BIOSYNTHESIS

OF AMINO ACIDS

Muntholib
Department of Chemistry
State University of Malang
BIOSYNTHESIS OF AMINO ACIDS
•Biosynthesis of the 20 common amino acids
is considered from the origins and fates of
their:
(1) Nitrogen atoms
(2) Carbon skeletons
•For mammals:
Essential amino acids must be obtained
from diet
Nonessential amino acids - can be
synthesized
The Nitrogen Cycle and Nitrogen Fixation

• Nitrogen is needed for amino acids synthesis

• Atmospheric N2 is the ultimate source of
biological nitrogen
• Nitrogen fixation: a few bacteria possess
nitrogenase which can reduce N2 to ammonia
• Nitrogen is recycled in nature through the
nitrogen cycle
The Nitrogen cycle
Nitrogenase

• An enzyme present in Rhizobium bacteria

that live in root nodules of leguminous plants
• Some free-living soil and aquatic bacteria
also possess nitrogenase (Clabsiela)
• Nitrogenase reaction:
N2 + 8 H+ + 8 e- + 16 ATP
2 NH3 + H2 + 16 ADP + 16 Pi
Assimilation of Ammonia

• Ammonia generated from N2 is assimilated

into low molecular weight metabolites such as
glutamate or glutamine
• At pH 7 ammonium ion predominates (NH4+)
• At enzyme reactive centers unprotonated NH3
is the nucleophilic reactive species
Ammonia Is Incorporated to α-Ketoglutarate
• Reductive amination of a-ketoglutarate by
glutamate dehydrogenase occurs in plants,
animals and microorganisms
• In mammals & plants, located in mitochondria.
Glutamine Is a Nitrogen Carrier in Many Biosynthetic Reactions

• A second important route in assimilation of

ammonia is via glutamine synthetase
Glutamate synthase transfers δ-amino of
glutamine to a-ketoglutarate
Alternate amino acid production
in prokaryotes

Especially used if [NH3] is low. Km of Gln

synthetase lower than Km of Glu dehydrogenase.
Regulation of Glutamine
Synthetase in E. coli

• Glutamine synthetase (GS) plays a critical

role in nitrogen metabolism
• E. coli enzyme regulated by:
(1) Cumulative feedback inhibition (9
allosteric inhibitors with additive effects)
(2) Covalent modification
(3) Regulation of enzyme synthesis
Allosteric inhibition of GS in E. coli
Regulation of E. coli GS by
covalent modification
Regulation of mammalian GS

• Regulation not as extensive as in

microorganisms
• No covalent regulation
• Allosteric inhibitors: glycine, serine, alanine,
and carbamoyl phosphate
• Allosteric activator: a-ketoglutarate
Note:
allosteric is the alteration of the activity of an enzyme by means of a
conformational change induced by a different molecule.
 Transamination Reactions

• Transfer of an amino group from an a-amino

acid to an a-keto acid
• In amino acid biosynthesis, the amino group of
glutamate is transferred to various a-keto acids
generating a-amino acids
• In amino acid catabolism, transamination
reactions generate glutamate or aspartate
Transamination reactions
 SEVERAL NOTES OF AMINO ACIDS
SYNTHESIS

All amino acids are synthesized from

intermediates of Glycolysis,TCA or PRPP.
Different organisms vary greatly in their
ability to synthesize the 20 amino acids.
Amino acids are grouped by their metabolic
precursors.
 Amino acid biosynthetic families grouped
by metabolic precursor
PEP+Erythrose- Ribose-
 -KG OAA 3-Phosphoglycerate Pyr
4-P 5-P
Glu Asp Trp* Ser Ala His*

Gln Asn Phe* Gly Val*

Pro Met* Tyr Cys Leu*

Arg~ Thr*

Lys*

Ile*

~ essential in the young

* Essential amino acids PVT TIM HALL
 Amino acid Biosynthesis is regulated
by feedback inhibition

Sequentialfeedback inhibition
Enzyme multiplicity
Concerted feedback inhibition
Cumulative feedback inhibition
Several enzyme cofactors play important
roles in amino acid metabolism
One carbon transfer is very important
◦ Biotin
◦ Tetrahydrofolate
◦ S-adenosylmethionine (SAM)
Some enzyme cofactors in C-transfer
reactions
Biotin
Tetrahydrofolate carries activated 1-C units at several
oxidation levels
SAM is more commonly used for CH transfer
3
Cys is made from Ser and HomoCys
Sulfurcomes from homoCys
The C skeleton comes from Ser
High homocysteine levels are associated with
vascular diseases
 Coronary heart disease
 Arteriosclerosis
 The molecular basis ???
 Perhaps:damage to cells lining blood vessels and
increase the growth of vascular smooth muscle cells
 Amino acids are precursors of many
biomolecules
Glutathione (GSH)
Nitric oxide (NO)
GSH serves as a buffer and antioxidant
 Protects cells from oxidative damage
 Presents at high levels (5 mM)
 It cycles between a reduced form (GSH) and an oxidized
form (GSSG)
 GSSG is reduced to GSH by GSH reductase
 The ratio of GSH/GSSG------>500
 GSH plays a key role in detoxification by reacting with
hydrogen peroxide and organic peroxides.
 Glutathione peroxidase is remarkable in having a modified
amino acid containing Se.
2GSH + ROOH------> GSSG + H2O + ROH
Nitric oxide is formed from Arg
NO is an important messenger
It is made by NO synthase
NADPH and Oxygen are required
 Amino acids are converted to specialized
products

