BIOMOLECULES: (INTRODUCTION, STRUCTURE &

FUNCTION)

Carbohydrates

Suman Khowala, Deepak Verma, Samudra P. Banik

Drug Developement and Biotechnology
Indian Institute of Chemical Biology
4, Raja S. C. Mullick Road.
Kolkata-700032. INDIA
Email: [email protected]

Revised 04-June-2008

CONTENTS
Introduction
Definition
Importance of carbohydrates
Biosynthesis of other compounds
Classification
Isomerism
Chirality
Structural isomerism
Stereoisomerism
Mutarotation
Configuration of glucose
Important reactions of Aldehydes and Ketones
Important reactions of sugars
Reactions of sugar due to hydroxyl groups
Monosaccharide, Disaccharides, Trisaccharide and Polysaccharide
Monosaccharide
Disaccharide
Trisaccharides
Polysaccharides
Homopolysaccharides
Heteropolysaccharides
Sugar derivatives
Derivatives of Monosaccharide
Amino sugars and N-acetylated sugars
Carboxylic acid sugars
Sugar phosphates
Sugar alcohols
Derivatives of polysaccharides
Carbohydrates in living system
ABO Blood group system
Sugars in the cell wall of bacteria
Sugars in the cell wall of fungus
Derivatives with proteins
Glycoproteins (Glycophorins, Lectins, Mucins)
 Proteoglycans
Conformation of polysaccharides
Three dimensional orientation
Orientation of the glycosidic groups
Rare sugars
Carbohydrate assays

Keywords
Carbohydrates; Sugars; Monosaccharides; Disaccharides; Trisachharides; Polysaccharides; Aldoses; Ketoses;
Stereoisomerism; Optical isomerism; Mutarotation; Conformation of sugars; Sugar derivatives; Reactions of
sugars.

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Introduction
Carbohydrates are the most abundant biomolecules belonging to class of organic
compounds found in living organisms on earth. Each year, more than 100 billion metric tons
of CO2 and H2O are converted into cellulose and other plant products due to photosynthesis.
Living matter is largely made of biomolecules consisting of water and complex polymers of
amino acids, lipids, nucleotides and carbohydrates. Carbohydrates are most special of them
in that they remain associated with the three other polymers mentioned. Carbohydrates are
linked with amino acid polymers (proteins) forming glycoproteins and with lipids as
glycolipids. Carbohydrates are present in DNA and RNA, which are essentially polymers of
D-ribose-phosphate and 2-deoxy-D-ribose phosphate to which purines and pyrimidines
bases are attached at the C-1 reducing position. Carbohydrates are a widely diverse group of
compounds that are ubiquitous in nature. More than 75% of the dry weight of the plant
world is carbohydrate in nature - particularly cellulose, hemicellulose and lignin.

Existence of sugars is confirmed before life itself appeared on earth. It is highly probable
that there was a relative abundance of various sugars and their phosphates in the prebiotic
world, where the basic building blocks must have polymerized and assembled, ultimately to
form a self-sustaining, self-reproducing, and adaptive entity. The reality or possibility that
carbohydrates will be found in fossils is almost zero because they are relatively unstable,
capable of being dehydrated and of combining with other molecules. At higher temperatures
they caramelize and char. It has been known for over a century that many sugars formed
from formaldehyde in alkaline solution. Several alternative, synthetic pathways and reaction
conditions have been proposed but specific details probably never be established.
Condensation of formaldehyde, a prebiotic constituent, led to formation of glycol-aldehyde,
trioses, tetroses, pentoses and hexoses in the laboratory. UV light, electric discharges and
ionization radiation at the right pH and temperature may also promote synthesis of sugars.
The phosphorylation of sugars is an indispensable step in the assembly of the building
blocks of living matter. Cyanogen, a likely prebiotic constituent, is capable of catalyzing the
synthesis of glucose mono- and diphosphate from glucose and orthophosphate.

Carbohydrates comprise a comprehensive group of naturally occurring substances, which

include innumerable sugars and sugar derivatives, as well as high-molecular weight
carbohydrates (polysaccharides) like starch and cellulose in plants and glycogen in animals.
A polysaccharide molecule is composed of a large number of sugar or sugar-like units.
Carbohydrates are of great importance in biology. The unique reaction, which makes life
possible on Earth, namely the assimilation of the green plants, produces sugar, from which
originate, not only all carbohydrates but, indirectly, also all other components of living
organisms.

The important role of carbohydrates, generally, in the metabolism of living organisms, is

well known. The biological breakdown of carbohydrates (often spoken of as "combustion")
supplies the principal part of the energy that every organism needs for various vital
processes. It is not surprising; therefore, that the carbohydrates and their metabolism have
been the subject of comprehensive and in many respects successful biochemical and
medical research for a long time.

This chapter is created in view of giving an idea about sugars (monosaccharides to

polysaccharides; their derivatives, their important reactions, structures, function and
biological importance. Efforts have made to explain the chemistry and organization of
biomolecules in terms of stereioisomerism, optical isomerism, anomeric forms,

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mutarotations etc. Information about polysaccharides in plants and living organisms, blood
sugars and rare sugars is also included.

Definition
Carbohydrates are polyhydroxylated aldehydes or ketones and their derivatives. The word
"carbohydrate" includes polymers and other compounds synthesized from polyhydroxylated
aldehydes and ketones. They can be synthesized in the laboratory or in living cells. Simple
carbohydrates or the entire carbohydrate family may also be called saccharides. In general
carbohydrates have the empirical formula (CH2O)n (Fig. 1). The term generated from carbon
and hydrate; though some also contain nitrogen, phosphorus, or sulfur. Chemically,
carbohydrates are molecules that are composed of carbon, along with hydrogen and oxygen
- usually in the same ratio as that found in water (H2O).

Fig. 1: Carbohydrate

They originate as products of photosynthesis, an endothermic reductive condensation of

carbon dioxide requiring light energy and the pigment chlorophyll.

nCO2 + nH2O + energy CnH2nOn + nO2

Typical carbohydrates are composed of strings or chains of monosaccharides - that is,

chains of individual sugars.

Importance of carbohydrates
Carbohydrates are of great importance in biology. The unique reaction, which makes life
possible on the Earth, namely the assimilation of the green plants, produces sugar, from
which originate, not only all carbohydrates but, directly or indirectly, all other components
of living organisms. The carbohydrates are a major source of metabolic energy, both for
plants and for animals that depend on plants for food. Aside from the sugars and starch that
meet this vital nutritional role, carbohydrates also serve as a structural material (cellulose), a
component of the energy transport compound ATP, recognition sites on cell surfaces, and
one of three essential components of DNA and RNA. Importance can be considered under
following headings;

Metabolic/Nutritional
The important role of carbohydrates, generally, in the metabolism of living organisms, is
well known. The biological breakdown of carbohydrates (often spoken of as "combustion")
supplies the principal part of the energy that every organism needs for various processes.

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Carbohydrates and their metabolism has been the subject of biochemical and medical
research for a long time.

Carbohydrates play a major role in promoting health fitness, form a major part of food and
help a great deal in building body strength, by generating energy. They are one among the
three prominent macronutrients that serve as excellent energy providers, the other two being
fats and proteins. Carbohydrate intake can take place in different forms like sugar, starch,
fibers etc., which are a dietary staple in most parts of the world, and the oxidation of
carbohydrates is the central energy-yielding pathway in most nonphotosynthetic organisms.

The functions of carbohydrates are multiple and it is owing to this fact that it becomes all
the more necessary to incorporate carbohydrates in our meal. For instant for energy
generation, sugars and starch act as the perfect fuel that enables us to carry out our physical
activities efficiently and effectively. Fiber does wonders in keeping your bowel function
going smooth. Carbohydrates add on to the taste and appearance of food item, thus making
the dish tempting and mouthwatering. They are sometimes used as flavors and sweeteners.
Carbohydrates aid in regulating blood glucose and also do good to our body by breaking
down fatty acids, thus preventing ketosis. Talking about the importance of carbohydrates,
apart from its direct benefits, there is also an added advantage of carbohydrate consumption
and that is that carbohydrates are found in different foods, which if eaten, also pave way for
consuming other essential nutrients. Therefore, it is preferable to go in for distinctive
carbohydrate food sources.

Structural
The structural diversity possible by linking the different, common sugar is immense:
theoretically far greater than that of proteins, which largely consist of 22 amino acids linked
by a single type of peptide bond. Linkages between sugars can occur through a glycoside
linkage between the anomeric, first carbon of a sugar in either α or β configuration with any
of a variety of hydroxyl groups on the adjacent sugar. In fact, many possible combinations
of sugars do not seem to exist.

Insoluble carbohydrate polymers serve as structural and protective elements in the cell walls
of bacteria and plants and in the connective tissues of animals. Plant cell walls are complex
arrangements of cellulose, hemicellulose and lignin. This contributes significantly to the
overall digestibility of the fiber. The proportion of each component depends on species and
age of the plant. Cellulose is the primary structural component of plants. It is found
primarily in the cells walls and is a primary fiber component of animal feeds.

Communication
Glycosaminoglycans as polymers of derivatives of carbohydrates are of critical importance
in intercellular communication in organisms. This ubiquitous class of linear polyanions
interact with a wide variety of proteins, including growth factors and chemokines, which
regulate important physiological processes. The presence of glycosaminoglycans on cell
membranes and in the extracellular matrix also has resulted in their exploitation by
infectious pathogens to gain access and entry into animal cells. Other carbohydrate
polymers lubricate skeletal joints and participate in recognition and adhesion between cells.

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More complex carbohydrate polymers covalently attached to proteins or lipids act as signals
that determine the intracellular location or metabolic fate of these hybrid molecules, called
glycoconjugates. Glycoconjugates carry various important functions of cell. Glycoproteins
act as receptors and integral membrane proteins in membranes, cytoskeletal proteins in
cytoplasm, extracellular proteins such as antibodies, hormones, collagen (found outside the
cell), enzymes (RNase, DNase, lipases, cholinesterase, phosphatase, pepsinogen,
glycosyltransferases) etc. Functions and locations of glycolipids within the cell are
diverse—take for example: GAGs: submaxillary secretions, human gastric mucin, RBC
membrane sialoglycoprotein, membrane protein, secretory proteins without enzymatic
functions, immunoglobins, enzymes.

Biosynthesis of other compounds

Carbohydates are source of carbon for biosynthesis of other compounds. Most people know
that the body uses carbohydrates for energy. For example, the simple carbohydrate glucose
(dextrose) gets oxidized by liver cells. In exchange, the cells produce adenosine
triphosphate (ATP), the main energy-providing compound in the cell. However,
carbohydrates are used in a number of ways by plants, animals and bacteria, not just for
energy.

In carbohydrate anabolism, simple organic acids can be converted into monosaccharides

such as glucose and then used to assemble polysaccharides such as starch.

In living cells, glucose is oxidized to give carbon dioxide and energy. The energy produced
is in the form of ATP and heat. This reaction is just like the combustion.

Glucose + O2 CO2 + energy

During photosynthesis in plants, glucose can be produced from CO2 and energy:

CO2 + energy glucose + O2

Here, the energy consumed is in the form of sunlight. This reaction is the reverse of the
combustion reaction.

Classification
Carbohydrates are called saccharides or, if they are relatively small, sugars. Classifications
of carbohydrates are outlined in the following table.

Table 1

Complexity Simple Carbohydrates Complex Carbohydrates disaccharides,

monosaccharides oligosaccharides & polysaccharides
Size Tetrose Pentose Hexose Heptose Octose Nonose
C4 sugars C5 C6 C7 sugars C8 C9
sugars sugars sugars sugars
C=O Aldose: sugars having an aldehyde function or an acetal equivalent.
Function
C=O Ketose: sugars having a ketone function or an acetal equivalent.
Function

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The compounds carbohydrates have common same functional groups, glyceraldehydes and
gulose are classifed as aldoses and ribulose and dihydroxyacetone as ketoses (Fig. 2). All of
these compounds are alcohols with many hydroxyl groups. They are polyhydroxylated and
either aldehydes or ketones.

Fig. 2: Aldose & Ketose

A. Monosaccharides
The simplest and smallest unit of the carbohydrates is the monosaccharide, (mono = one,
saccharide = sugar) from which disaccharides, oligosaccharides, and polysaccharides are
constructed. Monosaccharides are either aldehydes or ketones, with one or more hydroxyl
groups; the six-carbon monosaccharides glucose (an aldohexose) and fructose (a keto
hexose) have five hydroxyl groups. (Fig. 3) The carbon atoms, to which hydroxyl groups
are attached, are often chiral centers, and stereoisomerism is common among
monosaccharides.

Fig. 3: Monosaccharide

Simple monosaccharides with four, five, six, and seven carbon atoms are called tetroses,
pentoses, hexoses, and heptoses, respectively (Table1). Because these molecules have
multiple asymmetric carbons, they exist as diastereoisomers, isomers that are not mirror
images of each other, as well as enantiomers. In regard to these monosaccharides, the
symbols D and L designate the absolute configuration of the asymmetric carbon farthest
from the aldehyde or keto group. D-Ribose, the carbohydrate component of RNA, is a five-
carbon aldose. D-Glucose, D-mannose, and D-galactose are abundant six-carbon aldoses. It
may be noted that D-glucose and D-mannose differ in configuration only at C-2. Sugars
differing in configuration at a single asymmetric center are called epimers. Thus, D-glucose
and D-mannose are epimeric at C-2; D-glucose and D-galactose are epimers with respect to
C-4 (Fig. 4). (More examples of monosaccharide will appear subsequently later)

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 Fig. 4: Epimers

B. Disaccharides
A disaccharide consists of two monosaccharides joined by an O-glycosidic bond.
Disaccharides can be homo- and heterodisaccharide (Fig. 5). Three most abundant
disaccharides are sucrose, lactose, and maltose. In sucrose the anomeric carbon atoms of a
glucose unit and a fructose unit are joined. Lactose, the disaccharide of milk, consists of
galactose joined to glucose by a β (1→4) glycosidic linkage. In maltose, α (1→4) glycosidic
linkage joins two glucose units. Sucrose and lactose are heterosaccharides and maltose is
homosaccharide.

C. Oligosaccharide
An oligosaccharide is a saccharide polymer containing a small number (typically three to
ten) of component sugars, and is also known as simple sugars. They are generally found
either O- or N-linked to compatible amino acid side chains in proteins or to lipid moieties.
They (homo-and hetero-oligosaccharides) are also liberated as intermediate products of
saccharification by action of glycosidases on polysaccharides.

D. Polysaccharides
Polysaccharides are relatively complex carbohydrates. They are polymers made up of many
monosaccharides joined together by glycosidic bonds. They are, therefore, very large, often
branched, macromolecules. They tend to be amorphous, insoluble in water, and have no

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sweet taste. When all the monosaccharides in a polysaccharide are of the same type, the
polysaccharide is called a homopolysaccharide and when more than one type of
monosaccharide is present, they are called heteropolysaccharides. Examples include storage
polysaccharides such as starch and glycogen and structural polysaccharides such as
cellulose, and chitin. Xylan a hemicellulose is a heteropolysaccharide. Polysaccharides have
a general formula of Cn(H2O)n-1 where n can be any number between 200 and 2500.
Considering that the repeating units in the polymer backbone are often six-carbon
monosaccharides, the general formula can also be represented as (C6H10O5)n where
n={40...3000}.

Fig. 5: Disaccharide

E. Families of Monosaccharides
Monosaccharides are colorless, crystalline solids that are freely soluble in water but
insoluble in nonpolar solvents. Most have a sweet taste. The backbone of monosaccharides
is an unbranched carbon chain in which all the carbon atoms are linked by single bonds.
One of the carbon atoms is double-bonded to an oxygen atom to form a carbonyl group;
each of the other carbon atoms has a hydroxyl group. If the carbonyl group is at an end of
the carbon chain, the monosaccharide is an aldehyde and is called an aldose; if the carbonyl
group is at any other position, the monosaccharide is a ketone and is called a ketose. The
simplest monosaccharides are the two three-carbon trioses: glyceraldehyde, an aldose, and
dihydroxyacetone, a ketose.

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F. Structure of monosaccharide
Structures of monosaccharides are defined by Fischer projection, where all horizontal bonds
project toward the viewer, while vertical bonds project away from the viewer. Therefore, a
Fischer projection cannot be rotated by (2n+1)×90° in the plane of the page or the screen, as
the orientation of bonds relative to one another can change, converting a molecule to its
enantiomer (Fig. 4).

Examples of monosaccharide include glucose (dextrose), fructose, galactose, and ribose

(Fig. 15). Monosaccharides are the building blocks of disaccharides like sucrose (common
sugar) and polysaccharides (such as cellulose and starch and hemicellulose). Further, each
carbon atom that supports a hydroxyl group (except for the first and last) is chiral, giving
rise to a number of isomeric forms, all with the same chemical formula. Galactose and
glucose are both aldohexoses (Fig. 4), but they have different chemical and physical
properties.

With few exceptions (e.g., deoxyribose or dexyglucose), monosaccharides have the

chemical formula (CH2O)n + m with the chemical structure H (CHOH)nC=O(CHOH)mH. If
n or m is zero, it is an aldehyde and is termed an aldose; otherwise it is a ketone and is
termed a ketose. Examples of some aldo and keto sugars are presented in Table 2.
Monosaccharides contain a ketone or aldehyde functional group, and hydroxyl groups on
most or all of the non-carbonyl carbon atoms. Most monosaccharides form cyclic structures,
which predominate in aqueous solution, by forming hemiacetals or hemiketals (depending
on whether they are aldoses or ketoses) between an alcohol and the carbonyl group of the
same sugar. Glucose, for example, readily forms a hemiacetal linkage between its carbon-1
and the hydroxyl group of its carbon-5. Since such a reaction introduces an additional
stereogenic center, two anomers are formed (α-anomer and β-anomer) from each distinct
straight-chain monosaccharide.

Table 2: Monosaccharides

Monosaccharides Aldo form Keto form

Trioses Glyceraldehydes Dihydroxyacetone
Tetroses Erythrose and Threose Erythrulose
Pentoses Arabinose, Lyxose, Ribulose and
Ribose and Xylose Xylulose
Hexoses Allose, Altrose, Fructose, Psicose,
Galactose, Glucose, Sorbose and Tagatose
Gulose, Idose, Mannose
and Talose
Heptoses NA Mannoheptulose,
Sedoheptulose
Octoses NA 2-Keto-3-deoxy-
manno-octonate
Nonoses NA Sialose

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The cyclic structure of monosaccharides is represented by Haworth projection, where the
α-anomer has the OH- of the anomeric carbon under the ring structure, and the β-isomer,
has the OH- of the anomeric carbon on top of the ring structure (Fig. 6).

Fig. 6:Cyclic form

Haworth Projection: A Haworth projection is a common way of representing the cyclic

structure of monosaccharides with a simple three-dimensional perspective. The Haworth
projection was named after the English chemist Sir Walter N. Haworth.
A Haworth projection has the following characteristics:
Carbon is the implicit type of atom. In the example on the right, the atoms numbered
from 1 to 6 are all carbon atoms. Carbon 1 is known as the Anomeric Carbon.
Hydrogen atoms on carbon are implicit. In the example, atoms 1 to 6 have extra
hydrogen atoms not depicted.

A thicker line indicates atoms that are closer to the observer. In the following figure, atoms
2 and 3 (and their corresponding OH groups) are the closest to the observer, atoms 1 and 4
are further from the observer and finally the remaining atoms (5, etc.) are the furthest.

There is another way of representation of cyclic structure of saccharides; one is chair and
another is boat conformation. In chair conformation, the α-anomer has the OH- of the
anomeric carbon in an axial position, whereas the β-isomer has the OH- of the anomeric
carbon in equatorial position The lowest-energy chair conformation, 6 of the 12 hydrogens
are in axial positions their C-H bonds are parallel to each other and appear to stick up and
down from the ring structure, the other 6 are in equatorial positions.

On the other hand, boat conformation has a higher energy than the chair form due to steric
strain resulting from the two axial 1,4-hydrogen atoms. The torsional strain in the boat

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conformation has a maximum value because all the carbon bonds are eclipsed. The boat and
envelope forms are transition states between the twist forms and the twist and chair forms
respectively, and are impossible to isolate. The twist-boat conformation is less stable than
the chair conformation. The difference in energy between the chair and the twist-boat
conformation of monosaccharides can be measured indirectly by taking the difference in
activation energy for the conversion of the chair to the twist-boat conformation and that of
the reverse isomerization (Fig. 7).

Fig. 7: Chair and Boat form

Axial & equatorial position: The axial hydrogens are those sigma bonds that are parallel to
an imaginary axis running through the ring structure (Scheme 1a). The equatorial hydrogens
are those whose sigma bonds are perpendicular to that axis (Scheme 1b).

Scheme 1a Scheme 1b

In the figures given not all of the hydrogens attached to the ring carbons in cyclohexane are
equivalent. Replacing all but one of the 12 hydrogens with deuterium leaving one position
as regular hydrogen can prove this. Because the ring flip occurs so rapidly at room
temperature, there will be only one nuclear magnetic resonance (NMR) signal for the one
hydrogen. Deuterium atoms do not have a spin state that would generate an NMR signal.
However when we slow the molecular motion down by lowering the temperature of the
sample to an extremely low temperature so the ring flip occurs much less rapidly, we
observe two separate NMR signals with slightly different chemical shifts. This would
indicate that the hydrogen has changed positions as the ring underwent flipping so that the
two positions are non-equivalent. These two non-equivalent hydrogen positions are called
the axial and equatorial positions. The axial bonds run vertical to the molecule. The
equatorial bonds run approximately horizontal to the molecule. During the ring flip process
the axial hydrogens become equatorial and the equatorial hydrogens become axial. (Scheme
1b above)

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Isomerism
Isomers are defined as molecule with the same chemical formula and often with the same
kinds of chemical bonds between atoms, but in which the atoms are arranged differently
(analogous to a chemical anagram). That is to say, they have different structural formulae.
Many isomers share similar if not identical properties in most chemical contexts. Isomerism
can be of two types: Structural isomerism and Stereoisomerism

A. Chirality
A carbon is chiral if it is sp3 hybridized and it has 4 different groups attached to it.
Molecule is chiral if it is not superimposable on its mirror image. This means that none of
its conformations (out of the infinite number of them) has a plane of symmetry through it.
Remember, there are as many conformations in a molecule as there are rotations about
single bonds.

Chiral carbon centers

All chiral molecules have nonsuperimposable mirror images. And as a general rule of
thumb, chiral molecules must have one or more chiral centers -- that is, carbons that have
four non-identical substituents around it. (There are, of course, exceptions to this rule). A
classic case of a simple chiral molecule is the following halogenated methane derivative to
it. Chiral carbons result in stereoisomers.

B. Structural isomerism
In structural isomers, the atoms and functional groups are joined together in different ways.
This group includes chain isomerism, position isomerism and functional group isomerism.
This is also termed as constitutional isomerism.

Chain isomerism – Here hydrocarbon chains have variable amounts of branching. In

carbon-chain isomerism, the difference between the isomers is the length of the carbon
chain. For example, if the compound contains four carbon atoms, they can be arranged with
two different chain lengths as below:

Positional isomerism – This deals with the position of a functional group on a chain.
Positional isomers have the same functional group in different locations on the carbon
skeleton. For example, there are two isomers of molecular formula C3H8O. In one isomer
(propan-1-ol) the –OH group is bonded to an end carbon atom; in the other (propan-2-ol) it
is bonded to the middle carbon atom.

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Functional-group isomerism – Here one functional group is split up into different ones.
The isomers are members of different homologous series and, therefore, have different
functional groups. For example, there are two isomers of molecular formula C2H6O. One
isomer is the alcohol, ethanol, CH3CH2OH; the other is the ether, methoxymethane,
CH3OCH3.

