this chapter looked at the synthesis and degradation of different amino acids (put in bold). first it introduced the cofactors involved in these reactions: transamination reactions (such as the reaction involving glutamate introduced in chapter 38) require pyridoxal phosphate (PLP), which bonds its aldehyde carbon to the amino nitrogen and allows for different reactions to occur. FH4 is another cofactor that is involved in one carbon exchanges. BH4 is a cofactor that is involved in ring hydroxylations.
there are several amino acids that can be derived from the glycolytic intermediate, 3-phosphoglycerate. these include serine, cysteine, and glycine. serine is formed by oxidation, transamination to phosphoserine, then removal of the phosphate to form serine. it degrades in a separate pathway to form pyruvate. serine can then be converted to glycine in a reaction that involves both PLP and FH4. cysteine is also derived from serine- serine combines with homocysteine to form cystathione, which forms cysteine (and also succinyl CoA by way of alpha-keto butyrate- to be explained later).
amino acids can also be synthesized to TCA cycle intermediates. in particular, oxaloacetate and alpha-ketoglutarate. as we saw in the urea cycle, oxaloacetate can be transaminated to aspartate, which can be further converted into asparagate. alpha-ketoglutarate can be converted to glutamate in the glutamate dehydrogenase reaction. glutamate can then be converted to glutamine, or it can be converted to glutamate 5-semialdehyde. this compound can be converted to proline, or ornithine. ornithine can then be used to fuel the urea cycle, which produces arginine.
there are also several amino acids that can supply TCA cycle intermediates (an anaplerotic reaction); in particular, the intermediate succinyl CoA. the first was mentioned above- the homocysteine that reacts with serine to form cysteine actually is derived from methionine. in the last step of the cysteine synthesis pathway, the intermediate cystathione cleaves into cysteine and alpha-ketobutyrate, which is converted into propionyl CoA, and ultimately succinyl CoA.
valine and isoleucine are two branched chain amino acids that can replenish succinyl CoA. they are both transaminated into keto acids, then oxidatively decarboxylated into acyl CoA. these are oxidized in a way similar to fatty acid beta oxidation, ultimately producing FADH2, NADH, and propionyl CoA, which is converted to succinyl CoA.
finally, there are amino acids which are "ketogenic"- they produce ketone bodies, either acetyl CoA or acetoacetate, in their degradation. this includes leucine, isoleucine, tyrosine, phenylalanine, threonine, and tryptophan. isoleucine, as mentioned above, produces both succinyl CoA and acetyl CoA in its degradation, whereas leucine only produces acetyl CoA. phenylalanine is converted to tyrosine, which then produces acetoacetate and fumarate in its degradation. finally, tryptophan is an amino acid that produces formate, acetyl CoA, and alanine in its degradation.
questions
cofactors...
1. what are the three cofactors involved in amino acid metabolism?
2. how does pyridoxal phosphate aid in amino acid reactions?
3. how is FH4 involved in amino acid reactions? what is it derived from?
4. how is BH4 involved in amino acid reactions?
amino acids derived from glycolysis...
5. what are the amino acids derived from intermediates of glycolysis?
6. describe the synthesis of serine from glycolytic intermediates.
7. describe the degradation of serine.
8. how is serine synthesis regulated?
9. how is glycine synthesized?
10. how does glycine relate to kidney stones?
cysteine...
11. describe the synthesis of cysteine.
12. describe the regulation of the synthesis of cysteine.
13. how is methionine involved in cysteine synthesis?
14. describe the degradation of cysteine.
15. how is alanine synthesized?
amino acids related to TCA cycle intermediates...
16. which TCA cycle intermediates can be used to synthesize amino acids?
17. which TCA intermediates can be replenished by anaplerotic reactions via amino acids?
18. explain the statement "glutamate can be both derived from glucose and converted to glucose".
19. what are the three enzymes in the body that can "fix" free ammonia?
20. why is glutaminase important in the kidney?
alpha keto glutarate derived amino acids...
21. describe the synthesis of proline.
22. how is arginine synthesized?
23. what is the enzyme that transaminates glutamate 5-semialdehyde into ornithine?
24. describe the synthesis of aspartate and asparagine.
amino acids that supply succinyl CoA...
25. which amino acids degrade to form succinyl CoA?
26. describe the degradation of methionine to succinyl CoA.
27. describe the degradation of threonine to succinyl CoA.
28. where does most branched chain amino acid oxidation occur?
29. how are the degradations of valine and isoleucine both anaplerotic and energy producing?
30. what does degradation of leucine form?
ketogenic amino acids...
31. what are the main ketogenic amino acids?
32. describe how phenylalanine can produce ketone bodies.
33. what does tryptophan degradation produce?
34. what does degradation of lysine form?
answers
1. pyridoxal phosphate (PLP) (see chapter 38), FH4, and BH4.
2. the N on the amino acids bind to the aldehyde carbon of the PLP and pulls electrons away from the alpha carbon on the amino acid, allowing for different reactions to occur.
3. FH4 is required to donate or accept one carbon groups. it is derived from the vitamin folate.
4. BH4 is important for ring hydroxylation reactions.
5. serine, glycine, cysteine, and alanine.
