Protein Metabolism (FSV)

Amino acids are precursors for heme, purines, pyrimidines, hormones, neurotransmitters, and biologically active peptides.

Posttranslational modifications of amino acids enable proteins to perform specific functions by altering activity, localization, stability, and interactions.

Alanine carries ammonia and the carbon skeleton of pyruvate from muscle to liver: pyruvate + glutamate → alanine (in muscle), which is converted back to pyruvate in the liver for gluconeogenesis.

Alanine is present as a free amino acid in plasma and cycles between tissues such as muscle and liver.

Serotonin plays several physiological roles, including:

• Regulation of mood and anxiety.
• Modulation of sleep cycles.
• Influence on gastrointestinal function.
• Role in appetite control and satiety.

Ammonia is considered highly toxic due to its potential to disrupt cellular processes and cause damage to tissues.

A peptide bond (C-N bond) is formed between the two amino acids during dipeptide formation.

Pepsin is most active at a pH of 2.0 to 3.0 and becomes inactive at pH levels greater than 5.0.

The digestion and absorption of proteins involve several key processes:

1. Denaturation: Proteins are denatured by stomach acid (HCl), unfolding their structure.
2. Proteolysis: Enzymes like pepsin in the stomach and trypsin in the small intestine break down proteins into smaller peptides.
3. Peptide Absorption: Small peptides and amino acids are absorbed through the intestinal wall into the bloodstream via specific transporters.
4. Transport: Amino acids are transported to various tissues for protein synthesis or energy production.

The carbon skeletons of amino acids can undergo several metabolic fates:

1. Gluconeogenesis: Some amino acids can be converted into glucose, especially during fasting.
2. Ketogenesis: Certain amino acids can be converted into ketone bodies, which can be used as an energy source.
3. Energy Production: Carbon skeletons can enter the citric acid cycle (Krebs cycle) to produce ATP.
4. Fatty Acid Synthesis: Excess carbon skeletons can be converted into fatty acids and stored as fat.

Non-essential amino acids are synthesized from other compounds through various pathways:

1. Transamination: The transfer of an amino group from one amino acid to a keto acid, forming a new amino acid.
2. Deamination: Removal of an amino group, allowing the carbon skeleton to be used for other metabolic processes.
3. Regulation: Synthesis is regulated by the availability of substrates, the activity of enzymes involved, and feedback inhibition from the end products.

Non-protein nitrogenous compounds are formed through various metabolic pathways involving amino acids. Their clinical relevance includes roles in neurotransmitter synthesis, nucleotide formation, and detoxification processes. Understanding these compounds helps in analyzing metabolic disorders and their implications for human health.

Synthesizing information from primary research articles allows for a comprehensive understanding of how amino acid metabolism affects various physiological processes. This connection can reveal insights into metabolic disorders, nutritional deficiencies, and the role of amino acids in disease prevention and management.

Proteins are digested through a series of enzymatic reactions that break them down into smaller peptides and amino acids. The process involves:

1. Mechanical digestion in the mouth (chewing)
2. Chemical digestion in the stomach by gastric juices (pepsin)
3. Further breakdown in the small intestine by pancreatic enzymes (trypsin, chymotrypsin)
4. Absorption of amino acids and peptides through the intestinal wall into the bloodstream.

Amino acids in the body undergo several metabolic processes, including:

• Protein synthesis: Amino acids are used to build new proteins necessary for cellular functions.
• Energy production: Some amino acids can be converted into glucose or fatty acids for energy.
• Synthesis of non-protein compounds: Amino acids serve as precursors for hormones, neurotransmitters, and other nitrogenous compounds.
• Nitrogen balance: Amino acids contribute to the body's nitrogen pool, which is crucial for various metabolic processes.

Non-essential amino acids are synthesized in the body through various pathways, primarily involving:

1. Transamination: The transfer of an amino group from one amino acid to a keto acid, forming a new amino acid.
2. De novo synthesis: The body can create non-essential amino acids from simple precursors like glucose or other amino acids.
3. Utilization of intermediates: Some non-essential amino acids are synthesized from intermediates of metabolic pathways, such as the citric acid cycle.

