Protein Metabolism PDF

Protein Metabolism By Eklavya & Rokas With all the guidance by Dr. Mohammed Mansour Map of Metabolism 3  Protein Catabolism Core Deamination Concepts Urea Cycle Synthesis of Non-Essential Amino Acids Protein Catabolism Can...

Protein Metabolism By Eklavya & Rokas With all the guidance by Dr. Mohammed Mansour Map of Metabolism 3  Protein Catabolism Core Deamination Concepts Urea Cycle Synthesis of Non-Essential Amino Acids Protein Catabolism Can you think of some functions that proteins do in the body? Different Proteins in the body: Any Questions? Deamination/ Transamination Urea Cycle Urea Cycle: Overview Approx. 90% of nitrogen in urine is in the form of urea. One nitrogen of urea derived from ammonia, the other from aspartate. ✓ (both nitrogens from glutamate, from oxidative deamination and transamination, respectively.) CO2 provides C and O of urea. Urea is produced in the liver and transported to kidney for excretion in urine.  Distribution of N-containing compounds in urine Urea 86% Creatinine 5% NH4+ 3% Other 6%  The Urea Cycle Converts toxic NH3 to non-toxic urea Takes place in liver Partly mitochondrial (2 reactions) & partly cytosolic (3 reactions) Requires two nitrogen atoms:- One of the N atoms of urea is donated by ammonia (GDH & Glutaminase) the second N atom is donated by aspartate 7  Urea Cycle Reactions 1. Carbamoyl Phosphate Synthetase I (CPSI) 5. Arginase 4. Argininosuccinate Malate Lyase 2. Ornithine Transcarbamoylase Oxaloacetate Requires hydrolysis of 4 high energy bonds Gluconeogenesis 3. Argininosuccinate Synthetase -ketoglutarate Glutamate 8  Step 1: Formation of carbamoyl phosphate Catalyzed by mitochondrial carbamoyl phosphate synthetase I (CPS I) Rate-limiting step 2 ATPs needed to combine ammonia (from oxidative deamination) and CO2 to form carbamoyl phosphate. Requires N-acetyl glutamate as allosteric activator  Step 2: Formation of citrulline Catalyzed by mitochondrial ornithine transcarbamoylase. combines ornithine and carbamoyl phosphate. release of high-energy phosphate drives reaction citrulline is transported to the cytoplasm.  Step 3: Synthesis of arginosuccinate catalyzed by arginosuccinate synthase citrulline condenses with aspartate to form arginosuccinate source of second nitrogen atom in urea requires ATP, the third and final ATP needed for urea synthesis  Step 4: Cleavage of arginosuccinate catalyzed by arginosuccinate lyase forms fumarate and arginine. fumarate can be used to make malate (and glucose),or aspartate via oxaloacetate. arginine is the immediate precursor of urea. Step 5: Cleavage of arginine to urea and ornithine catalyzed by arginase. arginase only found in liver. Fate of Urea urea is transported to the kidney where it is excreted in urine. small part of urea is converted to NH3 and CO2 in the intestine by bacterial urease → NH3 excreted in feces In kidney failure, this becomes a significant source of hyperammonemia. Treatment with neomycin decreases urease-producing bacteria. Overall stoichiometry of urea cycle: Aspartate + NH3 + 3 ATP urea + 2 Pi + 2 ADP + Ppi + AMP 4 high energy P-bonds are consumed Flow of nitrogen from amino acids to urea. Positive feedback on Urea Cycle. 1. Regulation of CPS1 by N-acetylglutamate Synthesis of N-acetylglutamate dependent on [GLU]. Synthesis of N-acetylglutamate is stimulated by ARG (produced by urea cycle) 2. Regulation by substrate concentration (a.a.) The rate of NH4 + production 3. Induction (synthesis) of the cycle enzymes with increase in protein metabolism Fasting & high-protein diet Increased gene expression Liver has a large capacity to dispose of NH + 4 Importance of Urea Cycle: Overview of Nitrogen Metabolism Any Questions? Amino Acid Anabolism What do you think, energy will be produced or used? Process of Transamination in Amino Acid anabolism: Protein Synthesis: Protein Synthesis: Explanation Replication: In this Process, the DNA makes its exact copy which is crucial to pass the genes that contains specific codes for the protein. Transcription: Transcription is the first step in gene expression, where the DNA sequence of a gene is copied into a messenger RNA (mRNA) molecule. This mRNA molecule then carries the genetic information from the DNA to the ribosomes, where it is translated into a protein. Translation: Do you remember the location where these events happen inside the cell? Location of Events: Formation of Proteins: Synthesis of Non- Essential Amino Acids The body uses around 150 different amino acids but only 20 amino acids of which 9 are essential are used to produce between 80,000 and 400,000 distinct