Amino Acid Oxidation
and the Production
of Urea
chapter
18
1. Products of Amino Acid Transamination Name and draw the structure of the a-keto acid
resulting when each of the following amino acids undergoes transamination with a-ketoglutarate:
(a) aspartate, (b) glutamate, (c) alanine, (d) phenylalanine.
Answer
2. Measurement of Alanine Aminotransferase Activity The activity (reaction rate) of alanine
aminotransferase is usually measured by including an excess of pure lactate dehydrogenase and NADH
in the reaction system. The rate of alanine disappearance is equal to the rate of NADH disappearance
measured spectrophotometrically. Explain how this assay works.
Answer The measurement of the activity of alanine aminotransferase by measurement of the
3. Alanine and Glutamine in the Blood Normal human blood plasma contains all the amino acids re-
quired for the synthesis of body proteins, but not in equal concentrations. Alanine and glutamine are
present in much higher concentrations than any other amino acids. Suggest why.
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S-212 Chapter 18 Amino Acid Oxidation and the Production of Urea
4. Distribution of Amino Nitrogen If your diet is rich in alanine but deficient in aspartate, will you
show signs of aspartate deficiency? Explain.
5. Lactate versus Alanine as Metabolic Fuel: The Cost of Nitrogen Removal The three carbons in
lactate and alanine have identical oxidation states, and animals can use either carbon source as a meta-
bolic fuel. Compare the net ATP yield (moles of ATP per mole of substrate) for the complete oxidation
(to CO
2
and H
2
O) of lactate versus alanine when the cost of nitrogen excretion as urea is included.
Answer Lactate and alanine are converted to pyruvate by their respective dehydrogenases,
6. Ammonia Toxicity Resulting from an Arginine-Deficient Diet In a study conducted some years
ago, cats were fasted overnight then given a single meal complete in all amino acids except arginine.
Within 2 hours, blood ammonia levels increased from a normal level of 18 mg/L to 140 mg/L, and the cats
showed the clinical symptoms of ammonia toxicity. A control group fed a complete amino acid diet or
an amino acid diet in which arginine was replaced by ornithine showed no unusual clinical symptoms.
(a) What was the role of fasting in the experiment?
(b) What caused the ammonia levels to rise in the experimental group? Why did the absence of argi-
nine lead to ammonia toxicity? Is arginine an essential amino acid in cats? Why or why not?
(c) Why can ornithine be substituted for arginine?
A
O
COO
⫺
O
O
C
Lactate
A
A
H
HO OH
HH
C
A
⫹
O
COO
⫺
O
O
C
A
A
H
OH
HH
C
Alanine
H
3
N
7. Oxidation of Glutamate Write a series of balanced equations, and an overall equation for the net
reaction, describing the oxidation of 2 mol of glutamate to 2 mol of a-ketoglutarate and 1 mol of urea.
Answer
8. Transamination and the Urea Cycle Aspartate aminotransferase has the highest activity of all the
mammalian liver aminotransferases. Why?
9. The Case against the Liquid Protein Diet A weight-reducing diet heavily promoted some years
ago required the daily intake of “liquid protein” (soup of hydrolyzed gelatin), water, and an assortment
of vitamins. All other food and drink were to be avoided. People on this diet typically lost 10 to 14 lb in
the first week.
(a) Opponents argued that the weight loss was almost entirely due to water loss and would be regained
very soon after a normal diet was resumed. What is the biochemical basis for this argument?
(b) A number of people on this diet died. What are some of the dangers inherent in the diet and how
can they lead to death?
Answer
Chapter 18 Amino Acid Oxidation and the Production of Urea S-213
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S-214 Chapter 18 Amino Acid Oxidation and the Production of Urea
10. Ketogenic Amino Acids Which amino acids are exclusively ketogenic?
11. A Genetic Defect in Amino Acid Metabolism: A Case History A two-year-old child was taken to
the hospital. His mother said that he vomited frequently, especially after feedings. The child’s weight
and physical development were below normal. His hair, although dark, contained patches of white. A
urine sample treated with ferric chloride (FeCl
3
) gave a green color characteristic of the presence of
phenylpyruvate. Quantitative analysis of urine samples gave the results shown in the table.
