17' Nitrogen fixation and amino acid biosynthesis

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17. Nitrogen fixation and amino acid biosynthesis
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Nitrogen cycles between oxidized reduced forms
in the biosphere
degradation (animals microorganisms)
synthesis (microorganisms, plants animals)
(Rhizobium some other bacteria)
nitrification (Nitrosomonas other soil
bacteria)
nitrification (Nitrobacter other soil
bacteria)
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In the industrial Haber process, N2 is reduced to
NH3 by H2 at high temperature and pressure with
an iron oxide catalyst
The reaction is exothermic by 92.4 kJ/mol at
standard temperature pressure, but has a very
high activation energy
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The roots of leguminous plants have nodules
containing N2-fixing bacteria
Lehninger Fig. 22-4a
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Bacteroids containing nitrogenase are found
inside the nodule cells
bacteroids (rod-like bacteria)
plant cell nucleus
Lehninger Fig. 22-4b. (This electron micrograph
is colorized artificially.)
Nitrogenase is very sensitive to O2. It is
protected in the nodules by a high concentration
of leghemoglobin, a heme protein with a strong
affinity for O2. Leghemoglobin is produced by
the plant, but carries O2 for reduction by the
bacterial respiratory chain, keeping the O2
concentration low.
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Nitrogenase from Azobacter vinelandii contains
iron-sulfur and iron-molybdenum centers
Azotobacter are free-living, aerobic soil
bacteria.
Fe-Mo protein FeS cluster and Fe-Mo cofactor
Fe protein FeS cluster two ATP-binding sites
structurally homologous to G-proteins
1n2c.pdb
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Nitrogenase from Azobacter vinelandii
Mo-Fe-S cluster (Mo7Fe9S)
8Fe7S cluster
4Fe4S cluster
Mg ADP (2)
1n2c.pdb
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The Fe-Mo cofactor
Cys residue of the protein
Intermediates in which partially reduced
derivatives of N2 replace one of the O atoms
bound to the Mo have been proposed, but the
mechanism of the N2-fixation reaction is not
known.
Homocitrate (3-hydroxy-3-carboxyadipic acid)
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Nitrogenase uses 8 electrons and 16 ATP to
reduce N2 2 H to 2 NH4 H2
The Fe protein transfers one electron at a time
to the Fe-Mo protein.
The ATP stoichiometry is uncertain. Only 8 ATP
are needed under some conditions.
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Ammonia is incorporated into many biological
molecules through glutamate and glutamine
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Glutamine synthetase catalyzes formation of
glutamine from glutamate and NH4
glutamine synthetase
Glu
Gln
The reaction proceeds through an enzyme-bound
?-glutamylphosphate intermediate
glutaminase
In terrestrial animals, Gln serves to carry
ammonia in the blood to the liver kidneys,
where it is hydrolyzed for excretion as urea.
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Glutamine serves as a donor of amine groups for
synthesis of many other molecules
carbamoyl-phosphate
glucosamine-6-P
histidine
tryptophan
AMP
CTP
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Six of the end-products inhibit glutamine
synthetase allosterically
The inhibitory effect of the products acting
together is greater than the sum of their
individual effects.
glycine
alanine
Ser, Gly Ala inhibit at the substrate binding
site
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E. coli glutamine synthetase also is controlled
by covalent modification
Gln
ATP PPi
adenylylation
deadenylylation
ADP Pi
a-keto-glutarate
adenyl group
The regulation by Gln and a-ketoglutarate
involves similar covalent modifications
(uridylylation) of the enzymes that add or remove
the adenyl group.
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Bacterial glutamine synthetase has 12 identical
subunits
views of the Salmonella typhimurium enzyme
parallel and perpendicular to the 6-fold symmetry
axis
2gls.pdb
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The carbon chains of the common amino acids
provide materials that feed into the citric acid
cycle
isoleucine leucine threonine tryptophan
alanine cysteine glycine serine threonine tryptoph
an
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Amino acids can be classified as glucogenic or
ketogenic
leucine lysine phenylalanine tryptophan tyrosine
ketogenic
Some fall in both groups
acetoacetyl-coA
arginine glutamine histidine proline
glutamate
isoleucine leucine threonine tryptophan
acetyl-coA
?-ketoglutarate
isoleucine methionine threonine valine
succinyl-CoA
oxaloacetate
pyruvate
alanine cysteine glycine serine
threonine tryptophan
phenylalanine tyrosine
fumarate
asparagine aspartate
glucogenic
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Humans can synthesize 10 of the 20 common amino
acids
Arg is essential in infants and growing children
but not in adults.
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Building blocks for amino acid synthesis in
humans come from glycolysis and the citric acid
cycle
glucose
glycine
3-phosphoglycerate
serine
cysteine
pyruvate
alanine
proline
citrate
oxaloacetate
glutamate
glutamine
a-ketoglutarate
aspartate
arginine
asparagine
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Serine is formed via 3-phosphoglycerate
3-phosphoglycerate
3-phosphohydroxypyruvate
NADH
NAD
Glu
a-kG
serine
3-phosphoserine
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Plants and bacteria synthesize aromatic amino
acids from carbohydrates via shikimic acid
OH- CO2
prephenate
chorismate
I dont expect you to memorize this pathway.
Humans cant synthesize aromatic amino acids de
novo.