2. AMINO ACIDS
They are molecules containing an amine group, a
carboxylic acid group, and a side-chain that is specific
to each amino acid.
The key elements of amino acid are carbon,
hydrogen, oxygen, and nitrogen.
Amino acids are the basic structural building units of
protein and other biomolecules; they are also utilized
as an energy source.
5. Standard Amino Acids
Amino acids join together to form short polymer chains
called peptides or longer chains called either
polypeptidesor proteins.
These polymers are linear and unbranched, with each
amino acid within the chain attached to two neighboring
amino acids.
Twenty-two amino acids are naturally incorporated into polypeptides
and are called proteinogenic or natural amino acids. Of these, 20 are
encoded by the universal genetic code. The remaining 2 are
incorporated into proteins by unique synthetic mechanisms.
6.
7. Non-standard amino acids
Aside from the 22 standard amino acids, there are many
other amino acids that are called non-proteinogenic or
non-standard.
They are either not found in proteins (for example
carnitine, GABA), or are not produced directly.
Non-standard amino acids that are found in proteins are
formed by post-translational modification, which is
modification after translation during protein synthesis.
These modifications are often essential for the function or
regulation of a protein; for example, the carboxylation of
glutamate allows for better binding of calcium cations.
8. Some nonstandard amino acids are not found in
proteins. Examples include lanthionine, 2-
aminoisobutyric acid, dehydroalanine, and the
neurotransmitter gamma-aminobutyric acid.
Nonstandard amino acids often occur as
intermediates in the metabolic pathways for standard
amino acids — for example, ornithine and citrulline
occur in the urea cycle.
9. In human nutrition
When taken up into the human body from the diet, the 22
standard amino acids either are used to synthesize
proteins and other biomolecules or are oxidized to urea
and carbon dioxide as a source of energy.
The oxidation pathway starts with the removal of the
amino group by a transaminase, the amino group is then
fed into the urea cycle. The other product of
transamidation is a keto acid that enters the citric acid
cycle.
Glucogenic amino acids can also be converted into
glucose, through gluconeogenesis.
10. Difference between essential and
non-essential amino acids
There are 20 different amino that make up all proteins in the human
body.
These amino acids are needed to replenish tissue, red blood cells,
enzymes, and other substances.
9 - 12 can be manufactured by the body-nonessential amino acids, not
obtained from the diet.
The remaining 8 to 11 -essential amino acids, must be obtained from
the diet.
12. Non-protein functions
Many amino acids are used to synthesize other molecules,
for example:
Tryptophan is a precursor of the neurotransmitter
serotonin.
Tyrosine is a precursor of the neurotransmitter dopamine.
Glycine is a precursor of porphyrins such as heme.
Arginine is a precursor of nitric oxide.
Aspartate, glycine, and glutamine are precursors of
nucleotides.
13. Classification according to functions
Anabolic/Catabolic Responses and Tissue pH Regulation :-
Glutamic Acid
Glutamine
The Urea Cycle and Nitrogen Management
Arginine
Citrulline
Ornithine
Aspartic Acid
Asparagine
14. Essential Amino Acids for Proteins and Energy
Isoleucine
Leucine
Valine
Threonine
Histidine
Lysine
Alpha-Aminoadipic Acid
Sulfur Containing Amino Acids for Methylation and
Glutathione
Methionine
Cystine
Homocysteine
Cystathionine
Taurine
19. Synthesis of α-Amino Acids
Method#1- Amination of alpha-bromocarboxylic acids provides a straight forward
method for preparing alpha- aminocarboxylic acids. The bromoacid are
conveniently prepared from carboxylic acids by reaction with Br2 + PCl3.
21. Explaination of Method
#2
By modifying the nitrogen as a phthalimide salt the propensity of amines to
undergo multiple substitutions is removed, and a single clean substitution
reaction of 1º- and many 2º-alkylhalides takes place.
This procedure is known as the Gabriel synthesis, it can be used to advantage in
aminating bromomalonic esters, as shown in the upper equation of the following
scheme.
Since the phthalimide substituted malonic ester has an acidic hydrogen (colored
orange) activated by the two ester groups, this intermediate may be converted to
an ambident anion and alkylated.
Finally, base catalyzed hydrolysis of the phthalimide moiety and the esters,
followed by acidification and thermal decarboxylation, produces an amino acid
and phthalic acid (not shown).
