BIO 202 Biochemistry II

by
Seyhun YURDUGÜL
Lecture 10
Amino Acid Metabolism II:
Amino Acid Degradation
 Content Outline

• Catabolism of specific amino acids

• Urea Cycle
 Glutamine/Glutamate and
Asparagine/Aspartate Catabolism

• Glutaminase:
• an important kidney tubule enzyme;
• involved in converting glutamine (from
liver and from other tissue);
• to glutamate and NH3+, with the NH3+ being
excreted in the urine.
 Glutamine/Glutamate and
Asparagine/Aspartate Catabolism
• Glutaminase activity:
• present in many other tissues as well,
although its activity:
• is not nearly as prominent as in the kidney.
• The glutamate produced from glutamine is
converted to α-ketoglutarate,
• making glutamine a glucogenic amino acid.
 Glutamine/Glutamate and
Asparagine/Aspartate Catabolism
• Asparaginase:
• also widely distributed within the body,
• where it converts asparagine into ammonia
and aspartate.
• Aspartate transaminates to oxaloacetate,
• which follows the gluconeogenic pathway
to glucose.
 Glutamine/Glutamate and
Asparagine/Aspartate Catabolism
• Glutamate and aspartate:
• important in collecting and eliminating
amino nitrogen;
• via glutamine synthetase and the urea cycle,
respectively.
 Glutamine/Glutamate and
Asparagine/Aspartate Catabolism
• The catabolic path of the carbon skeletons
involves:
• simple 1-step aminotransferase reactions;
• that directly produce net quantities of a
TCA cycle intermediate.
 Glutamine/Glutamate and
Asparagine/Aspartate Catabolism
• The glutamate dehydrogenase reaction;
• operating in the direction of α-ketoglutarate
production:
• provides a second avenue leading from
glutamate to gluconeogenesis.
 Alanine Catabolism

• Alanine:
• also important in intertissue nitrogen
transport;
• as part of the glucose-alanine cycle.
• Alanine's catabolic pathway:
• involves a simple aminotransferase reaction
that directly produces pyruvate.
 Alanine Catabolism
• Generally pyruvate produced by this pathway:
• will result in the formation of oxaloacetate,
• although when the energy charge of a cell is low;
• the pyruvate will be oxidized to CO2 and H2O;
• via the pyruvate dehydrogenase complex;
• and the TCA cycle.
• This makes alanine: a glucogenic amino acid.
 Arginine, Ornithine and Proline
Catabolism

• The catabolism of arginine:

• begins within the context of the urea cycle:
• hydrolyzed to urea;
• and ornithine by arginase.
 Arginine, Ornithine and Proline
Catabolism
• Ornithine, in excess of urea cycle needs:
• transaminated to form glutamate
semialdehyde.
• Glutamate semialdehyde:
• can serve as the precursor for proline
biosynthesis as described above;
• or it can be converted to glutamate.
 Arginine, Ornithine and Proline
Catabolism
• Proline catabolism: a reversal of its synthesis
process.
• The glutamate semialdehyde;
• generated from ornithine and proline catabolism:
• oxidized to glutamate by an ATP-independent
glutamate semialdehyde dehydrogenase.
 Arginine, Ornithine and Proline
Catabolism
• The glutamate can then be converted to:
• α-ketoglutarate in a transamination reaction.
• Thus arginine, ornithine and proline, are
glucogenic.
 Serine Catabolism

• The conversion of serine to glycine;

• and then glycine oxidation to CO2 and NH3,
• with the production of two equivalents of
N5,N10-methylene tetrahydrofolate(THF).
 Serine Catabolism

• Serine can be catabolized back to the glycolytic

intermediate,
• 3-phosphoglycerate,
• by a pathway that is essentially a reversal of serine
biosynthesis.
• However, the enzymes are different.
• Serine can also be converted to pyruvate;
• through a deamination reaction catalyzed by
serine/threonine dehydratase
 Threonine Catabolism

• There are at least 3 pathways for threonine

catabolism.
• One involves a pathway initiated by
threonine dehydrogenase;
• yielding α-amino-β-ketobutyrate.
 Threonine Catabolism
• The α-amino-ketobutyrate is either
converted to acetyl-CoA;
• and glycine;
• or spontaneously degrades to aminoacetone
which is converted to pyruvate.
 Threonine Catabolism
• The second pathway:
• involves serine/threonine dehydratase;
• yielding α-ketobutyrate which is further
catabolized to propionyl-CoA;
• and finally the TCA cycle intermediate,
succinyl-CoA.
 Threonine Catabolism
• The third pathway utilizes threonine
aldolase.
• The products of this reaction are both
ketogenic (acetyl-CoA);
• and glucogenic (pyruvate).
 Glycine Catabolism