C. Stereoisomerism
The stereoisomers have same chemical formula and connectivity of atoms, but different
arrangements of those atoms. This is also termed as spatial isomerism. This class includes
enantiomers and diastereomers. Diastereomerism is of two types: conformational isomerism
(conformers) and cis-trans isomerism . Conformers can be referred to as having a
diastereomeric relationship; the isomers over all are not diastereomers, since bonds in
conformers can be rotated to make them mirror images.

a)

Enantiomers: Enantiomers are mirror images of chiral molecules. Enantiomers are not
superimposable on each other. Only chiral molecules will have a nonsuperimposable mirror
image. If two molecules are enantiomers, all of the chiral centers in it must have opposite
configurations.

The above carbon atom has four non-identical substituents around it, making this carbon a
chiral center, and as proof of its chirality the molecule has a non-superimposable mirror
image. A fancy term used in textbooks and in the literature to describe molecules that are
mirror images of each other are enantiomers, as in "the enantiomer of the left molecule
above is the molecule on the right, its mirror image."
To distinguish between enantiomers, chemists use the R and S classification system.
Stereocenters, (sometimes called chiral centers or stereogenic centers) are carbons that have
four non-identical substituents on them, and are designated as either of R stereochemistry or
S stereochemistry. If a molecule has one stereocenter of R configuration, then in the mirror
image of that molecule, the stereocenter would be of S configuration, and vice versa (Fig.
8).

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 Fig. 8: Enantiomers

Enantiomers have identical physical properties (b.p., m.p., density, etc.) with several
exceptions such as enantiomers have opposite specific rotations; they are distiguishable by
NMR spectroscopy in chiral media (but not achiral), they may exhibit different chemical
properties, such as very different rates of reaction.

Given the importance of stereochemistry in reactions between biomolecules, biochemists

must name and represent the structure of each biomolecule so that its stereochemistry is
unambiguous. For compounds with more than one chiral center, the most useful system of
nomenclature is the RS system. In this system, each group attached to a chiral carbon is
assigned a priority. The priorities of some common substituents are

ΟΟCΗ2 > ΟΟΗ> ΟΝΗ2 > ΟCΟΟΗ > ΟCΗΟ> ΟCΗ2ΟΗ > ΟCΗ3 > ΟΗ

For naming in the RS system, the chiral atom is viewed with the group of lowest priority (4
in the diagram on the next page) pointing away from the viewer. If the priority of the other
three groups (1 to 3) decreases in clockwise order, the configuration is (R) (Latin rectus,
“right”); if in counterclockwise order, the configuration is (S) (Latin sinister, “left”). In this
way each chiral carbon is designated either (R) or (S), and the inclusion of these
designations in the name of the compound provides an unambiguous description of the
stereochemistry at each chiral center.

Determination of R or S configuration can be applied in three steps:

1.Ordering of the substituents coming off the stereogenic carbon atom using the Cahn-
Ingold-Prelog rules.

[The Cahn-Ingold-Prelog priority rules, CIP system or CIP conventions are a set of rules
used in organic chemistry to name the stereoisomers of a molecule. A molecule may contain
any number of stereocenters and any number of double bonds, and each give rise to two
possible configurations. The purpose of the CIP system is to assign an R or S descriptor to
each stereocenter and an E or Z descriptor to each double bond so that the configuration of
the entire molecule can be specified uniquely by including the descriptors in its systematic
name.]

2. Rotation of the molecule until the lowest priority substituent is in the back

3. Depiction of a curve through the substituents in descending order of priority. If the curve
is clockwise, the stereocenter is of R configuration. If the curve is counterclockwise, the
stereocenter is of S configuration.

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1. Ordering the substituents
The substituents with higher molecular weight atoms are given a higher priority number. In
our example below, iodine would be 1, bromine 2, chlorine 3, and fluorine 4, because iodine
has the highest molecular weight (and is therefore highest priority) and fluorine has the
lowest molecular weight (and is therefore the lowest priority).

If the first atom of two substituents happen to be identical in molecular weight, go to the
next atom and make the molecular weight comparison (eg. an ethyl group would have
higher priority over a methyl group). Tthis applies in the same fashion to carbonyls, C=O,
and imines, C=N. A carbon with a double bond to another carbon is treated as a carbon
singly bonded to two carbons, as shown below. This means that, for example, an ethylene
substituent, R-CH=CH2, will have a higher priority then an ethyl substituent (R-CH2CH3).
Shown here is an ethylene substituent (often called an allyl substituent). By the Cahn-
Ingold-Prelog rules for assigning R and S nomenclature, this allyl group can be redrawn
with each double bond carbon singly bonded to an additional carbon with three "phantom
ligands," that are ignored.

Our example molecule can now be numbered as follows:

2. Rotation of the molecule

There are a couple of different ways to go from the priority numbering to determining R and
S configuration. One of the best methods is to rotate the molecule until the number 4
priority substituent is in the back, as shown below.

3. Draw the curve

A curve is then drawn from the 1 to 2 to 3 priority substituents, ignoring the 4th priority
subsituent (as shown below). If that curve goes clockwise then that stereocenter is of the R
configuration. If the curve goes in a counterclockwise direction, then that stereocenter is of
S configuration. In our example below, the curve goes counterclockwise so the stereocenter
is of S configuration.

16
The name of the compound above, then, would be (S)-bromo, chloro, fluoro, iodomethane,
and the name of its enantiomer, or its mirror image, would be (R)-bromo, chloro, fluoro,
iodomethane.

b) Diastereomers: Diastereomers are stereoisomers that are not enantiomers. If two

molecules differ only in the configuration of some of their stereocenters but all
stereocenters are not the opposite configuration, then the molecules are diastereomers (Fig.
9). In this class molecules do not have to be chiral to have a diastereomer, but they do have
to contain at least two chiral centers.

Fig. 9: Diasteromers

i) Conformational diastereomers: Conformational isomers are different conformers of a

diastereomer molecule. They differ only in how groups are rotated about single bonds.
Because at room temperature there is free rotation about single bonds, the conformation of a
given molecule will be changing constantly. There are an infinite number of conformations
for a given molecule as a result of an infinite number of posible rotations. A molecule does
not have to be chiral or contain chiral centers to have conformational isomers (Fig. 10).

Fig. 10: Conformational diasteromers

ii) Cis-Trans diastereomers: Cis-trans isomerism or geometric isomerism form of

stereoisomerism relates to the orientation of functional groups within a molecule. Such
isomers contain double bonds, which cannot rotate, but they can also arise from ring
structures, wherein the rotation of bonds is greatly restricted (Fig. 11).

17
 Fig. 11: Cis-Trans diasteromers

There are two forms of a cis-trans isomer, the cis and trans versions. When the substituent
groups are oriented in the same direction, the diastereomer is referred to as cis, whereas,
when the substituents are oriented in opposing directions, the diastereomer is referred to as
trans. An example of a small hydrocarbon displaying cis-trans isomerism is 2-butene.
Alicyclic compounds can also display cis-trans isomerism. As an example of a geometric
isomer due to a ring structure, consider 1,2-dichlorocyclohexane.

Structural isomers have different chemical properties; but stereoisomers behave identically
in most chemical reactions. Enzymes differentiate between stereoisomers of a compound,
and organisms do prefer one stereoisomer to the other. Some stereoisomers also differ in the
way they rotate polarized light.

There are other classes of isomers as below:

Tautomers are isomers of the same chemical substance that spontaneously convert to each
other, even when pure. They have different chemical properties, but cannot be isolated from
each other.

D. Mutarotation
The term for interconversion between the two anomers is called mutarotation. The two
different anomers are two distinct chemical structures, and thus have different physical and
chemical properties, notably optical rotation. For example, α-D-glucose has an optical
rotation of +112 degrees and its anomer, β-D-glucose, has an optical rotation of +19
degrees.
Isomeric forms of monosaccharides that differ only in their configuration about the
hemiacetal or hemiketal carbon atom are called anomers. The hemiacetal (or carbonyl)
carbon atom is called the anomeric carbon. The α and β anomers of D-glucose interconvert
in aqueous solution by a process called mutarotation (Fig. 12).

Fig. 12: Mutarotation

18
The figure is self-explanatory and shows that this mixture consists of about one-third α-D-
glucose, two-thirds β-D-glucose, and very small amounts of the linear and five-membered
ring (glucofuranose) forms (Fig. 13).

Fig. 13: Mutarotate forms of glucose

Anomers
In sugar chemistry, an anomer is a special type of epimer. It is a stereoisomer (diastereomer,
more exactly) of a saccharide (in the cyclic form) that differs only in its configuration at the
hemiacetal (or hemiketal) carbon, also called the anomeric carbon. If the structure is
analogous to one with the hydroxyl group on the anomeric carbon in the axial position of
glucose, then the sugar is an alpha anomer. If, however, that hydroxyl is in the equatorial
position, then the sugar is a beta anomer. For example, α-D-glucopyranose and β-D-
glucopyranose, the two cyclic forms of glucose, are anomers. For -L- the α and β are
contrarywise. The anomeric effect helps stabilize the α-anomer.

[The α- and β-anomers of D- glucopyranose]

E. Configuration of glucose
There are four chiral centers in glucose, which indicate possibility of sixteen stereoisomers
that would exist as eight diastereomeric pairs of enantiomers. German chemists Emil
Fischer in 1891 devised a method of representing the configuration of each chiral center in
an unambiguous manner. Fischer established a network of related aldose configurations
termed as D-family through an arbitrary choice for (+)-glucose. Consequently, The mirror
images of these configurations were designated the L-family of aldoses.

The last chiral center in an aldose chain (farthest from the aldehyde group) was chosen by
Fischer as the D / L designator site. If the hydroxyl group in the projection formula pointed

19
to the right, it was defined as a member of the D-family and a left directed hydroxyl group
(the mirror image) then represented the L-family. The sign of a compound's specific rotation
(an experimental number) does not correlate with its configuration (D or L) and optical
rotation can be measured by with a polarimeter.

Three-dimensional structure is described by Configuration and Conformation

The covalent bonds and functional groups of a biomolecule are, of course, central to its
function, but so also is the arrangement of the molecule’s constituent atoms in three-
dimensional space—its stereochemistry. A carbon-containing compound commonly exists
as stereoisomers, molecules with the same chemical bonds but different stereochemistry—
that is, different configuration, the fixed spatial arrangement of atoms. Interactions between
biomolecules are invariably stereospecific, requiring specific stereochemistry in the
interacting molecules.

Configuration is conferred by the presence of either (1) double bonds, around which there is
no freedom of rotation, or (2) chiral centers, around which substituent groups are arranged
in a specific sequence. The dentifying characteristic of configurational isomers is that they
cannot be interconverted without temporarily breaking one or more covalent bonds. A
binding site (on an enzyme, for example) that is complementary to one of these molecules
would not be a suitable binding site for the other, which explains why the two compounds
have distinct biological roles despite their similar chemistry.

In the second type of configurational isomer, four different substituents bonded to a

tetrahedral carbon atom may be arranged two different ways in space—that is, have two
configurations —yielding two stereoisomers with similar or identical chemical properties
but differing in certain physical and biological properties. A carbon atom with four different
substituents is said to be asymmetric, and asymmetric carbons are called chiral centers
(Greek chiros, “hand”; some stereoisomers are related structurally as the right hand is to the
left). A molecule with only one chiral carbon can have two stereoisomers; when two or
more (n) chiral carbons are present, there can be 2n stereoisomers. Some stereoisomers are
enantiomers and others, pairs of stereoisomers that are not mirror images of each other are
called diastereomer.

Distinct from configuration is molecular conformation, the spatial arrangement of

substituent groups that, without breaking any bonds, are free to assume different positions
in space because of the freedom of rotation about single bonds. In the simple hydrocarbon
ethane, for example, there is nearly complete freedom of rotation around the COC bond.
Many different, interconvertible conformations of ethane are possible, depending on the
degree of rotation. Two conformations are of special interest: the staggered, which is more
stable than all others and thus predominates, and the eclipsed, which are least stable. We
cannot isolate either of these conformational forms, because they are freely interconvertible.
However, when one or more of the hydrogen atoms on each carbon is replaced by a
functional group that is either very large or electrically charged, freedom of rotation around
the COC bond is hindered. This limits the number of stable conformations of the ethane
derivative.

Interactions between biomolecules are stereospecific

20
Biological interactions between molecules are stereospecific: the “fit” in such interactions
must be stereochemically correct. The three-dimensional structure of biomolecules large
and small—the combination of configuration and conformation—is of the utmost
importance in their biological interactions: reactant with enzyme, hormone with its receptor
on a cell surface, antigen with its specific antibody. The study of biomolecular
stereochemistry with precise physical methods is an important part of modern research on
cell structure and biochemical function. In living organisms, chiral molecules are usually
present in only one of their chiral forms. For example, the amino acids in proteins occur
only as their L isomers; glucose occurs only as its D isomer. In contrast, when a compound
with an asymmetric carbon atom is chemically synthesized in the laboratory, the reaction
usually produces all possible chiral forms: a mixture of the D and L forms, for example.
Living cells produce only one chiral form of biomolecules because the enzymes that
synthesize them are also chiral.

Stereospecificity, the ability to distinguish between stereoisomers, is a property of enzymes

and other proteins and a characteristic feature of the molecular logic of living cells. If the
binding site on a protein is complementary to one isomer of a chiral compound, it will not
be complementary to the other isomer, for the same reason that a left glove does not fit a
right hand.

Optical activity
Optical activity is the ability of a chiral molecule to rotate the plane of plane-polairsed light.
It is measured using a polarimeter, which consists of a light source, polarising lens, sample
tube and analysing lens. When light passes through a sample that can rotate plane polarised
light, the light appears to dim to the eye because it no longer passes straight through the
polarising filters. The amount of rotation is quantified as the number of degrees that the
analysing lens must be rotated by so that it appears as if no dimming, of the light has
occurred.
Louis Pasteur encountered the phenomenon of optical activity in 1843, during his
investigation of the crystalline sediment that accumulated in wine casks (a form of tartaric
acid called paratartaric acid—also called racemic acid, from Latin racemus, “bunch of
grapes”). He used fine forceps to separate two types of crystals identical in shape but mirror
images of each other. Both types proved to have all the chemical properties of tartaric acid,
but in solution one type rotated polarized light to the left (levorotatory), the other to the
right (dextro rotatory). Pasteur later described the experiment and its interpretation:

In isomeric bodies, the elements and the proportions in which they are combined are the
same, only the arrangement of the atoms is different. We know, on the one hand, that the
molecular arrangements of the two tartaric acids are asymmetric, and, on the other hand,
that these arrangements are absolutely identical, excepting that they exhibit asymmetry in
opposite directions. Are the atoms of the dextro acid grouped in the form of a right-handed
spiral, or are they placed at the apex of an irregular tetrahedron, or are they disposed
according to this or that asymmetric arrangement?

X-ray crystallographic studies in 1951 confirmed that the levorotatory and dextrorotatory
forms of tartaric acid are mirror images of each other at the molecular level and established
the absolute configuration of each.

21
Measurement of optical activity:
When rotation is quantified using a polarimeter it is known as an observed rotation, because
rotation is affected by path length (l), or the distance for which the light travels through a
sample and concentration (c), of the sample present to rotate the light. When these effects
are eliminated a standard for comparison of all molecules is obtained, the specific rotation,
[α], when concentration is expressed as sample in grams /100ml solution.

[α] = 100a / cl

Specific rotation is a physical property like the boiling point of a sample. Enantiomers will
rotate the plane of polarisation in exactly equal amounts (same magnitude) but in opposite
directions. Dextrorotary designated as (+), clockwise rotation (to the right) Levorotary
designated as (-), anti-clockwise rotation (to the left)

If only one enantiomer is present a sample is considered to be optically pure. When a

sample consists of a mixture of enantiomers, the effect of each enantiomer cancels out,
molecule for molecule. For example, a 50:50 mixture of two enantiomers or a racemic
mixture will not rotate plane polarised light and is optically inactive. A mixture that
contains one enantiomer excess, however, will display a net plane of polarisation in the
direction characteristic of the enantiomer that is in excess.

Determinination of optical purity

The optical purity or the enantiomeric excess (ee %) of a sample can be determined as
follows:

Optical purity = % enantiomeric excess = % enantiomer1 - % enantiomer2

= 100 [α]mixture / [α]pure sample

ee % = 100 ([R]-[S]) / ([R]+[S])

where [R] = concentration of the R-isomer

[S] = concentration of the S-isomer

Important reactions of Aldehydes and Ketones

Carbohydrates being polyhydroxylated aldehydes and ketones, it is important to know about
reactions of aldehyde and ketones, to understand reactivity of sugars.

A. Reversible Addition Reactions

a. Hydration and Hemiacetal Formation
Hydration of aldehydes leads to hemiacetal formation as shown below. It is well known that
water adds rapidly to the carbonyl function of aldehydes and ketones. The resulting hydrate
(hemiacetal) is unstable relative to the reactants and cannot be isolated. The addition
products are called hemiacetals and are unstable.

R2C=O + R’OH R’O–(R2) C–O–H (a hemiacetal)

b. Acetal Formation
Acetals are geminal-diether derivatives of aldehydes or ketones, formed by reaction with
two equivalents of an alcohol and elimination of water. Ketone derivatives of this kind were

22
once called ketals. The following equation shows the overall stoichiometric change in acetal
formation.
R2C=O + 2 R’OH R2C (OR')2 + H2O (an acetal)

For an effective acetal formation two additional features, an acid catalyst must be used; and
second, the water produced with the acetal must be removed from the reaction. The latter is
important, since acetal formation is reversible. The acetals may be hydrolyzed back by
treatment with aqueous acid. The mechanism shown here applies to both acetal formation
and acetal hydrolysis by the principle of microscopic reversiblity.

Reaction: Mechanism of acetal formation

The importance of acetals as carbonyl derivatives lies chiefly in their stability and lack of
reactivity in neutral to strongly basic environments. As long they do not get exposed to
acids, especially aqueous acid, acetals show lack of reactivity similar to ethers in general.

Among the most useful and characteristic reactions of aldehydes and ketones is their
reactivity toward strongly nucleophilic (and basic) metallo-hydride, alkyl and aryl reagents.
If the carbonyl functional group is converted to an acetal these powerful reagents have no
effect; thus, acetals are excellent protective groups, when these irreversible addition
reactions must be prevented.

c. Formation of Imines and Related Compounds

Imine derivatives are formed by the reaction of aldehydes and ketones with ammonia or 1º-
amines, also known as Schiff bases, (compounds having a C=N function). This reaction
plays an important role in the synthesis of 2º-amines. Water is eliminated in the reaction,
which is acid-catalyzed and reversible in the same sense as acetal formation.
R2C=O + R'NH2 R'NH–(R2)C–O–H R2C=NR' + H2O

B. Irreversible Addition Reactions

Most hydrates and hemiacetals (Y = OH & OR), are known to decompose spontaneously to
the corresponding carbonyl compounds. Aminols (Y = NHR) are intermediates in imine
formation, and also revert to their carbonyl precursors if dehydration conditions are not
employed. If substituent Y is an alkyl group or an aryl group, the resulting alcohol is a
stable compound and does not decompose with loss of hydrogen or hydrocarbons, even on

23
heating. It follows then, that if nucleophilic reagents corresponding to H:(–), R:(–) or Ar:(–)
add to aldehydes and ketones, the alcohol products of such additions will form irreversibly.
Free anions of this kind would be extremely strong bases and nucleophiles, but their
extraordinary reactivity would make them difficult to prepare and use.

a. Reduction by Complex Metal Hydrides

Addition of a hydride anion to an aldehyde or ketone would produce an alkoxide anion,
which on protonation should yield the corresponding alcohol. Aldehydes would give 1º-
alcohols and ketones would give 2º-alcohols.

RCH=O + H:(–) RCH2O(–) + H3O(–) RCH2OH

Reduction of α, β-unsaturated ketones by metal hydride reagents sometimes leads to a

saturated alcohol, especially with sodium borohydride. This product is formed by an initial
conjugate addition of hydride to the β-carbon atom, followed by ketonization of the enol
product and reduction of the resulting saturated ketone (equation 1 below).

NaBH4 (aq. + RCH2-

1) RCH=CHCOR' + ——> RCH=CHCH(OH)R'
alcohol) CH2CH(OH)R'
1,2-addition product 1,4-addition product
NaBH4 & CeCl3 -
2) RCH=CHCOR' + ——> RCH=CHCH(OH)R'
15º
1,2-addition product

Reaction: Reduction of α, β-unsaturated ketones by metal hydride reagents

C. Other Carbonyl group reactions

a. Oxidation
The most common and characteristic oxidation reaction is the conversion of aldehydes to
carboxylic acids. The carbon atom of a carbonyl group has a relatively high oxidation state.
This is reflected in the fact that most of the reactions described thus far either cause no
change in the oxidation state (e.g. acetal and imine formation) or effect a reduction (e.g.
organometallic additions and deoxygenations). In the shorthand equation shown here the
[O] symbol refers to unspecified oxidation conditions, which effect the desired change.
Several different methods of accomplishing this transformation will be described here.

RCH=O + [O] RC(OH)=O

In the oxidations of 1º and 2º-alcohols, aldehydes were converted to carboxylic acids,
presumably via the hydrate. Useful tests for aldehydes, Tollens' test, Benedict's test &
Fehling's test, take advantage of this ease of oxidation by using Ag(+) and Cu(2+) as
oxidizing agents (oxidants).

RCH=O + 2 [Ag(+) OH(–)] RC(OH)=O + 2 Ag (metallic mirror) + H2O

When silver cation is the oxidant, as in the above equation, it is reduced to metallic silver in
the course of the reaction, and this deposits as a mirror on the inner surface of the reaction
vessel. The Fehling and Benedict tests use cupric cation as the oxidant. This deep blue
reagent is reduced to cuprous oxide, which precipitates as a red to yellow solid. All these
cation oxidations are conducted under alkaline conditions. To avoid precipitation of the

24
insoluble metal hydroxides, the cations are stabilized as complexed ions. Silver is used as its
ammonia complex, Ag(NH3)2(+), and cupric ions are used as citrate or tartrate complexes.

Important reactions of sugars

A. Oxidation
Sugars are classified as reducing or non-reducing based on their reactivity with Tollens',
Benedict's or Fehling's reagents. If a sugar is oxidized by these reagents, it is called
reducing, since the oxidant (Ag+ or Cu+2) is reduced in the reaction, as evidenced by
formation of a silver mirror or precipitation of cuprous oxide. The Tollens' test is commonly
used to detect aldehyde functions; and because of the facile interconversion of ketoses and
aldoses under the basic conditions of this test, ketoses such as fructose also react and are
classified as reducing sugars.

When the aldehyde function of an aldose is oxidized to a carboxylic acid the product is
called an aldonic acid. Because of the 2º hydroxyl functions that are also present in these
compounds, a mild oxidizing agent such as hypobromite must be used for this conversion.

Oxidation of non anomeric hydroxyl groups can be achieved by the following oxydising
agents

a. Periodate oxidation
This reaction can be used quantitatively to measure the number of adjacent hydroxyl
group in a molecule; this is used in determination of polysaccharide structure.

25
 Aldose Alderic acid

b. Di nitrogen tetra oxide:

This reagent is specific for oxidation of primary alcohol groups. If we start with an aldose,
we get an alduronic acid. In case of a disaccharide, an aldobiouronic acid is obtained.

Methyl a-D- glucopyranoside Methyl a-D- glucopyranosiduronic acid

c. Hydrogen peroxide
It is a non-specific oxidant. It depolymerizes oligo- or polysaccharides and involves a free
radical mechanism. It also employs an Fe+2 catalyst.

Fe+2 + HO-OH Fe+3 + HO° + OH-

B. Reduction
Sodium borohydride reduction of an aldose makes the ends of the resulting alditol chain
identical, HOCH2(CHOH)nCH2OH, thereby accomplishing the same configurational change
produced by oxidation to an aldaric acid. Thus, allitol and galactitol from reduction of allose
and galactose are achiral, and altrose and talose are reduced to the same chiral alditol. A
summary of these redox reactions and derivative nomenclature is given in the following.

