Chapter 23

The Metabolism of
Nitrogen

Nitrogen Fixation
Nitrogen fixation is the reduction of N2 to NH3:
Bacteria are responsible for the reduction and typically
form symbiotic relationships that result in nodules on
the roots of leguminous plants
Reduction is catalyzed by the nitrogenase enzyme
complex
N2 to ammonium ion is a six-electron reduction

The Path of Electrons from Ferrodoxin to N2

Summary
Nitrogen enters the biosphere by the process of
nitrogen fixation.
Atmospheric nitrogen is converted to ammonia in its
conjugate acid form, ammonium ion.
The nitrogenase enzyme found in root nodules of
leguminous plants catalyzes crucial reactions in
nitrogen fixation

Feedback Inhibition in Nitrogen Metabolism

If there is a high level of
end product amino acid or
nucleotide, the cell saves
energy by not making the
compound through a
feedback mechanism
In summary, because the
biosynthetic pathways for
many nitrogen-containing
compounds are long and
complex, feedback
inhibition helps save
energy

Amino Acid Biosynthesis

Common features of amino acid biosynthesis include:
transamination and one-carbon transfers
Glutamate is formed by reductive amination of -ketoglutarate
and NH4+

Amidation of glutamate gives glutamine

All amino acids are grouped into families based on their

biosynthetic pathways

Amino Acid Biosynthesis (Contd)

Amino Acids and The Citric Acid Cycle

Role of Pyridoxal Phosphate in Amino Acid

Reactions
The biologically active form of vitamin B6 is pyridoxal
phosphate (PyrP)
PyrP participates in the catalysis of a wide variety of
reactions of amino acids, including transaminations
and decarboxylations
Pyridoxal phosphate forms an imine (a Schiff base)
with the -amino group of an amino acid
Rearrangement gives an isomeric imine
Hydrolysis of the isomeric imine gives an -ketoacid
and pyridoxamine
All reactions are reversible

Role of Pyridoxal Phosphate in Amino Acid

Reactions (Contd)

Role of Pyridoxal Phosphate in Amino Acid

Reactions (Contd)
Transamination reactions switch amino groups form
one amino acid to an -keto acid

A Transamination Reaction Results in

Generation of Serine

Serine to Glycine Involves the Transfer of a

One-Carbon Unit
Serine to glycine is an example of a one-carbon
transfer
The one-carbon acceptor is tetrahydrofolate, which
is derived from folic acid

Serine to Glycine Involves the Transfer of a

One-Carbon Unit (Contd)
Reduction of folic acid gives tetrahydrofolic acid
(THF), the reactive form of the coenzyme
Tetrahydrofolate is a carrier of the one-carbon
groups shown in Figure 23.11 (see next slide)

Structure and Reactions of Folic Acid

Serine to Cysteine
In plants and bacteria, serine is acetylated to form Oacetylserine
The source of sulfur in plants and bacteria differ from
that in animals
Sulfur donor comes from PAPS (3-Phospho5adenylylsulfate)

Serine to Cysteine (Contd)

Methionine
Methionine cannot be
produced in animals,
making it an essential
amino acid
Methionine reacts with
ATP to form Sadenosylmethionine
(SAM)

Cysteine in Animals
SAM is a methyl group carrier and this methyl group
can be transferred to a number of acceptors
producing S-adenosylhomocysteine

Summary
Two of the most important classes of reactions in the
biosynthesis of amino acids are transamination
reactions and one-carbon transfers
The amino acids glutamate and glutamine are the
principal donors of amino groups in transamination
reactions
Carriers of one-carbon groups include biotin, SAM,
and derivatives of folic acid

Essential Amino Acids

The biosynthesis of proteins requires the presence of all the
constituent amino acids
Some species, including humans, cannot produce all of the
amino acids and they must come from the diet, and are called
essential amino acids
In Summary:
Humans cannot produce some amino acids in sufficient
quantities to meet their metabolic needs. These are called
essential amino acids
The essential amino acids must come from other dietary
sources

