Comprehensive Biochemistry for Dentistry Textbook for Dental Students

7.3  Derived Lipids 125

Example: Lecithin, choline, sphingomyelin
• Glycolipids

Glycolipids are composed of fatty acids, alcohol, and carbohydrate residues.
Example: Cerebrosides and gangliosides.
• Lipoproteins

Lipoproteins are composed of lipids linked to proteins.
Example: HDL (High density lipoprotein), LDL (Low density lipoprotein),

VLDL (Very low density lipoprotein).
• Sulfolipids

Sulfolipids are lipids that possess sulfate residues.
Example: Sulfatide. It is synthesized in endoplasmic reticulum.

7.2.3 Derived Lipids

Derived lipids are obtained by hydrolysis of simple and compound lipids. They can
be the following types:

• Fatty acids
• Partial triglycerides like diglycerides and monoglycerides
• Alcohols: straight-chain alcohols like glycerol and cetyl alcohol and unsatu-

rated alcohols like sphingol and phytol.
• Steroids

–– C27steroids: Cholesterol, cholestanol, coprostanol
–– C28 steroids: Ergosterol
–– C18,19,21 steroids (gonadal and adrenal cortex hormones)
–– C24 steroids (bile acids)
–– Secosteroids: Cholecalciferol
• Terpenes
Squalene is a triterpene. It is found in the liver of shark and mammals and sebum
of humans.
• Carotenoids

7.3 Derived Lipids

7.3.1 F atty Acids

Fatty acids are organic compounds containing a hydrocarbon chain and a ter-
minal carboxylic group.

126 7 Lipids

7.3.2 T ypes of Fatty Acids

Fatty acids are various types which are described as follows:

Straight-Chain Saturated Fatty Acids
• These fatty acids have hydrocarbon straight chain without double bond.
• Their molecular formula is (Cn H2n+1 COOH).
• Examples:

Acetic acid (CH3COOH)
Propionic acid (C2H5COOH)
Butyric acid (C3H7COOH)
Palmitic acid (C15H31COOH)
Stearic acid (C17H35COOH)
• Depending on the number of carbon atoms in hydrocarbon chain, they are
sub-classified into different types.
• Types of straight-chain saturated fatty acids
–– Short-chain fatty acids: Straight-chain fatty acids containing up to eight car-

bon atoms
–– Example: Butyric acid (C4)
–– Medium-chain fatty acids: Straight-chain fatty acids containing up to 12

carbons atoms
–– Example: Capric acid (C10) and lauric acid (C12)
–– Long-chain fatty acids: Straight-chain fatty acids containing more than 12

carbon atoms
–– Example: Palmitic acid (C16), stearic acid (C18)
• Cow milk contains predominantly butyric acid, stearic acid, and palmitic
acid.

S traight-Chain Unsaturated Fatty Acids
• These fatty acids have hydrocarbon straight chain with double bonds.
• Depending on number of double bonds, they are sub-classified into different types.
• Types of straight-chain unsaturated fatty acids

–– Monounsaturated fatty acids (MUFA): They contain single double bond.
Their molecular formula is (CnH2n-1COOH).
Example:
Oleic acid (18:1;9).It contains C18 atoms with one double bond between C9
and C10 atoms in hydrocarbon chain. Oleic acid is present in milk.

–– Polyunsaturated fatty acids (PUFA): They contain two or more than two
double bonds.
Example:
Linoleic acid (C18), linolenic acid (C18), arachidonic acid (C20). They
have high biological importance for humans.

• Unsaturated fatty acids exhibit isomerism.
–– They have two isomeric forms.

7.3  Derived Lipids 127

–– In “cis” form, two hydrogen atoms around the double bond remain on the
same side of chain.

–– In “trans” form, two hydrogen atoms around the double bond are placed on
the opposite side of chain.

Example:
Oleic acid has cis configuration and elaidic acid has trans configuration.
Both have the same molecular formula.
• Trans fats.
–– Unsaturated fatty acids mostly exist in “cis” form in nature.
–– Trans fats are unsaturated straight-chain fatty acids with trans

configuration.
–– They are produced during partial hydrogenation of vegetable oils. The pro-

cess converts unsaturated vegetable oils into semisolid saturated fats.
Example: margarine. It is synthesized from vegetable oils by
hydrogenation.
–– During the process, a few unsaturated double bonds are converted into trans
form. Thus the vegetable fat contains trans fats.
–– The amount of trans fats in daily food should not be more than 1% of total
fats.
–– Natural trans fats are limited in number.
Example:
Conjugated linoleic acid and vaccenic acid. They are found in milk of cattle.
–– Trans fats have no known benefit to humans.
–– They increase the level of LDL and decrease the level of HDL. Tans fats
are implicated in atherosclerosis and coronary artery disease.

E ssential Fatty Acids
• Essential fatty acids are those polyunsaturated fatty acids which are essential for

physiological functions of the body. They are supplemented with diet.
Example:
Linoleic acid (C18), linolenic acid (C18), arachidonic acid (C20)

B ranched-Chain Fatty Acids (BCFA)
• These are basically saturated fatty acids with a branch on methyl group or on the

hydrocarbon chain.

• They are abundantly found in dairy products.
Example:
Phytanic acid

• They are structural component of bacterial cell membrane. Example: Lactobacilli.

Cyclic Fatty Acids
• They have a ring structure internally in the molecule.

Example:
Chaulmoogric acid

• It is derived from seeds of chaulmoogra. It is used in treatment of leprosy.

128 7 Lipids

7.4 E ssential Fatty Acids (EFA)

7.4.1 H istory

• In 1927, Herbert Evans and George Burr observed a deficiency in the growth of
rats. They hypothesized the necessity of a lipid substance (EFA) in diet and
called it “vitamin F.”

• In 1930, it was George Burr and his wife, Mildred Burr, who discovered linoleic
acid and coined the term “essential fatty acids” pertaining to their essentiality for
growth and overall health of experimental albino rats.

• In 1958, a deficiency of EFA was reported among infants who were fed upon a
diet deficient of EFA.

Definition

Essential fatty acids are polyunsaturated fatty acids which are not synthesized in the
body and need to be supplemented with diet to maintain normal health.

EFA are highly essential for physiological functions of the body. They are not
synthesized in the body. They are supplemented with diet.

7.4.2 T ypes of Essential Fatty Acids

Linoleic acid and linolenic acid are EFA. They are polyunsaturated fatty acids.

Linoleic Acid

• It is a C18 compound. It has two double bonds at C9 and C12 positions. They are
present between C9–C10 carbon atoms and C12–C13 carbon atoms. It is repre-
sented as (18:2;9,12).

• Linoleic acid is found in cottonseed oil, sunflower oil, soya bean oil, and egg
yolk.

• It exists as ester of triglyceride.
• Linoleic acid is a precursor to lipoxins, eicosanoids, and endocannabinoids.
• In fatty acids, carboxylic group is present at one end of molecule. The carbon

atom next to carboxylic carbon is called as α-carbon, and the carbon atom of
methyl group on the opposite end is called as ω-carbon (omega).
• Linoleic acid is called as “ω-6 fatty acid.” It has first double bond located at
ω-6 carbon atom.

Linolenic Acid

• It is a C18 compound. It has three double bonds at C9, C12, and C15 positions.
They are present between C9–C10, C12–C13, and C15–C16 atoms in hydrocar-
bon chain, respectively. It is represented as (18:3;9,12,15).

7.4  Essential Fatty Acids (EFA) 129

• Linolenic acid is found in rapeseed oil, sunflower oil, linseed oil, cod liver oil,

sea algae, and phytoplankton.
• Linolenic acid is called as “ω-3 fatty acid.” It has first double bond located

at ω-3 carbon atom.
• Three omega-3 fatty acids are biologically important for humans. They are

α-linolenic acid, eicosapentaenoic acid (EPA), and docosahexaenoic acid
(DHA).
• EFA cannot be synthesized in the body of mammals and humans. They lack
fatty acid desaturase enzyme which is necessary for biosynthesis of EFA.

Arachidonic Acid

• It is a C20 compound. It has four double bonds. They are present between C5–
C6, C8–C9, C11–C12, and C14–C15 carbon atoms. It is represented as
(20:4;5,8,11,14).

• Arachidonic acid is found in peanut oil, cod liver oil.
• It is synthesized from linoleic acid in the human body through chain elongation

and desaturation. It has high biological importance.
• Arachidonic acid is a precursor to prostaglandins, leukotrienes, and

thromboxane.

Conditionally Essential Fatty Acids

• These are polyunsaturated fatty acids that become essential in physiological
and/or pathological condition and need supplementation with diet.
Example: γ-Linolenic acid, DHA (docosahexaenoic acid)

7.4.3 Functions of EFA

• Essential fatty acids are vital for growth and normal health of individual.
• They are structural components of body tissues.
• Essential fatty acids are components of lipids in mitochondrial membrane. In

deficiency of EFA, oxidative phosphorylation is reduced.
• EFA are integral components of lipids in plasma membranes. Arachidonic acid

constitutes about 15% of the lipids in cell membranes.
• EFA are necessary for biosynthesis of prostaglandins from arachidonic acid

by cyclooxygenase enzyme activity.
• EFA are necessary for biosynthesis of leukotrienes through lipoxygenase

activity.
• Diet rich in EFA helps to lower low-density lipoprotein.
• Essential fatty acids help to minimize fatty liver condition.
• Docosahexaenoic acid (DHA) is abundantly found in the retina. It is biosyn-

thesized from dietary alpha linolenic acid. So EFA are necessary for normal
vision.

130 7 Lipids

• Docosahexaenoic acid (DHA) is the essential component of the plasma mem-
brane of brain tissues. DHA is essential in development of the brain and cog-
nitive functions among preschool children.

• Essential fatty acids have cis configuration. They provide fluidity to plasma
membranes.

