Dr.Rafi's Biochemistry PPTS Lwwatest.pdf

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Rafi MD: Textbook of Biochemistry (4th
Edition)
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Functional Organisation of
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Chapter 1
Learning Biochemistry

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Anatomy is the study of structure, Physiology is the
study of function. Biochemistry integrates both these
aspects—it describes the structure and function of living
things in molecular terms.
What is Biochemistry?

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Energy flow in the environment
Every organism needs energy for its survival.
Energy in Living Organisms

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Essential Elements in the Body

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Polar and Non- polar Molecules
• Water
• Hydrophilic, hydrophobic and amphipathic
molecules

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Major Biomolecules in the Body

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Rafi M D: Textbook of Biochemistry (4th
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CHAPTER 2
Chapter 2
The Cell and Biological
Membranes:
Structure and Function

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CHAPTER 2
Structure of a Human Cell

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Lipids

The major membrane lipids are phospholipids. These
are amphipathic molecules containing both hydrophilic
or polar (water soluble) and hydrophobic or non- polar
(water insoluble) groups.

The cell membrane also contains equal amounts of
cholesterol.
Composition of Membranes
Membranes are made of a double layer of lipid
molecules containing proteins which are embedded in
them.

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●
Proteins in membranes occur in two different ways.
Some proteins are located in the interior of the
membrane and are called integral membrane
proteins.
●
Others are located in the outer surface of the
membranes and are known as peripheral membrane
proteins.
●
Transmembrane proteins serve as:
a) Channels b) Carriers
c) Pumps d) Receptors
Proteins

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The extracellular surface of the plasma membrane
contains small amounts of carbohydrate structures
known as glycocalyx.
Carbohydrates

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Membranes are organised into a structure known as
the fluid mosaic model. It is called so because
membrane proteins float in a sea of lipids. This
model of the cell membrane was proposed by Singer
and Nicholson in 1972.
Fluid Mosaic Structure

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Fluid- Mosaic Model of
Membrane Structure

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Transport Across Biological Membranes
Passive Transport
Here, substances move across the cell membrane
without any energy expenditure by the cell. It includes
diffusion and osmosis.
1. Diffusion
Simple Diffusion
Facilitated Diffusion
2. Osmosis
Membrane Function

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
When substances are transported against their
chemical and electrical gradient requiring energy,
the process is called active transport. The main
types are
1. Primary active transport
2. Secondary active transport
3. Carrier transport
4. Vesicular transport
Active Transport

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1. Primary Active Transport
i) Sodium–potassium (Na+
–K+
) pump
ii) Calcium (Ca2+
) pump
iii) Potassium–hydrogen (K+
–H+
) pump
2. Secondary Active Transport

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3. Carrier Type Transport

Uniporters

Symporters

Antiporters
Carrier type processes

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Many substances are transported across the cell
membrane by endocytosis and exocytosis.
i) Endocytosis: pinocytosis, phagocytosis
4. Vesicular Transport or Transcytosis
Sequence of events in endocytosis

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Sequence of events in exocytosis
ii) Exocytosis

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Chapter 3
Carbohydrates

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
Carbohydrates are aldehyde or ketone compounds
with multiple hydroxyl groups.

Carbohydrates can be defined as aldehyde or ketone
derivatives of polyhydric alcohols. Most
carbohydrates taste sweet and hence they are
popularly known as sugars.

They are the chief source of energy for all
organisms including humans.
Carbohydrates

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Carbohydrates are classified into three major classes based
on the number of sugar units.
1. Monosaccharides
2. Oligosaccharides
3. Polysaccharides
Classification and Nomenclature

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They are categorised into two groups based on the
functional group they possess.
Aldoses: Monosaccharides with an aldehyde group
are known as aldoses. For example, ribose (5C), glucose
(6C).
Ketoses: Monosaccharides having a keto group
are called ketoses. For example, fructose (6C).
Monosaccharides

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Classification of Monosaccharides

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The spatial arrangement of –H and –OH groups on the
penultimate carbon atom in a monosaccharide (C2 for
glyceraldehyde, C5 for glucose) determines whether it
is a D- isomer or its mirror image L- isomer.
If the –OH group is on the right side, the sugar
belongs to the D- series, and if it is on the left side it
belongs to the L- series.
D and L Isomers

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D- and L- Isomerism

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Optical Isomerism

Optical isomerism is exhibited by those compounds
which possess asymmetric carbon(s).

Optical isomers are capable of rotating the plane of
polarised light either to the right or to the left.

A carbon atom which is attached to four different
groups is known as an 'asymmetric' or 'chiral' carbon.

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
The optical isomer which rotates the plane of
polarised light to the right (clockwise) is said to
be dextrorotatory [represented by ‘d’ or (+ )] and
the substance which rotates the plane of
polarised light to the same extent but to the left
(counter clockwise) is termed as levorotatory
[represented by ‘l’ or (–)].

A solution having equal concentrations of ‘d ’ and ‘l ’
forms, known as racemic mixture, cannot rotate the
plane of polarised light and hence shows zero
optical rotation.

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
Monosaccharides that differ only in their
configuration around one carbon atom (other
than anomeric) are known as epimers of one
another.

Thus, D- glucose and D- mannose are epimers
with respect to C2 and D- glucose and D-
galactose are epimers with regard to C4, that is,
they differ from each other in the arrangement of
–OH group around that particular carbon atom.
EPIMERS

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Epimers (glucose and mannose are C2 epimers, whereas glucose and
galactose are C4 epimers).
Epimers

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
The pair of stereoisomers that differ in
configuration around the carbonyl carbon are
called anomers.
The hemiacetal / hemiketal or carbonyl carbon is
called anomeric carbon.
In case of - anomer, the - OH group of the anomeric
carbon is on the opposite side of the terminal
primary alcohol group (C6) of the sugar ring.
If both groups are on the same side, it is a
- anomer.
Anomers

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and Anomers of Glucose
α β
(Fischer Projections)

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Pyranose and furanose forms of glucose (Haworth projections)
 &  Anomers

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 &  Anomers
Pyranose and furanose forms of fructose (Haworth projections)

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Mutarotation is defined as the change in optical rotation
representing interconversion of  and  forms of glucose
to an equilibrium mixture.
Mutarotation

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Formation of furfurals from monosaccharides upon dehydration
Properties and Reactions of
Monosaccharides

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Formation of a common enediol from glucose, fructose and mannose. ‘R’ represents
the common structure of all the three sugars C3 – C6.
Tautomerisation and Enediol formation

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Osazone Formation

Only the first two carbons are involved in osazone
formation.
The sugars which differ in configuration around the
first two carbons give identical osazones, since the
difference is masked by binding with phenyl
hydrazine.
This is the reason why glucose, fructose and mannose
give similar needle- shaped osazones.

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
Glucosazone and fructosazone – long needle-
shaped or broomstick- shaped crystals.

Maltosazone – Yellow coloured ‘petals of sun
flower’- shaped crystals.

