CHAPTER-1: CHEMISTRY OF CARBOHYDRATES

Carbohydrates form an important group of biomolecules which are the most abundant
biomolecule in nature. Carbohydrates are mainly composed of elements such as carbon,
Hydrogen and oxygen and are usually called as the hydrates of carbon (sometimes they contain
nitrogen, phospurus and sulphur also).

Definition:- Carbohydrates are defined as poly hydroxyl aldehydes or polyhydroxy ketones or

substances that yield such compounds on hydrolysis.

Biological importance of carbohydrates

1. Carbohydrates form the main source of energy for most organisms.

2. Certain carbohydrates form an important structural component of cell membranes.

3. Carbohydrate associate with proteins form glycoprotein and with lipids form Glycolipids.

4. Glycogen forms the stored form of energy in liver and skeletal muscles.

5. Ribose and deoxy ribose sugars form important structural component nuclic acids.

8. Cellulose is a structural polysaccharide present in the plant cellwall.

9. Chitin is a structural polysaccharide which is present in the exoskeleton of insects.

Classification of carbohydrates
The simplest unit of a carbohydrate is called a saccharide unit. The term saccharide came
from a Greek word “ saccharone” , meaning sweet to taste. The saccharide unit cannot be
hydrolysed in to simpler unit without the loss of its properties. Carbohydrate may differ in the
number of saccharide unit present ie. it may contain one, few or many numbers of saccharide
unit.

Based on the number of saccharide unit present i.e. based on the structural complexity,
carbohydrates are classified in to 3 major classes. They are:-

1. Monosaccharides:-contain only one saccharide unit. The sachharide unit may contain 3-7
carbon atoms.
2. Oligosaccharides:- contain 2-10 monosaccharide units which are linked together by
glycosidic linkages.
3. Polysaccharides:-contain more than ten monosaccharide units linked together by
glycosidic linkages. It may contain even hundreds or thousands of monosaccharide units
i.e. they are polymers of monosaccharide units.
1. Monosaccharides: Monosaccharides are the simplest carbohydrates. Monosaccharides
contain only one saccharide unit that cannot be hydrolysed in to simpler forms.
Monosaccharides are generally sweet to taste and are usually called as simple sugars.
Monosacharides contain 3-7 carbon atoms in their structure. The general formula of a
monosaccharide is C n H 2n On or (C H2O) n.

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 All monosaccharides posses either an aldehydes group (-CHO) or a keto (C=O) group as its
functional group. Due to the presence of this carbonyl group all monosaccharides are having the
property of reducing other compounds (getting themselves oxidized) and therefore they are also
called as reducing sugars.

Depending on the configuration of –OH group in the penultimate carbon atom

monosaccharides can exist in two forms –Dextro form or D-form and leavo form or L-form. If –
OH group is present in the right hand side, the monosaccaride is called D-form and when –OH
group is present in the left hand side, then it is called as L-form. Most of the monosaccharides
present in the biological system are in the D-form. L-form of monosaccharides is present in
certain bacterial polysaccharides.

Monosaccharides are further classified in to different groups based on different ways.

1. Based on the type of functional group present.

2. Based on the number of carbon atoms present
3. Based on the type of functional group present, monosaccharides are classified in to two
different groups. They are:-

a)Aldoses:-Aldoses are monosaccharides which contain an aldehydes group (- CHO) as its

functional group. Examples are Glucose, Ribose, Erythrose etc.

b)Ketoses:- Ketoses are monosaccharides which contain a keto group(-C=O) as its

functional group. Examples are Fructose, Erythrulose, Dihydroxyacetone etc.

2.Based on the number of carbon atoms present, monosaccharides are classified in to the
following groups and subgroups.

Groups Mol. Formulae sub-groups Examples

1. Trioses –contain 3 carbon atoms (C3 H6 O3) - aldotrioses Glyceraldehyde

-ketotrioses Dihydroxy acetone

2. Tetroses –contain 4 carbon atoms (C4 H8 O4) - aldotetroses Erythrose, Threose

- ketotetroses Erythrulose

3. Pentoses –contain 5 carbon atoms (C5 H10 O5) - aldopentoses Ribose, Xylose

Arabinose.

-ketopentoses Ribulose, Xylulose

4. Hexoses –contain 6 carbon atoms (C6 H12 O6) - aldohexoses Glucose, Mannose

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 Galactose.

- ketohexoses Fructose

5. Heptoses –contain 7 carbon atoms (C7 H14 O7) - aldoheptoses Sedoheptose

-ketoheptoses Sedoheptulose

I. Monosaccharides :Structure properties and functions

1. D-Glucose

D. Glucose is the most important (most abundant also) of all monosaccharides present in the
living system. It is also called as Dextrose (D-form of Glucose). Glucose is an aldohexose
sugar,containing six carbon atoms and an aldehydes group(-CHO) as the functional group. The
first carbon atom forms the functional group and this carbon is called the carbonyl carbon
atom. D-glucose forms the building blocks of polysaccharides such as starch, glycogen, cellulose
etc .In body D-glucose is oxidized (degraded) by a pathway called glycolysis. The structure of
Glucose molecule can be represented in different manner. These are:-

a) Open chain structure –simplified representation of glucose structure.

b. Fischer’s projection formula:-This structure was proposed by Emil Fischer. This is based on
the observation that in solutions glucose assumes a ring form. When D- glucose is put in a
watery medium , the 5th-OH group of the glucose molecule react with the carbonyl group (1st
carbon) resulting in the formation of a hemi-acetal linkage (also called hemi-acetal bridge)
between the two carbon atoms .

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c. Haworth ring structure :-This structure was proposed by Haworth. It is a modification of the
projection formula proposed by Fischer. Accordingly, in solution the carbon skeleton of glucose,
together with the oxygen atom of the hemi- acetal bridge form a 6- membered ring structure
that resembles a “pyran” ring. The chemical name of this structure is D-Glucopyranose.

Haworth ring structure

Functions-

1. D-Glucose is the major source of energy in our body (chief fuel molecule).

2. It is the only source of energy for the nervous system and RBCs.

3. Glucose is the precursor of starch, Cellulose, Glycogen, etc

2. D-Fructose

D-Fructose is the sweetest monosaccharide. D-fructose is also called as fruit sugar as it is

present abundantly in fruits. It is also present in honey. It is a keto hexose sugar containing 6 C-
atoms. It contains a keto group (C=O) attached with the second c-atom and this carbon is called
carbonyl carbon atom.

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 In aqueous solutions D-fructose usually exists as a 5-membered ring which resembles a furan
ring. Therefore this ring structure is known as D-Fructofuranose (very rarely Fructose can also
form 6-membered “pyran ring” and is then called as D- fructopyranose). Glucose and Fructose
are isomers. They possess the same molecular formulae, but different structural formulae and
functional groups

Functions

1. D-fructose is the only source of energy for spermatozoa.

2. D-fructose is oxidized via glycolytic pathway and yields energy.

3.D-fructose forms the building blocks of a plant polysaccharide called inulin.

3. D- Mannose

D-Mannose is an aldohexose sugar. It is commonly present in plants. Mannose is seen in some

glycoproteins. Within the cell D- Mannose is oxidized via glycolytic pathway and yields energy.
Mannose is the precursor of Mannuronic acid. The pyranose form of D- mannose is called D-
Manno pyranose.

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D-Mannose (open chain) alpha,D-Mannose (Haworth)

4. D- Galactose

D-Galactose is an aldo hexose sugar .Galactose is a component of the disaccharide Lactose

( Milk sugar).D-Glactose is a common monosaccharide present in glycoprotein and glycolipids.
Galactose is synthesized in mammary glands. D-galactose is oxidized via. the glycolytic pathway
and yields energy. The pyranose form is called D- Galactopyranose.

Alpha-D- Galactose
(Haworth)

5. D.Ribose , D.deoxy ribose ,Ribulose , Xylose ,Arabinose and Xylulose.

Ribose is an aldopentose sugar. It is formed in the body from D- Glucose by HMP shunt.
Ribose is the sugar present in Ribonucleotides which are the building blocks of RNA. 2-deoxy
ribose is the sugar present in deoxy ribonucleotides which build up DNA.

D-Ribose doesn’t have any role in energy production. Ribose and deoxy ribose in solution
form 5- membered furanose ring structures-D- Ribofuranose and 2-deoxy D-Ribofuranose
respectively.

Ribose and Ribulose are isomers. Arabinose and xylose are the 2’ and 3’epimers of D-Ribose
respectively. Xylulose is the 3’epimer of D- Ribulose. Arabinose and Xylose are present only in
Plants.

2 -deoxy beta- D-ribofuranose (found in DNA)

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 Beta- D-Ribofuranose (found in RNA)

D- Arabinose D-Xylose L- Xylulose

6. D. Erythrose and D. Erythrulose

These are tetrose sugars which contain 4 carbon atoms. Erythrose is an aldotetrose where as
Erythrulose is a ketotetrose. Erythrose and Erythrulose are formed in the body as intermediates
of metabolic pathways. They will not form ring structures in solutions. Erythrose and
Erythrulose are isomers.

D-Erythrose D- Threose

7. D.Glyceraldehyde and Dihydroxy acetone

They are the simplest of all monosaccharides and contain 3 carbon atoms. They cannot form
ring structures. Glyceraldehyde and Dihydroxy acetone are isomers. Dihydroxy acetone is
optically inactive as it does not contain an asymmetric carbon atom in its structure. So there is
no D&L as well as d & l forms for Dihydroxy acetone. Glyceraldehyde and Dihydroxy acetone
are formed in the body as metabolic intermediates.

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Epimers and Epimerism
Epimers are defined as monosaccharides which differ in the configuration of –OH group in
any one of the carbon atom other than the functional group carbon and the phenomenon is
known as epimerism.

Example

D-Mannose is the 2’ epimer of D-Glucose and vice versa i.e. they differ in the configuration
of
–OH group in the 2nd carbon only .

D-Galactose is the 4’ epimer of D-Glucose and vice versa i.e. they differ in the configuration
of
–OH group in the 4th carbon only .

D-Mannose (2’ epimer) D-Galactose (4’ epimer ) D-Glucose

Anomers and Anomerism

Anomers are defined as monosaccharides which differ in the configuration of –OH group in the
carbonyl carbon atom (functional group carbon) and the phenomenon is known as anomerism.

Examples.

a) Alpha D. Glucose and beta D. Glucose.

b) Alpha D. Galactose and beta D. Galactose

c) Alpha D. Mannose and beta D. Mannose

(In alpha form –OH group is in the right hand side in the case of Fischer’s projection /below the
plane in the case of Haworth structure ,where as in beta form –OH group is in the left hand
side in Fischer’s projection/above the plane in the case of Haworth structure .

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 Alpha, D- Glucose Beta, D- Glucose

II. Oligosaccharides
Carbohydrates containing 2-10 monosaccharide units are generally called as
oligosaccharides. The monosaccharide units are linked together by a special type of linkage
called glycosidic linkage. A glycosidic linkage is defined as a linkage formed by the reaction
between the –OH groups of two monosaccharide units with the elimination of one molecule of
water.Depending on the number of monosaccharide units present oligosaccharides may be
classified as Disaccharides (containing 2 monosccharide units), Trisaccharides (containing 3
monosccharide units),Tetrasaccharides, pentasaccharides and so on.

Among the oligosaccharides disaccharides are very common in living system and perform
important biological functions .Examples include sucrose, maltose, lactose, isomaltose
,cellobiose etc.

Trisaccharides are very rare. Only a very few are identified. Maltotriose is a very good
example. The structure consists of 3 molecules of D.Glucose molecules linked together by 2
alpha, 1-4 glycosidic linkages. Another example is Raffinose. Raffinose, also called melitose, is a
trisaccharide that is widely found in legumes and cruciferous vegetables, including beans, peas,
cabbage, brussels sprouts, and broccoli. It consists of galactose connected to sucrose via a 1α→6
glycosidic linkage. Humans cannot digest saccharides with this linkage and the saccharides are
fermented in the large intestine by gas-producing bacteria. Tablets containing the enzyme
alpha-galactosidase, such as Beano, are frequently used as digestive aids to prevent gas and
bloating. The enzyme is derived from selected strains of the food grade fungus Aspergillus niger.

Raffinose
Maltotriose

Other oligosaccharides are (tertra saccharides onwards) very rare and some are formed in the
digestive tract during the partial enzymatic digestion of polysaccharides.