7.4.4 C linical Significance of EFA

• Deficiency of EFA is rarely observed with normal diet.
• Essential fatty acids bring about esterification of cholesterol. They are helpful in

excretion of cholesterol.
• Deficiency of EFA may result into fatty liver.
• Deficiency of EFA results into excessive thickness of the stratum corneum

(hyperkeratosis) and epithelial hyperplasia of Malpighian layer with hyperpig-
mentation of the skin (acanthosis).
• Deficiency of EFA may be associated with abnormality in growth of body
tissues.
• EFA deficiency leads to Higher chances for retinitis pigmentosa disorder. It is a
hereditary degenerative disorder characterized by loss of retinal cells and
blindness.
• Diet with higher levels of trans fatty acids replaces EFA and predisposes to coro-
nary artery disease.

7.5 Cholesterol

Cholesterol is a biologically important sterol in the human body.
The word is derived from Greek words “chole” which means bile, “stereos”

which means solid, and “ol” which means alcohol.
It was first discovered by Francois Poulletier de la Salle from gallstones.

7.5.1 O ccurrence

• Cholesterol is distributed widely in body tissues. Healthy human body contains
about 2 g of cholesterol per kg of body weight. A person of 70 kg of body weight
has 140 g of cholesterol in the body.

• Normal serum total cholesterol level is 200–240 mg/dl.
• Brain tissues contain comparatively higher amount of cholesterol. It is around

25% of total cholesterol of the body.
• Adipose tissues contain around 30 g of cholesterol.
• The liver contains around 15 g of cholesterol.
• Almost all cells of the body can synthesize cholesterol.

7.5 Cholesterol 131

7.5.2 D ietary Sources

• Milk, cream, cheese, butter, eggs, meat, and shellfish are rich in cholesterol.

7.5.3 Properties

• It is a white to light yellowish, odorless crystalline solid.
• It is insoluble in water but soluble in alcohol, chloroform, ether, and other organic

solvents.
• It is an important animal sterol.
• It is absent in prokaryotes and plants.
• In animal tissues, cholesterol exists in “free state” as well as “esterified state.”

Brain tissues mainly contain free state of cholesterol, whereas the adrenal cortex
chiefly contains cholesterol ester.

7.5.4 C hemical Structure

• Molecular formula of cholesterol is (C27H45OH).
• It is a solid organic alcohol.
• Cholesterol has “cyclo-pentano-perhydro-phenanthrene nucleus.” It is also

called as “sterane ring” as in Fig. 7.3.
• The nucleus system is composed of four rings which are nonlinearly fused. Three

rings are designated as A, B, and C which are cyclohexane. Fourth ring is desig-
nated as D which is cyclopentane. The three cyclohexane rings together consti-
tute “phenanthrene” (polycyclic aromatic organic compound).
• Cholesterol has one hydroxyl group (OH) present at C3 position.
• It has one double bond between C5–C6 atoms.
• It possesses methyl groups at C10 and C13 atoms.
• It possesses a chain of eight carbon atoms linked to C17 atom as in Fig. 7.4.

Fig. 7.3  Structure of 18
Cholesterol
11 12 17
1 9C 13 16
D

2 10 B 14 15
8
A

357
46

Cyclopentanoper hydro Phenanthrene
nucleus

[Sterane nucleus]

132 7 Lipids
Fig. 7.4 Cholesterol
CH3 CH3

CH3 CH2– (CH2)3 – CH CH3
17 Aliphatic side

CH3 13 chain
2 1 10
15

3 45 6 Cyclopentane
OH Ring

Phenanthrene nucleus
[ Cholesterol ]

Fig. 7.5  7-Dehydro cholesterol CH2 CH2
CH2 CH2

CH2
1
2

345 7
OH 6

7-DEHYDRO CHOLESTROL

7.5.5 Functions

• Cholesterol is a structural component of plasma membrane.
• It helps to maintain fluidity of plasma membrane.
• It is necessary for biosynthesis of bile acids and bile salts.
• It is vital for biosynthesis of steroidal hormones like glucocorticoids, testoster-

one, and estrogen.
• Synthesis of calcitriol (vitamin D3) requires 7-dehydrocholesterol in the skin. It

is a precursor to vitamin D3 (Fig. 7.5).

7.6 Compound Lipids

7.6.1 P hospholipids

Phospholipids are compound lipids which contain nitrogenous base/additional sub-
stituents attached to phosphate residue in addition to fatty acids and alcohol.

7.6  Compound Lipids 133

They are also called as “phosphatides.”

Classification of Phospholipids
Celmer and Carter classified phospholipids on the basis of type of alcohol pres-
ent in phospholipids.

Phospholipids are classified into three groups as:

1 . Glycerophosphatides
2. Phosphoinositides
3. Phosphosphingosides

G lycerophosphatides

Composition
• They contain fatty acid + glycerol + phosphoric acid + nitrogenous base.

• Two fatty acid molecules are linked to glycerol at C1 and C2 positions. These
ester bonds are hydrophobic in nature and form the hydrophobic tail of

phospholipid.

• The phosphoric acid is attached to C3 of glycerol forming a hydrophilic head of
phospholipid. Glycerophosphatides have “amphipathic character.”

• Fatty acid, glycerol, and phosphate together form “phosphatidic acid.”

• Nitrogenous base is attached to phosphate residue through ester linkage.

Types
Depending on type of nitrogenous base, phospholipids are the following types:

Lecithin/Phosphatidylcholine
Occurrence

• Lecithin is the chief phospholipid in biological membranes of animals and
plants.

• It is abundantly found in the brain, liver, sperm, and egg yolk.
• It is present in sprouts and seeds. Important plant seeds with high lecithin content

are peanuts, flaxseeds, sunflower seeds, sesame seeds, and cottonseeds.

Composition

• It is composed of fatty acids  +  glycerol  +  phosphoric acid  +  choline as in
Fig. 7.6.

• Saturated fatty acid and unsaturated fatty acid are linked to C1 and C2 positions
on glycerol through ester linkage.

134 7 Lipids

Glycerol O
moiety ∝ CH2 – O – C – R1

O Fatty acids CH3
β CH – O – C – R2 CH3

O CH3
∝¢ CH2 – O – P – O – CH2 – CH2 – N+

OH

Phosphoric acid Polar choline

Fig. 7.6  Lecithin

• Phosphoric acid is linked to C3 position on glycerol through ester linkage. This
molecule is called as “phosphatidic acid.”

• Choline is linked to phosphate moiety through ester bond.

Hydrolysis of Lecithin
Lecithin is hydrolyzed by various phospholipases found in animal tissues.

Action of Phospholipases A1 and A2

• Phospholipases A1 andA2 are present in mammals and humans. Phospholipase
A1acts at SN-1 position of phospholipid (lecithin) and liberates fatty acid from
C1 of glycerol.

Phospholipase A1

Lecithin Lysolecithin + Fatty acid

• Phospholipase A2 is found in humans. It acts at SN-2 position of phospholipids
and liberates fatty acid from C2 of glycerol.

Phospholipase A 2

Lecithin Lysolecithin + Arachidonic acid

Action of Phospholipase B

• This enzyme is found in humans.
• It can act at SN-1 and SN-2 positions of phospholipid. Its substrate is

lysophospholipid.

7.6  Compound Lipids 135

• It is also called as lysophospholipase.

Phospholipase B

Lysolecithin Glyceryl phosphoryl choline + Fatty acid

Action of Phospholipase C

• It is found in humans, plants, and Clostridium welchii.
• It cleavages phosphate ester bond and releases 1,2-diacylglycerol and phospho-

ryl choline.

Phospholipase C

Lecithin 1,2Diacyl glycerol + Phosphoryl choline

Action of Phospholipase D

• This enzyme is found in plants, bacteria, and viruses.
• It cleavages phospholipid into phosphatidic acid and choline.

Phospholipase D

Lecithin Choline + Phosphatidic acid

Cephalin/Phosphatidylethanolamine
Occurrence

• Cephalin is the chief phospholipid of bacteria.
• It is found in biological membranes of animals and humans. It constitutes around

20% of total phospholipids.
• It is abundantly found in nervous tissues like white matter of the brain, spinal

cord, and nerve fibers. Cephalin constitutes around 50% of total phospholipids of
the brain.

Composition

• Cephalin is composed of fatty acids + glycerol + phosphoric acid + ethanol-
amine as in Fig. 7.7.

Plasmalogen
Plasmalogen is a class of ether phospholipid. It is different from other phospholip-
ids with the presence of ether bond at C1 and ester bond at C2 of glycerol.

136 7 Lipids

Occurrence

• It is found in biological membranes of animals.
• It is rich in brain tissues, mitochondria, and muscles.
• Plasmalogen constitutes about 15% of total phospholipids.

Composition

• Plasmalogen is composed of fatty acids + glycerol + phosphoric acid + etha-
nolamine/choline as in Fig. 7.8.

• In plasmalogen, saturated fatty acid is attached to C1 position of glycerol by ester
linkage, and PUFA is attached to C2 position of glycerol by ether linkage.

Cardiolipin
Occurrence

• Cardiolipin is a main phospholipid in inner mitochondrial membrane of animals
and plants.

• It was extracted from bovine heart. So it derived its name.
• It is also found in bacterial cell membrane.

Fig. 7.7  Chephalin ∝ CH2 – O – CO – R1
Fig. 7.8  Plasmalogen Fatty acids
(containing ethanolamine
moiety) β CH – O – CO – R2
O

∝¢ CH2 – O – P – O – CH2 – CH2 – NH2
OH

Ethanol amine

Phosphoric acid

CH2 – O – CH = CH – R1
CH – O – CO – R2

O
CH2 – O – P – O – CH2 – CH2 – NH2

OH
Ethanolamine

7.6  Compound Lipids 137

Composition

• It is composed of fatty acids + glycerol + phosphoric acids.
• Cardiolipin has a unique chemical structure. Glycerol molecule forms the back-

bone of the cardiolipin. It has two phosphatidic acid molecules. These are linked
at C1 and C3 positions on central glycerol moiety. So it is also called as “diphos-
phatidylglycerol” or “1,3-bis phosphatidylglycerol.”
• Cardiolipin contains two phosphoric acid molecules. So it has greater affinity to
proteins in inner mitochondrial membrane.

