Protein and Amino Acid Metabolism PDF

Proteins with short half-lives (< 30 mins) usually have PEST sequences Metabolism of amino acids → comprises a wide array of synthetic and which target them for rapid degradation degradati...

Proteins with short half-lives (< 30 mins) usually have PEST sequences Metabolism of amino acids → comprises a wide array of synthetic and which target them for rapid degradation degradative reactions by which amino acids are: o Regions rich in the amino acids Proline (P), Glutamate (E), Serine (S), o Assembled as precursors of polypeptides or other compounds and Threonine (T) o Broken down to recover metabolic energy Proteins with half-lives over 100 hours include Aldolase, Lactate Chemical transformations of amino acids are distinct from those of Dehydrogenase, and Cytochromes carbohydrates or lipids they involve the element Nitrogen o Aldolase is an enzyme in the Glycolytic Pathway – the enzyme that Bulk of the cell’s amino acid are incorporated into proteins Constantly splits Fructose 1,6-bisphosphate to Glyceraldehyde-3-Phosphate and being synthesized and degraded Dihydroxyacetone Phosphate There is no true storage form of amino acids analogous to glycogen or o Lactate Dehydrogenase is also in Glycolysis – the enzyme that converts triacylglycerols (TAGs) Pyruvate to Lactate and vice versa Mammals: o Cytochromes are involved in Electron Transport Chain o Synthesize certain amino acids The most rapidly degraded enzymes all occupy important metabolic o Obtain the rest from their diet or from food they eat control points, whereas the relatively stable enzymes have nearly constant Excess dietary amino acids: catalytic activities under all physiological conditions o Not simply excreted o All enzymes which are considered to be Rate-Limiting or Committed o Is converted to common metabolites: Enzymes have very short half-life → Glucose The rate of protein degradation in a cell varies with its nutritional and hormonal state → Fatty Acids o Example: under conditions of nutritional depravation, cells increase → Ketone Bodies their rate of protein degradation so as to provide the necessary nutrients for indispensable metabolic processes o This is because amino acids can be converted to glucose when the Amino Acid 3-Letter Code 1-Letter Code blood sugar is too low → Gluconeogenesis Alanine Ala A Cysteine Cys C Aspartic Acid / Aspartate Asp D Glutamic Acid / Glutamate Glu E Phenylalanine Phe F 1. Lysosomal Degradation Glycine Gly G o Lysosomes have a selective pathway, which is activated only after a Histidine His H prolonged fast, that imports and degrades cytosolic proteins Isoleucine Ile I containing the pentapeptide KFERQ (Lys-Phe-Glu-Arg-Gln) or a closely Lysine Lys K related sequenced Leucine Leu L 2. Ubiquitin Methionine Met M o Proteins are marked for degradation by covalently linking them to Asparagine Asn N ubiquitin Proline Pro P o Whether or not a given protein is derivatized by ubiquitin depends on Glutamine Gln Q which aminoacyl residue is present at its amino terminal (N-Terminal) Arginine Arg R Serine Ser S o Reaction with ubiquitin is retarded by amino terminal methionyl or Threonine Thr T seryl residue and is accelerated by amino terminal aspartyl or arginyl Valine Val V residues Tryptophan Trp W Tyrosine Tyr Y Is the continuous degradation and resynthesis of all cellular proteins It is a key physiologic process in all forms of life Each day, humans turn over 1-2% of their total body proteins, principally muscle proteins (200 to 300 g/day) o 75-80% → Percentage of amino acids reutilized for new protein synthesis (recycle) o 20-25% → Percentage of nitrogen that is converted to urea Urea is the final product of protein metabolism o The amount of Urea that you excrete is directly proportional to the amount of protein that you eat, that is assuming that your liver is functioning normally The carbon skeletons are then degraded to amphibolic intermediates The susceptibility of a protein to degradation is expressed as its Half-Life o How fast a protein can undergo degradation o It is the time required to reduce its concentration to 50% of its initial value Half-lives for liver proteins range from under 30 minutes to over 150 hours (6-7 days) Page 1 of 7  This is the overall scheme for Protein Metabolism in the body. You have What happens to these amino acids once they reach the liver? your collection of amino acids coming from 2 Sources: The most important is for these amino acids to be used for protein Exogenous – refers to the Dietary Proteins synthesis o What is your daily protein requirement? 