Biochemistry of GIT Module PDF

# Biochemistry of GIT ## Protein Metabolism 1. Protein Metabolism 2. Nucleotide Metabolism 3. Vitamins and Minerals ### The Genius in Biochemistry Dr. Mohamed Agha 2024-2025 ## Protein Metabolism ### **Contents** - Introduction - Nitrogen Balance - General Metabolism of proteins - Metabolism of Amm...

# Biochemistry of GIT ## Protein Metabolism 1. Protein Metabolism 2. Nucleotide Metabolism 3. Vitamins and Minerals ### The Genius in Biochemistry Dr. Mohamed Agha 2024-2025 ## Protein Metabolism ### **Contents** - Introduction - Nitrogen Balance - General Metabolism of proteins - Metabolism of Ammonia - Krebs urea cycle - Ammoniacal Encephalopathy - Metabolic fate of carbon skeleton of amino acids - Glycine - Serine - Alanine - Phenylalanine/Tyrosine - Tryptophan ### **Protein Metabolism** - Blood amino acid level is 3 – 6 mg/dl in fasting & rises 2 - 3 mg after protein meal. - 300 gm proteins (mainly muscle proteins) are degraded daily to amino acids. - Amino Acids share in Anabolic & Catabolic pathways:- - **Anabolic pathways:** - Formation of tissue protein for wear and tear. - Plasma proteins, Hb, Enzymes, Hormones. - Non Proteins Nitrogenous compounds «NPN» as Purines, Pyrimidines, Creatine and Thyroxine. - **Catabolic pathways:** - Urea → formed in the Liver → Main catabolic End product of protein catabolism. - Supplying Energy → 1gm protein → 4.1 Kcal, only if there is shortage in CHO and fats. ### **Nitrogen Balance** - There is no storage (depot) of protein, but there is a certain percentage of protein that undergoes breakdown & resynthesis (Turn over). - This is a normal process and essential feature of Nitrogen Balance. ### **Nitrogen Balance:** - Difference between total nitrogen intake (Dietary proteins) and total nitrogen loss (undigested protein in stools + urea and Ammonia in urine). - Also nitrogen output through nails, hairs, and desquamated skin. 1. **Nitrogen Equilibrium:** - N₂ losses (in urines & sweat) = N₂ intake (Diet). 2. **Positive Nitrogen Balance:** - Increased N2 intake over the output. - Occur in growth, pregnancy or convalescence from diseases. 3. **Negative Nitrogen Balance:** - N2 intake less than N2 output due to: - Decreased N2 intake as in starvation, poverty, malnutrition, maldigestion, malabsorption, severe vomiting and severe diarrhea. - Increased N2 output as in hemorrhage, burns, old age or debilitating diseases. ### **General Metabolism of Proteins** - Major pathway of amino acid excess after protein synthesis is removal of Amino group (Deamination) → a-Keto Acid + Free Ammonia → converted to Urea in Liver → Excreted by kidney. - Liver is the major site for the removal of amino group from amino acids. - Amino group is removed by different Mechanisms:- - **Major Process:** - Transdeamination (Transamination + Oxidative deamination by L- Glutamate Dehydrogenase) - **Minor Process:** - Oxidative Deamination by D- & L-Amino Acid Oxidase. - Non Oxidative Deamination. (specific for individual amino acids) ### **Transamination:** - Enzymes termed Transaminases which transfer NH2 from amino acid to a- keto Acid. - All amino acids can participate in transamination **Except Threonine, Lysine, Proline and Hydroxy Proline.** (last 2 → Imino acids) - Vitamin B6 (PLP) is required as a coenzyme. (intermediate carrier of NH2) - Pyridoxal Phosphate + NH₂ → Pyridoxamine Phosphate. - They are cytosolic and Mitochondrial Enzymes. - It is a freely Reversible process. - After protein meal → Transfer NH2 to a-Keto Glutarate. - Deficient protein meal → Transfer NH2 to a-Keto Acid → Amino acid. - Most transaminases require Glutamate and a-Keto Glutarate as one of the reacting pair → all can be called Glutamate Transaminase. - No uptake or release of free Ammonia. ### **Aspartate transaminase (AST=GOT)** - Aspartic Acid + a-Keto Glutarate → Oxaloacetate+ Glutamic acid - Enzyme found normally in Liver cells & to less extent in Cardiac and Skeletal muscles. - Non-functional plasma enzyme. - Its plasma Level increases in: - Chronic Liver diseases as Viral Hepatitis. - Skeletal Muscle damage or Myocardial Infarction. ### **Alanine transaminase (ALT=GPT)** - Alanine + a-Keto Glutarate → Pyruvate + Glutamic Acid - Enzyme found normally in Liver cells cytoplasm فقط - Non-functional plasma enzyme. - Its increase indicates Acute Liver cell damage as in Viral Hepatitis. ### **Biological importance of transamination:** 1. Synthesis of non-essential amino acids. 