IBB UNIVERSITY BIOCHEM LECTURE

IBB UNIVERSITY, LAPAI
2016/2017 ACADEMIC SESSION
BCH 201
General BiochemistryI
I. Introduction
II. Stereoisomerism
III. Carbohydrate Chemistry
IV. Lipid Chemistry
V. Protein and Amino Acid Chemistry
VI. Nucleic Acid Chemistry
VII. Enzymes, Vitamins and Coenzyme
Musa A. Dickson, PhD | Structure, Chemistry and Functions of Biomolecules 1

INTRODUCTION
Of the naturally occurring elements, 16 are known to be important constituents of living
systems. The important elements are:
C, H, O, N, P, S, K, Ca, Na, Cl, Mg, Fe, Cu, I, Mo, Zn
Distribution of the most important A Comparison of Elements Present in Non-living and

elements Living Matter
Earth (crust) Human body Percentage weight of
O 47.00% H 63.00% Element Earth (crust) Human body
Si 28.00% O 25.50% H 0.14 0.5
Al 7.90% C 9.50% C 0.03 18.5
Fe 4.50% N 1.4 5% O 46.6 65
Ca 3.50% Ca 0.31% N very little 3.3
Na 2.50% P 0.22% S 0.03 0.3
K 2.50% Cl 0.08 5% Na 2.8 0.2
Mg 2.20% K 0.06 5% Ca 3.6 1.5
Ti 0.46% S 0.05% Mg 2.1 0.1
H 0.22% Na 0.03% Si 27.7 negligible
C 0.19% Mg 0.01%
All important biological molecules contain carbon. All molecules that contain carbon are
called organic (except for CO2). Carbon has the unique ability to form a virtually infinite
number of compounds as a result of its capacity to make as many as four highly stable
covalent bonds (including single, double, and triple bonds) combined with ability to form
covalently linked C-C chains of unlimited extent.
The number of biological molecules is extremely large. However, the number of building
blocks used to make these molecules is surprisingly small. Most biological molecules have a
core made of carbon and hydrogen. Molecules differ in structure and function, in part,
because of different functional groups.
Biomolecules are the organic compounds which form the basis of life, i.e., they build up the
living system and responsible for their growth and maintenance.
The sequence that relates biomolecules to living organism is:

Biomolecules → Organelles → Cells → Tissues → Organs → Living organism

The molecules that form the building blocks of living organisms obey the same laws of
nature as all other “chemical molecules”. However, such molecules are different in a sense
that they have a function. They can be seen as highly efficient “tools” and/or “machines” or
as dedicated “building materials”. Certain biomolecules even have the ability to replicate
and repair themselves. As far as we know there are no biomolecules without function.
However, in a number of cases this function is not known. Many biological molecules form
complex and highly ordered structures. This order is maintained using energy from the
surrounding. The chemistry of such molecules is nevertheless an important basis for
understanding how biomolecules can fulfill their diverse functions. All biological phenomena
have a molecular and therefore a chemical basis.
The major classes of biological molecules that are important for all living things are
carbohydrates, lipids, proteins, and nucleic acids. Large biological molecules are called
macromolecules. Macromolecules are built by combining smaller building blocks into
polymers.
Examples of Biomolecules, their subunits and functions:

Macromolecules Sub units Function Examples
Proteins Elements- CHONS
Functional amino acids Catalysis, transport Heamoglobin
Structural amino acids Support Hair, silk
Carbohydrates Elements- CHO

Starch, Glycogen Glucose Energy storage potatoes, yam
Cellulose Glucose Cell walls Paper, strings
Chitin Modified glucose structural support crab shells
Nucleic Acids Elements- CHOP

DNA Nucleotides Encodes genes Chromosomes
Needed for gene
RNA Nucleotides Messenger RNA
expression
Lipids Elements- CHO

Fats Glycerol and fatty acids Energy storage Butter, corn oil, soap
Glycerol, fatty acids,
Phospholipids phosphate and polar R Cell membranes Lecithin
groups
carbon rings and non
Prostaglandins Chemical messengers Prostaglandin E
polar tails
Steroids Carbon rings Membranes, Hormones Cholesterol, oestrogen
Terpenes Long carbon chains pigments, structural Carotene, rubber

STEREOISOMERISM
ISOMERISM
Isomers are different compounds with the same molecular formula. Thus, isomerism is the
existence of two or more different compounds have the same molecular formula but,
different structural formula. Isomers have the same molecular formula, but different
structural formulas. Some organic and biochemical compounds may exist in different
isomeric forms. Many times, especially in biological systems, these different isomers have
different properties. The diversity of biomolecules and the many functional groups they
contain have increased their probability of occurring in an amazing number of isomers.
Isomers are classified into structural or constitutional or positional isomers, which occur
when atoms and groups are linked together in different ways; and stereo- or
configurational isomers, which occur when atoms and groups are connected in the same
way, yet having different arrangements in space.
Constitutional isomers:
 different IUPAC names;
 the same or different functional groups;
 different physical properties, so they are separable by physical techniques such as
distillation; and
 different chemical properties. They behave differently or give different products in
chemical reactions.
Structural isomerism occurs in biomolecules in a variety of forms; in carbohydrates the

pyran and furan ring structures and aldo- and keto- forms and in some carboxylic acids.

STEREOISOMERS
Stereoisomerism is the most important class of isomerism in biomolecules so far. And
almost all classes of biomolecules show stereoisomerism. Stereoisomers differ only in the
way atoms are oriented in space. A particular three-dimensional arrangement is called a
configuration. Thus, stereoisomers differ in configuration. Stereoisomers have identical
IUPAC names (except for a prefix like cis or trans). Because they differ only in the three
dimensional arrangement of atoms, stereoisomers always have the same functional
group(s).
Stereoisomers can be split up in accordance with the non-superimposability, into two

types; optical isomers (enantiomers, epimers, anomers) and geometric isomers
(diastereomers).
Stereoisomerism is found in carbohydrates in various forms; D and L isomers, α and β

anomers, and epimers. In lipids, it is found in the most important cis and trans forms, α and
β orientation especially in steroids. And in peptides and proteins only L isomer (L-
α-amino acids is found; this is true for humans but, in micro-organisms both D- and L-α-
amino acids are found.
The two most common types of isomers in biological systems are cis-trans isomers and
isomerism due to the presence of a chiral carbon.

Chirality
All substances have a mirror image however, what is important in chemistry is whether a
molecule is identical to or different from its mirror image. The presence of an asymmetric
or chiral carbon atom is sufficient to produce a “handed” molecule. Some molecules are like
hands. Left and right hands are mirror images of each other, but
they are not identical. If you try to mentally place one hand inside the other hand, you can
never superimpose either all the fingers, or the tops and palms. To superimpose an object
on its mirror image means to align all parts of the object with its mirror image. With
molecules, this means aligning all atoms and all bonds. If there is a chiral carbon atom
present, the mirror images are non-superimposable. Enantiomers are mirror images that
are not superimposable.
Other molecules are like socks. Two socks from a pair are mirror images that are
superimposable. One sock can fit inside another, aligning toes and heels, and tops and
bottoms. A sock and its mirror image are identical. A molecule (or object) that is
superimposable on its mirror image is said to be achiral. Achiral molecules usually contain a
plane of symmetry but chiral molecules do not. A plane of symmetry is a mirror plane that
cuts a molecule in half, so that one half of the molecule is a reflection of the other half.
Chirality of a compound is its existence in two non-superimposable forms (i.e mirror

images), thus, a molecule (or object) that is not superimposable on its mirror image is said
to be chiral. In order to be chiral a compound must possess at least one asymmetric or
stereogenic centre (i.e a carbon atom bonded to four different groups). The majority of
biological molecules have one or more chiral carbon atoms and, for this reason, they are
chiral.
Chirality is very important to discuss because biomolecules for the most part chiral and the
different chiral forms differ from each other in two aspects: How they affect light and how

they interact with other chiral substances (usually only one chiral form will be biologically
active)
To determine how a particular form affects light, it is necessary to use plane polarized light,
in which all the light waves vibrate in the same plane. Chiral compounds have the ability to
rotate plane polarized light (PPL), and this property has been used historically to
differentiate between enantiomers; when an enantiomer turns the PPL to the right it is
called dextrorotatory and, when it turns it to the left it is called levorotatory and
designated as (+) and (-) respectively. The dextrorotatory and levorotatory forms are
stereoisomers and are optically active. When a solution contains equivalent amounts of the
two enantiomers, it is referred to as a racemic mixture.
Many stereochemical descriptors are found which has nothing to do with the optical
activity, as they only describe how different groups are distributed around the chiral centre
(e.g.. D and L, R and S, E and Z). Nowadays their importance has lessened somewhat with
the development of powerful NMR and chiral chromatographic methods.
Chirality in biological world has great significance, as it affects enzyme-substrate, antigen-

antibody, hormone-receptor interactions and hence; the biological activities attained
through them, this because these interactions are highly enantio-selective or stereo-
selective in the biological world. For example, thalidomide, which contains one such
stereogenic center, was used as a popular sedative and anti-nausea drug for pregnant
women in Europe and Great Britain from 1959–1962. Unfortunately thalidomide was sold as
a mixture of its two enantiomers, and each of these stereoisomers has a different biological
activity.
Although one enantiomer had the desired therapeutic effect, the other enantiomer was
responsible for thousands of catastrophic birth defects in children born to women who took
the drug during pregnancy.

Assignment:
1. Classify each pair of compounds as constitutional isomers or stereoisomers.
2. Draw the mirror image of each compound below. Label each molecule as chiral or
achiral.
3. Locate any stereogenic center in the given molecules. (Some compounds contain no
stereogenic centers.)
a. CH3CH2CH(Cl)CH2CH3
b. (CH3)3CH
c. CH3CH(OH)CH=CH2
d. CH3CH2CH2OH
e. (CH3)2CHCH2CH2CH(CH3)CH2CH3
f. CH3CH2CH(CH3)CH2CH2CH3
4. Locate the stereogenic centers in each biomolecule

CARBOHYDRATE CHEMISTRY
INTRODUCTION
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.
Each year, more than 100 billion metric tons of CO2 and H2O are by photosynthesis
converted into biopolymers such as cellulose, hemicelluloses, chitin, starch and lignin, all
carbohydrates. Thus, making carbohydrates by far the most abundant biomolecules
belonging to class of organic compounds, i.e., a single class of natural products, found in
living organisms on earth, in fact about two thirds of the annually renewable biomass, are
carbohydrates.
The carbohydrates are a group of naturally occurring carbonyl compounds (aldehydes or

ketones) that also contain several hydroxyl groups. The carbohydrates, often termed as
sugars or saccharides, are the ‘staff of life’ for most organisms. Based on chemical
constitution, the carbohydrates or saccharides are most simply defined as polyhydroxy
aldehydes or ketones and their derivatives. The name carbohydrate arises from the basic
molecular formula (CH2O)n, where n = 3 or more. (CH2O)n can be rewritten (C.H2O)n to
show that these substances are hydrates of carbon. Chemically, carbohydrates are
composed of carbon, hydrogen and oxygen and most of them have hydrogen and oxygen in
the ratio of 2:1 for each carbon.
More complex carbohydrates may contain nitrogen, phosphorus or sulphur in addition to

carbon, hydrogen and oxygen. They are a major form of stored energy in organisms, and
they are the metabolic precursors of virtually all other biomolecules. Conjugates of
carbohydrates with proteins and lipids perform a variety of functions, including recognition
events that are important in cell growth, transformation and other processes.
OCCURENCE
Carbohydrates are the single most abundant class of organic molecules found in nature,
they constitute more than 50 % of the total biochemical matter. Energy from the sun
captured by green plants, algae, and some bacteria during photosynthesis converts more
than 250 billion kilograms of CO2 into carbohydrates every day on earth. They are widely
distributed in plants, animals and microbes. Animals have no way of synthesizing
carbohydrates from carbon dioxide and rely on plants for their supply. The carbohydrates
are then converted into other organic materials by a variety of biosynthetic pathways.

Included in the category of carbohydrates are the sugars, the glycogens, the starches and
the celluloses. In addition, there are complex carbohydrates such as glycoproteins,
glycolipids, lipopolysaccharides, etc.
PHYSIOLOGICAL ROLE AND BIOLOGICAL IMPORTANCE

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 serve many
functions in the living organism. Some of their vital functions are:
Metabolic/Nutritional
1. Chief source of energy (4 kcal/g). The biological breakdown of carbohydrates (often
spoken of as "combustion") supplies the principal part of the energy that every
organism needs for various processes.
2. Reserve or storage forms of energy in plants (starch, inulin) and animals (glycogen).
3. Carbohydrate fibre in our meals helps to keep bowel function going smooth.
4. Carbohydrates add on to the taste and appearance of food item
Structural
5. Insoluble carbohydrate polymers serve as structural and protective elements in the
cell walls of of certain microorganisms (peptidoglycans), exoskeleton of some insects
and crustacea (chitin) and in plant cell wall (cellulose).
6. They form a major portion of the supporting tissue and in the connective tissues of
animals (mucopolysaccharides).
Communications
7. Glycosaminoglycans as polymers of derivatives of carbohydrates are of critical
importance in intercellular communication in organisms. They are involved in cell
recognition, contact inhibition and also have antigenic properties of blood group
substances.
8. Some carbohydrate polymers lubricate skeletal joints and participate in recognition
and adhesion between cells
Biosynthesis of other compounds

9. Carbohydates are source of carbon for biosynthesis of other compounds. Important
components of nucleic acids, co-enzymes and flavoproteins (for example, ribose).