Phosphoinositide

Phosphatidylinositol
Occurrence

• It is found in biological membranes of animals and plants.
• It is more in brain tissues in mammals.

Composition

• It is composed of fatty acids + glycerol + phosphoric acids + inositol as in Fig. 7.9.
• Inositol is a cyclic polyhydroxy alcohol. It is a hexahydroxy cyclohexane. It is

the major structural constituent of phosphatidylinositol.

P hosphosphingosides

Sphingomyelin/Phosphatidyl-Sphingoside
Occurrence

• They are predominantly found in nervous tissues in the brain, spinal cord, and
nerves.

• They are the main phospholipid in myelin sheath of axons of nerves.

Fig. 7.9  Phosphatidyl O
inositol
CH2 – O – C – R1

CH – O – CO – R2
O

CH2 – O – P – O – CH2OH

OH OH
CH
H
C
H OH OH

OH H

138 7 Lipids

Phosphoric acid Choline
moiety

O= CH3
CH3 – (CH2)12 – CH = CH – CHOH – CH – CH2 – O – P – O – CH2 – CH2 – N+ CH3

NH H CH3
Fatty acid C = O

R

Fig. 7.10  Sphingomyelin

Composition

• They are composed of fatty acid + sphingol + phosphoric acid + choline as in
Fig. 7.10.

• Sphingol is a C18 amino alcohol. It is also called as “sphingosine.”
• Fatty acid molecule is attached to –NH2 group on sphingol. It results into forma-

tion of “ceramide.” It is a waxy lipid and important constituent of cell mem-
branes of animal cells.
• Ceramide is further linked to phosphoric acid to form “ceramide phosphate.”
Choline is attached to phosphate through ester bond to form sphingomyelin.

Functions of Phospholipids

• Phospholipids are structural constituents of biological cell membranes of ani-
mals, plants, and bacteria.

• Phospholipid like cardiolipins is an integral component of inner mitochondrial
membrane. It is associated with normal functioning of mitochondrial enzymes. It
helps in oxidative phosphorylation.

• Phospholipid like sphingomyelins is an integral component of myelin sheath of
myelinated nerve fibers. It forms an insulating layer over axon of nerve cells.

• Phospholipid like plasmalogens protects body tissues against oxidative damage
from reactive oxygen species.

• Phospholipids are necessary for blood coagulation along with blood clotting
factors.

• Phospholipid like lecithin decreases surface tension of water in intestinal lumen.
They are helpful in emulsification of fats.

• Phospholipids are helpful in the formation of chylomicrons within enterocytes.
They help in the transport of dietary triglycerides from the intestine to blood
circulation.

• Phospholipids help in the transport of endogenous triglycerides from the liver to
body tissues.

7.6  Compound Lipids 139

• Lecithin provides choline. It is a lipotropic factor and prevents fatty liver.
• Phospholipids of cell membranes provide arachidonic acid through enzymatic

action. It is a precursor for prostaglandins and leukotrienes.
• Phospholipids act as cofactor for tissue lipase.

Clinical Significance of Phospholipids

• Dipalmitoyl-Phosphatidyl-Choline (DPC)
–– It is lecithin which acts as “pulmonary surfactant.”
–– It is composed of two molecules of palmitic acids linked to
phosphatidylcholine.
–– It lowers the surface tension in pulmonary alveoli.
–– DPC increases the ability of pulmonary alveoli to expand (pulmonary
compliance).
–– DPC prevents the collapse of pulmonary alveoli after expiration
(atelectasis).

• Niemann-Pick Disease
–– It is a hereditary recessive disorder of lipid storage (lipidoses).
–– It is due to deficiency of sphingomyelinase enzyme.
–– It is characterized by excessive accumulation of sphingomyelin in the brain,
spleen, and liver.
–– Its onset is early in infancy. The affected children have enlargement of the
liver (hepatomegaly), enlargement of the spleen (splenomegaly), and progres-
sive degeneration of brain tissues.

7.6.2 Glycolipids

Glycolipids are compound lipids containing a carbohydrate moiety attached to
lipid molecule by glycosidic bond.

They are non-phosphorylated lipids.

Occurrence

• Glycolipids are found in white matter of the brain, spinal cord, myelin sheath,
spleen, and erythrocytes.

Composition

• They are fatty acids + sphingol + carbohydrates.

Types
Glycolipids are two types:

140 7 Lipids

Cerebrosides/Monoglucosylceramides
Occurrence

• Cerebrosides are abundantly found in white matter of the brain, spinal cord, and
myelin sheath of nerve fibers and dendrites.

Composition

• They are composed of fatty acids + sphingol + carbohydrates (galactose) or
(glucose).

• Cerebrosides are devoid of glycerol, phosphoric acid, and nitrogenous
base.

Types
Based on fatty acid in cerebrosides, they are the following four types:

• Kerasin
–– It contains lignoceric acid. It is a C24 fatty acid.

• Cerebron
–– It contains hydroxy lignoceric acid, called as cerebronic acid. It is a hydroxyl-
ated lignoceric acid.

• Nervon
–– It contains nervonic acid. It is a monosaturated fatty acid with C24 atoms.

• Oxynervon
–– It contains oxygenated nervonic acid.

Function

• Cerebrosides are structural components of white matter of the brain, myelin
sheath, and spinal cord.

• They are helpful in normal brain functioning.
• They modulate signal transduction.
• They are necessary for impulse conduction.

Clinical Significance

• Gaucher’s Disease
–– It is a hereditary autosomal recessive disorder of cerebroside metabolism.
–– The disorder is due to deficiency of beta-glucocerebrosidase enzyme.
–– It is characterized by excessive accumulation of glucocerebrosides (kerasin)
in the brain, liver, reticuloendothelial cells, and bone marrow.

7.6  Compound Lipids 141

–– Disease affects children and adults. Failure of growth, mental retardation, and
muscle spasticity are characteristic feature in infants and children. In adults,
bone marrow is infiltrated with histiocytes. Bone pain, anemia, and thrombo-
cytopenia are main manifestations in adults.

Ganglioside
Ganglioside is a carbohydrate-enriched glycolipid isolated from ganglionic cells

of bovine brain by Ernst Klenk in 1942.

Occurrence

• Gangliosides are found in the spleen, liver, and brain.
• They are predominantly found in white matter of the brain, spinal cord, gangli-

onic cells, spleen, and dendrites.

Composition

• They are composed of fatty acids + sphingol + carbohydrates (galactose) or
(glucose) + N-acetyl neuraminic acid (NANA) also called as sialic acid.

• Gangliosides contain 1–3 NANA residues.

Types
Based on number of sialic acid (NANA) residues, gangliosides are the following
types:

• One sialic acid residue containing gangliosides is designated as “GM.”
–– GM-1, GM-2, GM-3

• Two sialic acid residues containing gangliosides are designated as “GD.”
–– GD-1a, GD-1b, GD-2, GD-3

• Three sialic acid residues containing gangliosides are designated as “GT.”
–– GT-1b, GT-3

• Four sialic acid residues containing gangliosides are designated as “GQ.”
–– GQ-1

Function

• Gangliosides are structural components of biomembranes.
• They act as receptors for pituitary hormones.
• They modulate signal transduction.
• They have a role in cell recognition.
• They have a role in transportation of amines through plasma membranes.

142 7 Lipids

Clinical Significance

• Tay-Sachs Disease
–– It is a hereditary recessive disorder of ganglioside metabolism.
–– It is due to deficiency of hexosaminidase enzyme.
–– The disorder is characterized by excessive accumulation of GM-2 ganglioside
in the ganglionic cells and brain tissues.
–– Its onset is early in infancy. Ganglionic cells of the brain and retina are injured.
Infants suffer from blindness, mental retardation, and seizures.
–– Prognosis is extremely poor.

7.6.3 S ulfolipids

Sulfolipids are the compound lipids which possess sulfur groups. The sulfur group
is attached to glycolipid through esterification. Sulfolipids are abundantly found in
biomembranes of nervous tissues.

7.7 Simple Lipids

Neutral Fats
Neutral fats are the tri-esters of glycerol with similar or dissimilar fatty acids.

They are also called as “triacylglycerol” or “triglycerides.” The carbon atoms of
glycerol are designated as C1, C2, and C3. Esterification of glycerol with similar fatty
acids results into formation of simple triglycerides. Esterification with dissimilar
fatty acids results into mixed triglycerides.

Physical Properties

• Triglycerides are colorless, tasteless, and odorless.
• They are insoluble in water.
• Triglycerides containing higher proportion of unsaturated fatty acids are liquid

at room temperature and called as “oil.” Example: Cottonseed oil, sunflower
oil.
• Triglycerides with higher proportion of saturated fatty acids are semisolid at
room temperature and called as “fats.” Example: Butter (butyric acid),
coconut oil (lauric acid).
• Their specific gravity is <1. They float on the surface of water.
• They undergo emulsification in aqueous medium in the presence of bile salts,
soap, and proteins.
• Melting point of neutral fats with short-chain fatty acids is low, for example, but-
ter (MP = 35 °C), and fats with long-chain fatty acids is high, for example, tripal-
mitin (67 °C).

7.7  Simple Lipids 143

O

O CH2 – O – C – C17 H33 Hydrolysis CH2 OH

H33 C17 – C – O – CH O CH OH

CH2 – O – C – C17 H33 CH2 OH
Glycerol
Triglyceride +
[Triolein]
3 C17 H33 COOH
Oleic Acid

Fig. 7.11  Hydrolysis of triglyceride

Chemical Properties

• Hydrolysis
–– Neutral fats can be hydrolyzed by alkali, acids, or enzyme.
–– Lipase is found in saliva, gastric juice, pancreatic juice, intestinal juice, and
body tissues.
–– Lipase cleavages fats into glycerol and constituent fatty acids as in Fig. 7.11.