Lactosazone – ‘Hedgehog- shaped’ or powder- puff-
shaped crystals.
Differently shaped crystals (osazones)
from different carbohydrates

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As the name implies, disaccharides are
carbohydrates composed of two monosaccharides
linked together through a glycosidic linkage. They
are of two types.
Disaccharides
1. Reducing disaccharides: They possess a free
aldehyde or keto group, e.g., maltose, lactose.
2. Non- reducing disaccharides: They do not have
a free aldehyde or keto group,
e.g., sucrose.

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Maltose
Maltose is composed of two - D–glucose units held
together by  (1–4)- glycosidic linkage.

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Lactose is popularly known as milk sugar as it is
present in milk. Lactose is composed of - D-
galactose linked to - D- glucose through a - (1, 4)-
glycosidic bond.
Lactose

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
Sucrose is mostly present in sugarcane and fruits.
Hence it is also known as cane sugar. Sucrose is
synthesised by plants through photosynthesis.

Sucrose is composed of glucose and fructose linked
together through glycosidic linkage (1–2). The
aldehyde group of glucose and the keto group of
fructose are engaged in bond formation leaving no
free functional group thus making sucrose
essentially non- reducing.
Sucrose

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Formation of sucrose
Formation of sucrose [ -
α D- Glucopyranosyl- (1- 2)- -
β D- fructofuranose]

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Hundreds of monosaccharides are linked together
through glycosidic linkages to form polysaccharides.
Polysaccharides are of two types:
1. Homopolysaccharides
They are made up of a single variety of
monosaccharides. For example, starch is a polymer
of glucose.
Polysaccharides
2. Heteropolysaccharides
They are composed of different types of
monosaccharides or their derivatives, e.g.,
glycosaminoglycans.

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●
Starch is the high energy nutrient synthesised from
carbon dioxide and water by photosynthesis in
plants.
●
It is the chief carbohydrate fuel source for higher
animals, including humans. The dietary sources of
starch include cereals, tubers, roots, legumes and
vegetables.
●
Starch is composed of two components:
Amylose and Amylopectin.
●
Starch is digested by pancreatic amylase in the
intestine.
Starch

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Structure of Starch
Continues. . .

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Structure of Starch
. . . continued

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Glycogen is the storage form of carbohydrates in
animals, including humans, and hence is known as
animal starch. It is stored in muscle and in the liver.
Structure: Glycogen is composed of glucose units
linked by - (1–4) and - (1–6) glycosidic bonds. It is
structurally similar to amylopectin except in that
glycogen is more branched and well organised into a
number of concentric layers (about twelve). Hence,
glycogen is more compact than amylopectin (starch).
Glycogen

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Structure of glycogen
Glucose residues taking part in - 1- 6- glycosidic linkages are shown in
α pink colour.
Glycogen is the instant storage form of energy in animals, including humans.

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Glycogenin in the gylcogen structure
Glucose residues taking
part in α-1-6-glycosidic
linkages are shown in
orange colour. The green
ball represents glycogenin,
a protein that acts as
glycogen primer.

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CHAPTER 3
●
Cellulose is the most abundant carbohydrate in
nature. To be more precise, it is the most
abundant organic substance on earth. Cellulose
makes up most of the plant framework. It is absent
in animals.
●
Cellulose is the unbranched, linear polymer
composed of - D- glucose units linked through -
(1–4)- glycosidic bonds.
Cellulose

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Heteropolysaccharides
Glycosaminoglycans
Glycosamino glyc ans (GAGs), also known as
mucopolysaccharides, are made up of repeating units
of disaccharides containing amino sugars (glucosamine
or galactosamine) and uronic acids (glucuronic or
iduronic acids). Amino sugars are further acetylated and
sulphated.

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The major GAGs include:
1. Hyaluronic acid
2. Chondroitin sulphates
3. Keratan sulphates
4. Heparin and heparan sulphate
5. Dermatan sulphate

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Structures of Glycosaminoglycans
Hyaluronic acid
(Continues…
Chondroitin 4- sulphate

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Keratan sulphate
Heparin
(Continues…
…Continued)

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Dermatan sulphate
…Continued)

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Chapter 4
Lipids

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CHAPTER 4

Lipids can be defined as heterogeneous
substances grouped together under one class
based on their common property, of being
insoluble in water and soluble in organic solvents
(ether, benzene, chloroform).

They are predominantly composed of carbon and
hydrogen atoms. These atoms are linked together
through neutral covalent bonds making lipids
essentially non- polar.
Lipids

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1. Lipids are the structural components of biological
membranes (phospholipids and cholesterol) and
are responsible for the selective permeability of the
membranes.
2. They are the storage form of energy. Energy is
stored in the form of lipids (triacylgycerol) in
adipose tissue.
3. They act as electrical insulators (cholesterol and
glycolipids) helping in the propagation of nerve
impulse.
FUNCTIONS OF LIPIDS
(Continues…

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4. They act as thermal insulators (subcutaneous fat)
providing insulation against the changes in
external temperature.
…Continued)

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Lipids are classified based on 'Bloor's classification‘
(with a few modifications) into four groups.
1. Simple Lipids
They are fatty acid esters of alcohols
(Fatty acid + alcohol). They are of
two types.
a) Fats and oils
b) Waxes
Classification of Lipids

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2. Compound (Complex) Lipids

They are esters of fatty acids with alcohols having
additional groups like carbohydrates, proteins,
phosphoric acid

They are further classified into various subgroups
based on the type of additional group present.

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a) Phospholipids
i) Glycerophospholipids
ii) Sphingophospholipids
b) Glycolipids
c) Lipoproteins
3. Derived Lipids
4. Miscellaneous Lipids

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
Fatty acids are components of the majority of lipids.
They are carboxylic acids with a hydrocarbon side
chain.

The hydrocarbon chain accounts for the non- polar
nature of fatty acids.

Free and esterified fatty acids

Length of hydrocarbon chain

Even- and odd- number carbon fatty acids
Fatty Acids

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
Fatty acids which possess double bonds in their
structure are called 'Unsaturated fatty acids' (UFA)
and fatty acids with no double bonds are 'Saturated
fatty acids' (SFA).

Unsaturated fatty acids are further classified into
two subgroups based on the number of double
bonds.
Saturated and Unsaturated Fatty Acids
1. Monounsaturated fatty acids (MUFA) are
fatty acids with single double bond.
2. Polyunsaturated fatty acids (PUFA) are fatty
acids with two or more double bonds.

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Unsaturated Fatty Acids

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In this type of classification, the positions of the
double bonds are counted from the omega carbon end.
According to - classification, the unsaturated fatty
acids are broadly divided into three groups:
Omega () Classification o f Fatty Acids

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
Solubility

Melting point

Salt formation

Ester Formation

Hydrogenation

Halogenation

Soaps and detergents
Properties of Fatty Acids
Properties of fatty acids depend on chain length and
degree of unsaturation.