proteins across the body (depending on differing definitions of a new protein). These can come from our diet from sources such as meat, seafood, poultry, eggs and dairy as well as being anabolized(built up) but the essential amino acids can't The World Health Organization recommends a minimum daily intake for a health adult per kg of body weight Alanine Arginine (semi-essential, essential for children) Asparagine Aspartic acid Cysteine Glutamic acid Glutamine Glycine Histidine (essential) 10mg Isoleucine (essential) 20mg Leucine (essential) 39mg Lysine (essential) 30mg Methionine (essential) 10.4mg Phenylalanine (essential) 25mg Proline Serine Threonine (essential) 15mg Tryptophan (essential) 4mg Tyrosine Valine (essential) 26mg  Alanine Arginine (semi- Asparagine Aspartic acid -CH3 essential, essential for -CH₂CONH₂ -CH₂COO⁻ (Non-Polar, Hydrophobic) children) (Polar, Uncharged) (Negatively Charged) (CH₂)₃NHC(NH₂)₂⁺ (guanidino group) (Positively Charged) Cysteine Glutamic acid Glutamine Glycine -CH₂SH -CH₂CH₂COO⁻ -CH₂CH₂CONH₂ -H (Polar, Uncharged) (Negatively Charged) (Polar, Uncharged) (Non-Polar, Hydrophobic) Histidine (essential) 10mg Isoleucine (essential) 20mg Leucine (essential) 39mg Lysine (essential) 30mg CH₂(C₃H₃N₂) (imidazole -CH(CH₃)CH₂CH₃ -CH₂CH(CH₃)₂ (CH₂)₄NH₃⁺ ring, can carry a positive (Non-Polar, Hydrophobic) (Non-Polar, Hydrophobic) (Positively Charged) charge depending on pH) (Positively Charged) Methionine (essential) 10.4mg Phenylalanine (essential) 25m Proline Serine -CH₂CH₂SCH₃ g -(CH₂)₃ -CH₂OH (Non-Polar, Hydrophobic) -CH₂(C₆H₅) (benzene (Non-Polar, Hydrophobic) (Polar, Uncharged) ring, aromatic) (Non-Polar, Hydrophobic) Threonine (essential) 15mg Tryptophan (essential) 4mg Tyrosine Valine (essential) 26mg -CH(OH)CH₃ -CH₂(C₈H₆N) (indole ring) CH₂(C₆H₄OH) (phenol ring) -CH(CH3)2 (Polar, Uncharged) (Non-Polar, Hydrophobic) (Polar) (Non-Polar, Hydrophobic) Protein synthesis occurs in hepatocytes cells that make up 80% of the liver mass, taking intermediaries from the glycolytic and Krebs cycle(also know as citric acid cycle or tricarboxylic acid(TSA) cycle) specific molecules act as precursors to specific amino acids as well as provided the energy demand of anabolism. α-ketoglutarate is the precursor for the Biosynthetic Family of Glutamine; Glutamine, Proline and Argine. aspartate transaminase is the catalysis that allows the reaction α-Ketoglutarate + L-aspartate ⇌ Glutamate + Oxaloacetate undergoing transamination, the process of transferring an amino group. It uses the presence of Pyridoxal Phosphate(an active form of vitamin B6) as a co-factor to single for the reaction to occur in the direction of anabolism. Removing the alpha amino group from L-aspartate to form the keto acid Oxaloacetate, the group is transferred to the keto acid α-Ketoglutarate forming the amino acid Glutamate. Glutamate + NH3 + ATP → Glutamine + ADP + Pi To further convert to Glutamine, the enzyme Glutamine Synthetase hydrolyzes an ATP releasing a phosphate which provides the energy required to add Ammonia to Glutamate forming Glutamine. To further convert to Proline(cyclized derivative of glutamate) the enzyme glutamate kinase hydrolyzes an ATP releasing a phosphate and the Glutamate undergoes phosphorylation adding a phosphate to the gamma (γ) position of the side chain forming γ-Glutamyl Phosphate, overall undergoing the reaction Glutamate + ATP → γ-Glutamyl Phosphate + ADP + Pi which goes onto the reaction γ-Glutamyl Phosphate + NADPH + H+ → Proline + Pi + NADP+ where γ-Glutamyl Phosphate Reductase facilitates addition of electrons from NADPH and protons are added to the γ-Glutamyl Phosphate forming Proline, the oxidized NADPH leaves NADP+ as a byproduct To further convert to Argine contributing to the beginning of the Urea cycle, the Proline is oxidized by Proline Dehydrogenase releasing 2 electrons breaks the ring structure into pyrroline-5-carboxylate which bonds is unstable and spontaneously converted to glutamate, NAD accepts the electrons reducing it through the overall reaction of Proline + NAD + → Glutamate + NADH + H+ Then continues to the reaction Ornithine + Carbamoyl Phosphate → Citrulline + Pi. ornithine transcarbamylase transfers the carbamoyl group (NH₂-CO) from the carbamoyl phosphate to ornithine forming citrulline leaving behind a phosphate. Arginosuccinate catalyzes the formation of a high-energy bond between citrulline and aspartate in the reaction Citrulline + Aspartate + ATP → Arginosuccinate + AMP + PPi. Finally, Arginosuccinate Lyase splits Arginosuccinate into Arginine + Fumarate without needing any additional energy