• Saponification
–– Saponification is the hydrolysis of neutral fats by alkali. It results into forma-
tion of glycerol and alkali salts of fatty acids. These salts are called as
“soap.”

Tripalmitin + Sodium hydroxide Glycerol + Sodium palmitate
(Soap)

• Rancidity
–– The occurrence of unpleasant smell and bad taste in the neutral fats upon
aging is called rancidity.
–– Rancidity is hydrolytic rancidity and oxidative rancidity.
–– In hydrolytic rancidity, fats are hydrolyzed by lipase in the presence of mois-
ture and warm temperature. It yields glycerol, free fatty acids, and
monoacylglycerol.
–– In oxidative rancidity, unsaturated fatty acids in fats are oxidized to form per-
oxides and aldehydes. They have unpleasant smell and taste.
–– Natural oils possess antioxidants like vitamin E, hydroquinones, and phenols.
They prevent rancidity.
–– Natural oils containing higher quantity of PUFA are more prone to
rancidity.

144 7 Lipids

7.8 Applied Biochemistry

7.8.1 Dietary Omega: Three Fatty Acids and Dental Diseases

Periodontitis is a chronic and progressive inflammatory disease of periodontium
of teeth. It is a bacterial disease. It is characterized by inflammation of gums,
tooth mobility, pain, and suppuration. Polyunsaturated fatty acids like omega-3
fatty acids and omega-6 fatty acids have anti-inflammatory properties. Topical
application of omega-3 fatty acids on teeth and gums in experimental models has
proved beneficial in protection of tissue damage and bone loss associated with
periodontitis.

Randomized clinical trial in humans suffering from periodontitis had been done.
Systemic administration of eicosapentaenoic acid and gamma-linolenic acid was
followed for 12 weeks. Reduction in periodontal pockets in patients receiving EPA
and GLA was observed.

Suggested Readings

Campan P, Planchand PO, Duran D (1997) Pilot study on n-3 polyunsaturated fatty acids in the
treatment of human experimental gingivitis. J Clin Periodontol 24:907–913

Guan X, Wenk MR (2008) Biochemistry of inositol lipids. Front Biosci 13:3239–3251
Hasturk H, Kantarci A, Ohira T, Arita M, Ebrahimi N, Chiang N, Petasis NA, Levy BD, Serhan

CN, Van Dyke T (2006) RvE1 protects from local inflammation and osteoclast- mediated bone
destruction in periodontitis. FASEB J 20:401–403
Hunt SM, Groff JL, Gropper SA (1995) Advanced nutrition and human metabolism. West,
Belmont, CA
Hunter JE (2006) Dietary trans fatty acids: review of recent human studies and food industry
responses. Lipids 41(11):967–992
Rosenstein ED, Kushner LJ, Kramer N, Kazandjian G (2003) Pilot study of dietary fatty acid
supplementation in the treatment of adult periodontitis. Prostaglandins Leukot Essent Fatty
Acids 68:213–218
Vance JE, Vance DE (2002) Biochemistry of lipids, lipoproteins and membranes. Elsevier,
Amsterdam
Zhao G, Etherton TD, Martin KR, Gillies PJ, West SG, Kris-Etherton PM (2007) Dietary alpha-­
linolenic acid inhibits proinflammatory cytokine production by peripheral blood mononuclear
cells in hypercholesterolemic subjects. Am J Clin Nutr 85:385–391

Nucleic Acids 8

8.1 H istorical Background

• In 1868, Swiss physician, Friedrich Miescher, isolated nucleic acid from nuclei
of human WBC (pus cells). He called it as nuclein.

• In 1884, it was Oscar Hertwig who emphasized upon the importance of nuclein
as genetic material.

• In 1889, Altman named nuclein as nucleic acid.
• In 1919, Russian biochemist P. Levene proposed polynucleotide model of nucleic

acid of yeast. Later on, he suggested tetranucleotide model comprised of four
nucleotides arranged in the same order as G-C-T-A-G-C-T-A. Levene also
declared sequence (phosphate-sugar-base) of nucleotide constituents.
• In 1944, Oswald Avery postulated that DNA was the core molecule for inheri-
tance of information.
• In 1950, Erwin Chargaff, Austrian biochemist, concluded against Levene that
one nucleotide never replicates in the same sequence. He also noted that compo-
sition of nucleotide differs in different species.
• In 1950, Rosalind Franklin produced X-ray diffraction study of DNA structure.
Her pioneering work paved a way to 3D structure of DNA by Watson and Crick.
She remained unacknowledged.
• In 1953, American biologist, James Watson, and English physicist, Francis Crick,
restructured data regarding DNA and put forward a double-helix model of DNA.
• In 1961, DNA was synthesized by Kornberg.

Definition
Deoxyribonucleic Acid (DNA)
DNA is the largest biopolymer consisting of deoxyribonucleotides.

It constitutes genetic material of organisms. However, certain organisms like

tobacco mosaic virus (TMV) and human immunodeficiency virus (HIV) contain

ribonucleic acid (RNA) as a genetic material.

© Springer Nature Singapore Pte Ltd. 2019 145
A. Gupta, Comprehensive Biochemistry for Dentistry,
https://doi.org/10.1007/978-981-13-1035-5_8

146 8  Nucleic Acids

DNA as Genetic Material
In 1902, Sutton and Boveri promulgated the role of chromosomes in transmis-
sion of genetic information from one generation to another.

In 1952, the experiment conducted by Alfred Hershey and Martha Chase on
bacteriophage paved the way to declare DNA as genetic material due to follwo-
ing characteristics such as:

• DNA is present in all cells.
• It can replicate itself as carbon copy.
• It is inherited from parents to offspring.
• DNA can undergo mutations which are essential for adaptation and

variations.

8.2 Occurrence

In Eukaryotic Cells

• DNA is located within the nucleus of cell. It is associated with basic proteins and
forms chromosomes.
This may be called as nuclear DNA.

• DNA is also located within mitochondrial matrix.
This may be called as mitochondrial DNA (mtDNA).

In Prokaryotic Cells

• DNA is located in the cytoplasm of cell (nucleoid).

8.3 Chemical Composition of DNA

• DNA is a biomacromolecule. It is made up of two strands of
deoxyribonucleotides.

• Each deoxyribonucleotide is composed of three units as in Figs. 8.1, 8.2, and 8.3.
–– Nitrogenous bases
–– Deoxyribose sugar
–– Phosphoric acid

• Nitrogenous Bases
These are nitrogen-containing cyclic organic compounds. They are categorized
into two groups depending upon their chemical structure such as:
–– Purines
Purine is a nine-membered heterocyclic organic compound. Purine is com-
posed of pyrimidine ring attached to imidazole ring. Purine has four nitrogen
atoms at 1, 3, 7, and 9 positions as in Fig. 8.4.
Adenine and guanine are two purine bases in DNA.

8.3  Chemical Composition of DNA 147
Fig. 8.1  Ribose Sugar
HOH2C5 O H
C4 1C

HH H OH
C3 2C

OH OH

Fig. 8.2 Deoxyribose HOC5H2 O H
Sugar

C 4 1C

HH H OH
C3 2C

OH H

Fig. 8.3  Phosphoric acid H3PO4 OH
HO P O

OH

NH2 O

N1 C N HN 1 C N
HC 2
65 7 C2 65 7
H2N
C C

8 CH 8 CH

C 9 C 9

34 N 34 N
H H
N N

ADENINE GUANINE

PURINES

Fig. 8.4 Purines

–– Pyrimidines

Pyrimidine is a six-membered heterocyclic organic compound. Pyrimidine struc-

ture resembles benzene ring. It has two nitrogen atoms at 1 and 3 positions.
Thymine and cytosine are two pyrimidine bases in DNA.
• Deoxyribose Sugar

148 8  Nucleic Acids

–– It is an aldopentose. It contains five carbon atoms. Deoxyribose sugar
(C5H10O4) has one oxygen atom less than ribose sugar (C5H10O5). In deoxyri-
bose sugar, C2 contains H-C-H group, whereas ribose sugar contains H-C-OH
group.

• Phosphoric Acid
It forms phosphodiester bond with two sugar residues as in Fig. 8.5a.

a O CH3 NH2
5C
HN 1 C C

6 6

C 2 4 CH N 1 5 CH

3 C 2 4 CH

ON 3
H
ON
THYMINE H

CYTOSINE

PYRIMIDINES

b

Nitrogen Base + Deoxyribose Sugar

NUCLEOSIDE

Glycosidic Bond

c

NUCLEOSIDE + Phosphoric acid

NUCLEOTIDE
Esterification

Fig. 8.5 (b) Nucleoside structure. (c) Nucleotide structure

8.5  Structure of DNA Strand 149

In a Deoxyribonucleotide

Purines and pyrimidines are attached to deoxyribose sugar by glycosidic bond. The

nitrogen atom at position 9 in purines is linked to C1of deoxyribose sugar, whereas
nitrogen atom at position 1 in pyrimidines is linked to C1 of deoxyribose sugar as in
Fig. 8.5b.

Phosphodiester Bond
Phosphodiester bond is formed between two OH groups of phosphoric acid
and OH groups of sugar at 3′ and 5′ positions.

Polydeoxyribonucleotides in a strand are linked together by phosphodiester
bonding. These sugar-phosphate linkages constitute the backbone of DNA. It is
the structural basis of DNA.

The 3′ and 5′ positions in deoxyribose sugar are available for ester linkage.
Phosphoric acid is attached to OH group at 3′ carbon of deoxyribose sugar in one
nucleotide and OH group at 5′ carbon of deoxyribose sugar in adjacent nucleotide.