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
The fatty acids that are required by humans, but
are not synthesised in the body and hence need to
be supplied in the diet are known as essential
fatty acids (EFA).
1. Linoleic acid (18: 2; 9, 12)
2. Linolenic acid (18: 3; 9, 12, 15)

Arachidonic acid (20: 4; 5, 8, 11, 14) is considered
semiessential since it can be synthesised from
linoleic acid (note that both belong to - 6 series).
Essential Fatty Acids

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
Only linoleic acid and linolenic acid are essential
because humans lack the enzymes that can
introduce double bonds beyond carbon no. 9.

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
Oils rich in SFA: Palm oil, coconut oil, ghee.

Oils rich in MUFA: Groundnut oil, gingily oil,
mustard oil, sesame oil.

Oils rich in PUFA: Sunflower oil, cotton seed oil,
safflower oil, rice bran oil, soyabean oil, linseed oil,
corn oil.
Dietary Sources of Fatty Acids
Vegetable oils are the richest source of fatty
acids.

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
Eicosanoids are a group of biologically active molecules
synthesised from eicosaenoic acids (C20 PUFA).

Eicosanoids are a group of five types of molecules.
1. Prostaglandins (PG)
2. Prostacyclins (PI)
3. Thrombaxanes (TX)
4. Leukotrienes (LT)
5. Lipoxins (LX)

Most eicosanoids are synthesised from arachidonate.
Eicosanoids

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Eicosanoids act as local hormones.
1. Inflammation
Eicosanoids are the natural mediators of
inflammation. This is the basis of the use of
corticosteroids and various non- steroidal
antiinflammatory drugs (NSAID) (which inhibit
the eicosanoid synthesis) in the treatment of
various inflammatory disorders (e.g., rheumatoid
arthritis).
Biological Role and Therapeutic Applications
of Eicosanoids

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2. Regulation of Blood Pressure
Prostaglandins act as vasodilators. Hence, they
are used in the treatment of hypertension.
3. Effects on Platelet Aggregation
Thrombaxanes cause platelet aggregation.
Prostacyclins inhibit platelet aggregation.

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4. Effects on Reproduction
Prostaglandins are used in medical termination of
pregnancy (MTP).
5. Effects on the Gastrointestinal System
PGs increase intestinal motility and inhibit gastric
acid secretion. They are used in the treatment of
gastric ulcers.
6. Effects on the Respiratory System
PGEs are used in the treatment of bronchial asthma.

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Energy is stored as lipid droplets in adipose cells.
The storage lipids are chemically triacylglycerols.
They are insoluble in water and because of their
non- polar character.
Triacylglycerols

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Properties and reactions of tiracyl glycerols in relation
to nutritional value.
Saponification number
Saponification number is defined as the mg of KOH
required to saponify 1 g of fat or oil completely.
Saponification number is a measure of the average
molecular weight and chain length of the fatty acids
present.
Properties and Reactions

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Iodine Number
It is defined as the number of grams of iodine absorbed
by 100 g of fat or oil. Iodine number is used to assess
the degree of unsaturation of fat.
Reichert–Meissl Number (RM Number)
RM number is defined as the amount of 0.1 N KOH
required to neutralise the volatile fatty acids distilled
from 5 g of fat. It is employed to assess the purity of
fats having more volatile fatty acids.

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
They are the structural components of biological
membranes and are responsible for the selective
permeability of the membrane.
Phospholipids

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General structure of
phospholipids
I. Glycerophospholipids: They contain alcohol glycerol
(C3)
II. Sphingophospholipids: They contain alcohol
sphingosine (C18)

Phospholipids are divided into two classes based on
the type of alcohol present.

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It is a phosphatidic acid with ethanolamine as the
nitrogenous base. It is a component of membranes
along with other phospholipids.
It plays a role in blood coagulation.
Cephalin
Cephalin (Phosphatidyl
ethanolamine)

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
It is the phosphatidic acid with choline as the
base.
Lecithin
Lecithin (phosphatidyl choline)
• Lecithin is the predominant
glycerophospholipid in cell membranes.

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Dipalmitoyl Lecithin

Lung alveoli are coated with a surfactant which is
predominantly made up of dipalmitoyl lecithin.

Premature babies without sufficient
surfactant lining the alveolar walls can have
respiratory difficulties. This results in alveolar
collapse causing respiratory distress syndrome.

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Phosphatidyl Inositol
Phosphatidyl inositol

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Cardiolipin
Cardiolipin [diphosphatidyl glycerol]

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Ether Lipids
Plasmalogens

Plasmalogens are predominantly phophatidal
ethanolamines:

The brain and muscle tissue are rich in
plasmalogens.
Plasmalogen

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The numbers in circles represent the
number of carbon atoms in alcohol- sphingosine.
Sphingomyelin

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●
Lecithin- Sphingomyelin ratio (L/ S ratio) in amniotic
fluid is an indicator frequently used to evaluate fetal
lung maturity.
Prior to 34 weeks of gestation, the concentrations of
lecithin and sphingomyelin in amniotic fluid are
almost equal. Later, the concentration of lecithin
rises markedly and the L/ S ratio becomes 5 at term.
In preterm infants, the L/ S ratio is 1 or < 1,
resulting in respiratory distress.
L/ S Ratio

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
Glycolipids are high in nervous tissues

Types of glycolipids:
1. Cerebrosides
2. Globosides
3. Gangliosides
Glycolipids

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Structure Of Galactosyl Ceramide and
Sulphatide

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Cholesterol is a sterol that is exclusive to animals.
Cholesterol
Structure of cholesterol

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1. Cholesterol is an integral component of cell
membranes and hence influences membrane
permeability.
2. A number of biologically important substances are
synthesised from cholesterol (e.g. vitamin D, bile
acids, mineralocorticoids, glucocorticoids and
sex hormones).
3. Cholesterol acts as an electrical insulator and
helps in the propagation of nerve impulses.
Functions of Cholesterol

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General structures of various lipids (non-
polar and amphipathic

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Examples of Lipid Bilayers
Amphipathic lipids such as
phospholipids and cholesterol are
organised into bilayers in biological
membranes. Hydrophilic groups
are oriented towards the watery
phase (both ECF and ICF), while
hydrophobic groups are oriented
towards the oily phase (central
portion of membranes).

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CHAPTER 5
Chapter 5
Amino Acids and Proteins

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
Proteins are the building material for body
structure.

Proteins are composed of carbon, oxygen,
hydrogen, nitrogen and small amounts of other
elements, notably sulphur.
Proteins

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
Proteins play the role of ‘brick and mortar’ of the
body.

Proteins perform a number of roles including
biocatalysis, defence, hormonal function, transport,
storage and muscle contraction.

Proteins are polymers of amino acids

Standard amino acids

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
Amino acids are the structural units (monomers) of
proteins.

An amino acid is made up of two functional groups—
amino (–NH2), carboxyl (–COOH). They also contain a
hydrogen atom and a side chain (R) linked to the carbon
atom.