6. 3-phosphoglycerate is oxidized to 3-phosphohydroxypyruvate, by 3-pg dehydrogenase. 3-phosphohydroxypyruvate is then transaminated to phosphoserine. the phosphate from phosphoserine is then removed to form serine.
7. serine is transaminated to hydroxypyruvate. hydroxypyruvate is reduced and phosphorylated to form 2-phosphoglycerate, which then forms PEP and pyruvate.
8. when serine levels fall, higher levels of 3-phosphoglycerate dehydrogenase are induced, and inhibition of phosphoserine phosphatase by serine is relaxed.
9. the major pathway of glycine synthesis is a conversion of serine, involving FH4 and PLP. the minor pathway is through the degradation of threonine in an aldolase-like reaction.
10. glycine can be converted to glyoxalate, which can be oxidized to oxalate- the accumulation of which can cause kidney stones.
11. homocysteine combines with serine to form cystathione. cystathione is cleaved to form propionyl CoA (which is converted to succinyl CoA) and cysteine.
12. cysteine inhibits the cystathione synthase; thereby inhibiting its own production.
13. methionine, an essential amino acid, provides the sulfur for cysteine synthesis. if methionine is in short supply, cysteine can not be synthesized de novo and becomes an essential amino acid.
14. degradation of cysteine produces pyruvate, NH4, and sulfate.
15. alanine is synthesized from the transamination of pyruvate via alanine aminotransferase (ALT).
16. oxaloacetate, alpha-keto glutarate.
17. oxaloacetate, alpha-keto glutarate, succinyl CoA, fumarate.
18. glutamate is derived from alpha-ketoglutarate, which is derived from glucose via the TCA cycle. in the liver, it can be degraded back into alpha-ketoglutarate, which leads to the formation of malate, which produces glucose via gluconeogenesis.
19. carbamoyl phosphate synthetase I (first reaction from the urea cycle), glutamate dehydrogenase, and glutamine synthetase.
20. glutaminase catalyzes the release of NH3 from glutamine, which then is secreted into the renal tubules and is the basis of the ammonia buffer system which aids in the excretion of H+.
21. glutamate is reduced to glutamate 5-semialdehyde, which then spontaneously forms a cyclical structure. this is then reduced to proline.
22. glutamate 5-semialdehyde can be converted to ornithine via a transamination reaction. ornithine can then be used to fuel the urea cycle, which produces arginine.
23. ornithine aminotransferase.
24. aspartate is transaminated from oxaloacetate (see chapter 38 notes). aspartate can be converted to asparagine by aspargine synthetase.
25. methionine, valine, isoleucine, threonine.
26. see question 13. methionine is converted to S-adenhosylhomocysteine, which is converted to homocysteine, which combines with serine to form cystathione. cystathione cleaves to produce cysteine and alpha-keto butyrate, which can be converted to propionyl CoA and ultimately succinyl CoA.
27. threonine is converted to alpha-keto butyrate by a hydratase, using PLP as a cofactor. alpha-keto butyrate is converted to succinyl CoA in the same path as for methionine degradation to succinyl CoA.
28. in muscle.
29. in both degradation pathways, they are transaminated to the alpha keto acids, then oxidatively decarboxylated to acyl CoA's. at this point they are oxidized just like fatty acyl CoA's using beta oxidation, producing NADH, FADH2, and propionyl CoA, which can be converted to succinyl CoA. thus the NADH and FADH2 provides energy while the succinyl CoA replenishes the TCA cycle.
30. leucine, the third branched chain amino acid, does not form succinyl CoA- instead it just produces acetoacetate and acetyl CoA (and thus is "ketogenic")
31. phenylalanine, tyrosine, isoleucine, threonine, tryptophan.
32. phenylalanine is converted to tyrosine, which is ultimately converted into acetoacetate (a ketone body) and fumarate.
33. alanine, formate, and acetyl CoA.
34. acetyl CoA, and NADH, FADH2.
Showing posts with label amino acids. Show all posts
Showing posts with label amino acids. Show all posts
Thursday, February 19, 2009
Wednesday, February 18, 2009
biochem: mark's medical biochem chapter 38- urea cycle
this chapter looked at two aspects of nitrogen metabolism; the urea cycle in the liver, and supply of urea / nitrogen from different sources in the body.
the metabolism of amino acids releases carbon which can be used for ATP generation, as well as nitrogen in the form of NH4+/NH3. NH4+ is ammonium ion, which dissociates into NH3 and H+. at physiologic pH, NH4 predominates (it remains undissociated). NH4+/NH3 is toxic to the body and needs to be converted to urea in the liver; this chapter explains how the body transports nitrogen from amino acids to the liver for conversion in the urea cycle.
the most common reactions that frees nitrogen from amino acids are transamination reactions with glutamate. in this reaction, the amino group from the amino acid is transferred to an alpha keto-glutarate, forming glutamate and an alpha keto acid. glutamate can then receive another nitrogen and form glutamine, which is then released into the bloodstream. nitrogen in glutamine is one of the main transport mechanisms for nitrogen in the blood; the other is alanine, which is formed by transamination of pyruvate into alanine by glutamate.
