Ch 18 - Amino Acid Oxidation & Urea Production

Question 1

Q. 2: In animals and humans there are three different circumstances which will trigger the metabolic use of amino acids. Name those three.

Answer 1

1. During normal protein turnover some amino acids released from protein breakdown are not needed for the synthesis of new proteins.
2. When ingested amino acids exceeds the body’s requirement for protein synthesis, the surplus amino acids are catabolized (cannot be stored).
3. During starvation or uncontrolled diabetes mellitus, carbs are unavailable or improperly utilized, so cellular proteins are used as a fuel source.

Question 2

Q. 7: What is the name of the hormone which stimulates secretion of the inactive precursors (“zymogens”) of several enzymes? Which organ produces those “zymogens”.

Answer 2

Cholecystokinin - arrival of amino acids in the duodenum causes release.

Cholecystokinin stimulates secretion of several zymogens from the exocrine cells of the pancreas:

• Trypsinogen
• Chymotrypsinogen
• Procarboxypeptidases A & B

Question 3

Q. 8: Name the three important zymogens of produced and released by the pancreas and the proteolytic products of those. Why inactive precursors and not the final, active enzyme?

Answer 3

1. Trypsinogen –> trypsin
2. Chymotrypsinogen –> chymotrypsin
3. Procarboxypeptidases A and B –> carboxypeptidases A and B

Synthesis and secretion of enzymes as inactive precursors protects the exocrine cells of the pancreas from destructive proteolytic attack by the enzymes it is creating.

Question 4

Q. 9: During early protein catabolism in the small intestine, trypsinogen is converted to its active form, called ____________, by a proteolytic enzyme called ___________.

Answer 4

During early protein catabolism in the small intestine, trypsinogen is converted to its active form, called trypsin**, by a proteolytic enzyme called **enteropeptidase.

Question 5

Q. 10: After a protein-rich diet, the digested amino acids reach the ________. There the first step in the catabolism of most L-amino acids is the removal of the ________-amino groups by a class of enzymes called ___________.

Answer 5

After a protein-rich diet, the digested amino acids reach the liver**. There the first step in the catabolism of most L-amino acids is the removal of the **α-amino groups by a class of enzymes called aminotransferases (or transaminases).

Question 6

Q. 11: In physiological transamination reactions, the amino group is transferred to the alpha-carbon atom of _____________. The ultimate outcome of the numerous transamination reactions is to collect the amino groups from the ___+ different amino acids in the form of a “consensus amino acid” called ____________.

Answer 6

In physiological transamination reactions, the amino group is transferred to the alpha-carbon atom of α-ketoglutarate. The ultimate outcome of the numerous transamination reactions is to collect the amino groups from the ­20+ different amino acids in the form of a “consensus amino acid” called L-Glutamate.

Question 7

Q. 12: All aminotransferases share the same prosthetic group called _____________, which is the coenzyme form of ____________ , or vitamin ____.

Answer 7

All aminotransferases share the same prosthetic group called pyridoxal phosphate (PLP)**, which is the coenzyme form of **pyridoxine**, or vitamin **B₆.

Question 8

Q. 13: Pyridoxal phosphate functions as a coenzyme in many enzymes. What is its primary role in those enzymes? Which class of enzymes?

Answer 8

• PLP’s primary role is as an intermediate carrier of amino groups at the active site of aminotransferases. It transfers the α-amino group from an amino acid to the α-carbon of α-ketoglutarate.
• The class of enzymes known as aminotransferases all have pyridoxal phosphate (PLP) as a prosthetic group.

Question 9

Q. 15: What is the metabolic fate of the amino groups collected in the L-glutamate pool in the liver cells?

Answer 9

The amino groups must be removed via oxidative deamination from the glutamate to prepare them for excretion. Glutamate is transported from the cytosol into the mitochondria, where L-glutamate dehydrogenase catalyzes oxidative deamination.

Question 10

Q. 16: In hepatocytes, glutamate undergoes oxidative deamination which is catalyzed by an enzyme called ___________. Where is this enzyme located? Write down the chemical reaction catalyzed by this enzyme.