Amino acids differ from each other in their side chains.
Amino Acids

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I. Amino acids with aliphatic side chains
1. Glycine 2. Alanine
3. Valine 4. Leucine
5. Isoleucine
Classification of Amino Acids

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CHAPTER 5
II. Amino acids containing hydroxyl (–OH)
groups
6. Serine
7. Threonine

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III. Sulphur containing amino acids
8. Cysteine
9. Methionine

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IV. Acidic amino acids and their amides
10. Aspartic acid
11. Asparagine
12. Glutamic acid
13. Gultamine

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CHAPTER 5
V. Basic amino acids
14. Lysine
15. Arginine
16. Histidine

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CHAPTER 5
VI. Aromatic amino acids
17. Phenylalanine
18. Tyrosine
19. Tryptophan

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CHAPTER 5
VII. Imino acid
20. Proline

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
The amino acids which cannot be synthesised by the
body and hence need to be supplied through diet are
called essential amino acids. Some are
conditionally essential.

The ten essential amino acids in ascending order of
dietary requirement:
1. Arginine 6. Isoleucine
2. Tryptophan 7. Valine
3. Histidine 8. Phenylalanine
4. Methionine 9. Lysine
5. Threonine 10. Leucine
Essential or Indispensable Amino Acids

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Classification Based on Metabolic Fate

Ketogenic amino acids
Leucine is the only exclusive ketogenic amino acid.

Ketogenic and glucogenic amino acids
Isoleucine, lysine, phenylalanine, tyrosine and
tryptophan.

Glucogenic amino acids
The remaining 14 amino acids are used for the
synthesis of glucose or glycogen.

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CHAPTER 5
Classification Of Amino Acids Based On
Their Solubility

Polar (hydrophilic) amino acids
glycine, serine, threonine, cysteine, asparagine,
glutamine and tyrosine.

Non- polar (hydrophobic) amino acids
Phenyl alanine, tryptophan and proline.

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CHAPTER 5
Isoelectric pH
Various ionic forms of amino acid at different pH

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CHAPTER 5
Sorenson's titration curves of valine

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Colour Reactions of Amino Acids

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CHAPTER 5
Non- standard Amino Acids

D- amino acids

Non- Protein amino acids

Amino acid derivatives

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Precipitation Reactions of Proteins
1. Salting out
2. Isoelectric precipitation
3. Precipitation by heavy metal ions
4. Precipitation by alkaloidal reagents
5. Precipitation by alcohols
6. Heat coagulation

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Classification of Proteins

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Methods to Determine Protein Structure

Determination of amino acid composition in a
protein

Determination of the number of polypeptides in a
protein

Determination of amino acid sequence in a protein
Sanger's reagent
Edman's reagent
●
Automatic sequencing

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CHAPTER 5
Methods to Explore Higher Levels of
Protein Structure
1. Electron microscopy
2. X- ray crystallography
3. Nuclear magnetic resonance (NMR) spectroscopy

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Organisation of protein structure at
various levels

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CHAPTER 5
Formation of Peptide Bond

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CHAPTER 5
 (psi) and  (phi) angles in the peptide backbone
Primary Structure of Protein

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Forces Stabilising Protein Structure
Covalent bonds

Peptide and disulphide linkages
Non- covalent bonds

Hydrogen bonds

Hydrophobic interactions

Electrostatic interactions

Van der Waals interactions

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CHAPTER 5
Secondary Structure of Protein
The polypeptide chain folded into regular (- helix, -
sheet) and irregular forms (turns and loops)
characterises the secondary structure.

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CHAPTER 5
It is the first and the most common pattern (hence
designated a) of secondary structure.
Features of - helix
1. - helix is the most stable conformation formed
spontaneously with the lowest energy.
2. It is a coiled structure with the tightly coiled
polypeptide backbone forming the inner part of the
helix with the side chains extending outwards from
the central axis.
(Continues…

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CHAPTER 5
3. - helix can be either right handed or left handed.
But all a- helices found in proteins are right handed
(clockwise) because of the less probability of steric
clashes between the side chains and the backbone.
4. Covalent and various non- covalent forces stabilise
the - helix.
5. Except the first and last peptide bonds at both
ends of the chain all other NH and CO groups take
part in hydrogen bonding.
…Continued)
(Continues…

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CHAPTER 5
6. Each turn of the helix is 5.4 Å and accommodates 3.6
amino acid residues per turn of helix.
7. Thus, the amino acids spaced three to four residues
apart in sequence are spatially closer to one another
and each amino acid forms a hydrogen bond with the
fourth amino acid in linear sequence. In contrast,
amino acids which occur closer in linear sequence are
situated on opposite sides of the helix and hence
cannot make contact.
8. Proline fits only in the first turn of an - helix;
otherwise it is never found in an - helix.
…Continued)

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CHAPTER 5
- helix of a polypeptide chain
shown in a coiled structure
(right handed).
Only a few hydrogen bonds
are shown for clarity (dotted
lines).
Note that the side chains of
amino acids are not shown for
sake of clarity.
- Helix

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1. It is the second type of regular repetitive pattern
(thus the name ) occurring in the secondary
structure of a protein.
2. Unlike the coiled - helix, the peptide backbone of a
- sheet is partly extended with a 'pleated
appearance'.
3. The distance between adjacent amino acids along a
- strand is 3.5 Å, in contrast to a distance of 1.5 Å
along an - helix. The side chains of adjacent amino
acids orient in opposite directions to avoid steric
clashes.
Features of - Pleated Sheet
(Continues…

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CHAPTER 5
.
4 - Pleated sheet is stabilised by extensive
hydrogen bonding. Hydrogen bonds can be
formed between neighbouring polypeptide chains
or within a single polypeptide chain folded into
segments.
5. About two to fifteen strands are involved in the
formation of a - sheet. Adjacent chains in a -
sheet can run in opposite directions (antiparallel 
sheet), in same direction (parallel  sheet) or both
ways (mixed  sheets).
…Continued)

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CHAPTER 5
- pleated sheets shown as a folded sheet

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CHAPTER 5
- Pleated Sheets
Anti parallel
Parallel
Hydrogen bonds are formed between adjacent strands within a single polypeptide. Note that in beta
sheets running antiparallel, hydrogen bonds between NH and CO groups connect each amino acid to
a single amino acid on an adjacent strand. On the contrary, in a parallel beta sheet, hydrogen bonds
connect each amino acid on one strand with two different amino acids on the adjacent strand.

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CHAPTER 5
Tertiary Structure of Protein
Diagrammatic representation of super secondary motifs (- helix represented as
folded coil, - sheets as wide arrows and loops shown as connecting them).

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CHAPTER 5

Proteins consisting of more than one polypeptide
chain display quaternary structure.