Monosaccharides and Disaccharides are generally called as sugars because they are sweet to
taste. Monosaccharides are specifically called as simple sugars because they contain only one
saccharide unit.

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Examples of Disaccharides

Disaccharides can be divides in to 2 classes–reducing disaccharides and non-reducing

disaccharides. Reducing disaccharides contain a free aldehydes or ketone group in its structure.
Non reducing disaccharides do not contain a free aldehydes or ketone group in its structure.
Examples of reducing disaccharides are maltose and Lactose. An example for a non -reducing
disaccharide is Sucrose.

1.Maltose:- Maltose is reducing disaccharide. It is usually called as malt sugar because it is

present abundantly in malt (partially fermented starch). The structure of maltose consists of 2
molecules of D.Glucose units linked together by an alpha, 1-4 glycosidic linkage. Maltose is
formed in the digestive tract during the hydrolysis of starch and glycogen by an enzyme called
amylase. Maltose is hydrolysed in to 2 molecules of D-glucose by an enzyme called Maltase.

Maltose (alpha 1-4 linkage)

Chemical name: alpha D- glucopyranosyl (1-4)glucopyranoside

2. Lactose :- Lactose is a reducing disaccharide. It is usually called as milk sugar as it is

present abundantly in milk .The structure of Lactose consists of one molecules of α-D.Glucose
and one molecule of β -D. Galactose linked together by a β, 1-4 glycosidic linkage. Lactose is
hydrolysed by an enzyme called lactase to yield one molecules of D. Glucose and one molecule of
D.Galactose. Lactose is specifically called as beta lactose.

Lactose (β, 1-4 glycosidic linkage)

Chemical name : Beta,D- galactopyranosyl(1-4)glucopyranoside

3. Sucrose:-Sucrose is a non -reducing disaccharide as it lacks a free aldehydes or keto

group. It is usually called as table sugar as it is commonly used as a sweetening agent in foods
and drinks. The structure of sucrose consists of one molecules of alpha D.Glucose and one
molecule of beta D.Fructose linked together by an alpha, 1-2 glycosidic linkage (both functional
groups are involved in bond formation and are not free). Sucrose is hydrolysed by an enzyme
called sucrase to yield one molecules of D. Glucose and one molecule of D. Fructose.

Sucrose (alpha, 1-2 glycosidic linkage)

Chemical name: alpha D- glucopyranosyl(1-2)beta D- fructofuranoside

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4. Isomaltose and Cellobiose:-Isomaltose is reducing disaccharide. It is present in
plants. The structure of isomaltose consists of 2 molecules of D. Glucose units linked together by
an alpha, 1-6 glycosidic linkage. Isomaltose is formed in the digestive tract during the hydrolysis
of starch (amylopectin) and glycogen by an enzyme called amylase. Isomaltose is hydrolysed in
to 2 molecules of D-glucose by an enzyme called Isomaltase present in the intestinal juice which
specifically hydrolyzes the alpha 1-6 linkage.

Cellobiose is a reducing disaccharide which is formed during the partial digestion of cellulose
by the enzyme cellulase (specifically hydrolyzes the beta 1-4 glycosidic linkage). The structure
consists of 2 molecules of beta-D- Glucose linked together by a beta 1-4 glycosidic linkage. The
chemical structures of Isomaltose and cellobiose is shown below.

Structure of isomaltose

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Reducing and non- reducing sugars :-All reducing sugars give positive reaction with Benedict’s
reagent due to the presence of a free aldehydes or keto group. Whereas non reducing sugars will
not give positive reaction.

Examples

Reducing sugars –all monosaccharides and disaccharides such as maltose and lactose.

Non reducing sugars- Sucrose.

Benedict’s test is the commonly used test for the detection of reducing sugars in urine.

III. Polysaccharides
Carbohydrates which contain large numbers of monosaccharide units linked together by
glycosidic linkages are called polysaccharides. Polysaccharides are highly complex
carbohydrates which are polymers of monosaccharide units. Depending on the chemical
composition ie. based on the type of monosaccharide unit present polysaccharides are classified
in to two groups – Homopolysaccharides and heteropolysaccharides.

Homopolysaccharides also called homoglycans are polysaccharides which contain the same
type of monosaccharide units.

Examples –Starch (a homopolymer of alpha D- Glucose), Glycogen (a homo polymer of

alpha D- Glucose), Cellulose (a homopolymer of beta D- Glucose) and chitin (a homo polymer of
N- acetyl D-Glucosanine).

Starch – Structure and function:-Starch is a homopolysacchride composed of hundreds or

thousands of D- Glucose units which are joined by Glycosidic linkages. Generally starch is
composed of two different components-amyloses and amylopectins. The proportion of amylose
and amylopectin varies depending on the source from where the starch is obtained.

Amylose – amylose is a straight chain polymer of D-glucose in which the glucose units are
linked together by alpha,1-4 Glycosidic linkages.

Amylose

Amylopectin – amylopectin is a branched polymer of D-glucose in which the glucose units are
linked together by alpha, 1-4 and alpha,1-6 Glycosidic linkages. The 1-6 linkage is responsible
for the branching. The branching is seen in every 24-30 residues.

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 Amyolopectin

Amylose is soluble in water due to low molecular size, whereas amylopectin is insoluble in water
due to high molecular size. Starch, the mixture of amylose and amylopectin is partially soluble
in water.

Starch shows deep blue color with iodine reagent due to micelle (a blue colored complex with
iodine) formation. Starch is digested by enzymes called amylases.

Starch functions as the storage carbohydrate in plant tissue for future use by the germinating
seedlings. Starch is stored in different plant parts such as fruits (cereal grains such as rice,
wheat etc) stem (potato) and in roots (Tapioca).Starch is seen as small particles known as starch
granules within the cytoplasm of the cells of storage tissues. Starch is the main source of D-
Glucose in our diet.

Glycogen- Structure and function:- Glycogen is a homo polysaccharide composed of

hundreds or thousands of D- Glucose units which are joined by Glycosidic linkages. Glycogen is
the storage carbohydrate in animal tissues such as liver and skeletal muscles. Glycogen is also
called as animal starch. Muscle glycogen is a stored energy source for muscle functioning where
as liver glycogen is utilized in the maintenance of blood glucose level during hypoglycemia and
hyperglycemia. Glycogen can be seen as glycogen granules within the cytoplasm of hepatocytes
and myocytes.

Glycogen is a branched polymer of D-glucose in which the glucose units are linked together
by alpha, 1-4 and alpha, 1-6 Glycosidic linkages. The 1-6 linkage is responsible for the
branching. Glycogen is having a structure comparable to that of the amylopectin component of
starch, but the degree of branching is more in glycogen. The branch points are seen in every 9-
11 residues.

Glycogen is also hydrolyzed by amylases to yield maltose and iso-maltose. Glycogen gives
red color with iodine reagent

Cellulose –structure and functions

Cellulose is the most abundant carbohydrate and most abundant biomolecule in nature. It is
very amazing that the plant world synthesizes around 80Kgs of cellulose per individuals per day.

Cellulose is a structural polysaccharide present in plant cell wall. Cellulose provides protection
and mechanical support to plant cell. It is straight chain homo polysaccharide composed of
hundreds or thousands of beta, D- Glucose units which are joined by beta 1-4, glycosidic linkages.

Cellulose is not digested in humans as we lack the enzyme cellulase in the intestine and has no
nutritional value. But Cellulose is digested in ruminant animals with the help cellulase enzyme

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produced by symbiotic bacteria present in the rumen of the stomach. However Cellulose forms the
major component of dietary fibre in humans. It is helpful for the following.

a) It gives bulk to the food.

b) It increases the porosity and water retention capacity of food.
c) It increases the penetration of digestive secretions and enhances digestive process.
d) It helps in water re-absorption in the intestine.
e) It increases peristaltic movement and reduces constipation.

Heteropolysaccharides also called heteroglycans are polysaccharides which are formed of more
than one type of monosacchride units. Heteropolysacchrides containing repeating units of an
amino sugar and a sugar acid are very common and are generally called as glycosaminoglycans.
These are found mostly in association with protein in the extra cellular space. It holds large
quantity and increases the water retention capacity.

Examples- Hyaluronic acid, Heparin, Chondriotin sulphate etc. are very common.

Hyaluronic acid:-Hyaluronic acid is a hetero polysaccharide which is present in connective

tissue, bone cartilage and also in the synovial fluid of joints. It is a long polymeric chain
composed of alternating units of N-acetyl beta,D -Glucosamine and beta, D -glucuronic acid
which are joined by 2 different types of glycosidic linkages – beta 1-4 and beta 1-3 glycosidic
linkages.It forms an important component of bone and cartilage. In the synovial fluid it
functions as a shock absorber and a lubricant and reduces the friction during movement.

Heparin:- Heparin is a hetero polysaccharide which is present in the liver and lungs. It is a
long polymeric chain composed of alternating units of N-acetyl beta, D –Galactosamine -6-
sulphate and beta D-glucuronic acid which are joined by 2 different types of glycosidic linkages
– beta 1-4 and beta 1-3 glycosidic linkages.

Heparin is a natural anticoagulant which prevents blood coagulation in blood vessels.

CHAPTER-2: CHEMISTRY OF LIPIDS

Definition:- Lipids are a heterogeneous group of compounds composed of Carbon

Hydrogen and Oxygen, which are insoluble in water but soluble in non-polar solvents such
as chloroform, ether and benzene. These solvents are commonly called as fat solvents.

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Though this definition covers majority of the lipids, certain lipids will not come under this
definition. For example derived lipids like fatty acids are relatively soluble in water.

Lipids form an important group of biomolecules which are distributed in plants, animals and
microorganisms. They are organic molecules containing mainly of carbon, Hydrogen and
Oxygen and in some cases very less amounts of nitrogen and phosphorus. Lipids are usually
oily or greasy in its physical nature. Lipids present in plants animals and in microorganisms
vary greatly in its chemical nature.

General classification

Based on the general physical nature lipids are classified in to two groups. –Fats and oils.

1. Fats- Fats are defined as lipids which exist as solid at ordinary temperature
Eg. Animal fat

2. Oils-Oils are defined as lipids which exist as liquid at ordinary temperature.eg.

Cooking oil (vegetable oil).
General biological functions of lipids (in animals/humans)

3. It is the chief structural component of cell membrane phospholipids).

4. Lipids (fatty acids) are the second major source of energy.
5. Beta oxidation product of fatty acids, acetyl COA functions as the precursor for the
synthesis of a variety of important biomolecules ( steroid hormones , vit.D, Bile salts
etc.)
6. Fat deposition in the adipose tissue under the skin act as a heat insulation which
prevent the loss of body heat.
7. Fatty acid oxidation in the brown adipose tissue is essential for thermogenesis (heat
production) in cold conditions.
8. Lipids help in the packaging and protection of various internal organs.
9. Steroid hormones are chemically of lipid nature.
10. The fat stored in the adipose tissue functions as a shock absorber and protect the
internal organs.
11. The fat deposit around internal organs provide a cushioning effect and affords
protection.
12. The fat stored under the skin maintains the health of the skin and provides contour to
the body.
13. Lipid components in the food improves the taste and palatability.
14. The myelin sheath around the neurons function as an electrical insulator.
15.Lipids provide the shape to the body and attractiveness (contour) to the skin.
General biological functions of lipids in plants

Plant lipids are quite different from lipid seen in animals. They perform a great variety of
biological functions which can be summarized as follows.

16. Lipids functions as a storage biomolecule other than carbohydrates. Lipids are the
stored form of energy for future use. Lipids are mainly stored in seeds and are
utilized during germination. It is also a source of oil for human consumption.
17. Lipids (mainly phospholipids) form the chief structural component of cell
membranes.

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 3. Lipids yields large amounts of energy during its oxidation( beta oxidation)
4. Plant pigments such as chlorophylls Xanthophylls and carotenoids are also included
under a class of miscellaneous lipids. These pigments functions as the light harvesting
molecules (during photosynthesis) and also imparts attractive colors to different plant
parts which is helpful in pollination and seed dispersal.
5. Poly unsaturated fatty acids (PUFA) synthesized in plants are highly essential for the
animals to survive. They form essential fatty acids for humans.
Chemical Classification of Lipids

Based on the chemical nature and structural complexity, lipids are classified in to three
major groups – simple lipids compound lipids and derived lipids. Simple lipids are again
grouped in to two- neutral fats and waxes. Compound lipids are again grouped in to several
subgroups –the main types are phospholipids and glycolipids. Derived lipids include fatty
acids steroids etc. The classification if schematically represented as follows.

