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Amino acid, any of a group of organic molecules that consist of a basic amino group (―NH2), an acidic
carboxyl group (―COOH), and an organic R group (or side chain) that is unique to each amino acid. The
term amino acid is short for α-amino [alpha-amino] carboxylic acid. Each molecule contains a
central carbon (C) atom, called the α-carbon, to which both an amino and a carboxyl group are attached. The
remaining two bonds of the α-carbon atom are generally satisfied by a hydrogen (H) atom and the R group. The
formula of a general amino acid is:

The amino acids differ from each other in the particular chemical structure of the R group.

Building Blocks of Proteins

Proteins are of primary importance to the continuing functioning of life on Earth. Proteins catalyze the vast
majority of chemical reactions that occur in the cell. They provide many of the structural elements of a cell, and
they help to bind cells together into tissues. Some proteins act as contractile elements to make movement
possible. Others are responsible for the transport of vital materials from the outside of the cell (“extracellular”)
to its inside (“intracellular”). Proteins, in the form of antibodies, protect animals from disease and, in the form
of interferon, mount an intracellular attack against viruses that have eluded destruction by the antibodies and
other immune system defenses. Many hormones are proteins. Last but certainly not least, proteins control the
activity of genes (“gene expression”).

This plethora of vital tasks is reflected in the incredible spectrum of known proteins that vary markedly in their
overall size, shape, and charge. By the end of the 19th century, scientists appreciated that, although there exist
many different kinds of proteins in nature, all proteins upon their hydrolysis yield a class of simpler compounds,
the building blocks of proteins, called amino acids. The simplest amino acid is called glycine, named for its
sweet taste (glyco, “sugar”). It was one of the first amino acids to be identified, having been isolated from the
protein gelatin in 1820. In the mid-1950s scientists involved in elucidating the relationship between proteins and
genes agreed that 20 amino acids (called standard or common amino acids) were to be considered the essential
building blocks of all proteins. The last of these to be discovered, threonine, had been identified in 1935.

Chirality

All the amino acids but glycine are chiral molecules. That is, they exist in two optically active asymmetric
forms (called enantiomers) that are the mirror images of each other. (This property is conceptually similar to the
spatial relationship of the left hand to the right hand.) One enantiomer is designated D and the other L. It is
important to note that the amino acids found in proteins almost always possess only the L-configuration. This
reflects the fact that the enzymes responsible for protein synthesis have evolved to utilize only the L-
enantiomers. Reflecting this near universality, the prefix L is usually omitted. Some D-amino acids are found in
microorganisms, particularly in the cell walls of bacteria and in several of the antibiotics. However, these are
not synthesized in the ribosome.
Acid-Base Properties

Another important feature of free amino acids is the existence of both a basic and an acidic group at the α-
carbon. Compounds such as amino acids that can act as either an acid or a base are called amphoteric. The basic
amino group typically has a pKa between 9 and 10, while the acidic α-carboxyl group has a pKa that is usually
close to 2 (a very low value for carboxyls). The pKa of a group is the pH value at which the concentration of the
protonated group equals that of the unprotonated group. Thus, at physiological pH (about 7–7.4), the free amino
acids exist largely as dipolar ions or “zwitterions” (German for “hybrid ions”; a zwitterion carries an equal
number of positively and negatively charged groups). Any free amino acid and likewise any protein will, at
some specific pH, exist in the form of a zwitterion. That is, all amino acids and all proteins, when subjected to
changes in pH, pass through a state at which there is an equal number of positive and negative charges on the
molecule. The pH at which this occurs is known as the isoelectric point (or isoelectric pH) and is denoted as pI.
When dissolved in water, all amino acids and all proteins are present predominantly in their isoelectric form.
Stated another way, there is a pH (the isoelectric point) at which the molecule has a net zero charge (equal
number of positive and negative charges), but there is no pH at which the molecule has an absolute zero charge
(complete absence of positive and negative charges). That is, amino acids and proteins are always in the form of
ions; they always carry charged groups. This fact is vitally important in considering further the biochemistry of
amino acids and proteins.

STANDARD AMINO ACIDS

One of the most useful manners by which to classify the standard (or common) amino acids is based on
the polarity (that is, the distribution of electric charge) of the R group (e.g., side chain).