CLASSIFICATION
Carbohydrates are called saccharides or, if they are relatively small, sugars. They can be
classified based on complexities, size, and functional groups.
Description Classes
Simple carbohydrates Complex carbohydrates (Disaccharides,

Complexity
(Monosaccharides) Oligosaccharides & Polysaccharides)
Triose Tetrose Pentose Hexose Heptose Octose Nonose

Size
(C3 Sugars) (C4 Sugars) (C5 Sugars) (C6 Sugars) (C7 Sugars) (C8 Sugars) (C9 Sugars)
Functional Aldose: sugars having an Ketose: sugars having a ketone

group aldehyde functional group functional group
Carbohydrates can be classified based on complexities into three main groups as: a)
Monosaccharides (and their derivatives), b) Oligosaccharides and c) Polysaccharides, based
on number of monomeric sugar units present.
Monosaccharides are the simplest sugars consisting of single polyhydroxy aldehyde or

ketone group that cannot be hydrolyzed into smaller units under reasonable mild
conditions. They serve as the building-blocks for the more complex sugars.
Oligosaccharides (Greek Oligo 'few') contain from two to ten monosaccharide units joined
through glycosidic linkage or bond. They are hydrolyzable into constituent monosaccharide
units.
Polysaccharides are polymers of monosaccharide units joined in long linear or branched

chains through glycosidic bonds. Hydrolysis of polysaccharides yields many units of
constituent monosaccharides. Polysaccharides have two major biological functions:
a) as a storage form of fuels and

b) as structural elements in living organisms.
MONOSACCHARIDES
The term ‘monosaccharide’ denotes a single sugar unit without glycosidic connection to
other such units. Chemically, monosaccharides are either polyhydroxyaldehydes or aldoses
(e.g., glucose) or polyhydroxyketones or ketoses (e.g., fructose). I.e. they contain a short
chain of carbon atoms with one carbonyl group, each of the remaining carbon atoms
bearing a hydroxyl group. The suffix –ose is often used in describing and naming carbohydrates.

Monosaccharides are also called as simple sugars and they have the empirical formula
(CH2O)n, where n=3 or larger number. Monosaccharides consist typically of three to seven
carbon atoms and are described either as aldoses or ketoses, depending on whether the
molecule contains an aldehyde functional group or a ketone functional group. If the
carbonyl group is an aldehyde (-CHO) the sugar is called as an aldose and if a ketone (C=O) it
is a ketose. Monosaccharides are classified according to the number of carbon atoms they
contain, e.g. trioses (three carbons), tetroses (four carbons), pentoses (five carbons),
hexoses (six carbons), heptoses (seven carbons) and octoses (eight carbons).
The simplest aldose is glyceraldehyde, and the simplest ketose is dihydroxyacetone. These
two simple sugars are termed trioses because they each contain three carbon atoms.
Glyceraldehyde is an aldotriose; dihydroxyacetone is a ketotriose. Each exists in two series,

ie., aldotetroses and ketotetroses; aldopentoses and ketopentoses; aldohexoses and
ketohexoses, etc. Of these monosaccharides, hexoses (both aldoses and ketoses) are the
most abundant. Glucose (aldohexose) is the most abundant monosaccharide; serves as the
major fuel for most organisms and the- basic building-block of the many oligo- and
polysaccharides. However, aldopentoses are important components of nucleic acids (for
example, ribose) and various polysaccharides (for example, xylose and arabinose). Trioses,
tetroses and heptoses are important intermediates in carbohydrate metabolism.
General Properties
Some of the general properties of monosaccharides are summarized below:
1. Monosaccharides are polyhydroxy aldehydes or ketones and their derivatives having

either a potentially free aldehyde or a ketone group.
2. Simplest form of carbohydrates which cannot be hydrolyzed to other sugar units
under reasonably mild chemical conditions.
3. Generally monosaccharides are white crystalline solids, insoluble in ether, sparingly
soluble in alcohol but readily soluble in water.

4. Most of them have a sweet taste and char when heated.
5. Those with potentially a free aldehydic or a ketonic group are able to reduce metal
ions under alkaline conditions. Hence, they are excellent reducing agents.
6. Amphoteric nature i.e., they are capable of reacting as weak acids or weak bases
with strong acids or alkalies to form salts.
Stereochemistry
All the monosaccharides except dihydroxyacetone contain one or more asymmetric carbon
atom(s). If a molecule has more than one asymmetric carbon atom, it can exist in 2 n
stereoisomeric forms, where 'n' represents the number of asymmetric carbon atoms
present. Thus, aldotrioses. aldotetroses. aldopentoses and aldohexoses have 1, 2,3 and 4
asymmetric (chiral) carbon atoms and exist in 2, 4, 8 and 16 stereoisomeric forms
respectively.
Glyceraldehyde contains only one asymmetric carbon atom (carbon

atom, 2) and therefore can exist as two different stereoisomers, i.e., as
D- and L- glyceraldehyde. For sugars having two or more asymmetric
carbon atoms, the convention has been adopted that the prefixes D- and
L- designate the absolute configuration of the asymmetric carbon
farthest from the carbonyl carbon atom (or penultimate carbon atom or the last but one
carbon atom). The symbols D- and L- designate the absolute configuration of an isomer and
not the sign of rotation of plane-polarized light. The structure with -OH group on the right
and –CHO group on the top of the asymmetric carbon atom is designated as D-
glyceraldehyde. The structure in which the -OH group is to the left and -CHO group on the
top is designated as L-glyceraldehyde.
The D- and L-glyceraldehydes are used as reference or parent compounds for designating
the absolute configuration of all stereoisomeric compounds.
Assignment:
Derive the D- and L- hexose series from:
1. Glyceraldehyde
2. Dihydroxyacetone

Optical Activity
All the monosaccharides except dihydroxyacetone contain one are more asymmetric carbon
atom(s) and thus are optically active. Optical activity refers to the ability of a compound in
solution to rotate the plane of polarization of plane-polarized light when observed in a
polarimeter. Optical activity is shown by all compounds capable of existing in two forms that
are non-superimposable mirror images of each other. The optical activity is expressed
quantitatively as the specific rotation:
Observed rotation (in degrees) x 100

[α]D25 =
Optical path length (dm) x concentration (g/100ml)
Where, α = specific rotation in degrees at temperature usually 25 oC and the wavelength of

the light employed (usually the D line of sodium) is 589.3nm.
If the rotation of the beam of plane-polarized light is clockwise (to the right or rectus as the
observer looks towards the light source), the enantiomer is designated as dextrorotatory
(dextro, 'd' or '+' symbols) and if it is anticlockwise (to the left or sinister), the enantiomer is
designated as levorotatory (levo, 'l' or '-' symbols). For example, the specific rotation of a-D-
glucose is + 112.2o (dextrorotatory) and that of D-fructose is -930 (levorotatory). Thus, the
symbol '+' and '-' refer to the direction of rotation of the beam of plane-polarized light but
not the absolute configuration.
The D-and L-stereoisomers of any given compound have identical physical properties and
identical chemical reactivities, with two exceptions: (a) they rotate the plane of plane-
polarized light equally but in opposite directions and (b) they react at different rates with
reagents that are themselves asymmetric. The equimolar mixture of the D- and L-
stereoisomers, known as racemic mixture or racemate (designated as D L-) is optically
inactive as the asymmetric carbon atom passes through a symmetrical intermediate during
chemical reaction.
Enantiomers: Aldoses and ketoses of the L-series are mirror-images of their D-counterparts.
These two D- and L- forms of a sugar are known as enantiomers. L- sugars are found in
nature, but they are not so abundant as D-sugars.
Diastereoisomers: Two sugars having the same molecular formulae but not the mirror
images of each other are known as diastereoisomers. e.g. D-glucose and D-mannose.

Epimers: Two sugars differing only in the configuration around one specific carbon atom
are called epimers of each other. Thus, D-glucose and D-mannose are epimers (at C2) and D-
glucose and D-galactose are epimers (at C4).
Kiliani-Fischer Cyanohydrin Synthesis

A method for the synthesis of monosaccharides was first proposed by Heinrich Kiliani in
1886. It is, in fact, a method by which the chain length of a carbohydrate may be increased.
The application of Kiliani synthesis to D-glyceraldeyde resulting in the production of 2
tetroses, Derythrose and D-threose.
The Kiliani–Fischer synthesis proceeds through through cyanohydrin and aldonic acid
lactone intermediates. The process is based upon the addition of HCN to the carbonyl group
of aldehydes (or ketones) of the sugars forming cyanohydrin (Reaction-1). This reaction
creates a new asymmetric carbon atom. Thus, two compounds differing in conformation
about the newly-formed asymmetric carbon atom are formed. The cyanohydrin resulting
from this addition is heated in water, which hydrolyzes the cyanide into a carboxylic acid
group that quickly reacts with itself to form a more stable lactone. (Reaction2) which are
later converted to γ-lactones or inner esters (Reaction-3). Finally, the lactones are reduced
to the corresponding aldoses, containing one carbon atom more than their parent sugar
(Reaction-4). The process can be repeated and the 4 isomeric D-pentoses may be produced;
and from these the 8 isomeric D-hexoses would also result.

Application of the cyanohydrin synthesis to D-glyceraldehyde
The conversion of D-glyceraldehyde into an aldotetrose yields D-erythrose and D-threose.

These are called diastereoisomers i.e., isomers but not mirror images of each other. In fact,
diastereoisomers are different forms of a compound with two asymmetric centres. It may,
hence be inferred that if two optical isomers are not enantiomers, they are related as
diastereoisomers.

Ring Structure And Mutarotation
An aldehyde or a ketone can react with an alcohol to yield a hemiacetal or a hemiketal.
Hemiacetals and hemiketals are compounds that are derived from aldehydes and ketones
respectively.
The same way aldehydes and ketones react with alcohols to form hemiacetals and
hemiketals, respectively, carbohydrates react intermolecularly to form rings. When forming
a ring 5 or 6 membered ring is most favorable and will only be formed. The Carbon 1 will be
attacked by either the Carbon 5 or Carbon 6 hydroxyl group to form a 5 or 6 membered
(respectively) carbohydrate ring.
Up to this point we have been representing the sugars as "linear" molecules. In reality the
linear form is normally a minor species (often less than 0.1%). In the solid state and in
solution monosaccharides exist in a cyclic hemiacetal form, ring closure corresponding to
reaction between the aldehyde group and either the C-4-OH or C-5OH. Cyclization involving
O-4 results in a five membered ring structurally related to furan and therefore designated as
a furanose, whilst hemiacetal formation with O-5 gives rise to an essentially strain-free,
hence sterically more favored, six-membered ring, a derivative of pyran, hence termed a
pyranose.
Either ring formation generates a new asymmetric carbon atom at C-1, the anomeric center,
thereby giving rise to diastereomeric hemiacetals which are called and labeled α and β.
In aqueous solution, many monosaccharides act as if they have one more asymmetric center
than is given by the open chain structural formulae. D-glucose may exist in two different
isomeric forms differing in specific rotation, αD-glucose, for which [α]D20 = + 112.2°, and
β-D-glucose, for which [β]D20 = +18.7°. These two sugars do not differ in elementary
composition but differ in physical and chemical properties. When the α and β-isomers of D-
glucose are dissolved in water, the optical rotation of each gradually changes with time and
approaches a final equilibrium value of [αD20 = +52.7°. This change, called mutarotation is
due to the formation of an equilibrium mixture consisting of about one-third α-D-glucose
and two thirds β-D-glucose at 20°C. The ring forms of the sugars are the ones that
predominate in solution. For example, the proportion of the straight-chain form of glucose
is quite small, about 0.1% of the total molecules. Glucose slowly inter converts between the
three structures (half time ~ 1 hour).

Ring closure occurs by attack of a secondary -OH (presumably as the nucleophilic anion) on
the carbon of the electron deficient C=O . This attack can occur on either face of the planar
CHO with the result that the -OH group that is created at C1 can be oriented in either of two
directions (if attack is on the left structure the -OH created will point to the left and vice
versa). The two forms of glucose that are formed are called anomers and the C bearing the
C=O is the anomeric carbon. When the newly created -OH has the same orientation as the -
OH that did the attacking (the two -OH's are cis) we have the α-anomer, otherwise it is the
β-anomer. Usually the -OH that does the attacking is located on C5 and a 6-membered ring
is formed. This is called a pyranoside. Note that by closing the ring we have created another
chiral center so that the ring forms of aldohexoses have twice as many isomers as the
straight chain forms.
Less common is attack by the C4 -OH which leads to the sterically strained, 5-membered
furanoside. In ketohexoses the C=O is at C2 and so attack by C5 still yields a 5-membered
ring. The cyclic sugars are normally represented using Haworth structures; in this
representation the lines denote -OH and there is an implicit -H on the other end.
pyranoside fuanoside
Haworth formulae may be used to indicate the ring forms of monosaccharides. The
substituents on the carbon atoms are represented as extending above or below the plane of
the ring. The lower half of the ring is thickened to indicate that it is the portion of the ring
that is directed out of the plane of the paper towards the reader.

