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Nitrogen fixation and assimilation

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Amino acids are glucogenic, ketogenic, or both. Table 15.2 ... Aromatic amino acids: glucogenic (alanine or fumarate) and ketogenic amino acids (acetoacetate) ... – PowerPoint PPT presentation

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Title: Nitrogen fixation and assimilation


1
Ch. 15 Nitrogen metabolism
  • Nitrogen fixation and assimilation
  • Available fixed nitrogen nitrate(NO3-), nitrite
    (NO2-), ammonia (NH4)
  • Colonizing the root nodules of leguminous plants,
    some marine cyanobacteria
  • Artificial nitrogen fixation 300-500oC, 300 atm
  • Biological N2 reduction requires many ATP and a
    strong reducing agent, carried out by nitrogenase
    (inactivated by oxygen)

Figure 15.01 Root nodules from clover.
2
  • Other sources of fixed nitrogen
  • nitrate(NO3-) naturally present nitrogen,
    reduced to ammonia (NH4) by plants and bacteria
  • Nitrification
  • Denitrification

Figure 15.03 The nitrogen cycle.
3
  • Assimilation of ammonia
  • Glutamine synthetase
  • ? a metabolic entry point for fixed nitrogen
  • Glutamate ATP NH4 ? glutamine
    ADP Pi
  • tightly regulated allosteric regulation (E.
    coli, dodecamer)
  • Glutamate synthase provides glutamates for
    accepting amino group
  • a -ketoglutarate glutamine NADPH ? 2
    Glutamate NADP
  • Net result
  • a-ketoglutarate NADPH ATP NH4
  • ? Glutamate ADP Pi
    NADP

4
  • 2. Transamination
  • Glutamate served as a amino-group donor
  • Transaminase (fig 15.5)
  • catalyze the transfer of an amino group to an
    a-keto acid
  • ? Freely reversible, involved in synthesis and
    degradation of amino acids
  • PLP(Pyridoxal-5-phosphate)
  • ? a prosthetic group of pyridoxine to that the
    amino group is transiently attached
  • ? Linked to eamino group of lysine
  • Markers for damaged tissues SGOT, SGPT

5
Figure 15.05 PLP-catalyzed transamination.
6
  • 3. Amino acid biosynthesis
  • Synthesized from intermediates of glycolysis, the
    citric acid cycle, and the pentose phosphate
    pathway
  • Amino group donor glutamate, glutamine
  • 10 Essential amino acids

7
Figure 15.06 Nitrogen metabolism in context.
8
Synthesis of nonessential amino acids
9
Tetrahydrofolate a carrier of one-carbon units,
vitamin
Figure 15.07 Tetrahydrofolate.
10
  • Synthesis of essential amino acids
  • present only in microorgansims
  •  considerably more complex than for nonessential
    amino acids
  •   use familiar metabolic precursors
  •   show species variation
  • (1) Aspartate Family lysine,
    methionine,threonine
  •     (2) Pyruvate Family leucine, isoleucine,
    valine
  •     (3) Aromatic Family phenylalanine, tyrosine,
    tryptophan
  •     (4) Histidine

11
channeling movement of a reactant between two
active sites ex tryptophan synthase (a, b
subunit - indole)
Figure 15.08 Tryptophan synthase.
12
(4) Histidine
13
  • 4. Amino acids as metabolic precursors
  • Amino acids synthesized to proteins, converted
    to nucleotides, heme groups, neurotransmitters
  • Many neurotransmitters are amino acid
    derivatives
  • Neurotransmitters

Glutamate, Glycine GABA dopamine,
norepinephrine, epinephrine Serotonine
Prozac Melatonin NO (Box 15-A)
14
  • Nucleotides biosynthesis
  • Synthesized from several amino acids
  • No true dietary requirement efficient
    biosynthetic and salvage pathways

15
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17
Figure 15.09 AMP and GMP synthesis from IMP.
18
Pyrimidine biosynthesis     UMP synthesis
feedback inhibition by UMP, UDP, UTP   
19
  • Synthesis of CTP from UTP