1 gram per kg of the ideal Used for synthesis of Nitrogen-containing compounds body weight → Approx. 70 g/day The liver also acts as a central supplier of amino acids to other organs Endogenous – within the body It is also in the liver that you synthesize the Non-Essential Amino Acids o This comes from the amino acids that are synthesized in the body, If any amino acids are not used, it will undergo catabolism the so called “Non-Essential Amino Acids” and it also comes from the amino acids coming from the degradation of tissue proteins o Remember that there is a Protein Turnover, so you have amino acids coming from those proteins that undergo degradation Where do you use amino acids? Cannot be synthesized by the body so they must be provided in the diet The most important function of amino acids is for you to use them in Mnemonics: PVT TIM HALL Protein Synthesis Essential Amino Acids o You must synthesize all the proteins that your body needs P Phenylalanine T Tryptophan H Histidine o First, you synthesize Collagen, which is the most abundant protein V Valine I Isoleucine A Arginine in the body L Leucine T Threonine M Methionine o Next, you synthesize Hemoglobin, Plasma Proteins, and Enzymes L Lysine You also need amino acids to synthesize the Essential Non-Protein Nitrogenous Substances If all the 10 Essential Amino Acids are present in the protein, the protein is o These are substances that are not protein but you r equire amino called a Complete Protein or Protein of High Biological Value acids to synthesize them o Complete Protein o Example: → Can sustain life → Purines and Pyrimidines → Example: milk, meat, eggs → Porphyrins (Heme) – Glycine + Succinyl CoA are the → That’s why if babies drink milk alone, they can still live and grow precursors for Heme Synthesis because it is a Complete Protein → Some vitamins also require amino acids If one or more of the Essential Amino Acids are lacking in a protein → ✓ Folic Acid contains Glutamic Acid Incomplete Protein → Creatine is a tripeptide o Incomplete Protein ✓ 3 Amino Acids: Gly-Arg-Met → Cannot sustain life by itself → Glutathione is a tripeptide → Examples: ✓ 3 Amino Acids: Gly-Cys-Glu ✓ Fruits ✓ Vegetables If an amino acid is not used, it will undergo degradation or catabolism. You ✓ Cereals do not store amino acids. ✓ Oryzenin → found in rice Different ways to catabolize amino acids: ✓ Zein → found in corn (lacks Tryptophan) o Transamination o Limiting Amino Acid – amino acid that is lacking in an Incomplete o Deamination Protein o Decarboxylation, etc. Among this 10 Essential Amino Acids, 1 is considered to be Semi-Essential and that is Arginine o You can produce it in your body but you still have to provide it in your diet Protein o It satisfies both definitions → Semi-Essential or Conditionally Essential Synthesis Can be synthesized by the body so they need not be provided in the diet Includes all amino acids not included under Essential Amino Acids Synthesis of Synthesis of N- non-essential ctg amino acids Compounds Which is more important in synthesizing protein? They are equally important. Do not put in mind that Essential Amino Acids Liver are more important than the Non-Essential Amino Acids when synthesizing proteins. When you are synthesizing proteins, all the necessary amino acids must be there, whether it may be Essential or Non-Essential. When one of them is Catabolism of Delivery to other organs lacking, you cannot synthesize the protein. The phrase “Essential vs. Non- both C-Chain and of a balance mixture of Essential” only refers to their presence in the diet. They are Essential in the N of amino acids amino acids diet because you cannot synthesize them. They are Not Essential in the diet because you could synthesize them. This does not pertain to their role in protein synthesis. A protein will not be synthesized unless all the necessary After absorption, the amino acids will go to the liver amino acids are