Therefore, phosphodiester linkage at 3′ and 5′ positions provides stability to
DNA strand as in Fig. 8.5c.

8.4 T ypes of Deoxyribonucleotides in DNA

DNA contains four types of deoxyribonucleotides depending on the nature of
nitrogenous base.

1 . Deoxyadenosine Monophosphate (dAMP)
It is also called as 5′-deoxyadenylic acid or deoxyadenylate as in Fig. 8.6.

2. Deoxyguanosine Monophosphate (dGMP)
It is also called as 5′-deoxyguanylic acid or deoxyguanylate as in Fig. 8.7.

3 . Deoxythymidine Monophosphate (dTMP)
It is also called as 5′-deoxythymidylic acid or deoxythymidylate as in Fig. 8.8.

4. Deoxycytidine Monophosphate (dCMP)
It is also called as 5′-deoxycytidylic acid or deoxycytidylate as in Fig. 8.9.

8.5 Structure of DNA Strand

• It is polymer of deoxyribonucleotides. Adjacent nucleotides are linked together
by phosphodiester bond.

• Each DNA strand has polarity.
–– 3′ End (3 prime)
It is the end of DNA strand where C3 of deoxyribose sugar is not linked and
is free.
–– 5′ End (5 prime)
It is the end of DNA strand where C5 of deoxyribose sugar is not linked and
is free as in Figs. 8.10 and 8.11.

150 8  Nucleic Acids

Fig. 8.6 Adenosine NH2
monophosphate
(Adenylic acid) 6
51
O 7
OPO ADENINE
8
O 5CH2 42
9 3

N
O

41

SUGAR

32

OH

Fig. 8.7  O
Guanosine

monophosphate

(Guanylic acid)

O 7 51
OPO
8 GUANINE
O 5CH2
9 6

N NH2
O

41

SUGAR

32

OH

One strand of DNA molecule exhibits 3′–5′ polarity, whereas other strand
has 5′–3′ polarity.

Base Pair in DNA
Base pair signifies two nitrogenous bases held together through hydrogen bonding.
Each pair of base consists of purine in one strand and pyrimidine in another strand.
Particular purine always pairs with particular pyrimidine.

8.5  Structure of DNA Strand 151

Fig. 8.8  O CH3
Thymidine OPO
O
monophosphate O 5CH2
5
(Thymydlic acid)
4 6C
O THYMINE

41 N 3 1 NH

SUGAR 2

2 O

Fig. 8.9 Cytidine NH2
monophosphate (Cytidylic
C
acid)
6
O O
OPO 5 1N

O 5CH2 CYTOSINE

4 2C

3

N

O

41

32

This concept of base pair is called as complementary base pairs (base pair is
nonidentical).

Adenine pairs with thymine by two hydrogen bonds.
Guanine pairs with cytosine by three hydrogen bonds.

Justification of Complementary Base Pair

• Width of DNA helix is 20 Å. This space can be properly filled by a purine and a
pyrimidine. Contrarily, pairing between two purines would require space larger
than 20 Å. Furthermore, pairing between two pyrimidines would leave an empty
space, and hydrogen bonding could not be possible. A purine molecule has size
twice as wide as pyrimidine molecule.

• Three-dimensional arrangement of adenine and thymine is perfect to confer
hydrogen bonding between two bases.

152 8  Nucleic Acids

GLYCOSIDIC A Adenine
BOND C Cytosine
G Guanine
PHOSPHO DIESTER P P T Thymine
BOND SAT S RIBOSE SUGAR
P P PHOSPHATE GROUP
SCG S
P P
STA S
P P
SGC S
P P
SCG S
P P
SAT S
P P
SGA S
P P

HYDROGEN
BONDING

Fig. 8.10  Fragment of DNA molecule

• Similarly, guanine and cytosine alignment can only confer hydrogen bonding
between two bases.

Therefore, two DNA strands show:

• Polarity
Each strand shows polarity either in 3′–5′ direction or 5′–3′ direction.

• Complementary base pairing
A〓T, G≡C

• Antipolarity (antiparallel)
In DNA helix, two strands run in antiparallel direction.

8.6 Watson and Crick DNA Model

In 1953, American biologist, James D.  Watson, and British physicist, Francis
H.C.  Crick, postulated a 3D model of DNA.  They restructured X-ray diffraction
data provided by earlier pioneers, notably Franklin and Wilkins, regarding DNA.

CH3 3′ END 8.6  Watson and Crick DNA Model

H O O
H
3′ RIBOSE SUGAR
N H2 O
O 5′ END
OPO N N
7
O H
9 N
N
RIBOSE SUGAR O
ADENINE THYMINE
5′ CH2 5′ CH2 O
O OPO
O
H H 3′ 5′ HYDROGEN BONDING
H

H N H 5′
NH HO
O O 5′ CH2

OPO PHOSPHATE

O MOIETY C N HN G NO
OPO
5′ CH2 RIBOSE SUGAR N
CYTOSINE O
5O 1 O H N GUANINE
H 3′ H H 5′ END

O

3′ END 153
Fig. 8.11  Segment of DNA

154 8  Nucleic Acids

In 1962, Watson and Crick got Nobel Prize together with Wilkins.

Characteristics of DNA Model

• DNA molecule is made up of two polynucleotide strands that are linked with
each other by hydrogen bonds placed at regular intervals.

• DNA strands are antiparallel. One strand runs in 3′–5′ direction, while other
strand runs in 5′–3′ direction.

• Two polynucleotide strands are spirally coiled around an imaginary common
axis and form a double helix.

• Double helix has a diameter of 20 Å (2 nm). Diameter is uniform throughout the
DNA molecule as in Fig. 8.12.

• Grooves in double helix
–– Double helix contains major grooves and minor grooves that arise owing to
antiparallel nature of strands. Major and minor grooves oppose each other in
helix and are alternately placed along the entire length of DNA molecule.

Fig. 8.12  Watson - Crick
Model of DNA

3’
5’

5’
3’

PS TA S 34 A°
A P
S 3.4 A°
P TS

P

SG C S

8.6  Watson and Crick DNA Model 155

–– Width of major groove is 22 Å and minor groove is 12 Å.
–– Within grooves, base pairs are easily accessible to other molecules for interac-

tion. DNA-binding proteins have affinity for major grooves, for example,
transcription factors that attach major grooves and modulate transcription.
Histones, polymerases, and nucleases bind at major grooves.
• Spiral of double helix
–– One complete spiral (turn) of double helix has length of 34 Å (3.4 nm), called
pitch. It contains ten base pairs. A distance of 3.4  Å (0.34  nm) is present
between adjacent base pairs.
–– Nitrogenous bases are oriented to the interior of helix, while sugar-phosphate
backbone is directed outwardly. Purines and pyrimidines are oriented perpen-
dicular to sugar-phosphate backbone.
–– Adenine pairs with thymine through two hydrogen bonds, while guanine pairs
with cytosine through three hydrogen bonds. It is called as complementary
base pairing.
–– Double helix is coiled in right-hand direction. DNA turns are directed
clockwise.

DNA double helix is comparable to coiled ladder. Vertical bars of ladder repre-
sent sugar-phosphate components of DNA molecule. Horizontal steps of ladder rep-
resent nitrogenous bases which are linked to each other by hydrogen bonds, while
they remain attached to sugar-phosphate backbone.

Primarily, DNA double helix is stabilized by two forces such as:

• Hydrogen bonds
Forces of attraction between purines in one polynucleotide chain and pyrimi-
dines in other polynucleotide chain. This interchain hydrogen bonding is elusive
in defining the double helix.

• Phosphodiester bonds (covalent bond)
Present between two OH groups of phosphoric acid and OH groups of deoxyri-
bose sugars at 3′ and 5′ positions

• Nucleobase-stacking interactions
These are non-covalent forces of attraction between aromatic bases since they
contain pie bonds. Nitrogenous bases offer strong π-π stacking interactions.
Therefore, base-stacking interactions constitute other stabilizing forces in helix.
These forces are hydrophobic. These interactions are partially inter-strand and
partially intra-strand in DNA double helix.

Chargaff Rule
Erwin Chargaff states that in DNA of all organisms, the amount of adenine is equal
to the amount of thymine and the amount of guanine is equal to the amount of
cytosine.

The amount of purines should be equal to the amount of pyrimidines (1:1 ratio).
(A + G = T + C OR (A + G/T + C = 1)

156 8  Nucleic Acids

8.7 F unctions of DNA

1. DNA has a unique property of duplicating itself into an exact copy. It is essential
for transmission of characters from parents to offspring. Hence, it is a genetic
material of cells.

2 . DNA can transcribe mRNA on its strand. The mRNA contains codons for protein
synthesis.

3. DNA regulates synthesis of proteins through codons.
4. DNA controls gene expression. It can regulate cellular functions like secretion,

excretion, proliferation, and apoptosis.
5. DNA can undergo mutations which are essential for origin of species.
6. DNA is essential for crossing over and recombination during meiosis. They are

necessary for variation in same species.
7. It controls differentiation of cells in embryonic development.

8.8 T ypes of DNA

Linear DNA

• DNA molecule is linear in shape. It is made up of two strands. Each strand has
two free ends.

• Linear DNA is associated with nucleoprotein and is organized into
chromosome.

• It is found in eukaryotes.

Circular DNA

• DNA molecule is circular in shape. Ends of circular DNA are joined together. It
is not associated with protein.

• Circular DNA can be single stranded in viruses like chicken anemia virus
(CAV) and porcine circovirus 2 (PCV2). They are pathogenic organisms.

• Circular DNA can be double stranded in mitochondria, chloroplasts, bacteria,
and viruses.

Double-Stranded DNA

• DNA molecule has two strands which are helically coiled. It is found in
eukaryotes.

A-DNA

• It is a right-handed molecule.
• One turn of helix contains 11 base pairs.

