Amino Acid Metabolism Lectures
Amino Acid Biosynthesis
use Garrett and Grisham for illustrations
David Nelson Oct. 26, 2001
last revised Oct. 25, 2001 3:30 PM
You are now familiar with the central metabolic pathways of glycolysis,
Gluconeogenesis and the TCA cycle. Now we will look at the metabolism of the amino acids.
Before we start, I would like to introduce you to KEGG.
The Kyoto Encyclopedia of Genes and Genomes or KEGG has maps of many metabolic
pathways (About 100 maps). They are building a resource that will allow easy comparison
of pathways between genomes, and the assessment of an organism's biochemistry by
analysis of its pathways. The basic pathway maps have all known enzymes listed by their
Enzyme Commission number (EC number). Substrates and products are then placed in
order with the enzymes that either make them or modify them. The result is an automated
generation of all possible pathways. These can then be color coded for enzymes present in
a single species. Species maps are available by pull down menus. It is also possible to color
code human disease genes and these maps are available. The newest twist to this method is to
color code genes identified in gene chip arrays as being expressed in the same manner.
These may be genes in a single pathway or genes involved in the same process.
When whole genomes are analyzed, complete sets of pathways can be developed except for the 40-
50% of proteins that have no known function. Gaps in pathways can be identified, and
predictions made about an organism's metabolic strategies. Essential pathways present in
microorganisms but absent in humans are of course targets for antimicrobial drugs.
Obvious examples are the vitamin biosynthetic pathways in bacteria. Currently, the KEGG has
analyzed 67 complete genomes including 6 eukaryotes, and they also includes partial data on
mouse. They cover 56 species. You should try looking at some of the maps that are hyperlinked
in the text below. It may be interesting to compare yeast with E. coli and
Methanococcus jannaschiito get a feeling for similarities and differences between
the three main domains of life Archaea, Bacteria and Eukarya.
Clicking on an enzyme box will link you to the information on that gene, including the
enzyme name the protein sequence and the nucleotide sequence. If the Enzyme
Commission has not named the enzyme yet, then it will have a ? in the box. Related areas
on other maps are also linked. These are shown as circled regions with a label like urea
cycle. Clicking here will take you to the map that has that pathway. Clicking on a box in the
disease gene maps will take you to the OMIM entry for that gene.
Mammals don't make all 20 amino acids, so it will be necessary to consider some of
the pathways found in microorganisms. In bacteria and other microorganisms,
mutants that are defective for growth without a specific supplement are called
auxotrophs. Auxotrophs can be found in most biosynthetic pathways.
In going over these pathways, I will add information about some metabolic diseases.
These have similar features. Usually there is a build up of precursors in front of a block
in a pathway (see Fig. 18.12 p. 579 2nd ed., Fig. 17.17 p. 563 1st ed.).
After the block, intermediates are absent or depleted. The total absence of an
enzyme is not required to make people sick. Low activity of an enzyme due to a
point mutation or a premature stop codon can occur and this may lead to disease.
Since genes in eukaryotes are built from exons, alternative splicing or exon
skipping can cause disease. We will see that there are many more diseases caused
by defects in amino acid breakdown, than in amino acid biosynthesis. That is due
to accumulation of intermediates in the breakdown pathways that can act in
deleterious ways. Many amino acids are neurotransmitters and high concentrations of
them can lead to mental retardation. Some intermediates are inhibitors of other
enzymes and they can shut down needed metabolic activity. These types of problems
are not as likely in the biosynthetic pathways, because missing amino acids can be
obtained in the diet, and feedback inhibition of pathways can shut down a pathway
if intermediates accumulate to high levels. The loss of a biosynthetic pathway can
be harmful if an intermediate is required as a precursor in another pathway.