glutamate is a crucial molecule which serves as an intermediate in several different pathways in nitrogen metabolism. in the glutamate dehydrogenase reaction, glutamate is oxidized to alpha-keto glutarate via the enzyme glutamate dehydrogenase, releasing NH4+ (basically the opposite of the transamination reaction without the transfer to an amino acid). the glutaminase reaction was mentioned above- the enzyme glutaminase cleaves glutamine into glutamate and NH4+. the opposite reaction, glutamine synthetase, creates glutamine from glutamate. thus glutamate can serve as both the nitrogen acceptor and the nitrogen donor, aiding in amino acid degradation as well as synthesis.
when the nitrogen in the form of glutamine or alanine reaches the liver, it is cleaved into carbon, which can be used for metabolism or gluconeogenesis, and nitrogen in the form of ammonia. in the mitochondria, the urea cycle begins:
1. ammonium combines with bicarbonate, forming carbamoyl phosphate via carbamoyl phosphate synthetase I
2. carbamoyl phosphate combines with mitochondrial ornithine, forming citrulline via ornithine transcarbamoylase.
3. citrulline is transported out of the mitochondria into the cytoplasm, where it combines with aspartate to form argininosuccinate via argininosuccinate synthetase.
4. argininosuccinate is cleaved by argininosuccinate lyase into arginine and fumarate.
5. arginine is then cleaved into urea and ornithine via arginase.
6. ornithine is transported back into the mitochondria in exchange for citrulline formed in step 2.
in step 4, the fumarate that is created can be acted upon by the same enzymes from the TCA cycle- fumarase catalyzes the hydration reaction to malate, which is then oxidized by malate dehydrogenase into oxaloacetate. oxaloacetate can then be transaminated into aspartate. thus the net result is the recycling of fumarate back into aspartate, where it can be reused in the urea cycle in step 3.
the urea cycle is regulated by a "feed forward" positive feedback mechanism in which the relative activity of the urea cycle is dependent of substrate availability. thus in conditions of high amino acid availability such as fasting or a high protein diet, more NH4 will be transported to the liver, and the urea cycle will be stimulated. another regulatory mechanism is the allosteric activation of CPSI, the enzyme in the first step of the urea cycle, by a protein NAG. NAG is synthesized in response to high arginine levels- when arginine levels are high, this indicates the need for the urea cycle to be activated further.
questions
1. what is the main way by which nitrogen is removed from amino acids in the body?
2. describe the formation of an alpha keto acid from an amino acid.
3. which amino acids do not undergo transamination reactions?
4. what is the cofactor in transamination reactions?
5. what is another way that nitrogen is removed from amino acids?
6. what is the relative concentration of ammonia to ammonium in the body and why?
7. which can cross cell membranes, ammonia or ammonium?
8. which reaction does glutamate dehydrogenase catalyze?
9. how is histidine deaminated?
10. how are serine and threonine deaminated?
11. how are glutamine and asparagine deaminated?
12. why is the deamination of glutamine important in the kidney?
13. what occurs in the brain and muscle that allows NH4+ to be released from amino acids?
14. how does glutamate aid in amino acid synthesis?
15. how does glutamate supply nitrogen to the urea cycle?
16. what are the two transporters of nitrogen in the blood?
17. how is alanine formed in the muscles?
18. what happens to alanine in the liver?
18b. what is the glucose alanine cycle and when is it used?
19. what does the enzyme glutamine synthetase do?
20. describe the production of glutamine in the tissues.
21. what is glutamine used for in the liver, intestines, and kidney?
urea cycle...
22. describe the first step of the urea cycle. where does it occur?
23. describe the formation of citrulline.
24. describe the transport of citrulline.
25. describe the formation of argininosuccinate.
26. describe the formation of fumarate and arginine.
27. how is fumarate recycled?
28. describe the formation of urea from arginine.
29. how is the urea cycle regulated?
30. describe the regulation of CPSI.
31. describe the regulation of the urea cycle via induction of urea cycle enzymes.
32. why is urinary excretion of urea high during fasting?
33. why does urea excretion decrease during prolonged fasting?
answers
1. through transamination reactions.
2. via a transamination reaction where the amino group from the amino acid is transferred to alpha keto-glutarate, which forms an alpha keto acid from the amino acid, and glutamate from the alpha keto glutarate.
3. lysine and threonine.
4. pyridoxal phosphate.
5. through the release of ammonia and ammonium.
6. about one hundred times more ammonium, because the pKa of the dissociation reaction (NH4+ -> NH3 + H+) is 9.3. this means that at pH 9.3, 50% of the NH4+ is dissociated into ammonia, but at the lower body pH of 7.4, most of the NH4+ is undissociated.
7. ammonia (recall the ammonia buffer system from the kidney)
8. the oxidative deamination of glutamate, producing ammonium and alpha keto glutarate.
9. directly deaminated to form NH4 and urocanate.