2. Degradation of most amino acids except Threonine, Lysine and Proline. 3. Formation of components (filling up reactions) of Citric Acid Cycle. 4. Diagnosis and Prognosis of some diseases. - Hepatitis → ↑↑ ALT & AST → But more ALT ↑↑↑↑. ### **L-Glutamate dehydrogenase** $COO^-$ $CH_2$ $CH_2$ $H-C-NH_2$ $COOH$ Glutamate $NAD(P)^+$ $NAD(P)H+H^+$ Glutamate dehydrogenase $COO^-$ $CH_2$ $CH_2$ $C=O$ $COOH$ a-Ketoglutarate $COO^-$ $CH_2$ $CH_2$ $C-NH_2$ $COOH$ Glutamate $H_2O$ $NH_3$ Glutamate dehydrogenase $H_2O$ $COO^-$ $CH_2$ $CH_2$ $C=O$ $COOH$ a-Ketoglutarate - The reaction is both Mitochondrial ($NAD^+$) and Cytoplasmic ($NADP^+$). - It occurs mainly in Liver and Kidney. - Glutamate is the major amino acid in blood & major $NH_3$ donor to A.A. - Allosteric Activators: Enzyme: ADP, GDP - Allosteric Inhibitors: ATP, GTP - It is Reversible reaction that function in: 1. Amino acid Catabolism (Mitochondria)as it transmits nitrogen from glutamate to urea in urea cycle. 2. Amino acid Anabolism (Cytoplasm) as it catalyzes amination of a-keto glutarate to form glutamate by free ammonia. ### **Trans Deamination (Major Deamination Pathway):** - Transamination followed by Oxidative Deamination. - The net conversion of amino acid to ammonia requires action of glutamate transaminase and L-glutamate dehydrogenase. $R-CH-COOH$ $NH_2$ L-Amino acid $NAD(P)H + NH_3$ $a-Ketoglutarate$ $R-C-COOH$ $O$ $a-Keto acid$ $NAD(P)+ + H_2O$ $L-Glutamate$ $Glutamate$ $dehydrogenase$ $Transaminase$ $(aminotransferase)$ $pyridoxal phosphate$ $enzyme$ ###**Minor Deamination:** - **Oxidative Deamination by Amino acid oxidases:** - Occur in Liver and Kidney. - It Includes Removal of Hydrogen (Oxidation) and $NH_3$ (Deamination). $D-Amino Acid$ $Plants & Cell wall of$ $Microorganism$ $a- keto Acid + NH_3$ $D-Amino Acid Oxidase$ $FAD$ $FADH_2$ $L-Amino Acid$ $a- keto Acid + NH_3$ $L-Amino Acid Oxidase$ $FMN$ $FMNH_2$ - FAD has limited natural occurrence in mammals & high activity. - FMN has high natural occurrence and low activity. $R--COOH$ $NH_2$ $a-Amino acid$ $L-Amino acid$ $oxidase$ $Flavin$ $R--C--COO^-$ $NH_2$ $L-Amino acid$ $oxidase$ $R--C--COO^-$ $O$ $a-lmino acid$ $H_2O$ $NH_3$ $a-Keto acid$ $Flavin-H_2$ $H_2O_2$ $O_2$ $Catalase$ $H_2O + 1/2 O_2$ ### **Non-oxidative (Direct or Specific) Deamination:** - Serine → Serine Dehydratase (PLP) → Pyruvate + NH3. - Threonine → Threonine Dehydratase (PLP) → a-Keto Butyrate + NII3. - Glycine → Glycine Cleavage System → CO2 + NH3. - Glycine → Glycine Oxidase → Glyoxylic Acid + NH3. - Cysteine → Cysteine Desulfhydrase → Pyruvate + NH3. - Homoserine → Homoserine Deaminase → a-Keto Glutarate + NH3. - Histidine → Histidase → Urocanic Acid + NH3. ### **Hydrolytic Deamination:** - Glutamine → Glutaminase → Glutamate + NH3. - Asparagine → Asparaginase → Aspartate + NH3. ### **Reductive Deamination:** - Amino acids → large intestine Bacteria (Putrefaction) → Organic acids. ## Metabolism of Ammonia <start_of_image> схемы Non-Oxidative Deamination Oxidative Deamination Glutamine 4% NH3 Glutaminase Renal Intestinal 90% Trans Deamination Intestinal Bacterial putrefaction on proteins, amino acids and Urea Urea in bile by Bacterial Urease Monoamines by MAO & Pyrimidines Purines New amino acid Excretion in urine up to 1g/24h Urea Traces in blood up to 100 µg/dL ### **Fates of Ammonia (Removal of Ammonia):** - **Anabolic:** 1. Amination of a- keto acid to from non-essential amino acids. 2. Synthesis of Purines, Pyrimidines and Amino Sugars. - **Catabolic and Excretory pathways:** - **In the Liver:** 1. Majority of $NH_3$ (90%) produce Urea in Liver by Urea cycle → Blood → Kidney → Urine. 