Treatment of metabolic diseases is frequently dietary. The accumulation of amino
acids that are toxic can be controlled by a low protein diet supplemented with
essential amino acids. Other possible treatments are transplants of cells, that can
provide the missing enzyme. There have been several trials of treating Parkinson's
disease (defect in L-dopa synthesis, in the tyrosine biosynthetic pathway) by
surgical implants of fetal brain tissue into the brains of patients. This has
helped some patients. There was one dramatic case of a man who had taken a street
drug that was contaminated with a toxic chemical. This resulted in killing the
cells of his substantia nigra where dopamine is made and he became frozen,
completely unable to move. A transplant of fetal brain cells, done in Sweden,
helped him to regain some movement.
Not all defects in amino acid pathways result in disease. Failure to breakdown
proline for example causes proline to build up in the blood. It is excreted and no
ill effects are noted.
GETTING STARTED IN AMINO ACID BIOSYNTHESIS
In biosynthesis, all 20 amino acids are made from only 7 precursors from the
central metabolic pathways.
1. fructose 6 phosphate precursor to aromatic amino acids
2. glyceraldehyde 3 phosphate precursor to aromatic amino acids
3. 3-phosphoglycerate precursor to 3-phosphogycerate family of amino acids
4. phosphoenolpyruvate precursor to aromatic amino acids
5. pyruvate precursor to pyruvate family of amino acids
6. alpha ketoglutarate precursor to alpha ketoglutarate family of amino acids
7. oxaloacetate precursor to aspartate family of amino acids
The Kyoto Encyclopedia of Genes and Genomes has 16 maps on amino acid metabolism.
There is probably enough material for more than a dozen lectures, but
we have only two, so you will be getting just the highlights of amino acid
metabolism. To give you an idea of what we are not going to cover, here is the map
for phenylalanine metabolism.This does not include phenylalanine biosynthesis
that is shown as a small cirlce near the top of the figure.
SOURCES OF NITROGEN FOR SYNTHESIS,
GLUTAMATE AND GLUTAMINE
In plants and microorganisms, the 20 amino acids all receive their amino groups
from glutamate in a transamination reaction. In some pathways the transamination is the
first step (methionine, threonine). In other pathways, transamination is
the last step (valine, leucine and isoleucine). In mammals, only 10 amino acids
are synthesized. The rest are acquired in the diet.
The source of nitrogen is clearly important. The nitrogen in glutamate is
incorporated from ammonia. Ammonia is a reduced form of nitrogen that is created
by reduction of N2 gas (nitrogen fixation) or by reduction of nitrate (nitrate
assimilation).
Glutamate can be synthesized in two ways, by glutamate dehydrogenase in a reductive
amination that couples ammonia to alpha ketoglutarate(fig. 26.7, p. 832), or by
glutamate synthase that transfers the amide group from glutamine to alpha
ketoglutarate(fig. 26.9 p. 860 2nd ed., fig. 26.10, p. 834 1st ed). This last
reaction makes two glutamates, one from glutamine and one from alpha ketoglutarate.
The glutamine used in this reaction is made by glutamine synthase.
The two methods of forming glutamate are both present in bacteria. However, glutamate
dehydrogenase has a higher Km for ammonia than glutamate synthase. In real life situations,
where ammonia concentration is low, glutamate synthase is the preferred pathway. Since
glutamate synthase only transfers a nitrogen from glutamine, glutamine synthase is the key
enzyme for introducing ammonia into carbon compounds. Glutamine synthase is a highly
regulated enzyme in E. coli (see text, pp. 862-865 2nd ed., pp. 835-838 1st ed.)
AMINO ACID BIOSYNTHESIS
There are five families of amino acids. Four are based on the precursors they are
made from. The fifth, the aromatic amino acids, all share the first part of their
pathway up to chorismate. Histidine is in a group all by itself.
THE ALPHA KETOGLUTARATE FAMILY OF AMINO ACIDS
Glutamate, glutamine, proline, arginine and lysine(in fungi, and lower eukaryotes) are all
derived from alpha KG. We have already seen how glutamate and glutamine are made.