A few simple rules to transform Fischer's projection formula to correct Haworth perspective
formula are the following:
1. If the ring closes on a -OH which is on the right of the Fischer's projection, the
hydroxymethyl group (-CH20H 'tail') points up; if it closes on a -OH group on the left,
the tail points down
2. The ring -OHs points down if they are on the right in the Fisher's projection, and up if
they are on the left
3. The -OH group on the anomeric carbon atom in the D-series will be down if it is α- and
up if β-
Anomers
From various chemical considerations it has been deduced that the α- and β- isomers of D-
glucose are not open-chain structures in aqueous solution but six-membered ring structures
formed by the reaction of the alcoholic hydroxyl group at carbon atom 5 with the aldehydic
carbon atom 1 to form a hemiacetal which renders another chiral center at carbon atom 1,
also known as carbonyl carbon atom or anomeric carbon atom. Isomeric forms of
monosaccharides that differ from each other only in configuration about the carbonyl
carbon atom are known as anomers. Thus, D-glucose will have two anomers designated as
α-D-glucose and β-D-glucose.
As hemiacetal or hemiketal formation is reversible, if one of the anomers is dissolved in

water, an equilibrium mixture of the two anomers results. This interconversion between the
two anomers is due to mutarotation. The cyclic hemiacetal formation in the case of glucose
by the reaction of the alcoholic hydroxyl group at carbon 5 with the aldehydic carbon atom
1 results in formation of six-membered ring. The six-membered ring forms of sugars are
called pyranoses because they are derivatives of the heterocyclic compound pyran. Thus,
the systematic name for the ring form of α-D-glucose is α-D-glucopyranose.
In the case of fructose, the hemiketal is formed by reaction of the hydroxyl group on carbon
atom 5 with the carbonyl group at carbon atom 2 to yield a five-membered ring. The five-
membered ring forms of sugars are called furanoses as they are derivatives of heterocyclic
compound, furan as suggested by Haworth. The systematic name for the ring form of α-D-
fructose is α-D-fructofuranose.

Assignment:
1. Draw the Haworth projection formulae of the hexoaldoses

2. Draw the Haworth projection formulae of the hexoketoses
3. α-D-glucose has a specific rotation of *α+D20, of +112.20, whereas, β-D-
glucose has a specific rotation of +18.70. What is the composition of a
mixture of α-D-glucose and β-D-glucose which has a specific rotation of
+83.00
Sugar Conformation
Conformation denotes the arrangement in space of atoms in a molecule which can be
achieved by rotation about single bonds. Although, the Haworth formulae give a better
indication of the true structures of sugars than do the straight chain forms, they do not
represent the actual conformations. Hexoses and pentoses that have converted into
pyranoses or furanoses take on either chair, boat, or
envelope conformations due to the tetrahedral
geometry of their carbons. Pyranose rings can form
either chair or boat conformational isomers
(conformers) while furanose rings take on the
envelope (also called half-boat) conformation which
are comparatively stable.
Although there are exceptions, most aldohexoses

adopt the chair conformation that places the bulky
hydroxymethyl group at the C-5 terminus in the
equatorial position.
Reactions of Sugars
The carbohydrates, because of the various reactive groups present in the molecule, undergo
a large number of chemical reactions. Although monosaccharides exists predominantly as
hemiacetals, enough aldehyde or ketone is present at equilibrium that the sugars give most
of the reactions of these functional groups. In addition, monosaccharides exhibit reactions
of alcohol.

A. Reactions with the carbonyl group
1. With dilute alkali: Dilute aqueous bases at room temperature cause rearrangements
about the anomeric carbon atom and its adjacent carbon atom without affecting
substituents at other carbon atoms. Treatment of D-glucose with dilute alkali yields
an equilibrium mixture of D-glucose, D-fructose and D-mannose. This reaction
involves intermediate enol forms, called enediols of the hydroxy aldehyde and
hydroxy ketone structures of carbon atoms 1 and 2.
2. Reducing property of sugars: The enediols formed above are reactive species. They
are good reducing sugars. When glucose is heated with an alkaline solution of Cu2+
ions, the Cu2+ is reduced to Cu+ which is precipitated as Cu2O. This is the basis for
the estimation of reducing sugars.
3. Reduction to alcohols: The carboxyl group of monosaccharides can be reduced by
hydrogen gas in the presence of metal catalysts or by sodium amalgam in water to
form the corresponding sugar alcohols. For example, D-glucose on reduction yields
D-glucitol (also called L-sorbitol) while D-mannose yields D-mannitol. Sugar alcohols
occur in nature, particularly in plants. One such alcohol, glycerol is an essential
component of lipids. Myo-inositol, a stereoisomer of inositol is found as a
component of phosphoglycerides and also in phytic acid, the hexaphosphoric ester
of inositol.
4. Reactions with carbonyl reagents: The carbonyl group of monosaccharide reacts
with carbonyl reagents like hydrazine, phenyl hydrazine, hydroxylamine or
semicarbazide to yield crystalline hydrazone, phenylhydrazone, oxime or

semicarbazide respectively. Further, reaction of hydrazone or phenylhydrazone with
excess of the reagent gives rise to osazones whose characteristic crystalline
structures are used to identify the sugars.
5. Reactions with concentrated acids: Monosaccharides are generally stable to hot
dilute mineral acids even on heating. When aldohexoses are heated with strong
mineral acids, however, they are dehydrated, and 5-hydroxymethyl furfural is
formed. This dehydration reaction is the basis of certain qualitative tests for sugars,
since the furfurals can be reacted with α-napthnol and other aromatic compounds
to form characteristic coloured products.
6. Glycoside formation: Sugar hemiacetals and hemiketals can react with alcohol in the
presence of a mineral acid to form anomeric α- and β-glycosides. Glycosides are
asymmetric mixed acetals formed by the reaction of the anomeric carbon atom of
the intramolecular hemiacetal or pyranose form of the aldohexose with a hydroxyl
group of an alcohol. This is called a glycosidic bond. The anomeric carbon in such
glycosides is asymmetric. The glycoside linkage is also formed by the reaction of the
anomeric carbon of a monosaccharide with a hydroxyl group of another
monosaccharide to yield a disaccharide. Oligo- and polysaccharides are chains of
monosaccharides joined by glycosidic linkages.
B. Reactions of the carbonyl group

1. Acylation: The free hydroxyl groups of monosaccharides and polysaccharides can be
acylated by reaction with an acylchloride or acetic anhydride to yield O-acyl
derivatives which are useful in determining the structure. Treatment of α-D-glucose
with excess of acetic anhydride yields penta-O-acetyl αD-glucose. The resulting
esters can be hydrolyzed by alkali.
2. Methylation: The methylation of the hydroxyl group on the anomeric carbon atom
occurs readily with methanol in the presence of acid to yield methyl glycosides,
which are acetals. The remaining hydroxyl groups of monosaccharides require much
more drastic conditions for methylation, e.g. treatment with dimethyl sulfate or
methyl iodide and silver oxide which yield methyl ethers not methyl acetals.
Methylation of all the free hydroxyl groups of a carbohydrate is called exhaustive
methylation. These ether derivatives are resistant to hydrolysis unlike the
glycosides. Methylation studies are important in structural analysis of carbohydrates.

Methylation of methyl α-D-glucopyranoside for example, yields methy 1,2, 3 ,4, 6-
tetra-O-methyl-D- glucopyranoside.
3. Periodate oxidation: Periodic acid (HIO4) will oxidize and cleave the C-C bonds which
contain adjacent free hydroxyl groups or a hydroxyl group and a carbonyl grouping.
For example, in the case of glycerol, C-2 is oxidized two times so that it is converted
into formic acid while C-1 and C-3 are converted only to formaldehyde. In case of
free sugars, like glucose, all the bonds are broken by periodate oxidation. Periodate
oxidation studies like the exhaustive methylation technique have been useful in the
elucidation of the structure of carbohydrates.
Assignment:
Discuss sugar derivatives under:
1. Sugar acids
2. Sugar phosphates
OLIGOSACCHARIDES
These sugars consist of a short chain of 2 to 8 or 10 monosaccharide units linked by the
glycosidic bond (s) with the elimination of water molecule (s). The glycosidic bond is formed
most frequently between the anomeric carbon of one sugar residue and a hydroxyl group of
the other sugar residue. Depending on the number of monosaccharide units that are linked,
the oligosaccharides are further classified as disaccharides (two sugar units), trisaccharides
(three sugar units), tetrasaccharides (four sugar units), etc. Amongst these, disaccharides
are the most important class because of their biological role and relative abundance in
natural products.
Disaccharides (C12H22O11)
These are a group of compound sugars composed of two monosaccharides linked by the
glycosidic bond with the elimination of one molecule of water.
1. Those with potentially a free aldehyde or a ketone group can reduce Fehling's
solution, hence are called reducing disaccharides.

2. The reducing disaccharides have most of the properties of monosaccharides i.e., they
can form osazones and show mutarotation, etc.
3. Disaccharides can be hydrolyzed into their constituent monosaccharide units unlike
monosaccharides.
4. Some disaccharides may exist in white crystalline solids and are soluble in water and
sweet in taste.
5. Disaccharides are not fermented by yeast directly but they are first hydrolyzed to
constituent monosaccharides which in turn are fermented.
The most abundant disaccharides in nature are maltose, sucrose and lactose.
Sucrose (O-α-D-glucopyranosyl-(1→2)-β-D-fructofuranoside): Sucrose or cane sugar or

beet sugar or saccharose or invert sugar, affectionately called ‘‘the royal carbohydrate’’ is a
disaccharide made up of one molecule each of α-D-glucose and -D-fructose, the linkage
involving the potential aldehyde group of carbon atom 1 of glucose and the ketonic group
of the carbon atom 2 of fructose (,2->1) linkage. It is a non-reducing sugar because of the
absence of a potentially free aldehyde or ketonic group and forms no osazone. As it does
not exist in α- and β-forms, it fails to exhibit mutarotation. It is hydrolyzed by acid or
enzyme sucrase (invertase) into glucose and fructose. The specific rotation of sucrose is
+66.5° and after hydrolysis, the specific rotation of the mixture is -19.84°. Such a change in
specific rotation. from dextro- to levorotatory nature is called 'inversion' and hence the
name 'invert sugar'. The reason for the inversion is that fructose is more strongly
levorotatory (-93° than glucose which is dextrarotatory (+52.5°). It is the most abundant
oligosaccharide and is ubiquitous in plants. It is generally manufactured from sugarcane and
sugar beet.
Maltose (α-D-glucopyranosyl-(1→4)-D-glucopyranoside): It is a disaccharide formed by

linking two units of α-D-glucose through α-1,4 glycosidic bond with the elimination of one
molecule of water. It is a reducing sugar since the -OH group bound to carbon 1 of the
glucose residue is free and can exist in the aldehyde form. It exhibits mutarotation since it
exists in both α -and β-forms. It does not occur in nature but is only formed when starch is
hydrolyzed by the enzyme diastase. Sprouting cereal grains have a high content of amylases
which split the starch present to dextrins and maltose. Malt prepared from sprouting barely,
is an excellent, source of maltose. Starches are also split to maltose by the amylases present

in human saliva and in the pancreatic secretion of man and all animals. Maltose is
hydrolyzed to two units of glucose by the enzyme maltase of intestinal juice.
Lactose (β-D-galactopyranosyl-(1→4)-D-glucosepyranoside): Lactose or milk sugar is made

up of β-D-galactose and α-(in α-form) or β- (in β- form) D-glucose through -1, 4 glycosidic
bond. It is a reducing sugar, exhibits mutarotation and forms osazone. It reduces Fehling's
solution but not Barfoed's reagent and thus can be distinguished from other reducing
disaccharides. It is hydrolyzed by the enzyme lactase into its constituent hexoses. It does not
ferment as easily as glucose and hence makes an ideal constituent of milk of mammals
(about 5 g/100 ml milk). It is not produced in plants.
Isomaltose (α-D-glycopyranosyl-(1→6)-D-glucopyranoside): It is a product of partial

hydrolysis of amylopectin of starch and glycogen, made up of two glucose units joined
through α-1,6 linkage
Cellobiose (β-D-glucopyranosyl-(1→4)-D-glucopyranoside): It is a partial hydrolytic product

of cellulose, made up of two glucose units joined through β-1, 4 linkage. It is a reducing
sugar. It is probably present in only trace amounts in nature and formed during the
digestion of cellulose by the cellulases of microorganisms.
Trehalose (α-D-glucopyranosyl-(1→1)-α-D-glucopyranoside): Also known as mycose, is

made up of two glucose units linked through two anomeric carbon atoms. It is a non-
reducing sugar. It is the major carbohydrate present in insects and fungi where it serves as a
storage carbohydrate from which glucose may be obtained as required above. 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.
Assignment:
Draw the structures of all the disaccharides discussed above
Trisaccharides (C18H34O17):
A naturally occurring trisaccharide is raffinose [α-D-galactopyranosyl-O-( 1,6-α-D-
glucopyranosyl-O-(1,2) –β-D-fructofuranoside] found in sugar beet, coffee and other plant
materials. It is a non-reducing sugar. Melezitose [O-α-O-D-glucopyranosyl(1->3)-O-β-D-
fructofuranosyl(2,1)-α-D-glucopyranoside] is found in the sap of some coniferous trees.