Answer 10

In hepatocytes, glutamate undergoes oxidative deamination which is catalyzed by an enzyme called L-glutamate dehydrogenase. Where is this enzyme located? Write down the chemical reaction catalyzed by this enzyme.

The mitochondrial matrix of hepatocytes.

L-glutamate + H2O + NAD(P)+ <–> α-ketoglutarate + NAD(P)H + NH4+

Question 11

Q. 17: Ammonia (NH₄⁺) is a highly toxic molecule for humans. In humans much of the free ammonia is converted to a nontoxic compound, called ____________________ before export from extrahepatic tissues into the blood and transport to the liver or kidneys. What is the name of the enzyme which produces this molecule? Which chemical reaction does it catalyze?

Answer 11

Ammonia (NH₄⁺) is a highly toxic molecule for humans. In humans much of the free ammonia is converted to a nontoxic compound, called glutamine before export from extrahepatic tissues into the blood and transport to the liver or kidneys. What is the name of the enzyme which produces this molecule? Which chemical reaction does it catalyze?

Glutamine synthetase, and it catalyzes the ATP-dependent condensation of glutamate with ammonia to yield glutamine.

Question 12

Q. 18: Name the enzymes which play an important diagnostic role in medicine and which give valuable information for a number of disease conditions. Increased levels of those enzymes in blood are an indicator of which conditions?

Answer 12

Alanine aminotransferase (ALT, aka glutamate-pyruvate transaminase, GPT) and aspartate amino transferase (AST, aka glutamate-oxaloacetate transaminase, GOT) are important in the diagnosis of heart and liver damage due to heart attack, drug toxicity, or infection. Increased levels of GPT and GOT in the blood indicate damage to heart or liver cells causing GPT and GOT to leak into the blood. Measurement of blood serum concentrations of these two aminotransferases by SGPT and SGOT tests can provide information concerning the severity of damage to those tissue areas. Tests for these enzymes are also important in determining chemical exposure to carbon tetrachloride, chloroform, and other industrial solvents because damaged liver cells leak these enzymes into the blood. Aminotransferases are useful in monitoring exposure to these chemicals because these enzymes have high activity in hepatocytes and can be detected in small amounts.

Question 13

Q. 20: Ammonia is highly toxic to cells, particularly to specialized cells of the brain called ___________. The most common way for cells to remove excess ammonia happens though the activity of two enzymes, called ___________________________ and __________________________. Write down the chemical reactions catalyzed by those two enzymes. What is the problem with the end product of this ammonia removing reaction?

Answer 13

Q. 20: Ammonia is highly toxic to cells, particularly to specialized cells of the brain called astrocytes. The most common way for cells to remove excess ammonia happens though the activity of two enzymes, called glutamate dehydrogenase and glutamine synthetase. Write down the chemical reactions catalyzed by those two enzymes.

High levels of NH₄⁺ lead to increased levels of glutamine, which acts as an osmotically active solute in astrocytes, triggering an uptake of water into the astrocytes in an attempt to maintain osmotic balance. This leads to swelling and cerebral edema.

Question 14

Q. 21: Which cells of ureotelic organisms are responsible for the conversion of ammonia into urea? In which organelle(s) or compartments do the chemical reactions of the urea cycle take place? Give some examples of ureotelic life forms.

Answer 14

In the mitochondria of hepatocytes. Ureotelic life forms include amphibians and mammals. Humans are ureotelic.

Question 15

Q. 22: Which of the following scientists worked out the details of the urea cycle in 1932?

A) Max Delbrueck

B) Otto Warburg

C) Hans Krebs

D) Kurt Henseleit

E) both, c and d

Answer 15

Q. 22: Which of the following scientists worked out the details of the urea cycle in 1932?

A) Max Delbrueck

B) Otto Warburg

C) Hans Krebs

D) Kurt Henseleit

E) both, c and d

Question 16

Q. 24: Due to its high cytotoxicity, NH₄⁺ delivered to or generated in the mitochondria of hepatocytes is immediately metabolized. Write down the chemical (net) equation of the first chemical reaction of the urea cycle. Which enzyme catalyzes this chemical reaction?

Answer 16

Carbamoyl phosphate synthetase I

Question 17

Q. 25: Carbamoyl phosphate is the _____ substrate of the urea cycle, which has _____ enzymatic steps.

Answer 17

Carbamoyl phosphate is the first substrate of the urea cycle, which has four enzymatic steps.

Question 18

Q. 26: Write down the first chemical reaction happening within the urea cycle. Which enzyme catalyzes this chemical reaction? Where does it take place?

Answer 18

Ornithine transcarbamoylase catalyzes the formation of citrulline from ornithine and carbamoyl phosphate. This reaction takes place in the mitochondrial matrix.

Question 19

Q. 27: In the second chemical reaction of the urea cycle, citrulline reacts with ______________ to form ___________________________. What is the name of the enzyme which catalyzes this chemical reaction? Where does it take place? Write down the overall chemical reaction below.

Answer 19

In the second chemical reaction of the urea cycle, citrulline reacts with aspartate to form argininosuccinate. What is the name of the enzyme which catalyzes this chemical reaction? Where does it take place? Write down the overall chemical reaction below.

Argininosuccinate synthetase catalyzes the condensation reaction in the cytosol.

Question 20

Q. 28: Write down the overall chemical reaction of step 3 of the urea cycle. Which enzyme catalyzes this step? Explain the metabolic fate of the products of this reaction.

Answer 20

Argininosuccinase catalyzes the cleavage of argininosuccinate. Fumarate enters the mitochondria to join the pool of citric acid cycle intermediates. Arginine continues on in the urea cycle and is cleaved by arginase to yield urea and ornithine.

Question 21

Q. 29: What is the last reaction of the urea cycle? Which enzyme catalyzes this chemical reaction?

Answer 21

The last reaction is the cleavage of arginine by arginase to yield urea and ornithine.

Question 22

Q. 31: Like all other metabolic pathways, the urea cycle is neatly regulated. What is the name of the regulated key enzyme of the urea cycle? What kind of regulation takes place? Which molecules inhibit and which ones activate the enzyme?

Answer 22

Carbamoyl phosphate synthetase I is allosterically regulated to adjust the flux through the urea cycle. The kind of regulation is allosteric activation, and N-acetylglutamate is the allosteric activator. N-acetylglutamate is synthesized from acetyl-CoA and glutamate by N-acetylglutamate synthase. Arginine is an activator of N-acetylglutamate synthase, so arginine is, therefore, also an activator of the urea cycle.

Question 23

Q. 32: Genetic defects affecting enzymes of the urea cycle can lead to life threatening hyperammonemia in humans. One common treatment of this condition is the careful administration of two aromatic compounds in the diet. Name those two. How do they help to lower the excessively high ammonia levels in those patients?

Answer 23

Benzoate and phenylbutyrate can help lower the level of ammonia in the blood. Benzoate plus coenzyme A combines to form benzoyl-CoA, which combines with glycine to form hippurate. This reaction uses up glycine, which must be replenished, and ammonia is taken up in the glycine synthase reaction, thus lowering excessively high ammonia. Phenylbutyrate converts to phenylacetate by β-oxidation, which then converts to phenylacetyl-CoA. Phenylacetyl-CoA combines with glutamine to form phenylacetylglutamine. This uses glutamine in the synthesis process, triggering more glutamine synthesis by glutamine synthetase in a reaction that takes up ammonia, thus lowering excessively high ammonia levels.

Question 24

Q. 33: Why is a protein-less diet NOT a feasible solution to treat patients with hyperammonemia?

Answer 24

A protein-free diet is not a viable treatment option for patients with hyperammonemia because humans are incapable of synthesizing 9 of the 20 common amino acids, and these essential amino acids must be consumed in the diet.

Question 25

Q. 34: How many of the 20 most important amino acids found in humans are considered to be essential? What does “essential” mean? How many of those are “basic” (chemically speaking) amino acids?

Answer 25

9 of the 20 most important amino acids are considered essential. “Essential” means the amino acid cannot be synthesized de novo, so it must be supplied in the diet. 2 of the 9 essential amino acids are basic: histidine and lysine.

Question 26

Q. 35: The pathways of amino acid catabolism are not nearly as active as glycolysis and fatty acid oxidation. They normally account for only __ % of the human body’s energy production.

Answer 26

The pathways of amino acid catabolism are not nearly as active as glycolysis and fatty acid oxidation. They normally account for only 10 – 15 % of the human body’s energy production.

Question 27

Q. 36: The catabolic pathways of the 20 amino acids converge to form only ____ major metabolic products, all of which enter the Krebs cycle at some point. What happens with these amino acids-derived products there? Discuss this finding with respect to the often claimed benefits of a high protein/low carb diet with respect to energy expenditure and weight loss.

Answer 27

The catabolic pathways of the 20 amino acids converge to form only six major metabolic products, all of which enter the Krebs cycle at some point. What happens with these amino acids-derived products there? Discuss this finding with respect to the often claimed benefits of a high protein/low carb diet with respect to energy expenditure and weight loss.

Question 28

Q. 37: All or part of the carbon skeletons of ___ amino acids are ultimately broken down to acetyl-CoA. ____ amino acids are converted to alpha-ketoglutarate, ____ to succinyl-CoA, ___ to fumarate, and two to oxaloacetate. Name the amino acids which are catabolized to fumarate.

Answer 28

All or part of the carbon skeletons of ­seven amino acids are ultimately broken down to acetyl-CoA. Five amino acids are converted to alpha-ketoglutarate, four to succinyl-CoA, two to fumarate, and two to oxaloacetate. Name the amino acids which are catabolized to fumarate.

Phenylalanine and Tyrosine.

Question 29

Q. 38: Parts or all of ___ amino acids are converted to pyruvate. What is the metabolic fate of pyruvate?

Answer 29

Parts or all of six amino acids are converted to pyruvate. What is the metabolic fate of pyruvate?

Pyruvate can be converted to either acetyl-CoA or oxaloacetate.

Question 30

Q. 39: Seven amino acids are degraded (entirely or in part) to acetyl-CoA. Name those. Why are they called ketogenic amino acids?

Answer 30

Leucine, Isoleucine, Lysine, Phenylalanine, Tryptophan, Tyrosine, and Threonine. They are called ketogenic amino acids because they are degraded (entirely or in part) to acetyl-CoA and/or acetoacetyl-CoA; acetyl-CoA and acetoacetyl-CoA can undergo conversion to ketone bodies in the liver. Acetoacetyl-CoA is converted to acetoacetate and then to acetone and β-hydroxybutyrate. Therefore, these amino acids are ketogenic because they can make ketone bodies.

Question 31

Q. 40: The amino acids that are catabolized to pyruvate, alpha-ketoglutarate, succinyl-CoA, fumarate, and/or oxaloacetate are often refereed to as ________ amino acids.

Answer 31

The amino acids that are catabolized to pyruvate, alpha-ketoglutarate, succinyl-CoA, fumarate, and/or oxaloacetate are often refereed to as glucogenic amino acids.

Question 32

Q. 41: Catabolism of amino acids is of particular importance in humans on a high-protein diet, in diabetics or during starvation. Which of the 20 amino acids - which is very common in human proteins - is of particular importance under those conditions? Why? Which foods are particularly rich in this amino acid?

Answer 32

Leucine. Leucine is an exclusively ketogenic amino acid, and it is very common in proteins; therefore, the degradation of leucine makes a significant contribution to ketogenesis under conditions of high-protein diet, diabetes mellitus, or starvation. Dietary sources of leucine include: whey protein, soybeans, beef, peanuts, fish, wheat germ, almonds, chicken, and oats.

Question 33

Q. 42: Amino acids not only undergo transamination reactions, but very often are chemically modified by another (quite common) type of reaction. Which one is it?

Answer 33

One-carbon transfers.

Question 34

Q. 43: Metabolic activities involving one carbon transfers, e.g. carboxylation, methylation, involve(s) which of the following cofactors (Multiple answers possible)? Write down the correct vitamin annotation.

A) biotin = vitamin ___

B) ascorbic acid = vitamin ___

C) tetrahydrofolate = vitamin ___

D) S-adenosylmethionine = vitamin ___

E) cobalamin = vitamin ___

Answer 34

A) biotin = vitamin B7

B) ascorbic acid = vitamin C

C) tetrahydrofolate = vitamin B9 – tetrahydrofolate is also called as H₄ folate, and folate is vitamin B₉

D) S-adenosylmethionine = vitamin ___ - adoMet (or SAMe) is not a vitamin, but coenzyme B₁₂ is required to regenerate methionine from homocysteine in the activated-methyl cycle.

E) cobalamin = vitamin B12

Question 35

Q. 44: What is the name of the oxidized form of tetrahydrofolate (H4 folate)? What type of vitamin is it for humans? Where can it be found naturally? Where in the human diet?

Answer 35

Folate. It is a B-vitamin for humans (specifically, B₉). Animals, including humans, cannot synthesize folate and, therefore, must obtain folate from their diet. However, all plants and fungi and certain bacteria can synthesize tetrahydrofolate (H₄ folate). Therefore, folate can be found as a natural part of the diet from sources like asparagus, spinach, lettuce, broccoli, and nuts, to name a few. Furthermore, the U.S. mandates the fortification of enriched breads, cereals, flours, and other grains, and this fortification includes folate.

Question 36

Q. 45: Formation of the cofactor S-adenosylmethionine is a rather unusual ATP consuming chemical reaction. Why? Which enzyme catalyzes this chemical reaction in cells? What is the biological function of this cofactor?

Answer 36

The nucleophilic sulfur atom of methionine attacks the 5’ carbon of the ribose moiety of ATP instead of attacking one of the phosphorous atoms. Thus, triphosphate is released, cleaved into P_i and PP_i, and PP_i is cleaved by inorganic pyrophosphatase. This reaction is catalyzed by methionine adenosyl transferase. The biological function of S-adenosylmethionine is methyl group transfers. One-carbon transfers are a common type of reaction in amino acid catabolism.

Question 37

Q. 46: Transfer of methyl group from S-adenosylmethionine to an acceptor molecule yields S-adenosylhomocysteine, which is subsequently broken down to ___________________ and adenosine.

Answer 37

Transfer of methyl group from S-adenosylmethionine to an acceptor molecule yields S-adenosylhomocysteine, which is subsequently broken down to homocysteine and adenosine.

Question 38

Q. 47: During the “activated methyl cycle”, regeneration of the important amino acid methionine requires the transfer of a ________ group to homocysteine in a reaction catalyzed by the enzyme ______________________.

Answer 38

During the “activated methyl cycle”, regeneration of the important amino acid methionine requires the transfer of a methyl group to homocysteine in a reaction catalyzed by the enzyme methionine synthase.

Question 39

Q. 48: What is the name of the cofactor(s) required by the mammalian methionine synthase enzyme which ultimately donate the methyl groups transferred by this enzyme? Outline the basic methyl group transfer sequence on this enzyme.

Answer 39

The mammalian methionine synthase uses N⁵-methyltetrahydrofolate, but the methyl group is first transferred to cobalamin (derived from coenzyme B₁₂) to form methylcobalamin as the methyl donor in methionine formation.

Question 40

Q. 49: There are ____ amino acids which are both ketogenic AND glucogenic. Explain. Which amino acids are those?

Answer 40

The carbon skeletons of six amino acids are converted in whole or in part to pyruvate. Pyruvate can be converted to either acetyl-CoA (a ketone body precursor) or oxaloacetate (a gluconeogenesis precursor). Therefore, amino acids broken down to pyruvate are ketogenic and glucogenic. They are Ala, Trp, Cys, Ser, Gly, and Thr.

Question 41

Q. 50: The essential amino acid leucine is catabolized to ____________________ involving ____ enzymatic steps. Why is it considered a ketogenic amino acid? Explain. Would it make sense if it is taken by some athletes as a performance enhancing supplement?

Answer 41

The essential amino acid leucine is catabolized to acetyl-CoA involving six enzymatic steps. Why is it considered a ketogenic amino acid? Explain. Would it make sense if it is taken by some athletes as a performance enhancing supplement?

Leucine is considered ketogenic because its primary metabolic end products are acetyl-CoA and acetoacetate, both of which are part of the ketogenic pathway.

Question 42

Q. 51: Even though glycine is the smallest of all amino acids, cells catabolize it using ___ different pathways. In one reaction, glycine is hydroxymethylated to _______. Which enzyme catalyzes this reaction? Which coenzymes/cofactors does this enzyme require?

Answer 42

Even though glycine is the smallest of all amino acids, cells catabolize it using three different pathways. In one reaction, glycine is hydroxymethylated to serine. Which enzyme catalyzes this reaction? Which coenzymes/cofactors does this enzyme require?

Glycine conversion to serine is catalyzed by serine hydroxymethyl transferase and requires the coenzymes tetrahydrofolate (H₄ folate) and pyridoxal phosphate (PLP).

Question 43

Q. 52: In a second pathway (which is dominant in humans), glycine undergoes oxidative cleavage to CO₂, ammonia , and a methylene group which is catalyzed by the enzyme _________. If this enzyme is defective, a severe condition called ________ is the consequence. What are the telltale signs and symptoms of this fatal disease? Explain the neurological effects of this disease.

Answer 43

In a second pathway (which is dominant in humans), glycine undergoes oxidative cleavage to CO₂, ammonia, and a methylene group which is catalyzed by the enzyme glycine cleavage enzyme. If this enzyme is defective, a severe condition called nonketotic hyperglycinemia is the consequence. What are the telltale signs and symptoms of this fatal disease? Explain the neurological effects of this disease.

Nonketotic hyperglycinemia (NKH) is characterized by high serum levels of glycine. Symptoms of NKH appear shortly after birth, and affected infants experience lethargy, feeding difficulties, hypotonia, jerking movements, problems breathing, profound intellectual disability, seizures, and early childhood death. Mutations in the AMT and GLDC genes cause NKH. The AMT and GLDC genes encode proteins that are part of the glycine cleavage enzyme, responsible for breaking down glycine into CO₂, NH₄⁺, and methylene. When this enzyme is defective, excess glycine builds up to toxic levels in organs such as the brain. Since glycine is an inhibitory neurotransmitter in the brain, this may partly explain the neurological effects of NKH.

Question 44

Q. 53: Most of the catabolism of amino acids takes place in the liver. However, ____ amino acids are oxidized in the cells of other organs. Name those amino acids. What is so unique about those three amino acids? In which organs are they catabolized?

Answer 44

Most of the catabolism of amino acids takes place in the liver. However, three amino acids are oxidized in the cells of other organs. Name those amino acids. What is so unique about those three amino acids? In which organs are they catabolized?

Leu, Ile, and Val are oxidized in extrahepatic tissues. These three amino acids are unique because they are branched-chain amino acids (BCAAs). They have an aliphatic sidechain with a branch. Lue, Ile, and Val are oxidized as fuels primarily in muscle, adipose, kidney, and brain tissue.

Question 45

Q. 54: Extrahepatic tissues contain an aminotransferase complex which is absent in the liver. This multi-subunit enzyme complex, called_______, catalyzes the oxidative decarboxylation of _________ amino acids. What are the end products of this enzyme? Which cofactors/coenzymes are need by this enzyme complex?

Answer 45

Extrahepatic tissues contain an aminotransferase complex which is absent in the liver. This multi-subunit enzyme complex, called branched-chain α-keto acid dehydrogenase complex, catalyzes the oxidative decarboxylation of branched-chain amino acids. What are the end products of this enzyme? Which cofactors/coenzymes are need by this enzyme complex?

The end products of the branched-chain α-keto acid dehydrogenase complex are acyl-CoA derivatives. This enzyme requires five cofactors: thiamine pyrophosphate (TPP), lipoate, FAD, NAD⁺, and CoA.

Question 46

Q. 1: What is the name of the enzymes which play an important role in the degradation of proteins to the metabolically usable amino acids?

Answer 46

Proteases are enzymes that catalyze proteolysis, the breakdown of proteins into smaller polypeptides or single amino acids.

Question 47

Q. 4: In humans, most of the amino acids are derived from dietary protein. The amino groups are removed from the amino acids by a chemical reaction called ___________, and (initially) transferred ___________, which plays an especially critical role in cellular nitrogen metabolism.

Answer 47

In humans, most of the amino acids are derived from dietary protein. The amino groups are removed from the amino acids by a chemical reaction called transamination, and (initially) transferred to α-ketoglutarate, which plays an especially critical role in cellular nitrogen metabolism.