8.9  Replication of DNA 157

B-DNA

• It is a right-handed molecule.
• One turn of helix contains ten base pairs.
• Length of the helix is 34 Å.
• It is the Watson and Crick DNA.

C-DNA

• It is a right-handed molecule.
• One turn of helix has nine base pairs.

D-DNA

• It is a right-handed molecule.
• One turn of helix has eight base pairs.

Z-DNA

• This DNA molecule was observed by Robert Wells, and its structure was deci-
phered by Alexander Rich in 1979.

• It is a left-handed molecule.
• One turn of helix has 12 base pairs.
• Length of helix is 45 Å.
• Sugar-phosphate backbone adopts a zigzag pattern giving its name as Z-DNA.

Palindromic DNA

• A DNA molecule that contains palindromic sequence. Reading of sequence in
one strand in 5′ → 3′ direction exactly matches with sequence in other strand in
5′ → 3′ direction.

• 5′ G-G-A-T-G-T-G 3′
• 3’G-T-G-T-A-G-G 5′
• Palindrome sequence is found in prokaryotes and eukaryotes.
• It was described by Wilson and Thomas in 1974.

8.9 Replication of DNA
8.9.1 D efinition

Replication of DNA is an autocatalytic multistep biological process of synthesizing
two DNA molecules from a parental DNA molecule.

158 8  Nucleic Acids

8.9.2 S ite of Occurrence

In Eukaryotes

• DNA replication occurs in the nucleus during S-phase of interphase (interval
between two cell divisions).

• DNA replication is semiconservative, bidirectional, and
semi-discontinuous.

In Prokaryotes

• DNA replication occurs in cytoplasm of cell.
• DNA replication is semiconservative, bidirectional, and continuous.

8.9.3 Models of Replication of DNA

Three models of DNA replication have been proposed.

Semiconservative Model
Two parental strands of DNA molecule separate. Each strand serves as template for
synthesis of a new strand of DNA. After replication, each DNA molecule has one
parental strand and other new strand. Parental strands are semiconserved within
two daughter DNA molecules as in Fig. 8.13.

Conservative Model
Parent DNA molecule regulates synthesis of two new strands. After replication, new
strands coil helically to form a daughter DNA molecule. Parental strands are con-
served in one daughter DNA molecule as in Fig. 8.14.

Dispersive Model
Parental DNA double helix is broken into short double-helix segments. Each seg-
ment synthesizes short new double-helix segment. After replication, all segments
reassemble into two DNA molecules. Each daughter DNA molecule consists of
partially parental double helix and partially new double helix. Parental strands are
dispersed randomly in two daughter DNA molecules as in Fig. 8.15.

8.9.4 S emiconservative Model of DNA Replication

Historical Facts
• In 1953, Watson and Crick documented a semiconservative model of DNA rep-

lication in a paper. They commented that original strands of DNA served as tem-
plate in DNA replication.

8.9  Replication of DNA 159

Fig. 8.13 Semi- Parental DNA
conservative Model of
DNA Replication

Semi conservative model

• In 1957, Taylor described the semiconservative model of DNA replication in
eukaryotes.

• In 1958, Meselson and Stahl provided experimental evidence in favor of
semiconservative model of replication.

8.9.5 Mechanism of Semiconservative Model

Prerequisites of DNA Replication

1. Deoxyribonucleoside Monophosphates (dAMP, dGMP, dTMP, and dCMP)
• Deoxyribonucleoside monophosphates constitute raw material for DNA rep-
lication. They are present in nuclear sap.

2 . Enzymes
• DNA helicase
Helicase is a motor protein (molecular motor; able to move in a specific direc-
tion along the substrate; can utilize chemical energy released by hydrolysis of
ATP for mechanical movement).

160 8  Nucleic Acids
Parental DNA
Fig. 8.14 Conservative
Model of DNA Replication

Conservative model

Helicase is an essential enzyme in living organisms. Helicase traps chemi-
cal energy released from hydrolysis of ATP.  Helicase moves along the
sugar-p­hosphate backbone and disrupts hydrogen bonds in annealed
nucleotide bases (complementary bases held by hydrogen bonds).
Helicase does function to separate helically coiled DNA strands.
• DNA topoisomerase
–– This is an isomerase enzyme. It regulates geometry (topology) of DNA
molecule. It induces break in DNA strand to relive coiling stress.
• DNA ligase
–– It is a ligase enzyme. It brings about formation of phosphodiester bonds
between adjacent nucleotides and catalyzes polymerization.
–– It is helpful in DNA replication and repair. It helps to join two Okazaki
fragments after removal of RNA primer. It seals DNA segments after cor-
rection of mismatched nucleotide bases.
• Primase
–– It is a type of RNA polymerase. It catalyzes formation of RNA primer on
the DNA template.
–– DNA polymerases
These enzymes are essential for synthesis of DNA utilizing deoxyribonu-
cleoside triphosphates. However, DNA polymerase is unable to initiate

8.9  Replication of DNA 161

Fig. 8.15 Dispersive Parental DNA
Model of DNA Replication

Dispersive model

DNA synthesis. It can insert a free deoxyribonucleotide to 3′ end of a
newly synthesized strand. It helps to elongate a new strand in 5′–3′
direction.
In eukaryotes, DNA polymerase are the following types:
DNA polymerase α
It helps in the synthesis of RNA primer. It helps in the synthesis of lagging
DNA strand.
DNA polymerase β
It helps in DNA repair.
DNA polymerase γ
It has 3′ → 5′ exonuclease activity. It helps in the synthesis of mitochon-
drial DNA.
DNA polymerase δ
It helps in the synthesis of leading DNA strand. It inserts deoxyribonucleo-
tides after removal of RNA primer.
DNA polymerase ε
It helps to insert correct deoxyribonucleotides in growing DNA chain after
excision of mismatched nucleotide bases.
–– In prokaryotes, DNA polymerase are the following types:

162 8  Nucleic Acids

DNA polymerase I
This polymerase removes RNA primer between Okazaki fragments. It helps
to fill gap through its 5′ → 3′ synthesizing activity. It also has 3′ → 5′ exo-
nuclease activity which is involved in proofreading and DNA repair.
DNA polymerase II
This polymerase has activities similar to that of DNA polymerase I.
DNA polymerase III
It is mainly involved in 5′ → 3′ DNA replication. It promotes elongation of
DNA strand. It also has proofreading property.
• Proteins
Single-stranded DNA-binding protein
–– This protein has been found in prokaryotes and eukaryotes.
–– It binds with single strand of DNA. It prevents recoiling of single DNA
strand into duplex. It helps to stabilize uncoiled DNA strand.

Steps in DNA Replication

1. Phosphorylation of Deoxyribonucleoside Monophosphates
• Deoxyribonucleoside monophosphates constitute raw material for DNA rep-
lication. They are found in the nuclear sap. The four types are as follows:
–– dAMP (deoxyadenosine monophosphate)
–– dGMP (deoxyguanosine monophosphate)
–– dTMP (deoxythymidine monophosphate)
–– dCMP (deoxycytidine monophosphate)
• Deoxyribonucleoside monophosphates undergo phosphorylation to form
deoxyribonucleoside triphosphates as dATP, dGTP, dTTP, and dCTP.
• Reaction is catalyzed by phosphorylase enzyme in the presence of ATP
molecules.

2 . Origin of Replication
• Origin of replication is a specific sequence in DNA which leads to initiation
of DNA replication. Origin of replication is also called as Ori.
• Eukaryotes have linear double-stranded DNA molecule. It has multiple ori-
gins of replication.
• Prokaryotes have single circular DNA molecule. It has single origin of
replication.

3. Unwinding of Double Helix
DNA molecule is a double-stranded helix. Its unwinding is a complex proce-

dure and is catalyzed by enzymes as follows:
• Helicase (unwindase) enzyme acts upon origin of replication. It catalyzes

splitting of hydrogen bonds between purines and pyrimidines of two DNA
strands. Both the strands are separated at Ori.
• The separated DNA strands are stabilized by single-stranded DNA-­
binding proteins.
• Unwinding of DNA strands induces coiling tension on either side of origin of
replication. It results into the formation of supercoils in DNA molecule.

8.9  Replication of DNA 163

Topoisomerase

Parental DNA SSB Template 3'
double proteins strand RNA primer
strand
Gyrase 5'

5' Leading strand
3'
5' Okazaki fragments
RNA primer
3'
3'
Replication
fork 5'

Replication of DNA

Fig. 8.16  Replication of DNA

• Topoisomerase enzyme induces a nick in one strand of DNA to relieve coil-

ing tension. Later on, it seals the cut portions of DNA strand.

• Prokaryotes have gyrase enzyme. Its function is similar to action soft helicase

and topoisomerase.

• Separation of DNA strands proceeds toward both directions from origin of
replication. Separating strands appear like a Y-shaped structure and is
called as replication fork.

• Separated strands of DNA molecule serve as templates as in Fig. 8.16.
4 . Synthesis of RNA Primer

• RNA primer is a short chain of RNA. It is synthesized at 5′ end of DNA
template. Ribonucleotides are polymerized into RNA primer with the help of

primase enzyme.
• Number of RNA primers: there are two RNA primers, one on each DNA

strand. One RNA primer is formed at free end of DNA (3′ end of DNA strand)
template, and other RNA primer is synthesized at fork end of DNA (5′ end of
DNA strand) template.
• RNA primer helps to initiate synthesis of new strand. Afterward, RNA primer

is disassociated. The gap is filled by addition of deoxyribonucleotides through

action of DNA polymerase β and DNA polymerase I in eukaryotes and pro-
karyotes, respectively.
• DNA polymerase can continue the elongation of already initiated new
DNA strand.
5 . Complementary Base Pairing

• Deoxyribonucleoside triphosphates attach to complementary nitrogen bases

on the DNA templates, for example, dATP pairs with thymine, dTTP pairs

with adenine, dGTP pairs with cytosine, and dCTP pairs with guanine nitrog-

enous bases. It is called complementary base pairing.

