Elevate Your Exam Prep with This In-Depth Guide to Protein Metabolism | Self-study Guide/Notes for all

Protein metabolism is a vital topic for anyone pursuing a career in healthcare or the biological sciences. Whether you're studying to become a doctor, nurse, paramedic, or biochemist, a solid understanding of the biochemical reactions of amino acids is essential. In this article, we'll provide a comprehensive introduction to protein metabolism and the fate of amino acids after absorption in our body.

We'll explore the various pathways by which amino acids can be metabolized in the body, including transamination, deamination, transmethylation, transpeptidation, deamidation, decarboxylation, and inter-conversion of amino acids. Understanding these processes is crucial for anyone preparing for professional exams such as MBBS-I, MBDS-I, BS Nursing, Paramedics, BS Biochemistry, NEET, and other related tests.

We'll also delve into the concept of plasma amino acids and their significance in protein metabolism. By the end of this article, you'll have a clear and understandable understanding of the biochemical reactions of amino acids, ensuring maximum concept-gaining ability. This article serves as an important source for students looking to score higher marks on their professional exams, as well as for those seeking a deeper understanding of protein metabolism. So, let's get started and unlock the secrets of protein metabolism and amino acid biochemistry.

Biochemistry Notes for Medical and Professional Exams and Tests (MBBS, MBDS, BS Nursing, Paramedics, BS Biochemistry and othersNEET, MDCAT,)

Biochemistry Notes on Introduction to Protein and Amino Acid Metabolism
From the Biochemistry Library of H.E.S (Health, Education, and Skills)

Introduction to protein metabolism and amino acid biochemistry

Protein metabolism and amino acid biochemistry are essential topics for healthcare professionals to understand because they are fundamental to many important bodily functions and play a critical role in health and disease.

Protein metabolism refers to the processes by which the body breaks down dietary proteins into their constituent amino acids, which can then be used for a variety of purposes.
Understanding protein metabolism is important because it is essential for maintaining normal growth and development, repairing tissues, and supporting immune function.
Amino acids are the building blocks of proteins and are required for the synthesis of enzymes, hormones, and many other important molecules.
Amino acid biochemistry is equally important because it provides a detailed understanding of how different amino acids are metabolized and the roles they play in various physiological processes. For example, some amino acids are precursors to neurotransmitters, such as serotonin and dopamine, which are essential for proper brain function. Others are involved in the synthesis of hormones, such as insulin and glucagon, which regulate blood glucose levels.
Additionally, amino acids can be used for energy production when glucose is not available.
Amino acid biochemistry is also crucial for the diagnosis and treatment of many genetic disorders that affect amino acid metabolism. For example, phenylketonuria (PKU) is a genetic disorder in which the body cannot properly metabolize the amino acid phenylalanine, leading to the buildup of toxic byproducts that can cause intellectual disability and other serious health problems. Healthcare professionals need to be able to recognize the signs and symptoms of these disorders and understand the appropriate interventions to manage them.

Fate of Amino Acids after Absorption

i. Absorption and excretion of amino acids

Once the proteins are digested, amino acids are released and absorbed by the intestinal cells, they are passed into the blood and then taken up by the other cells of the body for different functions.
Amino acids, that are not utilized, pass out in the urine.

ii. Functions of Amino Acids

Amino acids are required by the body for the synthesis of important structural elements and metabolic processes. They are required for the synthesis of

Tissue proteins.
Enzymes.
Protein hormones e.g. insulin, glucagon, growth hormones, etc.
Hormones from single amino acids e.g. adrenaline, nor-adrenaline, thyroxine, etc.
Physiologically active peptides e.g. glutathione.
Vitamins e.g. niacin is formed from tryptophan.
Serotonin.
Body pigment e.g melanin.

The intracellular concentration of amino acids is much higher than that of extracellular fluid (ECF).
The active transport system, which requires ATPs, maintains the concentration gradient for the movement of amino acids from the EFC into the cells.
At least seven different transport systems are known for the transport of amino acids from EFC into the cells.
The most active system is Gamma (γ) Glutamyl Cycle.