Non-protein compounds are synthesized from amino acids through various biochemical pathways, including:

• Neurotransmitter synthesis: Amino acids like tryptophan and tyrosine are precursors for neurotransmitters (serotonin and dopamine, respectively).
• Hormone production: Certain amino acids are involved in the synthesis of hormones (e.g., tyrosine in thyroid hormones).
• Nitric oxide synthesis: Arginine is a precursor for nitric oxide, a signaling molecule.
• Creatine synthesis: Arginine, glycine, and methionine contribute to creatine production, important for energy metabolism.

Proteins are formed from multiple amino acids that are bound together by peptide linkages.

Pepsin provides 10 - 20% of total protein digestion and is capable of digesting collagen.

The end products of Pepsin digestion include proteoses, peptones, and a few polypeptides.

The process is called a condensation reaction, where a water molecule is removed to form a peptide bond between the two amino acids.

During hydrolysis, a water molecule is added to break the peptide bond, regenerating the original amino acids.

Each amino acid has a central carbon atom bonded to an amino group (NH2), a carboxyl group (COOH), a hydrogen atom (H), and a variable side chain (R).

The primary enzymes involved in protein digestion in the small intestine are pancreatic proteolytic enzymes, specifically trypsin, chymotrypsin, and carboxypolypeptidase.

Trypsin and chymotrypsin function by splitting proteins into small polypeptides during the digestion process.

Carboxypolypeptidase cleaves individual amino acids from the small polypeptides formed by trypsin and chymotrypsin.

Trypsinogen is activated to trypsin by membrane-bound enteropeptidase, while procarboxypeptidase is converted to carboxypeptidase by trypsin.

Enterocytes line the villi of the small intestine (duodenum and jejunum) and are responsible for the absorption of nutrients, primarily individual amino acids.

The peptidase enzymes produced by enterocytes include aminopolypeptidase and dipeptidase.

More than 99% of the final digestive products absorbed by enterocytes are individual amino acids, with only rare absorption of peptides and very rare absorption of whole protein molecules.

Enterocytes are responsible for the absorption of amino acids and peptides from the gut lumen. They transport amino acids into the bloodstream after further breaking down oligopeptides into dipeptides and tripeptides using specific enzymes like dipeptidases and tripeptidases.

The enzymes involved in the breakdown of polypeptides in the pancreas include trypsin, chymotrypsin, elastase, and carboxypeptidases. These enzymes act on polypeptides to form oligopeptides.

Amino acids are transported into enterocytes via H+-dependent symporters. This process is coupled with the transport of sodium ions (Na+), which is facilitated by the action of Na+/K+ ATPase in maintaining the sodium gradient.

Pepsin plays a crucial role in the initial digestion of proteins in the stomach by denaturing polypeptides and breaking them down into smaller peptides, which are further processed in the intestine.

Inside enterocytes, dipeptides and tripeptides are further broken down into individual amino acids by the action of dipeptidases and tripeptidases before being transported into the capillary system for distribution in the body.

PepT1 transporters facilitate the transport of small peptides (Pep) from the lumen into the enterocyte for further digestion.

Amino acids are transported from enterocytes into the blood after being broken down from peptides by peptidases inside the enterocyte.

1. PepT1 transport of peptides into the enterocyte
2. Tight junctions maintaining cell integrity
3. Transcytosis for peptide transport across the cell
4. Passive transcellular diffusion of amino acids into the blood

Peptidases break down small peptides into amino acids within the enterocyte, which are then transported into the bloodstream.

Pepsin is an enzyme that initiates the digestion of proteins in the stomach by breaking down proteins into smaller peptides, such as proteoses and peptones.

The enzymes involved in the further digestion of polypeptides include trypsin, chymotrypsin, carboxypolypeptidase, and elastase.

The final products of protein digestion are amino acids, which are produced from the breakdown of polypeptides by peptidases.

Proteins are absorbed through the luminal membranes of the intestinal epithelial cells as dipeptides, tripeptides, and free amino acids. This process is facilitated by the sodium co-transport mechanism, which provides the necessary energy for absorption.

The two categories are Ketogenic and Glucogenic amino acids.

