AMINO ACIDS
DEFINITION
Amino
acids are basic building block unit of protein. They are group of organic
compound containing two functional groups. The amino acids are named because
both amino (-NH2) and carboxyl (-COOH) groups are present in a
single molecule. The amino (-NH2) group is basic and carboxyl
(-COOH) group is acidic in nature. They are precursor molecules of many
important biological molecules e.g. Neurotransmitter, enzymes, proteins,
N-bases etc.
STRUCTURE OF THE AMINO ACIDS
Although more than 300 different
amino acids have been described in nature, only 20 are commonly found as
constituents of mammalian proteins. Each amino acid (except for proline, which
has a secondary amino group) has a carboxyl group, a primary amino group, and a
distinctive side chain (“R-group”) bonded to the α-carbon atom. At physiologic
pH (approximately pH 7.4), the carboxyl group is dissociated, forming the
negatively charged carboxylate ion (– COO–), and the amino group is
protonated (– NH3+). In proteins, almost all of these
carboxyl and amino groups are combined through peptide linkage and, in general,
are not available for chemical reaction except for hydrogen bond formation.
Thus, it is the nature of the side chains that ultimately dictates the role an
amino acid plays in a protein. It is, therefore, useful to classify the amino
acids according to the properties of their side chains, that is, whether they
are nonpolar (have an even distribution of electrons) or polar (Figures 1).
ABBREVIATIONS AND SYMBOLS FOR
COMMONLY OCCURRING AMINO ACIDS
Each amino acid name has an
associated three-letter abbreviation and a one-letter symbol. The one-letter
codes are determined by the following rules:
1. Unique first
letter: If only one amino acid begins with a particular letter, then
that letter is used as its symbol. For example, I = isoleucine.
2. Most commonly
occurring amino acids have priority: If more than one amino acid begins with a particular letter,
the most common of these amino acids receives this letter as its symbol. For
example, glycine is more common than glutamate, so G = glycine.
3. Similar
sounding names: Some one-letter symbols sound like the amino acid they
represent. For example, F = phenylalanine, or W = tryptophan (“twyptophan” as
Elmer Fudd would say).
4. Letter close
to initial letter: For the remaining amino acids, a one-letter symbol is
assigned that is as close in the alphabet as possible to the initial letter of
the amino acid, for example, K = lysine. Furthermore, B is assigned to Asx,
signifying either aspartic acid or asparagine, Z is assigned to Glx, signifying
either glutamic acid or glutamine, and X is assigned to an unidentified amino
acid (Figure 2).
Figure 1: Structural features of
amino acids
(Shown in their fully protonated
form)
Figure 2: Abbreviations and symbols used for amino acids
CLASSIFICATION OF AMINO ACIDS:
1.
Classification of amino acids on the basis of nature of side chains:
A. Amino acids with nonpolar side
chains
Each of these amino acids has a
nonpolar side chain that does not gain or lose protons or participate in
hydrogen or ionic bonds. The side chains of these amino acids can be thought of
as “oily” or lipid-like, a property that promotes hydrophobic interactions
(Figure 3).
Figure 3: Structures of amino
acids with non-polar side chains
B.
Polar amino acids with no charge on 'R‘ group:
These amino acids, as such, carry
no charge on the 'R‘ group. They however possess groups such as hydroxyl,
sulfhydryl and amide and participate in hydrogen bonding of protein structure. The
simple amino acid glycine (where R = H) is also considered in this category. The
amino acids in this group are glycine, serine, threonine, cysteine, glutamine,
asparagine and tyrosine (Figure 4).
Figure 4: Structures of polar amino
acids with no charge R groups
C.
Amino acids with acidic side chains
The amino acids aspartic and
glutamic acid are proton donors. At physiologic pH, the side chains of these
amino acids are fully ionized, containing a negatively charged carboxylate
group (–COO–). They are, therefore, called aspartate or glutamate to
emphasize that these amino acids are negatively charged at physiologic pH
(Figure 5).
Figure 5: Structures of amino
acids with acidic side chains
D.
Amino acids with basic side chains
The side chains of the basic
amino acids accept protons. At physiologic pH the side chains of lysine and
arginine are fully ionized and positively charged. In contrast, histidine is
weakly basic, and the free amino acid is largely uncharged at physiologic pH.
However, when histidine is incorporated into a protein, its side chain can be
either positively charged or neutral, depending on the ionic environment
provided by the polypeptide chains of the protein. This is an important
property of histidine that contributes to the role it plays in the functioning
of proteins such as hemoglobin (Figure 6).
Figure 6: Structures of amino
acids with basic side chains
2. Nutritional classification of amino acids:
The twenty
amino acids are required for the synthesis of variety of proteins, besides
other biological functions. However, all these 20 amino acids need not be taken
in the diet. Based on the nutritional requirements, amino acids are grouped
into two classes essential and nonessential.