Group I: Nonpolar amino acids

Group I amino acids are glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine,

and tryptophan. The R groups of these amino acids have either aliphatic or aromatic groups. This makes them
hydrophobic (“water fearing”). In aqueous solutions, globular proteins will fold into a three-dimensional shape
to bury these hydrophobic side chains in the protein interior. The chemical structures of Group I amino acids
are:
Isoleucine is an isomer of leucine, and it contains two chiral carbon atoms. Proline is unique among the standard
amino acids in that it does not have both free α-amino and free α-carboxyl groups. Instead, its side chain forms
a cyclic structure as the nitrogen atom of proline is linked to two carbon atoms. (Strictly speaking, this means
that proline is not an amino acid but rather an α-imino acid.) Phenylalanine, as the name implies, consists of a
phenyl group attached to alanine. Methionine is one of the two amino acids that possess a sulfur atom.
Methionine plays a central role in protein biosynthesis (translation) as it is almost always the initiating amino
acid. Methionine also provides methyl groups for metabolism. Tryptophan contains an indole ring attached to
the alanyl side chain.

Group II: Polar, uncharged amino acids

Group II amino acids are serine, cysteine, threonine, tyrosine, asparagine, and glutamine. The side chains in this

group possess a spectrum of functional groups. However, most have at least one atom (nitrogen, oxygen,
or sulfur) with electron pairs available for hydrogen bonding to water and other molecules. The chemical
structures of Group II amino acids are:
Two amino acids, serine and threonine, contain aliphatic hydroxyl groups (that is, an oxygen atom bonded to a
hydrogen atom, represented as ―OH). Tyrosine possesses a hydroxyl group in the aromatic ring, making it
a phenol derivative. The hydroxyl groups in these three amino acids are subject to an important type of
posttranslational modification: phosphorylation . Like methionine, cysteine contains a sulfur atom. Unlike
methionine’s sulfur atom, however, cysteine’s sulfur is very chemically reactive. Asparagine, first isolated
from asparagus, and glutamine both contain amide R groups. The carbonyl group can function as a hydrogen
bond acceptor, and the amino group (NH2) can function as a hydrogen bond donor.

Group III: Acidic amino acids

The two amino acids in this group are aspartic acid and glutamic acid. Each has a carboxylic acid on its side
chain that gives it acidic (proton-donating) properties. In an aqueous solution at physiological pH, all three
functional groups on these amino acids will ionize, thus giving an overall charge of −1. In the ionic forms, the
amino acids are called aspartate and glutamate. The chemical structures of Group III amino acids are
The side chains of aspartate and glutamate can form ionic bonds (“salt bridges”), and they can also function as
hydrogen bond acceptors. Many proteins that bind metal ions (“metalloproteins”) for structural or functional
purposes possess metal-binding sites containing aspartate or glutamate side chains or both. Free glutamate and
glutamine play a central role in amino acid metabolism. Glutamate is the most abundant
excitatory neurotransmitter in the central nervous system.

Group IV: Basic amino acids

The three amino acids in this group are arginine, histidine, and lysine. Each side chain is basic (i.e., can accept a
proton). Lysine and arginine both exist with an overall charge of +1 at physiological pH. The guanidine group
in arginine’s side chain is the most basic of all R groups (a fact reflected in its pKa value of 12.5). As mentioned
above for aspartate and glutamate, the side chains of arginine and lysine also form ionic bonds. The chemical
structures of Group IV amino acids are

The imidazole side chain of histidine allows it to function in both acid and base catalysis near physiological pH
values. None of the other standard amino acids possesses this important chemical property. Therefore, histidine
is an amino acid that most often makes up the active sites of protein enzymes.

The majority of amino acids in Groups II, III, and IV are hydrophilic (“water loving”). As a result, they are
often found clustered on the surface of globular proteins in aqueous solutions.