10. dehydration reactions that require pyridoxal phosphate as a cofactor and are catalyzed by serine dehydratase, releasing NH4+ in both cases. serine forms pyruvate, threonine forms alpha-ketobutyrate.
11. they both contain R group amides that may be released as NH4+ by deamidation.
12. because it produces ammonium, which is secreted directly into the renal tubules, which forms salts with metabolic acids and aids in their excretion.
13. the purine nucleotide cycle.
14. glutamate supplies nitrogen for amino acid synthesis; either from the glutamate dehydrogenase reaction or the transamination reaction. it then donates the amino group to an alpha keto acid to create an amino acid.
15. it supply nitrogen through NH4 produced in the glutamate dehydrogenase reaction, or it can transaminate oxaloacetate to aspartate, which then enters the urea cycle.
16. alanine and glutamine.
17. the metabolism of glucose in the muscles produces pyruvate, which can be transaminated by glutamate (see question 2) into alanine.
18. alanine is transaminated back to pyruvate, and the nitrogen will be used for urea synthesis. pyruvate can be used for gluconeogenesis and the glucose can be transported back to the muscles.
18b. the glucose/alanine cycle is the production of alanine via transamination of pyruvate in the muscles, and the breakdown of the alanine in the liver to ammonium and glucose. the cycle can take place in exercise, when the muscles "use blood borne glucose".
19. it is a cytoplasmic enzyme present in all cells that catalyzes the conversion of glutamate to glutamine.
20. in conditions of rapid amino acid degradation, glutamine is formed from glutamate via glutamine synthetase.
21. in the liver, glutamine is used in the urea cycle. in the intestines glutamine is used as fuel. in the kidney the NH4 released from glutamine degradations aids in excretion of metabolic salts.
22. in the mitochondria of liver and kidney cells: ammonium combines with bicarbonate and forms carbamoyl phosphate via CPSI and 2 ATP.
23. the carbomoyl phosphate formed in step one combines with ornithine to form citrulline, via ornithine transcarbamoylase.
24. citrulline is transported out of the mitochondria in exchange for cytoplasmic ornithine. =
25. citrulline in the cytoplasm combines with arginine (see question 15) to form argininosuccinate via argininosuccinate synthetase. this reactions costs 1 ATP
26. argininosuccinate is cleaved by argininosuccinate lyase to form fumarate and arginine.
27. fumarate is converted to malate via fumarase, which can be converted to oxaloacetate, which can then be transaminated to reform aspartate.
28. arginine is cleaved by arginine lyase into urea
29. by availability of substrates, regulation of CPSI, regulation of urea cycle enzymes.
30. high arginine levels stimulates NAG production from acetyl CoA, which activates CPSI.
31. during conditions of high protein metabolism (ie. high protein diet or fasting/starvation) causes urea cycle enzymes to be inducted.
32. because during fasting amino acids are used to supply substrates for gluconeogenesis; when an amino acid is converted to pyruvate, nitrogen is released and therefore excreted in the urine as urea.
33. during prolonged fasting ketone bodies are used for metabolism, sparing the need for amino acids as gluconeogenic precursors, which leads to less urea excretion.
the metabolism of amino acids releases carbon which can be used for ATP generation, as well as nitrogen in the form of NH4+/NH3. NH4+ is ammonium ion, which dissociates into NH3 and H+. at physiologic pH, NH4 predominates (it remains undissociated). NH4+/NH3 is toxic to the body and needs to be converted to urea in the liver; this chapter explains how the body transports nitrogen from amino acids to the liver for conversion in the urea cycle.
the most common reactions that frees nitrogen from amino acids are transamination reactions with glutamate. in this reaction, the amino group from the amino acid is transferred to an alpha keto-glutarate, forming glutamate and an alpha keto acid. glutamate can then receive another nitrogen and form glutamine, which is then released into the bloodstream. nitrogen in glutamine is one of the main transport mechanisms for nitrogen in the blood; the other is alanine, which is formed by transamination of pyruvate into alanine by glutamate.
glutamate is a crucial molecule which serves as an intermediate in several different pathways in nitrogen metabolism. in the glutamate dehydrogenase reaction, glutamate is oxidized to alpha-keto glutarate via the enzyme glutamate dehydrogenase, releasing NH4+ (basically the opposite of the transamination reaction without the transfer to an amino acid). the glutaminase reaction was mentioned above- the enzyme glutaminase cleaves glutamine into glutamate and NH4+. the opposite reaction, glutamine synthetase, creates glutamine from glutamate. thus glutamate can serve as both the nitrogen acceptor and the nitrogen donor, aiding in amino acid degradation as well as synthesis.
when the nitrogen in the form of glutamine or alanine reaches the liver, it is cleaved into carbon, which can be used for metabolism or gluconeogenesis, and nitrogen in the form of ammonia. in the mitochondria, the urea cycle begins:
1. ammonium combines with bicarbonate, forming carbamoyl phosphate via carbamoyl phosphate synthetase I
2. carbamoyl phosphate combines with mitochondrial ornithine, forming citrulline via ornithine transcarbamoylase.