Plasma Amino Acids

Nitrogen enters the body in the form of amino acids contained in dietary proteins.
Nitrogen leaves the body as urea, ammonia, and other products of amino acid metabolism.
Only 75% of the amino acids derived from the hydrolysis of body proteins are used for the biosynthesis of new tissue proteins.
The remainder serves as precursors for the compounds such as porphyrin, creatine, neurotransmitters, purines, pyrimidines, and other nitrogenous compounds.

Amino Acid pool

The amino acid pool consists of amino acids released by the hydrolysis of proteins plus free amino acids distributed throughout the body.

Formation of Plasma Proteins

These include enzymes, antibodies, hemoglobin, milk protein in lactating mammary glands, and proteinous hormones e.g insulin, and glucagon.

Formation of Nitrogenous compounds other than Proteins

These include thyroid hormones, catecholamines (adrenaline and nor-adrenaline), choline, creatine, purines, pyrimidines, nicotinic acid, tripeptides like glutathione, and pigments like melanin.

Formation of Ammonia and Keto Acids

Ammonia is formed by the deamination of amino acids. Deamination means simply the removal of an amino group from an amino acid. The removed amino acid is liberated as free ammonia and the remaining part of the amino acid is converted to its corresponding keto acid.

Protein Turnover

The total amount of protein in the body is constant because of the protein turnover i.e. the rate of protein synthesis is equal to the rate of protein degradation.

Clinical importance of Amino Acids

About 1 gm of amino acids is excreted in urine per day.
The amino acids in urine are found in free form e.g peptides and conjugated form e.g. hippuric acid.
Renal tubules absorb most of the amino acids filtered by glomeruli.
Amino acid levels in urine increase with the increase in plasma amino acid levels. This happens in diabetes mellitus, acute infections, liver diseases, and pregnancy.
A pathological condition associated with the loss of amino acids in urine is called Amino Aciduria.

Biochemical Reactions of Amino Acids in the Body

1. Transamination

Transamination is a biochemical reaction that involves the transfer of an amino group (-NH2) from an amino acid (glutamate, alanine, and aspartate) to a keto acid (pyruvate, oxaloacetate, and alpha-ketoglutarate), resulting in the formation of a new amino acid and a new keto acid.
The amino acid, after the removal of "NH2", becomes the corresponding ketoacid, and the ketoacid, after accepting "NH2", becomes the corresponding amino acid.
The reaction is catalyzed by a class of enzymes called transaminases, also known as aminotransferase.
The general reaction of transamination can be represented as:

amino acid 1 + alpha-keto acid 2 ⇌ alpha-keto acid 1 + amino acid 2

In this reaction, the amino group (-NH2) from amino acid 1 is transferred to the keto group (C=O) of alpha-keto acid 2, resulting in the formation of alpha-keto acid 1 and amino acid 2.

The transamination reaction is important in the metabolism of amino acids, as it allows for the synthesis of non-essential amino acids from essential amino acids. For example, the transamination of the essential amino acid valine with the keto acid alpha-ketoglutarate results in the formation of the non-essential amino acid glutamate and the keto acid alpha-ketoisocaproate. This reaction is catalyzed by the transaminase enzyme called branched-chain amino acid transaminase.

Valine + alpha-ketoglutarate ⇌ glutamate + alpha-ketoisocaproate

Transamination reactions also play a key role in the urea cycle.
Transaminases are of two types i.e. ALT (SGPT), and AST (SGOT), i.e.

A. Alanine Transaminase (ALT)

It is also called Serum Glutamate Pyruvate Transaminase (SGPT).
It is present only in the liver.
ALT catalyzes the transfer of "NH2" from glutamate to pyruvate forming alpha-ketoglutarate and alanine.
The reaction is readily reversible, however during amino acid catabolism, the enzyme functions in the direction of glutamate synthesis.

B. Aspartate transaminase (AST)

It is also called Serum Glutamate Oxaloacetate Transaminase (SGOT).
AST is present in the liver and cardiac muscles.
AST catalyzes the transfer of "NH2" from glutamate to oxaloacetate forming alpha-ketoglutarate and aspartate, which is a source of Nitrogen in the urea cycle.
The reaction is readily reversible, however, during amino acid catabolism, the enzyme functions in the direction of aspartate synthesis.