• classified as a glucogenic amino acid,

• since it can be converted to serine;
• by serine hydroxymethyltransferase,
• and serine can be converted back to the
glycolytic intermediate,
• 3-phosphoglycerate;
• or to pyruvate by serine/threonine
dehydratase.
 Glycine Catabolism

• Nevertheless, the main glycine catabolic

pathway:
• leads to the production of CO2,
• ammonia, and one equivalent of N5,N10-
methylene THF:
• by the mitochondrial glycine cleavage
complex.
 Cysteine Catabolism

• There are several pathways for cysteine

catabolism.
• The simplest, but least important pathway:
• catalyzed by a liver desulfurase and
produces hydrogen sulfide, (H2S) and
pyruvate.
 Cysteine Catabolism

• The major catabolic pathway in animals:

• via cysteine dioxygenase that oxidizes the
cysteine sulfhydryl to sulfinate,
• producing the intermediate cysteine
sulfinate.
 Cysteine Catabolism
• Cysteine sulfinate:
• can serve as a biosynthetic intermediate
undergoing decarboxylation;
• and oxidation to produce taurine.
• Catabolism of cysteine sulfinate proceeds through
transamination to β-sulfinylpyruvate;
• which then undergoes desulfuration yielding
bisulfite, (HSO3-);
• and the glucogenic product, pyruvate.
 Cysteine Catabolism
• The enzyme sulfite oxidase uses O2 and
H2O to convert HSO3- to sulfate, (SO4-) and
H2O2.
• The resultant sulfate:
• used as a precursor;
• for the formation of 3'-phosphoadenosine-
5'-phosphosulfate, PAPS
 Cysteine Catabolism
• PAPS: used for the transfer of sulfate:
• to biological molecules; such as the sugars
of the glycosphingolipids.
 Cysteine Catabolism
• Other than protein,
• the most important product of cysteine
metabolism:
• the bile salt precursor taurine,
• which is used to form the bile acid
conjugates taurocholate and
taurochenodeoxycholate.
 Cysteine Catabolism
• The enzyme cystathionase:
• can also transfer the sulfur;
• from one cysteine to another generating
thiocysteine and pyruvate.
• Transamination of cysteine yields β-
mercaptopyruvate which then reacts with sulfite,
(SO32-),
• to produce thiosulfate, (S2O32-) and pyruvate.
 Cysteine Catabolism
• Both thiocysteine and thiosulfate:
• can be used by the enzyme rhodanese;
• to incorporate sulfur into cyanide, (CN -),
• thereby detoxifying the cyanide to
thiocyanate.
 Methionine Catabolism

• The principal fates of the essential amino

acid methionine:
• incorporation into polypeptide chains,
• and use in the production of α-ketobutyrate;
• and cysteine via SAM as described above.
 Methionine Catabolism
• The transulfuration reactions that produce
cysteine from homocysteine and serine:
• also produce α-ketobutyrate,
• the latter being converted to succinyl-CoA.
 Methionine Catabolism
• Regulation of the methionine metabolic pathway:
• based on the availability of methionine and
cysteine.
• If both amino acids are present in adequate
quantities,
• SAM accumulates;
• and is a positive effector on cystathionine
synthase,
• encouraging the production of cysteine and α-
ketobutyrate (both of which are glucogenic).
 Methionine Catabolism
• However, if methionine is scarce,
• SAM will form only in small quantities,
• thus limiting cystathionine synthase activity.
• Under these conditions:
• accumulated homocysteine is remethylated to
methionine,
• using N5-methyl THF and other compounds as
methyl donors
 Valine, Leucine and Isoleucine
Catabolism

• This group of essential amino acids:

• identified as the branched-chain amino
acids, BCAAs.
• Because this arrangement of carbon atoms
cannot be made by humans,
• these amino acids are an essential element
in the diet.
 Valine, Leucine and Isoleucine
Catabolism

• The catabolism of all three compounds

initiates in muscle;
• and yields NADH and FADH2 which can be
utilized for ATP generation.
 Valine, Leucine and Isoleucine
Catabolism
• The catabolism of all three of these amino
acids:
• uses the same enzymes in the first two
steps.
• The first step in each case:
• a transamination using a single BCAA
aminotransferase,
• with α-ketoglutarate as amine acceptor.
 Valine, Leucine and Isoleucine
Catabolism
• As a result,
• three different α -keto acids:
• produced and are oxidized using a common
branched-chain α-keto acid dehydrogenase,
• yielding the three different CoA derivatives.
• Subsequently the metabolic pathways
diverge, producing many intermediates.
 Valine, Leucine and Isoleucine
Catabolism
• The principal product from valine is
propionylCoA,
• the glucogenic precursor of succinyl-CoA.
• Isoleucine catabolism terminates with
production of acetylCoA and
propionylCoA;
• thus isoleucine: both glucogenic and
ketogenic.
 Valine, Leucine and Isoleucine
Catabolism
• Leucine gives rise to acetyl CoA;
• and acetoacetyl CoA,
• and classified as strictly ketogenic.
 Phenylalanine Catabolism

