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Nitrogen Metabolism
Pratt and Cornely Chapter 18
• Nitrogen assimilation
• Amino acid biosynthesis
– Nonessential aa
– Essential aa
• Nucleotide biosynthesis
• Amino Acid Catabolism
• Urea Cycle
Juicy Steak Part 2
Nitrogen fixation
• Bacteria
• Nitrogenase
• Costly—16 ATP
per N2 molecule
Assimilation into Amino Acids
• In microorganisms/plants: assimilation of
ammonia is key—synthesis of most amino acids
– Glutamine synthetase incorporates amino group
– Coupled to glutamate synthase: reductive
amination of a-ketoglutarate to glutamate
Net Reaction
• a-KG + NH3 +ATP + NADPH  Glu + ADP + NADP+
• Ultimately, this is incorporation of ammonia into
an amino acid
• Glutamate can then be used to distribute
nitrogen into other amino acids (transamination)
Assimilation into Amino Acids
• In humans: acquire nitrogen in amino acids
– Amino acids in diet
– Glutamate distributes amino group to new amino
acids through transamination
– No need for glutamate synthase
– Glutamine synthetase used for different purpose:
to “mop up” ammonia
• Transfers assimilated nitrogen into all other
amino acids
• Requires PLP cofactor
• Dietary
• Ambiguous
– Stage of life (Arg)
– Precursor (Tyr, Cys)
• Mechanism of
biosynthesis can be
Amino Acid Biosynthesis
Non-essential Amino Acid Biosynthesis
• Transamination
– Pyruvatealanine
– Oxaloacetateaspartate
– a-ketoglutarateglutamate
• Amidation
– Glutamine (glutamine synthetase)
– Asparagine (asparagine synthetase)
Glutamate Backbone
• 3-phosphoglycerate Serine
• Serineglycine
– THF as a major one-carbon transfer vitamin
• Serinecysteine by incorporating sulfur from
homocysteine (Made from methionine)
• Monooxygenase uses O2 for hydroxylation
– Other atom ends up in water
– Requires a reducing cofactor called
• Also first step in catabolism of phenylalanine
• Which amino acid?
Nucleotide Biosynthesis
• 5-PRPP
• Purine: base built
onto ribose
– Asp, Gly, Glu,
THF, bicarbonate
• IMP produced
AMP/GMP Production
• Branched
• AMP: amination
• GMP: oxidation
• Branch allows for
• Contrast
• Base made
first, then
attached to
• Not branched:
UMP made to
UTP then to
Ribonucleotide Reductase
• Essential reaction: reduction
to make dNDP
• Very difficult reaction
• Free radical
• Enzyme is oxidized in the
– Reduced by thioredoxin
– In turn, thioredoxin reduced by
Production of TMP
• dUTP must be
converted to TMP
• Methylene donated
from THF by
thymidylate synthase
• THF oxidized to DHF
• Chemotherapy: dUMP
Regenerating THF
• DHF must be reduced to
THF by DHF reductase
• NADPH dependent
• Chemotherapy target
– DHF analogs such as
• Salvage pathway
through phosphorolysis
• Purines made into uric
acid (waste)
• Pyrimidines broken
down into catabolic
Amino acid catabolism
Ketogenic vs. Glucogenic
Problem 35
• The catabolic pathways for the 20 amino acids
vary considerably, but all amino acids are
degraded to one of seven metabolites:
pyruvate, a-ketoglutarate, succinyl-CoA,
fumarate, oxaloacetate, acetyl CoA, or
acetoacetate. What is the fate of each of these
Amino Acid Degradation
• Transamination and deamination
• Then carbon chain is metabolized
• Examples:
Pyruvate Producing
A variety of enzymes convert 3-C chains
Glutamate Family
• 25% of dietary intake
Thr: Both Glucogenic and Ketogenic
Many mammals:
In humans:
Glycine Cleavage system
Branched Amino Acids
• Major energy source in muscle
• Steps of degradation
– Transamination
– Oxidative decarboxylation (Pyruvate DH)
– Beta oxidation
• Valine: succinyl CoA
• Isoleucine: succinyl CoA and acetylCoA
• Leucine: acetyl CoA and ketone body
Problem 40
• Leucine is degraded to acetyl CoA and
acetoacetate by a pathway whose first two
steps are identical to those of valine
degradation (Figure 18-11). The third step is
the same as the first step of fatty acid
oxidation. The fourth step involves an ATPdependent carboxylation, the fifth step is a
hydration, and the last step is a cleavage
reaction to give products. Draw the
intermediates of leucine degradation.
Aromatic Amino Acids
• Monoxygenases and Dioxygenases
• First recognition of inborn errors of
• List all the reactions in this chapter that
generate free ammonia.
Ammonia Processing
• Most tissues: glutamine synthetase “mops up”
ammonium generated in metabolism
– glutamine then sent through blood to liver
– Deaminated in liver to give glutamic acid
• glutaminase
Ammonia Processing
• Muscle: The alanine-glucose cycle
• Glutamate also accepts amino group from
other amino acids
Glutamate Dehydrogenase
• Reversible reaction
• Grabs free ammonia and releases it in liver
Role of Liver Mitochondia
• Sequester toxic ammonia
• Make less toxic, execrable form
• Urea Cycle
Carbamoyl phosphate
• Cost of 2 ATP
– Phosphate leaving group
• Activation of ammonia for
– Excretion
– biosynthesis
Problem 52
• Which three mammalian enzymes can
potentially “mop up” excess NH4+?
Urea Cycle
Chemistry of Urea Cycle
• Catalytic
• Fumarate
• Urea = 4 ATP
Urea Cycle Regulation
• Carbamoyl phosphate synthetase
• Amino acid catabolism boosts acetyl CoA and
glutamate levels
• Produces activator
Problem 55
• An inborn error of metabolism results in the
deficiency of argininosuccinase. What could
be added to the diet to boost urea production
aid in ammonia secretion? (Argininosuccinate
can be excreted.)
Solving Metabolic Problems
• Arginosuccinase deficiency
• Low protein diet
– Minimize ammonium
• High arginine diet
– Provide carrier
Nitrogen Flow Overview
Summary: Main Players
• Glutamate: in liver, receives nitrogen from AA,
then ammonia is released in liver mitochondria
• Glutamine: ammonia transport; biosynthesis
• Alanine: ammonia transport
• Aspartate: nitrogen donor to urea
• Arginine: urea cycle