Lipids

Simple lipids Compound lipids Derived lipids

1. Neutral fat 1. Phospholipids 1.Fatty acids

2. Waxes 2. Glycolipids 2. Steroids etc.

3. Aminolipids etc.

I. Simple lipids :-Simple lipids are defined as esters of fatty acids with alcohol. The fatty
acids are estrified to the alcohol as a result of the reaction between the acidic carboxylic
group and the –OH group. Depending on the type of alcohol present simple lipids are again
classified in to two groups-neutral fats and waxes.

1.Neutral fats

Neutral fats are defined as esters of fatty acids with glycerol. Glycerol is a tri-hydroxy
alcohol. Chemically neutral fats are known as triglycerides or tri-acyl glycerol (TAG). The

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structure of TAG consists of one molecule of glycerol and three molecules of fatty acids. The
fatty acids are linked to the 1st 2nd and 3rd position of the glycerol molecule by ester linkages.

Tri acyl glycerol (TAG) /Triglyceride/Neutral fat

1, 3 Di acyl glycerol (DAG) 1, Mono acyl glycerol (MAG

Functions of neutral fat

1.TAG is the main storage lipids in plants. TAG stored in seeds is utilized by the embryo for
its development.

2. TAG forms stored lipid in the adipose tissue of animals which is

- oxidize to produce energy
- utilized for thermogenesis in cold conditions
- and effective as an insulation which prevents loss of body heat
3. TAG is the basis of all cooking oils.

Important reactions of neutral fats/oil

4.Hydrolysis with water and acid:-When TAG is boiled with water and little acid, the ester
linkages will be hydrolyzed liberating glycerol and free fatty acids.

H2 O / Acids

TAG Glycerol + 3, Free fatty acids

2.Saponification reaction :-When TAG is allowed to react with strong alkalies like NAOH
or KOH, all the ester linkages will be broken liberating glycerol and free fatty acids. The
liberated free fatty acids react with excess of alkali to yield the corresponding salts ( Na or
K salts)of fatty acids. These salts of fatty acid are known as soap and the reactions that lead
to the formation of soap is known as saponification reaction. Na salt of fatty acid is called

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washing soap and K salts of fatty acid is called bath soap. The reactions can be represented as
follows

Na OH / KOH/ H2O

TAG Glycerol + 3 Fatty acids

Fatty acids + NaOH / KOH R-COO K+ (Bath soap)

RCOO Na+ (Washing soap)

Saponification number- Saponification number can be defined as the no. of mgs of KOH
required to saponify one gm of fat or oil. Understanding of saponification number gives an
idea about the average mol. size of the fatty acids present in the particular fat sample.

3. Iodination:-Unsaturated fatty acids present in the fat can absorb iodine atoms at the point
of unsaturation converting the double bond in to single a bond. This process is called
iodination of fat. The amount of iodine absorbed is a measure of the degree of unsaturation of
fatty acids. The reaction can be represented as follows.

Iodine number – Iodine number can be defined as the number of gms of iodine utilized for
iodinating 100 gms of fat sample. Iodine number gives an idea about the degree of
unsaturation of fatty acids present in the fat.

When oils are kept open for a long time (months) in contact with the atmosphere we feel
some unusual smell and taste. This is because the fatty acids present in the fat are oxidized by
the effect of atmospheric oxygen and the free fatty acids are liberated, leading to the loss of
quality of the oil. Liberation of fatty acids leads to an increase in the acidity (decrease in PH)
of the oil making it inedible.

2. Waxes

Waxes are defined as esters of fatty acids with mono-hydroxy aliphatic alcohol and with
cholesterol.

Eg. Esters of butyl alcohol. A number of waxes are produced commercially in large amounts
for use in cosmetics, lubricants, polishes, surface coatings, inks and many other applications.
Some of these are of mineral origin (e.g. montan wax from brown coal/peat deposits), and
only those from living organisms are discussed here. Amongst them are -

1.Beeswax - Glands under the abdomen of bees secrete a wax, which they
use to construct the honeycomb. The wax is recovered as a by-product when the honey is
harvested and refined. It contains a high proportion of wax esters (35 to 80%).

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 2.Wool wax (lanolin) - The grease obtained from the wool of sheep
during the cleaning or refining process is rich in wax esters.

3. Plant Surface Waxes. Waxes found at the surface of plant.

II .Compound lipids

These are complex lipids which contain a non lipid part in its structure. Based on the
chemistry or chemical composition compound lipids are of two important types –
Phospholipids and glycolipids.

1.Phospholipids:- The structure of phospholipids consists of one molecule of Glycerol, 2

molecules of Fatty acids, one molecule of phosphoric acid and a nitrogenous base. The fatty
acids are estrified to the 1st and 2nd position of the glycerol molecule. Phosphoric acid is
estrified to the 3rd position of the glycerol molecule and the nitrogenous base is estrified to
the phosphoric acid group. Important examples of phospholipids are posphatidic acid,
phospahatidyl choline, phosphatidyl ethnolamine and phosphatidyl inositol. The
chemical structures of these compounds are given below.

Phosphatidyl choline (lecithin) Phosphatidyl ethanolamine (cephalin)

Phosphatidyl serine Phosphatidyl Inositol

Special Functions

1. Phospholipids form the chief constituent of the cell membrane structure.

2. Play an important role in the absorption of lipids and fat soluble vitamins in the intestine.

3. Phospholipids are involved in the storage and transport of other forms of lipids.

18
2)Glycolipids :-Glycolipids are defined as compound lipids which contain a carbohydrate as
a non-lipid component.

Functions

1. Form a minor constituent of cell membrane structure.

2. Responsible for maintaining the integrity of biological membranes.
3. Maintains cell – cell communication.
III. Derived lipids

This is the third group of lipids. As the name implies derived lipids are defined as less
complex forms of lipids which are derived from simple and compound lipids during its
degradation. They are relatively soluble in water. Derived lipids include a wide variety of
compounds. The most important type of derived lipids seen in plants are fatty acids and
steroids.

1. Fatty acids:-Fatty acids form an important group of derived lipids. Fatty acids are organic
acids containing a long hydrocarbon chain and an acidic carboxylic group as its functional
group. The length of hydrocarbon chain varies among fatty acids. Fatty acids are seen in two
different forms – Free fatty acid and esterified fatty acids. Free fatty acids are present in the
free form where as esterified fatty acids are found esterified to different types of alcohols.
( Glycerol, cholesterol etc.)

R-COOH

General structure of a fatty acid

(R- Represents the hydrocarbon chain)

Numbering of c- atoms

Fatty acids are having the general formula C n H (2n+1)-COOH. The ratio of hydrogen to
oxygen is very less in the case of fatty acids compared to carbohydrates Therefore fatty acids
are said to be more reduced than carbohydrates and therefore it yield more amount of energy
upon oxidation. Fatty acids are relatively soluble in water.

Classification of fatty acids based on different characteristics

1. Short chain, medium chain, long chain and very long chain fatty acids (VLFA)

Based on the length of the hydrocarbon chain fatty acids are grouped in to short chain (2-6
carbon), medium chain (8-10 carbon) long chain (12-20 carbon) and very long chin/VLFA
(more than 20 carbon).

19
2.Odd chain and even chain fatty acids:-It can also be classified in to odd chain fatty acids and
medium chain fatty acids based on whether it contain odd or even no. of carbon atoms. Most
of the fatty acids are even chain type.

3.Saturated and unsaturated fatty acids:- Based on the presence or absence of double bonds
fatty acids are grouped in to two – saturated fatty acids and unsaturated fatty acids . Saturated
fatty acids do not contain any double bonds in its structure. Unsaturated fatty acids contain
one or more double bond in its structure. If unsaturated fatty acids contain only one double
bond, they are called monounsaturated fatty acids. When the unsaturated fatty acids contain
more than one double bond in its structure, they are called polyunsaturated fatty acids
(PUFA).PUFA functions as essential fatty acids for human beings

4. Essential and non-essential fatty acids:-Based on the nutritional requirements fatty acids are
grouped under two classes – essential fatty acids and non essential fatty acids .Fatty acids
which are not synthesized in humans, but are highly essential for the metabolic activities
and are to be provided in the diet are called essential fatty acids. Examples are linoleic
acid, linolenic acid and arachidonic acid( PUFA). Fatty acids which are synthesized in
humans are called non-essential fatty acids. Palmitic acid, oleic acid etc.

5.Staight chain , branched chain(phytanic aicd) and cyclic fatty acids(chaulmoorgic acid).

Special functions of fatty acids

6.Fatty acids are the second major biomolecule that is oxidized for energy purpose. Fatty acids
are first degraded in to acetyl COA by a process called beta oxidation. Acetyl COA then
enters the TCA cycle and completely oxidized to CO2 and water. Since fatty acids are more
reduced than Glucose it will yield more amount of energy on oxidation.

7.Three of the PUFA are called essential fatty acids are called essential fatty acids as they are
not synthesized in humans and are to be supplied in the diet. Essential fatty acids are highly
essential for the synthesis of prostaglandins, prostacyclins and thromboxanes in humans.

8.Fatty acids are constituents of molecules like Neutral fat, waxes, glycolipids and
phospholipids. They perform diverse functions in plants and animals.

Functions of essential fatty acids:-

1. Arachidonic acid is required for the synthesis of biomolecules like

prostagalndins, prostacyclins and thromboxanes which perform important
physiological functions.
2. Essential fatty acids are present in the structure of phospholipids which forms an
important component of cell membrane structure

2. Steroids

Steroids are naturally occurring cyclic compounds containing a 5-membered perhydro-

cyclo-pentano-phenanthrene ring system in its structure. This ring system is generally known
as the steroid nucleus. The structure of steroid nucleus is shown below.

20
Steroids include different types of molecules such as

1.Sterols- cholesterol present in animals and phytosterols (eg. stegmasterol) present in plants.
cholesterol is a structural component of cell membrane. It also forms the precursor steroid
hormones, Vit. D , bile salt , bile acids etc.

2.Vitamin- vitamin D is a steroid which is formed in the skin by the action of UV -rays on
cholesterol.

3.Bile acids (bile salts) - cholic acid deoxy cholic acid and cheno deoxycholic acid
contain a steroid nucleus in their structures.

4.Steroid hormones – adreno corticosteroid hormones such as cortisone cortisol and

corticosterol are steroid derivatives. Sex hormones such as estrogen, progesterone and
estradiol (female) &Testosterone, esterone, androsterone (Male) etc. are steroids.

5. Drugs – Drugs commonly used in psychiatric medicine are mostly steroids.

CHAPTER 3: CHEMISTRY OF AMINO ACIDS AND

PROTEINS
Proteins are one of the chief biomolecules of living matter. Proteins may be defined
as high molecular weight mixed polymers of alpha amino acids linked together by special
types of linkage called peptide linkage. The total number of amino acids, the sequence in
which they are arranged and the overall three dimensional structure of the molecule are

21
characteristic of each protein and are responsible for its biological function. Proteins perform
a variety of functions in the living system.

Rubisco (The most abundant protein in the biosphere)

Collagen ( the most abundant protein in human body)

Amino acids

Amino acids are low molecular weight biomolecules containing a basic amino group (-
NH2/-NH3+) and an acidic carboxylic group (-COOH/-COO-) in its structure. Amino acids
are the building blocks of proteins. About 200 different types of amino acids are identified in
the living system so far. Of which only 20 amino acids are usually present in proteins. Other
amino acids are formed as intermediates of various metabolic pathways.

Based on their occurrence generally, amino acids can be grouped in to the following
categories.-protein amino acids and non protein amino acids

I. Protein amino acids:-

These are amino acids which are present in protein structure. Protein amino acids can be
divided in to two groups- common amino acids and Uncommon amino acids.

1.Common amino acids or Usual amino aids – These are amino acids which are
usually present in majority of the proteins. There are 20 amino acids which are commonly
present in proteins. Examples include Glycine, Alanine, Valine, Aspartic acid, serine,
cysteine etc.

2.Uncommon amino acids or Unusual amino acids - These are amino acids which are very
rarely present in proteins. Eg. 4-Hydroxy proline, 5-Hydroxy lysine and Selenocysteine.