Porphyrins and bile pigments

 Biosynthesis of porphyrins
Formation of ALA
Formation of porphobilinogen
Porphyrias
 Congenital erythropoietic porphyria
Other specialized products
Creatine
Histamine
Serotonin
Catecholamines
 Dopamine
 Norepinephrine
 Epinephrine
Melanin
Thyroid Hormones
Several of Amino Acids Biosynthesis
Humans are able to synthesize 11 of the 20 amino acids in
proteins, called nonessential amino acids
 The other 9 are called essential amino acids
◦ They are biosynthesized only in plants and
microorganisms
◦ Must be obtained in the human diet
Division between essential and nonessential is not clearcut
◦ Tyrosine is sometimes considered nonessential
because humans can produce it from phenylalanine,
but phenylalanine is essential and must be obtained in
the diet
◦ Arginine can be synthesized by humans, but much of
the arginine must come from the diet
Biosynthesis of Amino Acids
Biosynthesis of amino acids
 Essential amino acids
(red) are synthesized in
plants and bacteria and
must be obtained in our
diet
 Humans can synthesize
only the nonessential
amino acids (blue)
 Biosynthesis of Amino Acids
Alanine, Asparate, and Glutamate Biosynthesis
7 of the 11 nonessential amino acids are synthesized either from
pyruvate or from the citric-acid cycle intermediates oxaloacetate
and a-ketoglutarate
 Alanine is
biosynthesized by
PLP-dependent
transamination of
pyruvate
 Aspartate is made from
oxaloacetate
 Glutamate arises from
a-ketoglutarate
 Biosynthesis of Amino Acids
Asparagine and Glutamine Biosynthesis
Asparagine and glutamine are amides that are synthesized
from aspartate and glutamate
 Asparagine biosynthesis:
◦ Catalyzed by asparagine synthetase
◦ Requires ATP as cofactor
◦ Reaction proceeds through formation of an acyl
adenosyl monophosphate
◦ Acyl adenosyl monophosphate undergoes nucleophilic
acyl substitution by ammonia
 The ammonia is produced from glutamine by a nucleophilic
acyl substitution reaction with a cysteine residue in the
enzyme
Biosynthesis of Amino Acids
Glutamine biosynthesis:
◦ Catalyzed by glutamine synthetase
◦ Occurs by formation of the corresponding acyl
phosphate followed by nucleophilic acyl substitution
reaction with ammonia

The difference in activation strategies for the

asparagine and glutamine pathways is the result
of different evolutionary histories for the two
enzymes since both paths are energetically
favorable
 Biosynthesis of Amino Acids
Biosynthetic pathways for asparagine and glutamine by amide
formation from asparate and glutamate, respectively
 The mechanism of
the acyl
substitution
reactions are given
in abbreviated
form without
showing the
tetrahedral
intermediates
 Electron
movement is
shown as a heart-
shaped path
around the
carbonyl oxygen
to imply the full
mechanism
 Biosynthesis of Amino Acids
Arginine and Proline Biosynthesis
Arginine is synthesized from glutamate in humans
1. Reaction of glutamate with ATP gives an acyl phosphate
2. The acyl phosphate is reduced by NADH in a nucleophilic acyl
substitution reaction to yield glutamate 5-semialdehyde
3. PLP-mediated transamination of the glutamate 5-semialdehyde
carbonyl group by reaction with glutamate gives ornithine
4. Ornithine is converted to arginine in the urea cycle

Proline is synthesized from glutamate 5-semialdehyde, by

nonenzymatic formation of a cyclic imine, followed by enzymatic
reduction of the C=N bond with NADH
 Biosynthesis of Amino Acids

Biosynthesis of arginine and

proline from glutamate
Biosynthesis of Amino Acids
Biosynthesis of Threonine
Threonine is one the nine essential amino acids
 Biosynthesized in plants by a five-step sequence

◦ Starts with aspartate

◦ Initial phosphorylation with ATP forms an acyl
phosphate
◦ Acyl phosphate is partially reduced by reaction with
NADPH to give aspartate semialdehyde
◦ Further reduction of the aldehyde gives homoserine
◦ Homoserine undergoes phosphorylation and
rearrangement (The prefix homo- means “one more
carbon than,” so homoserine has one more carbon than
serine)
Biosynthesis of Amino Acids
Pathway for the biosynthesis of threonine