Tetrasaccharides
The important one among tetrasaccharides is the stachyose derived from raffinose.
Stachyose consists of galactose-galactose-glucose-fructose monosaccharide sugars linked
through α-1, 6, α-l, 6 and α-1, 2 glycosidic bonds, respectively. It occurs during
germination of seeds.
POLYSACCHARIDES (C5H10O5)n
These are complex carbohydrates which are polymerized anhydrides of a large but
undetermined number of the simple sugars which are joined by glycosidic bonds. Those
found in nature contain either five or six carbon monosaccharide units. The bulk of carbon
found in nature exists in the form of polysaccharides. These are involved in the majority of
biological processes although free monosaccharides and disaccharides occur in many
biological fluids and plants.
Polymers of the two

stereoisomers of glucose
produce polymers with very
different properties. Starch is a
polymer of α-glucose and readily
digestible. Cellulose is a polymer
of β-glucose and indigestible.
Some of the important properties of polysaccharides are as follows:
1. Complex sugars of high molecular weight; polymers of several units of

monosaccharides or either derivatives with linear or branched chains.
1. Upon hydrolysis by acids or enzymes, they are broken down into various
intermediate products and finally into their consituent monosaccharides or their
derivatives.
2. They are tasteless, apparently amorphous, some are crystalline
3. Mostly insoluble in cold water but form a sticky or gelatinous solutions
4. They differ in the nature of their recurring monosaccharides units, in the length of
their chains and in the degree of branching

Biological Role
Polysaccharides serve two main functions in the living organisms as:
1. Storage form of cellular fuel and

2. Structural elements in animal, plant and microbial systems
Classification
Polysaccharides can be classified in many ways:
A. Based on function:
1. Structural polysaccharides: These polysaccharides serve as structural components of
living organisms. e.g. cellulose (plant cell wall), chitin (exoskeleton of some insects),
etc.
2. Storage/ reserve / nutrient polysaccharides: These polysaccharides function as
reserve or storage form of fuel in living organisms e.g. starch (plants), glycogen
(animal cells) etc.
B. Based on composition
1. Homopolysaccharides: These are made up of single kind of monosaccharide
residues or their derivatives. e.g. Starch, glycogen, cellulose, chitin, inulin, etc.
2. Heteropolysaccharides: These are made up of two or more different kinds of
monosaccharide units or their derivatives. e.g. Hyaluronic acid, heparin, pectins,
gums, mucilages, chondroitins, etc.
Polysaccharides are often called as glycans. Those containing glucose are called as glycans
(starch and glycogen); those containing mannose are called mannans and those containing
galactose units are called galactans.
Structural polysaccharides
Cellulose: It is the most abundant organic compound of our planet accounting for about 50
per cent of all carbon. It is the principal constituent of cell walls in higher plants forming the
main structural element. It is a linear homopolymer of glucose units linked by β-1,4
glycosidic bonds. It is insoluble in water and all organic solvents. It dissolves in conc. H 2SO4,
on diluting the solution and boiling, glucose is formed as final product. Partial hydrolysis of
cellulose yields cellobiose, a disaccharide. Cellulase, a β-glucosidase produced by many
bacteria and fungi, hydrolyzes cellulose. The large amount of glucose present in cellulose is
not available as a source of energy for humans due to the lack of enzymes capable of

cleaving the β-1,4 bonds. However, ruminants can effectively use cellulose as they contain
a large bacterial population in their rumen capable of hydrolyzing it. In plant cell walls,
cellulose microfibrils are cemented together by other substances important among them
being pectin and hemicellulsoe. Pectins contain arabinose, galactose and glacturonic acid
while hemicelluloses are homopolymers of D-xylose linked by β- 1,4 bonds. The important
sources of cellulose are cotton fibers (98%), jute (50-70%), wood (40-50%), algae and
bacteria. Cellulose and its derivatives are widely used in textiles, films and plastics.
Chitin: It is a structural homopolysaccharide made up of N-acetyl glucosamine residues in β-

1,4 linkage. It is the principal structural polysaccharide present in the exoskeleton of
crustaceous insects, earthworms and mollusks. It is the second most abundant organic
substance on earth.
Peptidoglycan (murein): It is a structural heteropolysaccharide present in bacterial cell

walls. The repeating unit of peptidoglycan is the muropeptide which is a disaccharide
composed of N-acetyl- D-glucosamine (NAG) and N-acetyl muramic acid (NAMA) joined by a,
β-1,4 glycosidic bond. NAMA consists of a NAG unit which has its C-3 hydroxyl group joined
to the hydroxyl group of lactic acid by an ether linkage.. In the peptidoglycan the carboxyl
group of each lactic acid moiety is in turn linked to a tetrapeptide consisting of L-alanine, D-
isoglutamine, L-lysine and D-alanine. The terminal D-alanine residue of the side chain of one
polysaccharide chain is joined covalently with the peptide side chain of an adjacent
polysaccharide chain, either directly as in E. coli or through a short conneting peptide, e.g.
The pentaglycine in Staphylococcus aureus. The peptidoglycan structure of the bacterial cell
wall is resistant to the action of peptide-hydrolyzing enzymes, which do not attack peptides
containing D-amino acids. However, the enzyme lysozyme, found in tears and in egg white,
hydrolyzes the β(14) glycosidic bonds of the polysaccharide backbone of the peptidoglycan
structure.
Storage polysaccharides
Starch: It is a principal storage homopolysaccharide of the plant kingdom, made up of D-
glucose as repeating units. It is a mixture of two components amylose (about 20%) and
amylopectin (about 80%) Amylose consists of long unbranched chains of D-glucose units
which are linked by α-1, 4 glycosidic bonds. Its molecular weight ranges from a few
thousands of about 500,000. It gives blue colour with iodine due to the iodine- amylose
complex in which iodine molecule is occupying a position in the interior of the helical coil.

Amylopectin also has a backbone of α-1, 4 linkaged glucose units but in addition, branched
through α-1, 6 linkages. The average length of branching is from 24 to 30 glucose residues. It
gives a purple colour with iodine. Its molecular weight may range from 50,000 to 1,000,000.
Both amylose and amylopectin can be hydrolyzed by the enzymes α- and β- amylases. α-
amylases cleave α-1,4 linkages at random to give the mixture of maltose and glucose units
while the β-amylases, present in plants remove maltose units succcesively from the non-
reducing end. The intermediate product left after the cleavage of starch by α and β
amylases is called limit dextrins. Neither of these enzymes can hydrolyze α-1,6 linkages.
Microbial glucomylase can act on both α-1, 4 and α-1, 6 likages of starch to yield glucose.
Starch forms the major source of carbohydrates in the human diet and is of great economic
importance. The important source of starch are seeds, fruits, tubers, bulbs and cereal grains
varying from a few per cent of over 75 per cent. It is also found in some protozoa, bacteria
and algae.
Glycogen: It is the storage homopolysaccharide in animals and is often called ‘animal

starch’. It is present mainly in liver, skeletal muscle and in smaller amounts in all other
tissues. It is stored in liver and muscles of animals and split to glucose in the liver to
maintain proper concentration of glucose in the blood to furnish energy. The amount of
glycogen present in the animal varies widely among the different tissues with diet and
physiological state of the body. It is also aabundant in the mollusks while glycogens like
polysaccharides are found in some bacteria. Glycogen is a branched chain of D-glucose units
resembling amylopectin of starch. However, the branching through α-1, 6 linkages is more
extensive than amylopectin, with 8-10 glucose units between branching points. A glycogen
molecule may contain as many as 30,000 glucose units. It is readily dispersed in water to
form an opalescent solution which gives a reddish brown colour with iodine. It does not
reduce Fehling’s solution.
Dextrans: These are storage polysaccharides of some yeasts and bacteria. They consist of D-
glucose units joined by α-1, 6 glycosidic bonds primarily with cross linkages through α- 1,2
and and α-1, 3 linkages.
Inulin: It is a storage polysaccharide in the Compositae family (artichokes, dahlias,

dandelions, etc). It is a homopolymer made of D-Fructose units linked by β(2 -1) bonds.

Other polysaccharides
A plethora of other homo- and heteropolysaccharides are found in nature, most notably D-
xylans (hemicelluloses with linear chains of β -(1-4)-D-xylopyranosyl units), pectins (principal
constituent D-galacturonic acid), plant gums (building blocks D-galactose, L-arabinose, L-
rhamnose) and various algal and microbialpolysaccharideswith,inpart,unusual sugar units: L-
guluronic and D-mannuronic acids in alginates, glucuronic acid and pyruvate acetals in agar,
sulfated galactosyl residues in carrageenans, or ribitol phosphates in teichoic acids.
Assignment:
Discuss sugar derivatives under:
1. Amino sugars and N-acetylated sugars

2. Carboxylic acid sugars
3. Sugar alcohols
4. Glycosaminoglycans (GAGs)

LIPID CHEMISTRY
Lipids are a diverse group of fatty substances found in all living organisms. Lipids are any of a
diverse group of organic compounds including fats, oils, hormones, and certain components
of membranes that are grouped together because they do not interact appreciably with
water. Lipids can thus be defined fatty acids and their derivatives, and substances related
biosynthetically or functionally to these compounds.
They are the components of living systems consisting of basically carbon, hydrogen and
oxygen; in addition some have nitrogen and phosphorus. Fats and oils are widely distributed
in nature in both plant and animal tissues. They occur in relatively high concentration in
seeds of certain plants (oilseeds) where they function to supply food for use of the growing
seedlings. Animals store deposits of fats in their adipose tissues; these stored fats constitute
a reserve which can be used as the source of energy.
PHYSIOLOGICAL ROLE AND BIOLOGICAL IMPORTANCE

1. Major sources of metabolic energy in animals, insects, birds and high lipid containing
seeds
2. Basic structural components of cell membranes
3. As a protective water proof coating on the surface of cuticle of leaves or fruits of

plants, feathers of birds and as insect secretions
4. As cell surface components concerned in cell recognition, species specificity and

tissue immunity
5. Intense biological activity – some have profound biological activity; they include
some of the vitamins and hormones
6. Fats stored subcutaneously in warm blooded animals serve as insulation against an

unfavourable environment and also fatty tissues around vital organs give protection
against mechanical injuries and
7. As activators of enzymes – e.g., phosphatidylcholine micelles for activation of

microsomal enzymes
GENERAL PROPERTIES
Although the properties vary form one class to other, some of the general properties of
lipids are:
1. Soluble in nonpolar solvents but only sparingly soluble in water
2. Greasy or fat-like in nature and show translucent properties
3. Polar lipids are amphipathic i.e., one end of a lipid molecule, the head, is polar or
ionic and therefore, hydrophilic the other end, the tail (hydrocarbon) is nonpolar
and therefore hydrophobic.
4. Most lipids contain fatty acids. The glyceride esters of saturated fatty acids are
usually liquids at room temperature and
5. Fats and oils containing unsaturated fatty acids slowly become rancid when
exposed to light, heat, moisture and air.
CLASSIFICATION
Although the term lipid is sometimes used as a synonym for fats, fats are a subgroup of
lipids called triglycerides. Biological lipids originate entirely or in part from two distinct
types of biochemical subunits or "building-blocks": ketoacyl and isoprene groups.
There are eight categories of lipids defined by the LIPID MAPS Consortium, which classifies
them by their chemically functional backbones. The eight categories - fatty acyls,
glycerolipids, glycerophospholipids, sphingolipids, sterol lipids, prenol lipids,
saccharolipids, and polyketides - are then further divided into classes and subclasses. Based
on their reactivity with strong bases, lipids are classified into two major classes; saponifiable
and non-saponifiable lipids. The nonsaponifiable classes include the "fat-soluble" vitamins
(A, E) and cholesterol. The major saponifiable lipids are triacylglycerides,
glycerophospholipids, and the sphingolipids. The saponifiable lipids contain long chain
carboxylic acids, or fatty acids, esterified to a “backbone” molecule, which is either glycerol
or sphingosine. Saponification is the process that produces soaps from the reaction of lipids
and a strong base.
Lipids can also be broadly classified into simple lipids, complex lipids, derived lipids and
miscellaneous lipids based on their chemical composition
A. Simple Lipids
These lipids are the esters of fatty acids with alcohols. They are of two types.
1. Triglycerides (fats and oil): Found in adipose tissue, butterfat, lard, suet, fish oils,
olive oil, corn oil, etc. Esters of three molecules of fatty acids plus one molecule of

glycerol; the fatty acid may all be different. They are insoluble in water, non-polar in
character, and are commonly called neutral fats. They are called
fats if solid at room temperature and oils in they are liquids. Natural mixed
triglycerides have somewhat lower melting points, the melting point of lard being
near 300C, whereas olive oil melts near -60C. Since fats are valued over oils in some
populations because of features such as spreadability, texture, "mouth feel," and
increased shelf life, vegetable oils are extensively converted to solid triglycerides by
partial hydrogenation of their unsaturated components, producing some unintended
consequences. Some of the remaining double bonds are isomerized (to trans) in this
operation. These unnatural trans-fats in the diet appear to be associated with
increased heart disease, atherosclerosis, cancer, diabetes and obesity, as well as
immune response and reproductive problems.
2. Waxes: beeswax, head oil of sperm whale, cerumen, carnauba oil, and lanolin.
Composed of esters of fatty acids with alcohol other than glycerol; of industrial and
medicinal importance.
B. Complex (Compound) Lipids or Heterolipids

Complex lipids are Lipids with additional groups are called compound lipids. These lipids
are esters of fatty acids with alcohols and other groups such as phosphate, nitrogenous
base, etc. They are again divided into 3 types.
1. Phospholipids (phosphatids): Found chiefly in animal tissues. Substituted fats,

consisting of phosphatidic acid; composed of glycerol, fatty acids, and phosphoric
acid bound in ester linkage to a nitrogenous base. They are again sub-divided into:
a. Glycerophosphlipids: These contain glycerol as alcohol.