(Of these Hydroxy proline and Hydroxy lysine are formed in the protein structure after
protein synthesis by the chemical modification of proline and lysine respectively. These are
present in the structure of collagen, the most abundant protein in human body present in
bone, cartilage, skin and connective tissue.

Selenocysteine is present in an enzyme protein glutathione peroxidase. Selenocysteine is

discovered only recently and is found to be directly incorporated during protein synthesis.
Therefore selenocysteine can be considered as the 21st common amino acid).

II. Non-protein amino acids.

Amino acids which are not seen in protein structure are called as non- protein amino
acids. These are usually formed in the body as intermediates of various metabolic pathways.

Eg. Citrulline –is an intermediate in urea cycle.

22
 Taurine – present in bile acid.

Beta alanine – present in COASH

General Biological functions of amino acids

1. Amino acids are the building blocks of

proteins.

Amino acids present in protein structure are called protein amino acid and amino acids
seen as free form in the body are called free amino acids.

2.Amino acids are precursors of several important biomolecules.

a). Hormones –adrenaline, nor adrenaline thyroxine etc.

b) Biological amines – Tryptamine , Tyramine , Histamine
( allergic factor)etc
c) Neurotransmitters – gama amino butyric acid ( GABA)
d) Bile acid - Taurocholic acid.

e) Beta alanine is present in COA and Vitamin pantothenic acid.

f) Heme present in heamoglobin is synthesized from several

amino acids.

g)Nucleotides, the building blocks of nucleic acids are synthesized from certain amino
acids.

h)creatine- a component of creatine –P, a high energy molecule required for muscle
contraction.

i)glutathione – a reducing cofactor required by the antioxidant enzyme,

glutathione peroxidase.

3. Energy source -The carbon skeleton of amino acids are oxidized in the body to liberate
energy.

AMINO ACIDS PRESENT IN PROTEINS

There are 20 different amino acids which are usually seen in protein structure. These
amino acids are usually called as alpha amino acids. They contain two different types of
functional group, an amino group (-NH2) and a carboxyl group (-COOH) both attached to a
central carbon atom called alpha carbon atom and hence the name alpha amino acids. Of the
remaining two valancies of the alpha carbon one is occupied by a hydrogen atom and the
other is occupied by a group which is usually called as -R group or side chain. All the 20
different amino acids are having the same basic structure, but differ only in the structure of
their R- groups. The general chemical structure of an alpha amino acid can be represented as
follows.

23
 Classification of Amino acids

Amino acids are classified in three different ways.

I . Based on the chemistry of R- group.

II. Based on the metabolic fate.

III. Based on the nutritional requirement.

I Classification based on the chemistry of R- group .Based on the chemical nature of the R-
group amino acids are classified into the following groups.

1. Simple amino acids

They contain a simple R- group in their structure.

E.g. Glycine and Alanine

Glycine (G, Gly.) Alanine (A, Ala.)

2. Aliphatic amino acids

They contain an aliphatic R- group in their structure.

Eg. Valine. Leucine, Isoleucine

Valine (V, Val.) Leucine L, Leu.) Isoleucine (I, Ile.)

24
3. Hydroxyl (-OH) group containing amino acids.
They contain a hydroxyl group in their R- groups.

E.g. Serine, and Threonine

Serine (S, Ser,) Threonine (T,

Thr.)

4. Sulphur containing amino acids

They contain a sulphur atom in their R- group

Eg. Methionine and Cysteine

Methionine (M, Met.) Cysteine (C, Cys.)

( thio-ether group) ( sulfhydryl

group)

5. Acidic amino acids

They contain an acidic carboxylic group in their R- group

Eg. Apartic acid and Glutamic acid

Apartic acid (D, Asp.) Glutamic acid ( E , Glu.)

6. Basic amino acids.

They contain a basic amino group in their R- group

Eg. Histidine(Imidazole ring) , Arginine(Guanidum group) ,and Lysine

25
 Histidine (H, His.) Arginine (R, Arg.) Lysine (K, Lys.)

(Imidazole) (epsilon amino group)

(guanidium)

7. Amide group containing amino acids

They contain an amide group in their R- group
Eg. Asparagine and Glutamine

Asparagine (N, Asn.) Glutamine (Q, Gln.)

(amide) (amide)

8. Aromatic amino acids

They contain an aromatic ring in their R- group

Eg. Phenyl alanine(benzene) , Tyrosine(hydroxy benzene) ,

and Tryptophan(Indole ring)

Phenyl alanine (F, Phe.) Tyrosine (Y, Tyr.) Tryptophan (W, Trp.)

(Benzene) (phenolic) (Indole)

9. Imino acids

They
contain an
imino
group in
their
structure.
There fore
they are
also called
imino
acids.
Here the R- group is linked back to the alpha carbon
26 through the amino group forming an
imino group.

E.g. Proline
 Proline (P, Pro.)

(pyrrolidine)

10. Other important amino acids

Selenocysteine (SeCys.) Hydroxyproline (Hyp.) 5- Hydroxylysine (Hyl.)

II. Classification based on metabolic fate

During the catabolism of amino acid, the amino group is first removed as ammonia. The
remaining carbon skeleton enter either glucogenic or ketogenic pathway. Based on this
metabolic fate amino acids are grouped in to three classes.

1. Glucogenic amino acids

These are amino acids whose carbon skeleton enters the glucogenic pathway i.e. they
are
converted to either pyruvate or any of the intermediates in the TCA cycle from which glucose
can be synthesized by gluconeogenesis 14 out of 20 common amino acids are of glucogenic
type. E.g. Glycine, Alanine, Aspartic acid Glutamic acid etc.

1. Ketogenic amino acids

These are amino acids whose carbon skeleton is converted into either acetyl CoA or aceto
-
acetyl CoA which may give rise to ketone bodies. This group includes leucine and lysine.

3.Both Glucogenic and ketogenic group

This group include amino acids whose carbon skeleton are converted to two different types
of compound of which one is glucogenic and the other is ketogenic. This group includes
Isoleucine ,Tyrosine, Tryptophan and Phenylalanine.

III. Classification based on the nutritional requirement

Based on the nutritional requirement, amino acids are grouped in to three.

1. Essential amino acids.This group includes amino acids which are not synthesized in
the human body and are to be provided in the diet for maintaining the normal growth
and metabolism .There are 10 essential amino acids.They are:-
1. Methionine
2. Arginine
3. Threonine
4. Tryptophan 27
 5. Valine
6. Isoleucine
7. Leucine
8. Phenyl alanine
9. Histidine
10. Lysine
These can easily remembered by the code name “MATT V I L P H Ly”

11.Semi essential amino acids:Two out of the ten essential amino acids are synthesized in
our body to a limited extent ,and are to be supplied in the food additionally , especially
during the growing stages ( child hood) .They are called as semi -essential amino acids. It is
not highly essential in the adults.The semi essential amino acids are Histidine and Arginine.

12. Non essential amino acids :This group includes amino acids which can be synthesized in
human body and are not essentially required in the diet. 10 out of 20 common amino acids are
non essential type.

Eg. Gly. , Ala., Asp. , Glu. , Pro. ,Asn. , Gln. ,Ser. , Cys. and Tyr.

Important Physico -chemical Properties of Amino acids

1 .Meting point – All amino acids are having a very high melting point that is
above 200degree Celsius.

2. Solubility – Amino acids are generally soluble in polar solvents like water ethyl
and alcohol and insoluble in non-polar solvents like benzene.

3. L- amino acids and D- amino acids - Based on the configuration of different groups
around the alpha carbon, amino acids, alpha amino acids can be divided in to two groups- D-
alpha amino acids and L- alpha amino acids.

Most of the amino acids present in protein structure are of L- alpha amino acids. D- alpha
amino acids are very rare in protein structure and are present in certain bacterial proteins

28
such as gramicidin, polymixins,valinomycin (anti biotics) and peptido-glycan ( the cell wall
material of bacteria) .

4. Optical activity of amino acids

Optical activity of amino acid refers to the property of a solution of amino acid to rotate the
path of plane polarized light either towards the right or left side .Based on optical activity
amino acids are classified in to two groups .

a)Dextrorotatory amino acids or d – amino acids – which rotate path of plane

polarized light towards the right side and

b)Levorotatory amino acids or l -amino acids - which rotate path of plane

polarized light towards the left side.

The optical activity is a function of asymmetric carbon atom present in the structure of
amino acid. Most of the alpha amino acids contain an asymmetric carbon atom and are
optically active, i.e. they exist in two optical isomeric forms d and l. But, Glycine does not
posses any asymmetric carbon and is optically inactive i.e. it does not have d and l - forms.

5. Ionization of amino acids and Iso-electric pH

a) Ionization of amino acids.

All amino acids possess two ionizable groups in their structure – an acidic carboxylic
group and a basic amino group. In watery medium both of these group undergo ionization
and becomes charged groups– COO- and NH3 +. The extent of ionization is determined by
the pH of the medium.

In acidic medium the – NH2 group becomes accept a proton (H+) ion and become NH3 +
and the amino acid exist as positively charged molecule called cation. Where as in alkaline
pH, the -COOH group donates a proton (dissociation) to become COO- and the amino acid
exist as a negatively charge molecule called anion.

b) Zwittter ions

Amino acid which contains both its amino group and carboxyl group in the ionized
condition and possessing net zero charge is termed a zwitter ion. Zwittrer ionic form is
formed at a specific pH .The particular pH at which the amino acid exist as zwitter ionic
form is called iso-electric pH or pI.

c) Iso-electric pH (PI)- pI of an amino is defined as the particular pH at which the amino

acid behave as a zwitter ion. The values of pI vary for different amino acids
and buffering capacity are minimum at pI. Solubility

29
(acidic PH) (PI) (Alkaline pH)

d)Amino acid as Ampholytes – Ampholytes are compounds which can change its charge
depending on the pH of the medium. Amino acids can functions as ampholytes as it exist as
cation in the acidic medium, anions in the alkaline medium and as zwitter ions in a medium
pH. Cations move to the –vely charged electrode called cathode. Anions moves to the +vely
charged electrode called anode .Zwitter ions possesses net zero charge and will not move
under the influence of an electric field and remain in the centre.

e) p K or dissociation constant .

pK is the dissociation constant of an amino acids. pK value is defined as the pH at

which the different ionizable group groups dissociate. Since amino acids posses two
ionizable groups, there are two pK values.

pK1 the optimum PH at which the --COOH group

dissociate. pK2 is the optimum PH at which the –NH3+ group

dissociate.

For those amino acids which contain ionizable group in

the R- group there is pK3 also.

PI =

pK1+pK2 2

III .Classification of protein based on the biological Function

Based the biological function, proteins are classified in to the following categories.

30
1. Enzymes –enzymes are proteins specialized to catalyze biochemical reactions in the body
.All enzymes are chemically protein in nature.

2.Regulatory molecules –regulatory molecules such as hormones and growth factors are
mostly proteins in nature. Examples of protein hormone/peptide hormone – Insulin and
Glucagon.

3.Defense proteins –Defense proteins are proteins specialized in providing protection to

the body. E g. Antibodies or immuno globulins are involved in the neutralization of
antigens /pathogens. Fibrinogen is involved in blood clotting and prevents blood loss.
Interferons give protection against viral infection.

4.Structural proteins – Structural proteins are proteins that provide mechanical support to
the tissues. E.g. Keratin is fibrous protein present in hair nail and skin. Collagen is a
structural protein present in bone and cartilage. Fibroin present in silk

5.Contractile proteins- contractile proteins are involved in the muscle contraction

and cellular movements.E g. Actin and myosin present in muscle tissue are involved in
muscle contraction. Elastin present in tendons provide elasticity. Tubulin present in
microtubules and microfilaments helps in cell division

6.Transport protein-These are proteins which are involved in the transport of different
molecules in the blood and in to and out of the cell.

a) Blood transport proteins:-

Hemoglobin- involved in the transport of oxygen in the blood.

Transferrin –involved in the transport of iron in the blood plasma.

Ceruloplasmin – involved in the transport of copper in the blood plasma.

Albumin – involved in the transport of free fatty acid in the blood plasma.
b) Membrane transport proteins:-

Na + - K+ ATP ase- involved in the transport of Na + and K+ in to and out of the cell

Pyruvate transporter- involved in the transport of pyruvate in to the mitochondria.