26
 Derivatives of HOCH2(CHOH)nCHO

HOBr Oxidation ——> HO-CH2(CHOH)n-CO2H

an Aldonic Acid
HNO3 Oxidation ——> H2O-C(CHOH)n-CO2H
an Aldaric Acid
NaBH4 Reduction ——> HO-CH2(CHOH)n-CH2OH
an Alditol

Commercial examples

D-Glucose D-Glucitol (Sorbitol)

Sorbitol was discovered in the barriers of mountain ash (Sorbus aucuparia).

[Importance: Functions as humectant (water retainer), Non cariogenic (S. mutans can’t
metabolize). It is about 50% as sweet as sucrose, used in toothpaste, in sugarless gums,
mints, hard candies, cough drops. Used as a cryoprotectant in surimi, as a starting material
for sorbitan esters (emulsifiers) as well as for vitamin C synthesis].

[Importance: In the laboratory mannitol prepared by hydrogenation of D mannose, by

fermentation; and commercially by hydrogenolysis of sucrose. It is not a humectant,
crystallizes easily, moderately water soluble and 65% sweet as sucrose. It is used in making
candies, sugar free chocolate, mints and cough drops. It is also used as an anticaking agent
as well as dusting agent.]

27
  

[Importance: It has an endothermic heat of solution, and, therefore, cooling sensation in

mouth. It is 70% to 95% as sweet as sucrose and is non cariogenic.]

[Importance: It is used in making low calorie candies and miscellaneous other food items.]

C. Osazone Formation
The osazone reaction was developed and used by Emil Fischer to identify aldose sugars
differing in configuration only at the alpha-carbon. The equation shows the general form of
the osazone reaction, which effects an alpha-carbon oxidation with formation of a bis-
phenylhydrazone, known as an osazone. Application of the osazone reaction to D-glucose
and D-mannose demonstrates that these compounds differ in configuration only at C-2.

Reaction: Osazone Formation

28
D. Chain Shortening and Lengthening
These two procedures permit an aldose of a given size to be related to homologous smaller
and larger aldoses. Ruff degradation of the pentose arabinose gives the tetrose erythrose.
Working in the opposite direction, a Kiliani-Fischer synthesis applied to arabinose gives a
mixture of glucose and mannose.

Using these reactions we can now follow Fischer's train of logic in assigning the
configuration of D-glucose.
1. Ribose and arabinose (two well known pentoses) both gave erythrose on Ruff
degradation. As expected, Kiliani-Fischer synthesis applied to erythrose gave a
mixture of ribose and arabinose.
2. Oxidation of erythrose gave an achiral (optically inactive) aldaric acid. This defines
the configuration of erythrose.
3. Oxidation of ribose gave an achiral (optically inactive) aldaric acid. This defines the
configuration of both ribose and arabinose.
4. Ruff shortening of glucose gave arabinose, and Kiliani-Fischer synthesis applied to
arabinose gave a mixture of glucose and mannose.
5. Glucose and mannose are, therefore, epimers at C-2, a fact confirmed by the
common product from their osazone reactions.
6. A pair of structures for these epimers can be written, but which is glucose and which
is mannose?

Note: Fischer looked for and discovered a second aldohexose that represented the end group
exchange for the epimer lacking the latent C2 symmetry. This compound was L-(+)-gulose,
and its exchange relationship to D-(+)-glucose was demonstrated be oxidation to a common
aldaric acid product. The remaining epimer is, therefore, mannose.

29
Reactions of sugar due to hydroxyl groups
Chemical properties of monosaccharides are a consequence of different levels of reactivity
of primary and secondary alcohol groups. The alcohol group is nucleophilic, acidic (pKa
10-18), and is also easily oxidized by a wide range of reagents such as pyridinium
dichromate (PDC) and chromium trioxide (CrO3). A hydroxyl group can participate in
numerous transformations under relatively mild conditions.

The reactivity of sugar molecules (free or functionalized) is heavily governed by the

geometry of the molecule. The specific conformation of a sugar molecule (aldoses or
ketoses) causes different reactivities of its secondary alcohol group.

A. Ester formation
Reaction type: Nucleophilic Acyl Substitution

Reaction: Acylation of -OH

(preparation of esters)

Acetic anhydride in pyridine at 0ºC is used as a reagent for the above reaction. Esters are
also formed using acetyl chloride, benzoyl chloride, diphenylphosphorochloridate, and p-
toluenesulphonyl chloride.

Uses: Intermediates in the synthesis of glycosides and carbohydrate derivatives. Esters may
be used in determination of the monosaccharide composition of polysaccharides.

B. Ether formation
Reaction type: Nucleophilic Substitution (SN2)

Reaction: Alkylation of -OH group (preparation of ethers)

30
Methylations occur smoothly with methyl iodide in dimethyl sulfoxide (DMSO) using
DMSO anion as an acid acceptor. Reagents methyl iodide or dimethyl sulphate and an agent
to promote ionization of the hydroxyl groups and to accept the acid released are used. The
methyl ethers are stable under acidic and alkaline conditions. The -OR group at the acetal
center can be converted back to an -OH with aqueous acid.

Methyl and other stable ethers are used in proving structures of glycosides. S-Adenosyl
methionine is utilized for the methylation of many biologically important compounds such
as tRNA in which some of the bases and some of the riboses are methylated.

C. Acetals and ketals

General reaction: Pair of hydroxyl groups + aldehyde/ketone cyclic acetal/ketal

Acetone and other ketones react with sulfuric acid or copper sulphate, and zinc chloride to
produce cyclic ketals usually with five-membered dioxolane ring systems. Aldehyde
(Acetaldehyde, Formaldehyde, Benzaldehyde) gives cyclic acetals. The reaction is
reversible and the groups can be removed by acid hydrolysis.

D. Glycoside formation

Reaction: Glycoside formation

This reaction takes place with excess ROH and acid catalyst. Alternatively, the "ROH" can
be from another saccharide so joining two saccharide units. Glycosides are just acetals or
ketals. The chemistry and uses are similar to just that of simple acetals and ketals. In case of
a disaccharide formation the uses are indicated below.

E. Oxidation
General reaction: Alcohol aldehyde, ketone or acid

Reagents DMSO + dicyclohexylcarbodiimide can oxidize isolated secondary hydroxyl

groups to ketone and isolated primary hydroxyl groups to aldehyde. DMSO + acetic
anhydride or phosphrous oxychloride are capable of similar oxidation.

Analogous biochemical process: Many sugar, alcohols and cyclitols are oxidized by enzyme
utilizing the nicotinamide dinucleotides DPN+ and TPN+ .They are usually fairly specific
and do not oxidize all alditols.

Oxidized sugras are used for the synthesis of rare sugars.

F. Ring Closure
In this reaction the aldehyde or ketone of the sugar reacts with an alcohol (hydroxyl) at the
other end of the sugar. The alcohol group that reacts is the next-to-last one at the other end

31
of the chain. By tradition, the end alcohol group and the carbon it is bonded to are directed
up. The oxygen of the next-to-last hydroxyl group becomes the connecting oxygen of the
ether. The hydrogen of this group bonds with the alcohol of the aldehyde or ketone, creating
another hydroxyl group. This hydroxyl group can be oriented either up or down. The
alcohol groups in the middle should remain on the same side of the carbon as in the linear
version of the structure (Fig. 14).

Fig. 14: Ring closure

G. Polymerization
a) Chemical polymerization
1) The alcohol part of the hemiacetal (in the ring form of the sugar) reacts with an alcohol
in another sugar (also in the ring form). For eg. , reaction of glucose & fructose leads to
the production of sucrose.

D Glucose D Fructose Sucrose

2) Polycondensation and subsequent deprotection of a partially benzylated phenyl 1-thio-β-

malto octaoside having a sole hydroxyl group at the non-reducing end gives rise to an
amylase like α-(1,4)-glucan (Fig. 15).

32
 Fig. 15: Chemical polymerization

b) Enzymatic polymerization
Glycosyltransferases (EC 2.4) act as a catalyst for the transfer of a monosaccharide unit
from an activated sugar phosphate (known as the "glycosyl donor") to an acceptor molecule,
usually an alcohol. The result of glycosyl transfer can be a monosaccharide glycoside, an
oligosaccharide, or a polysaccharide, although some glycosyltransferases catalyse transfer
to inorganic phosphate or water. Glycosyl transfer can also occur to protein residues,
usually to tyrosine, serine or threonine to give O-linked glycoproteins, or to asparagine to
give N-linked glycoproteins. Mannosyl groups may be transferred to tryptophan to generate
C-mannosyl tryptophan, which is relatively abundant in eukaryotes.

Commonly, sugar nucleotide derivatives are used as glycosyl donors. However, certain
other glycosyltransferases utilize non-nucleotide donors, which may be polyprenol
pyrophosphates, polyprenol phosphates, sugar-1-phosphates or sugar-1-pyrophosphates.
Common examples include phosphorylase, glycogen synthase, chitinase, etc. (Fig. 16).

Fig. 16: Enzymatic polymerization

33
Monosaccharide, Disaccharides, Trisaccharide and Polysaccharide (Structure,
occurrence and biological importance)
A. Monosaccharide
a. Glucose
Systemic name: D-Glucose
Molecular formula: C6H12O6

Glucose (Glc), a monosaccharide (or simple sugar), is an important carbohydrate in biology.

The living cell uses it as a source of energy and metabolic intermediate. Glucose is one of
the main products of photosynthesis and starts cellular respiration in both prokaryotes and
eukaryotes. The name comes from the Greek word ‘glykys’, which means "sweet", plus the
suffix "-ose" which denotes a sugar.
Two stereoisomers of the aldohexose sugars are known as glucose, only one of which (D-
glucose) is biologically active (Figs 2-4). This form (D-glucose) is often referred to as
dextrose monohydrate, or, especially in the food industry, simply dextrose (from
dextrorotatory glucose). The mirror-image of the molecule, L-glucose, cannot be
metabolized by cells in the biochemical process known as glycolysis.

Function: Enzyme-regulated addition of glucose to proteins by glycosylation is often

essential to their function.
• As an energy source - Glucose is a ubiquitous fuel in biology. It is used as an energy
source in most organisms, from bacteria to humans. Use of glucose may be by either
aerobic or anaerobic respiration (fermentation). Carbohydrates are the human body's
key source of energy, through aerobic respiration, providing approximately 3.75
kilocalories (16 kilojoules) of food energy per gram. Breakdown of carbohydrates
(e.g. starch) yields mono- and disaccharides, most of which is glucose. Through
glycolysis and later in the reactions of the Citric acid cycle (TCA), glucose is
oxidized to eventually form CO2 and water, yielding energy, mostly in the form of
ATP. The insulin reaction and other mechanisms, regulate the concentration of
glucose in the blood.
• Use of glucose as an energy source in cells is via aerobic or anaerobic respiration.
Both of them start with the early steps of the glycolysis metabolic pathway. The first
step of this is the phosphorylation of glucose by hexokinase to prepare it for later
breakdown to provide energy.

As a precursor: Glucose is used as a precursor for the synthesis of several important

substances. Starch solution Starch, cellulose, and glycogen are common glucose polymers
(polysaccharides). Lactose, the predominant sugar in milk, is a glucose-galactose
disaccharide. In sucrose, another important disaccharide, glucose is joined to fructose.

b. Galactose
Systemic name: D-Galactose
Molecular formula: C6H12O6

Galactose (Gal) is a type of sugar, (Fig. 4) which is less sweet than glucose and not very
water-soluble. Galactose is more commonly found in the disaccharide, lactose or milk

34
sugar. It is found as the monosaccharide in peas. Galactose is classified as a
monosaccharide, an aldose, a hexose, and is a reducing sugar. It is considered a nutritive
sweetener because it has food energy. A genetic defect of not being able to utilize galactose
is called Galactosemia. The disorder is caused by a deficiency in one or more enzymes
required to metabolize galactose. Since galactose is in milk as part of lactose, it builds up in
the blood and urine. Undiagnosed it may lead to mental retardation, failure to grow,
formation of cataracts, and in severe cases death by liver damage.

c. Fructose
Systemic name: D-Fructose
Molecular formula: C6H12O6

Fructose or laevulose) is a simple reducing sugar (monosaccharide) (Fig. 3) found in many

foods and is one of the three most important blood sugars along with glucose and galactose.
Honey, tree fruits, berries, melons, and some root vegetables, such as beets, sweet potatoes,
parsnips, and onions, contain fructose, usually in combination with sucrose and glucose.
Fructose is also derived from the digestion of sucrose, a disaccharide consisting of glucose
and fructose that is broken down by glycoside hydrolase enzymes during digestion.
Fructose is the sweetest naturally occurring sugar, estimated to be twice as sweet as sucrose.

Fructose is often recommended for, and consumed by, people with diabetes mellitus or
hyperglycemia, because it has a very low glycemic index (GI) relative to cane sugar
(sucrose). The low GI is due to the unique and lengthy metabolic pathway of fructose,
which involves phosphorylation and a multi-step enzymatic process in the liver.

d. 2 Deoxy-D-glucose:
Systemic name: 2 Deoxy-D-arabino-hexose
Molecular formula: C6H12O5

2-Deoxy-D-glucose is a glucose molecule (Fig. 17), which has the 2-hydroxyl group,
replaced by hydrogen, so that it cannot undergo further glycolysis. It is also called as non-
metabolizable form of glucose. The sugar is responsible for inhibiting glycosylating of
proteins if used in culture medium.

Fig. 17: 2 Deoxy-D-glucose

e. Xylose
Systemic name: D-Xylose
Molecular formula: C5H10O5

35
Xylose or wood sugar is an aldopentose — a monosaccharide containing five carbon atoms
and including an aldehyde functional group (Fig. 4). It has chemical formula C5H10O5.
Xylose is found in the embryos of most edible plants.

Function
• Xylose is an antibacterial and antifungal, particularly with gram-negative organisms
and Candida sp.
• Absorption rate of Xylose is decreased in some patients with intestinal disorders,
including those with colitis and diabetes, suggesting that when absorption problems
are corrected, these conditions might also reverse themselves.
• Unlike sucrose or artificial sweeteners, xylose promotes the growth of "friendly
flora" in the intestines, thus increasing the manufacture and absorption of all nutrients
and strengthening the immune system to help fight off any type of illness.

f. Ribose
Systemic name: D-ribose
Molecular formula: C5H10O5

Ribose, primarily seen as D-ribose, is an aldopentose — a monosaccharide containing five

carbon atoms, and including an aldehyde functional group in its linear form. It has the
chemical formula C5H10O5, and was discovered in 1905 by Phoebus Levene (Fig. 18).

 
Fig. 18: Ribose

As a component of the RNA that is used for genetic transcription, ribose is critical to living
creatures. It is related to deoxyribose, which is a component of DNA. It is also a component
of ATP, NADH, and several other chemicals that are critical to metabolism.

g. Deoxyribose
Systemic name: 2 -Deoxy-D-erythro-pentoseD-ribose
Molecular formula: C5H10O4

Deoxyribose, also known as D-Deoxyribose and 2-deoxyribose, is an aldopentose — a

monosaccharide containing five carbon atoms, and including an aldehyde functional group
in its linear structure (Fig. 19). It is a deoxy sugar derived from the pentose sugar ribose by
the replacement of the hydroxyl group at the 2 position with hydrogen, leading to the net
loss of an oxygen atom.

Ribose forms a five-member ring composed of four carbon atoms and one oxygen.
Hydroxyl groups are attached to three of the carbons. The other carbon and a hydroxyl
group are attached to one of the carbon atoms adjacent to the oxygen. In deoxyribose, the
carbon furthest from the attached carbon is stripped of the oxygen atom in what would be a

36
hydroxyl group in ribose. Due to the common C3' and C4' stereochemistry of D-ribose and
D-arabinose, D-2-deoxyribose is also D-2-deoxyarabinose.

Fig. 19: Deoxyribose

Biological importance
Ribose and 2-deoxyribose derivatives have an important role in biology. Among the most
important derivatives are those with phosphate groups attached at the 5 position. Mono-, di-,
and triphosphate forms are important, as well as 3-5 cyclic monophosphates. Purines and
pyrimidines form an important class of compounds with ribose and deoxyribose. When
these purine and pyrimidine derivatives are coupled to a ribose sugar, they are called
nucleosides. In these compounds, the convention is to put a ′ (pronounced "prime") after the
carbon numbers of the sugar, so that in nucleoside derivatives a name might include, for
instance, the term "5′-monophosphate", meaning that the phosphate group is attached to the
fifth carbon of the sugar, and not to the base. The bases are attached to the 1′ ribose carbon
in the common nucleosides. Phosphorylated nucleosides are called nucleotides.

One of the common bases is adenine (a purine derivative); coupled to ribose it is called
adenosine; coupled to deoxyribose it is called deoxyadenosine. The 5′-triphosphate
derivative of adenosine, commonly called ATP, for adenosine triphosphate, is an important
energy transport molecule in cells.

2-Deoxyribose and ribose nucleotides are often found in unbranched 5′-3′ polymers. In
these structures, the 3′carbon of one monomer unit is linked to a phosphate that is attached
to the 5′carbon of the next unit, and so on. These polymer chains often contain many
millions of monomer units. Since long polymers have physical properties distinctly different
from those of small molecules, they are called macromolecules. The sugar-phosphate-sugar
chain is called the backbone of the polymer. One end of the backbone has a free
5′phosphate, and the other end has a free 3′OH group. The backbone structure is
independent of which particular bases are attached to the individual sugars.

Genetic material in earthly life often contains poly 5′-3′, 2′-deoxyribose nucleotides, in
structures called chromosomes, where each monomer is one of the nucleotides deoxy-
adenine, thymine, guanine or cytosine. This material is commonly called deoxyribonucleic
acid, or simply DNA for short. DNA in chromosomes forms very long helical structures
containing two molecules with the backbones running in opposite directions on the outside
of the helix and held together by hydrogen bonds between complementary nucleotide bases
lying between the helical backbones. The lack of the 2′ hydroxyl group in DNA appears to
allow the backbone the flexibility to assume the full conformation of the long double-helix,
which involves not only the basic helix, but additional coiling necessary to fit these very
long molecules into the very small volume of a cell nucleus.

37
In contrast, very similar molecules, containing ribose instead of deoxyribose, and known
generically as RNA, are known to form only relatively short double-helical complementary
base paired structures. These are well known, for instance, in ribosomal RNA molecules
and in transfer RNA (tRNA), where so-called hairpin structures from palindromic
sequences within one molecule.

B. Disaccharide
a. Sucrose
Systematic name: D-glucopyranosyl-(1↔2)-β-D-fructofuranoside
Molecular formula: C12H22O11

Sucrose (Fig. 5) (common name: table sugar, also called saccharose) is a disaccharide
(glucose + fructose) best known for its role in human nutrition and is formed by plants but
not by other organisms such as animals. Sucrose is an easily assimilated macronutrient that
provides a quick source of energy to the body, provoking a rapid rise in blood glucose upon
ingestion. However, pure sucrose is not normally part of a human diet balanced for good
nutrition, although it may be included sparingly to make certain foods more palatable.

Sucrose, as a pure carbohydrate, has an energy content of 3.94 kilocalories per gram (or 17
kilojoules per gram). When a large amount of foods that contain a high percentage of
sucrose is consumed, beneficial nutrients can be displaced from the diet, which can
contribute to an increased risk for chronic disease such as defect in glucose metabolism or
diabetes mettlitus

b. Cellobiose
Systemic name: 4-O- β-D-glucopyranosyl-D-glucose
Molecular formula C12H22O11

Cellobiose is a disaccharide derived from the condensation of two glucose molecules linked
in a β(1→4) bond. It can be hydrolyzed by bacteria or cationic ion exchange resins to give
glucose. Cellobiose has eight free alcohol (COH) groups and three ether linkages, which
give rise to strong inter- and intra-molecular hydrogen bonds.

c. Trehalose
Systemic name: α-D-glucopyranosyl- α-D-glucopyranoside
Molecular formula: C12H22O11

Trehalose, also known as mycose, is a natural alpha-linked disaccharide formed by an α, α-

1, 1-glucoside bond between two α-glucose units (Fig. 5). It can be synthesised by fungi,
plants, and invertebrate animals. It is implicated in anhydrobiosis — the ability of plants
and animals to withstand prolonged periods of desiccation. It has high water retention
capabilities and is used in food and cosmetics. The sugar forms a gel phase as cells
dehydrate, which prevents disruption of internal cell organelles by effectively splinting
them in position. Rehydration then allows normal cellular activity to be resumed without the
major, lethal damage that would normally follow a dehydration/reyhdration cycle.
Trehalose has the added advantage of being an antioxidant. Trehalose can be found in
nature, animals, plants, and microorganisms. In animals, trehalose is prevalent in shrimp,
and also in insects, including grasshoppers, locusts, butterflies, and bees, in which blood-
sugar is trehalose. The trehalose is then broken down into glucose by the catabolic enzyme

38
trehalase for use. In plants, the presence of trehalose is seen in sunflower seeds, selaginella
mosses, and sea algae. Within the fungus family, it is prevalent in mushrooms shiitake
(Lentinula edodes), maitake (Grifola fondosa), nameko (Pholiota nameko), and Judas's ear
(Auricularia auricula-judae) contain 1% to 17% percent of trehalose in dry weight form.
Trehalose is found in such microorganisms as baker's yeast and wine yeast. When
tardigrades (water bears) dry out, the glucose in their bodies changes to trehalose when they
enter a state called cryptobiosis - a state wherein they appear dead. However, when they
receive water, they revive and return to their metabolic state. Larva of sleeping chironomid
(polypedihum vanderplanki) and artemia (sea monkeys, brine shrimp) can withstand
dehydration, because they store trehalose within their cells. In the plant kingdom,
selaginella mosses that grow in desert and mountainous areas, although they may be
cracked and dried out, will turn green again and revive after a rain, because of the function
of Trehalose. Dried shitake mushrooms spring back into shape in water because they
contain trehalose.

Trehalose is metabolized by a number of bacteria, including Streptococcus mutans, the

common oral bacteria responsible for dental plaque. The enzyme trehalase, a glycoside
hydrolase, breaks trehalose into two glucose molecules, which can then be readily absorbed
in the gut. Trehalose is the major carbohydrate energy storage molecule used by insects for
flight to be used as glucose for the rapid energy requirement of flight.

d. Lactose
Systemic name: 4-O- β-D-galactopyranosyl-D-glucose
Molecular formula: C12H22O11

Lactose (also referred to as milk sugar) is a sugar, which is found most notably in milk (Fig.
5). Lactose makes up around 2–8% of milk (by weight). The name comes from the Latin
word for milk, plus the -ose ending used to name sugars. Lactose is the only significant
sugar or carbohydrate of animal origin. Lactose is a disaccharide that consists of β-D-
galactose and β-D-glucose fragments bonded through a β(1→4) glycosidic linkage.

An enzyme, lactase, is essential for digestion of lactose, and a majority of adults in this
country do not have lactase, which digests milk sugar, or lactose. Thus, it is very difficult
for them to digest milk and may contribute to gaseousness, cramping, and diarrhea.

e. Maltose
Systemic name: 4-O-α -D-glucopyranosyl-D-glucose
Molecular formula: C12H22O11

Maltose, or malt sugar, is a disaccharide formed from two units of glucose joined with an
α(1→4) linkage. It is the second member of an important biochemical series of glucose
chains. The addition of another glucose unit yields maltotriose; further additions will
produce dextrins (also called maltodextrins) and eventually starch.

Maltose can be broken down into two glucose molecules by hydrolysis. In living organisms,
the enzyme maltase can achieve this very rapidly. In the laboratory, heating with a strong
acid for several minutes will produce the same result. The production of maltose from
germinating cereals, such as barley, is an important part of the brewing process. When
barley is malted, it is brought into a condition in which the concentration of maltose-
producing amylases has been maximized. Mashing is the process by which these amylases

39
convert the cereal's starches into maltose. Metabolism of maltose by yeast during
fermentation then leads to the production of ethanol and carbon dioxide.