3. citrulline is transported out of the mitochondria into the cytoplasm, where it combines with aspartate to form argininosuccinate via argininosuccinate synthetase.
4. argininosuccinate is cleaved by argininosuccinate lyase into arginine and fumarate.
5. arginine is then cleaved into urea and ornithine via arginase.
6. ornithine is transported back into the mitochondria in exchange for citrulline formed in step 2.
in step 4, the fumarate that is created can be acted upon by the same enzymes from the TCA cycle- fumarase catalyzes the hydration reaction to malate, which is then oxidized by malate dehydrogenase into oxaloacetate. oxaloacetate can then be transaminated into aspartate. thus the net result is the recycling of fumarate back into aspartate, where it can be reused in the urea cycle in step 3.
the urea cycle is regulated by a "feed forward" positive feedback mechanism in which the relative activity of the urea cycle is dependent of substrate availability. thus in conditions of high amino acid availability such as fasting or a high protein diet, more NH4 will be transported to the liver, and the urea cycle will be stimulated. another regulatory mechanism is the allosteric activation of CPSI, the enzyme in the first step of the urea cycle, by a protein NAG. NAG is synthesized in response to high arginine levels- when arginine levels are high, this indicates the need for the urea cycle to be activated further.
questions
1. what is the main way by which nitrogen is removed from amino acids in the body?
2. describe the formation of an alpha keto acid from an amino acid.
3. which amino acids do not undergo transamination reactions?
4. what is the cofactor in transamination reactions?
5. what is another way that nitrogen is removed from amino acids?
6. what is the relative concentration of ammonia to ammonium in the body and why?
7. which can cross cell membranes, ammonia or ammonium?
8. which reaction does glutamate dehydrogenase catalyze?
9. how is histidine deaminated?
10. how are serine and threonine deaminated?
11. how are glutamine and asparagine deaminated?
12. why is the deamination of glutamine important in the kidney?
13. what occurs in the brain and muscle that allows NH4+ to be released from amino acids?
14. how does glutamate aid in amino acid synthesis?
15. how does glutamate supply nitrogen to the urea cycle?
16. what are the two transporters of nitrogen in the blood?
17. how is alanine formed in the muscles?
18. what happens to alanine in the liver?
18b. what is the glucose alanine cycle and when is it used?
19. what does the enzyme glutamine synthetase do?
20. describe the production of glutamine in the tissues.
21. what is glutamine used for in the liver, intestines, and kidney?
urea cycle...
22. describe the first step of the urea cycle. where does it occur?
23. describe the formation of citrulline.
24. describe the transport of citrulline.
25. describe the formation of argininosuccinate.
26. describe the formation of fumarate and arginine.
27. how is fumarate recycled?
28. describe the formation of urea from arginine.
29. how is the urea cycle regulated?
30. describe the regulation of CPSI.
31. describe the regulation of the urea cycle via induction of urea cycle enzymes.
32. why is urinary excretion of urea high during fasting?
33. why does urea excretion decrease during prolonged fasting?
answers
1. through transamination reactions.
2. via a transamination reaction where the amino group from the amino acid is transferred to alpha keto-glutarate, which forms an alpha keto acid from the amino acid, and glutamate from the alpha keto glutarate.
3. lysine and threonine.
4. pyridoxal phosphate.
5. through the release of ammonia and ammonium.
6. about one hundred times more ammonium, because the pKa of the dissociation reaction (NH4+ -> NH3 + H+) is 9.3. this means that at pH 9.3, 50% of the NH4+ is dissociated into ammonia, but at the lower body pH of 7.4, most of the NH4+ is undissociated.
7. ammonia (recall the ammonia buffer system from the kidney)
8. the oxidative deamination of glutamate, producing ammonium and alpha keto glutarate.
9. directly deaminated to form NH4 and urocanate.
10. dehydration reactions that require pyridoxal phosphate as a cofactor and are catalyzed by serine dehydratase, releasing NH4+ in both cases. serine forms pyruvate, threonine forms alpha-ketobutyrate.
11. they both contain R group amides that may be released as NH4+ by deamidation.
12. because it produces ammonium, which is secreted directly into the renal tubules, which forms salts with metabolic acids and aids in their excretion.
13. the purine nucleotide cycle.
14. glutamate supplies nitrogen for amino acid synthesis; either from the glutamate dehydrogenase reaction or the transamination reaction. it then donates the amino group to an alpha keto acid to create an amino acid.
15. it supply nitrogen through NH4 produced in the glutamate dehydrogenase reaction, or it can transaminate oxaloacetate to aspartate, which then enters the urea cycle.
16. alanine and glutamine.
17. the metabolism of glucose in the muscles produces pyruvate, which can be transaminated by glutamate (see question 2) into alanine.
18. alanine is transaminated back to pyruvate, and the nitrogen will be used for urea synthesis. pyruvate can be used for gluconeogenesis and the glucose can be transported back to the muscles.
18b. the glucose/alanine cycle is the production of alanine via transamination of pyruvate in the muscles, and the breakdown of the alanine in the liver to ammonium and glucose. the cycle can take place in exercise, when the muscles "use blood borne glucose".