The protein is known as a multimeric protein or
oligomeric protein. For example, hemoglobin, the
protein that transports oxygen in the blood is an
oligomeric protein with four polypeptide chains (2
and 2).
Quaternary Structure of Protein

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Denaturation
(a) Native protein (only
disulphide bridges are shown
which are intact)
(b) Denatured protein (note
that the disulphide linkages
are broken)

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CHAPTER 5
How Do Proteins Attain Their Native
Conformation?
Levinthal’s paradox

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CHAPTER 5
Principles of Protein Folding
1. The essence of protein folding is the retention of
partly correct intermediates.
2. Molten globule
3. Enzymes aiding protein folding:
Disulphide isomerase,
Cis- trans isomerase
4. Chaperone proteins

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
Prion diseases
Creutzfeldt- Jakob disease
Kuru
Mad cow disease

Alzheimer's disease
Diseases Related to Protein Folding

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CHAPTER 6
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Phone: 040-2766 5446/5447

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CHAPTER 6
Chapter 6
Nucleotides and Nucleic
Acids

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CHAPTER 6
Nucleotide, the basic unit of nucleic acids is
composed of three components.
Nucleotides
• Sugars in nucleic acids
• Phosphate group in nucleic acids
• Bases present in nucleic acids
Purines
Pyrimidines

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CHAPTER 6
X = H or ribose or ribose phosphate
depending upon whether it is just a
base or a nucleoside or a nucleotide,
respectively.
Structures of major purines (A, G) and
pyrimidines (C, T, U) found in nucleic acids

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CHAPTER 6
Nomenclature of Nucleotides

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CHAPTER 6
1. Nucleotides are the building blocks of nucleic
acids (DNA and RNA).
2. ATP is the universal energy currency of living
systems.
3. Cyclic nucleotides such as cAMP and cGMP act
as 'second messengers' .
4. Nucleotides are the structural components of a
number of coenzymes.
Functions of Nucleotides
(continued…

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CHAPTER 6
5. They act as the carriers of certain metabolic
intermediates of carbohydrates, (UDP- glucose),
lipids (CDP- acyl glycerol) and proteins (S- adenosyl
methionine- SAM).
6. UDP- Gal UDP- Glu, GDP- Man, CMP- NeuAc, GDPFuc,
UDP- Xyl, UDP- Gal Nac and UDP- Glu Nac - These
eight molecules are known as 'nucleotide- linked
sugars' and are important constituents of
glycoproteins.
…continues)

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Structures of biologically important
nucleotides

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Therapeutic applications
1. Synthetic nucleosides, cytarabine and vidarabine in
which ribose is replaced by arabinose are used in
chemotherapy to treat cancers.
2. Allopurinol is used in the treatment of
hyperuricemia and gout.
Synthetic Nucleotides
(continues…

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CHAPTER 6
3. Synthetic analogues such as 6- mercaptopurine, 5-
fluorouracil, 5- iodouracil, 3- deoxyuridine, 5 or 6-
azauridine, 5- or 6- azacytidine, 8- azaguanine, 6-
thioguanine are widely used by oncologists. They are
incorporated into DNA just before cell division, thus
blocking cell proliferation.
3. Drugs such as zidovudine which are used in the
treatment of AIDS are synthetic nucleotide analogues
with alterations in the sugar structure.
…continued)

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CHAPTER 6
The double helical structure of DNA was first proposed by
James Watson and Francis Crick in 1953.
Structure of DNA

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CHAPTER 6
Watson–Crick Model of DNA
Double Helix

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CHAPTER 6
Watson–Crick Model of
DNA Structure
1. A DNA molecule consists of two chains of
deoxyribonucleotides coiled around each other in
the form of a double helix. Two helical DNA chains
wind around each other on the same axis to form a
right- handed double helix.
(continues…
2. The two chains are antiparallel – one strand runs
in the 5' to 3' direction, while the opposite is in
the 3' to 5' direction. The terminal residue whose
C5' is not linked to another nucleotide is called the
5' end, and the terminal residue whose C3' is not
linked to another nucleotide is called the 3' end.

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CHAPTER 6
3. The two strands are held together by hydrogen
bonds between a purine base on one strand and a
pyrimidine base on the opposite strand. The ring
structure of each base occurs in a flat plane
perpendicular to the sugar–phosphate backbone,
resembling the steps on a spiral staircase. The base
pairing maintains a constant distance between the
sugar–phosphate backbones of the two strands as
they twist around each other.
…continues)
…continued )

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CHAPTER 6
4. The hydrogen bonds are formed between a purine
base and a pyrimidine base only. This specificity is
imposed on the base pairings by the fixed location
of the hydrogen bonds. If two purines face each
other, they would not fit into the space available
and two pyrimidines would be too far apart to form
hydrogen bonds. Each nucleotide base of one
strand is paired in the same plane with a base of
the opposite strand.
(continues…
…continued )

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CHAPTER 6
5. Three hydrogen bonds are formed between the
purine, guanine and the pyrimidine, cytosine (G–C
or C–G pairing), while only two hydrogen bonds can
be formed between the purine, adenine and the
pyrimidine, thymine (A–T or T–A pairing). As a
result, G always pairs with C, and A with T. This is
known as complementary base pairing. This
specificity has tremendous significance in DNA self
replication and transcription.
…continues)
…continued )

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6. It is more difficult to separate the paired DNA
strands rich in G–C pairing because
GC (three double bonds) pairing is stronger than
A= T (two double bonds) pairing.
7. The deoxyribose and phosphate groups (sugar–
phosphate backbone) are hydrophilic in nature and
hence are on the outside of the double helix
orienting towards the surrounding water molecules,
while the hydrophobic bases are stacked inside.
…continues)
…continued )

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CHAPTER 6
8. The coiling of two strands creates a major groove
and a minor groove on the surface of the duplex.
Proteins interact with DNA at these grooves without
disrupting the double helix.
9. Geometry of the DNA duplex: The width of a
double helix is 20 Å. Each turn of the helix is 34 Å
with 10 pairs of nucleotides, each pair is placed at a
distance of 3.4 Å.
…continues)
…continued )

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10. Because of their length, DNA chains are described
in terms of base pairs (bp) or thousands of base
pairs (kilobase pairs or kb), e.g. [5 kb (virus),
2,50,000 kb (humans)].
11. The two antiparallel strands of DNA are not
identical in either base sequence or composition,
but are complementary to each other. Wherever
adenine occurs in one chain, thymine is present in
the other and vice versa; similarly, wherever
guanine occurs in one strand, cytosine is found in
the other and vice versa.
…Continues)
…continued )

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12. The DNA duplex is stabilised by two forces; hydrogen
bonding between complementary base pairs and
nonspecific base- stacking interactions.
13. The strand that is transcribed or copied into the RNA
molecule is referred to as the template strand or anti
sense strand. The other strand is the sense or coding
strand of that gene. However it is noteworthy that each
DNA strand can act as a template for the synthesis of its
complementary strand and hence hereditary information
is encoded in the sequence of bases on either strand.
…continued )

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1. The base composition of DNA varies in different species.
2. DNA from different tissues of the same species have
the same base composition.
3. The base composition of DNA in a species does not
undergo any change with the organism's age,
nutritional status or changing environment.
4. In all species, the number of adenine is equal to the
number of thymine residues (A= T) and the number of
guanine is equal to the number of cytosine residues (G 
C). Thus, the sum of the purine residues equals the sum
of the pyrimidine residues; that is,
A+ G = T + C.
Chargaff's Rules