Amino Acid Catabolism

First step is removal of the -amino group by
transamination
-amino group is transferred to -ketoglutarate to give
glutamate and an -ketoacid

The breakdown of carbon skeletons follows two

pathways, depending on the type of endproduct
Glucogenic amino acid: one whose carbon skeleton
is degraded to pyruvate or oxaloacetate, both of which
may then be converted to glucose
Ketogenic amino acid: one whose carbon skeleton
is degraded to acetyl-CoA or acetoacetyl-CoA, both of
which may then be converted to ketone bodies

Amino Acid Catabolism (Contd)

Amino Acid Catabolism (Contd)

The -amino group which
has been transferred to ketoglutarate has one of
two fates:
It may be used for
biosynthesis
It may be excreted as a
part of a nitrogencontaining product

The Urea Cycle

The urea cycle is the central pathway in nitrogen
metabolism
The nitrogens come from several sources
Steps of the cycle are outlined in Figure 23.18 (see
next slide)

The Urea Cycle (Contd)

Summary
The carbon skeleton has two fates in the breakdown
process. Some carbon skeletons give rise to
pyruvate or oxaloacetate, which can be used in
gluconeogenesis. Others give rise to acetyl-CoA or
acetoacetyl-CoA, which can form lipids
The urea cycle, which has links to the citric acid
cycle, plays a central role in nitrogen metabolism. It
is involved in both the anabolism and the catabolism
of amino acids

Purine Biosynthesis
Where do the atoms of purines come from?

How is IMP converted to AMP and GMP

IMP is the precursor to AMP and GMP, and the
conversion takes place in 2 stages

Regulation of ATP and GTP by Feedback

Inhibition
Purine nucleotide biosynthesis is
regulated by feedback inhibition
In Summary:
The growing ring system of
purines is attached to ribose
phosphate during the synthesis
process
The biosynthesis of nucleotides
requires considerable
expenditures of energy by
organisms in long and complex
pathways. Feedback inhibition at
all stages plays a key role in
regulating the pathway

Purine Catabolism
The catabolism of purine nucleotides proceeds by
hydrolysis to the nucleoside and subsequently to the
free base, which is further degraded
Salvage reactions are important in the metabolism of
purine nucleotides because of the amount of energy
required for the synthesis of the purine bases
In Summary:
Purines are degraded to uric acid in primates and are
further degraded in other organisms. Overproduction
of uric acid causes gout in humans
Salvage reactions exist so that some purines can be
reused

Purine Catabolism (Contd)

Purine Salvage

Pyrimidine Biosynthesis and Catabolism

The overall scheme of pyrimidine biosynthesis differs
from that of purines because the pyrimidine ring is
assembled before it is attached to ribose-5phosphate
Carbon and Nitrogen atoms of the pyrimidine ring
come from carbamoyl phosphate and aspartate
The production of N-carbamoylaspartate is the
committed step in pyrimidine biosynthesis

Pyrimidine Biosynthesis and Catabolism

(Contd)

Pyrimidine Biosynthesis and Catabolism

(Contd)

Pyrimidine Biosynthesis and Catabolism

(Contd)
Feedback inhibition in
pyrimidine nucleotide
biosynthesis takes
place in several ways

Pyrimidine Biosynthesis and Catabolism

(Contd)
Pyrimidine catabolism involves the breakdown of the
molecule first to the nucleoside, and then to the base
This is similar to what happens in purine catabolism

Summary
The ring system of pyrimidines is assembled before
it is attached to ribose phosphate

During breakdown, the nucleoside is formed first,

then the base. Ring-opening reactions of the base
complete the degradation

Conversion of Ribonucleotides to
Deoxyribonucleotides
Ribonucleoside diphosphates are reduced to 2deoxyribonucleoside diphosphates in all organisms
NADPH is the reducing agent

Conversion of Ribonucleotides to
Deoxyribonucleotides (Contd)

Conversion of dUDP to dTTP

The addition of a methyl
group to uracil to
produce thymine
requires
tetrahydrofolate as the
one-carbon carrier. This
process is a target for
cancer chemotherapy

Thymidylate Synthase