Amino Acid Metabolism

Will be interested in two things:
1) origin of nitrogen atoms and their incorporation into amino group
2) origin of carbon skeletons
AMINO ACID SYNTHESIS
Nitrogen fixation
Gaseous nitrogen is chemically unreactive due to strong triple bond.
To reduce nitrogen gas to ammonia takes a strong enzyme --> reaction is called nitrogen fixation.
Only a few organisms are capable of fixing nitrogen and assembling amino acids from that.
Higher organisms cannot form NH4
+
from atmospheric N2.
Bacteria and blue-green algae (photosynthetic procaryotes) can because they possess nitrogenase.
Enzyme has two subunits:
1) strong reductase - has Fe-S cluster that supplies e- to second subunit
2) two re-dox centers, one of which is a nitrogenase
Composed of iron and molybdenum that reduces N2 to NH4
+
Reaction is ATP-dependent, but unstable in the presence of oxygen.
Enzyme is present in Rhizobium, symbiotic bacterium in roots of legumes (i.e. soybeans)
Nodules are pink inside due to presence of leghemoglobin (legume hemoglobin) that binds to oxygen
to keep environment around enzyme low in oxygen (nitrogen fixation requires the absence of
oxygen)
Plants and microorganisms can obtain NH3 by reducing nitrate (NO3
-) and nitrite (NO2
-
) --> used to
make amino acids, nucleotides, phospholipids.
Assimilation of Ammonia
Assimilation into amino acids occurs through glutamate and glutamine.
-amino group of most amino acids comes from -amino group of glutamate by transamination.
Glutamine contributes its side-chain nitrogen in other biosynthetic reactions.
Reaction:
NADPH +H
+
NADP
+
NH4
+
+ -ketoglutarate glutamate + H2O
glutamate dehydrogenase
Another reaction that occurs in some animals is the incorporation of ammonia into glutamine via
glutamine synthetase:
glutamate + NH4
+
+ ATP glutamine + ADP + Pi + H
+
2
When ammonium ion is limiting, most of glutamate is made by action of both enzymes to produce the
following (sum of both reactions):
NH4
+
+ -ketoglutarate + NADPH + ATP glutamate + NADP
+
+ ADP + Pi
Transamination Reactions
Having assimilated the ammonia, synthesis of nearly all amino acids is done via tranamination
reactions.
Glutamate is a key intermediate in amino acid metabolism
Amino group is transferred to produce the corresponding -amino acid.
transaminase
<------------->
-amino acid1 -keto acid2 -keto acid1 -amino acid2
Origins of Carbon Skeletons of the Amino Acids
Amino acids that must be supplied in diet are termed essential; others are nonessential.
Although the biosynthesis of specific amino acids is diverse, they all share a common feature -
carbon skeletons come from intermediates of glycolysis, PPP, or citric acid cycle.
There are only six biosynthetic families:
1) Derived from oxaloacetate --> Asp, Asn, Met, Thr, Ile, Lys
2) Drived from pyruvate --> Ala, Val, Leu
3) Derived from ribose 5-phosphate --> His
4) Derived from PEP and erythrose 4-phosphate --> Phe, Tyr, Trp
5) Derived from a-ketoglutarate --> Glu, Gln, Pro, Arg
6) Derived from 3-phosphoglycerate --> Ser, Cys, Gly
Porphyrin Synthesis
First step in biosynthesis of porphyrins is condensation of glycine and succinyl CoA to form -
aminolevulinate via -aminolevulinate synthase.
Translation of mRNA of this enzyme is feedback-inhibited by heme
Second step involves condensation of two molecules of -aminolevulinate to form porphobilinogen;
catalyzed by -aminolevulinate dehydrase.
Third step involves condensation of four porphobilinogens to form a linear tetrapyrrole via
porphobilinogen deaminase.
This is cyclized to form uroporphyrinogen III.
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Subsequent reactions alter side chains and degree of saturation of porphyrin ring to form
protoporphyrin IX.
Association of iron atom creates heme; iron atom transported in blood by transferrin.
Inherited or acquired disorders called porphyrias are result of deficiency in an enzyme in heme
biosynthetic pathway.
congenital erythropoietic porphyria - insufficient cosynthase (cyclizes tetrapyrrole)
Lots of uroporphyrinogen I, a useless isomer are made
RBCs prematurely destroyed
Patient’s urine is red because of excretion of uroporphyrin I
Heme Degradation:
Old RBCs are removed from circulation and degraded by spleen.
Apoprotein part of hemoglobin is hydrolyzed into amino acids.
First step in degradation of heme group is cleavage of -methene bridge to form biliverdin, a linear
tetrapyrrole; catalyzed by heme oxygenase; methene bridge released as CO.
Second step involved reduction of central methene bridge to form bilirubin; catalyzed by biliverdin
reductase.
Bilirubin is complexed with serum albumin --> liver --> sugar residues added to propionate side
chains.
2 glucuronates attached to bilirubin are secreted in bile.