Mechanism of action of Transaminases

Transaminases require the coenzyme Pyridoxal phosphate (Vitamin B6).
Transaminases transfer an amino group to the Pyridoxal part of the coenzyme to form Pyridoxamine.
Pyridoxamine then reacts with alpha-keto acid to form an amino acid and regenerates the original aldehyde form of the coenzyme i.e. pyridoxal phosphate.

Diagnostic value of Transaminases

Transaminases are intracellular enzymes of the liver and cardiac muscles.
Whenever there is damage to these cells, the serum level of these transaminases rises.
Raised serum ALT (GPT) level is diagnostic for liver diseases e.g. hepatitis, cirrhosis, etc.
Raised serum AST (GOT) level is diagnostic for cardiac diseases e.g. myocardial infarction (no more used as a diagnostic for myocardial injury).

2. Deamination

Deamination is a biochemical reaction in which an amino group (-NH2) is removed from an amino acid.
The removed amino group is released as free ammonia (NH3).
The amino acid, from which the amino group is removed, is converted to its corresponding keto-acid.
It occurs mainly in the liver.
This reaction plays a crucial role in the metabolism of amino acids in the body.

Two types of deamination reactions

I. Oxidative Deamination

This is a process by which an amino acid is converted into an alpha-keto acid by the removal of an amino group.
This process is catalyzed by an enzyme called amino acid oxidases in the presence of Oxygen.
The removed amino group is released as free NH3.
Hydrogen-per-oxide (H2O2) is produced and released. Since H2O2 is toxic, it is immediately decomposed by catalase.
Some amino acids (e.g. glutamic acid) are deaminated not by amino acid oxidases but by amino acid dehydrogenases resulting in the formation of an amino group as an intermediate product.
Another type of deamination involves specific amino acid oxidases e.g. glycine oxidase, which specifically deaminates glycine.

II. Non-oxidative Deamination

In this process, the amino group is removed from the amino acid and transferred to another molecule, rather than being converted into ammonia.
This process is catalyzed by a group of enzymes called transaminases.
These reactions do not require Oxygen.
For example, the amino acid glutamate is deaminated to produce alpha-ketoglutarate, which is an intermediate in the citric acid cycle, and ammonia. The ammonia is then combined with carbon dioxide to form urea, which is excreted by the body in the urine.
Hydroxy amino acids e.g. serine and threonine are deaminated by specific enzymes called dehydrases, which remove water from their molecules. This is followed by spontaneous deamination.

Deamination is an important process in the metabolism of amino acids, as it allows the body to break down excess amino acids and use them for energy or excrete them as waste. However, excessive deamination can lead to a buildup of ammonia in the body, which can be toxic. Therefore, the body tightly regulates the balance of amino acid metabolism to maintain proper levels of ammonia and other metabolic byproducts

3. Transmethylation

Transmethylation is a biochemical reaction that involves the transfer of a methyl group (-CH3), from a methyl donor e.g methionine to a methyl acceptor.
In order to donate its methyl group, methionine is first activated to S-Adenosyl Methionine (SAM) with the help of ATP.
SAM then donates its methyl group to substances to make other substances e.g. formation of creatine and adrenaline.
After donating methyl group, SAM becomes S-Adenosyl homocysteine.
The donated methyl group is known as the Labile methyl group.
The transmethylation reaction is mainly mediated by enzymes called methyltransferases.
One example of transmethylation in amino acid metabolism is the conversion of homocysteine to methionine. This reaction is catalyzed by the enzyme methionine synthase, which uses methylcobalamin (a form of vitamin B12) as a cofactor. The methyl group for this reaction comes from the SAM molecule, which donates a methyl group to homocysteine to form methionine.