Glycerophospholipids, usually referred to as phosphoglycerides, are
ubiquitous in nature and are key components of the lipid bilayer of cells, as
well as being involved in metabolism and cell signalling. Neural tissue
(including the brain) contains relatively high amounts of
glycerophospholipids, and alterations in their composition has been
implicated in various neurological disorders. They are further subdivided into:

i. Cerebroside: myline sheaths of nerves, brain, and other tissues. Yields
on hydrolysis of fatty acids, sphingosine, galactose (or glucose), but
not fatty acids; includes kerasin and phrenosin.
ii. Ganglioside: brain, nerve tissue, and other selected tissues, notably
spleen; contains a ceramide linked to hexose (glucose or galactose),
neuraminic acid, sphingosine, and fatty acids.
iii. Sulfolipid: white matter of brain, liver, and testicle; also plant
chloroplast. Sulfur-containing glycolipid; sulfate present in ester
linkage to galactose.
iv. Proteolipids: brain and nerve tissue. Complexes of protein and lipids
having solubility properties of lipids.
b. Sphingophospholipids: These contain sphingosine as alcohol. They are also
called as sphingomyelins. Found in nervous tissue, brain, and red blood cells.
Sphingosine-containing phosphatide; yields fatty acids, choline, sphingosine,
phosphoric acid, and no glycerol; source of phosphoric acid in body tissue.
c. Lecithin: Found in brain, egg yolk, and organ meats. Phosphatidyl choline or
serine; phosphatide linked to choline; a lipotropic agent; important in fat
metabolism and transport; used as emulsigying agent in the food industry.
d. Cephalin: Occurs predominantly in nervous tissue. Phosphatidyl
ethanolamine; phosphatide linage to serine or ethanolamine; plays a role in
blood clotting.
e. Plasmalogen: Found in brain, heart, and muscle. Phosphatidal ethanolamine
or choline; phosphatide containing an aliphatic aldehyde.
f. Lipositol: Found in brain, heart, kidneys, and plant tissues together with
phytic acid. Phosphatidyl inositol; phosphatide linked to inositol; rapid
synthesis and degradation in brain; evidence for role in cell transport
processes.
2. Glycolipids: They contain a fatty acid, carbohydrate and nitrogenous base but no
phosphorus. They are also called as glycosphingolipids. They have sphingosine as
alcohol.
3. Lipoproteins: These are the macromolecular complexes of lipids with proteins.
4. Apart from the above lipids some others like sulfolipids, aminolipids, and lipo
polysaccharides also come under complex lipids.

C. Derived Lipids
These lipids are obtained on hydrolysis of simple and complex lipids. These lipids
contain glycerol and other alcohols. This class of lipids include steroid hormones,
ketone bodies, hydrocarbons, fatty acids, fatty alcohols, mono and diglycerides,
terpenes and carotenoids. These are sometimes present as waste products of
metabolism.
1. Fatty acids: occur in plant and animal foods; also exhibit in complex forms with other
substances. Obtained from hydrolysis of fats; usually contains an even number of
carbon atoms and are straight chain derivatives. Classification of fatty acids is based
on the length of the carbon chain (short, medium, or long); the number of double
bonds (unsaturated, mono-, or polyunsaturated); or essentiality in the diet (essential
or non-essential). A current designation is based on the position of the endmost
double bond, counting from the methyl (CH3) carbon, called the omega end. The
most important omega fatty acids are: Omega 6 - linolein and arachidonic acids and
Omega 3 - linolenic, eicosapentaenoic, and docosahexaenoic acids.
Sample nomenclature for fatty acids:
Name - Carbon Length : Number of Double Bonds : (position of double bond)
Butyric acid - 4:0
Palmitic acid - 16:0
Oleic acid - 18:1 (9)
Linoleic acid - 18:2 (9,12)
Linolenic acid - 18:3 (9,12,15)
Arachidonic acid - 20:4 (5,8,11,14)
Eicosapentaenoic acid - 20:5 (5,8,11,14,17)
Docosahexaenoic acid - 22:6 (4,7,10,13,16,19).
Saturated Unsaturated
Common Melting Melting
Formula Formula Common Name
Name Point Point
CH3(CH2)10CO2H lauric acid 45 ºC CH3(CH2)5CH=CH(CH2)7CO2H palmitoleic acid 0 ºC
CH3(CH2)12CO2H myristic acid 55 ºC CH3(CH2)7CH=CH(CH2)7CO2H oleic acid 13 ºC
CH3(CH2)14CO2H palmitic acid 63 ºC CH3(CH2)4CH=CHCH2CH=CH(CH2)7CO2H linoleic acid -5 ºC
CH3(CH2)16CO2H stearic acid 69 ºC CH3CH2CH=CHCH2CH=CHCH2CH=CH(CH2)7CO2H linolenic acid -11 ºC
CH3(CH2)18CO2H arachidic acid 76 ºC CH3(CH2)4(CH=CHCH2)4(CH2)2CO2H arachidonic acid -49 ºC

As might be expected from the properties of the fatty acids, fats have a
predominance of saturated fatty acids, saturated fats have a regular structure, pack
tightly, and form solids at room temperature, most animal fats are of this type; and
oils are composed largely of unsaturated acids, unsaturated fats have an irregular
structure, do not pack tightly and are liquid at room temperature, most plant fats are
of this type. Two polyunsaturated fatty acids, linoleic and linolenic, are designated
"essential" because their absence in the human diet has been associated with health
problems, such as scaly skin, stunted growth and increased dehydration. These acids
are also precursors to the prostaglandins, a family of physiologically potent lipids
present in minute amounts in most body tissues.
2. Terpenes: Found in essential oils, resin acids, rubber, plant pigments such as
caotenese and lycopenes, Vitamin A, and camphor. Large group of compounds made
up of repeating isoprene units; Vitamin A of nutritional interest; fat soluble Vitamin E
and K, which are also related chemically to terpenes.
3. Sterols:
a. Cholesterol: found in egg yolk, dairy products, and animal tissues. A
consituent of bile acids and a precursor of Vitamin D. Cholesterol is a lipid-
like alcohol found in animal tissues. It has a structure different from other
lipids. It is relatively medium-sized molecule that contains four adjacent cyclic
hydrocarbon molecules with three six-member rings and one five-member
ring that has a hydroxyl and a saturated hydrocarbon chain terminals.
Cholesterol is amphipathic due to its polar hydroxyl group and non-polar
hydrocarbon body.
b. Ergosterol: found in plant tissues, yeast, and fungi. Converted to Vitamin D2
on irradiation.
c. 7-dehydrocholesterol: found in animal tissues and underneath skin.
Converted to D3 on irradiation.
4. Androgens and estrogens: (Sex hormones) Found in ovaries and testes.
5. Adrenal corticolsteroids: adrenal cortex, blood
Assignment:
Draw the structures of all the lipids discussed here

PROTEIN AND AMINO ACID CHEMISTRY
Proteins are complex organic nitrogenous substances found in the cells of the living beings.
Proteins are the most functionally diverse class of biomolecules. Protein diversity is the
basis of the diversity of life. Everything that organisms are composed of - all parts - are
made of, or by proteins. They are most abundant intracellular macro-molecules and
constitute over half the dry weight of most organisms. “Proteins occupy a central position in
the architecture and functioning of living matter.
Proteins serve for enzyme catalysis, defense, transport, support, motion, regulation and
storage.
Some proteins serve as important structural elements of the body, for example, as hair,
wool, fibrin which forms blood clots and collagen, an important constituent of connective
tissue. Proteins also serve as circulatory transporters such as haemoglobin and myoglobins,
and membrane transporters such as glucose transporters. Proteins such as immunoglobulins
and surface antigens serve as defence systems. Actin and mysosin which are protein
muscles participate in muscular contraction. other proteins may be enzymes, or regulators
such as osmotic proteins, gene regulators and hormones. Still other proteins, such as
camoldulin, ferritin and casein are storage proteins.
The constituent elements of proteins are carbon, hydrogen, oxygen, nitrogen and very
rarely sulphur also. In certain complex proteins, phosphorus occurs as well. All proteins are
macromolecules because of their very high molecular weights. They are polymers i.e., chain-
like molecules produced by joining a number of small units called monomers. The units
(monomers) that make up protein polymers are called amino acids.
AMINO ACIDS
Amino acids are the building blocks of proteins. The general formula of an amino acid is:
Each amino acid is a nitrogenous compound having both an acidic

carboxyl (— COOH) and a basic amino (— NH2) group. R stands for the
side chains that are different for each amino acid. R can be as simple as a
hydrogen atom (H) or a methyl group (— CH3) or a more complex structure. The first carbon
is the part of the carboxyl group. The second carbon, to which is attached the amino group,
is called the α-carbon. The α-carbon of most amino acids is joined by covalent bonds to 4
different groups. Thus, the α-carbon in all the amino acids is asymmetric except in glycine
where the α-carbon is symmetric. Because of this asymmetry, the amino acids (of course,
except glycine) exist in two
optically active forms: those
having — NH2 group to the right
are designated as D-forms and
those having — NH2 group to the
left as L-forms.
Only L-amino acids are constituents of proteins. Amino acids in solution at neutral pH exist
predominantly as dipolar ions (also called zwitterions). In the dipolar form, the amino group
is protonated (–NH3+) and the carboxyl group is deprotonated (–COO--). The ionization state
of an amino acid varies with pH. In acid solution (e.g., pH 1), the amino group is protonated
(–NH3+) and the carboxyl group is not dissociated (–COOH). As the pH is raised, the
carboxylic acid is the first group to give up a proton. The dipolar form persists until the pH
approaches 9, when the protonated amino group loses a proton. Thus, the zwitterionic form
predominates near physiological pH.
Although over 100 amino acids have been shown to be present in various plants and
animals, only 20 of them (L-isomers) are found as constituent of most proteins. These 20
amino acids of proteins are often referred to as proteigenic, standard, primary or normal
amino acids, to distinguish them from others. Their side chains vary in size, shape, charge,
hydrogen- bonding capacity, hydrophobic character, and chemical reactivity. Indeed, all
proteins in all species—bacterial, archaeal, and eukaryotic—are constructed from the same
set of 20 amino acids.
Table 1: The twenty proteigenic amino acids

3 Letter 1 Letter 3 Letter 1 Letter
S/N Amino Acid S/N Amino Acid
Abbreviation Abbreviation Abbreviation Abbreviation
1 Alanine Ala A 11 Leucine Leu L
2 Arginine Arg R 12 Lysine Lys K
3 Asparagine Asn N 13 Methionine Met M
4 Aspartic Acid Asp D 14 Phenylalanine Phe F
5 Cysteine Cys C 15 Proline Pro P
6 Glutamine Gln Q 16 Serine Ser S
7 Glutamic Acid Glu E 17 Threonine Thr T
8 Glycine Gly G 18 Tryptophan Trp W
9 Histidine His H 19 Tyrosine Tyr Y
10 Isoleucine Ile I 20 Valine Val V
Assignment:
 Draw the structures of all the 20 amino acids listed above
 List 10 non-standard and non-protein amino acids each

Classification of Amino Acids
A. Based on the composition of the side chain or R group: the twenty amino acids, may
be grouped into following 8 categories:
1. Simple amino acids:- These have no functional group in the side chain, e.g.,
glycine, alanine, valine, leucine and isoleucine.
2. Hydroxy amino acids:- These contain a hydroxyl group in their side chain, e.g.,
serine and threonine.
3. Sulphur-containing amino acids:- These possess a sulphur atom in the side
chain, e.g., cysteine and methionine.
4. Acidic amino acids:- These have a carboxyl group in the side chain, e.g.,
aspartic acid and glutamic acid
5. Amino acid amides:- These are derivatives of acidic amino acids in which one of
the carboxyl group has been transformed into an amide group (--CO.NH2), e.g.,
asparagine and glutamine.
6. Basic amino acids:- These possess an amino group in the side chain, e.g., lysine
and arginine
7. Heterocyclic amino acids:- These amino acids have in their side chain a ring
which possesses at least one atom other than the carbon, e.g., tryptophan,
histidine and proline.
8. Aromatic amino acids:- These have a benzene ring in the side chain, e.g.,
phenylalanine and tyrosine.
B. Based on the polarity of the side chain or R group
1. Non-polar R groups:- This group includes five amino acids with aliphatic R
groups (alanine, valine, leucine isoleucine, proline), two with aromatic rings
(phenylalanine, tryptophan) and one containing sulfur (methionine).
2. Polar but uncharged R groups:- This group includes 7 amino acids, viz.,
glycine, serine, threonine, tyrosine, cysteine, asparagine and glutamine.
3. Negatively charged (= acidic) R groups:- This group have side chain which
contains an extra carboxyl group with a dissociable proton e.g. aspartic and
glutamic acid
4. Positively charged (=basic) R groups:- This group have side chain which
contains an extra amino group which imparts basic properties to them e.g.
Lysine, arginine and histidine

C. Based on the number of amino and carboxylic groups:
1. Monoamino-monocarboxylic amino acids:
i. Unsubstituted: Glycine Alanine, Valine, Leucine, Isoleucine
ii. Heterocyclic: Proline
iii. Aromatic: Phenylalanine, Tyrosine,Tryptophan
iv. Thioether: Methionine
v. Hydroxy: Serine, Threonine
vi. Mercapto: Cysteine
vii. Carboxamide: Asparagine, Glutamine
2. Monoamino-dicarboxylic amnino acids : Aspartic acid, Glutamic acid
3. Diamino-monocaryboxylic amino acids : Lysine, Arginine, Histidine
Properties of Amino Acids

Physical Properties
1. Amino acids are colourless crystalline substances.
2. Amino acids may be either tasteless (tyrosine), sweet (glycine and alanine) or bitter
(arginine).
3. Amino acids have high melting points (above 200°C) and often result in
decomposition.
4. Amino acids are soluble in polar solvents such as water and ethanol but they are
insoluble in nonpolar solvents such as benzene and ether.
Acid-Base Properties
1. Amino acids form zwitterions (dipolar ions) at neutral pH.
2. Amino acids are all weak polyprotic acids.
3. Amino acids react with both acids and bases. Hence, they are amphoteric in nature.
Substances having this dual nature are often called ampholytes (from “amphoteric
electrolytes”).
Essential Amino Acids

Amino acids that cannot be synthesized by our body are known as essential amino acids.
They are necessary for growth and transmission of impulses in the nervous system. They
must be supplied to our body through our diet . Their deficiency results in many diseases.