Concentration (m
M
)
Substance Patient’s urine Normal urine
Phenylalanine 7.0 0.01
Phenylpyruvate 4.8 0
Phenyllactate 10.3 0
(a) Suggest which enzyme might be deficient in this child. Propose a treatment.
(b) Why does phenylalanine appear in the urine in large amounts?
(c) What is the source of phenylpyruvate and phenyllactate? Why does this pathway (normally not
functional) come into play when the concentration of phenylalanine rises?
(d) Why does the boy’s hair contain patches of white?
Answer
12. Role of Cobalamin in Amino Acid Catabolism Pernicious anemia is caused by impaired absorp-
tion of vitamin B
12
. What is the effect of this impairment on the catabolism of amino acids? Are all
amino acids equally affected? (Hint: see Box 17–2.)
13. Vegetarian Diets Vegetarian diets can provide high levels of antioxidants and a lipid profile that can
help prevent coronary disease. However, there can be some associated problems. Blood samples were
taken from a large group of volunteer subjects who were vegans (strict vegetarians: no animal prod-
ucts), lactovegetarians (vegetarians who eat dairy products), or omnivores (individuals with a normal,
varied diet including meat). In each case, the volunteers had followed the diet for several years. The
blood levels of both homocysteine and methylmalonate were elevated in the vegan group, somewhat
lower in the lactovegetarian group, and much lower in the omnivore group. Explain.
14. Pernicious Anemia Vitamin B
12
deficiency can arise from a few rare genetic diseases that lead to
low B
12
levels despite a normal diet that includes B
12
-rich meat and dairy sources. These conditions
cannot be treated with dietary B
12
supplements. Explain.
15. Pyridoxal Phosphate Reaction Mechanisms Threonine can be broken down by the enzyme threo-
nine dehydratase, which catalyzes the conversion of threonine to ␣-ketobutyrate and ammonia. The
enzyme uses PLP as a cofactor. Suggest a mechanism for this reaction, based on the mechanisms in
Figure 18–6. Note that this reaction includes an elimination at the carbon of threonine.
Chapter 18 Amino Acid Oxidation and the Production of Urea S-215
Threonine ␣-Ketobutyrate
threonine
dehydratase
PLP NH3
⫹
H2O
⫹
OCH3OCH2O
O
C
OH
O
AA
CH3OCH OCH
⫹
NH3
COO
⫺
COO
⫺
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S-216 Chapter 18 Amino Acid Oxidation and the Production of Urea
16. Pathway of Carbon and Nitrogen in Glutamate Metabolism When [2-
14
C,
15
N] glutamate under-
goes oxidative degradation in the liver of a rat, in which atoms of the following metabolites will each iso-
tope be found: (a) urea, (b) succinate, (c) arginine, (d) citrulline, (e) ornithine, (f) aspartate?
CH
2
H
COO
⫺
H
H
C
Labeled glutamate
COO
⫺
15
14
CH
2
H
N
⫹
Answer
17. Chemical Strategy of Isoleucine Catabolism Isoleucine is degraded in six steps to propionyl-CoA
and acetyl-CoA.
Chapter 18 Amino Acid Oxidation and the Production of Urea S-217
C
C
H
CH
2
Isoleucine
Propionyl-Co
A
CH
3
⫹
H
3
N
OO
⫺
C
S-CoA
CH
3
CH
3
O
C
H
CH
3
6 steps
C
S-CoA
CH
2
O
⫹
Acetyl-CoA
(a) The chemical process of isoleucine degradation includes strategies analogous to those used in
the citric acid cycle and the boxidation of fatty acids. The intermediates of isoleucine degradation
(I to V) shown below are not in the proper order. Use your knowledge and understanding of the
citric acid cycle and b-oxidation pathway to arrange the intermediates in the proper metabolic
sequence for isoleucine degradation.