A. Essential or indispensable amino acids:
The amino acids
which cannot be synthesized by the body and, therefore, need to be supplied
through the diet are called essential amino acids. They are required for proper
growth and maintenance of the individual. The ten amino acids listed below are
essential for humans (and also rats): Arginine, Valine, Histidine, lsoleucine,
Leucine, Lysine, Methionine, Phenylalanine, Threonine, and Tryptophan (For
remembrance use the code 'PVT TIM HALL'). The two amino acids namely
arginine and histidine can be synthesized by adults and not by growing
children, hence these are considered as semi-essential amino acids. HA
Thus, 8 amino
acids are absolutely essential while 2 are semi-essential.
B. Non-essential or dispensable amino acids:
The body can
synthesize about '10 amino acids to meet the biological needs, hence they need
not be consumed in the diet. These are glycine, alanine, serine, cysteine,
aspartate, asparagi ne, glutamate, glutamine, tyrosine and proline.
3. Amino acid classification based on their metabolic
fate
The carbon
skeleton of amino acids can serve as a precursor for the synthesis of glucose
(glycogenic) or fat (ketogenic) or both. From metabolic view point, amino acids
are divided into three groups.
A. Glycogenic amino acids:
These amino
acids can serve as precursors for the formation of glucose or glycogen. E.g. alanine,
aspartate, glycine, methionine etc.
B. Ketogenic amino acids:
Fat can be
synthesized from these amino acids. Two amino acids leucine and lysine are
exclusively ketogenic.
C. Glycogenic and ketogenic amino acids:
The four amino
acids isoleucine, phenylalanine, tryptophan, tyrosine are precursors for
synthesis of glucose as well as fat.
PROPERTIES OF AMINO ACIDS
A. Physical Properties of Amino acids:
The amino acids
differ in their physicochemical properties which ultimately determine the
characteristics of proteins.
1. Solubility:
Most of
the amino acids are usually soluble in water and insoluble in organic solvents.
2. Melting points:
Amino
acids generally melt at higher temperatures, often above 200°C.
3. Taste:
Amino
acids may be sweet (Gly, Ala, Val), tasteless (Leu) or bitter (Arg, lle).
Monosodium glutamate (MSC; ajinomoto) is used as a flavoring agent in food industry,
and Chinese foods to increase taste and flavor. Some individuals are intolerant
to MSC.
4. Optical property:
The α-carbon of an amino acid is
attached to four different chemical groups and is, therefore, a chiral or
optically active carbon atom. Glycine is the exception because its α-carbon has
two hydrogen substituents and, therefore, is optically inactive. Amino acids
that have an asymmetric center at the α-carbon can exist in two forms,
designated D (Dextro-dextrorotatory) and L (Levo-levorotatory) that are mirror
images of each other. The two forms in each pair are termed stereoisomers,
optical isomers, or enantiomers. All amino acids found in proteins are of the
L-configuration. However, D-amino acids are found in some antibiotics and in
plant and bacterial cell walls (Figure
7).
Figure 7: Mirror imaging of optical
isomers of amino acids
5. Amino acids as Ampholytes:
Amino acids contain both acidic (-COOH)
and basic (-NH2) groups. They can donate a proton or accept a proton;
hence amino acids are regarded as ampholytes. Zwitterion or dipolar ion: The
name zwitter is derived from the German word which means hybrid. Zwitter ion
(or dipolar ion) is a hybrid molecule containing positive and negative ionic
groups. The amino acids rarely exist in a neutral form with free carboxylic
(-COOH) and free amino (-NH2) groups. In strongly acidic pH (low
pH), the amino acid is positively charged (cation) while in strongly alkaline
pH (high pH), it is negatively charged (anion). Each amino acid has a
characteristic pH (e.g. leucine, pH 6.0) at which it carries both positive and
negative charges and exists as zwitterion. Isoelectric pH (symbol pl) is
defined as the pH at which a molecule exists as a zwitterion or dipolar ion and
carries no net charge. Thus, the molecule is electrically neutral.
Amino acids in aqueous solution contain
weakly acidic α-carboxyl groups and weakly basic α-amino groups. In addition,
each of the acidic and basic amino acids contains an ionizable group in its
side chain. Thus, both free amino acids and some amino acids combined in
peptide linkages can act as buffers. Recall that acids may be defined as proton
donors and bases as proton acceptors. Acids (or bases) described as “weak”
ionize to only a limited extent. The concentration of protons in aqueous
solution is expressed as pH, where pH = log 1/[H+] or –log [H+].
The quantitative relationship between the pH of the solution and concentration
of a weak acid (HA) and its conjugate base (A–) is described by the
Henderson-Hasselbalch equation.