C. Trisaccharides
a. Raffinose
Systemic name: β-D-Fructofuranosyl-O-α-D-galactopyrnosyl-(1→6)- α-D-
glucopyranoside
Molecular formula: C18H32O11

Raffinose is a trisaccharide composed of galactose, fructose, and glucose (Figure 20). It can
be found in beans, cabbage, brussels sprouts, broccoli, asparagus, other vegetables, and
whole grains. Raffinose can be hydrolyzed to D-galactose and sucrose by the enzyme α-
galactosidase (α-GAL), an enzyme not found in humans. α-GAL also hydrolyzes other α-
galactosides such as stachyose, verbascose, and galactinol, if present. The enzyme does not
cleave β-linked galactose, as in lactose. The raffinose families of oligosaccharides (RFOs)
are alpha-galactosyl derivatives of sucrose, and the most common are the trisaccharide
raffinose, the tetrasaccharide stachyose, and the pentasaccharide verbascose. RFOs are
almost ubiquitous in the plant kingdom, being found in a large variety of seeds from many
different families, and they rank second only to sucrose in abundance as soluble
carbohydrates. Raffinose is also used as a base substance for sucralose.

Fig. 20: Raffinose

Humans and other monogastric animals (pigs and poultry) do not possess the α-GAL
enzyme to break down RFOs and these oligosaccharides pass undigested through the
stomach and upper intestine. In the lower intestine, they are fermented by gas-producing
bacteria which do posses the α-GAL enzyme and make carbon dioxide, methane, and/or
hydrogen -- leading to the flatulence commonly associated with eating beans and other
vegetables. α-GAL is present in digestive aids such as the product Beano.

b. Acarbose
Systemic name: O-4,6-Dideoxy-4[[[1S-(1α,4α,5β,6α)]-4,5,6-trihydroxy-3-
(hydroxymethyl)-2-cyclohexen-1yl] amino]-α-D-glucopyranosyl-(1→4)-O- α-D-
glucopyranosyl-(1→4)-D-glucose
Molecular formula: C25H43NO18

Acarbose is an anti-diabetic drug used to treat type 2 diabetes mellitus and, in some
countries, prediabetes. (Fig. 21) It is an inhibitor of alpha glucosidase, an enteric enzyme
that releases glucose from larger carbohydrates.

40
  

Fig. 21: Acarbose

c. Melezitose
Systemic name: O- α -D-glucopyranosyl-(1→3)- β-D- fructofuranosyl- α-D-
glucopyranoside
Molecular formula: C18H32O16

Melezitose, also spelled melicitose, is a nonreducing trisaccharide sugar (Fig. 22)  that is
produced from lice such as Cinara pilicornis by an enzyme reaction. This is beneficial to
the insects, as it reduces the stress of osmosis by reducing their own water potential. The
melezitose is part of the honeydew of the honey produced by bees, and acts as an attractant
for ants. This is useful to the lice as they have a symbiotic relationship with ants. Melezitose
can be partially hydrolyzed to glucose and turanose, the latter of which is an isomer of
sucrose.

Since acarbose prevents the degradation of complex carbohydrates into glucose, the
carbohydrates will remain in the intestine. In the colon, bacteria will digest the complex
carbohydrates, thereby causing gastrointestinal side effects such as flatulence (78% of
patients) and diarrhea (14% of patients).

 
Fig. 22: Melezitose

D. Polysaccharides
Carbohydrate composed of ten or more monosaccharide units joined together by glycosidic
linkages are classified as polysaccharides. Most of the carbohydrates found in nature occur
as polysaccharides, polymers of high molecular weight; which on hydrolysis yield
monosaccharides or products related to monosaccharides, most frequently D-glucose.
Others monosaccharides obtained are D-mannose. D- and L-galactose, L-arabinose, D-
glucuronic acid, D- and L-galactose, L-arabinose. D-glucuronic acid, D-glucosamine, etc.
Polysaccharides, also called glycans, differ from each other in the identity of their recurring

41
monosaccharide units, in the length of their chains, in the types of bonds linking the units,
and in the degree of branching. Polysaccharides can be classified-as homopolysaccharidcs
and heleropolysciccharide (Fig. 23) depending on the variety of sugar moieties joined to the
sugar chain. Some are linear polymers and others are branched. Some typical
polysaccharides are starches, glycogens celluloses, agar, gum chitin, etc.

Fig. 23: Polysaccharide

Some homopolysaccharides serve as storage forms of monosaccharides used as fuels; starch

and glycogen are homopolysaccharides of this type. Other homopolysaccharides (cellulose
and chitin) serve as structural elements in plant cell walls and animal exoskeletons.
Heteropolysaccharides provide extracellular support for organisms of all kingdoms. The
rigid layer of the bacterial cell envelope (the peptidoglycan) is a heteropolysaccharide built
from two alternating monosaccharide units. In animal tissues, several
heteropolysaccharides, occupy the extracellular space forming a matrix that holds individual
cells together and provides protection, shape, and support to cells, tissues, or organs.
Hyaluronic acid accounts for the toughness and flexibility of cartilage and tendon, is among
this group of extracellular polysaccharides. Other heteropolysaccharides, sometimes in very
large aggregates with proteins (proteoglycans), account for the high viscosity and
lubricating properties of some extracellular secretions.

Unlike proteins, polysaccharides generally do not have definite molecular weights, due to
consequence of the mechanisms of assembly of the two types of polymers. Proteins are
synthesized on a template (messenger RNA) of defined sequence and length, by enzymes
that copy the template exactly. For polysaccharide synthesis, with no template; the program
for polysaccharide synthesis is intrinsic to the enzymes that catalyze the polymerization of
monomeric units. For each type of monosaccharide to be added to the growing polymer
there is a separate enzyme, which acts only when the enzyme that inserts the preceding
subunit has acted. The alternating action of several enzymes produces a polymer with a
precise repeating sequence, but the exact length varies from molecule to molecule, within a
general size class.

42
1. Homopolysaccharides
A homopolysaccharide is made up of a single kind of mono-saccharide. Starches,
glycogens, and celluloses, which are made up of only glucose residues, are example of
homopolysaccharides.

i) Starch
The starches occur widespread as reserve carbohydrate in tubers such as potatoes, in many
fruits, grains and seeds. In the grains, the starch is arranged in concentric layers. When
starch grains are treated with boiling water, the substance in the center passes into solution,
but the greater part of the grain is not soluble. This insoluble portion swells as it absorbs
water and the whole mass becomes starch paste. Both the soluble portion and the insoluble
portion are heterogeneous mixtures. The soluble fraction is referred to as amylose, and the
insoluble fraction as amylopectin. Most starches contain 80-90 per cent amylopectin and
10—20 per cent amylose. Amylose and amylopectin can be separated by taking advantage
of the difference in solubility in water. Both amylose and amylopectin are polymers of
glucose and upon hydrolysis with acid they give D-glucose as the product.

Structure of amylose: Amylose is an unbranched long chain polymer in which the glucose
residues are linked through α-1, 4- glycosidic linkages. The amylose structure may be
ragarded as a repeated maltose structure with a free sugar group (acetal group) at one end.
This is also known as the reducing end (nth residue), whereas, the opposite end (first
residue) is referred to as the non-reducing end. Any particular preparation of amylose
usually consists of a mixture of populations of molecules, which differ widely in chain
length (number of glucose residues per chain) (Fig. 24).

Fig. 24: Amylose

Structure of amylopectin: Amylopectin is also made of chains of glucose residues, but the
chains are highly branched. The glucose residue situated at the branching point is
substituted not only on carbon 4 but also on carbon 6 (Fig. 25). Both amylose and
amylopectin give characteristic colour reactions with iodine. Amylose produces a blue-
black colour, whereas, amylopectin gives a purple colour.

Saccharification of starch by amylases: Amylases are enzymes of plant and animal origin
and they hydrolyse starch. There are two kinds of amylases, alpha-amylases and beta-
amylases. Alpha-amylases are endo enzymes, act on amylose and amylopectin in a random
fashion. Initially more central linkages are cleaved and smaller polysaccharide chains are
formed. As the reaction proceeds, these are further hydrolysed to maltose and glucose.

α-amylases hydrolyse amylose and amylopectin in an orderly fashion. It acts from one end
of the polymer and cleaves off two glucose residues at a time, as a maltose unit. As the
reaction proceeds, amylose is completely hydrolysed to maltose. However, with the

43
amylopectin, the reaction stops as a branch point is approached. The terminal parts of the
branches are digested away as maltose units in an orderly fashion and the central core is left
behind as the enzyme is blocked at 1-6 glycosidic linkages or branch points. The
polysaccharide fragment that remains after such incomplete hydrolysis is called a dextrin.

Fig. 25: Amylopectin

Dextrins formed from amylopectin by β-amylase are highly branched and give a red colour
with iodine. Dextrins of relatively small molecular size do not give a colour with iodine.
The colour produced by reaction with iodine is used as an indication of the degree of
branching of starch. Starch is readily hydrolysed by dilute mineral acid with ultimate
formation of glucose in quantitative yield. The course of hydrolysis may be followed by the
gradual change in colour produced by iodine: blue-black-purple-red-colourless.

ii) Celluloses
Cellulose is the most abundant organic compound in nature and it is the chief constituent of
the fibrous parts of plants. The purest form of cellulose is usually obtained from cotton.
Cellulose is a polymer made up of glucose residues. Upon hydrolysis, cellulose yields D-
glucose as the product. Cellulose molecules are not branched and consist essentially of long
chains with glucose residues linked in repeating sequence of cellobiose structures. The
glucose residues are linked together through β-l, 4-glycosidic linkages. The celluloses
obtained from different sources differ in molecular size though they are all made up of
glucose. Cellulose is found in plants as microfibrils (2-20 nm diameter and 100 - 40 000 nm
long). These form the structurally strong framework in the cell walls.

Structural unit: Cellulose is a linear polymer of β-(1 4)-D-glucopyranose units in 4C1

conformation (Fig. 26). The fully equatorial conformation of β-linked glucopyranose
residues stabilizes the chair structure, minimizing its flexibility (for example, relative to the
slightly more flexible α-linked glucopyranose residues in amylose). Cellulose preparations
may contain trace amounts (~0.3%) of arabinoxylans

Molecular structure: Cellulose is an insoluble molecule consisting of between 2000 -

14000 residues with some preparations being somewhat shorter. It forms crystals (cellulose
Iα) where intra-molecular (O3-H O5' and O6 H-O2') and intra-strand (O6-H O3')
hydrogen bonds holds the network flat allowing the more hydrophobic ribbon faces to stack.
Each residue is oriented 180° to the next. Although individual strand of cellulose are
intrinsically no less hydrophilic, or no more hydrophobic, than some other soluble
polysaccharides (such as amylose) this tendency to form crystals utilizing extensive intra-

44
and intermolecular hydrogen bonding makes it completely insoluble in normal aqueous
solutions. It is thought that water molecules catalyze the formation of the natural cellulose
crystals by helping to align the chains through hydrogen-bonded bridging. Part of a
cellulose preparation is amorphous between these crystalline sections. The overall structure
is of aggregated particles with extensive pores capable of holding relatively large amounts
of water by capillarity. The natural crystal is made up from metastable Cellulose I with all
the cellulose strands parallel and no inter-sheet hydrogen bonding. This cellulose I (natural
cellulose) contains two coexisting phases cellulose Iα (triclinic) and cellulose Iβ
(monoclinic) in varying proportions dependent on its origin (Fig. 27).

Fig. 26: Cellulose

Function – Cellulose is the structural component of the primary cell wall of green plants,
many forms of algae and the oomycetes. Some species of bacteria secrete it to form
biofilms.

Fig. 27: Organization of glucose chains in cellulose

45
iii) Glycogen
Glycogen is the reserve carbohydrate in the animals and it is found in significant amounts in
the liver and muscle. Glycogen is made up of D-glucose residues. Upon hydrolysis, it yields
D-glucose as the product. Glycogen is a highly branched chain polysaccharide and it
resembles amylopectin in structure. Thus glucose residues are linked together through α-l,4-
glycosidic linkages except at the branch points. The branch is linked to the main chain
through α-l,6-glycosidic linkages. It is very similar to the structure of amylopectin. The
average molecular weights of glycogen preparations vary from 270,000 to 100,000,000. A
single preparation usually consists of a mixture of populations of molecules that differ in
molecular weight (Fig. 28). In the structure of glycogen, O represents glucose residues. The
arrows indicate the α-1→6 glycosidic linkage. All the other glycosidic linkage are α-1,4 .
The asterisks indicate the non—reducing end groups and r.e. strands for reducing end
group.

Fig. 28: Glycogen

In a wide range of organisms, excess glucose is stored not as monomer but converted to
polymeric forms for storage—glycogen in vertebrates and many microorganisms, starch in
plants. With two minor differences, glycogen has almost the same structure as amylopectin
(a constituent of starch). The glycogen molecule is roughly twice as large as amylopectin,
and branching frequency—that also controls the mobilization of stored polysaccharide.
Glycogen has roughly twice as many branches (branching occurs on an average after every
8-12 residues unlike amylopectin where it is after every 24-30 residues). There is an
advantage to branched polysaccharides such as amylopectin and glycogen. During times of
shortage, enzymes attack one end of the polymer chain and cut off glucose molecules, one
at a time. More the branches, more the points at which the enzyme attacks the
polysaccharide. Thus, a highly branched polysaccharide is better suited for the rapid release
of glucose than a linear polymer.

In vertebrates, glycogen is found primarily in the liver and skeletal muscle but can also be
made by the brain, uterus, and the vagina. However, muscle glycogen is not generally
available to other tissues, because muscle lacks the enzyme glucose-6-phosphatase.
Glycogen may represent up to 10% of the weight of liver and 1% to 2% of the weight of
muscle. Stores of glycogen in the liver are considered the main buffer of blood glucose
levels. If this much glucose was dissolved in the cytosol of a hepatocyte, its concentration
would be about 0.4 M, enough to dominate the osmotic properties of the cell. When stored
as a long polymer (glycogen), however, the same mass of glucose has a concentration of
only 0.01 µM. Glycogen is stored in large cytosolic granules. The elementary particle of
glycogen, the β particle, about 21 nm in diameter, consists of up to 55,000 glucose residues
with about 2,000 nonreducing ends. The major site of daily glucose consumption (75%) is
the brain via aerobic pathways. Most of the remainder of it is utilized by erythrocytes,
skeletal muscle, and heart muscle. Due to disbalance in glucose utilization iabetics may
experience

46
Glycogen degradation and synthesis are relatively simple biochemical processes. Glycogen
synthesis differs from glycogen breakdown. Unlike breakdown, synthesis is endergonic,
meaning that glycogen is not synthesized without the input of energy. Energy for glycogen
synthesis comes from UTP, which reacts with glucose-1-phosphate, forming UDP-glucose,
in reaction catalysed by UDP-glucose pyrophosphorylase. Glycogen is synthesized from
monomers of UDP-glucose by the enzyme Glycogen synthase, which progressively
lengthens the glycogen chain. As glycogen synthase can only lengthen an existing chain, the
protein glycogenin is needed to initiate the synthesis of glycogen.

Glycogen degradation consists of three steps: (1) the release of glucose 1-phosphate from
glycogen, (2) the remodeling of the glycogen substrate to permit further degradation, and
(3) the conversion of glucose 1-phosphate into glucose 6-phosphate for further metabolism.
It is cleaved from the nonreducing ends of the chain by the enzyme glycogen phosphorylase
to produce monomers of glucose-1-phosphate that is then converted to glucose 6-phosphate.
A special debranching enzyme is needed to remove the α (1-6) branches in branched
glycogen and reshape the chain into linear polymer. Debranching enzyme has two
independent active sites, consisting of residues in different segments of a single polypeptide
chain, that catalyze α(1-6) glucosidase and transferase (transglycosylase) reactions.

The transferase of the debranching enzyme transfers three glucose residues from a 4-residue
limit branch to the end of another branch, diminishing the limit branch to a single glucose
residue. The α(1-6) glucosidase moiety of the debranching enzyme then catalyzes
hydrolysis of the α(1-6) linkage, yielding free glucose. This is a minor fraction of glucose
released from glycogen. The major product of glycogen breakdown is glucose-1-phosphate,
arising from phosphorylase activity, which is subsequently converted, to glucose-6-
phosphate. The G6P monomers produced have three possible fates:
• G6P can continue on the glycolysis pathway and be used as fuel.
• G6P can enter the pentose phosphate pathway via the enzyme glucose-6-phosphate
dehydrogenase to produce NADPH and 5-carbon sugars.
• In the liver and kidney, G6P can be dephosphorylated back to glucose by the
enzyme glucose 6-phosphatase. This is the final step in the gluconeogenesis
pathway.

v) Chitin
Chitin is a linear homopolysacchande composed of N-acetyl- D-glucosamine residues in β-
linkage. The only chemical difference from cellulose is the replacement of a hydroxyl group
a: C-2 with an acetylated amino group. Chitin forms extended fibers similar to those of
cellulose, and structure of glycogen. Chitin like cellulose is indigestible by vertebrate
animals. It is the main component of the cell walls of fungi, the exoskeletons of arthropods,
such as crustaceans (like the crab, lobster and shrimp) and the insects, including ants,
beetles and butterflies, the radula of mollusks and the beaks of the cephalopods, including
squid and octopuses. Chitin is probably the second most abundant polysaccharide next to
cellulose, in nature (Fig. 29).

Chitin is used in water purification, and as an additive to thicken and stabilize foods and
pharmaceuticals. It also acts as a binder in dyes, fabrics, and adhesives. Industrial separation
membranes and ion-exchange resins can be made from chitin. Processes to size and
strengthen paper employ chitin. Its properties as a flexible and strong material make it
favorable as surgical thread. Its biodegradability means it wears away with time as the
wound heals. Moreover, the polysaccharide has some unusual properties that accelerate

47
healing of wounds in humans. Most recent studies point out that chitin is a good inductor
for defense mechanisms in plants. It is being tested as a fertilizer that can help plants
develop healthy immune responses, and have a much better yield and life expectancy.

Fig. 29: Chitin

2: Heteropolysaccharides
A heteropolysaccharide is made up of two or more different monosaccharides, or
monosaccharide derivatives.

i) Agar
Agar (agar-agar, kanten, agal-agal, ceylon agar, china grass) is a gelatinous substance
chiefly used as a solid substrate to culture medium for microbiological work. It is an
unbranched polysaccharide obtained from the cell membranes of some species of red algae
or seaweed. Chemically, agar is a polymer made up of subunits of the sugar galactose. Agar
polysaccharides serve as the primary structural support for the algae's cell walls. Agar is a
heterogeneous mixture of two classes of polysaccharide: agaropectin and agarose. Although
both polysaccharide classes share the same galactose-based backbone, agaropectin is
heavily modified with acidic side-groups, such as sulfate and pyruvate (Fig. 30). Agarose is
composed of agarobiose repeating disaccharide units alternating with 1, 3-linked-β-D-
galactopyranose and 1, 4-linked-3, 6-anhydro-α-L-galactopyranose. The agaropectin seems
to have the same backbone as the agarose, but contains considerable amount of acid groups
such as sulfate, pyruvate and glucuronate groups.

Fig. 30: Agar

Property Agar is insoluble in cold water but dissolves to give random coils in boiling
water. Gelation is reported to follow a phase separation process (although these findings
are disputed) and association on cooling (~35°C), forming gels with up to 99.5% water and
remaining solid up to about 85°C. It is derived primarily from Gracilaria species.

48
Uses: Agar has a major use in microbiological media as it is not easy for microorganisms to
metabolize and forms clear, stable and firm gels, but in the food area it is used in icings,
glazes, processed cheese, jelly sweets and marshmallows. It may be used in tropical
countries and by vegetarians as a substitute for gelatin.
Agar is used to form a surface for the growth of bacterial colonies. Another commercial use
of agar is for the capsules in which some vitamins and drugs are packaged; the dried agar
material dissolves readily in the stomach and is metabolically inert.

ii) Agarose: Certain marine red algae, including some of the seaweeds, have cell walls that
contain agar, a mixture of sulfated heteropolysaccharides made up of D-galactose and an L-
galactose derivative ether-linked between C-3 and C-6. The two major components of agar
(Fig. 31) are the unbranched polymer agarose (Mr ~120,000) (Figure 34) and a branched
component, agaropectin. The remarkable gel-forming property of agarose makes it useful in
the biochemistry. When a suspension of agarose in water is heated and cooled, the agarose
forms a double helix; two molecules in parallel orientation twist together with a helix repeat
of three residues; water molecules are trapped in the central cavity. These structures in turn
associate with each other to form a gel, a three-dimensional matrix that traps large amounts
of water. Exterior hydroxyl groups allow aggregation of up to 10,000 of these helices to
form suprafibers. Agarose gels are used as inert supports for the electrophoretic separation
of nucleic acids, an essential part of the DNA sequencing process.

Fig. 31: Agarose

iii) Xylan
Lignocelluloses in plant kingdom are composed of cellulose, hemicellulose and lignin. 15-
30% of the lignocellulose is hemicellulose, where xylan is the main component. They are
almost as ubiquitous as cellulose in plant-cell walls and contain predominantly beta-D-
xylose units linked as in cellulose. Xylan is a heteropolysaccharide found in plant cell walls
and some algae (Fig. 32). It is found in almost all parts of the plant, in the cell walls of some
green algae, especially macrophytic siphonous genera, where it replaces cellulose.
Similarly, it replaces the inner fibrillar cell-wall layer of cellulose in some red algae. Xylans
are polysaccarides mainly having backbone of 1,4 beta-linked xylose. The backbone is
branched with sugars like glucose, arabinose, acetylated sugars and esters through alpha
linkage. Xylans are of little commercial importance, but being associated with cellulose,
forms a part of sugar hydrolysis project to be converted to alcohol and other value added
products. In tune with the emergent need for production of ethanol from sugars xylan as
hemicellulose forms the main component, which supports complete utilization of cellulose
through enzymatic saccharification.

49
 Fig. 32: Xylan

iv) Alginate
Alginates are produced by brown seaweeds (Phaeophyceae, mainly Laminaria). Alginates
are linear unbranched polymers containing β-(1-4)-linked D-mannuronic acid (M) and α-(1-
4)-linked L-guluronic acid (G) residues (Fig. 33). Although these residues are epimers (D-
mannuronic acid residues being enzymatically converted to L-guluronic acid after
polymerizationa) and only differ at C5, they possess very different conformations; D-
mannuronic acid being 4C1 with diequatorial links between them and L-guluronic acid
being 1C4 with diaxial links between them. Bacterial alginates are additionally O-acetylated
on the 2 and/or 3 positions of the D-mannuronic acid residues. The bacterial O-acetylase
may be used to O-acetylate the algal alginates, so increasing their water binding.

Fig. 33: Alginate

Molecular structure: Alginates are not random copolymers but, according to the source
algae, consist of blocks of similar and strictly alternating residues (that is, MMMMMM,
GGGGGG and GMGMGMGM), each of which have different conformational preferences
and behavior (Fig. 33). As examples, the M/G ratio of alginate from Macrocystis pyrifera is
about 1.6 whereas that from Laminaria hyperborea is about 0.45.

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Functionality: The primary functions of the alginates are as thermally stable cold setting
gelling agents in the presence of calcium ions; gelling at far lower concentrations than
gelatin. Such gels can be heat treated without melting, although they may eventually
degrade.

Alginate's solubility and water-holding capacity depend on pH (precipitating below about

pH 3.5), molecular weight (lower molecular weight calcium alginate chains with less than
500 residues showing increasing water binding with increasing size), ionic strength (low
ionic strength increasing the extended nature of the chains) and the nature of the ions
present. Generally alginates show high water absorption and may be used as low viscosity
emulsifiers and shear-thinning thickeners. They can be used to stabilize phase separation in
low fat fat-substitutes.

Sugar derivatives (Structure, occurrence & functions)

Various sugar derivatives, which are essential participants in various reactions, are known
and well characterized. Some of them participate in the transformations of simple sugars to
other simple sugars or sugar derivatives. Here properties of some of the important
derivatives of the sugars will be presented.

1. Derivatives of Monosaccharide
Monosaccharide undergoes a number of reactions to form biologically important
derivatives. Three common types of monosaccharide derivatives are amino sugars,
carboxylic acid sugars and sugar alcohols.