there The liver plays a central role in Amino Acid Metabolism since all of the amino acids are metabolized in the liver There are 3 amino acids that are not metabolized in the liver: Glutamate Dehydrogenase o Valine, Leucine, Isoleucine – branched chain amino acids o Used to synthesize Glutamic Acids o They are metabolized in the brain and muscles Glutamine Synthetase o Used to synthesize Glutamine Aminotransferases / Transaminases o These are the enzymes that are used for Transamination o Can be used to synthesize many other amino acids Page 2 of 7 The combined effect of these 3 enzymes is to transform Ammonium ion into Example: the Alpha-Amino Nitrogen of various amino acids An amino acid has 3 3. D-Amino Acid Oxidase reactive parts: → You only have 2 D-Amino Acids: D-Aspartate and D-Serine Amino Group → We do not use the D-Amino Acid Oxidase Carboxyl Group R Group If you remove these groups one by one then you are catabolizing an Manifested by: Abnormal neural development, generalized amino acid. aminoaciduria, absence of peroxisomes in a liver biopsy The aminoaciduria is due to deficient L-Amino Acid Oxidase activity A. Removal of the Alpha-Amino Group (α-NH2) 1. Oxidative Deamination 2. Transamination Overall Reaction: 3. Non-Oxidative Deamination Amino Acid Keto Acid + NH3 B. Decarboxylation o Removal of Carboxyl Group Enzymes Involved: C. Oxygenation 1. Amino Acid Dehydrases o Add oxygen o Example: add O2 to Phe → converted to Tyrosine D. One-Carbon Transfer o Removal of R Group α → Requires B6PO4 (Pyridoxal Phosphate / Vitamin B6 Phosphate) as cofactor Overall Reaction: → Hydroxyl Amino Acids (Serine, Threonine, Tyrosine, Amino Acid Keto Acid + NH3 Homoserine) 2. Amino Acid Desulfhydrases Enzymes Involved: 1. Glutamate Dehydrogenase – Glu is the only amino acid that undergoes Oxidative Deamination at an appreciable rate in mammalian tissues → Most active enzyme for Oxidative Deamination → It converts Glutamic Acid to Alpha-Ketoglutarate + NH4 (Ammonia) → Requires B6PO4 (Pyridoxal Phosphate / Vitamin B6 Phosphate) → The Keto Acid that you derive from the catabolism of as cofactor Glutamic Acid is α-Ketoglutarate → Sulfur-containing Amino Acids (Cysteine, Homocysteine, → Since Glutamate Dehydrogenase is the most active enzyme, Methionine) it follows that Glutamic Acid is the most metabolically active amino acid Enzyme: Transaminase or Aminotransferase General Reaction: → If you reverse the reaction, you will get the Amino Acid using the same enzyme (Glutamate Dehydrogenase) ✓ Ex. Keto Acid + Ammonia = Amino Acid ✓ Because Alpha-Ketoglutarate is used again to accept the Example: Amino Group to convert it back to an Amino Acid, Alpha- o Enzyme: Aspartate Ketoglutarate is the most active amino group acceptor. Aminotransferase or Glutamate-Oxaloacetate 2. L-Amino Acid Oxidase Transaminase → Remember that in your body, your amino acids are L-Amino o Co-enzyme: Acids → Pyridoxal Phosphate → LAA converts Aspartic Acid to Oxaloacetate and Alanine to (Vit.B6) Pyruvate and Glycine to Glyoxylic Acid → Carrier between the amino acid and the keto acids Amino Acids that do not undergo Transamination: Lysine, Threonine, Proline, OHProline Page 3 of 7  For Transamination, the general reaction is that you’re going to transfer the Amino Group of an Amino Acid to a Keto Acid. Recall that Keto Acids do not One way to catabolize amino acid is by have Amino Groups so it will readily accept an Amino Group from the Amino removing the R-Group. If you remove Acid. the R-Group, it is no longer an amino When you transfer the amino group of Amino Acid 1 to Keto Acid 1 → Amino acid, it is what you call one carbon Acid 1 will become Keto Acid 2 and Keto Acid 1 will become Amino Acid 2 transfer Every time that you’re doing transamination, you are going to produce a New Keto Acid and a New Amino Acid. In oxygenation, you are not going The new amino acid that you’re going to form depends upon what keto acid to remove anything. You are just will accept the amino group. going to add O2 o Example: In the given example above, if you change Alpha- Example: When you add O2 to Ketoglutarate to Pyruvate, the new amino acid will be Alanine Phenylalanine, it will be converted to Tyrosine However, in Transamination, more often than not, the