group from amino acids occurs through a transamination reaction; the enzymes that catalyze this reaction are called transaminases (or amino transferases). These enzymes use an enzymatic cofactor called pyridoxal phosphate, which intervenes with its aldehyde group. Pyridoxal phosphate is the product of the phosphorylation of pyridoxine which is a vitamin (B6) contained mainly in vegetables.
Transaminases have the following properties:
High specificity for an α-ketoglutarate-glutamate pair;
They take their name from the second couple.
Transaminase enzymes always involve the α-ketoglutarate-glutamate pair and are distinguished by the second pair involved.
Examples:
Aspartate transaminase or GOT (glutamate-oxal acetate transaminase): the enzyme transfers the α-amino group from aspartate to α-ketoglutarate, obtaining oxalacetate and glutamate.
Alanine transaminase ie GTP (Glutamate-Pyruvate Transaminase): the enzyme transfers the α-amino group from alanine to α-ketoglutarate obtaining pyruvate and glutamate.
The various transaminases, use α-ketoglurate as an acceptor of the amino group of amino acids and convert it into glutamate; while, the amino acids that are formed are used in the path of ketone bodies.
This type of reaction can take place in both directions since they break and bonds with the same energy content are formed.
Transaminases are both in the cytoplasm and in the mitochondria (they are mostly active in the cytoplasm) and differ in their isoelectric point.
Transaminases are also able to decarboxylate amino acids.
There must be a way to convert glutamate back into α-ketoglutarate: this happens by deamination.
Glutamate dehydrogenase is an enzyme capable of transforming glutamate into α-ketoglutarate and, therefore, of converting the amino groups of the amino acids found in the form of glutamate into ammonia. What happens is an oxydoreductive process that passes through the intermediate α-amino glutarate: ammonia and α-ketoglutarate are released and return to circulation.
Thus, the disposal of the amino groups of the amino acids passes through the transaminases (different depending on the substrate) and the glutamate dehydrogenase, which determines the formation of ammonia.
There are two types of glutamate dehydrogenase: cytoplasmic and mitochondrial; the cofactor, which is also a co-constituent of this enzyme, is NAD (P) +: glutamate dehydrogenase uses NAD + or NADP + as acceptor of reducing power. The cytoplasmic form prefers, although not exclusively, NADP + whereas the mitochondrial form prefers NAD +. The mitochondrial form has the purpose of disposing of the amino groups: it leads to the formation of ammonia (which is a substrate for a specialized mitochondria enzyme) and NADH (which is sent to the respiratory chain). The cytoplasmic form works in the opposite direction, that is, it uses ammonia and α-ketoglutarate to give glutamate (which has a biosynthetic destination): this reaction is a reductive biosynthesis and the cofactor used is NADPH.
Glutamate dehydrogenase works when the amino groups of amino acids such as ammonia (via urine) need to be disposed of or when the skeletons of amino acids are needed to produce energy: this enzyme will therefore have systems that indicate good energy availability (ATP) as negative modulators. GTP and NAD (P) H) and as positive modulators, systems that indicate a need for energy (AMP, ADP, GDP, NAD (P) +, amino acids and thyroid hormones).
Amino acids (mainly leucine) are positive modulators of glutamate dehydrogenase: if amino acids are present in the cytoplasm, they can be used for protein synthesis, or they must be disposed of because they cannot be accumulated (this explains why amino acids are positive modulators) .
Ammonia disposal: urea cycle
Fish dispose of ammonia by introducing it into the water through the gills; the birds convert it into uric acid (which is a condensation product) and eliminate it with feces. Let's see what happens in humans: we have said that glutamate dehydrogenase converts glutamate into α-ketoglutarate and ammonia but we have not said that this happens only in the mitochondria of the liver.
A fundamental role of ammonia disposal, through the urea cycle, is covered by mitochondrial transaminases.
carbon dioxide, in the form of bicarbonate ion (HCO3-), is activated by the biotin cofactor forming the carboxy biotin which reacts with ammonia to give the carbamic acid; the subsequent reaction uses ATP to transfer a phosphate to the carbamic acid forming carbamyl phosphate and ADP (the conversion of ATP to ADP is the driving force for obtaining the carboxibiotine). This phase is catalyzed by carbamyl phosphate synthetase and occurs in the mitochondria. Carbamyl phosphate and ornithine, are substrates for the enzyme ornithine trans carbamylase which converts them to citrulline; this reaction occurs in the mitochondria (of hepatocytes). The citrulline produced comes out of the mitochondria and, in the cytoplasm, goes under the action of the arginine succinate synthase : there is the fusion between the carbon skeleton of citrulline and that of an aspartate through a nucleophilic attack and subsequent elimination of water. The enzyme arginine succinate synthase, requires an ATP molecule therefore there is an energetic coupling: the hydrolysis of ATP to AMP and pyrophosphate (the latter is then converted into two orthophosphate molecules) by expelling a molecule of water from the substrate and not due to the action of the water in the medium.
The next enzyme is arginine succinase : this enzyme is able to split the arginine succinate into arginine and fumarate inside the cytoplasm.
The urea cycle is completed by the enzyme arginase : urea and ornithine are obtained; urea is disposed of by the kidneys (urine) while the ornithine returns to the mitochondria and resumes the cycle.
The urea cycle is subject to indirect modulation by arginine: the accumulation of arginine, indicates that it is necessary to speed up the urea cycle; arginine modulation is indirect because arginine positively modulates the enzyme acetyl glutamate synthetase. The latter is able to transfer an acetyl group to the nitrogen of a glutamate: N-acetyl glutamate is formed which is a direct modulator of the enzyme carbamyl-phospho synthetase.
Arginine accumulates as a metabolite of the urea cycle if the production of carbamyl phosphate is not sufficient to dispose of ornithine.
Urea is only produced in the liver but there are other sites where initial reactions take place.
The brain and muscles use special strategies to eliminate amino groups. The brain uses a very efficient method in which an enzyme glutamine synthetase and an enzyme glutamase are used: the former is present in neurons, while the latter is found in the liver. This mechanism is very efficient for two reasons:
Two amino groups are transported from the brain to the liver with only one vehicle;
Glutamine is much less toxic than glutamate (glutamate also carries neuronal transfer and must not exceed physiological concentration).
In fish a similar mechanism brings the amino group of amino acids to the gills.
From the muscle (skeletal and cardiac), the amino groups reach the liver via the glucose-alanine cycle; the enzyme involved is glutamine-pyruvate transaminase: it allows the transposition of the amino groups (which are in the form of glutamate), converting the pyruvate into alanine and, simultaneously, the glutamate into α-ketoglutarate in the muscle and catalyzing the inverse process in liver.
Transaminases with different tasks or positions also have structural differences and can be determined by electrophoresis (they have different isoelectric points).
The presence of transaminases in the blood can be a symptom of hepatic or cardiopathic damage (ie tissue damage to liver or heart cells); transaminases, are in very high concentrations both in the liver and in the heart: through electrophoresis it can be established whether the damage occurred in liver or heart cells.