Proline is made starting from glutamate(see fig. 26.20 p. 868 2nd ed., fig 26.18,
p. 841 1st ed.) The gamma carboxyl group is activated by phosphorylation. This
compound is reduced and dephosphorylated to form glutamate gamma semialdehyde, a
compound we will see again in amino acid degradation. The aldehyde spontaneously
cyclizes by forming an internal Schiffs base with the alpha amino group. This is
then reduced to form proline.
Hydroxyproline is made in collagen after the protein is synthesized. The enzyme
prolyl hydroxylase is an ascorbate dependent enzyme. Lack of ascorbate causes
scurvy. Polar explorers traveling with Robert Scott to the South Pole in 1911/1912
developed scurvy. This weakens collagen tissue. One man who had suffered a bullet
wound during a war began to have his wound reopen. Ascorbate, or vitamin C is
required to maintain scar tissue and to keep blood vessels from becoming fragile.
None of Scott's polar expedition survived. They traveled 1400 miles and died
within 15 miles of their home base.
Arginine is also made from glutamate via an activated gamma carboxyl group.
However, the alpha amino group is acetylated first, so the gamma aldehyde cannot
react with the alpha amino group to form a cyclic product(fig. 26.21 p. 868 2nd
ed., fig. 26.19, p. 842 1st ed.). After this is done, the aldehyde is produced and
then glutamate donates the terminal amino group. The acetyl group is removed,
leaving ornithine. Ornithine is converted to arginine in the urea cycle. We will
talk about the urea cycle when we cover amino acid degradation, so we will stop at
ornithine for now. N-acetylglutamate is an activator of an important enzyme,
carbamoyl phosphate synthase I. This enzyme catalyzes a major route of ammonia
removal, so a defect in arginine biosynthesis leads to toxic levels of ammonia that
result in death a few days after birth.
Lysine can be made starting from alpha ketoglutarate in lower eukaryotes, but in
higher eukaryotes, it is made from aspartate. The fungal pathway of lysine
synthesis is shown in 26.24 p. 873 2nd ed., fig. 26.22, p. 846 1st ed. This
pathway has several steps similar
to the TCA cycle. Lysine has one more carbon than alpha ketoglutarate, so the
starting compound must be lengthened. This is done by reacting acetyl CoA with
alphaKG in a reaction that is similar to the citrate synthase reaction. The
product has an hydroxyl on the beta carbon, just like citrate. This has to be
moved to the alpha carbon in order to decarboxylate the homoisocitrate. Oxidation
of the hydroxyl group to a carbonyl cannot proceed on a teriary alcohol. It would
make a pentavalent carbon. The product alpha ketoadipate is similar to alpha
ketoglutarate in the TCA cycle. The compound is transaminated from glutamate to
make a new amino acid alpha aminoadipate. It is an amino acid that is next in the
series aspartate (4 carbons), glutamate (5 carbons), alpha aminoadipate (6
carbons). This compound is activated by phosphorylation and reduced to an aldehyde
as was seen in proline and ornithine biosynthesis. The aldehyde reacts with a
glutamate amino group to form an adduct that is hydrolyzed on the other side of the
nitrogen to form lysine and release alpha ketoglutarate. Remember in purine
biosynthesis that aspartate was an amino donor that was cleaved to release
fumarate. The main difference here is the hydrolytic cleavage adds an oxygen back
to the product.
THE ASPARTATE FAMILY OF AMINO ACIDS
The amino acids in this family include aspartate, asparagine, methionine, threonine,
isoleucine and lysine by a different pathway from the one seen in fungi.
Aspartate is formed by transamination of oxaloacetate from the TCA cycle. Both alpha
ketoglutarate and oxaloacetate are sources of carbon skeletons for amino acid synthesis.
