Amino acids

Group members:
Fizal Ali
Endra Rampersaud
Radha Ramkisson
Shoneza Kingston
Ameenah Khan
 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.
General Structure of
Amino acids.
 General Classification of
Amino acids

• Standard amino acids

• Non-standard amino
acids
 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.
 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.
• 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.
 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.
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.
 Essential Nonessential
Histidine Alanine
Isoleucine Arginine*
Leucine Asparagine
Lysine Aspartic acid
Methionine Cysteine*
Phenylalanine Glutamic acid
Threonine Glutamine*
Tryptophan Glycine
Valine Ornithine*
Proline*
Selenocysteine*
Serine*
Taurine*
Tyrosine*
 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.
 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
• 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
• Neurotransmitters and Precursors
– Phenylalanine
– Tyrosine
– Tryptophan
– Alpha-Amino-N-Butyric Acid
– Gamma-Aminobutyric Acid

• Methylhistidines
– 1-methylhistidine
– 3-methylhistidine
• Precursors to Heme, Nucleotides and Cell Membranes
– Glycine
– Serine
– Sarcosine
– Alanine
– Ethanolamine
– Phospethanolamine
– Phosphoserine
• Bone Collagen Specific Amino Acids
– Proline
– Hydroxyproline
– Hydroxylysine
α-AMINO- ACIDS
E.g of some α-Amino Acid
 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.
Method#2
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).
 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.
Method# 4
 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.
• 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.
• 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.
Method # 5 Petasis Reaction
 Reactions of α-Amino Acids

1. Carboxylic Acid Esterification.

2- Amine Acylation
3- The Ninhydrin Reaction
 4-Oxidative Coupling

Cysteine-Cystine Interconversion.
E.g of some α-Amino Acid Biosynthesis

• Glutamate.
Aspartate:
Cysteine Biosynthesis
Tyrosine Biosynthesis
Ornithine and Proline Biosynthesis
Serine Biosynthesis
Glycine Biosynthesis
Beta Amino
Acid
 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.
 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).
• 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.
 Secondary structure

• Because the backbones of β-peptides are longer than those of

peptides that consist of α-amino acids, β-peptides form
different secondary structures. The alkyl substituents at both
the α and β positions in a β amino acid favor a gauche
conformation about the bond between the α-carbon and β-
carbon.
• Many types of helix structures consisting of β-peptides have
been 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, β-
peptides form a more stable helix than α-peptides.
 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.
• 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.
 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.
• 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.
 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.

 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.
 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.
• 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.
Biosynthesis of Beta Alanine
• 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
γ-Aminobutyric acid (GABA
 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
 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.
• 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.
 Network of glucose and amino acid metabolism.

Li C et al. J. Biol. Chem. 2008;283:17238-17249

©2008 by American Society for Biochemistry and Molecular Biology

Delta Amino
Acids
 What is delta-
aminolevulinic acid?

• δ-Aminolevulinic acid (dALA or δ-ALA or 5ala or 5-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
 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.
 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
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)
• 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

– 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.
• 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.
4. Condensation of succinyl CoA and glycine to form enzyme-bound alpha-
amino-beta-ketoadipate.
5. 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.
There are two major means of regulating the activity of the enzyme.
• 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.
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:
6. acetic acid
7. propionic acid.
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.
 3) Uroporphyrinogen I
synthase and
uroporphyrinogen III
cosynthase
• Production of uroporphyrin III requires two enzymes.
• The substrates are four molecules of porphobilinogen.
• 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.
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.
 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.
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.")
 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.
 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.
 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.
• 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
 References

• en.wikipedia.org/wiki/Gamma-Aminobutyric_acid
• www.wormbook.org/chapters/www_gaba/gaba.html
• www.ebi.ac.uk/QuickGO/GTerm?id=GO:0009449
• www.integrativepsychiatry.net/natural_gaba.html
• American Medical Association Encyclopedia of Medicine, p. 94; Hillman,
Howard. Kitchen Science, Rev. ed., pp. 256-57 retrieved on 2012-04-13
from http://www.enotes.com/science/q-and-a/what-difference-between-
essential-nonessential-288712