A. Amino sugars and N-acetylated sugars

An amino sugar contains an amine group in place of a hydroxyl group. Derivatives of amine
containing sugars, such as N-acetylglucosamine and sialic acid, while not formally
containing an amine, are also considered amino sugars. N-acetylated sugars are derivatives
of amino sugars. The N in "N-acetyl" refers to the fact that the acetyl group is bonded to the
nitrogen. The acetyl group here replaces one of the amine hydrogens. Connective tissue
polysaccharides, such as cartilage, contain amino sugar and N-acetyl sugar monomers (Figs
34 and 35).

Significant amounts of glucosamine have been found in the intestinal mucin, which binds
chloresterol, thereby limiting its absorption. Glucosamine has proven to decrease insulin
secretion without suppressing liver glucose production.

i) Glucosamine
Systematic name: 2-Amino-2-deoxy-D-glucose
Molecular Formula: C6H13NO5
Glucosamine is an amino sugar derived from glucose, produced in the body from the sugar
glucose and the amino acid glutamine through the action of the enzyme glucosamine
synthetase (Fig. 34).

It’s used as a precursor in the biochemical synthesis of glycosylated proteins and lipids.
Glucosamine stimulates the synthesis of proteoglycans, glycosaminoglycans (more
commonly referred to as mucopolysaccharides), and collagen. It therefore plays a role in the
formation of cartilage and the cushioning synovial fluid between the joints; hence it’s

51
classified as "chondroprotective" agent. Supplementary glucosamine can be an important
source of this vital amino sugar for those with reduced capacity to produce glucosamine,
such as the elderly.

Fig. 34: Glucosamine

Glucosamine acts as an immune modulator with antitumor and antiviral properties, as well
as it has some activity against HIV. Oral glucosamine is commonly used for the treatment
of osteoarthritis. Since glucosamine is a precursor for glycosaminoglycans, and
glycosaminoglycans are a major component of joint cartilage, supplemental glucosamine
may help to rebuild cartilage and treat arthritis. Deficiencies or malfunctions in the ability to
metabolize this sugar have been linked to diseases of the bowel and bladder. Glucosamine
has been shown to help repair the mucosal-lining defensive barrier called the
glycosaminoglycan layer (GAG). Defects in the GAG layer have been implimented in
Crohn’s disease, ulcerative colitis, and interstitial cystitis.

One of the most striking effects of glucosamine is its ability to reduce the progression of
experimental cancers. Reductions in blood levels of Glucosamine have been found in those
with colon cancer. Distribution of the sugar is also altered when other cancerous tissues are
present. It has been found that, with some of the other essential sugars, glucosamine is also
vital to learning.

Retinal tissue from human eye donors showed that glucosamine preferred the photoreceptor
layer of the retina, suggesting that this sugar is needed in transplantation.

ii) N-Acetylglucosamine (N-Acetyl-D-Glucosamine, or GlcNAc, or NAG)

Systematic name: 2-(Acetylamino)-2-deoxy-D-glucose
Molecular formula: C8H15NO6
It is a monosaccharide derivative of glucose. Chemically it is an amide between
glucosamine and acetic acid; and is significant in several biological systems (Fig. 35).

Fig. 35: N-Acetylglucasamine

N-acetylglucosamine is part of a biopolymer in the bacterial cell wall, built from alternating
units of GlcNAc and N-acetylmuramic acid (MurNAc), cross-linked with oligopeptides at
the lactic acid residue of MurNAc. This layered structure is called peptidoglycan. GlcNAc
is the monomeric unit of the polymer chitin, which forms the outer coverings of insects and

52
crustaceans. GlcNAc is also of note in neurotransmission, where it is thought to be an
atypical neurotransmitter functioning in nocioceptive (pain) pathways.

N-acetylglucosamine (GlcNAc) carries out important roles in a broad range of cells from
bacteria to humans. One aspect of GlcNAc function is to mediate cellular signaling. In
bacteria, GlcNAc induces components that are important for colonization of human hosts,
including fimbrins that mediate adhesion to host cells, multidrug exporter genes and Curli
fibers that promote biofilm formation. In mammals, GlcNAc is a key sensor of nutrient
status that is involved in insulin signaling, cell cycle control, and other essential processes.
Nutritional effects that lead to increased GlcNAc levels result in its conversion to UDP-
GlcNAc and subsequent attachment to proteins on serine or threonine residues in a dynamic
manner that is analogous to modification of proteins by phosphorylation. In fact, the
interplay between O-GlcNAc modification and phosphorylation of proteins regulates many
critical transcription factors, such as c-myc and p53. O-GlcNAc modification also regulates
other processes including proteosome function. In addition to these regulatory roles,
GlcNAc contributes to the N-linked glycosylation, glycophosphatidylinositol (GPI) anchor
addition to proteins and is polymerized into chitin, which forms part of the fungal cell wall
and the exoskeletons of parasites, insects, and other organisms.

N-acetyl-D-glucosamine had been shown to possess an enhancing effect on the production

of IgG and IgM in mice. It also plays an important role in nutrient sensing and cellular
regulation in a wide range of organisms from bacteria to humans. N-acetylglucosamine
receptors are found in the thyroid gland, which indicates that it plays a role in the transport
of thyroglobulin (an iodine-containing glycoprotein). Concentrated amounts of N-
acetylglucosamine are found in the testes, liver, small intestines, epithelial cells of the
endocrine and sebaceous glands, and endothelial cells of blood vessels.

N-AcetylGlucosamine (or glucosamine its metabolic derivative) helps in immune system

functioning particular in regards to HIV and tumors. In addition, GlcNAc decreases pain
and inflammation and increases range of motion in osteoarthritis patients and helps repair
cartilage. GlcNAc has also been implicated as an aid to learning during certain mice studies.
The saccharide or its derivative is found in the brains of mammal implying a relation to
nerve functioning for learning.

In regards to disease processes, N-acetylglucosamine has been linked to Crohn's disease,

interstitial cystitis and ulcerative colitis. Deficiencies of GlcNAc have been linked to
diseases of the bowels and bladder. Those with colon cancer show particular deficiencies.

N-acetylglucosamine has been shown to repair the mucosal-lining defensive barrier called
the glycosaminoglycan layer (GAG). According to animal studies, N-acetylglucosamine
helped prevent the flu virus and herpes virus from occurring. N-acetylglucosamine also has
a hand in limiting chloresterol absorption and decreasing insulin secretion. It has been
proposed as a treatment for autoimmune diseases.

iii) Galactosamine
Systematic name: 2-Amino-2-deoxy-D-galactose
Molecular formula: C6H13NO5
Galactosamine is a hexosamine derived from galactose (Fig. 36).

53
 Fig. 36: Galactosamine

This amino sugar is a constituent of some glycoprotein hormones such as follicle-

stimulating hormone (FSH) and luteinizing hormone (LH).

iv) N-Acetylgalactosamine (GalNAc, 2-Acetamido-2-deoxy-D-galactopyranose or N-

Acetyl-D-galactosamine)
Systematic name: 2-(Acetylamino)-2-deoxy-D-galactose
Molecular formula: C8H15NO6
It is a monoacetylaminosaccharide derivative of galactose. Chemically it is an amide
between galactosamine and acetic acid (Fig. 37).

Fig. 37: N-Acetylgalactosamine

In humans it is the terminal carbohydrate forming the antigen of blood group A.

N-Acetylgalactosamine is necessary for intercellular communication, and is concentrated in

sensory nerve structures of both humans and animals. This saccharide may inhibit the
growth of some tumors.

Lower than normal levels of this sugar have been found in patients with heart disease
implying that these conditions may be reversed if a supplementation of N-
acetylgalactosamine were to be added to the diet. It appears that this sugar plays a role in
joint function, scavenging harmful radicals like superoxide generated during the course of
action of macrophage in inflammatory response

N-acetylgalactosamine also seems to play an important role in the immune system.

Contained in macrophages and neutrophils, it may play a significant role in the etiolology of
joint inflammation and could be important in such conditions as rheumatoid arthritis. N-
acetylgalactosamine is localized in the golgi apparatus and ER – found in cell organelles
and associated with synthesis of various proteins and enzymes.

It is also found on the surface of cortical neurons and involved in synaptic function of the
central nervous system and peripheral brain, suggesting its importance in nerve function. N-
acetylgalactosamine is also concentrated in other sensory nerve structures especially in the
retina, photoreceptors, optic nerve, and the epithelial pigment of the eyes of both humans
and animals. This suggests that it may be extremely important for optimal vision. N-

54
acetylgalactosamine is distributed to several other tissues, suggesting that it is important in
the functional role of these tissues. Some of these tissues include the ducts of the kidney, the
testes, the skin, and a variety of other structures including sweat glands, some blood vessel
cells, and hair follicles. It is known that concentrations of N-acetylgalactosamine decrease
with age.

v) Neuraminic acid & Sialic acid

Systematic name: (Neuraminic acid) 5-amino-3,5-dideoxy- D-glycero-D-galacto-non-2-
ulosonic acid
Molecular formula: C9H17N1O8
Neuraminic acid is a 9-carbon monosaccharide. It may be theoretically visualized as the
aldol-condensation product of pyruvic acid and D-mannosamine (2-amino-2-deoxy-
mannose). The N- or O-substituted derivatives of neuraminic acid are collectively and
commonly known as sialic acids, the predominant one being N-acetylneuraminic acid. The
amino group bears either an acetyl or a glycolyl group. The hydroxyl substituents may vary
considerably: acetyl, lactyl, methyl, sulfate and phosphate groups have been found (Fig.38).

Fig. 38: Neuraminic Acid

Neuraminic acid does not occur naturally, but many of its derivatives are found widely
distributed in animal tissues and in bacteria, especially in glycoproteins and gangliosides.
N-acetylneuraminic acid (is widely distributed throughout the tissues of the body (brain,
adrenal glands, and the heart). It is found mainly in the glycoproteins and glycolipids and
also in many fluids including saliva, urine, cerebrospinal fluid, amniotic fluid, and breast
milk.

It is important for brain development, learning, memory and cognitive performance. Cancer
cells that can metastasize often have a lot of sialic acid rich glycoproteins. This helps these
late stage cancer cells enter the blood stream.

During pregnancy, N-acetylneuraminic acid levels are raised suggesting its importance in
the immune system along with other physical and mental development systems for infants.
Disrupted N-acetylneuraminic acid metabolisms are seen in infants who are
developmentally delayed, show a coarsening of facial features, have enlarged livers and/or
spleens and fail to produce skin and hair pigmentation.

Like the other glyconutrients, N-acetylneuraminic acid is important for cellular

communication and is an immune system modulator. As an immune modulator, N-
acetylneuraminic acid affects the viscosity of mucus, which in turn repels viruses, bacteria
and other pathogens. In fact, N-acetylneuraminic acid has been shown to be effective in
defending against viruses that cause hepatitis, viral pneumonia and cold sores as well as the
common cold. This in turn decreased the severity of asthmatic bronchial spasms and allergic
reactions as well. N-acetylneuraminic acid is rapidly expelled from the kidneys and bladder.
N-acetylneuraminic acid also lowers the LDL (bad cholesterol) levels and influences blood
coagulation.

55
Sialic acid-rich oligosaccharides on the glycoconjugates found on surface membranes help
keep water at the surface of cells. The sialic acid-rich regions contribute to creating a
negative charge on the cells surface. Since water is a polar molecule, it has a partial positive
charge on both hydrogen molecules, it is attracted to cell surfaces and membranes. This also
contributes to cellular fluid uptake. Subjects with Sjogren's syndrome and alcohol
dependency show markedly low levels of N-acetylneuraminic acid.

vi) N-Acetylmuramic acid, or MurNAc

Systematic name: (R)-2-(acetylamino)-3-O-(1-carboxyethyl)-2-deoxy-D-glucose
Molecular formula: C11H19NO8
It is the ether of lactic acid and N-acetylglucosamine (Fig. 39).

Fig. 39: N-Acetylmuramic Acid

It is part of a biopolymer in the bacterial cell wall, built from alternating units of N-
acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc) linked by β(1→4)
glycosidic bonds, cross-linked with oligopeptides at the lactic acid residue of MurNAc. This
layered structure is called peptidoglycan. (see below for specific linkages).

vii) Peptidoglycan
Peptidoglycan, also known as murein, is a polymer consisting of sugars and amino acids
that forms a mesh-like layer outside the plasma membrane of eubacteria (Fig. 40a).
Structurally, it consists of linear chains of two alternating amino sugars, N-
acetylglucosamine (GlcNAc or NAG) and N-acetylmuramic acid (MurNAc or NAM). The
alternating sugars are connected by a β (1, 4) - glycosidic bond.

Fig. 40a: Structure of Peptidoglycan layer

56
Each MurNAc is attached to a short (4- to 5-residue) amino acid chain via its 3rd carbon,
normally containing D-alanine, D-glutamic acid, and mesodiaminopimelic acid (Fig. 40b).
These three amino acids do not occur in proteins and help protect against attacks by most
peptidases. Cross-linking between amino acids in different linear amino sugar chains by an
enzyme known as transpeptidase result in a 3-dimensional structure that is strong and rigid.
The specific amino acid sequence and molecular structure vary with the bacterial species
The peptide chain can be cross-linked to the peptide chain of another strand forming the 3D
mesh-like layer. Some Archaea have a similar layer of pseudopeptidoglycan.

Fig. 40b: Schematic representation of peptidoglycan

Peptidoglycan serves a structural role in the bacterial cell wall, giving structural strength, as
well as counteracting the osmotic pressure of the cytoplasm. A common misconception is
that peptidoglycan gives the cell its shape; however, whereas peptidoglycan helps maintain
the structure of the cell. Peptidoglycan is also involved in binary fission during bacterial cell
reproduction.The peptidoglycan layer is substantially thicker in Gram-positive bacteria (20
to 80 nm) than in Gram-negative bacteria (7 to 8 nm), with the attachment of the S-layer.
Peptidoglycan forms around 90% of the dry weight of Gram-positive bacteria but only 10%
of Gram-negative strains. In Gram-positive strains, it is important in attachment roles and
sterotyping purposes. For both Gram-positive and Gram-negative bacteria, particles of
approximately 2 nm can pass through the peptidoglycan.

B. Carboxylic acid sugars

The carbonyl group at C1 of monosaccharides may be oxidized to generate aldonic acids
while C-6 oxidation results in uronic acids.

i) Glucuronic acid
Systemic name: D-Glucuronic Acid
Molecular formula: C6H10O7
Glucuronic acid is a carboxylic acid. Its structure is similar to glucose. However glucuronic
acid's sixth carbon is oxidized to a carboxylic acid. The salts of glucuronic acid are known
as glucuronates; the anion C6H9O7− is the glucuronate ion (Fig. 41).

57
 ig. 41: Glucuronic Acid

Glucuronic acid is highly soluble in water. In the animal body, glucuronic acid is often
linked to poisonous substances, mainly in the liver, to allow for subsequent elimination, and
to hormones to allow for easier transport. These linkages involve O-glycosidic bonds. The
process is known as glucuronidation, and the resulting substances are known as
glucuronides (or glucuronosides).

ii) Gluconic acid

Systemic name: D-Gluconic Acid
Molecular formula: C6H12O7
Gluconic acid is the carboxylic acid formed by the oxidation of the first carbon of glucose
and. When dissolved in water, it forms the gluconate ion C6H11O7; the salts of gluconic acid
are also known as gluconates. The chemical structure of gluconic acid consists of a six-
carbon chain with five hydroxyl groups terminating in a carboxyl group (Fig. 42). This
latter group can lose a hydrogen ion and thus turns the molecule into an acid. In aqueous
solution, some gluconic acid molecules will convert to the cyclic ester Glucono delta
lactone (Fig. 43), and the two exist in equilibrium

Fig. 42: Gluconic Acid

Fig. 43: Glucurono delta lactone

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Occurrence & Uses: Gluconic acid occurs naturally in fruit, honey, kombucha tea and wine
and is used as a food additive, an acidity regulator. It is a strong chelating agent, especially
in alkaline solution.

C. Sugar phosphates
Phosphorylated sugars are another important class of derivatives of sugars. At the normal
pH of a cell, most of the hydroxyl groups (OH) on the phosphates are ionized (O-). The
hydroxyl group of sugars form ester bond with phosphates.

Phosphorylated sugars are key intermediates in energy generation and biosynthesis. Sugar
phosphates are intermediates in monosaccharide metabolism and are building blocks for
energy-providing nucleotides and for nucleic acids. Some important sugar phosphates are
listed below.

i) Glucose 6 phosphate
Molecular formula: C6H13O9P
Glucose 6-phosphate (Fig. 44) (also known as Robison ester) is glucose sugar
phosphorylated on carbon 6. This compound is very common in cells as the vast majority of
glucose entering a cell is phosphorylated in this way. Because of its prominent position in
cellular chemistry, glucose 6-phosphate has many roles within the cell. It lies at the start of
two major metabolic pathways: Glycolysis and Pentose phosphate pathway. In addition, it
may also be converted to glycogen or starch for storage. This storage is in the liver and
muscles in the form of glycogen for most multicellular animals, and in intracellular starch
or glycogen granules for most other organisms.

Fig. 44:Glucose 6 phosphate

ii) Adenosine triphosphate (ATP)

Molecular formula: C10H16N5O13P3
Adenosine 5'-triphosphate (ATP) (Fig. 45) is a multifunctional nucleotide that is most
important as a "molecular currency" of intracellular energy transfer. In this role, ATP
transports chemical energy within cells for metabolism. It is produced as an energy source
during the processes of photosynthesis and cellular respiration and consumed by many
enzymes and a multitude of cellular processes including biosynthetic reactions, motility and
cell division. In signal transduction pathways, ATP is used by kinases that phosphorylate
proteins and lipids, as well as by adenylate cyclase, which uses ATP to produce the second
messenger molecule cyclic AMP.

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 Fig. 45: Adenosine tri-phosphate

iii) Cyclic Adenosine MonoPhosphate (cAMP)

Molecular formula: C10H12N5O6P
Cyclic adenosine monophosphate (cAMP, cyclic AMP or 3'-5'-cyclic adenosine
monophosphate) is a molecule that is important in many biological processes (Fig. 46); it is
derived from adenosine triphosphate (ATP). cAMP is synthesised from ATP by adenylyl
cyclase which is located in the cell membranes. Adenylyl cyclase is activated by the
hormones glucagon and epinephrine. cAMP is a second messenger, used for intracellular
signal transduction, such as transferring the effects of hormones like glucagon and
adrenaline, which cannot get through the cell membrane. Its purposes include the activation
of protein kinases and regulating the effects of adrenaline and glucagon. It is also used to
regulate the passage of Ca2+ through ion channels.

Fig 46:Cyclic Adenosine monophosphate

D. Sugar alcohols
A sugar alcohol (also known as a polyol, polyhydric alcohol, or polyalcohol) is a
hydrogenated form of carbohydrate, whose carbonyl group (aldehyde or ketone, reducing
sugar) has been reduced to a primary or secondary hydroxyl group. Its general formula is
H(HCHO)n+1H, whereas sugar's is H(HCHO)nHCO.Some important sugar alcohols are as
follows. Lactitol, sorbitol, xylitol, mannitol, and maltitol are all sugar alcohols. The United
States Food and Drug Administration (FDA) classify sugar alcohols as "generally
recognized as safe" (GRAS). They are approved as food additives, and are recognized as not

60
contributing to tooth decay or causing increases in blood glucose. Few sugar alcohols are
discussed and illustrated below in table. (Table sugar alcohol)

i) Ethylene glycol
Systemic name: 1,2-Ethanediol
Molecular formula: C2H6O2
It is an alcohol with two -OH groups (a diol), a chemical compound.
C2H4O + H2O = HOCH2CH2OH
In its pure form, it is an odorless, colorless, syrupy liquid with a sweet taste. Ethylene glycol
is toxic, and its ingestion should be considered a medical emergency. (a Table sugar
alcohol)

ii) Glycerol
Systemic name: 1,2,3-Propanetriol
Molecular formula: C3H8O3
Glycerol has three hydrophilic alcoholic hydroxyl groups that are responsible for its
solubility in water and its hygroscopic nature. This colorless, odorless, viscous liquid is
widely used in pharmaceutical formulations. Also commonly called glycerin or glycerine, it
is a sugar alcohol, and is sweet-tasting and of low toxicity. It is a central component of
lipids. Glycerol is a precursor for synthesis of triacylglycerols and of phospholipids in the
liver and adipose tissue. When the body uses stored fat as a source of energy, glycerol and
fatty acids are released into the bloodstream. The glycerol component can be converted to
glucose by the liver and provides energy for cellular metabolism. (b Table sugar alcohol)

Table: Sugar alcohols

Sugar Alcohols Structure

a. Ethylene glycol

b. Glycerol

c. Erythritol

d. Xylitol

e. Mannitol

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 f. Sorbitol

g. Maltitol

h. Lactitol

iii) Erythritol
Systemic name: (2R, 3S)-butane-1,2,3,4-tetraol
Molecular formula: C4H10O4
Erythritol is alcohol derivative of erythrose. Erythritol is a natural sugar alcohol (a type of
sugar substitute), which has been approved for use in the United States and throughout
much of the world. It occurs naturally in fruits and fermented foods. At industrial level, it is
produced from glucose by fermentation with yeast, Moniliella pollinis. (c Table sugar
alcohol)

iv) Xylitol
Systemic name: Xylo-Pentane-1, 2, 3, 4, 5-pentol
Molecular formula: C5H12O5
Xylitol is derived from xylose. It is a five-carbon sugar alcohol that is used as a sugar
substitute. It naturally occurs in the fibers of many fruits and vegetables, including various
berries, cornhusks, oats, and mushrooms. Xylitol is roughly as sweet as sucrose but with
only two-thirds the food energy.

Possessing approximately 40% less food energy, xylitol is a low-calorie alternative to table
sugar. It is a "toothfriendly" sugar and may actively aid in repairing minor cavities caused
by dental caries. Xylitol also appears to have potential as a treatment for osteoporosis. The
open nature of xylitol and its ability to form many different sugar-like structures appears to
interfere with the ability of many bacteria to adhere. (d Table sugar alcohol)

v) Mannitol
Systemic name: Xylo-Pentane-1, 2, 3, 4, 5-pentol
Molecular formula: C5H14O6
Mannitol is a sorbitol stereoisomer. It is an osmotic diuretic agent and a weak renal
vasodilator. It was originally isolated from the secretions of the Flowering Ash, called
Manna after their resemblance to the Biblical food, and may also be referred to as Mannite
and Manna Sugar. (e Table sugar alcohol)

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Mannitol is used clinically to reduce acutely raised intracranial pressure, until more
definitive treatment can be given, and to treat patients with oliguric renal failure. Mannitol
can also be used to open the blood-brain barrier by temporarily shrinking the tightly coupled
endothelial cells that make up the barrier. This makes mannitol indispensable for delivering
various drugs directly to the brain (e.g. in the treatment of Alzheimer's disease). Mannitol is
also used as a sweetener for people with diabetes. Since mannitol has a negative heat of
solution, it is used as a sweetener in "breath-freshening" candies. It is sometimes used as an
adulterant or cutting agent for heroin, methamphetamines or other illicit drugs. It is a non-
permeating molecule; i.e., it cannot cross biological membranes. Mannitol is commonly
used in the circuit prime of a heart lung machine during cardiopulmonary bypass (CPB).
The presence of mannitol preserves renal function during the times of low blood flow and
pressure, while the patient is on bypass. The solution prevents the swelling of endothelial
cells in the kidney, which may have otherwise reduced blood flow to this area and resulted
in cell damage. Mannitol is also being developed as a treatment for cystic fibrosis and
bronchiectasis and as a diagnostic test for airway hyperresponsiveness. The mannitol is
orally inhaled as a dry powder through what is known as an osmohaler.

vi) Sorbitol
Systemic name: D-Glucitol
Molecular formula: C6H14O6
Sorbitol, also known as glucitol, is a sugar alcohol (Table f) metabolized slowly by the
body. It is obtained by reduction of glucose changing the aldehyde group to an additional
hydroxyl group hence the name sugar alcohol. (f Table sugar alcohol)

Sorbitol is a sugar substitute often used in diet foods and sugar-free chewing gum. It occurs
naturally in many stone fruits and berries from trees of the genus Sorbus. Sorbitol is a
nutritive sweetener and provides 65% dietary energy, while retaining 60% of the sweetness.
As a food additive it is categorized as a sweetener, emulsifier and humectant. Sorbitol can
be used as a non-stimulant laxative as either an oral suspension or suppository. Ingesting
large amounts of sorbitol can lead to some abdominal pain, gas, and mild to severe diarrhea.
Even in the absence of dietary sorbitol, cells also produce sorbitol naturally. Diabetic
retinopathy and neuropathy may be related to excess sorbitol in the cells of the eyes and
nerves. The source of this sorbitol in diabetics is excess glucose, which goes through the
polyol pathway. Sorbitol is often used in modern cosmetics as a humectant and thickener.
Some transparent gels can only be made with sorbitol as it has a refractive index sufficiently
high for transparent formulations. It is also used as a cryoprotectant additive (mixed with
sucrose and sodium polyphosphates) in the manufacture of surimi, a highly refined,
uncooked fish paste most commonly produced from Alaska (or walleye) pollock (Theragra
chalcogramma). Sorbitol is identified as a potential key chemical intermediate from biomass
resources. Complete reduction of sorbitol opens the way to alkanes such as hexane, which
can be used as a biofuel.

vii) Maltitol
Systemic name: 4-O-α-D-Glucopyranosyl-D-glucitol
Molecular formula: C12H24O11
Maltitol is a sugar alcohol (a polyol) used as a sugar substitute (g Table sugar alcohol)
because it has fewer calories, does not promote tooth decay and has a somewhat lesser
effect on blood glucose. It has 90% of the sweetness of sucrose (table sugar) and nearly
identical properties, except for browning. Unfortunately, maltitol is well known to cause
gastric distress if consumed in great quantities. Chemically, maltitol is also known as 4-O-a-

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 glucopyranosyl-D-sorbitol. Commercially, maltitol is a disaccharide produced by Corn
Products It is made by hydrogenation of maltose obtained from starch.