These amino acids are sources of nitrogen and carbon for building other amino acids and
nucleotides. These are exit points from the TCA cycle and these compounds have to be
replenished or the cycle will run out of oxaloacetate to react with acetyl CoA. (See
section 20.13 pp. 661-662 2nd ed., section 19.13, pp. 616-617 1st ed.) The cycle is
refilled by anaplerotic reactions that produce TCA cycle intermediates. (see section
20.14 p. 663 2nd ed., section 19.14, p. 618 1st ed.) The most important is pyruvate
carboxylase that makes oxaloacetate from pyruvate and CO2. When there is a deficit of
oxaloacetate, acetyl CoA builds up, because it cannot enter the TCA cycle. Acetyl CoA
activates pyruvate carboxylase. Malic enzyme is another anaplerotic enzyme that converts
pyruvate and CO2 to malate. We will see later that all amino acids are broken down to
TCA cycle intermediates, so amino acids can serve as sources of these intermediates to
keep the TCA cycle going, even if carbohydrates are not available.
Asparagine is made in two ways. In bacteria, the amide nitrogen comes from ammonia, as
in the glutamine synthase reaction. In other organisms glutamine is the amino group
donor to aspartate. This reaction requires ATP hydrolysis to AMP and PPi. (see fig.
26.26 p. 875 2nd ed., fig. 26.24, p. 848 1st ed.) The AMP group activates the carboxyl.
This is a recurring theme that you should be aware of.
Threonine, methionine and lysine are all made starting from aspartate(fig. 26.27 p. 876
2nd ed., fig. 26.25, p. 849 1st ed.). Since it is important to make the appropriate amount
of each amino acid, the first enzyme in the pathway, aspartokinase, is subject to
regulation. In fact in E. coli, there are three aspartokinase enzymes. Aspartokinase I
is feedback inhibited by threonine . Aspartokinase III is feedback inhibited by lysine.
Aspartokinase II is not feedback inhibited, but its gene expression is repressed by
methionine. Methionine is called a co-repressor(see fig. 31.21 p. 1036 2nd ed., fig.
17.16, p. 562 1st ed). Lysine is a co-repressor of aspartokinase III and threonine and
isoleucine (isoleucine is made from threonine) are co-repressors of aspartokinase I.
The pathways for these 4 amino acids all start the same way. Aspartate is phosphorylated
and reduced to form the aldehyde, just as we saw with proline, ornithine and fungal lysine
biosynthesis. This requires an ATP and NADPH. At this point lysine biosynthesis
branches off, through an 8 step pathway that we won't cover in detail. The main features
are addition of three carbons as pyruvate to make a 7 carbon skeleton. An extra amino
group is added from glutamate and one carbon is removed in a decarboxylation reaction at
the end of the pathway.
The three remaining amino acids have one more common step before they branch off.
This is the reduction of the aspartyl semialdehyde to an alcohol by NADPH. The alcohol
of aspartic acid is called homoserine. This is very similar to threonine except the
hydroxyl is on the gamma carbon instead of the beta carbon. A two step pathway
phosphorylates the gamma hydroxyl and shifts it to the beta carbon to make threonine.
Homoserine is also the precursor for methionine. Again the hydroxyl is activated, but
this time it is by succinyl CoA that transfers a succinyl group and releases CoA.
Methionine has a sulfur, and this is donated from cysteine. The whole cysteine molecule
is covalently attached to the activated carbon through the sulfur. This is cleaved off as
pyruvate and ammonia to leave the SH group on the product homocysteine. The terminal
methyl is donated by N5 methyl tetrahydrofolate.
Methionine can react with ATP to form S-adenosylmethionine (SAM). (see fig. 26.28 p. 878
2nd ed., fig. 26.26, p. 851 1st ed.) The ATP is hydrolyzed to release PPi and Pi, so SAM
costs three high energy phosphate bonds to make. The methyl group on SAM is readily
donated to methyl acceptors in synthetic reactions producing S-adenosyl homocysteine.
This product is cleaved to form adenosine and homocysteine that are recycled. Another
route SAM can enter is the decarboxylation of the methionine part of the molecule to make
decarboxylated SAM. This structure is now a propylamine donor rather than a methyl donor.