About 10 amino acids are essential. For example; arginine, valine, lysine, phenolalanine,
leucine, isoleucine, threonine, methionine, tryptophan, histidine.
The peptide bond

Amino acids in proteins are linked together through an acid- amide group type of bond
known as peptide bond. The peptide bond is formed between two amino acid molecules
when amino group of one amino acid is linked with the carboxylic group to the other amino
acid molecule by the elimination of water molecule.
PEPTIDES AND PROTEINS

The crucial feature of amino acids that allows them to polymerize to form peptides and
proteins is the existence of their two identifying chemical groups: the amino (-NH3+) and
carboxyl (-COO-) groups. The amino acid units are linked together through the carboxyl and
amino groups to produce the primary structure of the protein chain. The bond between two
adjacent amino acids is a special type of amide bond, in which the hydrogen atom of amino
(-NH2) group is replaced by an R radical. Such a substituted amide bond is known as the
peptide bond. And the chain, thus formed, by linking together of many amino acid units is
called a peptide chain. Peptides are classified by the number of amino acid units in the
chain. Dipeptides have two amino acid residues, tripeptides have three, tetrapeptides four,
and so on. After about 12 residues, this terminology becomes cumbersome, so peptide
chains of more than 12 and less than about 20 amino acid residues are usually referred to as
oligopeptides, and, when the chain exceeds several dozen amino acids in length, the term
polypeptide is used. Those containing more than around 100 amino acid residues are
described as proteins (polypeptides).
Chemically, proteins are unbranched polymers of amino acids linked head to tail, from
carboxyl group to amino group, through formation of covalent peptide bonds. Peptide bond
formation results in the release of H2O.

Each amino acid in the chain is termed a residue. The two ends of the peptide chain are
named as amino terminal and carboxyl terminal or simply as an N-terminal and C-terminal
respectively. These two terminal groups, one basic and another acidic, are the only ionizable
groups of any peptide chain except those present in the side chain. The terminal amino acid
with the free amino group is called as the N-terminal amino acid and the one with the free
carboxyl group at the other end as C-terminal amino acid.
Function of Proteins
1. Establishment and maintenance of structure:- Structural proteins are responsible for
the shape and stability of cells and tissues. Histones are examples of structural
proteins. They organize the arrangement of DNA in chromatin.
2. Transport:- A well-known transport protein is hemoglobin in the erythrocytes. It is
responsible for the transport of oxygen and carbon dioxide between the lungs and
tissues.
3. Protection and defence:- The immune system protects the body from pathogens and
foreign substances. An important component of this system is immunoglobulin G.
4. Control and regulation:- In biochemical signal chains, proteins function as signalling
substances (hormones) and as hormone receptors.
5. Catalysis:- Enzymes, with more than 2000 known representatives, are the largest
group of proteins in terms of numbers
6. Movement:- The interaction between actin and myosin is responsible for muscle
contraction and cell movement.
7. Storage:- Plants contain special storage proteins, which are also important for
human nutrition. In animals, muscle proteins constitute a nutrient reserve that can
be mobilized in emergencies.
GENERAL PROTEIN STRUCTURE

Chemical Bonds Involved In Protein Structure
A. Primary bond:- The principal linkage found in all proteins is the covalent peptide
bond (-CO-NH-).
B. Secondary bonds:-
1. Disulfide Bond (-S-S-):- In addition to the peptide bond, a second type of
covalent bond found between amino acid residues in proteins and polypeptides

is the disulfide bond, which is formed by the oxidation of the thiol or sulfhydryl (-
SH) groups of two cysteine residues to yield a mole of cystine, an amino acid
with a disulfide bridge.
2. Hydrogen Bond:- When a group containing a hydrogen atom, that is covalently-
bonded to an electronegative atom, such as oxygen or nitrogen, is in the vicinity
of a second group containing an electronegative atom, an energetically
favourable interaction occurs which is referred to as a hydrogen bond.
3. Nonpolar or Hydrophobic Bond:- Non polar amino acids have the side chains
which are essentially hydrophobic. Such R groups can unite among themselves
with elimination of water to form linkages between various segments of a chain
or between different chains. The association of various R groups in this manner
leads to a relatively strong bonding.
4. Ionic or Electrostatic Bond or Salt linkage or Salt bridge:- Ions possessing similar
charge repel each other whereas the ions having dissimilar charge attract each
other.
Protein Structure
Four basic structural levels of organization of proteins based on the degree of complexity of
their molecule have been recognized. The basic primary structure of a protein is relatively
simple and consists of one or more linear chains of a number of amino acid units. This linear,
unfolded structure or the polypeptide chain often assumes a helical shape to produce the
secondary structure. Secondary structure in a protein refers to the regular folding of regions
of the polypeptide chain. The two most common types of secondary structure are the α-
helix and the β-pleated sheet. The α-helix is a cylindrical, rod-like helical arrangement of the
amino acids in the polypeptide chain which is maintained by hydrogen bonds parallel to the
helix axis. In a β-pleated sheet, hydrogen bonds form between adjacent sections of
polypeptides that are either running in the same direction (parallel β-pleated sheet) or in
the opposite direction (antiparallel β-pleated sheet). The secondary structure, in turn, may
fold in certain specific patterns to produce the twisted three-dimensional or the tertiary
structure of the protein molecule. Finally, certain other proteins are made up of subunits of
similar or dissimilar types of the polypeptide chains. These subunits interact with each other
in a specific manner to give rise to the so-called quaternary structure of the protein.
Whereas the primary structure of a protein is determined by the covalently linked amino
acid residues in the polypeptide backbone, secondary and higher orders of structure are

determined principally by non-covalent forces such as hydrogen bonds and ionic, van der
Waals, and hydrophobic interactions.
Assignment:
 How do the chemical bonds discussed above help to stabilise the various levels of
protein structures?
PROTEINS CLASSIFICATION
Proteins are classified based on the following criteria:
A. Based on the origin of the protein

Proteins can be classified as animal proteins and plant proteins. Animal proteins are
the proteins derived from animal sources such as eggs, milk, meat and fish. They are
usually called higher-quality proteins because they contain (and hence supply)
adequate amounts of all the essential amino acids. On the other hand, plant proteins
are called lower-quality proteins since they have a low content of one or more of the
essential amino acids. The four most common limiting amino acids are methionine,
lysine, threonine and tryptophan
B. Based on the shape of protein molecule
Fibrous proteins tend to have relatively simple, regular linear structures. These
proteins often serve structural roles in cells. Typically, they are insoluble in water or
in dilute salt solutions. In contrast, globular proteins are roughly spherical in shape.
The polypeptide chain is compactly folded so that hydrophobic amino acid side
chains are in the interior of the molecule and the hydrophilic side chains are on the
outside exposed to the solvent, water. As a class, globular proteins are more
complex in conformation than fibrous proteins, have a far greater variety of
biological functions and are dynamic rather than static in their activities. Nearly all
enzymes are globular proteins, as are protein hormones, blood transport proteins,
antibodies and nutrient storage proteins. The fibrous proteins are extremely strong
and most fibrous proteins serve in a structural or protective role. They include
collagen, elastin, keratins and fibroins.
C. Based on composition and solubility

Based on their composition, proteins can be classified into simple, conjugated and
derived proteins.
1. Simple Proteins or Holoproteins: - These are of globular type except for
scleroproteins which are fibrous in nature. They include protamines and
histones (occurs almost entirely in animals, mainly in sperm cells), albumins
(widely distributed in nature but more abundant in seeds), globulins (found in
milk, blood plasma, muscles etc), glutelins and prolamines (found only in
plant seeds), and scleroproteins or albuminoids (which occur almost entirely
in animals and are, therefore, commonly known as the ‘animal skeleton
proteins’).
2. Conjugated or Complex Proteins or Heteroproteins: - These are also of
globular type except for the pigment in chicken feathers which is probably of
fibrous nature. The various sub-divisions under this group are
metalloproteins, chromoproteins, glycoproteins and mucoproteins,
phosphoproteins, lipoproteins and nucleoproteins.
3. Derived Proteins: - These are derivatives of proteins resulting from the action
of heat, enzymes or chemical reagents. This group also includes the
artificially-produced polypeptides. Examples are proteans, metaproteins or
infraproteins, coagulated proteins, proteoses and peptones.
D. Based on biological function
Depending upon their physical and chemical structure and location inside the cell,
different proteins perform various functions. As such diverse proteins may be
grouped under following categories, based on the metabolic functions they perform:
1. Enzymic proteins, they are biological catalysts and examples include urease,
amylase and catalase.
2. Structural proteins, they serve for strengthening or protecting biological
structures e.g. collagen, elastin, keratin and fibroin.
3. Transport or carrier proteins which transport ions or molecules in the body
e.g. myoglobin and haemoglobin.
4. Nutrient and storage proteins which provide nutrition to growing embryos
and store ions. E.g ovalbumin, casein and ferritin.
5. Contractile or motile proteins that function in the contractile system.Example
include actin, myosin and tubulin.

6. Defense proteins which serves to defend against other organisms. E.g.
antibodies, fibrinogen, thrombin.
7. Membrane proteins found in association with the various membrane systems
of cells. Membrane proteins characteristically have fewer hydrophilic amino
acids than cytosolic proteins.
8. Regulatory proteins that regulate cellular or metabolic activities. E.g. insulin,
G proteins and growth hormone.
9. Toxic proteins such as snake venom, ricin which hydrolyze (or degrade)
enzymes.
GENERAL PROPERTIES OF PROTEINS

Physical Properties
1. Proteins are colourless and usually tasteless. These are homogeneous and
crystalline.
2. The proteins range in shape from simple crystalloid spherical structures (globular
proteins) to long fibrillar structures (fibrous proteins).
3. Proteins generally have large molecular weights ranging between 5 × 10 3 and 1 × 106.
4. Proteins are colloidal in nature and exhibits many colloidal properties.
5. Proteins can be denatured. Denaturation refers to the changes in the properties of a
protein, i.e. loss of biologic activity. Denaturation may be followed by coagulation
and then precipitation from solution. Physical agents such as shaking, heat, cooling
and freezing and chemical agents such as ionizing radiations (like X-rays, radioactive
and ultrasonic radiations), organic solvents (acetone, alcohol), aromatic anions
(salicylates), some anionic detergents (like sodium dodecyl sulfate) can cause
denaturation.
6. Like amino acids, the proteins are amphoteric, i.e., they act as acids and alkalis. The
net charge is influenced by the pH value. Each protein has a fixed value of isoelectric
point (pl) at which it will move in an electric field. Isoelectric point (or isoionic point)
is the pH value at which the number of cations is equal to that of anions. Thus, at
isoelectric point, the net electric charge of a protein is always zero.
7. Being amphoteric in nature, the proteins can form salts with both cations and anions
based on their net charge.
8. The solubility of proteins is markedly influenced by pH. Solubility is lowest at
isoelectric point and increases with increasing acidity or alkalinity.

9. All protein solutions rotate the plane of polarized light to the left, i.e., these are
levoratotory.
Chemical Properties
1. Hydrolysis: Proteins are hydrolysed by a variety of hydrolytic agents:
a. By acidic agents. Proteins, upon hydrolysis with conc. HCl (6–12N) at 100–
110°C for 6 to 20 hrs, yield amino acids in the form of their hydrochlorides.
Undesirable side-effects of acid hydrolysis includes Asparagine and glutamine
are deamidated to aspartate and glutamate respectively; Tryptophan, serine
and threonine are destroyed.
b. By alkaline agents. Proteins may also be hydrolyzed with 2N NaOH. Alkaline
hydrolysis is, however, less used as it is highly disadvantageous because it
leads to the destruction of certain amino acids like arginine, cysteine, cystine,
serine, threonine etc. and It also causes loss of optical activity (or
racemization) of the amino acids.
c. By proteolytic enzymes. Under relatively mild conditions of temperature and
acidity, certain proteolytic enzymes like pepsin and trypsin hydrolyze the
proteins. Enzyme hydrolysis is used for the isolation of certain amino acids
like tryptophan, but it requires prolonged incubation and hydrolysis is
incomplete.
2. Reactions Involving COOH Group
a. Salt formation. The carboxylic group of amino acids can release a H+ ion with
the formation of carboxylate (COO—) ions. These may be neutralised by
cations like Na+ and Ca2+ to form salts. Thus, amino acids react with alkalies
to form salts.
b. Esterification. Carboxylic acids reacts with alcohols and corresponding esters
are produced. The esters, so obtained, are volatile in contrast to the free
amino acids.
c. Amino acids react with amines to form amides
3. Reactions Involving NH2 Group
a. Salt formation. When either free amino acids or proteins are treated with
acids like HCl, the acid salts are formed. The basic amino acids, arginine and
lysine react with CO2 in the presence of air to form carbonate salts.