4. Transpeptidation

Transpeptidation is a biochemical reaction that involves the formation of peptide bonds between amino acids. Thus Transpeptidation means the transfer or addition of an amino acid (not only the amino group).
This reaction is important in the synthesis of proteins (e.g. synthesis of glutathione, a tripeptide) and the maintenance of the structure and function of enzymes and other proteins in the body.
Another example is the transfer of glycine to Benzoic acid (a waste product) in the liver resulting in the formation of Hippuric acid, which is then excreted in the urine.
The transpeptidation reaction is catalyzed by enzymes called peptidyl transferases.
These enzymes bind to the growing polypeptide chain and facilitate the transfer of the amino group (-NH2) of one amino acid to the carboxyl group (-COOH) of another amino acid, forming a peptide bond (-CO-NH-) between them.
Transpeptidation in amino acid metabolism is the final step in the synthesis of the cell wall in bacteria.
The reaction involves the cross-linking of peptidoglycan chains by transpeptidation, which results in the formation of a rigid cell wall that protects the bacteria from osmotic pressure.
Transpeptidation also plays an important role in the function of enzymes and other proteins in the body. For example, in enzymes such as penicillin-binding proteins (PBPs), transpeptidation is involved in the cross-linking of peptidoglycan chains in bacterial cell walls, which is the target of antibiotics such as penicillin.

5. Deamidation

An amide is an amino acid that contains an additional amino (-NH2) group at C1.
Deamidation is simply the removal of this additional -NH2 group in the form of NH3.
Some amino acids e.g. glutamic acid and aspartic acid are also found in amid forms, which are glutamine and asparagine respectively.
These amides can be converted back to their original amino acid forms by the actions of glutaminase and asparaginase, which hydrolyze the amides and release the additional -NH2 group as NH3.
The deamidation reaction is catalyzed by a group of enzymes called deamidases, which are present in various tissues throughout the body.
The reaction can occur spontaneously under certain conditions, such as exposure to high temperature, extreme pH, or radiation.
Deamidation can have important physiological implications. For example, in the brain, deamidation of asparagine to aspartic acid can regulate the activity of neurotransmitters, affecting cognitive function and behavior.

6. Decarboxylation

Decarboxylation is a biochemical reaction that involves the removal of a carboxyl group (-COOH) from a molecule, typically in the form of carbon dioxide (CO2).
This reaction is important in the metabolism of amino acids in the body, as many amino acids can be converted into neurotransmitters or other molecules through the process of decarboxylation.
One example of an amino acid that undergoes decarboxylation is histidine. Histidine is an essential amino acid that is involved in many important processes in the body, including the synthesis of proteins and the regulation of pH levels. In order to be converted into the neurotransmitter histamine, histidine must first undergo decarboxylation. This reaction is catalyzed by the enzyme histidine decarboxylase, which removes the carboxyl group from histidine and releases carbon dioxide.
Another example of an amino acid that undergoes decarboxylation is glutamate. Glutamate is an amino acid that is involved in many important processes in the body, including the synthesis of proteins and the regulation of neurotransmitter levels. In order to be converted into the neurotransmitter gamma-aminobutyric acid (GABA), glutamate must first undergo decarboxylation. This reaction is catalyzed by the enzyme glutamate decarboxylase, which removes the carboxyl group from glutamate and releases carbon dioxide.

7. Inter-conversion of amino acids

Many amino acids can be converted to other amino acids e.g.

Methionine can be converted to Cysteine.
Cysteine can also be converted to Alanine.
Glycine can be converted to Serine.
Phenylalanine can be converted to Tyrosine.
Tyrosine can be converted to DOPA.

Formation of specialized products from Amino Acids

In addition to protein synthesis, amino acids can also be metabolized into a variety of specialized products with important biological functions. Here are some examples of specialized products that can be formed from amino acids:

I. Porphyrins

They are synthesized from the condensation of glycine and succinyl CoA.
They are cyclic compounds known as metalloporphyrins because they bind metal ions, usually Fe+2 or Fe+3.
In humans, the most prevalent metalloporphyrin is heme, which is a prosthetic group of myoglobin, hemoglobin, cytochrome, and catalase.
The formation and degradation of the porphyrin component of hemoglobin are of quantitative importance in the Nitrogen balance of the body.

II. Creatine

Creatine phosphate (a phosphorylated form of creatine), found in muscles, is a high-energy phosphate compound, which can reversibly donate its phosphate group to ADP to form ATP. This transfer of Pi from creatine phosphate to ADP is catalyzed by creatine kinase.
Creatine is synthesized from the amino acids arginine, glycine, and methionine.
It maintains the intracellular levels of ATP during the first few minutes of intense muscular exercise.
The presence of creatine kinase (CK) in the plasma indicates tissue damage and is diagnostic of myocardial infarction as well as a skeletal muscle injury.
The amount of creatine phosphate is proportional to the muscle mass.
Creatine can be used as a supplement by athletes to improve athletic performance.