one that is used to accept the amino group is Alpha-Ketoglutarate o α-Ketoglutarate is referred to as the major amino group acceptor in transamination The major difference between the general reaction in transamination and oxidative and non-oxidative deamination is that in transamination you do The body produces ammonia whether we like it or not because the not see ammonia being released. different catabolic pathways can produce ammonia → Our body is equipped with fighting mechanism The body prefers to do transamination because the body does not want 1. Reversal of the Glutamate Dehydrogenase Reaction ammonia to accumulate since it is toxic when ammonia accumulates 2. Glutamine Formation 3. Urea Formation 4. Asparagine Formation Manifestations: o Initially, you will have nausea and headache which will progress to vomiting o Eventually, there will be blurring of vision, slurring of speech o Convulsive seizures o Unconsciousness o Comatose → Death Ammonia may be toxic to the brain in part because it reacts with α- ketoglutarate to form glutamate. The resulting depletion of levels of Alpha-Ketoglutarate + Ammonia → convert it back to Glutamic Acid α-ketoglutarate then impairs function of the tricarboxylic acid (TCA) You are using the NH3 to convert the keto acid back to the amino acid cycle in neurons Glutamine Formation is the major means by Removal of the Alpha-Carboxyl which the brain detoxifies ammonia Group → Released as CO2 Whenever ammonia reaches the brain, the Amino Group + Alpha-Carbon + brain combines it with Glutamic Acid, Hydrogen + R Group = Amine converting it to Glutamine using the enzyme Decarboxylation → produces Glutamine Synthetase CO2 and an Amine from the The Glutamine that is formed in the brain will Amino Acid be brought to the kidneys and once it reaches Leads to the formation of the kidneys, the reaction will be reversed Biogenic Amines Glutamine will be converted back to Glutamic Examples: Acid and Ammonia using the enzyme o Serotonin or 5-hydroxytryptamine – Tryptophan Glutaminase → Neurotransmitter, Vasoconstrictor Because this reversal happens in the kidneys, o Histamine – Histidine the ammonia now can be released directly into → Substance released when you have allergies the urine o Catecholamines → Dopamine, Norepinephrine, Epinephrine – Tyrosine and Phenylalanine What is the major source of ammonia excreted in → Epinephrine the urine? Glutamine ✓ Activates muscle Adenylyl Cyclase ✓ Stimulates synthesis of cAMP ✓ Promotes Glycogen breakdown → Dopamine ✓ Deficiency in Dopamine Production = associated with Parkinson’s Disease → degenerative condition cause Asparagine Formation is similar to Glutamine Formation, you just change “shaking palsy” Glutamic Acid to Aspartic Acid and you will form Asparagine → GABA Uses the enzyme Asparagine Synthetase ✓ One of the brain’s major inhibitory neurotransmitter Page 4 of 7  Urea Formation is the major means by which the liver detoxifies ammonia Happens inside the Mitochondria In as much as the catabolism of amino acid takes place primarily in the liver, 2 Moles of ATP + CO2 + Ammonia + H2O Urea Formation is the most active way of detoxifying ammonia among all → reacts to form Carbamoyl these 4 ways. Phosphate Enzyme: Carbamoyl PO4 Synthetase I (CPS I) Differences between CPS I and CPS II CPS I CPS II Urea Cycle Pyrimidine Biosynthesis Ammonia as Nitrogen Donor Glutamine as Nitrogen Donor Mitochondria Cytosol Requires N-Acetyl Glutamic Acid as Does not require N-AGA as its activator activator Ornithine reacts with Carbamoyl Phosphate → produce Citrulline Enzyme: Ornithine Transcarbamoylase Note that in the 2nd reaction, Ornithine came from the cytosol and enters the mitochondria using a transporter → Ornithine Transporter Gene Urea Cycle is also called Krebs-Henseleit Cycle The ammonia deposited in the mitochondria of hepatocytes is converted to urea through the urea cycle Urea production occurs in the liver It has 2 compartments: cytosol and mitochondria o Like Gluconeogenesis, it also involves both cytosol and mitochondria o Heme Synthesis Normal Human Adult is in Nitrogen Balance → the amount of nitrogen ingested each day (mainly in the form of dietary protein) is equal to the amount of nitrogen excreted Major nitrogenous excretory