This group is transferred to a putrescine amino group (made by decarboxylation of
ornithine) to make spermidine. One more propylamine can be added to the other amino group
of spermidine to make spermine.
Isoleucine is made from threonine after it is oxidatively deaminated to form alpha
ketobutyrate. This compound is similar to pyruvate, except it has one more methylene
group. (see fig. 26.29 p. 880 2nd ed., fig. 26.27, p. 852 1st ed.) Pyruvate and alpha
ketobutyrate are both processed by the same four enzymes to make valine and isoleucine.
We will go over these in the pyruvate family of amino acids. Since the deamination of
threonine is unique to the isoleucine pathway, this step is feedback inhibited by
isoleucine. The next step is feedback inhibited by valine, so valine inhibits its own
synthesis and isoleucine's as well, but isoleucine only inhibits its own pathway, not
valine's. (Remember isoleucine also inhibits aspartokinase I at the first step in its
pathway.)
THE PYRUVATE FAMILY OF AMINO ACIDS
Alanine valine and leucine are the three members of this family. Alanine is formed by
transamination of pyruvate from glutamate. Valine is made by the same pathway as
isoleucine starting from the alpha keto acids pyruvate and alpha ketobutyrate. In the
first common step, pyruvate donates an hydroxyethyl group to the alpha carbon of the keto
acid. In the next step, the newly added acetyl group inserts itself between the alpha and
beta carbons, forming a dihydroxy acid. This is then dehydrated to make the alpha keto
acids that are directly transaminated by glutamate to make valine and isoleucine.
Leucine biosynthesis branches from alpha ketoisovalerate, the immediate precursor to
valine. This compound undergoes a reaction similar to oxaloacetate in the citrate
synthase reaction. It reacts with acetyl CoA to make a product that is both
hydroxylated and carboxylated at the beta carbon. As in the TCA cycle conversion of
citrate, the hydroxyl is shifted to the alpha carbon and the carboxyl is removed as CO2.
This forms a new alpha keto acid that is transaminated to form leucine.
THE 3-PHOSPHOGLYCERATE FAMILY OF AMINO ACIDS
Serine, glycine and cysteine belong in this group. 3-phosphoglycerate is oxidized to
convert the alpha hydroxyl to a keto group. This is then transaminated and
dephosphorylated to make serine. (see fig 26.31 p. 881 2nd ed., fig. 26.29, p. 854 1st
ed.)
Glycine is made from serine in two different ways. In the first, an hydroxymethyl group
is transferred from serine to tetrahydrofolate to make N5 N10 methylenetetrahydrofolate.
The second pathway is the glycine oxidase reaction acting in reverse. Here CO2, NH4+ and
N5 N10 methylenetetrahydrofolate condense to form glycine. Serine is the source for one
carbon units used in biosynthesis of many products like lipids, purines, thymine,
tryptophan, cysteine and methionine. Glycine is used in purine, glutathione and heme
synthesis.
There are several ways to make cysteine. In bacteria, H2S can react with serine to make
cysteine directly. This requires a pyridoxal phosphate dependent enzyme. In other
organisms the hydroxyl is first activated by adding an acetyl group from acetyl CoA. The
acetyl group is then displaced by H2S to form cysteine.
Through this series of reactions, you should be noticing that there are common principles
that are used in the pathways again and again. Often, carboxyl groups are activated by
phosphorylation and then reduced to make an aldehyde before some other reaction occurs.
The series of reactions seen in the TCA cycle that react acetyl CoA with an alpha keto acid
and then proceed to shift an hydroxyl group and decarboxylate the product, are used in the
fungal lysine pathway and the leucine pathway. There are a variety of activating groups
that can be added to carboxyls and hydroxyls. These include phosphates, CoA, succinate,
acetyl groups or AMP. You should be aware of similarities in the different pathways.
