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Amino acid
metabolism,
concluded
Andy Howard
Introductory Biochemistry
24 April 2008
What we’ll cover

Amino acid
metabolism




Non-essential amino
acids
Branched-chain
Aromatics
Histidine

Amino acids as
metabolites




Amino Acid metabolism
Glucogenic amino
acids
Ketogenic amino
acids
Serine biproducts
Glycine
biproducts
p. 2 of 44
24 April 2008
Essential and non-essential
amino acids



An amino acid is defined as essential if it
must be obtained within the diet
In general the essential amino acids are
the ones that have complicated and
highly ATP-dependent biosynthetic
pathways
Of course, it depends on the organism
Amino Acid metabolism
p. 3 of 44
24 April 2008
The human list
(cf. box 17.3)
AA
moles ATP
Asp
Asn
Lys
Met
Thr
Ala
Val
Leu
Ile
21
22-24
50-51
44
31
20
39
47
55
Glu
Gln
30
31
essential?
no
no
yes
yes
yes
no
yes
yes
yes
no
no
Amino Acid metabolism
AA
moles ATP
Arg
Pro
Ser
Gly
Cys
Phe
Tyr
Trp
His
44
39
18
12
19
65
62
78
42
p. 4 of 44
essential?
no
no
no
no
no
yes
no*
yes
yes
24 April 2008
Examples of transaminases
Reactants
Products
Keto acid
amino acid
Pyruvate
glutamate
Pyruvate
aspartate
Oxaloacetate glutamate
3-P-OH-pyr glutamate
3-OH-phenyl- glutamate
pyruvate
Glu-g(glu)
semialdehyde
N-acylglutamate
2-amino6-oxopimelate
keto acid
-k-glutarate
oxaloacetate
-k-glutarate
-k-glutarate
-k-glutarate
amino acid
alanine pyruvate
alanine pyruvate
aspartate aspartate
P-ser
phosphoserine
tyrosine tyrosine
(-k-g)
ornithine ornithine
Amino Acid metabolism
Transaminase
-k-glutarate N-acyl- 2.3.1.89
2-6,diaminopimelate
p. 5 of 44
24 April 2008
Marching through the list of
twenty amino acids

Amino acids we’ve
already covered



Acids and amides:
glu, gln, asp, asn
Simple:
ala, ser, gly
New but nonessential


arg, pro
cys
Amino Acid metabolism

Essential but
straightforward



lys, met, thr
val, leu, ile
Essential & Ugly


phe, tyr, trp
his
p. 6 of 44
24 April 2008
Glutamate
semialdehyde
Arginine and proline


Two routes:
Glutamate to glutamate semialdehyde



that cyclizes to 1-pyrroline 5-carboxylate
and thence to proline
Glutamate semialdehyde can also be
converted to ornithine and thence to arg
Alternative: glutamate acetylated to Nacetyl-glutamate-5-semialdehyde and
thence to ornithine
Amino Acid metabolism
p. 7 of 44
ornithine
24 April 2008
Glutamate
to P5C


Single enzyme can
interconvert glutamate and
1-pyrroline carboxylate:
1-pyrroline-5-carboxylate
dehydrogenase
3-layer  sandwich
protein
Amino Acid metabolism
p. 8 of 44
PDB 2BJA
170 kDa trimer
monomer
shown
Thermus
thermophilus
24 April 2008
Pyrroline-5-carboxylate
to proline


Pyrroline-5carboxylate
reduced to
proline
Large, NAD(P)dependent
enzyme
Amino Acid metabolism
Pyrroline-5-carboxylate
reductase
PDB 2IZZ
354 kDa decamer
pentamer shown
Human
p. 9 of 44
24 April 2008
Glutamate to Glu
semialdehyde


Glu-5-P
Glu is -phosphorylated:
glu + ATP  glu-5-P +
ADP (2.7.2.11)
Glu-5-P is reduced and
dephosphorylated:
glu-5-P + NADPH + H+

glu-5-semialdehyde +
-glutamyl phosphate
NADP+
Amino Acid metabolism
reductase
PDB 1O20
47 kDa monomer
Thermatoga maritima
p. 10 of 44
24 April 2008
Glu semialdehyde
to ornithine

ornithine

This is just another
transamination,
catalyzed by ornithine
aminotransferase:
glu-5-semialdehyde +
glu/asp  ornithine +
-keto-glutarate /
oxaloacetate
Typical PLPdependent reaction
Amino Acid metabolism
p. 11 of 44
PDB 2OAT
193 kDa tetramer
human
24 April 2008
Ornithine to
citrulline

Carbamoyl
phosphate
Ornithine
condenses with
carbamoyl
phosphate to form
citrulline with the
help of ornithine
transcarbamoylase
Amino Acid metabolism
citrulline
PDB 1DUV
110 kDa trimer
E.coil
p. 12 of 44
24 April 2008
Citrulline to
arginosuccinate