19. it is a cytoplasmic enzyme present in all cells that catalyzes the conversion of glutamate to glutamine.
20. in conditions of rapid amino acid degradation, glutamine is formed from glutamate via glutamine synthetase.
21. in the liver, glutamine is used in the urea cycle. in the intestines glutamine is used as fuel. in the kidney the NH4 released from glutamine degradations aids in excretion of metabolic salts.
22. in the mitochondria of liver and kidney cells: ammonium combines with bicarbonate and forms carbamoyl phosphate via CPSI and 2 ATP.
23. the carbomoyl phosphate formed in step one combines with ornithine to form citrulline, via ornithine transcarbamoylase.
24. citrulline is transported out of the mitochondria in exchange for cytoplasmic ornithine. =
25. citrulline in the cytoplasm combines with arginine (see question 15) to form argininosuccinate via argininosuccinate synthetase. this reactions costs 1 ATP
26. argininosuccinate is cleaved by argininosuccinate lyase to form fumarate and arginine.
27. fumarate is converted to malate via fumarase, which can be converted to oxaloacetate, which can then be transaminated to reform aspartate.
28. arginine is cleaved by arginine lyase into urea
29. by availability of substrates, regulation of CPSI, regulation of urea cycle enzymes.
30. high arginine levels stimulates NAG production from acetyl CoA, which activates CPSI.
31. during conditions of high protein metabolism (ie. high protein diet or fasting/starvation) causes urea cycle enzymes to be inducted.
32. because during fasting amino acids are used to supply substrates for gluconeogenesis; when an amino acid is converted to pyruvate, nitrogen is released and therefore excreted in the urine as urea.
33. during prolonged fasting ketone bodies are used for metabolism, sparing the need for amino acids as gluconeogenic precursors, which leads to less urea excretion.
Monday, February 16, 2009
biochem: mark's medical biochem chapter 37- protein digestion
this chapter looked at the digestion, absorption, and transport of proteins. digestion of proteins begins in the stomach, when the zymogen pepsinogen (recall that this is secreted by the parietal cells in the gastric pits) is autocatalytically cleaved to pepsin. pepsin works as an endopeptidase, randomly cleaving peptide bonds within the protein.
in the intestine, protein digestion continues with enzymes secreted from the pancreas, in zymogenic (inactive) form: trypsinogen, chymotrypsinogen, proelastase, procarboxypeptidase. trypsinogen is cleaved first by enteropeptidase into trypsin. trypsin both works to digest proteins directly by cleaving peptide bonds adjacent to carboxyl groups contained by arginine or lysine, and more importantly, it activates the other digestive enzymes.
it converts chymotrypsinogen to chymotrypsin, which then cleaves peptide bonds adjacent to carboxyl groups from acidic or hydrophobic amino acids. it converts proelastase to elastase, which then cleaves peptide bonds in elastin as well as those next to carboxyl groups contained by small chain amino acids such as alanine, glycine, and serine. finally, it activates carboxypeptidase from procarboxypeptidase, which acts an exopeptidase; cleaving amino acids one at a time from the outside edges of the protein fragments created by digestion via the other pancreatic enzymes.
in addition to pancreatic enzymes, the intestinal epithelial cells also contain protein digesting enzymes; these include aminopeptidases, which also act as exopeptidases, and intracellular peptidases, which break down protein fragments that have been absorbed by the enterocytes.
the amino acids produced from degradation of proteins are transported into enterocytes via Na+ cotransporters, similar to the glucose / Na+ cotransporters seen in carbohydrate digestion. these transporters are powered by the low Na+ concentration in the cells which is manufactured by the Na+/K+ pumps. thus amino acids are absorbed via secondary active transport- and then they diffuse out of the serosal side via facilitated transport proteins.
the "intracellular amino acid pool" is a measure of how much amino acid there is at any given moment within a cell. this is a dynamic balance between proteins acquired from the diet vs. the degradation of proteins. the "half life" of a protein refers to the point at which 50% of the protein has been degraded; proteins in muscle cells, digestive enzymes, or hemoglobin, are all examples of proteins which have a short half life and therefore a high "turnover" rate.
a few notes about intracellular protein digestion: cells can digest proteins by the process of "autophagy", in which proteins in extracellular vesicles fuse with lysosomes, which contain proteases which degrade the proteins into amino acids, which then are absorbed into the cytoplasm. another method of protein digestion is through the ubiquitin / proteasome pathway, in which ubiquitin is attached to proteins, "tagging" them for digestion via proteasomes, which are large barrel shaped proteins with multiple internal proteolytic sites.
questions
1. what form are the protein digesting enzymes secreted in?
2. where are parietal and chief cells located and what do they secrete?
3. how is pepsinogen activated?
4. describe the action of pepsin on proteins.
5. what are the zymogens that are secreted by the pancreas into the intestine?
6. describe trypsinogen's role in protein digestion in the intestine.
7. how is trypsinogen activated?
8. how does trypsin directly digest proteins?
9. describe the digestive action of chymotrypsin on proteins.
10. describe the digestive action of elastase on proteins.