AROMATIC AMINO ACIDS
The aromatic amino acids do not derive from a single metabolic intermediate starting point,
like the other families of amino acids we already discussed. It takes three intermediates
from the glycolysis pathway to start aromatic amino acid biosynthesis. Fructose-6-
phosphate and glyceraldehyde-3-phosphate are reconfigured by transketolase (see Fig. 23.33
p. 767 2nd ed., Fig 21.42 page 691 1st ed.). If you remember from the pentose phosphate
pathway, transketolase moves a two carbon ketol group from a keto sugar to an aldose. So
the 6 carbon fructose-6-P becomes the four carbon erythrose-4-P and glyceraldehyde-3P picks
up two carbons to become the 5 carbon xylulose-5-P (precursor to PRPP). The erythrose-4-P
reacts with phosphoenolpyruvate to start biosynthesis of the aromatic amino acids.
Phenylalanine, tyrosine and tryptophan are synthesized from the intermediate chorismate.
This is also a precursor of many compounds in biology that contain a benzene ring.
Vitamins E, K, folic acid, ubiquinone, plastoquinone and lignin are all made from
chorismate(see fig. 26.35 p. 885 2nd ed., fig. 26.33, p. 857 1st ed). Two carbohydrate
skeletons phosphoenol pyruvate and erythrose 4 phosphate are condensed to form a seven
carbon compound called 2-keto-3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP). (see fig.
26.34, p. 858) This compound is cyclized with loss of the phosphate to form a six membered
ring that undergoes dehydration and reduction to form shikimate. This pathway is referred
to as the shikimate pathway. Shikimate is phosphorylated and then reacts with PEP, with the
loss of phosphate from PEP to make the intermediate 3-enolpyruvyl-shikimate-5-phosphate.
This loses its phosphate to become chorismate.
Here the pathway branches in two directions to make trp on one branch and tyr and phe on
the other branch.
Tyrosine and phenylalanine are similar amino acids and their synthesis is similar(fig. 26.37
p. 886 2nd ed., fig. 26.35, p. 859 1st ed). The enolpyruvyl group on chorismate is shifted
to the para position of the ring to make prephenate. At this point the pathway diverges
again. If the carboxyl group is oxidized to CO2, the resulting alpha keto acid is 4-
hydroxyphenylpyruvate, which is transaminated from glutamate to form tyrosine. If the
carboxyl and the hydroxyl are both removed, the resulting alpha keto acid is phenylpyruvate.
This is also transaminated to form phenylalanine.
Tryptophan is also formed from chorismate, in a five enzyme pathway. In the first step of
this pathway, the enolpyruvyl group and the hydroxyl are removed and an amino group
from glutamine is added to the ring, which is now aromatic. This compound, anthranilate
is condensed with PRPP, which you saw in purine biosynthesis. The phosphoribosyl
group is added to the amino group. In step three, the ribose sugar is isomerized to a
ribulose sugar. The enzyme that catalyzes this step is one of the common genes in yeast
that is used as a selectable marker TRP1. Yeast that have a mutation in TRP1 cannot grow
on media lacking tryptophan. A functional copy of TRP1 on a plasmid complements this
defect and can be selected for in a yeast transformation, on tryptophan minus plates. If
your favorite gene is on this plasmid, you can select for your gene at the same time, by
selecting for trp plus colonies from a trp1 auxotrophic yeast.
In step 4, the intermediate made by TRP1 is decarboxylated and dehydrated to form the
indole ring of tryptophan, attached to glycerol three phosphate. The last enzyme,
tryptophan synthase actually has two active sites and two different steps are carried out on
the alpha and beta subunits. The glycerol three phosphate is removed as glyceraldehyde 3
phosphate, on the alpha subunit and serine is added to replace it on the beta subunit. The
intermediate is transferred from the alpha to the beta subunit active sites through a tunnel
on the enzyme. This is called channeling. (see fig. 26.39 p. 888 2nd ed., fig. 26.37, p.
861 1st ed).