• Deoxyribonucleoside triphosphates are linked to nitrogen bases by formation

of hydrogen bonds.
6. Synthesis of New Strand of DNA

164 8  Nucleic Acids

• Deoxyribonucleoside triphosphates are held through hydrogen bonds with
complementary nitrogen bases on the DNA template.

• Deoxyribonucleoside triphosphates undergo hydrolysis into deoxyribo-
nucleoside monophosphates with release of pyrophosphates.

• Pyrophosphates undergo hydrolysis by pyrophosphatase enzyme to form
inorganic phosphate. In this reaction, energy is released.

• The energy is utilized in the formation of phosphodiester bonds between adja-
cent deoxyribonucleoside monophosphates on DNA template. This process
is called polymerization of deoxyribonucleoside monophosphates. It leads
to the formation of a new DNA strand on DNA template.

• In prokaryotes, DNA polymerase III and, in eukaryotes, DNA polymerase
δ catalyze synthesis of new DNA strands. Reaction requires Mg++ ions and
ATP molecules.

7 . Formation of Leading and Lagging DNA Strands
• DNA polymerase brings about synthesis of new strand in 5′ → 3′direction on
DNA template.
• Two DNA templates are antiparallel in nature. One template runs in
5′ → 3′direction, while the other template runs in 3′ → 5′direction. Therefore,
two new DNA strands are synthesized in opposite directions.
• Leading strand
–– Leading strand is formed on a DNA template which has polarity in
3′ → 5′direction.
• Leading strand is continuously elongated. Its 3′ end grows by addition of new
nucleotides. It is also called as continuous strand as in Fig. 8.16.
• Lagging strand
–– Lagging strand is formed on a DNA template which has polarity in
5′ → 3′direction.
• Lagging strand is discontinuously formed. It is due to exposure of a small
segment of DNA template over which new nucleotides are polymerized. In
this way, a short segment of new DNA strand is synthesized which is called
as Okazaki fragment as in Fig. 8.16.
–– Okazaki fragment (naming is based on scientist Reiji Okazaki who dis-
covered). Each fragment has nearly 200 base pairs in eukaryotes and 2000
base pairs in prokaryotes. A separate RNA primer is necessary for synthe-
sis of each Okazaki fragment. RNA primers are removed, and gaps are
sealed with deoxyribonucleotides through action of DNA polymerase β
and DNA polymerase I in eukaryotes and prokaryotes, respectively.
–– Individual Okazaki fragments are joined together by action of DNA ligase
enzyme.
• Lagging or discontinuous strand is composed of Okazaki fragments
joined together by DNA ligase.

8. Proofreading (Editing) and DNA Repair
Proofreading is a process of correcting errors in replication of DNA.

• Common error in DNA replication is the incorporation of incorrect nitroge-
nous base in growing DNA chain.
–– Nitrogenous bases in DNA molecule exist in common forms in which protons
occupy specific positions. These are keto forms. Due to a proton shift in a

8.10 Transcription 165

base, it is transformed from a common form into rare form which is called as
tautomerization. It is the most common cause for mismatch in base pairing.
–– The frequency of base-pairing mismatch is 0.001% (1 nucleotide in 10,000
nucleotides).
• In prokaryotes, DNA polymerase III can recognize mismatched nitrogenous
base in DNA chain. It is a 3′  →  5′ exonuclease enzyme. It excises incorrect
nucleotide from the end of chain in a direction opposite to DNA replication. It
inserts correct nucleotide. DNA ligase seals the repaired segment of DNA strand.
• In eukaryotes, DNA polymerase δ (3′ → 5′ exonuclease enzyme) performs
proofreading and repair.
• Proofreading corrects most of the base-pairing mismatch during the process
of DNA replication, while some are corrected after replication.
9 . DNA Helix Formation
• Newly formed DNA strands are coiled spirally to form a DNA duplex.

8.10 T ranscription

Definition
Transcription is defined as enzyme-controlled multistep biological process of syn-
thesis of RNA from a template of DNA. Etymologically, transcript means “writing
consisted of same words as original.”

Overview

1 . Sense strand of DNA is transcribed and it is identical to a single strand of RNA.
2. DNA molecule contains genetic information. This information is preserved

through DNA replication. This information is expressed through transcrip-
tion and translation.
3 . Transcription involves copying a template strand of DNA into a single-stranded
mRNA molecule. RNA molecule is complementary to template strand of
DNA and identical to non-template strand of DNA.
4. Transcription is a biological activity of rewriting an identical genetic
message.

8.10.1 Site of Occurrence

• Transcription occurs during G1 and G2 phases in interphase of cell cycle.

8.10.2 Prerequisites of Transcription

RNA Polymerase
This enzyme is essential for polymerization of ribonucleotides. It catalyzes synthe-
sis of RNA from a template strand of DNA:

166 8  Nucleic Acids

• In prokaryotes, one type of RNA polymerase is present. It can catalyze transcrip-
tion of RNA.

• In eukaryotes, three types of RNA polymerases are present which are essential
for synthesis of different types of RNA molecules as follows:
–– RNA polymerase I
It catalyzes synthesis of rRNA except 5S ribosomal RNA.
–– RNA polymerase II
It catalyzes synthesis of mRNA and snRNA (small nuclear RNA).
–– RNA polymerase III
It catalyzes synthesis of tRNA, 5S RNA, and snRNA.

Ribonucleoside Monophosphates

• Ribonucleoside monophosphates constitute raw material for synthesis of RNA.

Transcription Unit
Transcription unit is a specific sequence in DNA which is involved in transcrip-
tion. It has following components such as:

• Promoter
Promoter is a particular sequence in DNA that initiates transcription. Promoter is
located upstream on DNA toward 5′ end of sense strand and 3′ end of antisense
strand. Promoter is located nearby transcriptional start site. The size of promoter
can vary between 100 and 200 base pairs. RNA polymerase and transcription
factors bind to promoter region.

• Enhancer
Enhancer is a specific sequence in DNA that activates transcription. It is located
at a distance of about 2000 to 1 million base pairs from gene to be transcribed.
Its position is either downstream or upstream of transcription start site. Enhancer
in eukaryotes binds with activators to increase chances of transcription.
Promoter and enhancer are together described as cis-acting elements.
Transcription factors bind with cis-acting elements.

• Terminator
Terminator is a specific sequence of DNA that terminates transcription and
brings about release of mRNA.
–– In prokaryotes, Rho factor is a protein which stops transcription. It brings
about dissociation of RNA polymerase from DNA and terminates transcription.
–– In eukaryotes, proteins associated with RNA polymerase II signal the termi-
nation of transcription as in Figs. 8.17 and 8.18.

• Structural gene
It is the gene which codes for the synthesis of RNA or proteins. Structural gene
has two strands that serve different functions such as:
–– Sense strand (+)
DNA strand that has 5′ → 3′ polarity is called as sense strand. It is also called
as coding strand or non-template strand.

8.10 Transcription 167
Double stranded
3'
helix (DNA Molecule) 5'
5'

3'
Fig. 8.17  Double Stranded DNA Molecule and Cistron

5' 3'

3' 5'
[GENE] cistron

Fig. 8.18  Sites on Cistron

Promoter Transcription Termination
site site site
3'
5'

Core RNA (RNAP) Coding strand
enzyme polymerase (sense strand)
Sigma factor Template strand
3' 5' Non-coding or
anti sense strand
[GENE] Showing
cistron strands

Fig. 8.19  Attachment of RNA Polymerase (RNAP) to Promoter Region of Cistron

Sense strand of DNA has sequence (parallel) identical to sequence in RNA strand.
–– Antisense strand (─)

DNA strand that has 3′ → 5′ polarity is called as antisense strand. It is also
called as noncoding strand or template strand.
Antisense strand of DNA has sequence complementary (antiparallel) to
sequence in RNA. It acts as a template strand for synthesis of RNA strand as
in Fig. 8.19.
• Transcription factor
Transcription factor is a protein that binds with sequence of DNA. It controls
gene expression. Transcription factor binds with promoter. It can bring about
either upregulation or downregulation of transcription.

168 8  Nucleic Acids

8.10.3 M echanism of Transcription

Steps in Transcription

1 . Phosphorylation of Ribonucleoside Monophosphates
• Ribonucleoside monophosphates constitute raw material for synthesis of
mRNA. These are found in the nuclear sap. The four types are as follows:
–– AMP (adenosine monophosphate)
–– GMP (guanosine monophosphate)
–– UMP (uridine monophosphate)
–– CMP (cytidine monophosphate)
• Ribonucleoside monophosphates undergo phosphorylation to form ribonu-
cleoside triphosphates such as ATP, GTP, UTP, and CTP.
• Reaction is catalyzed by phosphorylase enzyme in the presence of ATP
molecules.

2. Initiation
• RNA polymerase binds to promoter on gene. Promoter is a sequence of gene
which starts transcription of a specific gene. They are located around tran-
scription start site of gene. They can be around 100 base pairs.
• Promoters in prokaryotes and eukaryotes are as follows:
• Promoters in prokaryotes
–– Pribnow box
Pribnow box in eukaryotes is called as TATA box. It is a specific sequence
of six nucleotides (TATAAT). It is located at ten nucleotides upstream from
transcription start site of DNA.
–– “35” sequence
It is a consensus sequence of TTGACA nucleotides. It is located at 35
nucleotides upstream of transcription start site of genome.
• Promoters in eukaryotes
–– TATA box
It is also called as Goldberg-Hogness box. It is located at 25 nucleotides
upstream of transcription start site of DNA.
–– CAAT box
It is a specific sequence of nine nucleotide bases (GGCCAATCT). This region
is located at 90 nucleotides upstream from transcription start site of DNA.
• In prokaryotes, single RNA polymerase can synthesize all types of RNAs. In
eukaryotes, specific RNA polymerases synthesize specific RNAs.
• In prokaryotes, RNA polymerase (holoenzyme) is made up of a core
enzyme (2α, 1β, and 1β′ polypeptide subunits) and a sigma factor.
A sigma factor helps in the recognition of promoter region of DNA.
• In eukaryotes, separate RNA polymerases (Pol I-rRNA, Pol II-mRNA, and
Pol III-tRNA) are necessary for transcription. RNA polymerase is associated
with general transcription factors (proteins).
General transcription factors help in recognition and binding with pro-
moter region of DNA.