22. Method#3
An elegant procedure known as the Strecker synthesis, assembles an alpha-amino acid from
ammonia (the amine precursor), cyanide (the carboxyl precursor) and an aldehyde. This
reaction is essentially an imino analog of cyanohydrin formation. The alpha-amino nitrile
formed in this way can then be hydrolyzed to an amino acid by either acid or base catalysis.
24. Explaination of Method # 4
Resolution The three synthetic procedures described above and many others that
can be conceived, give racemic amino acid products. If pure L or D enantiomers are
desired, it is necessary to resolve these racemic mixtures.
A common method of resolving racemates is by diastereomeric salt formation with a
pure chiral acid or base.
This is illustrated for a generic amino acid in the following diagram. Be careful to
distinguish charge symbols shown in colored circles, from optical rotation signs
shown in parenthesis.
25. In the initial display, the carboxylic acid function contributes to diastereomeric salt formation.
The racemic amino acid is first converted to a benzamide derivative to remove the basic
character of the amino group.
Next, an ammonium salt is formed by combining the carboxylic acid with an optically pure
amine, such as brucine (a relative of strychnine).
The structure of this amine is not shown, because it is not a critical factor in the logical
progression of steps.
Since the amino acid moiety is racemic and the base is a single enantiomer (levorotatory in this
example), an equimolar mixture of diastereomeric salts is formed (drawn in the green shaded
box).
Diastereomers may be separated by crystallization, chromatography or other physical
manipulation and in this way one of the isomers may be isolated for further treatment, in this
illustration it is the (+):(-) diastereomer.
Finally the salt is broken by acid treatment, giving the resolved (+)-amino acid derivative
together with the recovered resolving agent (the optically active amine). Of course, the same
procedure could be used to obtain the (-)-enantiomer of the amino acid.
26. Since amino acids are amphoteric, resolution could also be achieved by using the basic character
of the amine function. For this approach we would need an enantiomerically pure chiral acid
such as tartaric acid to use as the resolving agent.
Note that the carboxylic acid function is first esterified, so that it will not compete with the
resolving acid.
Resolution of aminoacid derivatives may also be achieved by enzymatic discrimination in the
hydrolysis of amides. For example, an aminoacylase enzyme from pig kidneys cleaves an amide
derivative of a natural L-amino acid much faster than it does the D-enantiomer.
If the racemic mixture of amides shown in the green shaded box above is treated with this
enzyme, the L-enantiomer (whatever its rotation) will be rapidly converted to its free zwitterionic
form, whereas the D-enantiomer will remain largely unchanged.
the diastereomeric species are transition states rather than isolable intermediates.
This separation of enantiomers, based on very different rates of reaction is called kinetic
resolution.
42. Beta amino acid
β amino acids, which have their amino group bonded to the β carbon rather
than the α carbon as in the 20 standard biological amino acids.
The only commonly naturally occurring β amino acid is β-alanine; although it
is used as a component of larger bioactive molecules, β-peptides in general do
not appear in nature.
Only glycine lacks a β carbon, which means that β-glycine is not possible.
43. Chemical synthesis
The chemical synthesis of β amino acids can be
challenging, especially given the diversity of functional
groups bonded to the β carbon and the necessity of
maintaining chirality.
In the alanine molecule shown, the β carbon is achiral;
however, most larger amino acids have a chiral atom.
A number of synthesis mechanisms have been introduced
to efficiently form β amino acids and their derivatives
notably those based on the Arndt-Eistert synthesis (A
method of increasing the length of an aliphatic acid by one
carbon by reacting diazomethane with acid chloride).
44. Two main types of β-peptides exist:
those with the organic residue (R) next
to the amine are called β3-peptides and
those with position next to the carbonyl
group are called β2-peptides.
45. Secondary structure
Because the backbones of -peptides are longer than those of peptidesβ
that consist of -amino acids, -peptides form different secondaryα β
structures. The alkyl substituents at both the and positions in aα β β
amino acid favor a gauche conformation about the bond between the
-carbon and -carbon.α β
Many types of helix structures consisting of -peptides have beenβ
reported. These conformation types are distinguished by the number
of atoms in the hydrogen-bonded ring that is formed in solution; 8-
helix, 10-helix, 12-helix, 14-helix, and 10/12-helix have been
reported. Generally speaking, -peptides form a more stable helixβ
than -peptides.α
46. Arndt–Eistert reaction
The Arndt-Eistert synthesis is a series of chemical
reactions designed to convert a carboxylic acid to a
higher carboxylic acid homologue (i.e. contains one
additional carbon atom) and is considered a
homologation process.