It is used especially in production of sweets: sugarless hard candies, chewing gum,

chocolates, baked goods, and ice cream. It is not metabolized by oral bacteria, so it does not
promote tooth decay. It is somewhat more slowly absorbed than sucrose, which makes it
somewhat more suitable for people with diabetes than sucrose. Due to its slow absorption,
excessive consumption can have laxative effect and sometimes can cause gas and/or
bloating. This means that maltitol is particularly associated with gastric issues.

viii) Lactitol
Systemic name: 4-O- β-D-galactocopyranosyl-D-glucitol
Molecular formula: C12H24O11
Lactitol is a sugar alcohol used as a replacement bulk sweetener for low calorie foods with
approximately 40% of the sweetness of sugar. (h Table sugar alcohol)

Lactitol is used in a variety of low food energy or low fat foods. High stability makes it
popular for baking. It is used in sugar-free candies, cookies (biscuits), chocolate, and ice
cream. Lactitol also promotes colon health as a prebiotic. Lactitol only has 60% calories,
compared for typical carbohydrates. Lactitol is also approved for use in foods in most
countries around the world, though lactitol can cause cramping, flatulence, and diarrhoea in
some individuals.

2. Derivatives of polysaccharides
(Glycosaminoglycans (GAGs) or mucopolysaccharides)
Classification: Glycosaminoglycans (GAGs) or mucopolysaccharides are long unbranched
anionic polysaccharides consisting of a repeating disaccharide unit (sugar 1 and sugar 2)
Table below. Members of the glycosaminoglycan family vary in the type of hexosamine,
hexose or hexuronic acid unit they contain (e.g. glucuronic acid, iduronic acid, galactose,
galactosamine, glucosamine). They also vary in the geometry of the glycosidic linkage.
They are synthesized in either endoplasmic reticulum and/or Golgi.

Examples of GAGs:

Name Sugar 1 Sugar 2 Linkage Unique features

Chondroitin N- Glucuronic acid β (1→3) Most prevalent GAG
sulphate acetylgalactosamine
Dermatan Iduronic acid N_Acetylgalactosa β (1→3) Only one with iduronic
sulphate mine acid
Keratan Galactose (varies) β (1→4) Very variable
sulphate
Heparin Glucuronic acid Glucosamine α (1→4) Only one intracellular;
high negative charge
density
Heparan Glucuronic acid Glucosamine α (1→4) Similar to heparin but
sulphate extracellular
Hyaluronan Glucuronic acid N- β (1→3) Only bacterial one, only
Acetylglucosamine one without sulfur

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A glycosaminoglycans unit consists of an N-acetyl-hexosamine and a hexose or hexuronic
acid, either or both of which may be sulfated. The combination of the sulfate group and the
carboxylate groups of the uronic acid residues gives them a very high density of negative
charge.

This family of carbohydrates is essential or important for the life of vertebrates and an
assortment of lower animals. It is present on the cell surface and in the extracellular matrix
of animals. GAGs form an important component of connective tissues. GAG chains may be
covalently linked to a protein to form proteoglycans.

i) Chondroitin sulfate
Chondroitin sulfate is a sulfated glycosaminoglycan (GAG) composed of a chain of
alternating sugars (N-acetylgalactosamine and glucuronic acid) (Fig. 47). It is usually found
attached to proteins as part of a proteoglycan. A chondroitin chain can have over 100
individual sugars, each of which can be sulfated in variable positions and quantities.
Understanding the functions of such diversity in chondroitin sulfate and related
glycosaminoglycans is a major goal of glycobiology. Chondroitin sulfate is an important
structural component of cartilage and provides much of its resistance to compression.
Chondroitin sulfate chains are unbranched polysaccharides of variable length containing
two alternating monosaccharides: D-glucuronic acid (GlcA) and N-acetyl-D-galactosamine
(GalNac). Some GlcA residues are epimerized into L-iduronic acid (IdoA); the resulting
disaccharide is then referred to as dermatan sulfate.

Fig. 47: Chondroitin sulfate

Protein attachment: Chondroitin sulfate chains are linked to hydroxyl groups on serine
residues of certain proteins. Exactly how proteins are selected for attachment of
glycosaminoglycans is not understood. Empirically, glycosylated serines are often followed
by a glycine and have neighboring acidic residues, but this motif does not always predict
glycosylation.

Attachment of the GAG chain begins with four monosaccharides in a fixed pattern: Xyl -
Gal - Gal - GlcA. Each sugar is attached by a specific enzyme, allowing for multiple levels
of control over GAG synthesis. Xylose begins to be attached to proteins in the endoplasmic
reticulum, while the rest of the sugars are attached in the Golgi apparatus.

Sulfation: Each monosaccharide may be left unsulfated, sulfated once, or sulfated twice.
Most commonly the hydroxyls of the 4 and 6 positions of the N-acetyl-galactosamine are
sulfated. Sulfation is mediated by specific sulfotransferases.

Functions: Chondroitin's functions largely depend on the properties of the overall

proteoglycan of which it is a part. These functions can be broadly divided into structural and

65
regulatory roles. However, this division is not absolute and some proteoglycans have both
structural and regulatory roles.
Structural: Chondroitin sulfate is a major component of extracellular matrix, and is
important in maintaining the structural integrity of the tissue. This function is typical of the
large aggregating proteoglycans: aggrecan, versican, brevican, and neurocan. As part of
aggrecan, chondroitin sulfate is a major component of cartilage. The tightly packed and
highly charged sulfate groups of chondroitin sulfate generate electrostatic repulsion that
provides much of the resistance of cartilage to compression. Loss of chondroitin sulfate
from the cartilage is a major cause of osteoarthritis.

Regulatory: Chondroitin sulfate readily interacts with proteins in the extracellular matrix
due to its negative charges. These interactions are important for regulating a diverse array of
cellular activities. In the nervous system, chondroitin sulfate proteoglycans regulate the
growth and development of the nervous system as well as the nervous system response to
injury.

Medical use: Chondroitin is an ingredient found commonly in dietary supplements used as

an alternative medicine to treat osteoarthritis. It is commonly sold together with
glucosamine.

ii) Dermatan sulfate

Dermatan sulfate is a glycosaminoglycan (formerly called a mucopolysaccharide) found
mostly in skin, but also in blood vessels, heart valves, tendons, and lungs.

Function: Dermatan sulfate may have roles in coagulation, cardiovascular disease,

carcinogenesis, infection, wound repair, and fibrosis. Dermatan sulfate accumulates
abnormally in several of the mucopolysaccharidosis disorders.

iii) Keratan sulfate

Keratan sulfate is any of several sulfated glycosaminoglycans that have been found
especially in the cornea, cartilage, and bone. It is a large, highly hydrated structural
carbohydrates molecule, which in joints can act as a cushion. There are two main types.
Type I is found in the cornea, and Type II is found in cartilage.

iv) Heparin
Heparin is a member of the glycosaminoglycan family of carbohydrates (which includes the
closely related molecule heparan sulfate). It is widely used as an injectable anticoagulant
and has the highest negative charge density of any known biological molecule. It can also
be used to form an inner anticoagulant surface on various experimental and medical devices
such as test tubes and renal dialysis machines.

Structure: Native heparin is a polymer with a molecular weight ranging from 3 kDa to 40
kDa although the average molecular weight of most commercial heparin preparations is in
the range of 12 kDa to 15 kDa. Heparin is a member of the glycosaminoglycan family of
carbohydrates (which includes the closely related molecule heparan sulfate) and consists of
a variably sulfated repeating disaccharide unit (Fig. 48). The main disaccharide units that
occur in heparin are shown below. The most common disaccharide unit is composed of a 2-
O-sulfated iduronic acid and 6-O-sulfated, N-sulfated glucosamine, IdoA(2S)-GlcNS(6S).
Under physiological conditions the ester and amide sulfate groups are deprotonated and
attract positively charged counterions to form a heparin salt. It is in this form that heparin is
usually administered as an anticoagulant.

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 Fig. 48: Heparin

Mechanism of action: Heparin is a naturally occurring anticoagulant produced by

basophils and mast cells. Heparin binds to the enzyme inhibitor antithrombin III (AT-III)
causing a conformational changes which results in its active site being exposed. The
activated AT-III then inactivates thrombin and other proteases involved in blood
clotting, most notably factor Xa.

Heparin's exact physiological role is still unclear, because blood anti-coagulation is

mostly achieved by endothelial cell-derived heparan sulfate proteoglycans. Heparin is
usually stored within the secretory granules of mast cells and only released into the
vasculature at sites of tissue injury. It has been proposed that rather than anticoagulation
the main purpose of heparin is in a defensive mechanism at sites of tissue injury against
invading bacteria and other foreign materials.

v) Heparan sulfate
Heparan sulfate (HS) is a linear polysaccharide found in all animal tissues. It occurs as a
proteoglycan (PG) in which two or three HS chains are attached in close proximity to
cell suface or extracellular matrix proteins. It is in this form that HS binds to a variety of
protein ligands and regulates a wide variety of biological activities, including
developmental processes, angiogenesis, blood coagulation and tumour metastasis.

HS structure and differences from heparin: Heparan sulfate is a member of the

glycosaminoglycan family of carbohydrates and is very closely related in structure to
heparin. Both consist of a variably sulfated repeating disaccharide unit. The most
common disaccharide unit within heparan sulfate is composed of a glucuronic (GlcA)
linked to N-acetyl glucosamine (GlcNAc) typically making up around 50% of the total
disaccharide units. It has been suggested that a GAG should qualify as heparin only if its
content of N-sulfate groups largely exceeds that of N-acetyl groups and the
concentration of O-sulfate groups exceeds those of N-sulfate (Fig. 49). Under
physiological conditions the ester and amide sulfate groups are deprotonated and attract
positively charged counterions to form a salt. It is in this form that HS is thought to exist
at the cell surface. Heparan sulfate is initially synthesized on a membrane-embedded
core protein as a polymer of alternating glucuronate and N-acetylglucosamine residues.
Later, in segments of the polymer, glucuronate residues may be converted to the sulfated
sugar iduronic acid, while N-acetylglucosamine residues may be deacetylated and/or
sulfated. Some cell surface heparan sulfate glycosaminoglycans remain covalently linked
to core proteins embedded in the plasma membrane. Proteins involved in signaling and
adhesion at the cell surface recognize and bind segments of heparan sulfate chains
having particular patterns of sulfation (Fig. 50).

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 Fig. 49: Heparan sulfate

Fig. 50: Heparan sulfate chains

vi) Hyaluronan
Hyaluronan (also called hyaluronic acid or hyaluronate) is a non-sulfated
glycosaminoglycan distributed widely throughout connective, epithelial, and neural
tissues. Hyaluronan is a polymer of disaccharides themselves composed of D-glucuronic
acid and D-N-acetylglucosamine, linked together via alternating β-1,4 and β-1,3
glycosidic bonds. Hyaluronan can be 25,000 disaccharide repeats in length. Polymers of
hyaluronan can range in size from 5,000 to 20,000,000 Da in vivo. The average
molecular weight in human synovial fluid is 3−4,000,000 Da and hyaluronan purified
from human umbilical cord is 3,140,000 Da.

It is one of the chief components of the extracellular matrix, contributes significantly to

cell proliferation and migration, and may also be involved in the progression of some
malignant tumors. The average 70 kg man has roughly 15 grams of hyaluronan in his
body, one third of which is turned over (degraded and synthesised) every day.

Fig. 51: Hyaluronan

Functions: Until the late 1970s, hyaluronan was described as a "goo" molecule, a
ubiquitous carbohydrate polymer that is part of the extracellular matrix. For example,
hyaluronan is a major component of the synovial fluid and was found to increase the

68
viscosity of the fluid. Along with lubricin, it is one of the fluid's main lubricating
components. Hyaluronan is an important component of articular cartilage, where it is
present as a coat around each cell (chondrocyte). When aggrecan monomers bind to
hyaluronan in the presence of link protein, large highly negatively charged aggregates
form. These aggregates imbibe water and are responsible for the resilience of cartilage
(its resistance to compression). The molecular weight (size) of hyaluronan in cartilage
decreases with age however the amount increases.

Hyaluronan is also a major component of skin, where it is involved in tissue repair. When
skin is excessively exposed to UV-B rays, it becomes inflamed (sunburn) and the cells in
the dermis stop producing as much hyaluronan and increase the rate of its degradation.
Hyaluronan degradation products also accumulate in the skin after UV exposure.

While it is abundant in extracellular matrices, hyaluronan also contributes to tissue

hydrodynamics, movement and proliferation of cells, and participates in a number of cell
surface receptor interactions, notably those including its primary receptor, CD44. CD44
participates in cell adhesion interactions required by tumor cells.

Carbohydrates in living system

A: ABO Blood group system
The International Society of Blood Transfusion currently recognizes 29 blood group
systems (including the ABO and Rh systems). ABO blood types are also present in
some animals, for example; apes such as chimpanzees, bonobos and gorillas.

Carbohydrates form the most important part of blood group system in human blood
transfusion. The associated anti-A antibodies and anti-B antibodies are usually IgM
antibodies, which are usually produced in the first years of life by sensitization to
environmental substances such as food, bacteria and viruses. The corresponding blood
group carbohydrate structures, designated ABH, are found at the termini of
oligosaccharide chains on glycoproteins and glycolipids on the surface of RBC &
endothelial & most epithelial cells. The immunodominant monosaccharide that
determines blood group A, is a terminal α-1,3-linked N-acetylgalactosamine (GalNAc),
whereas the corresponding monosaccharide of blood group B specificity is an α-1,3-
linked galactose. Group O cells lack chains, which instead are terminated with α-1,2-
linked-fucose.

The ABO blood group system is widely credited to have been discovered by the
Austrian scientist Karl Landsteiner, who found three different blood types A, B, and O
in 1900; Czech serologist Jan Janský independently pioneered the classification of
human blood into four groups. Decastrello and Sturli discovered the fourth type, AB, in
1902. Ludwik Hirszfeld and E. von Dungern discovered the heritability of ABO blood
groups in 1910-11, with Felix Bernstein demonstrating the correct blood group
inheritance pattern of multiple alleles at one locus in 1924.

Chemical nature & Structure: The antigens, which determine blood types belong to
glycoproteins and glycolipids. There are three types of blood-group antigens: O, A, and
B. They differ only slightly in the composition of carbohydrates. The A antigen and the

69
B antigen are derived from a common precursor known as the H antigen (or H
substance). The H antigen is a carbohydrate sequence with carbohydrates linked mainly
to protein (with a minor fraction attached to ceramide moiety). The majority of the ABO
determinants are expressed on the ends of long polylactosamine chains attached mainly
to Band 3 protein

(1), the anion exchange protein of the red cell membrane, and a minority of the epitopes is
expressed on neutral glycosphingolipids (1). In blood group O, the H antigen remains
unchanged and consists of a chain of beta-D-galactose, beta-D-N-Acetylglucosamine, beta-
D-galactose, and 2-linked, alpha-L-fucose, the chain being attached to the protein or
ceramide. H antigens can be changed into A or B antigens by enzymes coded by the blood
group A or B genes, which are sugar (glycosyl) tranferases. Type A has an extra alpha-N-
Acetyl-D-galactosamine bonded to the D-galactose at the end, while type B has an extra
alpha-D-galactose bonded to the D-galactose at the end.
• Individuals with Type A blood can receive blood from donors of type A and type
O blood.
• Individuals with type B blood can receive blood from donors of type B and type
O blood.
• Individuals with type AB blood can receive blood from donors of type A, type
B, type AB, or type O blood. Type AB blood is referred to as the universal
recipient.
• Individuals with of O blood can receive blood from donors of only type O.
• Individuals of type A, B, AB and O blood can receive blood from donors of type
O blood. Type O blood is called the universal donor.
• Antibodies are not formed against the H antigen except by those with the
Bombay phenotype.

In ABH secretors, ABH antigens are secreted by most mucus-producing cells of the
body interfacing with the environment, including lung, skin, liver, pancreas, stomach,
intestines, ovaries and prostate.

Blood-group antigens
All humans contain enzymes, which catalyze the synthesis of the O antigen. Humans with
A-type blood also contain an additional enzyme (called A-type enzyme here), which adds
N-acetylgalactosamine to the O antigen. Humans with B-type blood contain another
enzyme (called B-type enzyme here), which adds galactose to the O antigen. Humans with
AB-type blood contain both A-type and B-type enzymes while humans with O-type blood
lack both types of enzymes (Fig. 52).

The Rh System
Rh antigens are transmembrane proteins with loops exposed at the surface of red blood
cells. They appear to be used for the transport of carbon dioxide and/or ammonia across the
plasma membrane. They are named for the rhesus monkey in which they were first
discovered. There are a number of Rh antigens. Red cells that are "Rh positive" are
designated as D. About 15% of the population have no RhD antigens and thus are "Rh
negative". The major importance of the Rh system for human health is to avoid the danger
of RhD incompatibility between mother and fetus.

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 Fig. 52: Blood group antigens

During birth, there is often a leakage of the baby's red blood cells into the mother's
circulation. If the baby is Rh positive (having inherited the trait from its father) and the
mother Rh-negative, these red cells will cause her to develop antibodies against the Rh D
antigen. The antibodies, usually of the IgG class, do not cause any problems for that child,
but can cross the placenta and attack the red cells of a subsequent Rh+ fetus. This destroys
the red cells producing anemia and jaundice. The disease, called erythroblastosis fetalis or
hemolytic disease of the newborn may be so severe as to kill the fetus or even the newborn
infant. It is an example of an antibody-mediated cytotoxicity disorder.

B: Sugars in the cell wall of bacteria

In contrast to eukaryotic cells, bacterial cells have a cell wall in addition to a lipid bilayer
membrane. These are essentially carbohydrate polymers, which offer protection from
exterior hypotonic condition and the high internal osmotic pressures, preventing swelling
and bursting of the cells. The membrane consists of a peptidoglycan (Fig. 53).

a) In Gram positive bacteria

Gram-positive bacteria can be stained with Gram stain. The wall consists of a GlcNAc (b
1->4) MurNAc repeat (like that in chitin which is a polymer of GlcNAc in (b 1->4)
links, but in which the OH of lactate is in ether-linkage to C3 to form N-Acetylmuramic
acid). A tetrapeptide (Ala-D-isoGlu-Lys-D-Ala) is attached in amide link to the
carboxyl group of the lactate in MurNAc. The GlcNAc (b 1->4) MurNAc strands are
covalently connected by a pentaglycine bridge through the epsilon amino group of the
tetrapeptide Lys on one strand and the D-Ala of a tetrapeptide on another strand (Fig.
54).

Techioic acids are often attached to the C6 of MurNAc. Teichoic acid is a polymer of
glycerol or ribitol to which alternative GlcNAc and D-Ala are linked to the middle C of
the glycerol. Multiple glycerols are linked through phosphodiester bonds. These teichoic
acids often make up 50% of the dry weight of the cell wall, and present a foreign (or

71
antigenic) surface to infected hosts. These often serve as receptors for viruses that infect
bacteria (bacteriophages)
.

Fig. 53: Bacterial cell wall

Fig. 54: Gram positive bacterial cell wall

72
b) In Gram negative bacteria
These bacterial cannot be stained with Gram stain. The wall consists of the same
structure as in Gram positive bacteria, but the GlcNAc (b 1->4) MurNAc strands are
covalently connected through a direct amide bond between the epsilon amino group of
the tetrapeptide Lys on one strand and the D-Ala of a tetrapeptide on another strand. (i.e.
no pentaGly spacer). In addition, Gram negative bacteria don't have teichoic acid
polymers. Rather they have a second, outer lipid bilayer. The cell wall is sandwiched
between the inner and outer bilayers. The space between the lipid bilayers is called the
periplasmic space. A hydrophobic protein covalently attaches (through an amide link
from a protein Lys) to the cell wall at the last amino acid in the tetrapeptide unit of the
wall (actually diaminopimelic acid which replaces about 10% of the D-Ala in the cell
wall). The N-terminal of the hydrophobic proteins attaches to the outer lipid
membrane through a Ser (Fig. 55). The outer membrane is coated with a
lipopolysaccharide (LPS) of varying composition. The LPS determines the antigenicity
of the bacteria. The different LPS are called the O-antigens (Fig. 56).

Fig. 55: Gram Negative bacterial cell wall

C: Sugars in the cell wall of fungus

The composition of the fungal cell wall is characterized as a relatively simple structure
made up of "cellulose" and chitin. The fungal cell wall can make up 30% or more of the
dry weight of the fungus, and the fungi are characterized by external digestion of food
followed by selective absorption of the digestion products. So the fungal cell walls are a
complex, specialized and highly dynamic system, constantly being regenerated and
remodeled according to the needs. Therefore, many of the cell wall-associated proteins

73
enzymes do hydrolyze chitin and polysaccharides. The fungal cell wall is very different
from insect exoskeletons or plant cell walls, which are terminally differentiated structures.

Fig. 56: Liposaccharide organization in bacteria

The cell wall is generally constructed of three layers: (1) An α-glucan layer (a glucan is a
polymer of glucose), (2) A β-glucan layer, and (3) An outer layer of glycoprotein.

In addition, chitin may be a significant component of certain cell wall structures. The α-
glucan layer, if present, is generally composed of the α (1→3)-glucan polymer. However, α
(1→4) glycosides are variably present. Compare glycogen, which is α (1→4)-glucan with
(1→6) side chains. Where present, the α-glucan material appears as a fibrillar layer
adjacent to the plasma membrane and is thought to serve a largely structural role, stiffening
the basal layer of the cell wall. The α-glucan layer is rarely represented in diagrams of the
fungal cell wall because it does not occur in Saccharomyces, the usual model system.
Among ascomycetes, the alpha glucan is found in Schizosaccharomyces, but is not known
from any other yeasts. The material is common among all groups in the Pezizomycotina.
However, in Lecanoromycetes, a very large proportion tends to be in the α (1→4) form.
Alpha glucans form a significant part of the cell wall in many basidiomycetes.