Amino Acid Reactions

Amino acids via their various chemical functionalities (carboxyl, amino, and R groups) can undergo
numerous chemical reactions. However, two reactions (peptide bond and cysteine oxidation) are of particular
importance because of their effect on protein structure.
Peptide bond

Amino acids can be linked by a condensation reaction in which an ―OH is lost from the carboxyl group of one
amino acid along with a hydrogen from the amino group of a second, forming a molecule of water and leaving
the two amino acids linked via an amide—called, in this case, a peptide bond. At the turn of the 20th century,
German chemist Emil Fischer first proposed this linking together of amino acids. Note that when individual
amino acids are combined to form proteins, their carboxyl and amino groups are no longer able to act
as acids or bases, since they have reacted to form the peptide bond. Therefore, the acid-base properties of
proteins are dependent upon the overall ionization characteristics of the individual R groups of the component
amino acids.

Amino acids joined by a series of peptide bonds are said to constitute a peptide. After they are incorporated into
a peptide, the individual amino acids are referred to as amino acid residues. Small polymers of amino acids
(fewer than 50) are called oligopeptides, while larger ones (more than 50) are referred to as polypeptides.
Hence, a protein molecule is a polypeptide chain composed of many amino acid residues, with each residue
joined to the next by a peptide bond. The lengths for different proteins range from a few dozen to thousands of
amino acids, and each protein contains different relative proportions of the 20 standard amino acids.

Many amino acids (more than 100) are joined to form a polypeptide chain. A polypeptide chain has direction
because it has 2 different ends α-amino, and α-COOH groups. An amino acid unit in a polypeptide chain is
written by starting with amino terminal residue and ending with -COOH terminal. One is basic and the other is
acidic and these two are the only ionizable groups of the peptide chain except those present in side chain. A
polypeptide thus consists of a regularly repeating part called the main chain or backbone and the variable part
comprising the side chain. The names are written by adding the suffix –yl except in last amino acid which is
written full. Peptides have different structure- 1. Linear peptides- with a free -NH2 and +COOH at the ends. 2.
Branched peptides- where branching of one of several amino acid on a linear chain takes place either by
-COOH or -NH2 groups of ω carboxylic group of dicarboxylic amino acid or amino group of lysine. 3. Cyclic
peptides- do not have N and C terminal ends. 4. Semi-cyclic peptides- have only one end if only N terminal end,
the α-COOH of last amino acid is linked with -NH2 of an endopeptide lysine, inversely when there is only one
-COOH terminal end the αNH2 of first amino acid is linked with ω -COOH of dicarboxylic amino acid.
Peptides may consist of same amino acids - homopeptides like triglycine, polyphenylalanine or may be
heteropeptides.

IMPORTANT PEPTIDES1. Glutathione- this is a tripeptide (γ-L-glutamyl-L-cysteinyl-glycine) a linear

peptide. It exists in reduced form (thiol) and oxidized form in which 2 molecules are linked by disulphide
bridge and play a role in redox reactions. 2. Peptide hormones- e.g- pituitary hormones, oxytocin, vasopressin.
These are cyclic due to a disulphide bridge and side chain. 3. Insulin- secreted by pancreas. It has 2 chains- A
chain of 21 amino acid (free from basic amino acid) and B chain of 30 amino acid (with basic amino acid) 3
disulphide bridges, 2 inter-chain bridges and 1 intra-chain bridge. 4. Penicillin- has valine and cystine but
besides peptide linkage other linkage are also present. They possess antibacterial activities present in fungus and
bacteria Peptides like amino acid can be distinguished by their ionization behavior showing characteristic
titration curves and isoelectric pH.