Arndt-Eistert synthesis is a popular method of
producing β-amino acids from α-amino acids. Acid
chlorides react with diazomethane to give
diazoketones. In the presence of a nucleophile (water)
and a metal catalyst (Ag2O), diazoketones will form
the desired acid homologue.
47. While the classic Arndt-Eistert synthesis uses thionyl
chloride to convert the starting acid to an acid chloride,
any procedure can be used that will generate an acid
chloride.
3 RCOOH + PCl3(phosphorus trichloride) 3 RCOCl + H3PO3→
RCOOH + PCl5(phosphorus pentachloride) RCOCl + POCl3 + HCl→
Diazoketones are typically generated as described here,
but other methods such as diazo-group transfer can also
apply.
48. Reaction mechanism
The key step in the Arndt-Eistert synthesis is the metal-catalyzed Wolff
rearrangement of the diazoketone to form a ketene.
In the insertion homologation of t-BOC (Di-tert-butyl dicarbonate)
protected (S)-phenylalanine (2-amino-3-phenylpropanoic acid), t-BOC
protected (S)-3-amino-4-phenylbutanoic acid is formed.
49. Wolff rearrangement of the α-diazoketone
intermediate forms a ketene via a 1,2-rearrangement,
which is subsequently hydrolysed to form the
carboxylic acid. The consequence of the 1,2-
rearrangement is that the methylene group α- to the
carboxyl group in the product is the methylene group
from the diazomethane reagant.
It has been demonstrated that the rearrangement
preserves the stereochemistry of the chiral centre as
the product formed from t-BOC protected (S)-
phenylalanine retains the (S) stereochemistry
Heat, light, platinum, silver, and copper salts will also
catalyze the Wolff rearrangement to produce the
desired acid homologue.
50. Wolff rearrangement
The Wolff rearrangement is a rearrangement
reaction converting a α-diazo-ketone into a ketene.
1,2-rearrangement is the key step in the Arndt-Eistert
synthesis.
51. Clinical potential
β-peptides are stable against proteolytic degradation in vitro and in vivo, an
important advantage over natural peptides in the preparation of peptide-
based drugs.
β-Peptides have been used to mimic natural peptide-based antibiotics such as
magainins (A family of peptides with broad-spectrum antimicrobial activity
has been isolated from the skin of the African clawed frog Xenopus laevis),
which are highly potent but difficult to use as drugs because they are
degraded by proteolytic enzymes in the body.
52. BETA ALANINE
Also known as 3-aminopropanoic acid,
It is a non-essential amino acid and is the only
naturally occurring beta-amino acid.
Not to be confused with alanine, beta- alanine is
classified as a non-proteinogenic amino acid as it is
not used in the building of proteins.
53. β-Alanine is not used in the biosynthesis of any major
proteins or enzymes. It is formed in vivo by the
degradation of dihydrouracil and carnosine. It is a
component of the naturally occurring peptides carnosine
and anserine and also of pantothenic acid (vitamin B5),
which itself is a component of coenzyme A. Under normal
conditions, β-alanine is metabolized into acetic acid.
β-Alanine is the rate-limiting precursor of carnosine,
which is to say carnosine levels are limited by the amount
of available β-alanine.
Supplementation with β-alanine has been shown to
increase the concentration of carnosine in muscles,
decrease fatigue in athletes and increase total muscular
work done.
55. Carnosine (beta-alanyl-L-histidine) is a dipeptide of
the amino acids beta-alanine and histidine. It is
highly concentrated in muscle and brain tissues.
Anserine (beta-alanyl-N-methylhistidine) is a
dipeptide found in the skeletal muscle and brain of
mammals, and birds.
It is an antioxidant (about 5 times that of carnosine)
and helps reduce fatigue
59. Functions
It plays a role in regulating neuronal excitability throughout the
nervous system. In humans, GABA is also directly responsible for the
regulation of muscle tone.
GABA acts at inhibitory synapses in the brain by binding to specific
transmembrane receptors in the plasma membrane of both pre- and
postsynaptic neuronal processes.
This binding causes the opening of ion channels to allow the flow of
either negatively charged chloride ions into the cell or positively
charged potassium ions out of the cell.
In both cases, the membrane potential is decreased. This action results
in a negative change in the transmembrane potential, usually causing
hyperpolarization
60. Synthesis
GABA does not penetrate the blood-brain
barrier; it is synthesized in the brain.