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Different Types (Forms) of DNA
• B- DNA
• A- DNA
• Z- DNA
Unusual structures in DNA
• Hoogsteen pairing
• Triplex DNAs
• Tetraplex
• Palindromes
Denaturation of DNA

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Organisation of DNA
• Supercoiling of DNA
• Topoisomerases
• Nucleoproteins
Histones
Chromatin
Covalent modifications
Nucleosomes

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Mitochondrial DNA
• Apart from the nucleus, eukaryotic cells also have
other organelles such as mitochondria and
chloroplasts, which contain DNA. Mitochondrial
DNA is capable of encoding certain proteins and
RNA in mitochondria. The synthesis of about 13
proteins of the respiratory chain, are encoded by
mtDNA.
• mtDNA is inherited only from the mother!
• Leber's hereditary optic neuropathy

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Genes
• Can a single gene be expressed into multiple
gene products?
• Coding and noncoding sequences in genes
Introns
Exons
• Transposons

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• The nucleoproteins which link the chromosome to
the mitotic spindle during cell division are anchored
to a specific region on the DNA known as the
centromere.
• This ensures an equal distribution of chromosome
sets to daughter cells.
• The guanine- rich sequences at the ends of
eukaryotic chromosomes are known as telomeres.
Centromeres and Telomeres
(continues…

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• Telomeric DNA is synthesised and maintained by an
enzyme known as telomerase.
The somatic cells of multicellular organisms lack
telomerase activity; however their germ cells have
active telomerase function.
The loss of telomerase activity allows the gradual
shortening of chromosomes with each cycle of DNA
replication and cell division until they reach
senescence (a stage at which there will be no more
division). Perhaps this is the basis of ageing.
…continued)

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• Endonucleases
• Exonucleases
• Restriction endonucleases
Nucleases
Nucleases are enzymes that are capable of
degrading nucleic acids.

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CHAPTER 6
1. Messenger RNA (m- RNA)
Messenger RNA is located in the cytoplasm and
transfers genetic information from the DNA to the
protein- synthesising machinery on ribosomes.
2. Transfer RNA (t- RNA)
It also occurs in cytoplasm, it translates the
information carried by m- RNA into a specific
sequence of amino acids that are incorporated
into protein.
Types of RNA
(Continues…

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CHAPTER 6
3. Ribosomal RNA (r- RNA)
It is a component of ribosomes which are the sites
for protein biosynthesis.
4. Heterogenous nuclear RNA (hnRNA)
It is the primary form of RNA in nucleus processed
into mature m- RNA.
…Continued

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CHAPTER 6

Messenger RNA is synthesised as the primary
transcript from the template strand of DNA and
later processed to m- RNA.

5 capping

Poly ‘A’ tail

Heterogeneous nuclear RNA (hnRNA)
Messenger RNA (m- RNA)

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• Acceptor arm
• Anticodon arm
• D arm
• T  C arm
Transfer RNA (t- RNA)
Transfer RNA is the adapter molecule that translates
the information carried by m- RNA into specific
sequences of amino acids.
tRNA contains mainly four arms.

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Structure of t- RNA

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CHAPTER 7
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Chapter 7
Enzymes

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
Enzymes are highly specialised proteins that act as
catalysts in biological systems (biocatalysts).

Enzymes are highly specific for their substrates
Enzymes

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Nomenclature and Classification
of Enzymes

International Union of Biochemistry (IUB) devised a new
system of nomenclature in 1964.

A four- digit Enzyme Commission (E.C.) number is
assigned to each enzyme. The first digit represents the
class, the second digit indicates the subclass, the third
digit represents the sub- subclass and the fourth digit
specifies the individual enzyme.

Enzymes are classified into six major classes as per
the IUB system of enzyme classification.

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CHAPTER 7
Classification of Enzymes
(Continues…

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CHAPTER 7
Classification of Enzymes
…Continued)

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CHAPTER 7
• Enzymes are proteins.
• Apoenzyme
• Coenzyme
• Holoenzyme
Enzyme Structure

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CHAPTER 7
The small cleft- like portion of an enzyme where the
substrate(s) binds and catalysis occurs is known as the
active site or active centre.
Active Site
• Substrate binding site
• Catalytic site
A diagrammatic representation of
an enzyme and its active site

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Coenzymes
Coenzymes of B- complex vitamins

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Coenzymes which are not related to vitamins

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CHAPTER 7
Enzyme Specificity
The active site in a specified conformation on an
intact enzyme molecule is largely responsible for
the enzyme specificity.
There are three types of specificity:
1. Stereo specificity
2. Substrate specificity
3. Reaction specificity

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CHAPTER 7
How Do Enzymes Work?
• Transition state
• Ground state
• Activation energy
• Enzymes act by reducing the activation energies
• Binding energy

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S = substrate
P = product
Effect of enzyme on activation
energy in a reaction

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CHAPTER 7
To summarise, the energy required to surmount the
activation barrier is the activation energy. Enzymes
catalyse the reactions by lowering the activation
barrier. The binding energy resulting from weak
non- covalent interactions between the substrate
and the enzyme reduces the activation energy.
Enzymes do not alter the reaction equilibria, they
only enhance the reaction rates by lowering
activation energies.

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1. Lock and key model
2. Induced fit theory
3. Substrate strain theory
Mechanism of Enzyme Action

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(A) Lock and key model
(B) Induced fit theory
(C) (C) Substrate strain theory
Different models explaining
enzyme–substrate (ES) complex
formation

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CHAPTER 7
Mechanism of Catalysis
• Acid- base catalysis
• Covalent catalysis
• Metal ion catalysis

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The various factors that influence enzyme activity
are
Factors Affecting Enzyme Activity
1. Concentration of enzyme
2. Concentration of substrate
3. Concentration of product
4. Temperature
5. pH

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
The rate of an enzyme catalysed reaction increases
as the substrate concentration increases until it
reaches a maximal rate, which remains constant
despite further increases in substrate concentration.

The substrate concentration (expressed in moles/ L)
required to produce half- maximum velocity (1/ 2
Vmax) is known as Km or Michaelis–Menten constant.
Effect of Concentration of Substrate
on Enzyme Velocity

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Effect of substrate concentration on enzyme velocity

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Derivation of Km or Michaelis–Menten Constant
(Continues…

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…Continued
(Continues…

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CHAPTER 7
…Continued

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Effect of Temperature on Enzyme Velocity

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Effect of pH on Enzyme Velocity

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CHAPTER 7
Enzyme inhibition can be broadly classified into three
categories:
1. Competitive inhibition
2. Non- competitive inhibition
3. Allosteric inhibition
Enzyme Inhibition

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
The inhibitor binds with the enzyme through non-
covalent interactions and hence the pro cess is
readily reversible.
 In competitive inhibition, the Km value increases
whereas Vmax is unchanged.
Competitive Inhibition

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Velocity versus substrate plot in
competitive inhibition

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Drugs acting as competitive
inhibitors