2. Glutamine synthesis especially in Acidosis. - **In the Kidney:** 1. Excretion in Urine (40% of Urinary Ammonia). - **In Extra-renal tissues:** 1. Converted to Glutamine especially in Brain. 2. Glutamine → Blood → kidney → Renal - Glutaminase → Glutamic Acid + Ammonia (60% of Urinary Ammonia). - Glutaminase $COOH$ $HCNH_2$ $CH_2$ $CH_2$ $COOH$ $NH_3$ $Glutaminase$ $COOH$ $HCNH_2$ $CH_2$ $CH_2$ $CONH_2$ $GLUTAMATE$ $Glutamine Synthetase$ $ATP ADP$ $NH_3$ $GLUTAMINE$ ### **Ammonia Transport in Circulation** - Ammonia level in blood is very low due to: - Rapid removal of Ammonia from blood by Liver. - Many tissues as muscles release nitrogen as Glutamine and Alanine. - Ammonia is transported in circulation as Urea and Glutamine (Non-Toxic forms of Ammonia). - **Glutamine** - Amide of Glutamic Acid → Non-toxic storage and transport of $NH_3$. - Glutamine formation occurs in Muscle and Liver. - Major Mechanism of Ammonia removal from Brain. - Its blood level is higher than other amino acids (Transport Function). - Removed by Renal Glutaminase (Deaminated). $Kidney$ $H^+$ $glutaminase$ $Glutamine$ $NH_3$ $Glutamine$ $H_2O$ $Glutamine$ $synthetase$ $ATP$ $H_2O$ $Glutamate$ $Glutamate$ $H_2O$ $Glutamate$ $Bloodstream$ $Brain$ - **Urea** - The most important disposal form of Ammonia. - It is the major End product of Nitrogen (Protein) catabolism representing 90% of nitrogen Excreted. $CO_2$ $H_2N$ $C$ $NH_2$ $Free NH_3$ $Aspartate$ ### **Kerbs Urea Cycle (Krebs Hensleit Cycle)** - Urea is formed in Liver from 1 $CO_2$ + 2 $NH_3$ using 3 ATPs + Break 4 high energy bonds. - Urea is the only product in this cycle. Other intermediates are regenerated. - First 2 reactions → Mitochondria - Rest 3 reactions → Cytoplasmic $Urea$ $HO$ $CO_2 +NH_3$ $1 -2 ATP$ $N-Acetyl$ $Glutamate$ $2 ADP+Pi$ $Ornithine$ $Carbamoyl Phosphate$ $2$ $Arginine$ $Fumarate$ $4$ $Pi$ $Citrulline$ $Arginino Succinate$ $3$ $Aspartate$ $ATP$ $AMP + Pi$ 1. → Carbamoyl Phosphate Synthetase I 2. → Citrulline Synthase (Ornithine Trans Carbamoylase) 3. → Arginino Succinate Synthetase 4. → Arginino Succinase 5. → Arginase ### **Link between Krebs Urea Cycle & Krebs T.C.A (C.A.C):** 1. Fumarate is hydrated to Malate which is either: - Oxidized in C.A.C in mitochondria → Energy. - Oxidized in Cytosol to Oxaloacetate which is either: - Transaminated to Aspartate → Re-enter Urea Cycle. - Used in Glucose synthesis (by Gluconeogenesis GNG). 2. $CO_2$ used in Urea cycle comes from T.C.A. ### **N.B:** - 1st $NH_2$ comes from L-glutamic Acid by L-glutamate Dehydrogenase. - 2nd $NH_2$ comes from amino group of Aspartate. - Ornithine and Citrulline are amino acids in Urea Cycle, but not in tissue proteins (They have no codons on DNA). - ### **Short Term Regulation of Urea cycle:** 1. Carbamoyl Phosphate Synthetase I (rate limiting Enzyme). - Active only in the presence of N-Acetyl glutamate (Allosteric activator). 2. Excess $NH_3$ → stimulate Urea formation. 3. High Urea level inhibit CPS I (reaction 1), Ornithine Trans carbamoylase (reaction 2) and Arginase (reaction 5). 4. Arginine activates N-acetyl Glutamate synthase (Cytosol) → ↑↑ N-Acetyl glutamate → ↑↑↑ Urea. $N-Acetyl Glutamate Hydrolase$ $N-Acetyl Glutamate$ $Acetate + Glutamate.$ ### **Long Term Regulation of Urea cycle:** 1. Protein Free diet decreases enzymes Level. 2. Increase dietary protein or Starvation increase enzymes Level. ### **Glutamate importance in Urea cycle:** 1. Forms N-Acetyl Glutamate (Activator of CPS-I) 2. By L-Glutamate Dehydrogenase gives $NH_3$. 3. Glutamate & Oxaloacetate transamination → Aspartate. ### **Urea Fate:** 1. Liver Urea → Blood (10-50 mg/dL) → Kidney → Excreted in Urine. 2. Little Urea is excreted in sweat and bile. 3. Bile Urea → Bacterial Urease in intestine → $CO_2$ + $NH_3$. 4. Part of $NH_3$ is lost in feces & part is reabsorbed to liver to re-form Urea. | Organ | Site | CPS II | |-------------|-----------------------------|-------------------------------| | Liver only | Mitochondria | Widely distributed | | | | Cytoplasm | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |