Unit 20 Question Bank
Format note: the TMU Biochemistry paper gives five suggested
answers (A–E), not four — these MCQs match that. Items tagged TMU 2019 or
TMU 2020/21 come from the real papers. Answers are verified against Harper's
Illustrated Biochemistry; the "marking schemes" in the source folder are other students'
answer sheets, not official, so they are never used as the authority.
0 / 25 answered
1Transamination is best defined as ( ).
Answer: A
⭐ Set in Section I of BOTH papers. Say reversible and name pyridoxal phosphate — the reaction is freely reversible, with an equilibrium constant close to unity, and PLP sits at the catalytic site of every aminotransferase. Option B is glutaminase, option C oxidative deamination.Harper's ch.28, pp.290–291
2The coenzyme of all aminotransferases is derived from which vitamin?
Answer: B
Pyridoxal phosphate (PLP), a derivative of vitamin B₆. During transamination it serves as a “carrier” of amino groups: an enzyme-bound Schiff base forms with the α-amino group, and rearrangement yields the α-keto acid plus enzyme-bound pyridoxamine phosphate.Harper's ch.28, p.291
3Which amino acids do NOT participate in transamination?
Answer: C
A precise fact worth memorising as a set of four. Note a related subtlety: transamination is not restricted to α-amino groups — the δ-amino group of ornithine (but not the ε-amino group of lysine) readily undergoes transamination.Harper's ch.28, p.291
4All amino acid nitrogen is funnelled into glutamate because ( ).
Answer: D
This is the reasoning the examiner is really testing. There is essentially one door out of the amino acid pool, and it is glutamate's. Since alanine is also a substrate for glutamate aminotransferase, the α-amino nitrogen from all amino acids that undergo transamination can be concentrated in glutamate — transamination is the collection system, deamination the release step.Harper's ch.28, p.291
5Glutamate dehydrogenase is allosterically ( ).
Answer: E
Read it as an energy statement: GDH runs when the cell is energy-poor. Deaminating glutamate yields α-ketoglutarate, a citric acid cycle fuel, so a cell rich in ATP has no reason to dismantle amino acids. The same logic governs isocitrate dehydrogenase in Unit 11. GDH can use either NAD⁺ or NADP⁺.Harper's ch.28, p.291
6“Transdeamination” refers to ( ).
Answer: A
Transamination collects the nitrogen onto α-ketoglutarate to form glutamate; oxidative deamination then strips it off as ammonia and regenerates the α-ketoglutarate. The regeneration is what makes it a cycle rather than a consumption — one α-ketoglutarate molecule can process nitrogen indefinitely.Harper's ch.28, p.291
7Which enzyme fixes ammonia as glutamine, and where?
Answer: B
Because amide bond synthesis is coupled to the hydrolysis of ATP to ADP and Pi, the reaction strongly favours glutamine synthesis. The ATP is the price of safe carriage: glutamine is a harmless parcel in which toxic ammonia travels to the liver. A rare neonatal deficiency causes severe brain damage, multiorgan failure and death.Harper's ch.28, p.292
8Glutaminase removes which nitrogen from glutamine?
Answer: C
Harper's puts this in italics for a reason. The amide nitrogen is released as ammonia, leaving glutamate — which still carries its α-amino group, ready for glutamate dehydrogenase. The reaction proceeds essentially irreversibly.Harper's ch.28, p.292
9Renal glutaminase activity increases in ( ).
Answer: D
Ammonia excreted by renal tubular cells facilitates cation conservation and regulation of acid-base balance — NH₃ buffers a secreted proton as NH₄⁺, so H⁺ leaves without the loss of Na⁺ or K⁺. Note the contrast with the other isoform: hepatic glutaminase rises in response to high protein intake, renal in acidosis. Different genes, different regulation.Harper's ch.28, p.292
10Ammonia is thought to be toxic to the brain in part because ( ).
Answer: E
This is Unit 11's anaplerosis problem in clinical dress — the citric acid cycle is catalytic, so removing an intermediate stops it turning. The neuron is uniquely exposed because it depends almost entirely on oxidative phosphorylation. Symptoms follow in order: tremor, slurred speech, blurred vision, coma, death.Harper's ch.28, p.292
11Normal peripheral blood ammonia concentration is about ( ).
Answer: A
Only traces, because ammonia from enteric bacteria and from tissues is rapidly removed from the circulation by the liver. Toxic levels arise when portal blood bypasses the liver — in severely impaired hepatic function, or through collateral links between portal and systemic veins in cirrhosis.Harper's ch.28, pp.291–292
12Fish, birds and humans excrete excess nitrogen respectively as ( ).
Answer: B
Each solution fits an ecological constraint. Fish are ammonotelic because their aqueous environment permits continuous water excretion to dilute the toxin. Birds are uricotelic because they must conserve water and maintain low weight — uric acid leaves as semisolid guano. Humans are ureotelic: urea is nontoxic and highly water-soluble.Harper's ch.28, p.290
13Synthesis of one mole of urea requires ( ).
Answer: C
Learn the line verbatim; it earns marks on its own. Note where the ATP goes: 2 mol are consumed by carbamoyl phosphate synthase I alone — one as the phosphoryl donor for the mixed anhydride bond, one to drive the amide bond — and the third at argininosuccinate synthase, which cleaves ATP to AMP + PPi.Harper's ch.28, p.292
14The atoms of urea are provided by ( ).
Answer: D
Trace each nitrogen. The first enters as free ammonium ion at reaction 1, built into carbamoyl phosphate. The second enters at reaction 3, where argininosuccinate synthase links aspartate and citrulline via the amino group of aspartate — it never appears as free ammonia at all.Harper's ch.28, pp.292–294
15Which reactions of the urea cycle occur in the mitochondrial matrix?
Answer: E
Reactions 1 and 2 occur in the matrix of liver mitochondria; reactions 3, 4 and 5 in liver cytosol. The split has a practical consequence: CO₂ (as bicarbonate), ammonium ion, ornithine and citrulline must cross the inner membrane on specific carriers — and a mutation in one of those carriers is itself a disease (HHH syndrome).Harper's ch.28, p.293
16The rate-limiting enzyme of the urea cycle, and its obligatory activator, are ( ).
Answer: A
The enzyme is active only in the presence of N-acetylglutamate, an allosteric activator that enhances the affinity of the synthase for ATP. And note why that signal is well chosen: it is made from acetyl-CoA and glutamate — glutamate reports the nitrogen load, acetyl-CoA reports that fuel is available to pay for disposal.Harper's ch.28, pp.293–294
17Carbamoyl phosphate synthase II differs from CPS-I in that it ( ).
Answer: B
A classic discrimination question, and one that connects to Unit 21. Two enzymes, the same product name, entirely different jobs: I — mitochondrial, ammonia, urea, needs N-acetylglutamate; II — cytosolic, glutamine, pyrimidines, no such activator.Harper's ch.28, p.293
18Cleavage of argininosuccinate by argininosuccinate lyase releases ( ).
Answer: C
The reaction proceeds with retention of all three nitrogens in arginine and release of the aspartate skeleton as fumarate. That fumarate is the link between the urea cycle and the citric acid cycle: it is hydrated to malate and oxidised to oxaloacetate by cytosolic fumarase and malate dehydrogenase, then transaminated back to aspartate. Aspartate is a shuttle, not a consumable.Harper's ch.28, p.294
19Which urea cycle disorder is X-chromosome linked?
Answer: D
Termed hyperammonemia type 2. A clinical detail worth carrying: the mothers also exhibit hyperammonemia and an aversion to high-protein foods — an aversion that is, in effect, self-prescribed dietary therapy. Glutamine is elevated in blood, CSF and urine, from enhanced glutamine synthesis in response to the ammonia.Harper's ch.28, p.295
20Ammonia intoxication is MOST severe when the urea cycle block occurs at ( ).
Answer: E
Harper's gives the reason exactly: if citrulline can be synthesized, some ammonia has already been removed by being covalently linked to an organic metabolite. A late block leaves the nitrogen already trapped in a harmless intermediate; an early block leaves it as free ammonia.Harper's ch.28, p.295
21Which pair of amino acids is EXCLUSIVELY ketogenic?
Answer: A
Only these two. Isoleucine, phenylalanine, tryptophan and tyrosine are BOTH glucogenic and ketogenic; everything else is glucogenic. Note that TMU Lecture 19 slide 58 lists seven “ketogenic” amino acids including threonine — that is the “ketogenic or partly ketogenic” list, and Harper's Table 29-1 classifies threonine as glycogenic. The lecture's own question slide asks for the exclusively ketogenic pair.Harper's ch.29, Table 29-1, p.298 · TMU Lecture 19 slides 58, 70
22An amino acid degraded to acetyl-CoA cannot give rise to glucose because ( ).
Answer: B
One reaction explains two facts — this is also exactly why fatty acids are not glucogenic (Unit 17). The two carbons entering as acetyl-CoA are balanced by two leaving as CO₂ in the same turn of the cycle, so there is no net gain of oxaloacetate. State the reason rather than reciting the list and you can never get this wrong.Harper's ch.19, p.193 · Harper's ch.29
23Which six amino acids are degraded to pyruvate?
Answer: C
Set as a question on the lecturer's own final slide. Pyruvate can then go either to acetyl-CoA (a ketone body precursor) or to oxaloacetate (gluconeogenesis). Option D is the succinyl-CoA group, option E the α-ketoglutarate group.TMU Lecture 19 slide 54 · Harper's ch.29
24Branched-chain amino acids are degraded only in extrahepatic tissues because ( ).
Answer: D
They are oxidised as fuels in muscle, adipose tissue and kidney. This explains two earlier observations at once: why branched-chain amino acids are spared by the liver after a meal and extracted by muscle, and why valine is released by muscle and taken up predominantly by the brain in fasting.TMU Lecture 19 slide 61 · Harper's ch.28, p.290
25The enzyme deficient in classic phenylketonuria is ( ).
Answer: E
Type I (classic) PKU, frequency 1 in 10,000 births. Note that TMU Lecture 19 slides 59–60 say “phenylalanine carboxylase” — that is an error; the lecture's own slide 66 and Harper's both give hydroxylase, and the name describes the chemistry (a hydroxyl inserted into the ring to make tyrosine). Dihydrobiopterin reductase is types II and III — the cofactor forms.Harper's ch.29, p.304 · TMU Lecture 19 slides 59–60 vs 66
1 Transamination — 3′ — PROVEN in BOTH papers+
The reversible transfer of an α-amino group from an α-amino acid to an α-keto acid, interconverting pairs of α-amino acids and α-keto acids.
It is catalysed by aminotransferases (transaminases), all of which carry pyridoxal phosphate (PLP), a derivative of vitamin B₆, at the catalytic site, where it acts as the carrier of the amino group via an enzyme-bound Schiff base. The mechanism is “ping-pong” — alternate addition of a substrate and release of a product.
The reaction is freely reversible, with an equilibrium constant close to unity, so it serves in both amino acid catabolism and biosynthesis. All the common amino acids except lysine, threonine, proline and hydroxyproline participate.
Significance: since alanine is also a substrate for glutamate aminotransferase, the α-amino nitrogen of all amino acids that undergo transamination can be concentrated in glutamate — the only amino acid oxidatively deaminated at an appreciable rate. Clinically, AST (SGOT) is raised in myocardial infarction and ALT (SGPT) in viral hepatitis.Harper's ch.28, pp.290–291 · 2019 and 2020/21 papers, Section I
It is catalysed by aminotransferases (transaminases), all of which carry pyridoxal phosphate (PLP), a derivative of vitamin B₆, at the catalytic site, where it acts as the carrier of the amino group via an enzyme-bound Schiff base. The mechanism is “ping-pong” — alternate addition of a substrate and release of a product.
The reaction is freely reversible, with an equilibrium constant close to unity, so it serves in both amino acid catabolism and biosynthesis. All the common amino acids except lysine, threonine, proline and hydroxyproline participate.
Significance: since alanine is also a substrate for glutamate aminotransferase, the α-amino nitrogen of all amino acids that undergo transamination can be concentrated in glutamate — the only amino acid oxidatively deaminated at an appreciable rate. Clinically, AST (SGOT) is raised in myocardial infarction and ALT (SGPT) in viral hepatitis.Harper's ch.28, pp.290–291 · 2019 and 2020/21 papers, Section I
2 The urea cycle — 3′+
The hepatic cyclic pathway that converts toxic ammonia into nontoxic, water-soluble urea for excretion — the final stage of nitrogen disposal in ureotelic animals.
Synthesis of 1 mol of urea requires 3 mol of ATP, 1 mol each of ammonium ion and of aspartate, and employs five enzymes. NH₃, CO₂ and the amide nitrogen of aspartate provide the atoms of urea.
1 · CO₂ + NH₄⁺ + 2 ATP → carbamoyl phosphate (carbamoyl phosphate synthase I, the rate-limiting enzyme, activated by N-acetylglutamate) — mitochondrial
2 · + ornithine → citrulline (ornithine transcarbamoylase) — mitochondrial
3 · + aspartate + ATP → argininosuccinate (argininosuccinate synthase) — cytosolic
4 · → arginine + fumarate (argininosuccinate lyase) — cytosolic
5 · → urea + ornithine (arginase) — cytosolic
Ornithine is regenerated, so there is no net loss or gain of ornithine, citrulline, argininosuccinate or arginine. The fumarate links the cycle to the citric acid cycle.Harper's ch.28, pp.292–294
Synthesis of 1 mol of urea requires 3 mol of ATP, 1 mol each of ammonium ion and of aspartate, and employs five enzymes. NH₃, CO₂ and the amide nitrogen of aspartate provide the atoms of urea.
1 · CO₂ + NH₄⁺ + 2 ATP → carbamoyl phosphate (carbamoyl phosphate synthase I, the rate-limiting enzyme, activated by N-acetylglutamate) — mitochondrial
2 · + ornithine → citrulline (ornithine transcarbamoylase) — mitochondrial
3 · + aspartate + ATP → argininosuccinate (argininosuccinate synthase) — cytosolic
4 · → arginine + fumarate (argininosuccinate lyase) — cytosolic
5 · → urea + ornithine (arginase) — cytosolic
Ornithine is regenerated, so there is no net loss or gain of ornithine, citrulline, argininosuccinate or arginine. The fumarate links the cycle to the citric acid cycle.Harper's ch.28, pp.292–294
3 Nitrogen balance — 2′+
Nitrogen balance = nitrogen ingested (primarily as protein) − nitrogen excreted (primarily as urea).
Nitrogen equilibrium (balance = 0): protein synthesis = protein degradation — the normal adult state.
Positive nitrogen balance: an excess of ingested over excreted nitrogen; synthesis exceeds degradation. Accompanies growth and pregnancy.
Negative nitrogen balance: output exceeds intake. May follow surgery, advanced cancer, and the nutritional disorders kwashiorkor and marasmus.
Related: humans turn over 1% to 2% of their total body protein each day, principally muscle protein, and about 75% of the liberated amino acids are reutilized. Excess amino acids are not stored — those not immediately incorporated into protein are rapidly degraded.Harper's ch.28, pp.287–288
Nitrogen equilibrium (balance = 0): protein synthesis = protein degradation — the normal adult state.
Positive nitrogen balance: an excess of ingested over excreted nitrogen; synthesis exceeds degradation. Accompanies growth and pregnancy.
Negative nitrogen balance: output exceeds intake. May follow surgery, advanced cancer, and the nutritional disorders kwashiorkor and marasmus.
Related: humans turn over 1% to 2% of their total body protein each day, principally muscle protein, and about 75% of the liberated amino acids are reutilized. Excess amino acids are not stored — those not immediately incorporated into protein are rapidly degraded.Harper's ch.28, pp.287–288
4 Glutamate dehydrogenase (GDH) — 2′+
The hepatic enzyme that occupies a central position in nitrogen metabolism, catalysing the oxidative deamination of L-glutamate: L-glutamate + NAD(P)⁺ + H₂O → α-ketoglutarate + NH₃ + NAD(P)H.
It can use either NAD⁺ or NADP⁺. The reaction is reversible but strongly favours glutamate formation, and therefore serves in amino acid biosynthesis as well as catabolism.
Allosterically inhibited by ATP, GTP and NADH; activated by ADP — it runs when the cell needs fuel.
Its concerted action with glutamate aminotransferase is termed transdeamination, and it is the route by which the formation of ammonia from α-amino groups mainly occurs.Harper's ch.28, p.291
It can use either NAD⁺ or NADP⁺. The reaction is reversible but strongly favours glutamate formation, and therefore serves in amino acid biosynthesis as well as catabolism.
Allosterically inhibited by ATP, GTP and NADH; activated by ADP — it runs when the cell needs fuel.
Its concerted action with glutamate aminotransferase is termed transdeamination, and it is the route by which the formation of ammonia from α-amino groups mainly occurs.Harper's ch.28, p.291
5 Ammonia intoxication — 2′+
The clinical syndrome of hyperammonemia, arising when ammonia is not cleared by the liver.
Normally only traces (10–20 μg/dL) are present in peripheral blood, because ammonia from enteric bacteria and from tissues is rapidly removed by the liver and converted to urea. Toxic levels arise if portal blood bypasses the liver — in severely impaired hepatic function, or through collateral portal-systemic links in cirrhosis — or in inherited urea cycle defects.
Symptoms: tremor, slurred speech, blurred vision, coma and ultimately death.
Mechanism: ammonia reacts with α-ketoglutarate to form glutamate; the resulting depletion of α-ketoglutarate impairs function of the TCA cycle in neurons.Harper's ch.28, pp.291–292
Normally only traces (10–20 μg/dL) are present in peripheral blood, because ammonia from enteric bacteria and from tissues is rapidly removed by the liver and converted to urea. Toxic levels arise if portal blood bypasses the liver — in severely impaired hepatic function, or through collateral portal-systemic links in cirrhosis — or in inherited urea cycle defects.
Symptoms: tremor, slurred speech, blurred vision, coma and ultimately death.
Mechanism: ammonia reacts with α-ketoglutarate to form glutamate; the resulting depletion of α-ketoglutarate impairs function of the TCA cycle in neurons.Harper's ch.28, pp.291–292
6 Glucogenic and ketogenic amino acids — 2′+
Glucogenic (glycogenic): the carbon skeleton is degraded to pyruvate or a citric acid cycle intermediate — α-ketoglutarate, succinyl-CoA, fumarate or oxaloacetate — and can give rise to glucose by gluconeogenesis.
Ketogenic: the skeleton is degraded to acetyl-CoA, acetoacetyl-CoA or acetoacetate, and can give rise to ketone bodies and fat but never to glucose, because pyruvate dehydrogenase is essentially irreversible.
Exclusively ketogenic: LEUCINE and LYSINE only.
Both: isoleucine, phenylalanine, tryptophan, tyrosine.
All the remainder are glucogenic.Harper's ch.29, Table 29-1, p.298
Ketogenic: the skeleton is degraded to acetyl-CoA, acetoacetyl-CoA or acetoacetate, and can give rise to ketone bodies and fat but never to glucose, because pyruvate dehydrogenase is essentially irreversible.
Exclusively ketogenic: LEUCINE and LYSINE only.
Both: isoleucine, phenylalanine, tryptophan, tyrosine.
All the remainder are glucogenic.Harper's ch.29, Table 29-1, p.298
1
Describe the urea cycle and its regulation.
10′
Why urea at all
Excess amino acids are not stored, so their nitrogen must be disposed of continuously — and that nitrogen is ammonia, which is highly toxic to the central nervous system. Humans are ureotelic: they convert it to urea, which is nontoxic and highly water-soluble. (Fish are ammonotelic, birds uricotelic.)
The four stages of urea biosynthesis
Harper's divides the process into (1) transamination, (2) oxidative deamination of glutamate, (3) ammonia transport, and (4) the reactions of the urea cycle.
- Transamination channels the α-amino nitrogen of all amino acids into glutamate, because L-glutamate is the only amino acid that undergoes oxidative deamination at an appreciable rate.
- Glutamate dehydrogenase then releases that nitrogen as ammonia, regenerating α-ketoglutarate. The two reactions coupled are transdeamination.
- Transport: glutamine synthase fixes ammonia as harmless glutamine in peripheral tissue at the cost of one ATP; glutaminase releases it again in the liver. Muscle also exports nitrogen as alanine, through the glucose-alanine cycle.
The cycle itself
Synthesis of 1 mol of urea requires 3 mol of ATP, 1 mol each of ammonium ion and of aspartate, and employs five enzymes.
| # | Reaction | Enzyme | Where |
|---|---|---|---|
| 1 | CO₂ + NH₄⁺ + 2 ATP → carbamoyl phosphate | Carbamoyl phosphate synthase I | Matrix |
| 2 | + ornithine → citrulline | Ornithine transcarbamoylase | Matrix |
| 3 | + aspartate + ATP → argininosuccinate | Argininosuccinate synthase | Cytosol |
| 4 | → arginine + fumarate | Argininosuccinate lyase | Cytosol |
| 5 | → urea + ornithine | Arginase | Cytosol |
Ornithine consumed in reaction 2 is regenerated in reaction 5, so there is no net loss or gain of ornithine, citrulline, argininosuccinate or arginine. Because the pathway is split between compartments, CO₂, ammonium ion, ornithine and citrulline cross the inner mitochondrial membrane on specific carriers.
The two nitrogens
NH₃, CO₂ and the amide nitrogen of aspartate provide the atoms of urea. The first nitrogen enters as free ammonium ion at reaction 1; the second enters at reaction 3, where argininosuccinate synthase links aspartate and citrulline via the amino group of aspartate. Reaction 4 retains all three nitrogens in arginine and releases the aspartate skeleton as fumarate, which is hydrated to malate and oxidised to oxaloacetate by cytosolic fumarase and malate dehydrogenase, then transaminated back to aspartate. The aspartate-fumarate skeleton is therefore a carrier, not a consumable — and that fumarate is the link between the urea cycle and the citric acid cycle.
Regulation
- Allosteric. Carbamoyl phosphate synthase I is the rate-limiting (pacemaker) enzyme and is active only in the presence of N-acetylglutamate, which enhances the affinity of the synthase for ATP. Its level is set by the balance between N-acetylglutamate synthase and N-acetylglutamate deacylase. Since it is made from acetyl-CoA and glutamate, it rises exactly when there is both a nitrogen load and the energy to dispose of it.
- Enzyme induction. Major changes in diet can increase the concentrations of individual urea cycle enzymes 10- to 20-fold; starvation elevates the levels, presumably to handle the ammonia from starvation-induced protein degradation.
Clinical significance
Defects in each enzyme are known. Urea cycle disorders are characterized by hyperammonemia, encephalopathy and respiratory alkalosis, with vomiting, avoidance of high-protein foods, intermittent ataxia, irritability, lethargy and severe mental retardation. Ammonia intoxication is most severe when the block occurs at reactions 1 or 2, for if citrulline can be synthesized some ammonia has already been removed by being covalently linked to an organic metabolite. Treatment is a low-protein diet as frequent small meals with sufficient arginine and energy — not a protein-free diet, since mammals cannot synthesise all 20 amino acids.
Marking guide: the four stages named 1.5 · the five reactions with correct enzymes 3 · compartmentation correctly stated 1 · the source of the two nitrogens 1.5 · stoichiometry, 3 ATP 0.5 · N-acetylglutamate and CPS-I 1.5 · one clinical consequence 1. Both marking schemes reward the sentence 'NH₃, CO₂ and the amide nitrogen of aspartate provide the atoms of urea' — write it verbatim.
2
How is amino acid nitrogen transported to the liver and converted to ammonia?
6′
The problem
Nitrogen is released from amino acids all over the body, but only the liver has the urea cycle enzymes. The nitrogen must therefore travel — and it cannot travel as free ammonia, which is toxic to the central nervous system and is normally present in peripheral blood at only 10–20 μg/dL.
Step 1 — collection by transamination
Transamination reactions interconvert pairs of α-amino acids and α-keto acids, catalysed by aminotransferases with pyridoxal phosphate. Because each aminotransferase is specific for one pair of substrates but nonspecific for the other, and because alanine is itself a substrate for glutamate aminotransferase, the α-amino nitrogen of all amino acids that undergo transamination can be concentrated in glutamate. Only lysine, threonine, proline and hydroxyproline stand outside this system.
Step 2 — two carriers in the blood
- Glutamine. Mitochondrial glutamine synthase fixes ammonia as glutamine, the reaction being pulled forward by coupling to ATP hydrolysis. Glutamine is a harmless amide in which the nitrogen travels safely; in the liver and kidney, glutaminase hydrolytically releases the AMIDE nitrogen as ammonia, essentially irreversibly. The concerted action of the two enzymes interconverts free ammonium ion and glutamine — a delivery service rather than a futile cycle, because the two enzymes act in different organs.
- Alanine. In the glucose-alanine cycle, muscle transaminates glucose-derived pyruvate to alanine, exporting nitrogen and carbon together. Alanine is extracted primarily by the liver, where the nitrogen enters the urea cycle and the carbon skeleton enters gluconeogenesis; the rate of hepatic gluconeogenesis from alanine is far higher than from all other amino acids.
Step 3 — release as ammonia
Hepatic L-glutamate dehydrogenase, which can use either NAD⁺ or NADP⁺, releases the nitrogen of glutamate as ammonia. The coupled action of glutamate aminotransferase and GDH is transdeamination. GDH is allosterically inhibited by ATP, GTP and NADH and activated by ADP, so deamination proceeds when the cell needs fuel. Note that although the reaction strongly favours glutamate formation, it is pulled in the deaminating direction because the ammonia is immediately consumed by carbamoyl phosphate synthase I.
A minor additional route is L-amino acid oxidase of liver and kidney, which forms an unstable α-imino acid that decomposes to an α-keto acid and ammonium ion; the H₂O₂ generated is destroyed by catalase.
Renal ammonia
Ammonia formed in renal tubular cells, especially from glutamine, increases in metabolic acidosis and decreases in metabolic alkalosis. Its excretion facilitates cation conservation and regulation of acid-base balance.
Marking guide: transamination as the collection step, with the glutamate rationale 2 · glutamine synthase/glutaminase pair 1.5 · glucose-alanine cycle 1 · glutamate dehydrogenase and transdeamination 1.5. Naming pyridoxal phosphate and stating that glutaminase removes the AMIDE nitrogen each earn a half-mark.
3
What happens to the carbon skeletons of amino acids after their nitrogen is removed?
6′
The general answer
Excess amino acids are catabolized to amphibolic intermediates used as sources of energy or for carbohydrate and lipid biosynthesis. After transamination, the remaining carbon skeleton — an α-keto acid — is restructured for conversion to oxaloacetate, α-ketoglutarate, pyruvate or acetyl-CoA.
The dividing line
Glucogenic skeletons enter as pyruvate or a citric acid cycle intermediate and can therefore yield glucose. Ketogenic skeletons enter as acetyl-CoA, acetoacetyl-CoA or acetoacetate and can yield only ketone bodies and fat.
The reason for the line is a single irreversible reaction: pyruvate dehydrogenase. Carbon entering as acetyl-CoA cannot return to pyruvate, and the two carbons of acetyl-CoA that enter the citric acid cycle are balanced by two leaving as CO₂ — so there is no net oxaloacetate and therefore no net glucose. The same reaction is why fatty acids are not glucogenic.
| Class | Amino acids |
|---|---|
| Exclusively ketogenic | Leucine, lysine |
| Both | Isoleucine, phenylalanine, tryptophan, tyrosine |
| Glucogenic | All the rest — Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Hyp, Met, Pro, Ser, Thr, Val |
Entry points into the citric acid cycle
| Enters as | From |
|---|---|
| Pyruvate | Alanine, tryptophan, cysteine, serine, glycine, threonine |
| Oxaloacetate | Asparagine, aspartate |
| α-Ketoglutarate | Arginine, histidine, glutamine, proline, glutamate |
| Succinyl-CoA | Isoleucine, methionine, valine |
| Fumarate | Phenylalanine, tyrosine |
| Acetyl-CoA / acetoacetyl-CoA | Leucine, lysine, phenylalanine, tryptophan, tyrosine |
Two special cases worth naming
- Glycine has three routes: to serine and thence pyruvate via serine hydroxymethyltransferase; oxidative cleavage by the glycine cleavage enzyme to CO₂, NH₄⁺ and a methylene group — defects cause elevated serum glycine and mental retardation; and conversion to glyoxylate and thence oxalate — calcium oxalate crystals account for 75% of all kidney stones.
- Branched-chain amino acids (Ile, Leu, Val) are degraded only in extrahepatic tissues — muscle, adipose tissue and kidney — because the branched-chain α-ketoacid dehydrogenase complex is absent from the liver. That complex is analogous to pyruvate dehydrogenase, and the subsequent reactions are analogous to fatty acid β-oxidation.
Clinical correlates
Phenylketonuria — phenylalanine hydroxylase, 1 in 10,000. Maple syrup urine disease — the branched-chain α-ketoacid dehydrogenase complex. Alkaptonuria — homogentisate oxidase, the urine darkening in air, the disorder from which Garrod derived the whole concept of an inborn error of metabolism.
Marking guide: the glucogenic/ketogenic distinction defined 1.5 · Leu and Lys named as exclusively ketogenic 1 · the pyruvate dehydrogenase reason 1 · at least three entry points correct 1.5 · one special case or clinical correlate 1.