(b) For each step you propose, describe the chemical process, provide an analogous example from
the citric acid cycle or b-oxidation pathway (where possible), and indicate any necessary
cofactors.
Answer
C
CCH
2
OO
⫺
C
S-Co
A
OC H
CH
3
S-CoAO
C
CH
3
C
CH
3
C
C
HCH
3
O
CH
3
III
III IV V
H
C
S-CoA
O
CH
3
C
CCH
3
O
CH
2
H
CH
3
C
S-CoA
CH
3
C
C
O
HH
CH
3
HO
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S-218 Chapter 18 Amino Acid Oxidation and the Production of Urea
18. Role of Pyridoxal Phosphate in Glycine Metabolism The enzyme serine hydroxymethyltrans-
ferase requires pyridoxal phosphate as cofactor. Propose a mechanism for the reaction catalyzed by this
enzyme, in the direction of serine degradation (glycine production). (Hint: see Figs 18–19 and 18–20b.)
19. Parallel Pathways for Amino Acid and Fatty Acid Degradation The carbon skeleton of leucine
is degraded by a series of reactions closely analogous to those of the citric acid cycle and boxidation.
For each reaction, (a) through (f), indicate its type, provide an analogous example from the citric
acid cycle or b-oxidation pathway (where possible), and note any necessary cofactors.
Chapter 18 Amino Acid Oxidation and the Production of Urea S-219
⫺
OOC
CH
3
NH
3
CH
2
O
CO
2
⫹CCH
3
Acetyl-CoA
(b)
CH
3
COO
⫺
CH
2
C
C
H
H
2
O
Leucine
(c)
CoA-SH
CH
3
COO
⫺
CH
2
C
O
C
H
CH
3
␣-Ketoisocaproate
(e)
S-Co
A
CH
3
CH
2
C
O
C
CH
3
Isovaleryl-CoA
S-CoA
C
H
(f )
H
C
C C
O
S-CoA
H
-Methylcrotonyl-CoA
(d)
⫺
OOC CCH
2
O
C
H
3
C
-Methylglutaconyl-CoA
C S-CoA
H
⫺
OOC CH
2
O
C
CH
3
-Hydroxy--methylglutaryl-CoA
C S-CoA
(a)
CH
2
OH
CH
3
O
Acetoacetate
CH
3
⫺
HCO
3
H
3
C
⫹
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S-220 Chapter 18 Amino Acid Oxidation and the Production of Urea
Answer
Data Analysis Problem
20. Maple Syrup Urine Disease Figure 18–28 shows the pathway for the degradation of branched-chain
amino acids and the site of the biochemical defect that causes maple syrup urine disease. The initial
findings that eventually led to the discovery of the defect in this disease were presented in three pa-
pers published in the late 1950s and early 1960s. This problem traces the history of the findings from
initial clinical observations to proposal of a biochemical mechanism.
Menkes, Hurst, and Craig (1954) presented the cases of four siblings, all of whom died following a
similar course of symptoms. In all four cases, the mother’s pregnancy and the birth had been normal.
The first 3 to 5 days of each child’s life were also normal. But soon thereafter each child began having
convulsions, and the children died between the ages of 11 days and 3 months. Autopsy showed consid-
erable swelling of the brain in all cases. The children’s urine had a strong, unusual “maple syrup” odor,
starting from about the third day of life.
Menkes (1959) reported data collected from six more children. All showed symptoms similar
to those described above, and died within 15 days to 20 months of birth. In one case, Menkes was able
to obtain urine samples during the last months of the infant’s life. When he treated the urine with
2,4-dinitrophenylhydrazone, which forms colored precipitates with keto compounds, he found three
␣-keto acids in unusually large amounts:
(a) These ␣-keto acids are produced by the deamination of amino acids. For each of the ␣-keto acids
above, draw and name the amino acid from which it was derived.