The bulk material of the cell wall is usually in the form of β (1→3)-glucan. This forms a
very stable hydrogen-bonded triple helix in solution, and probably in vivo. The packing of
these triple helix structures is controlled by the size and frequency of very short (1→6) side
chains, sometimes consisting of a single glucose monomer.

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In addition to β(1→3)-glucan, the cell wall contains β(1→6)-glucan. It may be described as
a β(1→3)-glucan with big side-chains, with a true β(1→6) backbone. This material may be
peripheral to the bulk β(1→3)-glucan and is strongly involved in cross-linking the various
components of the cell wall, as shown in the figure.

The outermost layer of the cell wall is composed of diverse proteins with polysaccharide
side chains composed of mannose. These are attached through their mannan side chains via
a (1→3) linkage with the β(1→6)-glucan. In reality the structure is much more complex,
involving a wide variety of different interactions between glycoproteins and bulk cell wall
materials.

Finally, the fungal cell wall contains also contains variable amounts of chitin. In many
systems chitin is a major constituent of the cell wall. In others, it is involved only in cell
division or reproductive structures or is virtually absent otherwise.

D: Derivatives with proteins

Sugars combine with proteins in different ways to create glycoproteins, proteoglycans etc.

a. Glycoproteins
A glycoprotein is a biomolecule composed of a protein and a carbohydrate (an
oligosaccharide). The carbohydrate is attached to the protein in a co-translational or post-
translational modification. This process is known as glycosylation. The addition of sugar
chains can happen either at asparagines (N-glycosylation); or at hydroxylysine,
hydroxyproline, serine, or threonine (O-glycosylation). Monosaccharides commonly found
in eukaryotic glycoproteins include glucose, N-acetylglucosamine, galactose, N-
acetylgalactosamine, mannose, fucose, xylose and N-acetylneuraminic acid (also known as
sialic acid). In proteins that have segments extending extracellularly, the extracellular
segments are often glycosylated.

Important facts
a) Glycoproteins have carbohydrate attached to them and this attachment is a covalent
linkage to:
• The hydroxyl (-OH) group of the R group of serine or threonine - called "O-linked"
in both cases.
• The amino group (-NH2) in the R group of asparagine - called "N-linked".

b) The carbohydrate consists of short, usually branched, chains of

• Simple sugars (e.g., glucose, galactose)
• Amino sugars (sugars with an amino group, e.g., N-acetylglucosamine), and
• Acidic sugars (sugars with a carboxyl group, e.g., sialic acid)

Sugars are very hydrophilic thanks to their many -OH groups. Their presence makes
glycoproteins far more hydrophilic than they would be otherwise and essential for the
proper folding of the protein into its tertiary structure. Most of the proteins exposed to the
watery surroundings at the surface of cells are glycoproteins. Soluble glycoproteins often
show a high viscosity, for example, in egg white and blood plasma.

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Types of glycoproteins
Broadly, they can be classified into two types according to the site of glycosylation.

A) In N-glycosylation (Fig. 57), the addition of sugar chains can happen at the amide
nitrogen on the side chain of the asparagines.

N-linked glycosylation is important for the folding of some eukaryotic proteins. The N-
linked glycosylation process occurs in eukaryotes and widely in archaea, but very rarely in
bacteria. For N-linked oligosaccharides, a 14-sugar precursor is first added to the asparagine
in the polypeptide chain of the target protein. The structure of this precursor is common to
most eukaryotes, and contains 3 glucose, 9 mannose, and 2 N-acetylglucosamine molecules.
A complex set of reactions attaches this branched chain to a carrier molecule called
dolichol, and then it is transferred to the appropriate point on the polypeptide chain as it is
translocated into the ER lumen.

Fig. 57: Overview of the major types of vertebrate N-linked glycan glycosylation

There are two major types of N-linked saccharides: high-mannose oligosaccharides, in

essence, just two N-acetylglucosamines with many mannose residues, and complex
oligosaccharides, containing almost any number of the other types of saccharides, including
more than the original two N-acetylglucosamines.

The oligosaccharide chain is attached by oligosaccharyltransferase to asparagine occurring

in the tripeptide sequence Asn-X-Ser, Asn-X-Thr or Asn-X-Cys, where X could be any
amino acid except Pro. This sequence is known as a glycosylation sequon. After attachment,
once the protein is correctly folded, the three glucose residues are removed from the chain
and the protein is available for export from the ER. The glycoprotein thus formed is then
transported to the Golgi where removal of further mannose residues may take place.
However, glycosylation itself does not seem to be as necessary for correct transport
targeting of the protein, as one might think. Studies involving drugs that block certain steps
in glycosylation, or mutant cells deficient in a glycosylation enzyme, still produce
otherwise-structurally-normal proteins that are correctly targeted, and this interference does
not seem to interfere severely with the viability of the cells. Mature glycoproteins may
contain a variety of oligomannose N-linked oligosaccharides containing between 5 and 9

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mannose residues. Further removal of mannose residues leads to a 'core' structure
containing 3 mannose, and 2 N-acetylglucosamine residues, which may then be elongated
with a variety of different monosaccharides including galactose N-acetylglucosamine, N-
acetylgalactosamine, fucose and sialic acid.

B) In O-glycosylation (Fig. 58), the addition of sugar chains can happen on the hydroxyl
oxygen on the side chain of hydroxylysine, hydroxyproline, serine or threonine. It can again
be of the following types depending on the sugar moiety being attached:

a) O-N-acetylgalactosamine (O-GalNAc)- O-linked glycosylation occurs at a later

stage during protein processing, probably in the Golgi apparatus. This is the addition
of N-acetyl-galactosamine to serine or threonine residues by the enzyme UDP-N-
acetyl-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase (EC
2.4.1.41), followed by other carbohydrates (such as galactose and sialic acid). This
process is important for certain types of proteins such as proteoglycans, which
involves the addition of glycosaminoglycan chains to an initially unglycosylated
"proteoglycan core protein." These additions are usually serine O-linked
glycoproteins, which seem to have one of two main functions. One function involves
secretion to form components of the extracellular matrix, adhering one cell to
another by interactions between the large sugar complexes of proteoglycans. The
other main function is to act as a component of mucosal secretions, and it is the high
concentration of carbohydrates that tends to give mucus its "slimy" feel. Proteins
that circulate in the blood are not normally O-glycosylated, with the exception of
IgA1 and IgD (two types of antibody) and C1-inhibitor.

Fig. 58: Overview of the major O-linked glycan types glycosylation

b) O-fucose - O-fucose is added between the second and third conserved cysteines of EGF-
like repeats in the Notch protein, and possibly other substrates by GDP-fucose protein O-
fucosyltransferase 1, and to Thrombospondin repeats by GDP-fucose protein O-

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fucosyltransferase 2. In the case of EGF-like repeats, the O-fucose may be further elongated
to a tetrasaccharide by sequential addition of N-acetylglucoasamine (GlcNAc), galactose
and sialic acids, and for Thrombospondin repeats, may be elongated to a disaccharide by the
addition of glucose. Both of these fucosyltransferases have been localized to the
endoplasmic reticulum, which is unusual for glycosyltransferases, most of which function in
the Golgi apparatus.

c) O-glucose - O-glucose is added between the first and second conserved cysteines of
EGF-like repeats in the Notch protein, and possibly other substrates by an unidentified O-
glucosyltransferase.

d) O-N-acetylglucosamine (O-GlcNAc) - O-GlcNAc is added to serines or threonines by

O-GlcNAc transferase. O-GlcNAc appears to occur on serines and threonines that would
otherwise be phosphorylated by serine/threonine kinases. Thus, if phosphorylation occurs,
O-GlcNAc does not, and vice versa. This is an incredibly important finding because
phosphorylation/dephosphorylation has become a scientific paradigm for the regulation of
signaling within cells. A massive amount of cancer research is focused on phosphorylation.
Ignoring the involvement of this form of glycosylation, which clearly appears to act in
concert with phosphorylation, means that a lot of current research is missing at least half of
the picture. O-GlcNAc addition and removal also appear to be key regulators of the
pathways that are deregulated in diabetes mellitus. The gene encoding the O-GlcNAc
removal enzyme has been linked to non-insulin dependent diabetes mellitus. It is the
terminal step in a nutrient-sensing hexosamine signaling pathway.

e) GPI anchor - A special form of glycosylation is the GPI anchor. This form of
glycosylation functions to attach a protein to a hydrophobic lipid anchor, via a glycan chain.

f) C-mannosylation – A mannose sugar is added to tryptophan residues in

Thrombospondin repeats. This is an unusual modification both because the sugar is linked
to a carbon rather than a reactive atom like a nitrogen or oxygen and because the sugar is
linked to a tryptophan residue rathen than an asparagines or serine/threonine.

Functions of Glycoproteins
In vivo, glycan moieties of glycoproteins has been known to play important roles in -
maintenance of protein conformation and solubility, - proteolytic processing and
stabilization of the polypeptide, - mediation of biological activity, - intracellular sorting and
externalization of glycoproteins, and – embryonic development and differentiation.
Glycosylation on protein residues confers on them a host of physiological functions, which
are vital for maintenance of life processes. Some of these are enlisted below:

Structural: Glycoproteins are found throughout matrices. They act as receptors on cell
surfaces that bring other cells and proteins (collagen) together giving strength and support
to a matrix (Ivatt). Proteoglycan-linking glycoproteins cross links proteoglycan molecules
and is involved in the formation of the ordered structure within cartilage tissue. In nerve
tissue glycoproteins are abundant in gray matter and appear to be associated with
synaptosomes, axons, and microsomes. Prothrombin, thrombin, and fibrinogen are all
glycoproteins that play an intricate role in the blood clotting mechanism (Gottschalk). In
certain bacteria the slime layer that surrounds the outermost components of cell walls are
made up of glycoproteins of high molecular weight. In addition to forming these s-layers,

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glycoproteins also function as bacterial flagella. These are made up of bundles of
glycoproteins protruding from the cell's surface. Their rotation provides propulsion. In
plants, glycoproteins have roles in cell wall formation, tissue differentiation,
embryogenesis, and sexual adhesion (certain algal species).

Protection: High molecular weight polymers called mucins are found on internal epithelial
surfaces. They form a highly viscous gel that protects epithelium form chemical, physical,
and microbial disturbances. Examples of mucin sites are the human digestive tract, urinary
tract, and respiratory tracts. "Cervical mucin" is a glycoprotein found in the cervix of
animals that regulates access of spermatozoa to the upper reproductive tract. Mucins are
also found on the outer body surfaces of fish to protect the skin. Mucins also acts as a
lubricant. Human lacrimal glands produce a glycoprotein, which protects the corneal
epithelium from desiccation and foreign particles. Human sweat glands secrete
glycoproteins, which protect the skin from the other excretory products that could harm the
skin.

Reproduction: Glycoproteins found on the surface of spermatozoa appear to increase a

sperm cell's attraction for the egg by altering the electrophoretic mobility of the plasma
membrane. Actual binding of the sperm cell to the egg is mediated by glycoproteins serving
as receptors on the surface of each the two membranes. The zona pellucida is an envelope
made of glycoprotein that surrounds the egg and prevents polyspermy from occurring after
the first sperm cell has penetrated the egg's plasma membrane. Hen ovalbumin is a
glycoprotein found in egg white that serves as a food storage unit for the embryo.

Adhesion: Glycoproteins serve to adhere cells to cells and cells to substratum. Cell-cell
adhesion is the basis for the development of functional tissues in the body. The interactions
between cells are mediated by the glycoproteins on those cell's surfaces. In different
domains of the body, different glycoproteins act to unite cells. For example, nerve cells
recognize and bind to one another via the glycoprotein N-CAM (nerve cell adhesion
molecule). N-CAM is also found on muscle cells indicating a role in the formation of
myoneural junctions. With cell-substratum adhesion, glycoproteins serve as cell surface
receptors for certain adhesion ligands that mediate and coordinate the interaction of cells.
Substrates with the appropriate receptor will bind to the cell related to that receptor. For
example, a substrate containing the glycoprotein fibronectin will be recognized and adhered
to by fibroblasts. The fibroblasts will then secrete adhesion molecules and continue to
spread, producing a pericellular matrix.

Hormones: There are many glycoproteins that function as hormones such as human
chorionic gonadotropin (HCG), which is present in human pregnancy urine. Another
example is erythropoietin, which regulates erythrocyte production.

Enzymes: Glycoprotein enzymes are of three types. These are oxidoreductases, transferases,
and hydrolases. Majority of fungal enzymes are glycosylated.

Carriers: Glycoproteins can bind to certain molecules and serve as vehicles of transport.
They can bind to vitamins, hormones, cations, and other substances.

Inhibitors: Many glycoproteins in blood plasma have shown antiproteolytic activity. For
example, the glycoprotein a1-antichymotrypsin inhibits chymotrypsin.

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Defense: In beetles pygidial glands secrete a glycoprotein disinfecting paste that covers the
body and hardens. This shell provides protection against attack by bacteria and fungi
(Gottschalk).

Vision: In bovine visual pigment a glycoprotein forms the outer membranes of retinal rods.

Immunological: The interaction of blood group substances with antibodies is determined

by the glycoproteins on erythrocytes. Adding or removing just one monosaccharide from a
blood group structure, the antigenicity and therefore a person's blood type can be altered.
Many immunoglobulins are actually glycoproteins. Soluble immune mediators such as
helper, suppressor, and activator cell have been shown to bind to glycoproteins found on the
surface of their target cells. B and T cells contain surface glycoproteins that attract bacteria
to these sites and bind them. In much the same manner, glycoproteins can direct
phagocytosis. Because the HIV virus recognizes the receptor protein CD4, it binds to helper
T cells that contain it.

Table: Functions of glycoproteins

Function Glycoproteins
Structural molecule Collagens
Lubricant and protective agent Mucins
Transport molecule Transferrin, ceruloplasmin
Immunologic molecule Immunoglobins histocompatibility antigens
Chorionic gonadotropin thyroid-stimulating hormone
Hormone
(TSH)
Various, e.g. alkaline phosphatase, cellulases, xylanases,
Enzyme
amylases
Various proteins involved in cell-cell (sperm-oocyte),
Cell attachment-recognition site
virus-cell, bacterium-cell, and hormone cell interactions
Interact with specific
Lectins, selectins (cell adhesion lectins), antibodies
carbohydrates
Receptor Various proteins involved in hormone and drug action
Affect folding of certain proteins Calnexin, Calreticuluin
Regulation of development Notch and its analogs, key proteins in development
Specific glycoproteins on the surface membranes of
Homostasis and thrmbosis
platelets

Other specialized functions

As an antifreeze: The blood serums of Antarctic fishes freeze at -2°C, which is
approximately 1°C below the melting points of their serums. This thermal hysteresis is due
to the influence of some serum glycoproteins designated as antifreeze glycoproteins. They
were first discovered by Arthur L. DeVries in the 1960's The temperatures of freezing and
melting of aqueous solutions of the purified glycoproteins suggest that this thermal
hysteresis results from the adsorption of the glycoprotein molecule onto the surface of ice

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crystals. Antifreeze proteins are found in some fish, insects and plants. They bind to ice
crystals and prevent them from growing to a size where they would damage the host.
Specific hydrogen bonds form on the surface where protein meets ice and inhibits crystal
growth. The antifreeze molecules accumulate at the interface between ice and water, not at
the interface between ice and a vacuum. So it is hypothesised that a hydrophobic reaction
between the protein and the neighboring water prevents the water from forming ice crystals.

As an anticancer agent: Normal Gc protein (also called vitamin D binding protein), an

abundant glyco-protein found in human blood serum, becomes the molecular switch to
activate macrophages when it is converted to its active form, called Gc macrophage
activating factor (Gc-MAF). Gc protein is normally activated by conversion to Gc-MAF
with the help of the B and T cells (bone marrow-made and thymus gland-made white blood
cells). Cancer cells secrete an enzyme known as alpha-N-acetylgalactosaminidase (also
called Nagalase) that completely blocks conversion of Gc protein to Gc-MAF, preventing
tumor-cell killing by the macrophages. This is the way cancer cells escape detection and
destruction, by disengaging the human immune system. This also leaves cancer patients
prone to infections and many then succumb to pneumonia or other infections. The once-
weekly injection of minute amounts of Gc-MAF, just 100 nanograms (billionths of a gram),
activate macrophages and allow the immune system to pursue cancer cells with vigor,
sufficient to produce total long-term cures in humans.

In protein folding: Glycoproteins also play important roles in mediating proper folding of
proteins in the ER, which accounts for the observations that glycan addition to proteins in
the ER is a cotranslational event. When inhibitors of ER glycosylation are added to cells,
protein misfolding and aggregation are observed. The extent of misfolding depends on the
particular protein and particular glycosylation sites with the protein. The polar CHO
residues help promote solubility of folding intermediates, similar to the effects of many
chaperone proteins. Some of the typical sugars found frequently in eukaryotic glycoproteins
which assist in protein folding as also imparts solubility to the proteins include the
following.

Sugar Type Abbreviation

Galactose Hexose Gal
Glucose Hexose Glc
Mannose Hexose Man
N-Acetylneuraminic acid Sialic acid (nine C atoms) NeuAc
Fucose Deoxyhexose Fuc
N-Acetylgalactosamine Aminohexase GalNAc
N-Acetylglucosamine Aminohexase GlcNac
Xylose Pentose Xyl

The glycan moieties of the folding glycoprotein also lead to binding of the protein to lectins
in the ER, which serve as molecular chaperones. The most studied of these chaperones are
involved in the calnexin-calreticulin cycle, and facilitate correct disulfide bond formation in
the protein. After two glucose residues are removed by glucosidase I and II, the
monoglucosylated protein binds to calnexin (CNX) and/or calreticulin (CRT), two

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homologous ER lectins specific for monoglucosylated proteins. Once bound, another
protein, ERp57, a molecular chaperone with a disulfide bond interacts with the protein.
This protein has protein disulfide isomerase activity. If a glycoprotein has not folded
completely, it is recognized by a glycoprotein glucosyltransferase, which adds glucose to it.
This then promotes reentry into the calnexin/calreticulin cycle. Ideally, unfolded or
misfolded proteins would be targeted from degradation and elimination from cells. The ER
has evolved a system to accomplish this. Since folding occurs in the ER, to prevent
misfolding and aggregation, the ER also contains chaperones and folding catalysts. Stress
(such as through heat shock) stimulates ER chaperone activity. As a final defense
mechanism, unfolded or aberrantly-folded proteins are degraded by the cytoplasmic
proteasome complex. Nonnative forms of some proteins that "escape" this surveillance
system can accumulate and result in disease (for example neurodegenerative diseases like
Alzheimers and Parkinson's disease).

Synthesis & Regulation

Regulation and control of glycoproteins is not as straightforward as some might think. To
understand regulation in glycoproteins, the enzymes that are involved in the biosynthesis
pathway of these molecules are monitored. Control of glycoproteins can be seen through
biosynthesis and degradation.

Synthesis: The protein part of the glycoprotein is formed at the ribosomes, where all
proteins are synthesized on template represented by RNA and DNA. As a result, its
structure can change only through the mutation of the genetic material of the cell. On the
other hand, the carbohydrate component of a glycoprotein is not a product of the ribosome;
it is synthesized somewhere in the cytoplasm, the exact site of synthesis has not been
established. Since it is not directly genetically controlled, the oligosaccharide part shows a
much greater variation.

In contrast with O-linked glycoproteins, where oligosaccharide assemble occurs on the

polypeptide chain, N-linked glycoproteins assemble their oligosaccharide portions on a lipid
linked intermediate, dolichol phosphate. The first step in oligosaccharide synthesis is the
formation of that intermediate. In subsequent steps, sugars, the first being always N-
acetylglucosamine (GlcNAc), are chain-like connected to dolichol phosphate. One more
GlcNAc and three more mannose sugars are linked to the first GlcNAc to form the typical
core of N-linked glycoproteins. Addition of any other sugar can be in any possible
combination, according to the desired resulting functions. The specificity of the enzymes is
very important in the synthesis process. Every sugar added, is catalyzed by a different
enzyme. These group of enzymes are called glycosyltransferases. The first addition of
GlcNAc to dolichol phosphate is catalyzed by the specific enzyme that cleave peptide
bonds, and glycosidases (e.g example), enzymes that remove sugars one at a time from the
end of an oligosaccharide chain. Both of these groups are contained in lysozomes. The
lysosome attaches to a phagocyte, which has engulfed a substance that needs to be broken
down, and releases its enzymes in it. Next, these enzymes begin their catalytic action. In
degradation, ad in synthesis, the enzymes involved are very specific. After the glycoprotein
is broken down, its amino acid and sugar components are either metabolized or can be used
in the formation of another glycoprotein. Enzymatic degradation can provide much
information about the structure of the oligosaccharide chains, as well as about the
carbohydrate peptide linkage. For example, if a glycoprotein is treated with mannosidase
(removes mannose), and mannose is released, one can conclude that mannose residues were
located at the periphery of the molecule since glycosidases remove sugars from the end of

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the oligosaccharide chain. Regulation and control is the organism's ultimate tool to monitor
and adjust the production or degradation of different molecules.

Glycobiology and Glycomics

Our understanding of the synthesis and structure of glycan portions of glycoproteins has
lagged behind our understanding of protein and nucleic acid structure and synthesis.
Several reasons account for this:
• Carbohydrates are much more complex with more functional groups per carbon and
with a much larger number of stereocenters, making chemical synthesis and
structure determination more difficult.
• Carbohydrate chain synthesis is not directed by a template as is the synthesis of
DNA, RNA, and proteins
• Synthesis is spread over two different organelles, and which allows great
heterogeneity in main chain and branch chain synthesis, which provides
heterogeneous samples for analysis

New techniques in analysis and synthesis of carbohydrate analogs and inhibitors of enzymes
involved in CHO synthesis and degradation, as well as in genetic manipulations of gene for
these enzymes, are revolutionizing our understanding of the function of carbohydrate
groups on lipids and proteins. New methods to synthesize glycoproteins using recombinant
DNA technology have been developed that allow synthesis of therapeutic human
glycoproteins in yeast. Although they share many of the same synthetic steps, yeast
glycoproteins are enriched in the high-mannose type, making them targets of the human
immune system. Human and yeast glycoproteins synthesis produce the same mannose core
in the ER. However, differences in synthesis occur in the Golgi. Human Golgi contain a-
mannosidases I and II, which remove all but 3 Man residues from the final product. In
yeast, however, these mannosidases appear to be missing so more Man residues are added
(as many as 100). Human proteins made in yeast, therefore, contain many Man residues,
which are recognized by the human immune system. Mutants of the yeast Pichia pastoris
that localized glycoprotein synthesis proteins for mannosidase I and II, as well as other
human glycoprotein synthesis genes, to the correct intracellular location while inactivating
normal yeast gene, resulted in the production of human glycoproteins with the correct CHO
structure in yeast. This may prove to have widespread use in the production of therapeutic
human proteins

Examples
1. Glycophorin A, a glycoprotein that spans the plasma membrane ("Lipid bilayer") of
human red blood cells. Each RBC has some 500,000 copies of the molecule embedded in its
plasma membrane. Fifteen carbohydrate chains are "O-linked" to serine (Ser) and threonine
(Thr) residues. One carbohydrate chain is "N-linked" to the asparagine (Asn) at position 26
(Fig. 59).

There are two polymorphic versions of glycophorin A, which differ only at residues 1 and
5, occur in humans. These give rise to the MN blood groups.

Glycophorin A is the most important attachment site by which the parasite Plasmodium
falciparum invades human red blood cells.

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 Fig. 59: Glycophorin

2. Lectins – These are sugar-binding proteins, which are highly specific for their sugar
moieties. Lectins are basically non-enzymic in action and non-immune in origin. Lectins
occur ubiquitously in nature. They may bind to a soluble carbohydrate or to a carbohydrate
moiety that is a part of a glycoprotein or glycolipid. They typically agglutinate certain
animal cells and/or precipitate glycoconjugates. They influence the biological recognition
phenomena involving cells and proteins. For example, some bacteria use lectins to attach
themselves to the cells of the host organism during infection.