product Synthesized almost exclusively in the liver Serves as the disposal form of ammonia → Toxic particularly to the brain and CNS o Normally, little ammonia is present in the blood Concentration ranges between 30 and 60 μm Ammonia is rapidly removed from the blood Converted to urea by the Citrulline gets out from the mitochondria to the cytosol → reacts with one liver or more ammonia in the form of Aspartic Acid, along with 1 ATP to form Argininosuccinate Enzyme: Argnininosuccinate Synthetase 1. Carbamoyl PO4 Synthetase I Note that the 2nd ammonia that enters the Urea Cycle is in the form of 2. Ornithine Transcarbamoylase Aspartic Acid – not as free ammonia 3. Argininosuccinate Synthetase 4. Argininosuccinase 5. Arginase Page 5 of 7  Argininosuccinate is cleaved to form If you want to stimulate or inhibit the pathway, you stimulate or inhibit Fumarate and Arginine the control enzymes Enzyme: Argininosuccinase Recall: Arginine can be synthesized in the body through the Urea Cycle Because it is a gene, there could be a mutation of that transporter gene thereby destroying its function Syndrome wherein Ornithine Transporter Gene undergoes mutation → If that happens, there will be no Ornithine that will enter the Urea Cycle → There will be no step 2 of the Urea Cycle → Urea Cycle stops after the 1st step What happens if the Urea Cycle stops? o Ammonia accumulates (instead of ammonia being converted to Urea, it will now accumulate) leading to Hyperammonemia → Accumulation of Ammonia in the blood Because Ornithine cannot enter the mitochondria, it will accumulate → Hyperornithinemia → Increased level of Ornithine in the blood The Citrulline will come out in the urine → Homocitrullinuria Due to mutation of the Ornithine Transporter Gene (ORNT1) 3 Manifestations: o Hyperammonemia o Hyperornithinemia o Homocitrullinuria Results from mutation of the ORNT1 gene that encodes the mitochondrial membrane Ornithine Transporter. Failure to import cytosolic Ornithine into the mitochondrial matrix renders the Urea Cycle inoperable with consequent hyperammonemia and the accumulation of cytosolic Ornithine results in hyperornithinemia Arginine is immediately converted to Urea and Ornithine Enzyme: Arginase Ornithine is transported back to mitochondria to begin another cycle In the 4th Reaction, Argininosuccinate is cleaved to form Fumarate and Urea is excreted in the urine Arginine The more protein that you eat, the more Urea that you are going to excrete Arginine can be synthesized in the body through the Urea Cycle – Non- o Increase Urine Volume = because it is a diuretic Essential o Increase Specific Gravity = because it is solid o Arginine that is synthesized in the Urea Cycle is immediately converted to Urea and Ornithine Urea is the final end product of protein metabolism in the body and it is o It does not stay long as Arginine in the body. excreted in the urine. The amount of Urea you excrete depends on how If you need Arginine to be used for Protein Synthesis, you must have much protein you eat. Arginine provided in the diet (Essential) – that is why it is considered as Urea is a diuretic so when you go on a high protein diet, expect that there “Semi-Essential Amino Acid” would be an increase in urine volume because you will have a high urea excretion. Urea is solid, the specific gravity of urine will also go up. None, you do not produce ATPs, you only use it. 2 ATPs used in the 1st step 1 ATP used in the 3rd step o ATP here is converted to AMP + PPi o Usually, when ATP undergoes hydrolysis, the products are ADP + Pi but in here, the products are AMP + PPi o The PPi should be further converted to 2 Pi and that will require 1 In the 4th Reaction, Argininosuccinate is cleaved to form Fumarate and more ATP Arginine o Total of ATPs used in the 3rd Reaction → 2 ATPs Fumarate is an intermediate of the Krebs Cycle Total of 4 ATPs used per turn of the Urea Cycle Krebs Cycle can be linked to Urea Cycle through Fumarate → Krebs Bicycle / Aspartate-Argininosuccinate Shunt 1st Step: 1 ammonia enters 3rd Step: 1 ammonia enters Total of 2 ammonias are detoxified per turn of the Urea Cycle 1. 1st Step – Carbamoyl Phosphate Synthetase I 2. 2nd Step – Ornithine Transcarbamoylase 3. 