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
The inhibitor binds to the enzyme covalently and
inactivates it making the process essentially
irreversible.
 In non- competitive inhibition, the Km value is
unchanged while Vmax is lowered.
Non- competitive Inhibition

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Velocity versus substrate plot in non-
competitive inhibition

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1. Allosteric regulation
2. Covalent modulation
3. Proteolytic trimming
4. Compartmentation
5. Control of enzyme synthesis and degradation
Regulation of Enzyme Activity

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Allosteric Regulation

Allosteric enzymes

Allosteric modulators

Cooperativity of allosteric enzymes

Classification of allosteric enzymes

K class allosteric enzymes

V class allosteric enzymes

Feedback regulation

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Effect of substrate
concentration on allosteric
enzymes

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Examples of allosteric enzymes

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Covalent Modulation

Regulatory enzymes or rate- limiting enzymes

Reversible protein phosphorylation

Protein kinases

Protein phosphatases

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Regulatory enzymes (rate- limiting enzymes) controlled by
covalent modulation

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The multiple molecular forms of an enzyme catalysing
the same reaction are called isoenzymes.
They differ in their physical and chemical properties
such as structure, Km, Vmax, pH, electrophoretic mobility
and their susceptibility to inhibitors.
Isoenzymes

Isoenzyme variants are coded by different genes.

Allelozymes

Hybrid isoenzymes

Isoforms

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CHAPTER 7
Creatine Kinase (CK)

Normal serum levels of CK are 15–100 U/ L in males
and 10–80 U/ L in females.

Lohmann’s reaction

In myocardial infarction, CK levels (CK–MB
isoenzyme) start to rise within 3–6 hours of
infarction.
Isoenzymes of CK

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CHAPTER 7
Lactate Dehydrogenase (LDH)
Normal levels of LDH in serum are 100–200 U/ L.
Isoenzymes of LDH

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CHAPTER 7
Alkaline Phosphatase (ALP)
• The normal serum
levels of ALP range
between 40 and 125
U/ L.
• Increased ALP levels
are most commonly
associated with
bone disease and
hepatobiliary
disease.
Isoenzymes of ALP

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CHAPTER 7
• Plasma specific enzymes
• Plasma nonspecific enzymes
• Units of enzyme activity
Clinical Enzymology

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CHAPTER 7
Diagnostic Markers of Myocardial
Infarction (MI)

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Enzymes Used As Therapeutic Agents

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Enzymes used in Laboratory
Measurements and Gene Transfer

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CHAPTER 8
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Section II
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Phone: 040-2766 5446/5447

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Chapter 8
Vitamins

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Classification of Vitamins

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Differences between fat- soluble and water- soluble
vitamins

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CHAPTER 8
Vitamin A
• Chemistry
Retinol
Retinal
Retinoic acid
- Carotene

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CHAPTER 8
Summary of kinetics and mechanism of action of vitamin A
(Continues …

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CHAPTER 8
…Continued)

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CHAPTER 8
Wald’s Visual Cycle

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CHAPTER 8
1. Retinol and retinoic acid act like steroid hormones.
They regulate the synthesis of proteins involved in
cell growth and differentiation. Vitamin A is
required for normal reproduction.
2. Vitamin A is required for maintenance of healthy
epithelial tissue. It maintains moist and pliable
epithelium by inhibiting the synthesis of excess
keratin (responsible for horny surfaces).
Other Biochemical Functions of
Vitamin A
(Continues…

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CHAPTER 8
3. Retinoyl phosphate synthesised from retinoic acid
participates in glycoprotein synthesis.
Glycoproteins are important constituents of
mucus. In vitamin A deficiency, lack of mucus
secretion results in drying of epithelial tissues.
4. Vitamin A is essential for the formation of
mucopolysaccharides in the extracellular matrix.
(Continues…
…Continued)

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CHAPTER 8
5. Vitamin A is essential for the maintenance of the
immune system. Its deficiency causes
keratinisation of the mucosal lining of the
respiratory, gastrointestinal and genitourinary
tracts making them susceptible to frequent
infections.
6. Retinol and retinoic acid are essential for the
synthesis of transferrin, the iron transportaing
protein. Irondeficiency anemia may occur in
vitamin A deficiency.
…Continued)

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CHAPTER 8
Daily Requirements and Dietary Sources
1 RE = 1 g retinol
= 6 g - carotene
1 IU = 0.3 g retinol
The RDA for vitamin A are as follows
Men 1000 RE (3500 IU)
Women 800 RE (2800 IU)

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CHAPTER 8
• Animal foods: Liver, whole milk, eggs, butter,
cheese, fish and meat. Fish (cod or shark) liver oils
are the richest sources of vitamin A. However, they
are generally used as nutritional supplements rather
than as food sources.
Dietary Sources
(Continues…

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CHAPTER 8
• Plant foods: Among the best sources are green
leafy vegetables such as spinach and amaranthus,
which are available in all seasons.
The darker the green leaves, the higher is its carotene
content.
Vitamin A also occurs in vegetables and fruits such as
papaya, pumpkin and mango. Carrots is also a good
source of vitamin A.
…Continued)

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CHAPTER 8
Deficiency Manifestations
The clinical signs of vitamin A deficiency mostly
involve the eye. Vitamin A deficiency is one of the
major causes of preventable blindness.
Night blindness
Night blindness (Nyctalopia) or the inability to see in
dim light is the earliest symptom of vitamin A
deficiency. It occurs due to impairment of dark
adaptation.
(Continues…

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CHAPTER 8
Xerophthalmia
Night blindness, if left untreated, causes dryness of the
conjunctiva and the cornea.
The conjunctiva becomes thick and wrinkled; the
cornea loses its mucosal cells and become dull, hazy
due to keratinisation and loses its transparency. These
changes are described as xerophthalmia.
…Continued)

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CHAPTER 8
Bitot's spots
Bitot's spots are triangular, white patches on the
conjunctiva on either side of the cornea. They are usually
bilateral.
Keratomalacia
If the condition progresses beyond xerophthalmia, there
is ulceration and necrosis of the cornea (keratomalacia)
which results in total blindness. Keratomalacia is one of
the major causes of blindness in developing countries
and is usually associated with protein energy
malnutrition (PEM).
…Continued
(Continues…

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CHAPTER 8
…Continued
Manifestation of vitamin A deficiency in the eye

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CHAPTER 8
Formation and Activation of Vitamin D
Vitamin D

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CHAPTER 8
Metabolism and Biochemical
Functions of Vitamin D
(Continues…

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CHAPTER 8

The recommended dietary allowance (RDA) is about
400 international units (IU) or 10 g. However, in
places with good sunlight (like the Indian
subcontinent), the daily requirement is about 200 IU
or 5 g. In growing children, during pregnancy and
lactation, it should be 10 g (400 IU).

Vitamin D can be derived both from sunlight and
food. The human body manufactures vitamin D with
the help of sunlight. It also occurs mainly in foods of
animal origin.
Daily Requirements and Sources
(Continues…

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CHAPTER 8
Oily fish, egg yolk, liver, butter and cheese contain
good quantities. Fish liver oils, although not
considered a food, are the richest source of vitamin
D. Plant sterol, ergosterol provides a dietary source.