Degradation of Creatine

The final degradation product of creatine and creatine phosphate is creatinine, which is excreted in the urine.
The amount of creatinine excreted from the body is proportional to the total content of creatine phosphate of the body, and thus can be used to estimate muscle mass.
When muscle mass decreases e.g. in paralysis or muscular dystrophy, the creatinine content of urine falls.
Creatinine is a sensitive indicator of renal function because normally creatinine is rapidly removed from the blood and excreted, thus any rise in the blood creatinine indicates a renal malfunction.

Creatinine clearance

It is the indicator of renal function. it is defined as "the volume of serum or plasma that would be cleared of creatinine by one minute's excretion of urine".
Creatinine excretion in a typical adult is 14 - 26 mg/kg/day.

III. Histamine

It is formed by the decarboxylation of histidine (semi-essential amino acid).
It is a chemical messenger and is secreted by mast cells in response to trauma or inflammatory reactions.
It mediates a wide range of cellular responses, including allergic and inflammatory reactions, gastric acid secretion, and neurotransmission in some parts of the brain.
It has no clinical applications, but agents interfering with the action of histamine have important therapeutic benefits.

IV. Serotonin

It is also called 5-hydroxytryptamine and is synthesized from tryptophan.
It acts as a neurotransmitter.
The largest amount is found in gastric mucosa and a smaller amount is found in platelets and CNS.
It has multiple physiological roles including pain perception, normal and abnormal behavior (affective disorders), regulation of food intake, sleep, temperature, blood pressure, and neuroendocrine functions.
It participates in the regulation of hormonal secretion of the pituitary gland e.g. it stimulates the release of adrenocorticotropic hormone (ACTH), growth hormone, and prolactin and it inhibits the secretion of luteinizing hormone (LH), follicle-stimulating hormone (FSH), and thyroid stimulating hormone (TSH).
Serotonin appears to be involved in migraine headaches (the actual cause of this type of headache is still unknown).
Serotonin is an arteriolar constrictor and may thus cause decreased cerebral blood flow during an attack of migraine headaches.
Serotonin also increases the sensitivity of pain receptors.

V. Catecholamines

Catecholamines are a class of neurotransmitters and hormones that play a crucial role in the body's response to stress and various physiological processes.
The three primary catecholamines are dopamine, norepinephrine, and epinephrine, all of which are synthesized from the amino acid tyrosine.
All of the catecholamines act as neurotransmitters in the brain and autonomic nervous system, whereas epinephrine and nor-epinephrine also act as hormones.
Nor-epinephrine and epinephrine are released from the adrenal medulla in response to fright, flight, exercise, cold, low blood glucose, and low blood pressure.

Synthesis of Catecholamines

The synthesis of catecholamines begins with the conversion of tyrosine to L-dopa by the enzyme tyrosine hydroxylase, which requires oxygen, tetrahydrobiopterin, and iron as cofactors.
L-dopa is then decarboxylated by the enzyme aromatic L-amino acid decarboxylase to produce dopamine.
Dopamine can then be further converted to norepinephrine by the enzyme dopamine β-hydroxylase, which requires ascorbic acid as a cofactor.
Norepinephrine can be further converted to epinephrine by the enzyme phenylethanolamine N-methyltransferase, which requires S-adenosylmethionine as a cofactor.
This synthesis occurs primarily in the adrenal medulla, but norepinephrine can also be synthesized in the sympathetic nerve terminals.

Functions of Catecholamines

a. Regulation of the sympathetic nervous system: Catecholamines are released in response to stress, leading to increased heart rate, blood pressure, and respiration. These effects prepare the body for the "fight or flight" response.

b. Mood regulation: Dopamine plays a role in the brain's reward and pleasure pathways and is involved in motivation and mood regulation.

c. Attention and arousal: Norepinephrine plays a role in attention and arousal by increasing alertness and vigilance.

d. Metabolism: Catecholamines increase the breakdown of glycogen in the liver, leading to increased glucose production and release into the bloodstream. This effect helps to provide energy during periods of stress.

e. Blood pressure regulation: Epinephrine and norepinephrine can constrict blood vessels, leading to an increase in blood pressure.

f. Immune function: Catecholamines can modulate immune function by regulating the activity of immune cells, such as T cells and natural killer cells.

g. Pain perception: Catecholamines can modulate pain perception by acting on opioid receptors in the brain and spinal cord.