11. describe the action of carboxypeptidase on proteins.
12. what is the difference between carboxypeptidase A and B?
13. where are aminopeptidases located and what do they do?
14. what are intracellular peptidases?
15. describe the transport of amino acids from the intestinal lumen into enterocytes.
16. describe the transport of amino acids from the enterocyte to the portal vein.
17. describe the diversity of amino acid transport proteins on the apical side of enterocytes.
18. how do amino acids get transported into cells of peripheral tissues?
19. in what way does transport and absorption of amino acids into peripheral tissues differ from that of carbohydrates?
20. what is the half life of a protein?
21. what are some examples of proteins that undergo extensive synthesis and degradation in the body?
22. how much of the cells lining the intestinal wall are replaced each day?
23. what percentage of proteins that are absorbed from the intestines are excreted?
24. what is autophagy?
25. which enzymes in lysosomes aid in protein digestion?
26. what is the ubiquitin-proteasoms pathway?
27. how does ubiquitin "tag" proteins?
28. what is a proteasome?
answers
1. zymogenic: an inactive, larger form of the enzyme that is activated by proteolytic cleavage once in the digestive tract.
2. in the gastric pits / epithelium of the stomach. parietal cells secrete HCl and chief cells secrete pepsinogen.
3. the acidity in the stomach allows pepsinogen to be cleaved to its active form, pepsin.
4. pepsin acts as an endopeptidase, cleaving peptide bonds at random intervals within the denatured protein.
5. trypsinogen, pepsinogen, proelastase, procarboxypeptidase.
6. trypsin (the activated form of trypsinogen) catalyzes the activation of the other pancreatic enzymes to their active forms, as well as directly aiding in the digestion of proteins.
7. through enteropeptidase.
8. trypsin cleaves peptide bonds adjacent to carboxyl groups that are provided by lysine or arginine.
9. chymotrypsin cleaves peptide bonds next to residues that contain hydrophobic or acidic amino acids.
10. elastase cleaves peptide bonds within elastase as well as bonds next to residues with small side chains (alanine, glycine, serine)
11. carboxypeptidase acts an exopeptidase, removing amino acids one at a time from the carboxyl end, from the smaller peptides resulting from breakdown of the other pancreatic enzymes mentioned above.
12. A preferentially cleaves hydrophobic amino acids while B preferentially cleaves basic amino acids.
13. they are located on the epithelial wall of the intestine and act as exopeptidases, removing one amino acid at a time.
14. the enzymes within cells that break down peptides which are absorbed.
15. a Na+/K+ pump in the enterocyte creates a low concentration of Na+ in the enterocyte. The resulting influx of Na+ is coupled with amino acid transport, this is called secondary active transport.
16. the amino acids in the enterocytes are transported into the portal vein via "facilitated transporters"
17. there are at least 6 such transport proteins which have overlapping specificities for different types of amino acids.
18. mainly through Na+ cotransporters.
19. amino acids are transported into cells mainly by Na+ cotransporters wheras in peripheral tissues carbohydrates are transported by facilitated transporters (recall the GLUT transporters). in the intestine and renal cells the absorption of both amino acids and carbohydrates are Na+ coupled.
20. the point at which 50% of the protein in a cell has been degraded.
21. hemoglobin, muscle proteins, digestive enzymes.
22. roughly 1/4th.
23. roughly 6%.
24. the process by which cells digest proteins using lysosomal enzymes.
25. the cathepin family of proteases.
26. a method of intracellular protein digestion using ubiquitin tagging and degradation via proteosomes.
27. by covalently binding to the epsilon-amino group of lysine residues.
28. a cylindrical 20S protein complex with multiple internal proteolytic sites.
in the intestine, protein digestion continues with enzymes secreted from the pancreas, in zymogenic (inactive) form: trypsinogen, chymotrypsinogen, proelastase, procarboxypeptidase. trypsinogen is cleaved first by enteropeptidase into trypsin. trypsin both works to digest proteins directly by cleaving peptide bonds adjacent to carboxyl groups contained by arginine or lysine, and more importantly, it activates the other digestive enzymes.
it converts chymotrypsinogen to chymotrypsin, which then cleaves peptide bonds adjacent to carboxyl groups from acidic or hydrophobic amino acids. it converts proelastase to elastase, which then cleaves peptide bonds in elastin as well as those next to carboxyl groups contained by small chain amino acids such as alanine, glycine, and serine. finally, it activates carboxypeptidase from procarboxypeptidase, which acts an exopeptidase; cleaving amino acids one at a time from the outside edges of the protein fragments created by digestion via the other pancreatic enzymes.
in addition to pancreatic enzymes, the intestinal epithelial cells also contain protein digesting enzymes; these include aminopeptidases, which also act as exopeptidases, and intracellular peptidases, which break down protein fragments that have been absorbed by the enterocytes.
the amino acids produced from degradation of proteins are transported into enterocytes via Na+ cotransporters, similar to the glucose / Na+ cotransporters seen in carbohydrate digestion. these transporters are powered by the low Na+ concentration in the cells which is manufactured by the Na+/K+ pumps. thus amino acids are absorbed via secondary active transport- and then they diffuse out of the serosal side via facilitated transport proteins.