7.Storage proteins-stored source of energy for future use. Eg. Egg proteins (ovalbumin
and ovaglobulin), milk protein (casein).

STRUCTURE OF PROTEINS

Proteins are the polymers of amino acids. There are 21 different types of amino acids
which are commonly incorporated into proteins during protein synthesis. The structure of

31
protein is very complex and consists of four different levels of organization - primary
secondary, tertiary and quaternary structures.

Every proteins are first synthesized as a long polypeptide chains (primary structure).The
primary structure undergo coiling and folding to form different types of helices and sheet
structures ( Secondary structures ) .The secondary structures are further folded and packed in
to a most comfortable 3-D conformation which is called the tertiary structure. In the case of
proteins consisting of more than one polypeptide chains (eg. Hb, Insulin), each polypeptide
chain forms separate tertiary structures, called subunits. These subunits then associate to form
the multi-subunit structure called quaternary structure. In proteins with only one polypeptide
chain there is no quaternary structure.

Peptide linkage

Peptide linkage is a linkage formed between the carboxyl group of one amino acid and the
amino group of the second amino acid with the elimination of one molecule of water.Peptide
linkage forms the back bone of the protein structure.

32
 The important features of peptide linkage are the following:-

a)Peptide linkage is considered as a partial double bond as it is intermediate between a

single bond and a double bond in bond length and bond strength. Average bond length of
single bond is 1.42 Ao, and that of a double bond is 1.28 Ao. Peptide bond is having a bond
length of 1.32 Ao

b) Peptide bonds are very rigid and it will not allow any flexibility or rotation around its axis.

c) Peptide bonds are very stable and are not destroyed during denaturation of proteins.

d)Peptide bonds are hydrolyzed by peptidases and proteases in the intestinal tract to
liberate free amino acids.

1.Primary structure

Primary structure refers to the number and sequence of amino acid in the polypeptide chain.
A polypeptide chain may contain hundreds to several thousand amino acids. Different
proteins differs in their primary structures, ie. in the number and sequence of amino acid in
the primary structure. Primary structure determines secondary structure and other higher
levels of organizations in protein structure. In the primary structure the amino acids are
joined by peptide linkages.

33
 The primary structure, i.e. the structure of the polypeptide chain is having two ends– the
amino terminal end or N-terminus and the carboxy terminal end or C- terminus. Usually the
amino acid sequence of a polypeptide chain is written from the N to C terminal direction .ie.
the N-terminal amino acid is considered as the 1st amino acid .

All the three atoms in the structure of an amino acid which are involved in the
formation of the primary structure are called the back bone atoms. The back bone atoms have
the repeating sequence of ----N-C-C---N-C-C--- N-C-C-- N-C-C--- N-C-C--- N-C-C--- N-C-
C--- N-C-C--- N-C-C---N-C-C

Importance of primary structure

1. Primary structure determines the secondary and tertiary structure of protein.

2.Primary structure is responsible for the biological function of the protein. When there is a
minute change in the amino acid number or sequence in the primary structure that may
severely alter the tertiary structure and thereby the biological function of the protein.

For example, a single amino acid substitution in the beta subunit (Glutamic acid in the 6th
position is replaced by Valine) of the Hb molecule lead to the formation of an abnormal Hb
called sickle cell Hb. which is having a low oxygen carrying capacity. This condition is
called sickle cell anemia and is characterized by sickle shaped RBCs.

3. The amino acid sequence in the primary structure is determined by the nucleotide sequence
of the corresponding gene.

4. Secondary structure

The primary structure undergoes coiling and folding in different manner to form different
type of secondary structure such as helices and sheets. The peptide bond is very rigid and it
will not allow any kind of flexibility of the chain around its axis. But flexibility is allowed
around the two other bonds in the back bone ie. around the N-C and C-C bonds in the
structure of each amino acid.This flexibility is responsible for the formation of different types
of secondary structures. Secondary structures which are commonly found in protein
structures are of two major types.

1. Helix
2. Sheets ( beta pleated sheets )
1. Helices Helices are the commonest type of secondary structures. The elongated
polypeptide chain undergoes coiling around a central imaginary axis to form coils called
Helices. The structure of helical structures is stabilized by weak force of interactions called
H-bonds. H- bonds are formed between the amide hydrogen and carboxyl oxygen of the
peptide bonds of distantly placed amino acids.

34
3.Tertiary structure.

Tertiary structure is the 3rd level of organization of the protein structure. The secondary
structure of the poly peptide chain consisting of different types of secondary structures
undergo further coiling and folding and become packed in a most comfortable manner to
form a spherical 3-D structure called tertiary structure. The packing of the secondary
structures such as helices and sheets are achieved by the formation of different types of non-
covalent forces .The different non covalent forces involved are the following.

a) H-bonds
b) Hydrophobic interaction forces
c) Van der Waals forces
d) Electrostatic forces ( ionic bonds )
Hydrogen bond is a weak force of attraction between a hydrogen atom and an electronegative
atom such as oxygen. H-bonds are formed between the hydrogen atoms present in the side

35
chain of one amino acid and the oxygen present in the side chain of other amino acids. It
forms a major non covalent force that stabilizes protein structure.

Hydrophobic interaction refers to the tendency of an atom or a group to keep away from a
watery phase. Based on the charged nature of the side chains, amino acids present in the
protein structure are of 2 different categories – polar amino acids (posses either a +vely
charged or –vely charged R-group) and non polar amino acid (possessing an uncharged R-
group). Polar amino acids always found towards the periphery of the 3-D structure because of
the affinity towards water outside(hydrophilic), whereas non polar amino acid always try to
avoid water and are found towards the centre of the structure(hydrophobic). Hydrophobic
interaction force play a major role in the packing of amino acid side chains in the protein
structure.

Vander Waals forces are weak force of attraction or repulsion formed between two
uncharged atoms which are already covalently bonded to other atoms. Accordingly they are
of two types
- Vander Waals force of attraction and Vander Waals force of repulsion.

Electrostatic forces or ionic bonds refers to the weak force of attraction between
oppositely charged atoms and weak force repulsion between similarly charged atoms –
electrostatic force of attraction and electrostatic force of repulsion respectively. Electrostatic
forces of attraction and repulsion are formed between the charged groups in the side chains of
amino acids such as Asp., Glu. (-COO- group) and Lys, Arg. (NH3+) etc.

Apart from the non-covalent interactions in some cases the tertiary structure is stabilized by
a covalent linkage called disulphide linkage also called –S-S-linkage. This linkage is formed
between the sulphydril groups (-SH groups) of two cysteine residues present in different
locations in the chain. The –SS- linkage seen within the tertiay structure is more specifically
called as intra-chain disulphide linkage.
36
Importance of tertiary structure

1.Tertiary structure is essential for maintaining the biological activity of a protein. Once the
tertiary structure is lost, the protein will loose its biological activity.

The loss of tertiary structure due to the destruction of non-covalent interaction is called
protein denaturation. During denaturtion the primary structure is not affected. The agent used
for deanturation is called denaturating agent–physical (heat, x-ray, U-V) and chemical
(urea). The conversion of a denatured protein back to its original native and biologically
active form is called protein renaturation.

2. Tertiary structure gives the particular shape to the protein molecule.

Protein coagulation

Loss of tertiary/secondary as well as primary structures - by coagulating agents-heat ,UVetc.

Precipitation of protein

Soluble protein become insoluble-by precipitating agent-by acids, heavy metal ions etc.

4. Quaternary structure.

Two or more poly peptide chain each has its own 3 –D structure associate to form quaternary
structure. It is seen only in proteins which consists more than one polypeptide chain. Each
polypeptide chain having a 3-D structure is called a subunit.

37
 Based on the number of subunit present proteins may be classified in to monomeric, dimeric,
trimetric tetrameric and so on. If all the subunits are of the same type then the protein is
called a homomeric protein. When the subunit is of different types, it is called a
heteteromeric protein.

The forces involved in subunit association include both covalent and non-covalent forces.

Covalent forces :-Disulphide linkages formed between different subunits form the only
covalent force that binds the subunits together. These disulphide linkages are specifically
called as inter chain disulphide linkages. (These are formed between two different
polypeptide chains).

Non-covalent forces

These include:-

a..H-bonds

b..Hydrophobic interaction forces

c..Van der Waals forces

d..Electrostatic forces (ionic bonds).

Quaternary structure can be better

analyzed by taking hemoglobin
molecule as a example.

Structure of Hb:- Quaternary structure is well studied in Hemoglobin molecule. Hemoglobin

molecule consists of a protein part called globin and a non- protein part called heme and is a
conjugated protein. Globin molecule is a hetero tetramer (α2 β2).The structure of the globin
molecule consists of four poly peptide chains -2 alpha chains and 2 beta chains(forming
alpha subunits and beta subunits respectively ).The two alpha chains are identical and the
beta chains are also identical. Each subunit contain a cleft called heme pocket in which the
38
heme ( tera -pyrrol ring) is covalently bound to some of the histidine residues of the globin
part , i.e. there are total 4 heme units in a hemoglobin molecule and can carry 4 molecules
of oxygen at a time.

Each of the alpha chain is composed of 141 amino acids and each of the beta chain
consists of 146 amino acids. Both alpha and beta chain contain only alpha helix and no
beta sheet.

The subunits are associated by different non-covalent forces such as H-bonds,

hydrophobic interaction forces, Van der Waals forces, and Electrostatic forces (ionic
bonds). There is no –S-S- linkage in the quaternary structure of Hb molecule.

CHAPTER- 4: METABOLISM
Metabolism: The term “metabolism” refers to the sum total of all biochemical reactions/
biochemical pathways taking place in the body of an organism that is essential for the
maintenance of life. Metabolism include three different groups of reactions .They are

1. Anabolic (anabolism) –include all anabolic reactions / anabolic pathways.

2. Catabolic (catabolism)-include all catabolic reactions / catabolic pathways.
3. Amphibolic (amphibolism) –refers to reactions /pathways which are both anabolic
and catabolic in nature.
Anabolism includes those reactions / pathways in which complex biomolecules
are
synthesized from simpler molecules at the expense of energy. These are biosynthetic reactions.
Eg. Glycogenesis, Gluconeogenesis, Fatty acid biosynthesis, cholesterol biosynthesis, protein
biosynthesis etc. Catabolism includes those reactions (or pathways) in which complex
biomolecules are degraded in to simpler molecules with the liberation of energy. These are
degradative (or oxidative reactions) reactions. Eg. Glycolysis, Glycogenolysis, Beta –oxidation etc.

Citric acid cycle is considered as an amphibolic pathway because it is both synthetic (anabolic) and
degradative (catabolic) in nature.

The study of metabolism is important to understand, how the life processes are maintained in an
organism. The living body is a biochemical factory. Metabolism includes areas like:-

4. Carbohydrate metabolism

5. Lipid metabolism

39
 3. Amino acid and protein metabolism

4. Nucleic acid metabolism

5. Water and mineral metabolism etc.

4.1. CARBOHYDRATE METABOLISM

1.GLYCOLYSIS ( Embedden – Mayerhoff- Paranas Pathway)

Glycolysis is a biochemical pathway in which the 6- carbon glucose is enzymatically degraded

in to 2 molecules of 3- carbon pyruvate. It is the chief oxidative (degradative) pathway of D-
Glucose. It takes place in the cytosol ( soluble fraction of the cytoplasm ) of the cell. The pathway
consist of 10 steps, each steps being catalyzed by separate enzymes ie. There are 10 enzymes.
Glycolysis is the only source of energy for the RBC s as they do not contain mitochondria or any
other cell organelle for further degradation of pyruvate. Glycolytic pathway is having two phases.

Phase - I : Praparatory phase: –consists of the first five reactions during which
one molecule of D- Glucose is converted in two 2 molecules of Glyceraldehyde -3-P.

Phase - II : Pay off phase or energy conserving phase : –consists of the last
five reactions during which 2 molecules of Glyceraldehyde 3-P is converted to 2 molecules of
puruvate. In addition to Glucose Glycolysis is also a pathway for the oxidation of other hexoses
such as mannose, Galactose and Fructose which are usually present in the food stuffs. Glycolytic
pathway can be outlined as follows.