• Phenylalanine normally has only two fates:

• incorporation into polypeptide chains,
• and production of tyrosine;
• via the tetrahydrobiopterin-requiring
phenylalanine hydroxylase.
• Thus, phenylalanine catabolism always
follows the pathway of tyrosine catabolism.
 Phenylalanine Catabolism
• The main pathway for tyrosine degradation:
• involves conversion to fumarate and
acetoacetate,
• allowing phenylalanine and tyrosine to be
classified as:
• both glucogenic and ketogenic.
 Tyrosine Catabolism
• Tyrosine is equally important for protein
biosynthesis;
• as well as an intermediate in the
biosynthesis of several physiologically
important metabolites
• e.g. dopamine, norepinephrine and
epinephrine
 Lysine Catabolism

• Lysine catabolism:
• unusual in the way that the Epsilon-amino
group:
• transferred to α-ketoglutarate and into the
general nitrogen pool.
 Lysine Catabolism
• The reaction:
• a transamination in which the epsilon-
amino group is transferred to the α-keto
carbon;
• of α-ketoglutarate forming the metabolite,
• saccharopine.
 Lysine Catabolism
• Unlike the majority of transamination
reactions,
• this one does not employ pyridoxal
phosphate as a cofactor.
 Lysine Catabolism
• Saccharopine:
• immediately hydrolyzed by the enzyme α-
aminoadipic semialdehyde synthase;
• in such a way that the amino nitrogen
remains with the α -carbon of α
-ketoglutarate,
• producing glutamate and α -aminoadipic
semialdehyde.
 Lysine Catabolism
• Because this transamination reaction is not
reversible,
• Lysine: an essential amino acid.
• The ultimate end-product of lysine
catabolism: acetoacetyl-CoA
 The Urea Cycle

• Earlier it was noted that:

• kidney glutaminase was responsible for converting
excess glutamine;
• from the liver to urine ammonium.
 The Urea Cycle
• However, about 80% of the excreted nitrogen:
• in the form of urea which is also largely made in the
liver,
• in a series of reactions;
• that are distributed:
• between the mitochondrial matrix;
• and the cytosol.
 The Urea Cycle
• The series of reactions that form urea:
• known as the Urea Cycle;
• or the Krebs-Henseleit Cycle.
 The Urea Cycle
• The essential features of the urea cycle
reactions;
• and their metabolic regulation are as
follows:
• Arginine from the diet or from protein
breakdown:
• cleaved by the cytosolic enzyme arginase,
generating urea and ornithine.
 The Urea Cycle
• In subsequent reactions of the urea cycle;
• a new urea residue is built on the ornithine,
• regenerating arginine;
• and perpetuating the cycle.
 The Urea Cycle
• Ornithine arising in the cytosol:
• transported to the mitochondrial matrix,
• where ornithine transcarbamoylase:
• catalyzes the condensation of ornithine with
carbamoyl phosphate,
• producing citrulline.
 The Urea Cycle
• The energy for the reaction:
• provided by the high-energy anhydride of
carbamoyl phosphate.
• The product, citrulline:
• then transported to the cytosol, where the
remaining reactions of the cycle take place.
 The Urea Cycle
• The synthesis of citrulline:
• requires a prior activation of carbon and
nitrogen as carbamoyl phosphate (CP).
• The activation step:
• requires 2 equivalents of ATP;
• and the mitochondrial matrix enzyme
carbamoyl phosphate synthetase-I (CPS-I).
 The Urea Cycle
• There are two CP synthetases:
• a mitochondrial enzyme, CPS-I,
• which forms CP destined for inclusion in
the urea cycle,
• and a cytosolic CP synthatase (CPS-II),
which is involved in pyrimidine nucleotide
biosynthesis.
 The Urea Cycle
• CPS-I:
• positively regulated by the allosteric
effector N-acetyl-glutamate,
• while the cytosolic enzyme:
• acetylglutamate independent
 The Urea Cycle
• In a two-step reaction,
• catalyzed by cytosolic argininosuccinate
synthetase,
• citrulline and aspartate are condensed to
form argininosuccinate.
 The Urea Cycle
• The reaction involves the addition of AMP
(from ATP)
• to the amido carbonyl of citrulline,
• forming an activated intermediate on the
enzyme surface (AMP-citrulline),
• and the subsequent addition of aspartate to
form argininosuccinate.
 The Urea Cycle
• Arginine and fumarate:
• produced from argininosuccinate;
• by the cytosolic enzyme argininosuccinate
lyase (also called argininosuccinase).
 The Urea Cycle
• In the final step of the cycle;
• arginase cleaves urea from aspartate,
• regenerating cytosolic ornithine,
• which can be transported to the
mitochondrial matrix
• for another round of urea synthesis.
 The Urea Cycle
• The fumarate,
• generated via the action of
argininosuccinate lyase,
• reconverted to aspartate for use in the
argininosuccinate synthetase reaction.
 The Urea Cycle
• This occurs through the actions of cytosolic
versions of the TCA cycle enzymes,
• fumarase (which yields malate) and malate
dehydrogenase (which yields oxaloacetate).
• The oxaloacetate:
• then transaminated to aspartate by AST
 The Urea Cycle
• Beginning and ending with ornithine,
• the reactions of the cycle consumes 3
equivalents of ATP;
• and a total of 4 high-energy nucleotide
phosphates.
 The Urea Cycle
• Urea:
• the only new compound generated by the cycle;
• all other intermediates and reactants are recycled.
• The energy consumed in the production of urea:
• more than recovered;
• by the release of energy formed;
• during the synthesis of the urea cycle
intermediates.
 The Urea Cycle
• Ammonia released during the glutamate
dehydrogenase reaction:
• coupled to the formation of NADH.
• In addition, when fumarate is converted
back to aspartate,
• the malate dehydrogenase reaction used to
convert malate;
• to oxaloacetate generates a mole of NADH.
 The Urea Cycle
• These two moles of NADH:
• oxidized in the mitochondria yielding 6
moles of ATP.
 Histidine Catabolism