ESSENTIAL AND NON-ESSENTIAL AMINO ACIDS

Amino acids can be called the “building blocks” of protein and are an important part of every human body.
There are 20 different amino acids – nine of which are called “essential” and 11 of which are labeled as “non-
essential.” The human body needs all 20 of these amino acids, in varying degrees, to be healthy and fully
functional. All 20 have distinct chemical structures and are used for different roles – such as forming
neurotransmitters, forming hormones and producing energy. But their primary role is to build proteins. Protein
is part of every single cell in the human body and is essential to the body’s functioning. Protein helps build and
repair tissues like skin and muscle, and it helps produce antibodies and insulin. From only 20 amino acids, the
body is able to generate many thousands of unique proteins with different functions. Each one of these proteins
contains between 50 and 2000 amino acids, connected in varying sequences. After all of these amino acids are
joined together, they are folded and twisted to make a specific shape. This unique shape is the determining
factor for what the protein does for the body. From only 9 essential and 11 non-essential amino acids, the body
is able to generate many thousands of unique proteins with different functions. Essential Amino Acids Essential
amino acid, or indispensable amino acid, is an amino acid that cannot be synthesized de novo by the organism
at a rate as per its demand, and thus must be supplied in its diet. These are the nine amino acids that cannot be
create on its own, and which must obtain by eating various foods. Adults need to eat foods that contain the
following nine amino acids phenylalanine, valine, threonine, tryptophan, methionine, leucine, isoleucine, lysine,
and histidine. Instead of storing up a supply of the essential acids, the body uses them to create new proteins on
a regular basis. Therefore, the body needs a continuous supply of these amino acids to stay healthy. Non-
Essential Amino Acids The other type is the non-essential amino acid, 11 of which exist and are synthesized by
the body- alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline,
serine, and tyrosine. Thus, although they are an important part of building proteins, they do not need to be
included in an everyday diet. Six of these non-essential acids are also known as “conditional,” meaning that the
body may not be capable of producing enough of them when presented with substantial stress or illness These
are arginine, cysteine, glycine, glutamine, proline, and tyrosine.. The limiting amino acid is the essential amino
acid found in the smallest quantity in the foodstuff, most plant-based foods have a limiting amino acid.
 PROTEINS

The basic structural units of proteins are amino acid however since protein is a macromolecule four basic
structural levels of organizations are present:

1. PRIMARY STRUCTURE: this refers to the basic amino acid sequence in a polypeptide chain. Amino acid
consists of an amino group, carboxyl group, a H atom and a distinctive R group bonded to ‘C’ atom which is
called α-carbon. Amino acids are linked by polypeptide chain. A peptide (-CONH) bond links αcarboxyl group
of one amino acid to the α-amino group of other. A protein consists of one or more polypeptide chain. Each
kind of protein has a unique amino acid sequence that is genetically determined. An amino acid unit in a
polypeptide chain is called a residue.

2. SECONDARY STRUCTURE: many structural proteins eg. Silk fibroin are linear unfolded t ype having
gly-alan – ser units. A polypeptide chain has a spatial organization. This refers to the regular folding of the
chain due to presence of intramolecular H bonds. Folding and H bonding between amino acids results in a rigid
stale structure called 1. Helix and 2. Sheets.

The secondary structure includes the polypeptide amino acid side chain because secondary structure is
stabilized by H bonding between peptide imide and carboxyl groups of polypeptide and not the side chain. The
peptide bond has a planar structure and the electrons are delocalized in amide linkage giving a double bond
nature to C=N bonds. Since the C-N bond is double the α-C to carboxyl C and imide N to α-carbon bond result
in rotation. The chain thus assumes either a helical configuration or two degenerate forms of a circle (very rare)
or a zigzag structure. Of these, the most abundant are α-helix, parallel β pleated sheets and anti- parallel β-
pleated sheets.

α-helix is a right handed helix i.e, the chain rotates clockwise. The α-helix has 3.6 amino acids residue per turn
and is stabilized by a nearly straight H bonding between an imide (NH) group and a carboxyl (COO) group at a
position 4 residues away in the same chain. α-keratin is example of fibrous protein. Haemoglobin and
myoglobin are example of globular protein.

β-pleated sheets: The atoms lie in folded plane and the side chains of succeeding residues along the
polypeptide chain protrude alternatively above and below the general plain of the structure. There is a
maximum H bonding between -NH and -CO group of different polypeptide chain and the H bonds are straight
enough to be stable. They are not only pleated but slightly twisted. The polypeptide chain lies in a extended or
β- form with the C=O and N-H group. Hydrogen atom are bonded to those of neighboring chain which maybe
the same chain folded back or separate chain. It is named β-form because it was first founded in β-keratin. It is
pleated because successive α-carbon atoms of amino acids residue lie slightly above and below the plane of β-
sheet. The adjacent polypeptide chain in same direction is parallel or opposite direction is anti-parallel.