• Ketogenic only (2): Leucine, Lysine
• Glucogenic only (14): Arginine, Methionine, Cysteine, Valine, Glycine, Glutamate, Threonine, Glutamine, Serine, Histidine, Asparagine, Histidine, Aspartate, Tyrosine
• Both (4): Tryptophan, Phenylalanine, Tyrosine, Isoleucine

The amino acids that lead to Citrate are Ala, Cys, Gly, Hyp, Ser, Thr, Ile, Leu, and Trp.

The amino acids associated with alpha-Ketoglutarate are Arg, His, Gln, and Pro.

Succinyl-CoA is associated with the amino acids Ile, Met, and Val.

Fumarate is related to the amino acids Tyr and Phe.

Acetyl-CoA can convert to Acetoacetyl-CoA, which is connected to the amino acids Leu, Lys, Phe, Trp, and Tyr.

Oxaloacetate is related to the amino acids Aspartate and Asn.

The glucogenic amino acids include:

• Asparagine
• Aspartate
• Alanine
• Cysteine
• Glycine
• Serine
• Threonine
• Tryptophan
• Valine
• Methionine
• Isoleucine
• Phenylalanine
• Tyrosine
• Histidine
• Proline
• Arginine
• Glutamate
• Glutamine
• Threonine
• Tryptophan

The ketogenic amino acids include:

• Leucine
• Lysine
• Phenylalanine
• Tryptophan
• Tyrosine
• Isoleucine
• Threonine

Glucogenic amino acids are converted into various metabolic intermediates such as:

• Pyruvate
• Oxaloacetate
• Fumarate
• Succinyl CoA
• Phosphoenol-pyruvate

Ketogenic amino acids are converted into:

• Acetyl CoA
• Acetoacetyl CoA
• Citrate

The amino acids converted to carbohydrates (glycogenic) are:

1. Ala (Alanine)
2. Arg (Arginine)
3. Asp (Aspartate)
4. Cys (Cysteine)
5. Glu (Glutamate)
6. Gly (Glycine)
7. His (Histidine)

The amino acids classified as ketogenic are:

1. Hyp (Hydroxyproline)
2. Met (Methionine)
3. Pro (Proline)
4. Ser (Serine)
5. Thr (Threonine)
6. Val (Valine)

The amino acids that can form both glycogen and fat (glycogenic and ketogenic) are:

1. Ile (Isoleucine)
2. Lys (Lysine)
3. Phe (Phenylalanine)
4. Trp (Tryptophan)
5. Tyr (Tyrosine)

A positive nitrogen balance occurs when ingested nitrogen is greater than excreted nitrogen. This is typically observed during growth and pregnancy.

A negative nitrogen balance occurs when excreted nitrogen is greater than ingested nitrogen. This is typically observed in situations such as surgery, advanced cancer, and nutritional disorders.

Ammonia arises primarily from the α-amino nitrogen of amino acids.

Ammonia is converted to urea, which is then excreted in the urine.

The first step of the Urea Cycle involves the conversion of CO2 and NH4+ into carbamoyl phosphate, catalyzed by the enzyme carbamoyl phosphate synthase I.

The cleavage of argininosuccinate by argininosuccinate lyase produces fumarate and L-arginine.

L-ornithine is regenerated at the end of the Urea Cycle after the cleavage of L-arginine by arginase, allowing it to re-enter the mitochondria and participate in the cycle again.

L-citrulline is formed from carbamoyl phosphate and ornithine by the action of ornithine carbamoyltransferase and is then converted to argininosuccinate, continuing the cycle.

N-acetylglutamate acts as an essential allosteric activator for carbamoyl phosphate synthase I, facilitating the first step of the Urea Cycle.

Birds excrete uric acid, which is a white, pasty substance. This is because birds have a unique way of excreting nitrogenous waste, allowing them to conserve water. The white color comes from the uric acid, while any yellow or brownish solids are typically from other waste materials.

The amino acids that are both gluconeogenic and ketogenic include isoleucine, phenylalanine, threonine, and tryptophan.

The main entry point for glucogenic amino acid carbon skeletons in the TCA cycle is oxaloacetate.