There are three irreversible steps in glycolysis which are called rate limiting steps or key enzyme
steps. The steps are step I (HK) step III (PFK) and step X( PK). Glycolysis is regulated mainly by
controlling the activity of these key enzymes

Steps Enzyme ATP /NADH (produced or utilized)

Step I HK/GK -1 ATP

StepII PFK -1ATP

StepVI Gly.3-P-DH +2 NADH+H+(=+6ATP)

StepVII PGK +2 ATP

Step X PK + 2ATP

Total Yield of ATP = 10

40
 Total no. of ATP utilized =2

Net yield of ATP= 8/ Glucose molecule

When the blood Glucose level increases

1. Insulin will be secreted which induces the synthesis of enzymes like HK and PFK This
stimulate glycolysis and helps to decrease the blood sugar level.

2. HK is inhibited by Glucose- 6 P in a feedback manner.

3. ATP inhibits PFK.

4. Citrate inhibits PFK.

Regulation of Glycolysis
When the blood Glucose level decreases

5.Glucagon and Epinephrine are released which activate protein kinases (enzymes). Protein
kinases phosphorylate pyruvate kinase leading to its inactivation. Thus the rate of Glycolysis
decreases.

6. AMP is an inhibitor for PFK.

41
42
 Fate of pyruvate

2 Ethyl alcohol (in yeast)

Glucose 2pyruvate 2-AcetylCOA (under aerobic condition)

2Lactate(in SKELETALmuscle)

1. Oxidative decarboxylation of to acetyl COA (under

pyruvate condition)
aerobic
Pyruvate is transported to the mit.matrix with the help of a transport protein called pyruvate
transporter which is present in the inner mit. membrane. In the mit. matrix pyruvate is oxidatively
decarboxylated to acetyl COA. This process takes place with the help of an enzyme complex called
Pyruvate Dehydrogenase Complex (PDC). Pyruvate dehydrogenase is a multienzyme complex
consisting of 3 enzymes and five co-enzymes. The enzymes and co enzymes are listed below.

Enzymes Co-enzymes

1. Pyruvate dehydrogenase 1. Thiamine pyrophosphate (TPP)

2. Dihydrolipoyil trans acetylase 2. COASH

3. Dihydrolipoyil dehydrogenase 3. FAD

4. NAD+

5. Lipoic acid

The oxidative decarboxylation of pyruvate can be represented as follows.

Oxidative decarboxylation is an irreversible reaction. It yields 2 NADH (for 2 molecules of

pyruvate formed from 1 molecule of Glucose) which on oxidation yield a total of 6 molecules of
ATP .

1. Anaerobic glycolysis ( under anaerobic condition)

In the absence of sufficient oxygen pyruvate is reduced to lactate. This process is called anaerobic
glycolysis. It takes place in the cytosol of skeletal muscle cells. The reaction is catalyzed by an
enzyme called Lactate dehydrogenase (LDH) which requires NADH+H+ as a co-enzyme.

43
The net energy production in anaerobic glycolysis is only 2 molecules of ATP per molecule of
Glucose.

Energy yield of anaerobic glycolysis

steps Enzyme ATP /NADH (produced or utilized)

Step I HK/GK -1 ATP

StepII PFK -1ATP

StepVI Gly.3-P-DH +2 NADH+2H

StepVII PGK +2 ATP

Step X PK +2ATP

Step XI LDH - 2 NADH+2H+

Total Yield of ATP = 4

Total no. of ATP utilized =2

Net yield of ATP= 2 ATP/ Glucose molecule

2. Alcoholic fermentation ( in Yeast)

Alcoholic fermentation is a modified pathway of Glycolysis. It is seen in microorganisms like Yeast
(fungi). Here pyruvate formed during glycolysis is converted to ethyl alcohol by a 2 step pathway.
The enzymes involved are puruvate decarboxylase and alcohol dehydrogenase.

Alcoholic fermentation technique is widely utilized in the production of wine, beer and other
alcoholic products. It is also employed in the preparation of bread.

Mechanism of NADH transport from cytosol to Mit. Matrix

44
 Malate shuttle

3. CITRIC ACID CYCLE

Under aerobic condition pyruvate formed by glycolysis enters the mitochondria and undergo
oxidative decarboxylation to form acetyl COA. Acetyl COA is completely oxidized in the
mitochondrial matrix in to CO2 and H2O in a cyclic pathway known as Citric acid cycle. Citric acid
cycle is also known as Krebs cycle because it was elucidated by a scientist named Hans Krebs. It is
also called as tricarboxylic acid cycle because; citrate the first intermediate in this cycle is a
tricarboxylic acid.

Citric acid cycle consists of 8 steps and 8 enzymes and all these reactions are taking place in the
mitochondrial matrix. All enzymes except one are present in the matrix in a soluble form and are
called soluble enzymes. But succinate dehydrogenase(SDH) is present bound to the inner
membrane and is called a membrane bound enzyme.

There are three irreversible steps in citric acid cycle which are called rate limiting steps or key
enzyme steps. The steps are step I (Citrate synthase), step III (ICDH) and step IV (alpha
ketoglutarate dehydrogenase).

The citric acid cycle can be represented as follows.

Fatty acids acetyl COA Pyruvate Glucose

45
 During each turn of the cycle 1 molecule of Acetyl COA enters the cycle and 3 NADH, 1 FADH2 , 1
GTP , 2 CO2 and 1 COASH are produced in the cycle. Citric acid cycle is considered as an amphibolic
cycle rather than catabolic or anabolic because it is having both catabolic and anabolic roles.

Catabolic role- It is a pathway for the complete oxidation of carbohydrates amino acids and
fatty acids.

Anabolic role – The intermediates of this cycle form the precursors of several amino acids,
steroids, cholesterol etc.

Energy yield of Citric acid cycle( 2 turns of the cycle / 2 acetyl COA /1 Glucose)

steps Enzyme ATP /NADH (produced or utilized)

Step III ICDH + 2 NADH + 2H+ ( =+ 6 ATP)

StepIV Alpha KGDH + 2 NADH + 2H+ ( =+ 6 ATP)

StepV Succynyl COA synthetase + 2 GTP (=+ 2 ATP)

StepVI SDH + 2 FADH2 (=+ 4 ATP)

Step VIII MDH + 2 NADH + 2H+ (= +6 ATP)

Total no. of ATP utilized =0

Net yield of ATP= 2 4ATP/ Glucose molecule

Total energy yield during the complete oxidation of one molecule of Glucose via. glycolysis, PDC
and Citric acid cycle

46
 Pathway Energy yield

Glycolysis 8 ATP

Oxidative decarboxylation of 6 ATP

pyruvate to acetyl COA ( PDC)

Citric acid cycle 24 ATP

Total energy yield = 38 molecules of ATP / Glucose molecule

Regulation of citric acid cycle

Key enzymes are the regulatory points in citric acid cycle.

1. The key enzymes are stimulated by Ca++ ions which are liberated during increased
muscular work / energy demand.
2. The key enzymes are activated by NAD + and ADP.
3. The key enzymes are inhibited by NADH + H+ and ATP.
Citric acid cycle is activated when there is an increased energy demand and

inhibited
when the energy level is sufficient in the body.

47
 5.GLYCOGEN METABOLISM
Glycogen is a polysaccharide which is the reserve carbohydrate in animal tissue. It is the stored
form of energy. Glycogen is synthesized from excess glucose in the body and is stored in liver (liver
glycogen) or skeletal muscles (muscle glycogen). Liver glycogen is involved in the maintenance of
blood glucose level, where as muscle glycogen provides energy for muscle contraction.

Glycogen metabolism includes two processes. They are:-

1. Glycogen synthesis (Glycogenesis) – anabolic pathway.

2. Glycogen breakdown (Glycogenolysis) –Catabolic pathway.

Glycogen synthesis ( Glycogenesis)

Glycogen synthesis refers to the synthesis of complex glycogen molecule by the polymerization of
hundreds or thousands of D- Glucose molecules. This takes place in the cytosol of liver cells
(hepatocytes) and muscle cells. Glycogenesis takes place with the help of a number of enzymes.
They are:-

1. Hexokinase / Glucokinase
2. Phosphoglucomutase
3. UDP glucose pyrrophosphorylase
4. Glycosyl transferase
5. Glycogen synthase ( Glycogen synthetase )
6.Branching enzyme ( amylo 4-6 trans glycosylase )
The process can be described under 4 headings

1.Activation of D-Glucose :-This involves the

conversion of D Glucose in to UDP- Glucose
.This takes place in three steps.

Step- I – The phosphorylation of Glucose to form Glucose

-6- p by an enzyme called Hexokinase
/Glucokinase.

Step -II- The conversion of Glucose -6-p to Glucose 1 –P by an enzyme called phosphoglucomutase
(PGM). 48
Step- III- The conversion of Glucose 1-P to UDP Glucose by an enzyme called UDP-Glucose
pyrrophosphorylase. UDP- Glucose is the activated Glucose or substrate for glycogenesis .

2. Synthesis of Glycogen primer with the help of a protein called Glycogenin:-

A glycogen primer containing 8 glucose units is first synthesized on the glycogenin protein with the
help of an enzyme called glycosyl transferase.

This is achived by the successive addition of glucose units from UDP glucose to the non reducing
end of the growing fragment resulting in the formation of alpha-1-4 glycosidic linkages. The primer
remains attached to the glycogenin protein at its Tyrosine residue.

3.Extension of the primer by glycogen synthase enzyme:- Glycogen synthase

cannot initiates polymerization de novo. But, once the primer is synthesized, Glycogen synthase
catalyzes the addition of glucose residues to the non reducing end of the primer together with the
formation of alpha1-4 glycosidic linkages, resulting in the extension of chain. In this way a long
unbranched polymer of D-Glucose with only alpha1-4 linkage is synthesized.

4.Branching:- An enzyme called amylo 4-6 transferase catalyzes the cleavage of an alpha1-4
linkage and the transfer of the resulting oligosaccharide fragment to another position in the chain.
The fragment becomes attached to the main chain by an alpha1-6 linkage. This results in the
branching of the molecule.

Glycogen breakdown (Glycogenolysis)

Glycogenolysis refers to the process of degradation of the highly branched glycogen molecule to
liberate D- Glucose molecules. This takes place in liver and muscle. The end product of
Glycogenolysis in liver is D-Glucose. In muscle the end product is Glucose-6-P due to the absence
of an enzyme called glucose -6- phosphatase. Glycogenolysis takes place in the cytosol. The
enzymes involved in glycogenolysis are:-

49
 1. Glycogen phosphorylase.
2. Debranching enzyme- is having two different enzymatic activities.
a) Amylo, 4-4 trans glycosylase activity and

b) Alpha 1-6 glucosidase activity.

3. Phospho glucomutase ( PGM) and

4. Glucose -6- phosphatase .
The process of glycogenolysis can be described under three headings.

5.Action of Glycogen phosphorylase enzyme:-Glycogen phosphorylase catalyses the

cleavage of alpha, 1-4 glycosidic linkages present in the glycogen molecule, resulting in the
liberation of Glucose -1- P.

6.Action of debranching enzyme –( debranching) :-Glycogen phosphorylase can

proceed only up to four glucose residue prior to a branch point. The debranching is done by the
debranching enzyme which is having two enzymatic activities.

The amylo, 4-4 transglycosylase enzyme catalyses the cleavage of an alpha,1-4 linkage one
residue prior to the branch point and transfer the oligosaccharide to the non- reducing end of the
adjacent chain. This can again be acted upon by glycogen phosphorylase liberating glucose-1-P.
The alpha,1-6 Glucosidase enzyme cleaves the alpha1-6 linkage in the branch point liberating the
D- glucose molecule.

3.The conversion of Glucose -1-P to D-Glucose ( Free Blood Glucose ) :- This

takes place in two steps with the help of two different enzymes.

Step-I :- The conversion of Glucose -1-P to Glucose-6-P by Phospho Glucomutase.

Step-II: -The conversion of Glucose -6-P to D- Glucose by an enzyme called Glucose- 6-

Phosphatase. The enzyme Glucose-6- phosphatase is absent in muscle and therefore the end
product of glycogenolysis in muscle is Glucose -6- phosphate which enter the glycolytic pathway.

REGULATION OF BLOOD SUGAR (GLUCOSE) LEVEL

50
The normal blood glucose level in the body is 70-110mg/100ml in the fasting condition. It is called
fasting blood glucose level. When the fasting blood glucose level is above 110mg/ 100ml, the
condition is called as hyperglycemia. When the fasting blood glucose level is below 70mg/100ml,
the condition is called hypoglycemia. During hyperglycemia and hypoglycemia, the blood glucose
level is brought to the normal range by regulation over two processes – Glycogenolysis and
Glycogenesis. This is achieved through hormonal means involving three different hormones.