β-pleated sheet differ from α–helix in having a polypeptide arranged side by side resembling a sheet rather than
a rod. The chain is fully extended in a zigzag fashion rather than being lightly coiled as in a helix. In fibrous
proteins parallel β sheet is β- keratin and antiparallel is silk. In globular proteins antiparallel – β sheet are 6
stranded bovine pancreatic Chymotrypsin and 4 parallel stranded globular protein 4 stranded parallel β sheet in
Glutathione Reductase.

Super secondary structure- In fibrous protein collagen 3 left handed α helix coil in parallel around each other
to form a right handed super secondary structure which is stabilized by inter chain H bond. This is mainly due
to presence of glycine and no α helix is formed. The special structure of fibrous protein is super secondary
structure. Super secondary structures are also motif or folds are stable arrangement of several elements of
secondary structure and their connections. Motifs are the basis of protein structural classification (SCOP) in
which proteins are divided into 4 classes all α, all β, α/β in which α+β segments alternate and α+β in which α+β
regions are segregated. Within each class are 10 to 100s of different folding arrangements. The top two level
class and folds are purely structural. Proteins with significant primary sequence similarity or similar structure
and function form family. eg., globin family. Two or more families having same major structural motif and
functional similarities are grouped as super families. Polypeptides with more than a few hundred amino acid
residues after fold into two or more stable globular units are called domains. In many cases a domain from a
large protein will retain its correct 3-D structure even when it is separated from the remainder of the polypeptide
chain. A protein with multiple domains may appear to have distinct globular lobe for each domain. Different
domains have distinct functions. Two simple motifs the β-α-β and α-α corner are involved.

3. TERTIARY STRUCTURE: refers to the three dimensional structure especially the bonds between amino
acids residue that are distant from each other in a polypeptide chain and the arrangement of secondary elements
relative to one another. The term conformation refers to secondary and tertiary structure i.e, the folding pattern
of polypeptide chain and all contacts between amino acid side chain of that polypeptide chain. The biological
activity of protein molecule is due to its well defined 3-D structure. The steric relationship between amino acid
residue that lie far part in a linear sequence and relative arrangements of the secondary structure elements to
another in a polypeptide chain is the tertiary structure. The tertiary structure is stabilized by side chains of
amino acids. e.g., Ribonuclease is a single polypeptide chain of 124 AA residues. It has 4 disulphide bonds
which can be reversibly cleaved by reducing them with reagent like β-mercaptoethanol so that disulphide
(cystine) all converts to sulfhydrul (cysteine). If urea is added the protein is totally denatured by unfolding. The
reduced unfolded inactive RNase regains its enzyme activity when oxidised with air after removal of urea +
mercaptoethanol to give S-S. Thus the four disulphide bond pairing gives the 3-D structure to RNase and
determines its activity.

4. QUARTERNARY STRUCTURE: Oligomeric proteins that contain more than one polypeptide chains have
an additional structure which refers to the way in which the chain is folded together in relation to each other.
Each polypeptide subunit or protomer (repeating subunit or a group of subunit) has its own primary, secondary
and tertiary structure (a multi subunit protein is also referred to as multimer.). Thus quarternary structure
defines the structure resulting from interaction between separate polypeptide units of protein containing more
than one subunit. It maybe homogeneous when subunits have similar structure example phosphorylase which
has 2 sub identical subunits that are inactive separately but when they join as dimers they become active.
Heterogeneous quaternary structure when subunits are dissimilar example hemoglobin has two identical α-
chains and β-chains i.e. protomers are α2 β2; Ribulose bisphosphate carboxylase has 8 small and 8 large
subunits. Random coil or loop region- of a polypeptide chain is neither random nor a coil. The term indicates a
section of polypeptide in a protein whose conformation is not responsible as one of defined structure above. A
more common term is connecting loop region. The structure of random coil in a protein is mainly determined by
side chain interactions and it is fixed within a protein. The structure maybe along conformation as determined
by various group interactions in protein structure despite named coil. Since structure of random coil does not
satisfy the H bonding potentials of C=O and N-H group of the backbone or those of side groups, such section
are found at the exterior of proteins, in contact with water.
 CLASSIFICATION OF PROTEIN
A. Fibrous Protein

Scleroproteins- insoluble in water, dilute acids, bases and salts. e.g animal fibres like collagen, keratin, elastin,
fibroin.