The first step of the urea cycle occurs in the mitochondria of liver cells.

The immediate precursor of urea is arginine.

The amino acid that transports ammonia from muscle to liver for detoxification is glutamine.

The defect in MSUD is in the α-keto acid decarboxylase complex.

Increased levels of leucine, isoleucine, and valine, along with their α-keto acids and α-hydroxy acids, are observed in MSUD.

Nutritionally essential amino acids must be obtained from the diet, while non-essential amino acids can be synthesized by the body.

The essential amino acid Phenylalanine requires 10 enzymes for its synthesis.

The nutritionally nonessential amino acid Proline requires 3 enzymes for its synthesis.

The term 'nutritionally semiessential' refers to amino acids that are synthesized at rates inadequate to support the growth of children, meaning they may not be sufficient for their needs during growth periods.

Kwashiorkor is a form of malnutrition caused by a starchy, protein-poor diet. Characteristics include:

• Distended or protuberant belly
• Presence of subcutaneous fat
• Itchy rash
• Xerosis (dry skin)
• Poor wound healing

Marasmus is a severe form of malnutrition characterized by both caloric deficit and protein deficit. Key differences from Kwashiorkor include:

• Extreme thinness with prominent bones
• Very low body weight
• Decreased subcutaneous fat

The reductive amidation of α-ketoglutarate involves the conversion of α-ketoglutarate into L-Glutamate through a reversible reaction catalyzed by glutamate dehydrogenase. This process is significant because it allows for the incorporation of ammonium ions (NH4+) into the amino acid structure, facilitating the synthesis of glutamate, which is a key amino acid in nitrogen metabolism and neurotransmission.

The process of amidation of glutamate involves the conversion of L-Glutamate to L-Glutamine. This reaction is catalyzed by the enzyme glutamine synthetase. During this reaction, an ammonium ion (NH4+) is added to L-Glutamate, resulting in the formation of L-Glutamine, which contains an amide group (H2N) instead of the ammonium group.

Alanine is formed from pyruvate through transamination, where an amino group is transferred from an amino donor (such as glutamate or aspartate) to pyruvate. This reaction results in the formation of alanine and either alpha-ketoglutarate or oxaloacetate as the other product.

Oxaloacetate acts as the amino acceptor in the transamination reaction, where it combines with glutamate to produce aspartate and alpha-ketoglutarate.

The transamination reaction produces aspartate and alpha-ketoglutarate from oxaloacetate and glutamate.

Aspartate has a nitrogen atom in place of the oxygen atom on the central carbon, which is present in glutamate. Both have similar structures otherwise, with carboxylate groups and a central carbon.

The amidation of aspartate involves the conversion of L-Aspartate to L-Asparagine through a reaction catalyzed by asparagine synthetase (EC 6.3.5.4). This reaction utilizes glutamine as a nitrogen source and requires ATP for energy, resulting in the formation of L-Asparagine and the byproducts AMP and PPi.

Glycine is synthesized from glyoxylate and glutamate or alanine through the action of aminotransferases.

Glycine can be formed from:

1. Choline

   • Through a series of reactions involving choline dehydrogenase and other enzymes.

2. Serine

   • Interconversion between serine and glycine is catalyzed by serine hydroxymethyltransferase, and this reaction is freely reversible.

Tyrosine is converted to dopamine, which is then further converted to norepinephrine in neural cells.

The sulfur in cysteine derives from methionine. The process involves the conversion of methionine to homocysteine, which then reacts with serine to form cystathionine. Hydrolysis of cystathionine results in the formation of cysteine and homoserine.

Hydroxylation catalyzed by phenylalanine hydroxylase (PAH). Reaction uses tetrahydrobiopterin (BH4) and O2: phenylalanine + O2 + BH4 → tyrosine + H2O + BH2. Dihydropteridine reductase regenerates BH4 from BH2 using NADPH.

Peptidyl prolyl 4-hydroxylase (EC 1.14.11.2) is a mixed-function oxidase that incorporates molecular oxygen into succinate and proline during the hydroxylation of peptidyl proline residues.