It is synthesized from glutamate using the
enzyme L-glutamic acid decarboxylase ( GAD)
and pyridoxal phosphate (which is the active
form of vitamin B6) as a cofactor via a
metabolic pathway called the GABA shunt.
The synthesis of GABA is linked to the Kreb's
cycle.
61. This process converts glutamate, the principal
excitatory neurotransmitter, into the principal
inhibitory neurotransmitter (GABA).
GABA is destroyed by a transamination reaction,
in which the amino group is transferred to alpha-
oxoglutaric acid (to yield glutamate), with the
production of succinic semialdehyde, and then
succinic acid. The reaction is catalysed by GABA
transaminase.
62. Network of glucose and amino acid metabolism.
Li C et al. J. Biol. Chem. 2008;283:17238-17249
65. What is delta-aminolevulinic
acid?
-Aminolevulinic acidδ (dALA or -ALA or 5ala or 5-δ
aminolevulinic acid ) is the first compound in the porphyrin
synthesis pathway, the pathway that leads to heme in
mammals and chlorophyll in plants.
STRUCTURE dALA
66. Heme Synthesis
Heme synthesis occurs partly in the mitochondria and partly in
the cytoplasm.
The process begins in the mitochondria because one of the
precursors is found only there. Since this reaction is regulated in
part by the concentration of heme, the final step (which
produces the heme) is also mitochondrial.
Many of the intermediate steps are cytoplasmic. Notice in the
diagram of the pathway that there is a branch with no apparent
useful endproduct.
67.
68. Outline of the porphyrin synthesis
pathway.
1) delta-aminolevulinic acid synthase (ALA synthase).
2) delta-aminolevulinic acid dehydratase (ALA
dehydratase)
3) uroporphyrinogen I synthase and
uroporphyrinogen III cosynthase
4) uroporphyrinogen decarboxylase
5) coproporphyrinogen III oxidase
6) protoporphyrinogen IX oxidase
7) ferrochelatase
69. 1) Delta-aminolevulinic acid
synthase (ALA synthase)
The delta-aminolevulinic acid synthase (ALA synthase) reaction
occurs in the mitochondria.
The substrates are
succinyl CoA (from the tricarboxylic acid cycle)
glycine (from the general amino acid pool)
70. An essential cofactor is pyridoxal phosphate (vitamin
B-6).
The reaction is sensitive to nutritional deficiency of this vitamin.
Drugs which are antagonistic to pyridoxal phosphate will inhibit
it. Such drugs include
1. penicillamine, is used as a form of immunosuppression to treat rheumatoid
arthritis. It works by reducing numbers of T-lymphocytes, inhibiting macrophage
function, decreasing IL-1, decreasing rheumatoid factor, and preventing collagen
from cross-linking.
71. It is used as a chelating agent: Wilson's disease and cystinuria,
Penicillamine is the second line treatment for arsenic poisoning, after dimercaprol
(BAL)
2. isoniazid also known as isonicotinylhydrazine (INH), is an organic compound
that is the first-line anti tuberculosis medication in prevention and treatment.
The reaction occurs in two steps.
1. Condensation of succinyl CoA and glycine to form enzyme-bound alpha-amino-
beta-ketoadipate.
2. Decarboxylation of alpha-amino-beta-ketoadipate to form delta-aminolevulinate.
This is the rate-limiting reaction of heme synthesis in all tissues, and it is therefore
tightly regulated.
72.
73. There are two major means of regulating the activity of the enzyme.
1. The first is by regulating the synthesis of the enzyme protein. This is important
because its half life is only about one hour.
Enzyme synthesis is repressed by heme and hematin.
It is stimulated by barbiturates (as a result, these drugs exacerbate certain
porphyrias).
steroids with a 4,5 double bond, such as testosterone and certain oral
contraceptives. This double bond can be reduced by two different reductases to
form either a 5-alpha or a 5-beta product. Only the 5-beta product affects synthesis
of ALA synthase. Since the 5-beta reductase appears at puberty, some porphyrias are
not manifested until this age.
2. The second control is feedback inhibition by heme and hematin, presumably by an
allosteric mechanism. Hence, heme has a dual role in decreasing its own rate of
synthesis.
The product of the reaction, ALA, diffuses into the cytoplasm, where the next
several steps of heme synthesis occur.
74. 2) delta-aminolevulinic acid
dehydratase (ALA dehydratase)
The ALA dehydratase reaction occurs in the cytoplasm; the product is
porphobilinogen
The substrates are two molecules of ALA.