B. Globular Protein

1. Simple proteins- this group includes proteins containing only amino acids as structural components. On
decomposition with acids they liberate constituent acid. On the basis of solubility these maybe
a) Protamines and histones- posses a simple structure, low molecular weight (approx 5000), water soluble,
heat resistant, strongly basic due to high content of basic amino acids (lysine, arginine) form salts with mineral
acids and nucleic proteins. Mainly found in animal sperm cells etc.
b) Albumins- abundant in seeds, water soluble, soluble in dilute solution of acids and bases or salts, heat labile
(coagulation) precipitated by saturated solution of acid salt (NH4)2SO4 or neutral salt Na2SO4 e.g., leucosine
in cereals, legumelline in legumes.
c) Globulin- soluble in water are pseudoglobulin (milk whey) and insoluble are euglobulin (more common),
coagulated by heat, precipitated by solution of (NH4)SO4 . Euglobulin e.g., glycine (soybean) legumine
(peas).
d) Glutelins- isolated from plant seeds, insoluble in water, dilute salt and alcohol solutions, soluble in dilute
acids and alkaline, coagulated by heat e.g., glutenin (wheat), glutelin (maize, oryzin (rice).
e) Prolamines- insoluble in water and dilute salt solution but soluble in dilute acid and alkaline and alcohol (60-
80%), not coagulated by heat e.g gliadin (wheat), zein (corn), hordein (oat).

2. Conjugated or Complex proteins:- these are linked with a separable non protein part or prosthetic group.
This prosthetic group maybe metal or an organic compound. On decomposition they liberate amino acids and
prosthetic group.
a) Metalloproteins- proteins linked with metals. Maybe stable or labile.

Metals strongly bound by proteins- some heavy metals like Hg, Ag, Cu, Zn are strongly bound to protein by –
SH group of side chain. Some have strong affinity for Fe (siderophilin) and Cu (ceruloplasmin).
Metals loosely bound- e.g Ca.
Metals which do not bind with proteins- Na and K form compounds with nucleic acids by electrostatic bonds.

b) Chromoproteins- these are proteins coupled with colored pigments. Chlorophyll is present in leaf
cells as chloroplastin which readily dissolves in water and is readily denatured. eg haem protein in
haemoglobin, cytochromes, flavoproteins- flavin nucleic acid (FAD).
c) Glycoprotein- egg albumin.
d) Mucoprotein- large amount of carbohydrates e.g mucin
e) Phospholipids- casein, vitellin
f) Lipoprotein- lipovitellin.
g) Nucleoprotein- nucleohistones from nuclei.
 BIOLOGICAL FUNCTIONS OF PROTEINS

1. Enzymes- most varied and highly specialized proteins with catalytic activity are the enzymes.
2. Transport proteins- bind and carry specific molecule or ions from one organ to another e.g lipoproteins,
ceruloplasmin (Cu), siderophilin (Fe).
3. Nutrient storage- seeds of many plants store nutrient proteins. Ovalbumin, egg white, casein milk, ferritin-
Fe protein plant, haemoglobin.
4. Contractile or motile protein- Actin and mycin in contractile system. Tubulin is protein from which micro
tubule is built.
5. Structural proteins- Supporting filaments gives structural strength or protection. Fibrous protein e.g.-
collagen, cartilage, elastin in ligaments, hair, finger nails- keratin. Silk fibers and spider web- fibroid, resilin in
wings of insect.
6. Defense proteins- The immunoglobulins or antibodies which can recognize and precipitate invading viruses ,
bacteria and foreign protein e.g. fibrinogen, thrombin, snake venom, ricin- plant toxic protein have defensive
function.
7. Regulatory protein- Help to regulate cellular or physiological activity. eg.- hormones in cellular response to
many hormonal signals is mediated by a loss of ATP binding protein called G- proteins. Other regulatory
proteins bind to amino acid and regulate the biosynthesis of enzymes. t- RNA molecule involved in cell
division.
8. Other proteins- Function cannot be classified. Monellin- African plant sweet protein. Also antifreeze protein
in Antarctic fish.

REFERENCES

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