b. Reaction with formaldehyde. With formaldehyde, the hydroxy-methyl
derivatives are formed. These derivatives are insoluble in water and resistant
to attack by microorganisms. Because of this action, formaldehyde is the
principal reagent in embalming fluids and is used to harden and preserve
certain fibres obtained from globular proteins.
c. Reaction with benzaldehyde tof form Schiff 's bases.
d. Reaction with nitrous acid (Van Slyke reaction). The amino acids react with
HNO2 to liberate N2 gas and to produce the corresponding α-hydroxy acids.
e. Acylation. Acylation is brought about by many acid chlorides and acid
anhydrides, when amino acids in alkaline medium react with them.
f. Reaction with FDNB or Sanger's reagent. In mildly alkaline solution, FDNB (1-
fluoro- 2, 4-dinitrobenzene) reacts with α-amino acids to produce yellow
coloured derivative, DNBamino acid. This reaction is valuable in elucidation of
protein structure.
g. Reaction with dansyl chloride. The N-terminal amino acid of the protein also
combines with 1-dimethylaminonaphthalene-5-sulfonyl chloride (or dansyl
chloride) to form a fluorescent dansyl derivative.
4. Reactions Involving both COOH and NH2 Groups
a. Reaction with triketohydrindene hydrate (Ninhydrin reaction). Ninhydrin is
widely used for detecting amino acids, forms a purple product with α-amino
acids and a yellow adduct with the imine groups of proline and
hydroxyproline.
b. Reaction with phenyl isocyanate. With phenyl isocyanate, hydantoic acid is
formed which in turn can be converted to hydantoin.
c. Reaction with phenyl isothiocyanate or Edman reagent. Phenyl
isothiocyanate also reacts similarly with amino acids to produce
thiohydantoic acid. On treatment with acids in nonhydroxylic solvents, the
latter cyclize to thiohydantoin. This reaction has proved useful in the studies
of protein structure.
d. Reaction with phosgene. With phosgene, N-carboxyanhydride is formed.
e. Reaction with carbon disulfide. With carbon disulfide, 2-thio-5-thiozolidone
is produced.
f. Reaction with carbon disulfide. With carbon disulfide, 2-thio-5-thiozolidone
is produced.
5. Reactions Involving R Group or Side Chain
a. Biuret test. Compounds containing peptide bonds produce a characteristic
purple colour when treated with an alkaline 0.2% copper sulfate solution (or
biuret reagent). This reaction is termed as ‘biuret reaction’ since it is also
given by the substance biuret. The colour deepens as the number of peptide
bonds is increased and the proteins produce a deep blue-violet colour due to
the probable formation of a coordination complex. All proteins except
dipeptides, respond to this reaction. This reaction is widely used both as a
qualitative test for the detection of proteins and as a quantitative measure of
protein concentration.
b. Xanthoproteic test. Yellow colour develops on boiling proteins with conc.
HNO3 due to the presence of benzene ring. This reaction is due to the
nitration of the phenyl rings (of tyrosine, tryptophan and phenylalanine) to
yield yellow substitution products, which turn orange upon addition of alkali.
c. Millon's test. Red colour develops when proteins are heated with Hg.NO 3 in
HNO2. The reaction is specific for tyrosine and takes place between mercuric
and mercurous nitrates and tyrosine residues of the protein. Tryptophan also
responds to this reaction.
d. Hopkins–Cole test or Glyoxylic acid test. Violet ring develops on addition of
conc. H2SO4 at the junction of protein and glyoxylic acid solutions. The test is
specific for tryptophan.
e. Folin's test. Blue colour develops with phosphomolybdotungstic acid in
alkaline solution due to the presence of phenol group. The test is specific for
tyrosine.
f. Sakaguchi test. Red colour develops with a-naphthol and sodium
hypochlorite. The test is applied for the detection of arginine.
g. Pauly test. Red colour develops with diazotized sulfanilic acid in alkaline
solution. The reaction is specific for tyrosine and histidine.
h. Ehrlich test. With p-dimethylaminobenzaldehyde in 12 N HCl, tryptophan
develops a blue colour.
6. Reactions Involving SH Group
a. Nitroprusside test. Red colour develops with sodium nitroprusside in dilute
NH4.OH. The test is specific for cysteine.

b. Sullivan test. Cysteine develops red colour in the presence of sodium 1, 2-
naphthoquinone-4-sulfonate and sodium hydrosulfite.

NUCLEIC ACID CHEMISTRY
INTRODUCTION
Nucleotides are energy-rich biological compounds that possess a heterocyclic nitrogenous

base, a five-carbon sugar (pentose), and phosphate as principal components of their
structure. The biochemical roles of nucleotides are numerous; they participate as essential
intermediates in virtually all aspects of cellular metabolism especially biosynthetic
pathways. They also serve as chemical signals, key links in cellular systems that respond to
hormones and other extracellular stimuli, and are structural components of a number of
enzyme cofactors and metabolic intermediates.
Serving an even more central biological purpose are the nucleic acids, the elements of
heredity and the agents of genetic information transfer. Nucleic acids are high molecular
weight biopolymers of nucleotides as repeating units which are linked by characteristic 3’-5’
phosphodiester bonds. Nucleic acids are one of the major components of all cells, making
up from 5 to 15 per cent of their dry weight. They are also present in viruses. They are
responsible for the storage and transmission of genetic information and translation of this
information for a precise synthesis of proteins characteristics of the individual cell. Like the
letters in this sentence, the orderly sequence of nucleotide residues in a nucleic acid can
encode information. The two basic kinds of nucleic acids are deoxyribonucleic acid (DNA)
and ribonucleic acid (RNA).
Based on the nature of sugar moiety and the nitrogenous bases present, two types of
nucleic acids are recognized: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
Although the name nucleic acid suggests their location in the nuclei of cells, certain of them
are, however, also present in the cytoplasm. Complete hydrolysis of nucleic acids by acids,
bases or specific enzymes yields three characteristics components: (a) heterocyclic bases (b)
sugar and (c) phosphoric acid.
Heterocyclic Nitrogenous bases

The bases of nucleotides and nucleic acids are derivatives of either pyrimidine or purine.
Pyrimidines are six-membered heterocyclic aromatic rings containing two nitrogen atoms.
The purine ring system consists of two rings of atoms: one resembling the pyrimidine ring
and another resembling the imidazole ring. The common naturally occurring pyrimidines are
cytosine, uracil, and thymine (5-methyluracil). Cytosine and thymine are the pyrimidines
typically found in DNA, whereas cytosine and uracil are common in RNA.

Adenine (6-amino purine) and guanine (2-amino-6-oxy purine), the two common purines,
are found in both DNA and RNA. Other naturally occurring purine derivatives include
hypoxanthine, xanthine, and uric acid
Pentose Sugar
The two types of nucleic acids are distinguished primarily on the basis of the 5-carbon keto
sugar or pentose which they possess. One possesses D-2-deoxyribose, hence the name
deoxyribose nucleic acid or deoxyribonucleic acid, while the other contains D-ribose, hence
the name ribouncleic acid. Both these sugars in nucleic acids are present in the furanose
form and are of β configuration.
NUCLEOSIDES
The nucleosides are compounds formed by linking purine and pyrimidine bases to either D-
ribose or 2'-deoxy-D-ribiose in a N--glycosidic bound. The point of attachment of the bases
to the sugar is N-9 of the purines or N- 1-of the pyrimidines to C-1 or D-ribose or 2'-deoxy-D-
ribose. The carbon atoms of the sugar are designated by prime numbers (i.e., C-1’, C-5’),
while the atoms in the bases lack the prime sign. Nucleosides are named by adding the
ending –idine to the root name of a pyrimidine or –osine to the root name of a purine. The
common nucleosides are thus cytidine, uridine, thymidine, adenosine, and guanosine.
Nucleosides are more water soluble than the free bases, because of the hydrophilicity of the
pentose.

Recently two nucleoside analogues, 3′-azidodeoxythymidine (AZT) and 2′, 3′dideoxycytidine
(DDC), have been therapeutically used for the treatment of acquired immune deficiency
syndrome (AIDS) patients. The disease is caused by the human immunodeficiency viurs
(HIV), which is an RNA virus that requires a specific enzyme, an RNA-dependent DNA
polymerase, for its replication. When given to AIDS patients, AZT and DDC are converted
into their triphosphate forms, which can then compete with dTTP and dCTP, respectively, as
substrates for DNA synthesis. When incorporated, the analogues terminate DNA synthesis
because the absence of a 3′-OH group in them prevents continued elongation of the DNA
molecule being synthesized. As the DNA-synthesizing enzyme of HIV is much more sensitive
to AZT and DDC inhibition than are the analogous enzymes of its host cell, these nucleoside
analogues offer some hope as an effective treatment, if not a cure, for AIDS patients.
NUCLEOTIDES
A nucleotide results when phosphoric acid is esterified to a sugar -OH group of a nucleoside.
The nucleoside ribose ring has three -OH groups available for esterification, at C-2’, C-3’, and
C-5’ (although 2’-deoxyribose has only two). The vast majority of monomeric nucleotides in
the cell are ribonucleotides having 5’-phosphate groups. Therefore, 2’, 3’ or 5’
ribonucleoside monophosphate and 3’ or 5’ deoxyribonucleoside monophosphtes can be
formed. However, the 5’ position is most commonly phosphorylated.
Nucleoside monophosphates can be linked to a phosphate or pyrophosphate group through

anhydride bonds to give nucleoside di-and triphosphate, respectively. In the absence of
oxygen atom at C-2’ of the sugar ring, the structures are correspondingly known as
deoxyadenosine-5’-monophosphate (dAMP), deoxyadenosine-5’-diphosphate (dADP) and
deoxyadenosine-5’-triphopshate (dATP), respectively.
Nucleoside monophosphates in which the phosphoric acid is esterified to two of the

available ribose hydroxyl groups are found in all cells. Forming two such ester linkages with
one phosphate results in a cyclic phosphodiester structure. 3’, 5’-cyclic AMP, often
abbreviated cAMP, and its guanine analog 3’, 5’-cyclic GMP, or cGMP, are important
regulators of cellular metabolism.
Nucleoside 5’-triphosphates are indispensable agents in metabolism because the

phosphoric anhydride bonds they possess are a prime source of chemical energy to do

biological work. Virtually all of the biochemical reactions of nucleotides involve either
phosphate or pyrophosphate group transfer: the release of a phosphoryl group from an NTP
to give an NDP, the release of a pyrophosphoryl group to give an NMP unit, or the
acceptance of a phosphoryl group by an NMP or an NDP to give an NDP or an NTP. ATP to
serve as the primary nucleotide in central pathways of energy metabolism, whereas GTP is
used to drive protein synthesis.
BASE SUGAR NUCLEOTIDE NAME ABBREVIATION

DNA Nucleotides
Adenine deoxyribose deoxyadenosine 5'-monophosphate dAMP
Guanine deoxyribose deoxyguanosine 5'-monophosphate dGMP
Cytosine deoxyribose deoxycytidine 5'-monophosphate dCMP
Thymine deoxyribose deoxythymidine 5'-monophosphate dTMP
RNA Nucleotides
Adenine ribose adenosine 5'-monophosphate AMP
Guanine ribose guanosine 5'-monophosphate GMP
Cytosine ribose cytidine 5'-monophosphate CMP
Uracil ribose uridine 5'-monophosphate UMP
METABOLIC FUNCTIONS
1. Role in energy metabolism: ATP is the main form of chemical energy available to the
cells. It is generated in cells by oxidative phosphorylation and substrate level
phosphorylation .
2. Monomeric units of nucleic acids: The nucleic acids, DNA and RNA are composed of
monomeric units of the nucleotides as building-blocks.
3. Physiological mediators: cAMP plays an important role as a ‘second messenger’

4. Components of coenzymes: Coenzymes such as NAD+ FAD and coenzyme A are
important metabolic constitutes of cells and are involved in many metabolic
pathways.
5. Activated intermediates: The nucleotides also serve as carriers of activated

intermediates required for a variety of reactions.
6. Allosteric effectors: Many of the regulated steps of the metabolic pathways are
controlled by the intracellular concentrations of nucleotides.
DNA
The DNA isolated from different cells and viruses characteristically consists of two
polynucleotide strands wound together to form a long, slender, helical molecule, the DNA
double helix (exceeding 2 x 109 in molecular weight). The strands run in opposite directions;
that is, they are antiparallel. The two strands are held together in the double helical
structure through inter-chain hydrogen bonds. An important feature of the double helix is
the specificity of the pairing of bases. Pairing always occurs between adenine and thymine
and between guanine and cytosine
DNA occurs in various forms in different cells. The single chromosome of prokaryotic cells is
typically a circular DNA molecule. In diploid eukaryotic cells nearly all the DNA molecules
are present in the cell nucleus, where they are combined with s class of arginine- and lysine-
rich basic proteins called histones.
Characteristics and properties

1. Genetic material: DNA is the molecule of heredity and is responsible for the
progeny to have the same characteristics as their parents.
2. DNA content: The DNA content of a cell is remarkably constant for each species
3. Base composition: DNA isolated from different tissues of the same organism has the
same base composition
4. Effect of pH: DNA is a polybasic acid due to the presence of phosphate groups which
are fully ionized at physiological pH.