Citrulline condenses with
aspartate using ATP
hydrolysis to drive it
forward to Larginosuccinate:
citrulline + aspartate +
ATP  L-arginosuccinate
+ AMP + PPi
Amino Acid metabolism
p. 13 of 44
Arginosuccinate
synthase
200 kDa tetramer
monomer shown
24 April 2008
Arginosuccinate
to arginine


fumarate
Fumarate extracted,
leaving arginine
Arginosuccinate lyase
is also -crystallin,
one of the
moonlighting proteins:
it’s a component of
eye lenses
Amino Acid metabolism
p. 14 of 44
PDB 1TJ7
100 kDa dimer
(really!)
E.coli
24 April 2008
Why all that detail?


These reactions form 75% of the urea
cycle, which is an important path for
amino acid and nucleic acid degradation.
So we’ll need this later.
Amino Acid metabolism
p. 15 of 44
24 April 2008
Cysteine synthesis
in plants and
bacteria



serine + Acetyl CoA 
O-acetylserine + HSCoA
O-acetylserine + S2- + H+
 cysteine + acetate
Ser acetyltransferase is
inhibited by cysteine
Serine
acetyltransferase
PDB 1SSQ
176 kDa hexamer
dimer shown
Haemophilus
O-acetylserine
Amino Acid metabolism
p. 16 of 44
24 April 2008
Animal pathway
to cys


cystathionine
Ser +
homocysteine
(from met) fuse to
form cystathionine
+ H2O
Cystathionine +
H2O  NH4+ +
Cystathionine -lyase
cysteine + PDB 1N8P
ketobutyrate
173 kDa tetramer
yeast
Amino Acid metabolism
p. 17 of 44
24 April 2008
Lys, met, thr





asp gets phosphorylated and
becomes a source for all of these:
Asp + ATP
-aspartyl phosphate + ADP
via aspartate kinase
-asp P + NADPH + H+ -> Pi +
aspartate -semialdehyde +NADP+
This heads to lys or to homoserine
Homoserine converts in a few steps
to met or thr
Amino Acid metabolism
p. 18 of 44
Aspartate
kinase
112 kDa
PDB 2CDQ
dimer
Arabidopsis
24 April 2008
Asp -semialdehyde
to homoserine




-aldehyde reduced to secalcohol, which is homoserine
Homo is generally a prefix
meaning containing an extra
methylene group
This is precursor to
homocysteine  methionine
It also leads to threonine
Amino Acid metabolism
p. 19 of 44
homoserine
24 April 2008
Homoserine
to threonine


Phosphohomoserine
Homoserine phosphorylated
with ATP as phosphate
donor
threonine
Phosphohomoserine
dephosporylated with
movement of -OH from one
carbon to another: threonine
results
Amino Acid metabolism
p. 20 of 44
24 April 2008
Homoserine to
methionine




Three reactions convert
homoserine to homocysteine
5-methyltetrahydrofolate serves as
a methyl donor to convert
homocysteine to methionine via
methionine synthase
This enzyme exists in humans but
its activity is low and
[homocysteine] is low;
So methionine is essential in
humans
Amino Acid metabolism
p. 21 of 44
homocysteine
24 April 2008
Specifics
for lysine




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

2,3-dihydropicolinate
Aspartyl semialdehyde condenses with
pyruvate to form 2-3-dihydropicolinate
Reduced again to 2,3,4,5-tetrahydropicolinate
Acylated (via AcylCoA) to N-acyl-2-amino-6oxopimelate
Transaminated to N-acyl-2,6-diaminopimelate
Deacylated to L,L-N-acyl-2,6-diaminopimelate
Epimerase converts that to meso form
That’s decarboxylated to lysine
Amino Acid metabolism
p. 22 of 44
24 April 2008
The human list
(cf. box 17.3)
AA
moles ATP
Asp
Asn
Lys
Met
Thr
Ala
Val
Leu
Ile
21
22-24
50-51
44
31
20
39
47
55
Glu
Gln
30
31
essential?
no
no
yes
yes
yes
no
yes
yes
yes
no
no
Amino Acid metabolism
AA
moles ATP
Arg
Pro
Ser
Gly
Cys
Phe
Tyr
Trp
His
44
39
18
12
19
65
62
78
42
p. 23 of 44
essential?
no
no
no
no
no
yes
no*
yes
yes
24 April 2008
Branched-chain aliphatics:
isoleucine and valine -ketobutyrate




Derived from pyruvate or ketobutyrate
2 pyruvate 
-ketoisovalerate + CO2
pyr + -ketobutyrate 
-keto--methylvalerate + CO2
These products are
transaminated to ile and val
Amino Acid metabolism
p. 24 of 44
-keto
-methylvalerate
24 April 2008
Leucine