The reaction is a condensation to form porphobilinogen, the
first pyrrole.
Two molecules of water are released. The asymmetry of the reaction
relative to the two molecules of substrate results in the pyrrole ring
having two different substituent groups:
1. acetic acid
2. propionic acid.
75.
76. ALA dehydratase is a -SH containing enzyme.
It is very susceptible to inhibition by heavy metals, especially
lead.
increased urinary excretion of its substrate is a good indicator of
lead poisoning.
This is because when ALA dehydratase is inhibited its substrate,
delta-aminolevulinate (ALA), accumulates. This is in part simply
because it is no longer being used, and in part because it can no
longer continue down the pathway to form heme, which would
serve as a feedback inhibitor of further ALA synthesis. ALA
continues to be made, and the excess is excreted in the urine.
77. 3) Uroporphyrinogen I synthase
and uroporphyrinogen III
cosynthase
Production of uroporphyrin III requires two enzymes.
The substrates are four molecules of porphobilinogen.
1. The first reaction is catalyzed by uroporphyrinogen I synthase.
The porphobilinogen molecules lose their amino groups.
A linear tetrapyrrole with alternating acetic acid and propionic acid groups is
produced. This linear molecule cyclizes slowly (nonenzymatically) to yield
uroporphyrinogen I. Without the second reaction (below), the heme synthesis
pathway would end with porphyrinogens of the I series, which have no known
function.
78. 2. The second reaction is catalyzed by uroporphyrinogen III
cosynthase. This enzyme rapidly converts the alternating linear
tetrapyrrole to the cyclic uroporphyrinogen III, which has the
substituents of its IV ring reversed: AP AP AP PA. This is the
physiologically useful product.
79.
80. 4) Uroporphyrinogen
decarboxylase
Uroporphyrinogen decarboxylase decarboxylates the acetic acid groups, converting them
to methyl groups.
The physiologically significant substrate is uroporphyrinogen III.
The product is coproporphyrinogen III, which is transported back to the mitochondria,
where the remainder of heme synthesis occurs.
The substituent pattern in the coproporphyrinogen is MP MP MP PM.
Uroporphyrinogen decarboxylase also acts on uroporphyrinogen I, yielding
coproporphyrinogen I. Coproporphyrinogen I has no known function, and its formation
is thought to be a blind pathway.
81.
82. 5) Coproporphyrinogen III oxidase
The mitochondrial enzyme, coproporphyrinogen III oxidase, catalyzes the next
reaction.
The substrate is coproporphyrinogen III.
The reaction is conversion of the propionic acid groups of rings I and III to vinyl
groups. We now have the final substituent pattern of MV MV MP PM (note that
"Petrarchan" pattern of the last four substituent groups).
The product is protoporphyrinogen IX. (Some naming systems would call this
protoporphyrinogen III to preserve the logic of the nomenclature, but
"protoporphyrinogen III" is a departure from a time-honored tradition of referring to
this and subsequent compounds by the number "IX.")
83.
84. 6) Protoporphyrinogen IX oxidase
Protoporphyrinogen IX oxidase converts the methylene bridges
between the pyrrole rings to methenyl bridges. Resonance of
double bonds around the entire great ring, with its resulting
stabilization, is now possible.
85.
86. 7) Ferrochelatase
Ferrochelatase adds iron (II) to protoporphyrin IX, forming
heme
The enzyme requires iron (II), ascorbic acid and cysteine
(reducing agents).
Ferrochelatase is inhibited by lead.
87.
88. Physiological regulation of heme
synthesis
Substrate availability: iron (II) must be available for ferrochelatase.
Feedback regulation: heme is a feedback inhibitor of ALA synthase.
Subcellular localization: ALA synthase is in the mitochondria, where the substrate,
succinyl CoA, is produced. ALA synthase is synthesized in the cytoplasm, and is
transported into the mitochondria (like many other mitochondrial proteins). Its transport
across the mitochondrial membrane may be regulated.
89. In erythropoietic cells, heme synthesis is coordinated with globin
synthesis. If heme is available, globin synthesis proceeds. If heme
is absent:
a cAMP independent protein kinase is active.
the kinase phosphorylates and thereby inactivates, the eukaryotic
initiation factor, eIF-2. This prevents further globin synthesis
Effects of drugs and steroids: Remember, certain drugs and
steroids can increase heme synthesis via increased production of
the rate-limiting enzyme, ALA synthase