Dancis, Levitz, and Westall (1960) collected further data that led them to propose the biochemical
defect shown in Figure 18–28. In one case, they examined a patient whose urine first showed the
maple syrup odor when he was 4 months old. At the age of 10 months (March 1956), the child was
admitted to the hospital because he had a fever, and he showed grossly retarded motor development.
␣
-Ketoisocaproate
␣
-Ketoisovalerate
␣
-Keto-

-methyl-n-valerate
OC
CH
3
CH
CH
2
CH
3
COO
⫺
OC
CH
3
CH
CH
3
COO
⫺
OC
CH
2
CH
3
CH
CH
3
COO
⫺
At the age of 20 months (January 1957), he was readmitted and was found to have the degenerative
neurological symptoms seen in previous cases of maple syrup urine disease; he died soon after.
Results of his blood and urine analyses are shown in the table below, along with normal values for
each component.
Chapter 18 Amino Acid Oxidation and the Production of Urea S-221
Urine (mg/24 h) Plasma (mg/ml)
Normal Patient Normal Patient
Amino acid(s) Mar. 1956 Jan. 1957 Jan. 1957
Alanine 5–15 0.2 0.4 3.0–4.8 0.6
Asparagine and glutamine 5–15 0.4 0 3.0–5.0 2.0
Aspartic acid 1–2 0.2 1.5 0.1–0.2 0.04
Arginine 1.5–3 0.3 0.7 0.8–1.4 0.8
Cystine 2–4 0.5 0.3 1.0–1.5 0
Glutamic acid 1.5–3 0.7 1.6 1.0–1.5 0.9
Glycine 20–40 4.6 20.7 1.0–2.0 1.5
Histidine 8–15 0.3 4.7 1.0–1.7 0.7
Isoleucine 2–5 2.0 13.5 0.8–1.5 2.2
Leucine 3–8 2.7 39.4 1.7–2.4 14.5
Lysine 2–12 1.6 4.3 1.5–2.7 1.1
Methionine 2–5 1.4 1.4 0.3–0.6 2.7
Ornithine 1–2 0 1.3 0.6–0.8 0.5
Phenylalanine 2–4 0.4 2.6 1.0–1.7 0.8
Proline 2–4 0.5 0.3 1.5–3.0 0.9
Serine 5–15 1.2 0 1.3–2.2 0.9
Taurine 1–10 0.2 18.7 0.9–1.8 0.4
Threonine 5–10 0.6 0 1.2–1.6 0.3
Tryptophan 3–8 0.9 2.3 Not measured 0
Tyrosine 4–8 0.3 3.7 1.5–2.3 0.7
Valine 2–4 1.6 15.4 2.0–3.0 13.1
(b) The table includes taurine, an amino acid not normally found in proteins. Taurine is often pro-
duced as a by-product of cell damage. Its structure is:
CH
2
CH
2
O
O
S
H
3
N
⫺
⫹
O
Based on its structure and the information in this chapter, what is the most likely amino acid pre-
cursor of taurine? Explain your reasoning.
(c) Compared with the normal values given in the table, which amino acids showed significantly ele-
vated levels in the patient’s blood in January 1957? Which ones in the patient’s urine?
Based on their results and their knowledge of the pathway shown in Figure 18–28, Dancis and
coauthors concluded: “although it appears most likely to the authors that the primary block is in the
metabolic degradative pathway of the branched-chain amino acids, this cannot be considered estab-
lished beyond question.”
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S-222 Chapter 18 Amino Acid Oxidation and the Production of Urea
(d) How do the data presented here support this conclusion?
(e) Which data presented here do not fit this model of maple syrup urine disease? How do you
explain these seemingly contradictory data?
(f) What data would you need to collect to be more secure in your conclusion?
Answer