5. Effect of temperature : when highly polymerized double stranded DNA is slowly
heated, the double helix ‘melts’, as a result the double-stranded structure is
converted to a random coil over a range of a few degrees of temperature.
6. Absorbance: The purine and pyrimidine bases found in the DNA and also RNA
strongly absorb ultraviolet radiation of wave-length at 260 nm. This property is used
to identify and estimate nucleic acids.
7. Hydroysis: Gentle acid hydrolysis of DNA at pH 3.0 causes selective hydrolytic

removal of all its purine bases without affecting the pyrimidine-deoxyribose bonds or
the phosphodiester bonds of the backbone.
Biological role
1. It contains the genetic information that is transmitted from generation to
generation, which is achieved by self-replication of DNA during cell growth and
division so that two daughter double helical molecules of DNA are obtained, each
identical to parent DNA.
2. It expresses it encoded genetic information for the synthesis of RNA and proteins for
metabolic function and control of all cellular activities.
The genetic information is carried in the form of genes and expressed at appropriate
times. A gene is defined as a sequence of bases in DNA which specifies the complete
amino acid sequence of polypeptide chain or the base sequence of an RNA molecule
(rRNA, tRNA).
RNA
RNA occurs in all prokaryotic and eukaryotic cells and in some viruses. RNA is present mainly
in the cytosol. Unlike DNA, RNA is essentially a single stranded molecule. Although DNA is
the primary genetic material within the cells, many RNA molecules participate in the
processes by which this genetic information is expressed.
Differences with DNA

Although sharing many features with DNA, the RNA molecules possess several specific
differences:

1. The sugar moiety in RNA, to which the phosphate and the nitrogen bases are
attached, is ribose rather than 2′- deoxyribose of DNA. Ribose contains a 2′-hydroxyl
group not present in deoxyribose.
2. RNA contains the pyrimidine uracil (U) in place of thymine which is characteristic of
DNA molecule.
3. The native RNA is single-stranded rather than a double-stranded helical structure
characteristic of DNA.
4. Since the RNA molecule is single-stranded and complementary to only one of the
two strands of a gene, it need not have complementary base ratios.
5. RNA is alkali-labile whereas DNA is alkali-stable.
Types of RNA
Based on cellular location and function, three major types of RNA have been identified in all
cells:
1. messenger RNA (mRNA),

2. ribosomal RNA (rRNA) and
3. transfer RNA (tRNA).
mRNA: This is also known as a template RNA. Messenger RNA (mRNA) serves to carry the
information or “message” that is encoded in genes to the sites of protein synthesis in the
cell, where this information is translated into a polypeptide sequence. That is mRNA
molecules are transcribed copies of the protein-coding genetic units of DNA. It has a primary
structure complementary to a portion of one of the stands of DNA; In bacterial cells, mRNA
is highly unstable i.e., it is constantly being degraded and re-synthesized. In eukaryotic cells,
the turnover rate of mRNA is much lower.
rRNA: This is also known as a high- molecular RNA and constitutes up to 65 per cent of the
mass of ribiosomes. The major portion of the total RNA of a cell is ribiosomal RNA. The
different species of rRNA are generally referred to according to their sedimentation
coefficients. There are three types of rRNA; 5S, 15S and 23S in prokaryotic cells and four
types – 5S, 5.8S, 18S and 28S in eukaryotic cells. The rRNA is presumed to play a role in
maintenance of structure of ribosomes.

tRNA: This is also known as a soluble and acceptor RNA because of its high solubility and
acceptor and transfer of amino acid carrying function in the synthesis of protein,
respectively. Transfer RNAs (tRNAs) serve as the carrier of amino acids for protein synthesis.
tRNA molecules also fold into a characteristic secondary structure This RNA consists of some
of the unusual nucleotide residues like –ribothymidylic acid (T), pseudouridylic acid ( ),
dihydouracil (D) and methylguanine (mG). Additional evidence suggests that 60-70 per cent
of the tRNA exists as a helical ‘cloverleaf’ structure with the anticodon (i.e., the nucleotide
triplet necessary for the positioning of the specific RNA in the mRNA template during
protein synthesis) located in the central petal of cloverleaf.

ENZYMES, VITAMINS AND COENZYME
ENZYMES
At any moment, thousands of chemical reactions are taking place in any living cell. Enzymes
are essential for these reactions to proceed at rates fast enough to sustain life. Enzymes are
macromolecules of biological origin that help accelerate (catalyse) biochemical reactions
(chemical reactions in biological systems). This is usually done by accelerating reactions by
lowering the transition state or decreasing the activation energy.
The orderly course of metabolic processes is only possible because each cell is equipped
with its own genetically determined set of enzymes. It is only this that allows coordinated
sequences of reactions. An important point about enzymes is that they are very specific
about what they can catalyse. Even small changes in the reactant molecule can stop the
enzyme from catalysing its reaction. The reason for this lies in the active site present in the
enzyme
Enzymes as biological catalysts
 Speed up the rate of a chemical reaction

o Lower activation energy by holding molecule in a favourable place
 Not consumed or permanently changed
 Highly specific
o Will react some with similar molecules especially if their concentration is
high.
Almost all enzymes are proteins, with the exception of a few catalytically active ribonucleic
acids (catalytic RNA molecules), or ribozymes. Their catalytic activity depends on the
integrity of their native protein conformation. If an enzyme is broken down into its
component amino acids, its catalytic activity is always destroyed. Thus the primary,
secondary, tertiary, and quaternary structures of protein enzymes are essential to their
catalytic activity.
Some enzymes require no chemical groups for activity other than their amino acid residues.
Others require an additional chemical component called a cofactor - either one or more
inorganic ions, such as Fe2+, Mg2+, Mn2+, or Zn2+, or a complex organic or metalloorganic
molecule called a coenzyme. Cofactors are generally stable to heat while the enzyme
protein loses its activity on heating.

A coenzyme or metal ion that is very tightly or even covalently bound to the enzyme protein
is called a prosthetic group. A complete, catalytically active enzyme together with its bound
coenzyme and/or metal ions is called a holoenzyme. The protein part of such an enzyme is
called the apoenzyme or apoprotein. Coenzymes act as transient carriers of specific
functional groups. Most are derived from vitamins, organic nutrients required in small
amounts in the diet
VITAMINS AND COENZYMES

Reactions within the cells work to either break down nutrients or combine molecules for
cellular activities that keep the cells alive. Without enzymes, these reactions may not occur.
Most of these biochemical pathways in living things are enhanced by enzymes. The
efficiency of the enzyme-catalysed reactions is often increased by the presence of “helper
molecules” called coenzymes. Enzymes speed up these reactions. Coenzymes, in turn,
support the functions of enzymes. They loosely bind to enzymes to help them complete
their activities.
Coenzymes are non-protein, organic molecules that facilitate the catalysis, or reaction, of its
enzyme. Coenzymes are one of two types of cofactors used by enzymes in these enzymatic
reactions. The other types of cofactors are inorganic ions.
Coenzymes work by binding to the active side of the enzymes, the side that works in the
reaction. Since enzymes and coenzymes are non-metal organic molecules, they bind
together by forming covalent bonds. The coenzymes share electrons with the enzymes,
rather than lose or gain electrons. When they form this bond, they only help the reaction to
occur by carrying and transferring electrons through the reaction. Coenzymes do not
become integral parts of the enzymatic reaction. Instead, the covalent bonds are broken at
the end of the reaction, and the coenzyme returns back to free circulation within the cell
until it is used again.
Taking vitamins, whether from eating foods or in supplement form, increases the amount of
coenzymes in the body. Some vitamins help the body produce coenzymes, such as folic acid
and some of the B vitamins, while other vitamins directly act as coenzymes, such as vitamin
C. Without vitamins, the body would be unable to produce coenzymes. A vitamin is defined
as an organic compound that is required in the diet in small amounts for the maintenance of
normal metabolic integrity. There are two types of vitamins; fat-soluble and water-soluble,

neither of which is produced by the human body. Therefore, it is essential that our daily diet consists
of vitamin-rich foods.
Water-Soluble Vitamins Function As Coenzymes

The water-soluble vitamins are ascorbic acid (vitamin C) and a series known as the vitamin B
complex.
Riboflavin (B2)
Thiamine (B1)
Pyridoxine (B6) Cobalamine
Fat-Soluble Vitamins Participate in Diverse Processes

Not all vitamins function as coenzymes. The fat-soluble vitamins, which are designated by
the letters A, D, E, and K, have a diverse array of functions. Vitamin K, which is required for
normal blood clotting (K from the German koagulation), participates in the carboxylation of
glutamate residues to γ-carboxyglutamate, which makes modified glutamic acid a much
stronger chelator of Ca2+.
Vitamin A (retinol) is the precursor of retinal, the light-sensitive group in rhodopsin and
other visual pigments. Retinoic acid, which contains a terminal carboxylate in place of the
alcohol terminus of retinol, serves as a signal molecule and activates the transcription of
specific genes that mediate growth and development.

A metabolite of vitamin D is a hormone that regulates the metabolism of calcium and
phosphorus. A deficiency in vitamin D impairs bone formation in growing animals. Vitamin E
(α-tocopherol) reacts with and neutralizes reactive oxygen species such as hydroxyl, radicals
before they can oxidize unsaturated membrane lipids, damaging cell structures.
Important Coenzymes
Coenzymes fall into two groups:
 Metabolite coenzymes, most of which are derived from nucleotides
 Vitamin-derived coenzymes, which are synthesized from required dietary precursors.
Vitamins and derivatives:
Coenzyme Vitamin Chemical groups transferred

Thiamine pyrophosphate Thiamine (B1) 2-carbon groups, α cleavage
FMN, FAD and Coenzyme F420 Riboflavin (B2) Electrons
NAD+ , NADP+ Niacin (B3) Electrons
Coenzyme A Panthothenic acid (B5) Acetyl, acyl groups
Pyridoxal phosphate Pyridoxine (B6) Amino and carboxyl groups
Tetrahydrofolic acid Folic acid(B9) Methylene groups

Cobalamine Cobalamine (B12) hydrogen, alkyl groups
Ascorbic acid Vitamin C Electrons
Biocytin Biotin (H) CO2
Menoquinone Vitamin K Carbonyl groups, electrons
Lipoamide Lipoic acid electrons, acyl groups

Non-Vitamins:
Coenzyme Chemical groups transferred

Adenosine triphosphate Phosphate group
S-Adenosyl methionine Methyl group
Coenzyme Q Electrons
Coenzyme M Methyl group
Coenzyme B Electrons
Gluthatione Electrons
Cytidine triphosphate Diacylglycerols and lipid head groups
Methanofuran Formyl group
Molybdopterin Oxygen atoms
3'-Phosphoadenosine-5'-phosphosulfate Sulfate group

IBB UNIVERSITY BIOCHEM LECTURE

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IBB UNIVERSITY BIOCHEM LECTURE

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IBB UNIVERSITY, LAPAI

2016/2017 ACADEMIC SESSION

III. Carbohydrate Chemistry

IV. Lipid Chemistry

V. Protein and Amino Acid Chemistry

VI. Nucleic Acid Chemistry

VII. Enzymes, Vitamins and Coenzyme

Musa A. Dickson, PhD | Structure, Chemistry and Functions of Biomolecules 1

Distribution of the most important A Comparison of Elements Present in Non-living and

Earth (crust) Human body Percentage weight of

O 47.00% H 63.00% Element Earth (crust) Human body

Si 28.00% O 25.50% H 0.14 0.5

Al 7.90% C 9.50% C 0.03 18.5

Fe 4.50% N 1.4 5% O 46.6 65

Ca 3.50% Ca 0.31% N very little 3.3

Na 2.50% P 0.22% S 0.03 0.3

K 2.50% Cl 0.08 5% Na 2.8 0.2

Mg 2.20% K 0.06 5% Ca 3.6 1.5

Ti 0.46% S 0.05% Mg 2.1 0.1

H 0.22% Na 0.03% Si 27.7 negligible

The sequence that relates biomolecules to living organism is:

Musa A. Dickson, PhD | Structure, Chemistry and Functions of Biomolecules 2

Examples of Biomolecules, their subunits and functions:

Carbohydrates Elements- CHO

Nucleic Acids Elements- CHOP

Lipids Elements- CHO

Musa A. Dickson, PhD | Structure, Chemistry and Functions of Biomolecules 3

Structural isomerism occurs in biomolecules in a variety of forms; in carbohydrates the

Musa A. Dickson, PhD | Structure, Chemistry and Functions of Biomolecules 4

Stereoisomers can be split up in accordance with the non-superimposability, into two

Stereoisomerism is found in carbohydrates in various forms; D and L isomers, α and β

Musa A. Dickson, PhD | Structure, Chemistry and Functions of Biomolecules 5

Chirality of a compound is its existence in two non-superimposable forms (i.e mirror

Musa A. Dickson, PhD | Structure, Chemistry and Functions of Biomolecules 6

Chirality in biological world has great significance, as it affects enzyme-substrate, antigen-

Musa A. Dickson, PhD | Structure, Chemistry and Functions of Biomolecules 7

1. Classify each pair of compounds as constitutional isomers or stereoisomers.

4. Locate the stereogenic centers in each biomolecule

Musa A. Dickson, PhD | Structure, Chemistry and Functions of Biomolecules 8

The carbohydrates are a group of naturally occurring carbonyl compounds (aldehydes or

More complex carbohydrates may contain nitrogen, phosphorus or sulphur in addition to

Musa A. Dickson, PhD | Structure, Chemistry and Functions of Biomolecules 9

PHYSIOLOGICAL ROLE AND BIOLOGICAL IMPORTANCE

Biosynthesis of other compounds

Musa A. Dickson, PhD | Structure, Chemistry and Functions of Biomolecules 10

Simple carbohydrates Complex carbohydrates (Disaccharides,

Triose Tetrose Pentose Hexose Heptose Octose Nonose

Functional Aldose: sugars having an Ketose: sugars having a ketone

Monosaccharides are the simplest sugars consisting of single polyhydroxy aldehyde or

Polysaccharides are polymers of monosaccharide units joined in long linear or branched

a) as a storage form of fuels and

Musa A. Dickson, PhD | Structure, Chemistry and Functions of Biomolecules 11

Glyceraldehyde is an aldotriose; dihydroxyacetone is a ketotriose. Each exists in two series,

1. Monosaccharides are polyhydroxy aldehydes or ketones and their derivatives having

Musa A. Dickson, PhD | Structure, Chemistry and Functions of Biomolecules 12

Glyceraldehyde contains only one asymmetric carbon atom (carbon

Derive the D- and L- hexose series from:

Musa A. Dickson, PhD | Structure, Chemistry and Functions of Biomolecules 13

Observed rotation (in degrees) x 100

Where, α = specific rotation in degrees at temperature usually 25 oC and the wavelength of

Musa A. Dickson, PhD | Structure, Chemistry and Functions of Biomolecules 14

Kiliani-Fischer Cyanohydrin Synthesis