Catecholamine Degradation

Catecholamines are degraded by Oxidative deamination, catalyzed by Monoamine Oxidase (MAO), and by O-methylation carried by catechol-O-methyltransferase.
The end products of these reactions are excreted in urine as VMA (Vanillylmendelic Acid), metanephrine, and nor-metanephrine.

Monoamine Oxidase (MAO)

It is an enzyme found in natural and other tissues such as the intestine and liver.
In Neurons, MAO functions as a "safety valve" against an excess of neurotransmitters, which are dopamine, nor-epinephrine, and serotonin. MAO oxidatively deaminates and inactivates excess of these neurotransmitters.
MAO-Inhibitors are drugs that cause inhibition of MAO resulting in the activation and prolonged action of nor-epinephrine and serotonin receptors and may be responsible for the antidepressant action of these drugs.

VI. Nitric Oxide:

Nitric oxide (NO) is a gas that acts as a signaling molecule in the body.
It is synthesized from the amino acid arginine by an enzyme called nitric oxide synthase.
Nitric oxide is involved in regulating blood flow, immune function, and neurotransmission.

VII. Glutathione

Glutathione is a molecule that plays an important role in detoxification and antioxidant defense.
It is synthesized from the amino acids glutamate, cysteine, and glycine.
Glutathione helps to neutralize harmful toxins and free radicals in the body.

VIII. Melanin

Melanin is a pigment that gives color to skin, hair, and eyes.
It is synthesized from the amino acid tyrosine by specialized cells called melanocytes.
Synthesis is catalyzed by tyrosinase or occurs simultaneously.
Melanin helps to protect the skin from UV radiation and other environmental stressors.

IX. Thyroid hormones:

The thyroid hormones triiodothyronine (T3) and thyroxine (T4) are important regulators of metabolism and growth.
They are synthesized from the amino acid tyrosine and the mineral iodine.
Thyroid hormones play important roles in regulating body temperature, heart rate, and energy metabolism.

Clinical Applications and Significance

Clinical applications of protein and amino acid metabolism include diagnosis, treatment, and monitoring of various diseases and disorders.

Diagnosis of Inherited Disorders: Inherited disorders of protein and amino acid metabolism can lead to the accumulation of toxic metabolites, resulting in various disorders such as phenylketonuria (PKU), maple syrup urine disease, and homocystinuria. Diagnosis of these disorders involves measuring the levels of amino acids and their metabolites in blood and urine. Early diagnosis and treatment can prevent the progression of these disorders and improve the quality of life of affected individuals.
Nutritional Assessment: The levels of amino acids in blood and urine can be used to assess the nutritional status of individuals. Malnutrition can lead to a decrease in the levels of essential amino acids, which can have adverse effects on various physiological processes. Nutritional assessment can be used to identify individuals who may require dietary interventions or supplements to meet their amino acid requirements.
Monitoring of Disease Progression: Alterations in protein and amino acid metabolism are associated with various diseases such as cancer, liver disease, and diabetes. Monitoring the levels of amino acids and their metabolites in blood and urine can provide insights into disease progression and response to therapy.
Treatment of Inborn Errors of Metabolism: Inborn errors of metabolism are genetic disorders that affect the metabolism of proteins and amino acids. Treatment of these disorders involves dietary modifications, supplementation of deficient amino acids, and enzyme replacement therapy. These treatments can prevent the accumulation of toxic metabolites and improve the quality of life of affected individuals.
Sports Nutrition: Amino acids play an essential role in muscle protein synthesis and repair, making them essential for athletes and individuals involved in physical activity. Supplementation with specific amino acids such as branched-chain amino acids (BCAAs) can improve exercise performance and reduce muscle damage.

Maximizing Your Exams Performance | The Ultimate Protein Metabolism Guide for Professionals