8.10 Transcription 169

RNA polymerase II is associated with TFIIA, TFIIB, TFIID, TFIIE, TFIIF,
and TFIIH.
A particular RNA polymerase binds to a specific promoter in DNA.
Activity of promoter can be increased or decreased by enhancers and silenc-
ers (sequence of nucleotides) which are placed either upstream or downstream
from promoter.
• RNA polymerase along with sigma factor or general transcription factor binds
to promoter region on gene and forms a RNA polymerase-promoter closed
complex (DNA is double stranded).
• Helicase enzyme brings about localized unwinding and separation of two
strands of DNA. Now RNA polymerase-promoter open complex is formed.
This complex has unwound DNA strands and is called as transcription
bubble as in Figs. 8.20, 8.21, and 8.22.
• RNA polymerase has binding site to bind with ribonucleoside triphosphate
(NTP). The first NTP is generally A or G nucleoside triphosphate. The first
NTP binds to RNA polymerase at transcription start site and undergoes
hydrogen bonding with complementary base of template strand. First NTP
binds through its 3′ end and its 5′ end is free.
• Selection of second NTP depends on the base pairing with sequence of tran-
scription start site. It forms H-bond with complementary base. RNA
­polymerase brings about phosphodiester bond formation that results in an
initial RNA product.
3. Elongation
• RNA polymerase moves downstream over template strand in 3′ to 5′ direc-
tion. It is coupled with unwinding of DNA duplex downstream toward 5′ end
of the template strand.
• Successive nucleoside triphosphates are added to 3′ end of newly synthesiz-
ing ribonucleotide chain by RNA polymerase. These NTPs form phosphodi-
ester bonds with already existing NTP.
• Sense strand helps to select incoming NTP. Around 35–40 NTPs are added in
a second.

Fig. 8.20  Release of Promoter Attachment of Sense strand
Sigma factor from RNAP site RNAP 3'

5' 5'
Template
RNA P strand

3'
Sigma

170 8  Nucleic Acids

Fig. 8.21 Showing Promoter Transcription Termination
release of sigma factor site site site

5' 3'

RNA P 5'

3'

Movement of RNAP

Sigma factor
released

Fig. 8.22 Showing Sense strand
transciption bubble

5' 3'

5' Nascent RNA 3'

U A AG C
A T TC G

3' 5'
RNAP

Uncoiled
DNA strands
Template
strand [transcription bubble]

• The uncoiled DNA rewinds upstream of RNA polymerase toward 3′ end of
template strand as in Fig. 8.23.

4. Termination
• Specific sequence present on template strand of DNA terminates elongation
of RNA molecule.
• As RNA polymerase approaches a specific sequence, Rho protein binds with
RNA and stops transcription.
• RNA molecule and RNA polymerase are dissociated from template strand.
• Single-stranded RNA transcribed from DNA template is called as primary
transcript as in Fig. 8.23.

8.11 Ribonucleic Acid (RNA) 171

Transcription Codind
bubble strand

Recoiling 5' Nascent RNA 3' 5'
DNA
3' 3' 3'
3' RNA 5' Uncoiling

5' RNAP DNA

5' Template
strand
Fig. 8.23  Synthesis of RNA

Important Terms
Gene Expression Gene expression is a biological process through which genetic

information within a gene is utilized in synthesis of gene product.

Gene Product
Gene products are biomolecules produced by gene expression. They are either a
polypeptide or a RNA molecule.

Transcription
Transcription is a biological process by which a template strand of DNA is copied
into single-stranded RNA molecule (primary transcript). It undergoes processing
(posttranscriptional modifications) to become functional RNA.

Single strand of RNA is complementary (antiparallel) to template strand of DNA.
Single strand of RNA is identical (parallel) to non-template strand of DNA.

• Transcription factor
A protein which binds with DNA template and controls gene expression
through promotion or suppression of transcription

• Transcriptional regulation
An act of controlling gene expression

• Transcription upregulation
Promoting the rate of gene expression

• Transcription downregulation
Repression of gene expression

8.11 R ibonucleic Acid (RNA)

8.11.1 Structure

RNA is a single-stranded polymer of ribonucleotides. RNA is an unbranched and
linear molecule.

172 8  Nucleic Acids

RNA is composed of three components such as:

• Phosphate group
• Ribose sugar (5C)
• Nitrogenous bases

RNA molecule contains four types of nitrogenous bases such as adenine, gua-
nine, uracil, and cytosine.

8.11.2 Types of RNA

Depending upon the function, RNA molecules are grouped into three types such as:

• mRNA
• tRNA
• rRNA

Messenger RNA (mRNA)
The mRNA is a type of ribonucleic acid which contains genetic information
(message) in the form of codons from DNA to ribosomes for protein synthesis.

Occurrence

• The mRNA is transcribed in nucleus. It is translocated from nucleus to cyto-
plasm to control protein synthesis.

Types of mRNA

• It has numerous types depending upon the type of polypeptide chain.

Synthesis of mRNA

• The mRNA is synthesized by RNA polymerase II (in eukaryotes) and RNA poly-
merase in prokaryotes from template strand of DNA.

Structure
• The mRNA constitutes about 5% of the total ribonucleic acid of cell.
• It is a linear molecule. Its length is dependent on the length of polypeptide chain.

The mRNA is the longest among all RNA molecules.
• The mRNA carries genetic message (genetic code) from DNA in the form of a

unique sequence of three nucleotides, called as codon as in Fig. 8.23.
• Structurally, a mRNA is made up of about 500–1500 ribonucleotides. It has

five regions based on different functions such as:
–– Cap region (5′ end)

8.11  Ribonucleic Acid (RNA) 173

Its 5′ end is called as cap region. It contains a methylated guanylate nucleo-
tide. Cap region serves as an attachment site to bind with small subunit of
ribosome. It also functions to protect the mRNA from damage by ribonucle-
ase (RNase) as in Fig. 8.24.
Cap region is followed by a small noncoding region, and it is called as
leader segment. This region does not code for protein synthesis. It is rich
in A and U nucleotides.
–– Initiation codon region
This region contains an initiation or start codon. It is AUG and start codon is
universal in living organisms. In eukaryotes, AUG codes for methionine
(MET) as in Fig.  8.24. In prokaryotes, AUG codes for formylmethionine
(fMet).
This region marks the initiation of polypeptide chain synthesis.
–– Coding region
This region contains about 1500 ribonucleotides. This region contains codons
for amino acids. It is necessary for elongation of polypeptide chain.
–– Termination codon region
This region contains termination or stop codons to terminate the elongation of
polypeptide chain. Termination codons are UAG, UGA, and UAA.
A small noncoding region follows the termination codon region and is
called as called as trailer segment. This region is rich in A and U nucleo-
tides as in Fig. 8.24.
–– Tail region (3′ end)
Tail region is the 3′ end of mRNA.  This end contains a sequence of
multiple adenosine monophosphate ribonucleotides which is called as
poly-(A) tail as in Fig. 8.24.
It protects mRNA from hydrolytic action of RNases. It also prompts
translocation of mRNA from nucleus to cytoplasm and protein
synthesis.

Function
• The mRNA carries genetic information from DNA regarding the sequence of

amino acids in polypeptide chain.

Leader Trailer
(non-coding region) (non-coding region)

5' Coding region 3'

Initiation Termination Poly A
codon codon cap
region region
Fig. 8.24  mRNA Molecule

174 8  Nucleic Acids

• In eukaryotes, a single gene (cistron) transcribes mRNA which controls synthe-
sis of one polypeptide chain (monocistronic).

• In prokaryotes, multiple genes transcribe a mRNA which controls synthesis of
more than one polypeptide chains (polycistronic).

Transfer RNA (tRNA)
It is a type of ribonucleic acid that serves to transfer activated amino acid from
cytoplasm to surface of ribosome for protein synthesis.

Occurrence

• The tRNA is located in nucleus. It is translocated to cytoplasm.

Types of tRNA

• There are about 60 tRNA molecules that exist.

Synthesis of tRNA

• The tRNA is synthesized by action of RNA polymerase III (eukaryotes) and
RNA polymerase (prokaryotes) from template strand of DNA.

Structure
• tRNA molecule constitutes about 15% of the total RNA of cell.
• tRNA is the smallest size among all three RNAs of cell.
• The shape of tRNA resembles the shape of a leaf of clover plant. Its clover leaf

shape was proposed by RW Holley in 1965. It is due to auto folding and base
pairing in tRNA molecule.
• Structurally, tRNA is made up of 70–95 ribonucleotide residues. It is folded
and undergoes base pairing to assume an L-shaped form with five arms as
described below:
• Each arm has stem (paired bases) and a loop (unpaired bases) except acceptor
arm that is without loop and variable arm that is without stem as in Fig. 8.25.
–– Anticodon arm or loop

In anticodon arm, stem contains five paired bases, and loop contains seven
unpaired bases. The three unpaired bases in loop are complementary to bases
in mRNA codons. Anticodon arm reads codons in mRNA and is essential
to recognize amino acids for activation and attachment to acceptor arm.
–– Acceptor arm
Acceptor arm is without a loop. In acceptor arm, 5′ end and 3′ end of RNA
molecule come closer to each owing to its folding. Stem contains seven to
nine nucleotide base pairs. Terminus of 5′ end has either guanine or cytosine