The five enzymes in this pathway have been studied in many different organisms, including
bacteria, fungi and yeast. (see handout) Some of the genes are fused together, so two
enzymes are on one polypeptide chain. Some of the enzymes have alpha and beta
subunits, that are coded in separate proteins, but they have no activity unless they are
associated with each other. Anthranilate synthase is like this in all species, tryptophan
synthase is like this in some species, in other species the alpha and beta subunit are fused
as one protein. Some of the proteins that are not sequential in the pathway are covalently
linked by disulfide bonds. All this points to the existence of a super complex of all the
tryptophan biosynthetic enzymes. However, this complex is pretty loose, since it cannot
be isolated intact.
REGULATION OF AROMATIC AMINO ACID BIOSYNTHESIS
In E. coli, there are three different DAHP synthase enzymes (first step in chorismate
synthesis). This is similar to aspartokinase in the thr, ile, met and lys pathways. Each
product, trp, tyr and phe inhibits one of the three different DAHP synthases. The gene
expression of these three enzymes is also repressed by the end products. Trp represses the
five enzymes unique to the trp pathway, since they are in a single operon.
In Bacillus subtilis, there is just one enzyme and it is not inhibited by the three amino
acid products of the pathway. Instead it is inhibited by chorismate and prephenate, the
products that occur at the two branch points of the pathway. The branches that lead to tyr
and phe are inhibited by these amino acids, at the first step after prephenate is formed.
HISTIDINE BIOSYNTHESIS
The first step of histidine biosynthesis couples PRPP and ATP to make an unusual
compound that has two ribose rings attached to the same adenine ring. The compound
has four phosphates. (see fig. 26.40 p. 889 2nd ed., fig. 26.38, p. 862 1st ed.) Two of
these are cleaved off and then the adenine ring is broken. The ribose from PRPP is
isomerized to the open chain conformation then, in reaction 5, glutamine donates its amide
and displaces the remainder of the ATP molecule, leaving behind one nitrogen and one carbon
from the adenine ring that was broken. This cyclizes to make the imidazole ring. Here we
see imidazole coupled to glycerol phosphate. This is like the tryptophan pathway, where the
indole ring was coupled to glycerol phosphate. Rather than swapping the glycerol phosphate
for serine like we saw in the tryptophan pathway, histidine is made by dehydrating to make
an alpha keto group (in yeast this enzyme is HIS3, a common auxotrophic marker) this
compound is transaminated by glutamate. The product is dephosphorylated and oxidized twice
by the same enzyme histidinol dehydrogenase to make the carboxyl.
The genes of the histidine biosynthetic pathway are in a single operon and they are
repressed by histidine.
The histidine biosynthetic pathway is the basis for the Ames mutagenesis test. Mutants in
the histidine pathway are plated on a his minus medium and a test substance is included.
The number of his+ colonies that appear compared to a control shows that a compound is
mutagenic. It changes the his minus mutants back to wild type and restores growth.
EXPLOITING INHIBITORS OF MISSING PATHWAYS
Plants make all twenty amino acids, but humans make only 10. Therefore, inhibitors of
the pathways that are present in plants but not humans should not affect humans (and
other mammals). These are useful as herbicides. (see p. 888 2nd ed. p. 863 1st ed.) The
aromatic amino acids and histidine as well as the branched chain amino acids are all
essential in humans, meaning we cannot make them. (We can convert phenylalanine to tyrosine
by a phenylalanine breakdown pathway, but we are missing the shikimate pathway.) There are
three inhibitors listed in your book that block three of these pathways: the shikimate
pathway, the histidine pathway, and an enzyme used in common to make Ile, Leu and Val.
The popular garden weed killer Roundup inhibits the shikimate pathway.
Recently, malaria has been shown to have an organelle called an apicoplast. All members of the
apicomplexan parasites have this plastid. It appears to derive from a chloroplast like ancestor
but it has lost the ability to make chlorophyll. This makes malaria plant like because this
essential plastid has the shikimate pathway. Treatment of malaria infected mice with roundup
kills the malaria and cures the mice. This should also work on humans safely, since we do not
have the shikimate pathway.