B. Chemical Properties of Amino acids:
The general
reactions of mostly due to the presence groups namely carboxyl (-COOH) group
and amino (-NH2) group.
Reactions due to -COOH group:
1. Salt formation: Amino acids form salts (-COONa) with bases and esters
(-COOR') with alcohols.
2. Decarboxylation: Amino acids undergo decarboxylation to produce
corresponding amines.
R-CH(NH3+ )-COO ® R-CH2(NH3+)
+ CO2
This reaction
assumes significance in the living cells due to the formation of many
biologically important amines. These include histamine, tyramine and g-amino butyric
acid (GABA) from the amino acids histidine, tyrosine and glutamate,
respectively.
3. Reaction with ammonia: The carboxyl group of dicarboxylic
amino acids reacts with NH3 to form amide
Aspartic
acid + NH3 ® Asparagine
Glutamic
acid + NH3 ® Glutamine
Reactions due to -NH2 group:
4. Acts as bases: The amino groups behave as bases and combine with acids
(e.g. HCI) to form salts (-NH3+Cl-).
5. Reaction with ninhydrin: In the pH range of 4-8, all α- amino
acids react with ninhydrin (triketohydrindene hydrate), a powerful oxidizing
agent to give a purple colored product (diketohydrin) termed Rhuemann’s purple.
All primary amines and ammonia react similarly but without the liberation of
carbon dioxide. The imino acids proline and hydroxyproline also react with
ninhydrin, but they give a yellow colored complex instead of a purple one.
Besides amino acids, other complex structures such as peptides, peptones and
proteins also react positively when subjected to the ninhydrin reaction (Note:
Proline and hydroxyproline give yellow color with ninhydrin).
6. Color reactions of amino acids: Amino acids can be
identified by specific color reactions:
a. Xanthoproteic acid test
Aromatic amino
acids, such as Phenyl alanine, tyrosine and tryptophan, respond to this test.
In the presence of concentrated nitric acid, the aromatic phenyl ring is
nitrated to give yellow colored nitro-derivatives. At alkaline pH, the color
changes to orange due to the ionization of the phenolic group.
b. Pauly's diazo Test
This test is specific for the detection of Tryptophan or
Histidine. The reagent used for this test contains sulphanilic acid dissolved
in hydrochloric acid. Sulphanilic acid upon diazotization in the presence of
sodium nitrite and hydrochloric acid results in the formation a diazonium salt.
The diazonium salt formed couples with either tyrosine or histidine in alkaline
medium to give a red coloured chromogen (azo dye).
c. Millon's test
Phenolic amino
acids such as Tyrosine and its derivatives respond to this test. Compounds with
a hydroxybenzene radical react with Millon’s reagent to form a red colored
complex. Millon’s reagent is a solution of mercuric sulphate in sulphuric acid.
d. Histidine test
This test was discovered by Knoop. This reaction involves
bromination of histidine in acid solution, followed by neutralization of the
acid with excess of ammonia. Heating of alkaline solution develops a blue
or violet coloration.
e. Hopkins cole test
This test is specific test for detecting tryptophan. The
indole moiety of tryptophan reacts with glyoxilic acid in the presence of
concentrated sulphuric acid to give a purple colored product. Glyoxilic acid is
prepared from glacial acetic acid by being exposed to sunlight.
f. Sakaguchi test
Under alkaline condition, α- naphthol (1-hydroxy
naphthalene) reacts with a mono-substituted guanidine compound like arginine
which upon treatment with hypobromite or hypochlorite produces a characteristic
red color.
g. Lead sulphide test
Sulphur containing amino acids, such as cysteine and
cystine upon boiling with sodium hydroxide (hot alkali), yield sodium sulphide.
This reaction is due to partial conversion of the organic sulphur to inorganic
sulphide, which can be detected by precipitating it to lead sulphide, using
lead acetate solution.
h. Folin's McCarthy Sullivan Test
Imino acids such as Proline and hydroxyproline condense
with isatin reagent under alkaline condition to yield blue colored adduct.
Addition to sodium nitroprusside [Na2Fe(CN)5NO] to
an alkaline solution of methionine followed by the acidification of the
reaction yields a red color. This reaction also forms the basis for the
quantitative determination of methionine.
i. Isatin test
Imino acids such as Proline and hydroxyproline condense
with isatin reagent under alkaline condition to yield blue colored adduct.
7. Transamination: Transfer of an amino group from an amino acid to a keto
acid to form a new amino acid is a very important reaction in amino acid
metabolism.
8. Oxidative deamination: The amino acids undergo oxidative
deamination to liberate free ammonia.
References:
Lippincott's Bichemistry
&
Satyanarayan's Text Book of Biochemistry