Lysyl 5-hydroxylase (EC 1.14.11.4) catalyzes the hydroxylation of lysine residues, analogous to peptidyl prolyl 4-hydroxylase acting on proline.

Hydroxyproline and hydroxylysine stabilize collagen by contributing to the hydrogen-bonding network and enabling cross-linking between alpha chains, essential for collagen's triple-helical structure.

Tissue aminotransferases reversibly interconvert leucine, valine, and isoleucine with their corresponding α-keto acids, allowing dietary replacement of these amino acids by their α-keto acids.

The branched-chain amino acids involved in transamination pathways are leucine, valine, and isoleucine.

In transamination of branched-chain amino acids, α-ketoglutarate accepts the amino group and is converted to glutamate.

Branched-chain transaminase catalyzes the transamination of leucine, valine, and isoleucine.

1. α-Ketoisocaproate (from leucine)
2. α-Ketoisovalerate (from valine)
3. α-Keto-β-methylvalerate (from isoleucine)

Selenocysteine (the 21st amino acid) is incorporated into selenoproteins via a specific tRNA and UGA recoding. It is essential for enzymes involved in antioxidant defense and thyroid hormone metabolism.

Primary products from arginine include:

• Urea
• Nitric oxide (NO)
• Creatine (and creatine phosphate/creatinine)
• Arginine phosphate Arginine also connects to ornithine and the polyamine pathway, producing putrescine, spermidine, and spermine; glutamate-γ-semialdehyde derived from ornithine can be converted to glutamate.

Arginine serves as a carrier of nitrogen atoms in urea biosynthesis; arginase cleaves arginine to form urea and ornithine, facilitating ammonia detoxification.

In the kidney, arginine and glycine react via arginine:glycine amidinotransferase (AGAT) to form guanidinoacetate (GAA) and ornithine. In the liver, GAA is methylated by guanidinoacetate N-methyltransferase (GAMT), using S-adenosylmethionine (SAM), to produce creatine.

Arginase converts arginine to ornithine; ornithine decarboxylase (ODC) decarboxylates ornithine to form putrescine. Putrescine is converted to spermidine and then to spermine by spermidine synthase and spermine synthase, using decarboxylated S-adenosylmethionine (dcSAM) as the aminopropyl donor.

Nitric oxide synthase (NOS) oxidizes arginine to produce nitric oxide (NO) and citrulline, using O2 and NADPH as cofactors.

Cysteine, pantothenate (vitamin B5), and adenosine are the components involved in coenzyme A biosynthesis.

Cysteine contributes to formation of 4-phosphopantothenoyl-cysteine during CoA biosynthesis and provides the thiol group essential for CoA's biochemical functions.

1. Cysteine dioxygenase converts cysteine to sulfinoalanine (requires O2 and Fe2+).
2. Sulfinoalanine decarboxylase decarboxylates sulfinoalanine to form hypotaurine (releasing CO2).
3. Hypotaurine is oxidized by hypotaurine dehydrogenase to form taurine, with NAD+ reduced to NADH.

Glycine conjugates with xenobiotics and endogenous metabolites to increase water solubility and facilitate excretion.

Decarboxylation of histidine produces histamine.

Histamine mediates allergic reactions and stimulates gastric acid secretion.

Major compounds derived from histidine include carnosine, ergothioneine, and anserine.

S-adenosylmethionine (SAM) is the major methyl-group donor in the body.

Hypermethioninemia is a clinical disorder associated with altered methionine metabolism.

Methionine is converted to S-adenosylmethionine (SAM). SAM is decarboxylated to decarboxylated SAM (dcSAM), which donates aminopropyl groups to putrescine to form spermidine and to spermidine to form spermine (enzymes: spermidine synthase, spermine synthase).

Serine participates in biosynthesis of sphingosine and provides one-carbon units for purine and pyrimidine synthesis.

Genetic defects in cystathionine ß-synthase result in homocystinuria.

The reaction is: Serine + Homocysteine → Cystathionine + H₂O.

Serotonin is a potent vasoconstrictor and stimulates smooth muscle contraction.

Melatonin regulates sleep-wake cycles.