Jaundice - yellow pigmentation in sclera of eye and in skin --> excessive bilirubin levels in blood
Caused by excessive breakdown of RBCs, impaired liver function, mechanical obstruction of
bile duct.
Common in newborns as fetal hemoglobin is broken down and replaced by adult hemoglobin.
AMINO ACID CATABOLISM
Excess amino acids (those not used for protein synthesis or synthesis of other macromolecules)
cannot be stored.
Surplus amino acids are used as metabolic fuel.
-amino group is removed; carbon skeleton is converted into major metabolic intermediate
Amino group converted to urea; carbon skeletons converted into acetyl CoA, acetoacetyl CoA,
pyruvate, or citric acid intermediate.
Fatty acids, ketone bodies, and glucose can be formed from amino acids.
Major site of amino acid degradation is the liver.
First step is the transfer of -amino group to -ketoglutarate to form glutamate, which is
oxidatively deaminated to yield NH4
+
(see pathway sheet).
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Some of NH4
+ is consumed in biosynthesis of nitrogen compounds; most terrestrial vertebrates
convert NH4
+ into urea, which is then excreted (considered ureotelic).
Terrestrial reptiles and birds convert NH4
+
into uric acid for excretion (considered uricotelic).
Aquatic animals excrete NH4+ (considered ammontelic).
In terrestrial vertebrates NH4
+ is converted to urea via urea cycle.
One of nitrogen atoms in urea is transferred from aspartate; other is derived from NH4
+
; carbon
atom comes from CO2.
UREA CYCLE
There are six steps of the urea cycle:
1) Bicarbonate ion, NH4
+
and 2 ATP necessary to form carbamoyl phosphate via carbamoyl
phosphate synthetase I (found in mitochondrial matrix).
2) Carbamoyl phosphate and ornithine (carrier or carbon and nitrogen atoms; an amino acid,
but not a building block of proteins) combine to form citrulline via ornithine
transcarbamoylase
3) Citruilline is transported out of mitochondrial matrix in exchange for ornithine
4) Citruilline condenses with aspartate --> arginosuccinate via an ATP-dependent reaction via
arginosuccinate synthetase
5) Arginosuccinate cleaved to form fumarate and arginine via arginosuccinate lyase
fumarate --> malate--> oxaloacetate --> gluconeogenesis
oxaloacetate has four possible fates:
1) transamination to aspartate
2) conversion into glucose via gluconeogenesis
3) condensation with acetyl CoA to form citrate
4) conversion into pyruvate
6) Two -NH2 groups and terminal carbon of arginine cleaved to form ornithine and urea via
arginase
Ornithine is transported into mitochondrion to repeat cycle
Overall reaction:
CO2 + NH4
+ + 3 ATP + aspartate + 2 H2O ---> urea + 2 ADP + 2 Pi + AMP + PPi + fumarate
Inherited defects in urea cycle:
1) Blockage of carbamoyl phosphate synthesis leads to hyperammonemia (elevated levels of
ammonia in blood)
2) argininosuccinase deficiency
Providing surplus of arginine in diet and restricting total protein intake
Nitrogen is excreted in the form of argininosuccinate
3) carbamoyl phosphate synthetase deficiency or ornithine transcarbamoylase deficiency
5
Excess nitrogen accumulates in glycine and glutamine; must then get rid of these
amino acids
Done by supplementation with benzoate and phenylacetate (both substitute for urea
in the disposal of nitrogen)
benzoate --> benzoyl CoA --> hippurate
phenylacetate --> phenylacetyl CoA --> phenylacetylglutamine
Fate of Carbon Skeleton of Amino Acids
Used to form major metabolic intermediates that can be converted into glucose or oxidized by
citric acid cycle.
All 20 amino acids are funneled into seven molecules:
1) pyruvate
2) acetyl CoA
3) acetoacetyl CoA
4) -ketoglutarate
5) succinyl CoA
6) fumarate
7) oxaloacetate
Those that are degraded to acetyl CoA or acetoacetyl Coa are termed ketogenic because they give
rise to ketone bodies.
Those that are degraded to pyruvate or citric acid cycle intermediates are termed glucogenic.
Leucine and lysine are only ketogenic --> cannot be converted to glucose
Isoleucine, phenylalanine, tryptophan, tyrosine are both.
All others are glucogenic only.
C3 family (alanine, serine, cysteine) ---> pyruvate
C4 family(aspartate and asparagine) ---> oxaloacetate
C5 family (glutamine, proline, arginine, histidine) ---> glutamate ---> -ketoglutarate
Methionine, isoleucine, valine, threonine --> succinyl CoA
Leucine --> acetyl CoA and acetoacetate
Phenylalanine and tyrosine --> acetoacetate and fumarate
Tryptophan --> pyruvate
Regulation of the Urea Cycle
The main allosteric enzyme is glutamate dehydrogenase.
It is inhibited by high GTP and ATP levels.
It is stimulated by high GDP and ADP levels.