the "intracellular amino acid pool" is a measure of how much amino acid there is at any given moment within a cell. this is a dynamic balance between proteins acquired from the diet vs. the degradation of proteins. the "half life" of a protein refers to the point at which 50% of the protein has been degraded; proteins in muscle cells, digestive enzymes, or hemoglobin, are all examples of proteins which have a short half life and therefore a high "turnover" rate.
a few notes about intracellular protein digestion: cells can digest proteins by the process of "autophagy", in which proteins in extracellular vesicles fuse with lysosomes, which contain proteases which degrade the proteins into amino acids, which then are absorbed into the cytoplasm. another method of protein digestion is through the ubiquitin / proteasome pathway, in which ubiquitin is attached to proteins, "tagging" them for digestion via proteasomes, which are large barrel shaped proteins with multiple internal proteolytic sites.
questions
1. what form are the protein digesting enzymes secreted in?
2. where are parietal and chief cells located and what do they secrete?
3. how is pepsinogen activated?
4. describe the action of pepsin on proteins.
5. what are the zymogens that are secreted by the pancreas into the intestine?
6. describe trypsinogen's role in protein digestion in the intestine.
7. how is trypsinogen activated?
8. how does trypsin directly digest proteins?
9. describe the digestive action of chymotrypsin on proteins.
10. describe the digestive action of elastase on proteins.
11. describe the action of carboxypeptidase on proteins.
12. what is the difference between carboxypeptidase A and B?
13. where are aminopeptidases located and what do they do?
14. what are intracellular peptidases?
15. describe the transport of amino acids from the intestinal lumen into enterocytes.
16. describe the transport of amino acids from the enterocyte to the portal vein.
17. describe the diversity of amino acid transport proteins on the apical side of enterocytes.
18. how do amino acids get transported into cells of peripheral tissues?
19. in what way does transport and absorption of amino acids into peripheral tissues differ from that of carbohydrates?
20. what is the half life of a protein?
21. what are some examples of proteins that undergo extensive synthesis and degradation in the body?
22. how much of the cells lining the intestinal wall are replaced each day?
23. what percentage of proteins that are absorbed from the intestines are excreted?
24. what is autophagy?
25. which enzymes in lysosomes aid in protein digestion?
26. what is the ubiquitin-proteasoms pathway?
27. how does ubiquitin "tag" proteins?
28. what is a proteasome?
answers
1. zymogenic: an inactive, larger form of the enzyme that is activated by proteolytic cleavage once in the digestive tract.
2. in the gastric pits / epithelium of the stomach. parietal cells secrete HCl and chief cells secrete pepsinogen.
3. the acidity in the stomach allows pepsinogen to be cleaved to its active form, pepsin.
4. pepsin acts as an endopeptidase, cleaving peptide bonds at random intervals within the denatured protein.
5. trypsinogen, pepsinogen, proelastase, procarboxypeptidase.
6. trypsin (the activated form of trypsinogen) catalyzes the activation of the other pancreatic enzymes to their active forms, as well as directly aiding in the digestion of proteins.
7. through enteropeptidase.
8. trypsin cleaves peptide bonds adjacent to carboxyl groups that are provided by lysine or arginine.
9. chymotrypsin cleaves peptide bonds next to residues that contain hydrophobic or acidic amino acids.
10. elastase cleaves peptide bonds within elastase as well as bonds next to residues with small side chains (alanine, glycine, serine)
11. carboxypeptidase acts an exopeptidase, removing amino acids one at a time from the carboxyl end, from the smaller peptides resulting from breakdown of the other pancreatic enzymes mentioned above.
12. A preferentially cleaves hydrophobic amino acids while B preferentially cleaves basic amino acids.
13. they are located on the epithelial wall of the intestine and act as exopeptidases, removing one amino acid at a time.
14. the enzymes within cells that break down peptides which are absorbed.
15. a Na+/K+ pump in the enterocyte creates a low concentration of Na+ in the enterocyte. The resulting influx of Na+ is coupled with amino acid transport, this is called secondary active transport.
16. the amino acids in the enterocytes are transported into the portal vein via "facilitated transporters"
17. there are at least 6 such transport proteins which have overlapping specificities for different types of amino acids.
18. mainly through Na+ cotransporters.
19. amino acids are transported into cells mainly by Na+ cotransporters wheras in peripheral tissues carbohydrates are transported by facilitated transporters (recall the GLUT transporters). in the intestine and renal cells the absorption of both amino acids and carbohydrates are Na+ coupled.
20. the point at which 50% of the protein in a cell has been degraded.
21. hemoglobin, muscle proteins, digestive enzymes.
22. roughly 1/4th.
23. roughly 6%.
24. the process by which cells digest proteins using lysosomal enzymes.
25. the cathepin family of proteases.
26. a method of intracellular protein digestion using ubiquitin tagging and degradation via proteosomes.
27. by covalently binding to the epsilon-amino group of lysine residues.
28. a cylindrical 20S protein complex with multiple internal proteolytic sites.
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