They are:-

1. Glucagon:–Glucagon is secreted by the alpha cells of the islets of Langerhans of the pancreas
.It is a hyperglycemic hormone. It is secreted during hypoglycemia. Glucagon increases the rate of
glycogenolysis in the liver and increases blood glucose level.

2.Epinephrine: – Epinephrine or adrenalin is secreted by the medulla of adrenal gland.

Epinephrine is a hyperglycemic hormone which increases the rate of glycogenolysis in the liver and
skeletal muscle. Epinephrine is also called as emergency hormone as it is secreted during
emergency situations.

3.Insulin:–Insulin is secreted by the beta cells of the islets of Langerhans of the pancreas. Insulin
is secreted during hyperglycemia. .Insulin is a hypoglycemic hormone that lowers the blood
glucose level by three different mechanisms:-

a) Increases the uptake of Glucose in the cells.

b) It increases the rate of Glycolysis by increasing the activity of two enzymes –
Phosphofructokinase and pyriuvate kinase.
c)Increases the rate of Glycogen synthesis.
GLYCOGEN SRTORAGE DISEASES

Genetic deficiency of various enzymes involved in the metabolism of glycogen lead to the
manifestation of various disorders which are collectively known as glycogen storage diseases.

51
 6.GLUCONEOGENESIS
Gluconeogenesis is a biochemical pathway in which D-Glucose is synthesized from non-
carbohydarte precussors such as pyruvate, Lactate, Oxaloacetate, certain amino acid etc.
Gluconeogenesis is an anabolic pathway which takes place mainly in the liver and to a lesser
extent in the renal cortex. This pathway is operated partially in the mitochondria and partially in
the cytosol. Gluconeogenesis takes place when there is a lack of sufficient glucose in the body and
during starvation.

Most of the enzymes involved in gluconeogenesis are the same as those involved in Glycolysis.
The three irreversible steps in glycolysis are bypassed in gluconeogenesis with the help of 4
additional enzymes which are designated as the key enzymes of gluconeogenesis. They are

1. Pyruvate carboxylase
2. Phospho-enol pyruvate carboxykinase
3. Fructose 1,6-bisphosphatase &
4.Glucose -6-phosphatase.
Substrate for Gluconeogenesis.

5. Pyruvate – It is the end

product of aerobic glycolysis.

6.Lactate- It is formed in the muscle during anaerobic glycolysis. Lactate is transported to the liver
where it gets oxidized to pyruvate by Lactate dehydrogenase enzyme (LDH). Puruvate enters the
gluconeogenic pathway.

7.Glucogenic amino acids – Certain amino acids can act as precursors of Glucose under emergency
conditions. Such amino acids are called Glucogenic amino acids. Examples include alanine,
aspartic acid , glutamic acid, etc. These amino acids are either de-aminated or transaminated to
form corresponding keto acids (carbon skeleton). These keto acids enter the Citric acid cycle and
are converted to oxalo-acetate which is the direct substrate for Gluconeogenesis.

Trans amination /Alanine transaminase ( ALT)

Alanine Pyruvate.

Trans amination /Aspartate transaminase ( AST)

Aspartic acid Oxalo acetic acid.

Deamination/ Glutamate dehydrogenase

Glutamic acid alpha keto glutarate.

Glucose – Alanine cycle

The cyclic pathway involved in the interconvert ion between Alnine and Glucose in the body is
called Glucose –Alanine cycle. This can be represented as follows.

52
4.Glycerol– Glycerol is a part of neutral fat TAG) which is absorbed in the intestine and assimilated
in the body. Glycerol portion of the TAG will be liberated during lipid mobilization (associated with
fasting and hypoglycemia). Glycerol is first phosphorylated to Glycerol-3-P by an enzyme called
Glyceol kinase.

Digestion / Absorption /assimilation

Glycerol-3-P is then oxidized to Dihydroxy acetone –P, an intermediate in gluconeogenic pathway

(also glycolysis). This reaction is catalyzed by glycerol-3-P dehydrogenase enzyme which requires
NAD+ as a coenzyme.

5. Propionyl COA (activated propionic acid)-

Propionyl COA is mainly formed during the beta-oxidation of odd-chain fatty acid. It is also
formed during the catabolism of certain amino acid. Propionyl COA is converted to succinyl COA
which is an intermediate of Citric acid cycle. Succinyl COA is then converted to Oxalo acetate
which enters the gluconeogenic pathway.

The pathway of Gluconeogenesis starting from Lactate can be outlined as follows.

Significance of Gluconeogenesis

1. Gluconeogenesis is involved in the maintenance of blood glucose level during starvation /

hypoglycemia.
D- Glucose is the only source of energy for NS

2. Gluconeogenesis help to utilize the lactate formed during anaerobic glycolysis and glycerol
produced in adipose tissue.
3. Only liver can replenish D- Glucose through Gluconeogenesis because Glucose-6-
Phosphatase enzyme is present only in liver.
4. Propionic acid (a 3-carbon fatty acid) is converted to glucose by gluconeogenesis and is
the only glucogenic fatty acid.
Regulation

Glycolysis and gluconeogenesis are reciprocally regulated so that one pathway is relatively
inactive when the other is active. The key enzymes are the regulatory steps in
gluconeogenesis.

6. Glucagon enhances gluconeogenesis by inducing the synthesis of key enzymes.

7. Glucocorticoids (cortisol, cortisone and corticosterone) enhances gluconeogenesis.

8. ATP enhances gluconeogenesis

9. AMP inhibit gluconeogenesis.

10.Insulin inhibit gluconeogenesis.

53
 4.2. LIPID METABOLISM
LIPID MOBILIZATION
When there is sufficient concentration of D- Glucose in the body, the body derives energy
from glucose oxidation and the fatty acid oxidation rate will be less. The fatty acids are then
stored in the adipose tissue in the form of neutral fat or Tri-acyl Glycerol (TAG). But when the
concentration of D- Glucose becomes insufficient i.e. during starvation, the glycogen (stored D-
Glucose) will be degraded to maintain the normal energy production. If the starvation is continued
further the neutral fat stored in the adipose tissue (adipocytes) is used for oxidation to liberate
energy.

The process of degradation of neutral fat (TAG) in the adipose to liberate glycerol and free
fatty acid is called lipid mobilization. This takes place with the help of an enzyme called hormone
sensitive lipase .The production of this enzyme is induced by the hormone glucagon and hence the
name hormone sensitive lipase.

The glycerol will be converted to dihydroxy acetone with the help of enzymes like Glycerol kinase
and glycerol -3- P dehydrogenase.

The liberated fatty acids are transported to different target tissues concerned with fatty acid
oxidation. These tissues include liver, brain, adipose tissue, muscle, heart, lungs, testis and kidney.

FATTY ACID OXIDATION

The complete oxidation of the long chain fatty acid in to CO2 and water takes place in two
different stages. They are:-

54
Stage I : Beta - oxidation –The degradation of fatty acid in to acetyl COA.

Stage II : Citric acid Cycle – The degradation of acetyl COA in to CO2 and water.

Stage I : Beta Oxidation

Beta oxidation refers to the successive oxidative removal of 2- carbon fragments in the form of
acetyl COA from the C-terminal end of the long chain fatty acid. It is the first stage in the oxidation
of fatty acids. Beta- oxidation takes place with the help of a group of enzyme which are collectively
called as fatty acid oxidase complex.

The process of beta oxidation takes place in tissues such as adipose tissue, brain, kidney heart,
lungs, muscles, testis etc. Mitochondrion is the site of beta oxidation. In the body the chief fatty
acid oxidized is palmitic acid (16-C).

The process of beta-oxidation can be described under the following headings.

1. Activation of fatty acid:-

Fatty acid activation refers to the conversion of fatty acid to fatty acyl COA. This takes place in
the
cytosol .The enzyme that carries out this reaction is called fatty acyl COA synthetase or
thiokinase.
The reaction can be represented as follows.

Palmitic acid is activated to palmitoyil COA by the enzyme palmitoyil COA synthetase.

2. Transport of fatty acyl COA in to the mitochondrial matrix.

The fatty acyl COA is freely permeable through the outer mitochondrial membrane, but the inner
membrane is impermeable. Fatty acyl COA is transported across the inner membrane with the
help of a molecule called carnitine present in the inter membrane space. This process involves the
following steps.

55
 Step-I: Fatty acyl COA react with carnitine in the intermembrane space to form fatty acyl carnitine
.This reaction is catalyzed by an enzyme called carnitine acyl transferase (CAT I) which is a
membrane bound enzyme present in the outer surface of the inner membrane).

Step-II: The fatty acyl carnitine is transported to the mit. matrix by a transporter protein called
traslocase.

Step-III: Fatty acyl carnitine react with COASH in the mitochondrial matrix to form fatty acyl COA
and carnitine .This reaction is catalyzes by an enzyme called carnitine acyl transferase -II
(CAT II) which is present in the inner surface of the inner membrane. Thus fatty acyl COA is
regenerated in the mit. matrix.

3. Beta- oxidation (Beta -oxidation cycle)

The removal of each 2-carbon unit in the form of acetyl COA takes place in four steps.

Step I: Dehydrogenation: The fatty acyl COA undergo dehydrogenation at its alpha and beta carbon atoms
(2&3) resulting in the formation of an unsaturated fatty acyl COA called trans- ∆ 2 enoyil COA. This
reaction is catalyzed by an enzyme called fatty acyl COA dehydrogenase. One molecule of FADH 2
is formed in this step.

56
Step II. Hydration: One molecule of water is added to the trans ∆2 enoyil COA so that it is converted to 3 –
hydroxyl (β-hydroxy)acyl COA. This reaction is catalyzed by an enzyme called trans ∆ 2 enoyil COA
hydratase.
Step III: Dehydrogenation: 3- hydroxyl acyl COA undergo dehydrogenation in the 3rd carbon so that it is
converted to 3 – keto acyl COA. This reaction is catalyzed by an enzyme called 3- hydroxyl
acyl COA dehydrogenase. One molecule of NADH+ H+ is formed in this step.
Step-IV: Thiolytic cleavage : 3-keto acyl COA undergo a cleavage between its alpha and beta carbon atom
to form one molecule of acetyl COA and a fatty acyl COA containing 2 carbon atoms less. This reaction is
catalyzed by an enzyme called acyl CoA acetyl transferase (thiolase) which requires a COASH.

Thus for the complete degradation of a C-16 palmitoyil COA to 8 molecules of acetyl -COA the beta-
oxidation steps have to repeat 6 more times (Total 7 cycles).The overall reaction for the beta-oxidation of
one molecule of palmitoyil COA can be written as follows.

Palmitoyil COA + 7 FAD +7 H2O +7 NAD+ + 7 COASH

8 Acetyl COA + 7 FADH2+7 NADH+H+

Stage II Citric acid Cycle
This is the second stage in the oxidation of fatty acid. Each molecule of acetyl COA produced in the
beta-oxidation are further oxidized in the citric acid cycle to form CO2 and water. During the
oxidation of each acetyl COA 12 molecules of ATP are formed in the citric acid cycle.

Energetic of fatty acid oxidation (Palmitic acid)

Beta-oxidation

No. of FADH2…………………….7 = + 14 ATP

No. Of NADH……………………..7 = + 21 ATP

Citric acid Cycle

No. of FADH2……………………. 8 = + 16ATP

No. Of NADH……………………..24 = + 72ATP

No 0f GTP …………………………8 = + 8 ATP

Total ATP production = 131 ATP / molecule of palmitic

acid
Net production of ATP = 131-2 = 129 ATP (2 molecules of ATP are
used during the activation step)

57
4.3: AMINO ACID METABOLISM
SOURCES OF AMINO ACIDS
1. Digestion of protein and absorption of amino acids (Exogenous source)
2. Intracellular protein Degradation (Endogenous source)

I. Digestion of proteins and absorption of amino acids

1. In Mouth- No digestion

2. In Stomach- gastric juice – Enzymes, HCL and Mucous.

- Highly acidic (very low pH) due to the presence of H Cl.