5th Step – Arginase Page 6 of 7  Remember that the only reason why α-KG is being used up is to produce If any of the enzymes are deficient, you now produce the so-called Inborn Glutamic Acid. Errors of Urea Cycle So, if there is an external source for Glutamic Acid, then there is no need for Enzymes are deficient → Urea Cycle will stop → Ammonia accumulates → your brain to use up all the α-KG in the body. Hyperammonemia Inborn Error Enzyme Deficient Hyperammonemia Type 1 Carbamoyl Phosphate Synthetase I Aims of Treatment Hyperammonemia Type 2 Ornithine Transcarbamoylase o Elimination or treatment of precipitating factors Citrullinemia Argininosuccinate Synthetase o Lowering of blood NH3 levels by decreasing absorption of proteins and nitrogenous products from the intestine Argininosuccinate Aciduria Argininosuccinase Arginemia Arginase Modes of Therapy o Low Protein Diet All of them are manifested by Hyperammonemia → leading to Ammonia → Limit protein intake → ammonia comes from protein Intoxication → You cannot totally stop taking protein → remember that there are important proteins that our body must synthesize Severe Liver Disease → You need proteins for your hemoglobin, plasma proteins, It is in the liver where you have Urea Formation enzymes, etc → that is why you cannot stop eating protein Among all the ways by which your body detoxifies ammonia, Urea o Administration of Lactulose (Levulose) Formation is the most active → If you have liver diseases, urea formation → Lactulose / Levulose → prevent absorption of ammonia in the will stop → Urea Cycle stops → NH3 accumulates in the liver → NH3 gets GI Tract out in the systemic circulation to the different parts of the body → reaches → Ammonia is not absorbed → excreted in the stool the brain. Brain detoxifies NH3 through Glutamine Formation → Glutamine goes to o Oral Administration of Antibiotics the kidneys, reversed back to Glu and NH3 → NH3 is excreted through the → Bacteria in the GI tract → Harmless → Normal Flora →Do not urine. produce disease → However, the normal bacteria in the intestines produces In Severe Liver Diseases, the ammonia that enters the brain will be too ammonia through fermentation. So as not to produce much. Until such time, your Glutamic Acid will be all used up. What will the ammonia, might as well kill them by giving antibiotics brain do now? → Antibiotics here is not for infection → Given to kill the bacteria Too much NH3 going to the brain → Glu will all be used up → brain will that produces ammonia convert α-KG to Glu o Binding Compounds The source of α-KG is the Krebs Cycle → Krebs Cycle will be depleted of α- → You have to remove excess ammonia by giving binding compounds. These are compounds that can bind to amino acids KG → Krebs Cycle will stop → ATP formation stops → Comatose → Remember: For every amino acid, there is always an ammonia This is the reason why it is so easy to go into coma when you have severe in it. So, when you bind that amino acid and excrete it through liver diseases. This is exactly the way you die when you have Hepatitis B. the urine, it is like excreting one ammonia per amino acid Most common deficiency involving Urea Cycle Enzymes Mental retardation and death often result Gene for ornithine transcarbamoylase is on X chromosome → Males generally are more seriously affected than heterozygotic females Ammonia and amino acids in blood is increased Orotic Acid also increased o Presumably due to Carbamoyl Phosphate that cannot be used to form Citrulline diffuses to the cytosol → Condenses with Aspartate → Form Orotic Acid 1. To limit protein intake and potential build up of ammonia o Limit ingestions of amino acids o Give Levulose to promote excretion of ammonia in feces o Give Antibiotics to kill NH3-producing bacteria 2. To remove excess ammonia o Give binding compounds that bind covalently to amino acids and produce N-containing molecules that are excreted in the urine o Example: → Benzoate + Glycine = Hippuric Acid → Phenylacetate + Glutamine = Phenylacetylglutamine 3. Replace any intermediates missing from the Urea Cycle o Best treatment Reason for Comatose would be α-KG depletion. In order to reverse this, you have to replace α-KG. However, there is no external source of α-KG that you can get and the best to give is Glutamic Acid. Page 7 of 7