• Histidine catabolism begins with release of

the α-amino group catalyzed by histidase,
• introducing a double bond into the
molecule.
• As a result, the deaminated product,
urocanate,
• is not the usual α -keto acid associated with
loss of α -amino nitrogens.
 Histidine Catabolism

• The end product of histidine catabolism:

• glutamate, making histidine one of the
glucogenic amino acids.
 Histidine Catabolism

• Another key feature of histidine catabolism:

• it serves as a source of ring nitrogen to
combine with tetrahydrofolate (THF),
• producing the 1-carbon THF intermediate
known as N5-formiminoTHF.
• The latter reaction:
• one of two routes to N5-formiminoTHF.
 Tryptophan Catabolism

• A number of important side reactions occur

• during the catabolism of tryptophan on the
pathway to acetoacetate.
• The first enzyme of the catabolic pathway:
• an iron porphyrin oxygenase that opens the indole
ring.
• The latter enzyme:
• highly inducible, its concentration rising almost
10-fold on a diet high in tryptophan.
 Tryptophan Catabolism
• Kynurenine:
• the first key branch point intermediate in the
pathway.
• undergoes deamination in a standard
transamination reaction;
• yielding kynurenic acid.
• Kynurenic acid and metabolites:
• have been shown to act as antiexcitotoxics and
anticonvulsives.
 Tryptophan Catabolism
• A second side branch reaction:
• produces anthranilic acid plus alanine.
• Another equivalent of alanine:
• produced further along the main catabolic
pathway,
• and it is the production of these alanine:
• residues that allows tryptophan to be classified
among the glucogenic and ketogenic amino acids.
 Tryptophan Catabolism
• The second important branch point converts
kynurenine:
• into 2-amino-3-carboxymuconic
semialdehyde,
• which has two fates.
• The main flow of carbon elements from this
intermediate:
• to glutarate.
 Tryptophan Catabolism
• An important side reaction in liver:
• a transamination;
• and several rearrangements to produce
limited amounts of nicotinic acid,
• which leads to production of a small
amount of NAD+ and NADP+
 Tryptophan Catabolism
• Aside from its role as an amino acid in
protein biosynthesis,
• tryptophan also serves as a precursor:
• for the synthesis of serotonin;
• and melatonin.
 LITERATURE CITED
• Devlin,T.M. Textbook of Biochemistry with
Clinical Correlations,Fifth Edition,Wiley-Liss
Publications,New York, USA, 2002.
• Lehninger, A. Principles of Biochemistry, Second
edition, Worth Publishers Co., New York, USA,
1993.
• Matthews, C.K. and van Holde, K.E.,
Biochemistry, Second edition, Benjamin /
Cummings Publishing Company Inc., San
Francisco, 1996.