20
Synthesis of dNTPs reduction of ADP, GDP, CDP,
UDP to dADP, dGDP, dCDP, dUDP by ribonucleotide
reductase (box 15.B)
Ribonucleotide reductase
21
Synthesis of dTMP from dUMP
Thymidylate synthase dihydrofolate reductase vs
cancer          Anticancer agent inhibitor of
thymidylate synthase dihydrofolate reductase ,
eg 5-fluorodeoxyuridylate, methotrexate
22
Thymidylate synthase dihydrofolate reductase
in one enzyme in plant and protozoa Figure 15.10
The bifunctional thymidylate synthase-dihydrofolat
e reductase of the protozoan Leishmania.
23
  • 5. Amino acids catabolism
  • Amino acids as metabolic fuel
  • Cells lining small intestine use dietary amino
    acids as E source
  • liver aa originated from the diet, biosynthetic
    reactions and turnover of intracellular proteins
    (breakdown of muscle tissue)
  • ? the catabolism of aa in the liver is not
    complete synthesized to glucose and exported to
    other tissues

24
  • Amino acids are glucogenic, ketogenic, or both
  • glucogenic amino acids
  • ketogenic amino acids
  • Both glucogenic and ketogenic amino acids
  • Table 15.2
  • Ala, Asp, Glu converted to gluconeogenic
    substrates by transamination (Pyruvate, OAA,
    a-ketoglu)
  • ? Asn, Gln, Ser deamination (Asp, glu, pyruvate)
  • ? Pro, Arg, His converted to aketoglutarate via
    Glu
  • ? Cys release ammonia and sulfur and converted
    to pyruvate

25
  • Amino acids are glucogenic, ketogenic, or both
  • Table 15.2
  • Ala, Asp, Glu converted to gluconeogenic
    substrates by transamination (Pyruvate, OAA,
    a-ketoglu)
  • ? Asn, Gln, Ser deamination (Asp, glu, pyruvate)
  • ? Pro, Arg, His converted to aketoglutarate via
    Glu
  • Cys release ammonia and sulfur and converted to
    pyruvate
  • ? Thr glucogenic and ketogenic and converted to
    glycine actyl-CoA
  • ? Gly converted to methylene-tetrahydrofolate by
    glycine cleavage system (a multiprotein complex)
  • ? Branched chain amino acids transamination,
    oxidative decarboxylation (fig 15.11)
  • ? Aromatic amino acids glucogenic (alanine or
    fumarate) and ketogenic amino acids
    (acetoacetate)
  • tetrahydrobiopterine

26
Figure 15.11 The initial steps of valine
degradation.
27
First step of phenylalanine degradation.
28
Inborn errors of metabolism (Box 15.C)
29
  • 6. Nitrogen disposal The urea cycle
  • Urea 80 of the bodys excess nitrogen is
    excreted as urea
  • cf ammonia not a good form of disposal of
    excess nitrogen (neurotoxicity)
  • Glutamate supplies nitrogen to the urea cycle
  • Glutamate one of the most abundant amino acids
    inside cells
  • Glutamate dehydrogenase mitochondrial enzyme,
    reversible
  • ? Carbamoyl phosphate synthetase

The carbamoyl phosphate synthetase reaction.
30
The urea cycle consists of four reactions Also
synthesized arginine (BUT essential?)
Figure 15.13 The four reactions of the urea
cycle.
31
The urea cycle consists of four reactions
Figure 15.14 The urea cycle and related
reactions.
32
  • The urea cycle consists of four reactions
  • Six enzymes mitochondrial and cytosolic,
  • i) citrullinemitochondria ? ctyosol
  • ii) ornithine ctyosol? mitochondria
  • E consideration 4 ATP consumption/urea, but
    2NADH generation/urea ? 2 ATP gaining
  • Regulation carbamoyl phosphate synthetase by
    N-acetylglutamate

Figure 15.14 The urea cycle and related
reactions.
33
  • Other mechanisms for nitrogen disposal
  • Uric acids birds, reptile, WHY NOT UREA?
  • Problem of uric acids kidney stone,
    precipitation in joint
  • Excess pyrimidine bases can be degraded to CoA
    adducts
  • ? Excess purine bases excreted
  • Urease breaks down urea
  • Urea H2O ? 2 NH3 CO2
  • Present in bacteria, fungi
  • ? The first enzyme to be crystalized (in 1926)

Figure 15.15 Urease.
34
Uric acid is an end product of purine
catabolism - Catabolism and Salvage of Purine
Nucleotides         
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