Also derived from -ketoisovalerate;
An extra methylene is inserted between
the polar end and the isopropyl group
Final reaction is another transamination
Amino Acid metabolism
p. 25 of 44
24 April 2008
shikimate
Aromatics:
phe and tyr



Common pathways for
phe,tyr,trp via shikimate and
chorismate
For phe, tyr: chorismate
converted to prephenate
Prephenate can be aromatized
with or without a 4-OH group to
lead to phe,tyr
Amino Acid metabolism
p. 26 of 44
chorismate
24 April 2008
Reaction specifics



Prephenate is oxidized
and dehydroxylated in two
steps to phenylpyruvate
Or it is oxidized to 4-OHphenylpyruvate
Transaminations of those
-ketoacids yield the final
amino acids
Amino Acid metabolism
p. 27 of 44
prephenate
4-hydroxyphenylpyruvate
24 April 2008
Chorismate
mutase




Isomerase, converts chorismate
to prephenate
In E.coli: 2 versions depending
on which path the product is
heading to
Active sites are similar in all
organisms but architecture is
very different
Catalytic triad similar to serine
proteases
Amino Acid metabolism
p. 28 of 44
PDB 1DBF
42 kDa trimer
B.subtilis
24 April 2008
Path to tryptophan:
anthranilate synthase

anthranilate
Chorismate reacts
with glutamine and
is aromatized to
anthranilate:
chorismate + gln 
anthranilate +
pyruvate +
glutamate
Amino Acid metabolism
p. 29 of 44
PDB 1I1Q
157 kDa
heterotetramer
heterodimer
shown
Salmonella
24 April 2008
Anthranilate
to indole

Four-step pathway:




phosphoribosyl pyrophosphate (PRPP)
contributes a phosphoribosyl group
Sugar ring opens and rearranges
Result is decarboxylated and forms a second
ring to form indole 3-glycerinphosphate
Glyceraldehyde-3-P is released to leave
indole
Amino Acid metabolism
p. 30 of 44
24 April 2008
Tryptophan
synthase


Indole + ser 
tryptophan + H2O
PLP-dependent enzyme, but
different in how it uses PLP
from the transaminases
Amino Acid metabolism
p. 31 of 44
PDB 2CLF
146 kDa
heterotetramer;
heterodimer
shown
Salmonella
24 April 2008
Genetic control of
aromatic aa synthesis

In E.coli and other bacteria, a single
operon controls several chorismaterelated genes
Amino Acid metabolism
p. 32 of 44
24 April 2008
Histidine (fig. 17.22)



Start with PRPP and ATP: form
phosphoribosyl ATP
3 reactions involving glutamine as
nitrogen donor for ring lead to imidazole
glycerol phosphate
That gets modified and transaminated t
make histidine
Amino Acid metabolism
p. 33 of 44
24 April 2008
What do we do
with amino acids?


Obviously a lot of them serve as buildingblocks for protein and peptide synthesis
via ribosomal mechanisms
Also serve as metabolites, getting
converted to other compounds or getting
oxidized as fuel
Amino Acid metabolism
p. 34 of 44
24 April 2008
Gluogenic and
ketogenic amino acids

Degradation of many amino acids lead to
TCA cycle intermediates or pyruvate



therefore these can be built back up to glucose;
these are called glucogenic
Degradation of others leads to acetyl CoA
and related compounds


these cannot be built back up to glucose except
via the glyoxalate shuttle
these are called ketogenic
Amino Acid metabolism
p. 35 of 44
24 April 2008
Serine-based metabolites


Serine is a building block for sphinganine
and therefore for sphingolipids
Serine also leads to phosphatidylserine,
which is important by itself and can be
metabolized to phosphatidylethanolamine
and phosphatidylcholine
Amino Acid metabolism
p. 36 of 44
24 April 2008
Glycine-based
metabolites

porphobilinogen
Glycine is a source for purines,
glyoxylate, creatine phosphate, and (with
the help of succinyl CoA)
porphobilinogen, whence we get
porphyrins, and from those we get
chlorophyll, heme, and cobalamin
Amino Acid metabolism
p. 37 of 44
24 April 2008
We’ll continue amino acids
next time…

But first, a sneak preview of our coverage
of nucleic acid chemistry, which we’ll do
on Tuesday!
Amino Acid metabolism
p. 38 of 44
24 April 2008
6
5
Pyrimidines






N
4
2
N
3
Single-ring nucleic acid bases
pyrimidine
6-atom ring; always two nitrogens in the ring,
meta to one another
Based on pyrimidine, although pyrimidine itself
is not a biologically important molecule
Variations depend on oxygens and nitrogens
attached to ring carbons
Tautomerization possible
Note line of symmetry in pyrimidine structure
Amino Acid metabolism
p. 39 of 44
1
24 April 2008