-Secreted by gastric mucosa

-chief cells (enzymes) and parietal cells (HCl).
The enzymes are:-

a) Pepsin (zymogen- pepsinogen)-

-hydrolyze peptide bonds involving aromatic amino acids. It is an endo-peptidase.

b)Rennin (also called as chymosin)- present only in infants . It is involved in the

digestion of milk protein, casein.

3. In Intestine
A.ByPancreatic juice – alkaline due to the presence of HCO3-ions. It contains a number of
proteolytic enzymes.
Enzymes include:-
a)Trypsin – (zymogen form-Trypsinogen)- hydrolyze peptide bonds involving
Lysine and Arginine. It is an endopeptidase (activated by enterokinase).
b)Chymotrypsin (chymotrypsinogen)- hydrolyze peptide bonds involving aromatic
amino acids. It is an endopeptidase. (actvated by trypsin)
c)Carboxypeptidase –A (zymogen form-pro carboxy peptidase A)-hydrolyzes peptide
bonds involving acidic amino acids &
d)Carboxypeptidase -B (zymogen form- Pro carboxypeptidase B)-hydrolyzes
peptide bonds involving basic amino acids . Both carboxy peptidases are
exopeptidases.
e)Elastase(zymogen form -proelastase – specifically involved in the digestion of
elastin (protein) present in tendons of meat.
B) Intestinal juice (succus entericus)
It contains the following enzymes.
a)Aminopeptidases-exo-peptidase acts from the amino terminal end liberating free
amino acids.
b) Tripeptidases – hydrolysis of tri-peptides to liberate amino acids.
c) Dipeptidases – hydrolysis of di-peptides in to amino acids.

58
Absorption of amino acids

In the small intestine absorption takes place by ATP dependent symport mechanism ( active
absorption)
Five different types of carrier proteins are there.
1. For neutral amino acids 2. Basic amino acids 3. Imino acids and Glycine 4.
Acidic amino acids and 5. Beta amino acids .

Transport of amino acids

In the blood, amino acids are transported in a free form in the plasma (Free amino acids). The
absorbed amino acids are liberated in to the body’s amino acid pool (blood, other body fluids,
extracellular space and cytoplasm).

Uptake of amino acids in the tissues

In the Intestine kidney tubules and and brain amino acid absorption takes place by Gamma
glutamyl cycle or Miester cycle involving Glutathione. The cycle is shown below.

II. Intra cellular Protein Degradation

Body proteins are continuously renewed /replaced with new ones. The intracellular degradation
of body proteins takes place by 2 different mechanisms.
1. Lysosome dependent (within the lysosome)
Non- functional and old proteins are endocytosed and taken in to the lysosome and digested by
intracellular proteases, called cathepsins –present in the lysosome. There are 18 different types of
cathepsins in our body, Cathepsin (A to T).These enzymes are active only at the acidic PH inside
the lysosome. Sometimes Proteins are taken in to the cells by carrier mediated endocytosis. The
endocytic vesicle fuse with lysosome to form digestive vesicle. Within the digestive vesicles the
proteins are degraded in to amino acids by the action of cathepsins. The proteins present in the
dead cells are usually degraded / removed by this mechanism.
2. Lysosome independent( in the cytosol)
This takes place with the help of a protein called ubiquitin. Ubiquituitins are certain adaptor
proteins which has a binding site for the protein to be degaraded. Once the ubiquitin – protein
complex is formed, the complex will be taken in to an assembly of proteases called proteasome.
Proteasome complex is formed of large number of proteases which are arranged in the form of a
cylinder/barrel. Inside the proteasome the target protein is digested in to amino acids by the
surrounding proteases. (Nobel Prize work- 2004).The liberated amino acids become a part of
amino acid pool from which new body proteins can be synthesized.
The representation of a proteasome complex:-

The replacement of body protein by new and fresh protein is called protein turn over.

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This is a normal process taking place in a healthy individual. In children the rate of protein
synthesis will exceed that of protein degradation that is why the body is growing (increase in
weight).In adults the rate of protein degradation almost balances with that of protein synthesis. In
an old individual the rate of protein degradation exceeds the rate of protein synthesis, i e. the
renewal efficiency is less in an old individual compared youngsters.
Fasting and protein degradation
Intracellular protein degradation is accelerated during fasting to supply amino acids for
the following essential processes.
1. For gluconeogenesis and

2. For energy production –amino acid catabolism.

During severe fasting the synthesis of urea cycle enzymes become accelerated to support the process of
amino acid catabolism. This is because there will be an increase production of NH3 during fasting due to an
increase in the rate of amino acid catabolism.

Fate of amino acids in the amino acid pool

The amino acids present in the amino acid pool are having different fates. These are:

-1.Synthesis of new body proteins.

2. Catabolised for energy production(This process is accelerated during severe fasting)

3.Acts as a precursor for the synthesis of several other compounds – heme, neurotransmitters,
hormones ,glutathione ,nucleic acids, creatine etc.

Diet (Exogeneous) Catabolism - (57%)

Amino acid pool Body protein synthesis

(21%)

Body protein degradation Remain as free amino acid

(22%) (endogenous) (This forms the precursors of other
biomolecules)

GENERAL CATABOLISM OF AMINO ACIDS

There are two stages in the catabolism of amino acids.
Stage I – Removal of amino group in the form of Ammonia.

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Stage II- Utilization of the carbon skeleton for energy production and biosynthetic
processes.
Removal of Amino group
The removal of amino group takes place by different mechanism.

1.Trans-amination
Most of the amino acids undergo trans-amination reactions. It takes place in all the cells and
all tissues.
THE PROCESS INVOLVES THE TRANSFER OF AMINO GORUP FROM AN AMINO ACID TO A KETO ACID
RESULTING IN THE FORMATION OF A NEW AMINO ACID AND A NEW KETO ACID. During this reaction the
amino group of all amino acids are transferred to alpha ketoglutarate, as areult , alphaketo
glutarate is converted to glutamate.
Amino acid + alpha keto glutarate transaminases
PLP
Corresponding ketoacid + Glutamate
Transamination is also a process in which certain amino acids are synthesized in the body.

Thus glutamate is produced in tissues in large quantities. Glutamate is transported to the

liver where it is de-aminated by glutamate dehydrogenase enzyme and NH3 is liberated. The
enzymes that catalyse transamination reactions are generally called as transaminases. All
trans-aminases require PLP as a co-enzyme. Eg. AST (GOT/SGOT), ALT (GPT/SGPT), Tyrosine
transaminase etc.
AST and ALT are clinically important marker enzymes in case of liver diseases whose serum level
are elevated during liver damage due to any cause.

2. Deamination

Deamination lead to the removal of amino group in the form of free ammonia. It takes
place by two mechanisms – oxidative deamination and Non- oxidative deamination.

a) Oxidative de-maination :
This type of deamination is associated with the oxidation of amino acid. It takes place by 2
different ways- oxidative de-amination by glutamate dehydrogenase and oxidative
domination by amino acid oxidases.

i) Oxidative deamination by glutamate dehydrogenase:- This is highly specific to glutamate

and it takes place only in liver. During this process NADH is produced.

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 ii) Oxidative deamination by amino acid oxidases:-This type of oxidative de-amination
takes place in all the tissues and for most amino acids. FMN / FAD acts as a coenzyme in
these reactions.

Amino acid +FMN ketoacid + FMNH2+NH3 AMINOACID

OXIDASES

b) Non oxidative de-amination

This type of deamination is not associated with oxidation of amino acids. Only some amino acids
are de-aminated by this mechanism. There are three different mechanisms.

i)by amino acid dehydratases :-Hydroxyl group containing amino acids are de-aminated mainly
by this mechanism. Pyruvic acid is formed .Eg. Serine dehydratases and Threonine dehydratases

serine dehydratase

Serine
pyruvate +H2O+NH3

Threonine Threonine dehydratase

pyruvate +H2O+NH3

ii)byamino acid desulfhydratases:- Cysteine is mainly de-aminated by this mechanism. The

enzyme involved is cysteine desulfhydrases. Pyruvic acid is produced .The sulfur atom is liberated
as H2S.

cysteine desufhydratase

Cysteine + H2O

pyruvic acid+ NH3+H2S

ii) by Histidase :-Histidine is de-aminated mainly by this mechanism . The enzyme

involved is histidase. Urocanic acid is produced.
Histidine Histidase Uro canic acid +
NH3

Transport of ammonia
1. In the brain Ammonia is captured immediately after its formation and is utilized for the
synthesis of glutamine by glutamine synthetase enzyme. (Present only in brain).
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Glutamic acid + NH3+ ATP Glutamine+ ADP
2.From other tissues ammonia is transported in the form of Glutamic acid or as free
ammonia .Ammonia generated in the intestinal as a result of intestinal putrefaction is
transported as free ammonia.

3.In the liver ammonia present in the form of Glutamic acid and glutamine are liberated
by the help of 2 enzymes glutamate dehydrogenase and glutaminase .

Glutamine

Glutaminase

Glutamic acid + NH3

Glutamate
dehydrogenas
e

Alphaketo
glutarate + NH3

Stage II: Oxidation of

Carbon skeleton and
production of energy

As a result of various mechanisms amino group is removed from the amino acids and the
corresponding carbon skeletons are formed. The carbon skeleton can be any of the keto acids
(pyruvic acid, alphaketoglutaric acid, fumeric acid or oxaloacetic acid ) or acetyl CoA or succinyl
CoA. Depending on the type of carbon skeleton amino acids are classified in to glucogenic
ketogenic and both glucogenic and ketogenic group (classification based on metabolic fate).
If the carbon skeleton is acetyl COA the amino acid is called ketogenic because during strvation
there will be excessive accumulation of acetyl coA which is then converted to ketone bodies. (leu,
Lys. and Trp.)
If the carbon skeleton is a keto acid or any other intermediate in TCA cycle, the amino acid is
called glucogenic because during starvation they can contribute to the formation of D- Glucose by
gluconeogenesis.( Asp, Glu.Gly etc-total 14).Certain amino acid gives two carbon skeleton-of which
one is glucogenic and other is ketogenic such an amino acid is called both glucogenic and
ketogenic amino acids.( Ile, Phe and Tyr.)

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 DISPOSAL OF AMMONIA
(URIA CYCLE /KREBS-HANSLEIT CYCLE)
Ammonia is formed in the body as a result of various transamination and de amination
mechanisms. This ammonia is circulated in the blood as free ammonium ion. Ammonia is highly
toxic to the tissues especially to the CNS. The toxic ammonia is converted to less toxic and water
soluble uria in the liver by a cycle of reaction which is known as uria cycle. Urea cycle is postulated
by Hans Kreb and Hansleit and therefore it is also known as Kreb – Hansleit cycle. Urea can be
filtered out by the kidney via the urine as it is water soluble. Urea cycle is operated only in the
liver. It takes place partially in the cytosol and partially in the mitochondria.

There are five different steps –

The reactions can be represented as follows.

Step 1 &2 takes place in the mitochondrial matrix where as 3, 4 &5 takes place in the cytosol of
liver cell. Urea cycle is also known as uria bicycle because it is linked with TCA cycle through
fumerate. Fumerate is a common intermediate in both the pathways. Urea cycle is energy
consuming pathway 1 ATP is required for the formation of every molecule of Urea.

DECARBOXYLATION REACTIONS
Decarboxylation of amino acid lead to the production of corresponding amines, generally called as
biological amines. The enzymes are generally called as decarboxylases which require PLP as a
coenzyme. Decarboxylation reactions take place mainly in the liver, kidney and brain. Many of
these amines perform important physiological functions.

Decarboxylases

Amino acid PLP Amines + CO2

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Sl.No Amino acid Amines Functions
1 Tyrosine Tyramine Present in chocolate , dry meat ,dry fish
and it may cause migraine
2 Tryptophan Tryptamine 1.5-hydroxyl tryptamine is seratonin –
vaso-dialator
2.Melatonin is another derivative which
is a sleep wake-up hormone secreted by
pineal gland .

3 Histidine Histamine Manifestation of allergic response

4 Glutamic acid GABA Inhibitory neurotransmitter
5 Threonine Propanolamine Component of vit B12
6 Cysteine betamercaptoethanol Present in COASH
7 Aspartic acids Beta alanine Present in COASH
8 Lysine Cadavarine Intestinal putrefaction product
9 Ornithine Putrecine Intestinal putrefaction product
10 Arginine Agmatine Intestinal putrefaction product

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