Biological function: While the function of lectins in plants is believed to be the binding of
glycoproteins on the surface of parasitic cells, their role in animals also includes the binding
of soluble extracellular and intercellular glycoproteins. For example, lectins found on the
surface of mammalian liver cells specifically recognize galactose residues. It is believed that
these cell-surface receptors are responsible for the removal of certain glycoproteins from the
circulatory system. Another example is the mannose-6-phosphate receptor that recognizes
hydrolytic enzymes containing this residue and subsequently targets these proteins for
delivery to the lysosomes. (one defect in this particular system is known as I-cell disease.)
Lectins serve many different biological functions from the regulation of cell adhesion to
glycoprotein synthesis and the control of protein levels in the blood. Lectins are also known
to play important roles in the immune system by recognizing carbohydrates that are found
exclusively on pathogens, or that are inaccessible on host cells. Examples are the lectin
complement activation pathway and Mannose binding lectin.

The function of lectins in plants is still uncertain. Once thought to be necessary for rhizobia
binding, this proposed function was ruled out through lectin-knockout transgene studies.
The large concentration of lectins in plant seeds decreases with growth, and suggests a role
in plant germination and perhaps in the seed's survival itself.

3. Mucins – Mucins are secreted in the mucus of the respiratory and digestive tracts. The
sugars attached to mucins give them considerable water-holding capacity and also make
them resistant to proteolysis by digestive enzymes. Glycoproteins are important for immune
cell recognition, especially in mammals. Examples of glycoproteins in the immune system
are:

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 • Molecules such as antibodies (immunoglobulins), which interact directly with
antigens
• Molecules of the major histocompatibility complex (or MHC), which are expressed
on the surface of cells and interact with T-cells as part of the adaptive immune
response.

Other examples of glycoproteins include:

• Components of the zona pellucida, which surrounds the oocyte, and is important for
sperm-egg interaction.
• Structural glycoproteins, which occur in connective tissue. These help bind together
the fibers, cells, and ground substance of connective tissue. They may also help
components of the tissue bind to inorganic substances, such as calcium in bone.
• Enzymes, immunoglobulins etc. are glycoproteins with various applications.

Proteoglycans
Proteoglycans represent a special class of glycoproteins that are heavily glycosylated. They
consist of a core protein with one or more covalently attached glycosaminoglycan chain(s).
These glycosaminoglycan (GAG) chains are long, linear carbohydrate polymers that are
negatively charged under physiological conditions, due to the occurrence of sulphate and
uronic acid groups (Fig. 60). Proteoglycans can be categorised depending upon the nature of
their glycosaminoglycan chains. These chains may be:
• chondroitin sulfate and dermatan sulfate
• heparin and heparan sulfate
• keratan sulfate
(These have been described in derivatives of polysaccharides part earlier.)

Fig. 60: Structure of proteoglycan

Proteoglycans can also be categorized by size. Examples of large proteoglycans are

aggrecan, the major proteoglycan in cartilage, and versican, present in many adult tissues
including blood vessels and skin. The small leucine rich repeat proteoglycans (SLRPs)
include decorin, biglycan, fibromodulin and lumican.

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Synthesis: The protein component of proteoglycans is synthesized by ribosomes and
translocated into the lumen of the rough endoplasmic reticulum. Glycosylation of the
proteoglycan occurs in the Golgi apparatus in multiple enzymatic steps. First a special link
tetrasaccharide is attached to a serine side chain on the core protein to serve as a primer for
polysaccharide growth. Then sugars are added one at the time by glycosyl transferase. The
completed proteoglycan is then exported in secretory vesicles to the extracellular matrix of
the cell.

Function: Proteoglycans are a major component of the animal extracellular matrix, the
'filler' substance existing between cells in an organism. Here they form large complexes,
both to other proteoglycans, to hyaluronan and to fibrous matrix proteins (such as collagen).
They are involved in binding cations (such as sodium, potassium and calcium) and water,
and also regulating the movement of molecules through the matrix. Evidences shows that
they can affect the activity and stability of proteins and signalling molecules within the
matrix. Individual functions of proteoglycans can be attributed to either the protein core or
the attached GAG chain.

Proteoglycans and disease: An inability to break down proteoglycans is characteristic of a

group of genetic disorders, called mucopolysaccharidoses. The inactivity of specific
lysozomal enzymes that normally degrade glycosaminoglycans leads to the accumulation of
proteoglycans within cells. This leads to a variety of disease symptoms, depending upon the
type of proteoglycan that is not degraded.

Structure of proteo glycans

Glycoforms are types of proteins (isoforms) with specific type of glycoprotein attached to
them by either posttranslational or cotranslational modifications. In other words, two
proteins would be of the same glycoform if they carried the same glycoprotein. Glycoform
is defined as a subunit of molecules with identical polypeptide sequences but with different
glycans present at the sites of glycosylation. It is very important to analyze the glycoform,
because different glycoforms of the same glycoprotein have different biological properties.
It has been estimated, for example, that recombinant tissue plasminogen activator (rtPA)
may contain as many as 11,500 different glycoforms. One interesting example appears to be
Glycodelin, a human secreted glycoprotein that appears in a small number of glycoforms,
exhibits diverse biological activities, such as in contraception and immunosuppression.
Moreover, different tissue-specific glycoforms appear to mediate diverse functions. Quite
unusually, the glycodelin N-linked glycans differ between the male and female glycoforms.
The fact that these glycans are fundamental for exerting the physiological activities of the
different glycoforms makes them an interesting target for glycobiology research.

Conformation of polysaccharides
Conformation of the polysaccharides gives the idea of three-dimensional orientation of a
specific polysaccharide in space and the orientation of the glycosidic groups about
projections of sugar moieties in the chain.

A. Three-dimensional orientation
In order to completely describe the three dimensional orientation of a specific
polysaccharide in space, we need to know the following general notations.

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Direction of Numbering: The chain is numbered from the reducing glycose residue to the
non-reducing glycosyl group. Thus i refers to a particular saccharide unit in the polymer
chain, (i - 1) to the adjacent unit in the direction away from the non-reducing end and (i + 1)
in the direction of the non-reducing end. This direction of numbering is chosen so that gain
or loss of a residue at the non-reducing end by transfer of a glycosyl group does not change
the numbering of every unit in the chain. Some polysaccharides lack reducing end groups
and are initiated by formation of a glycosidic linkage, e.g. to O1 of another sugar, to an
alditol or to an alcohol. For these polysaccharides the residue forming this glycosidic
linkage is regarded as the first member of the chain.

Monomeric unit: The monomeric unit is the monosaccharide. The oxygen of the glycosidic
bond is part of the residue glycosylated. Since its position is of importance in specifying the
unit, the torsion angle at the glycosidic bond is included in the characteristics of the sugar
residue.

Atomic numbering: The notation used conforms with that being proposed for specifying
polynucleotide conformation. Atoms are thus designated C3, O2, H4, etc. The hydrogen
atoms of a methylene group may be distinguished by an additional number, e.g. H61 and
H62. When it is necessary to indicate the particular saccharide unit its number may be
added in parenthesis, e.g. O3(i ), C4(i+1), H61(i-1) (Fig. 61).

Fig. 61: Atomic numbering

Notation for atomic numbering of (A) a hexopyranose and (B) a hexofuranose unit

Interatomic distance: In tabulating interatomic distances, non-bonded atoms are

represented with a single dot between them, e.g. O2.C3, and covalent bonds are represented
by hyphens between atoms, e.g. C1-C2. Hydrogen bonds are denoted by dotted lines
whether or not the hydrogen is shown, e.g. O6...O5 or O6-H...O5. The atom donating the
hydrogen is written first if specification is possible.

Bond Angles: The bond angle included between three atoms A-B-C is written 'tau' as τ (A,
B, C). If there is no ambiguity because the central atom is bivalent, this may be abbreviated
to τ (B). The angle at the ring-oxygen atom of an aldopyranose may thus be written as τ
(C1, O5, C5) or τ (O5).

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Ring Shape: The ring shape of a sugar residue can be defined either by the endocyclic
torsion angles or in terms of the notation for conformations of five and six-membered
monosaccharide rings.

Endocyclic Torsion Angles: To provide a complete description of the sugar ring

conformation, it is necessary to specify the endocyclic torsion angles about at least some of
the ring bonds, in addition to the bond lengths and bond angles. These ring torsion angles,
denoted by the symbol υ (nu), can be described by adding a number indicating the bond as
listed in. The torsion angle of the atoms A-B-C-D is the angle between A-B and C-D in a
projection of the four atoms on to a plane normal to B-C. It is considered positive when the
bond to the front, viewed along the central bond, must be rotated clockwise to eclipse the
bond to the rear.

Conformation of Side Groups: A ring substituent of a pyranosidic sugar unit. e.g. a

hydroxyl group, may be designated as being axial or equatorial in a given conformation. For
the precise specification of the orientation of a polyatomic ring substituent, it is necessary to
specify the torsion angle about the exocyclic bond. The reference atom in the ring is the
carbon atom with the number one lower than that of the substituted carbon, unless
substitution is on the anomeric carbon, when the ring oxygen is the reference atom. The
reference atom in an exocyclic-CH2X group is X. The exocyclic torsion angle is denoted by
χ (chi), followed by the atoms to which it refers. e.g. (C1-C2-O2-H) or, if no ambiguity
arises, simply by χ2.

B. Orientation of the glycosidic groups

The structures are more precisely defined with repect to the following notations
corresponding to the orientation of the glycosidic groups.

Designation of Bonds: The glycosidic bonds are part of the backbone of the
polysaccharide. The glycosidic linkage is most easily described using the symbols for the
monomeric units and the locants together with the anomeric descriptor, e.g. in cellobiose:
Glc (i)(β 1→4) Glc (i-1). If a more detailed description is necessary, this can be given in the
form C1(i)-O4(i-1)-C4(i-1). (Fig. 62)

Fig. 62: Designation of bonds

Notation for the torsion angles specifying the orientation of glycosidic bonds for a pyranose
unit (A) varrying a ring hydroxyl that is glycosylated and (B) in which the glycosylated
hydroxyl group is on an exocyclic carbon. The limits of the i th residue are indicated by the
vertical dash lines. The residue number attached to φ, ψ and ω is conventionally that of the
glycosylating residue.

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Torsion Angles: Two torsion angles, φ (phi) and ψ (psi), are required to describe the
glycosidic bond from the i th unit to a carbon atom located in the ring of the (i-1) th unit.
The angle φ about the bond from the anomeric carbon to the oxygen that joins the two
residues is specified using the ring oxygen as a reference atom. The torsion angle ψ about
the bond from the glycosylated oxygen of the (i-1) th residue to a carbon of this residue uses
the carbon atom one lower in numbering as a reference atom. Since this angle relates to the
mode of attachment of the ith residue, it may be designated ψ (i). When the glycosidic bond
does not involve a carbon atom located in the ring, but rather on a side chain, the angle ω
(omega), around the next C-C bond is also of importance. For a 1→6 linked
aldohexopyranose, this angle is the exocyclic angle c5 of the (i-1) th residue. Nevertheless it
may be designated as ω (i ) since it refers to attachment of the i th residue. The torsion angle
is that of the atoms OX-CX-C -C . where X is the number of the carbon atom whose
hydroxyl group if glycosylated.

Helix Characteristics: In the description of helices or helical segments the following

symbols may be used:
n = number of repeating units per turn
h = unit height (translation per repeating unit along the helix axis)
t = 360deg./n = unit twist (angle of rotation per repeating unit about the helix axis)
p = pitch height of helix = n . h.
Note. The repeating unit in a homopolysaccharide is a sugar residue. Heteropolysaccharides
may possess repeating units of two or more residues.

Rare sugars
Rare sugars are defined by the International Society of Rare Sugars (ISRS) as
monosaccharides and their derivatives that are rare in nature. They are hardly available for
research purposes because of their expensiveness. "Izumoring", a structural framework
containing all 34 six-carbon monosaccharides linked by enzymatic reactions, has been
proposed following the discovery of a key enzyme that converts abundantly occurring
monosaccharides in nature into rare sugars. This has made possible the mass production of
rare sugars from inexpensive sugars such as D-glucose or D-fructose.

Rare Sugars are mostly used in pharmaceuticals as precursors for a wide variety of
carbohydrate-based drugs. These include nucleoside analogues, which are used in antiviral
applications such as HIV, HBV and HCV. Another important class of compounds is
complex oligosaccharides and olignonucleotides, which may be used as anti-inflammatory
or anti-cancer agents, as well as in highly specific chronic pain relievers. They are also
being used as precursors in the production of flavor chemicals, such as natural furanones
and Maillard reaction savoury flavours. Furthermore, some of the rare sugars products have
applications as nutraceuticals or they may be used in high-end cosmetic products. They are
enlisted under the D & L series depending on their chirality.

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 D series L series
D- Sorbose L- Sorbose
L- Fructose
D- Psicose L- Psicose
D- Tagatose L- Tagatose
D- Gulose D- Gulitol L- Gulose L- Gulitol
D- Idose D- Iditol L- Idose L- Iditol
D- Talose D- Talitol L- Talose L- Talitol
D- Galactitol L- Galactose L- Galactitol
D- Mannitol L- Mannose L- Mannitol
D- Glucitol L- Glucose L- Glucitol
D- Altrose D- Altritol L- Altrose L- Altritol
D- Allose D- Allitol L- Allose L- Allitol

Carbohydrate assays
Carbohydrates can be assayed using the methods below

Molisch Test (Carbohydrates): The Molisch test is a general test for the presence of
carbohydrates. Molisch reagent is a solution of alpha-naphthol in 95% ethanol. This test is
useful for identifying any compound, which can be dehydrated to furfural or
hydroxymethylfurfural in the presence of H2SO4. Furfural is derived from the dehydration
of pentoses and pentosans, while hydroxymethylfurfural is produced from hexoses and
hexosans. Oligosaccharides and polysaccharides are hydrolyzed to yield their repeating
monomers by the acid. The alpha-naphthol reacts with the cyclic aldehydes to form purple
colored condensation products. Although this test will detect compounds other than
carbohydrates (i.e. glycoproteins), a negative result indicates the ABSENCE of
carbohydrates.
[Prepare Molisch's reagent by dissolving 0.5 g reagent grade α-naphthol in10 mL of 95%
ethanol. Store the reagent, protected from light, at room temperature. To test for
carbohydrates, add 0.02 mL of the reagent to 1 mL of 0.1% carbohydrate (1 mg/mL)
solution in a small test tube. After mixing, tilt the tube and carefully add without mixing,
0.5 mL of concentrated sulfuric acid by pouring it down the side of the tube. A red-violet
layer at the interface between the acid (bottom) and aqueous (upper) layers is a positive test
for carbohydrates]

Bial's Test (Pentoses): Bial's reagent uses orcinol, HCl, and FeCl3. Orcinol forms colored
condensation products with furfural generated by the dehydration of pentoses and
pentosans. It is necessary to keep the concentration of the sugar solution around 0.2M by
appropriate dilutions in this test.
[Prepare Bial's reagent by dissolving 0.3 g reagent-grade orcinol and 0.05 g ferric chloride
in 100 mL of concentrated (12 M) HCl. Store the reagent protected from light. To test for
pentoses, add 0.05 mL of 0.1% carbohydrate solution in water to 1 mL of Bial's reagent, and
heat the solution in a boiling water bath for 2 minutes. * A blue-green color indicates

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pentoses or nucleotides containing pentoses; a yellow-green color indicates hexoses, and
disaccharides are yellow.]

Resorcinol (Seliwanoff's) Test (Ketohexoses): Seliwanoff's reagent contains resorcinol in

6 M hydrochloric acid. Hexoses undergo dehydration when heated in this reagent to form
hydroxymethylfurfural, which condenses with resorcinol to give a red product. Ketohexoses
(such as fructose) and disaccharides containing a ketohexose (such as sucrose) form a
cherry-red condensation product. Other sugars may produce yellow to faint pink colors.
[Prepare Seliwanoff's reagent by dissolving 0.05 g of reagent-grade resorcinol in 100 mL of
3 M HCl. Store protected from light. To test for ketohexoses, add 0.1 mL of a 1%
carbohydrate solution in water to 1 mL of the reagent, and heat the solution in a boiling
water bath for 5 minutes.* A deep red colored precipitate within 5 minute indicates
ketohexoses. Sucrose gives a positive ketohexose test because of partial hydrolysis to
glucose and fructose. Other sugars give a red color upon prolonged heating.]

Benedict's Test (Reducing sugars): Alkaline solutions of copper are reduced by sugars
having a free aldehyde or ketone group, with the formation of colored cuprous oxide.
Benedict's solution is composed of copper sulfate, sodium carbonate, and sodium citrate
(pH 10.5). The citrate will form soluble complex ions with Cu++, preventing the
precipitation of CuCO3 in alkaline solutions.
[Dissolve 1.73 g trisodium citrate (dihydrate) and 1.0 g anhydrous sodium carbonate in 8
mL of warm distil H2O (Solution A). Dissolve copper sulfate (pentahydrate) (1.73 g)
separately in 20 mL of distil H2O (Solution B). Immediately before using, prepare
Benedict's reagent by mixing 0.8 mL of Solution A with 0.2 mL of Solution B. To test for
reducing sugars, add 0.2 mL of a 1% carbohydrate solution to 1 mL of Benedict's reagent
and heat in a boiling water bath for 5 minutes. A brick-red precipitate indicates a positive
test for reducing sugars.]

Barfoed's Test (Reducing monosaccharides): This reaction detects reducing

monosaccharides in the presence of disaccharides. This reagent uses copper ions to detect
reducing sugars in an acidic solution. Barfoed's reagent is copper acetate in dilute acetic
acid (pH 4.6). The color changes are the same as that in Benedict's test.
[Prepare Barfoed's reagent by dissolving 0.66 g cupric acetate (monohydrate) and 0.18 mL
glacial acetic acid in 10 mL of distil H2O. To test for reducing monosaccharides, add 0.3
mL of 1% carbohydrate solution to 0.6 mL of Barfoed's reagent and heat in a boiling-water
bath for 5 minutes,* then cool to room temperature. A copious amount of brick-red
precipitate indicates a reducing monosaccharide. Some hydrolysis of disaccharides may
lead to trace precipitates.]

Iodine Test (Starch/Amylose): The use of Lugol's iodine reagent (IKI) is useful to
distinguish starch and glycogen from other polysaccharides. Lugol's iodine yields a blue-
black color in the presence of starch. Glycogen reacts with Lugol's reagent to give a brown-
blue color. Other polysaccharides and monosaccharides yield no color change; the test
solution remains the characteristic brown-yellow of the reagent. It is thought that starch and
glycogen form helical coils. Iodine atoms can then fit into the helices to form a starch-
iodine or glycogen-iodine complex. Starch in the form of amylose and amylopectin has less
branches than glycogen. This means that the helices of starch are longer than glycogen,
therefore binding more iodine atoms. The result is that the color produced by a starch-iodine
complex is more intense than that obtained with a glycogen-iodine complex.
[A few drops of 0.01 M iodine in 0.12 M KI are added to a 1% solution of the carbohydrate
in question. The immediate formation of a vivid blue color indicates amylose.]

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Glucose Test (GOD-PAP): This method involves colorimetric determination of glucose by
employing two successive enzymatic reactions; Glucose is first oxidized to gluconic acid by
glucose oxidase with the concomitant production of hydrogen peroxide. This is
subsequently converted to a quinone by peroxidase. The red quinone generated is then
measured colorimetrically to determine the amount of glucose present initially
[Prepare the assay reagent by dissolving a capsule (Sigma 510-6) containing 500 units of
glucose oxidase and 100 units of horseradish peroxidase with buffer salts in 100 mL of
distilled water, and adding 1.6 mL of 2.5 mg/mL o-dianisidine dihydrochloride (Sigma 510-
50). Combine 0.1 mL of a sample solution containing 0.25 to 3 mg/mL of carbohydrate
with 1 mL of the assay reagent. A brown color within 30 minutes indicates glucose. * Heat
in a fume hood.
Precaution:
1. Use a glass Pasteur pipette to add the H2SO4.
2. Do not use a mechanical pipettor with concentrated acids.
Reminder: Always add acid to water.]

Mucic Acid Test for Galactose: Oxidation of most monosaccharides by nitric acid yields
soluble dicarboxylic acids. However, oxidation of galactose yields an insoluble mucic acid.
Lactose also yields a mucic acid, due to hydrolysis of the glycosidic linkage between its
glucose and galactose subunits.

Summary of carbohydrate assay

Sugar Molisch Bial (φ)2NH G.O.§ Resorcinol Benedict Barfoed Iodine

Ribose + (r/v) (bl/gr) - - - +(r ppt) + (r ppt) -
DNA* + (r/v) (y) (bl/gr) - - +(r ppt) + (r ppt) -
Fructose + (r/v) (y/gr) - - + (r) +(r ppt) + (r ppt) -
Galactose + (r/v) (y/gr) - - - +(r ppt) + (r ppt) -
Glucose + (r/v) (y/gr) - +(br) - +(r ppt) + (r ppt) -
Sucrose + (r/v) (y) - - + (r) - - -
Lactose + (r/v) (y) - - - +(r ppt) - -
Maltose + (r/v) (y) - - - +(r ppt) - -
Amylose + (r/v) (y) - - - - - + (bl)
Glycogen + (r/v) (y) - - - - - + (br)
+ = positive; - = negative; bl = blue; br = brown; gr = green; r = red; v = violet; y = yellow; ppt = precipitate
* To test for DNA, the sample is first hydrolyzed in 10% trichloroacetic acid at 95°C for 10 minutes then
diluted with two volumes of water before assaying with the diphenylamine test.
§
GO = glucose oxidase

Suggested Reading
1. Morrison, R.T. & Boyd, R.N. (1992) Organic Chemistry, 6th edn, Benjamin Cummings, San
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reactions of carbohydrates.
2. Pigman, W. & Horton, D. (Eds) (1970, 1972, 1980) the Carbohydrates: Chemistry and Biochemistry,
Vols IA, IB, IIA, and IIB, Academic Press, Inc., New York. Comprehensive treatise on carbohydrate
chemistry.
3. Fukuda, M. & Hindsgaul, O. (1994) Molecular Glycobiology, IRL Press at Oxford University Press,
Inc., New York. Thorough, advanced treatment of the chemistry and biology of cell surface

92
 carbohydrates. Good chapters on lectins, carbohydrate recognition in cell-cell interactions, and
chemical synthesis of oligosaccharides.
4. David L. Nelson. Michael M. Cox. Principles of Biochemistry; 4th edition, 2006, W. H. Freeman and
Company. NY. 2006.
5. KleinKauf . Dohren. Jaenicke. The roots of modern biochemistry. Waller De Gruyter Berlin. NY.
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6. Stryer Lubert. Biochemistry. 4th edition. 1995. W. H. Freeman and Company. NY.
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Oxford,
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Inc. New York.
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16. www.wikiepedia.com
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Jean Spence, Edward Nudelman, Steven B Levery, Thayer White, John M Neveu, William S Lane,
Yves Bourne, Martin L Olsson, Bernard Henrissat & Henrik Clausen. Bacterial glycosidases for the
production of universal red blood cells; 2007 Nature biotechnology; Edward Nudelman. Nature
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18. Pei Zhang, Scott Snyder, Peter Feng, Parastoo Azadi, Shusheng Zhang, Silvia Bulgheresi, Kenneth E.
Sanderson, Johnny He, John Klena, and Tie Chen; Role of N-Acetylglucosamine within Core
Lipopolysaccharide of Several Species of Gram-Negative Bacteria in Targeting the DC-SIGN
(CD209). The Journal of Immunology, 177: 4002-4011(2006).
19. Francisco J. Alvarez* and James B. Konopka. Identification of an N-Acetylglucosamine Transporter
That Mediates Hyphal Induction in Candida albicans. Mol Biol Cell. March; 18(3): 965–975. (2007)
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M Pfender, John F Morrison, Jeffrey Ockuly, Carl Stafstrom, Thomas Sutula & Avtar Roopra, "2-
Deoxy-D-glucose reduces epilepsy progression by NRSF-CtBP–dependent metabolic regulation of
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