In the adrenal medulla, tyrosine is converted to L-DOPA and then to dopamine; dopamine is converted to norepinephrine by dopamine β-hydroxylase. Norepinephrine is subsequently methylated by phenylethanolamine N-methyltransferase (PNMT) to form epinephrine in the adrenal medulla.

L-Phenylalanine → L-Tyrosine (phenylalanine hydroxylase) → L-DOPA → dopaquinone (tyrosinase-mediated steps). From dopaquinone: either conversion through DOPAchrome → DHICA → IQCA → Eumelanin, or addition of cysteine/GSH to form cysteinyldopa → benzothiazine intermediates → Pheomelanin. Reactive oxygen species (ROS) can be generated during several oxidation steps.

Tyrosine is a precursor of thyroid hormones such as Thyroxine (T4) and Triiodothyronine (T3).

Phosphoserine, phosphothreonine, and phosphotyrosine are involved in the phosphorylation and dephosphorylation of specific residues in proteins. This process regulates the activity of certain enzymes involved in lipid and carbohydrate metabolism, as well as proteins that participate in signal transduction cascades.

1. From dimethylglycine: dimethylglycine is converted to sarcosine by dimethylglycine dehydrogenase (one-carbon transfer pathways involving folate cofactors).

2. From glycine: glycine is methylated by glycine N-methyltransferase using S-adenosylmethionine (SAM) to produce sarcosine and S-adenosylhomocysteine.

Creatinine is formed in muscle through irreversible, nonenzymatic dehydration and loss of phosphate from creatine phosphate.

The formation of creatine involves the amino acids glycine, arginine, and methionine.

ẞ-Alanine is present in combined form in coenzyme A and in the ẞ-alanyl dipeptides carnosine, anserine, and homocarnosine.

ẞ-Alanine is formed during the catabolism of uracil, while ẞ-aminoisobutyrate is formed during the catabolism of thymine.

Disorders arise from defects in enzymes of the pyrimidine catabolic pathway.

The β-alanyl dipeptides carnosine and anserine (N-methyl-carnosine) have several important functions:

1. Activate myosin ATPase - This enhances muscle contraction efficiency.
2. Chelate copper - They bind to copper ions, which can help in regulating copper levels in the body.
3. Enhance copper uptake - They facilitate the absorption of copper, which is essential for various physiological processes.

GABA functions as an inhibitory neurotransmitter in brain tissue.

The metabolism of γ-aminobutyrate starts with L-Glutamate.

The products of the metabolism of γ-aminobutyrate include γ-Hydroxybutyrate, Succinate semialdehyde, Succinate, and α-Ketoglutarate.

The enzyme responsible for this conversion is L-Glutamate decarboxylase.

The amino acid precursor is tryptophan, which is the precursor for serotonin synthesis.

Key enzymes:

1. Tryptophan hydroxylase – converts tryptophan to 5-hydroxytryptophan (5-HTP).
2. Aromatic L-amino acid decarboxylase (AAAD) – converts 5-HTP to serotonin (5-HT).

(for catabolism) Monoamine oxidase A (MAO-A) oxidatively deaminates serotonin to 5-hydroxyindoleacetaldehyde, which is further converted to 5-hydroxyindoleacetic acid (5-HIAA).

Clinical correlations include:

• Depression and anxiety disorders: Low levels of serotonin are linked to mood disorders.
• Serotonin syndrome: A potentially life-threatening condition caused by excessive serotonin activity.
• Irritable bowel syndrome (IBS): Altered serotonin levels can affect gut motility and function.

Glycolysis occurs in the cytosol. Gluconeogenesis uses both mitochondrial and cytosolic compartments — pyruvate is converted to oxaloacetate in mitochondria (pyruvate carboxylase), oxaloacetate is converted to PEP either in mitochondria (mitochondrial PEPCK) or after transport to cytosol (cytosolic PEPCK), and later gluconeogenic steps occur in the cytosol.

Fatty acid synthesis occurs primarily in the cytosol (with later elongation/desaturation in the endoplasmic reticulum). Fatty acid β-oxidation occurs mainly in the mitochondrial matrix; very-long-chain fatty acids are first shortened in peroxisomes before mitochondrial β-oxidation.