Breastmilk contains relatively small amounts of
vitamin D and infants are at risk of developing
vitamin D deficiency, particularly premature infants
(since the vitamin is transported across the placenta
mainly in the last trimester of pregnancy).
…Continued)

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CHAPTER 8
Skeletal deformities seen in
rickets

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CHAPTER 8
Rickets
• improper mineralisation
• bow- legs, knock- knees, pigeon chest,
kyphoscoliosis.
• ('rickety rosary')
• (Harrison's sulcus)
Osteomalacia
• Renal rickets
• Vitami- D resistant rickets

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Functions of Vitamin E
• Vitamin E plays a vital role in safeguarding the
structural integrity of biological membranes.
Its antioxidant property prevents the oxidation of
polyunsaturated fatty acids (PUFA) of membrane
phospholipids.
By inhibiting lipid peroxidation in cell membranes,
it protects the structural integrity of the cell. By
the same mechanism, vitamin E is responsible for
the resistance of RBC to hemolysis (caused by
oxidising agents such as hydrogen peroxide).
(Continues…

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CHAPTER 8
It is observed that vitamin E is essential for normal
reproduction and fertility in experimental animals.
Hence, it is known as the ‘anti- sterility vitamin’.
It helps in maintaining intact germinal epithelium
(gonads).
Deficiency of vitamin E adversely affects
spermatogenesis and motility of sperms. However,
the effects of vitamin E on reproduction in humans
is controversial and evidence of any direct effect is
not fully established.
…Continued)
(Continues…

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CHAPTER 8
…Continued)
• It protects low- density lipoproteins (LDL)
from oxidation. (Note that oxidised LDL is
implicated in heart disease.) By doing so,
vitamin E reduces the risk of myocardial
infarction.

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CHAPTER 8
RDA and dietary sources of vitamin E
Men – 10 mg
Women – 8 mg
Vegetable oils are rich in vitamin E especially wheat
germ oil. Sunflower, safflower, cotton seed oils; corn
and soyabean oils are good sources.

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CHAPTER 8
Vitamin K – Biochemical Functions
Vitamin K acts as a cofactor in the formation of - carboxyglutamate.
Vitamin K is required for blood coagulation.
Clotting factors II (prothrombin), VII, IX and X need
vitamin K for their activation.

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CHAPTER 8
Vitamin K cycle in hepatocytes
Biochemical Functions

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CHAPTER 8
Daily Requirement and Dietary Sources

Since vitamin K is synthesised by the intestinal
bacteria, its requirement in the diet is very low. A
recommended daily allowance (RDA) of 70–140
mg/ day would suffice for adult human needs.

Green leafy vegetables are an excellent source of
vitamin K. It is also present in eggs and diary
products.

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CHAPTER 8
●
Vitamin K deficiency leads to prolonged
coagulation and bleeding. Newborns, especially
preterm infants are more susceptible to vitamin K
deficiency
(Continues…

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CHAPTER 8
●
Vitamin K deficiency is seen in adults suffering from
obstructive jaundice and other diseases causing
severe fat malabsorption. Patients suffering from
small bowel diseases such as celiac disease, Crohn's
disease suffer from vitamin K deficiency.
Patients on long- term antibiotic therapy (antibiotic
drugs kill vitamin K synthesising bacteria in the
intestine) are also at risk of developing vitamin K
deficiency.
Deficiency manifestations
…Continued)

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CHAPTER 8
Vitamin C
Different forms of vitamin C and its derivatives

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CHAPTER 8

Collagen formation
Vitamin C plays a role in the maintenance of
normal connective tissue and is essential for
wound healing.
Deficiency of vitamin C results in local hemorrhages
and bones become susceptible to fractures.
Collagen is also a constituent of the ground
substance surrounding capillary walls, hence
vitamin C deficiency causes capillary fragility.
Biochemical Role
(Continues…

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CHAPTER 8

Antioxidant: Vitamin C plays a role in eliminating
potentially dangerous free- radicals from the
biological system.

Role in metabolism
Vitamin C plays a role in the metabolism of amino
acids
Tyrosine; Tryptophan
Biochemical Role
…Continued)
(Continues…

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CHAPTER 8
Role in lipid metabolism
Role in iron metabolism
Role in hemoglobin metabolism

It spares vitamins A, E and some B- complex
vitamins from oxidation.

Phagocytosis
…Continued)

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CHAPTER 8

Recommended daily allowance is about 60–75
mg/ day. About 100 mg/ day is required during
pregnancy and lactation. Smokers, chronic
alcoholics and women on oral contraceptives
require up to 125 mg/ day.

The main dietary sources of vitamin C are fresh
fruits and green leafy vegetables. Citrus fruits,
Indian gooseberry (amla), guava, cabbage, spinach
are very high in vitamin C content. Germinating
pulses contain large amounts of vitamin C.

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CHAPTER 8
Vitamin C deficiency causes scurvy. Symptoms of
scurvy reflect impaired collagen synthesis resulting in
defective connective tissue.

Capillary fragility: Petechiae (small, pinpoint
hemorrhages under the skin), ecchymoses or
even hematomas. Internal bleeding into the
gastrointestinal tract, peritoneal cavity,
pericardium and the adrenal glands may occur.
(Continues…

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CHAPTER 8
• Swollen and painful gums
• Teeth get loosened
• Poor wound healing and anemia
• Osteoporosis
• Barlow's disease
…Continued)

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CHAPTER 8
Thiamine (Vitamin B1)
Structure of thiamine and thiamine pyrophosphate (TPP)

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CHAPTER 8

Thiamine exerts its biochemical functions
through its coenzyme form, thiamine
pyrophosphate (TPP).

Pyruvate dehydrogenase requires TPP as one of
the coenzymes.

- ketoglutarate dehydrogenase is also dependent
on TPP a a coenzyme.

Oxidative decarboxylation reaction involving
branched chain amino acids requires TPP.
(Continues…

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CHAPTER 8

Enzyme transketolase of hexose monophosphate
shunt (HMP shunt) utilises TPP as the coenzyme.

TPP plays a role in the transmission of nerve
impulses.
…Continued

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CHAPTER 8

The recommended dietary allowance (RDA) for
adults is 1–1.5 mg/ day.

Whole grain cereals, yeast, legumes, oilseeds and
nuts, especially groundnut, are important sources
of thiamine. Animal foods such as pork, beef and
sheep liver are also good sources.

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CHAPTER 8
• Wet beri- beri
It is characterised by cardiovascular signs and
symptoms such as edema of legs, face, trunk
and serous cavities.
• Dry beri- beri
In this type, the nervous system is affected. It
presents with progressive muscle wasting,
peripheral neuropathy of the motor and sensory
systems with diminished reflexes.
• Mixed beri- beri
• Infantile beri- beri
• Wernicke–Korsakoff syndrome

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CHAPTER 8
Riboflavin (Vitamin B2)
Coenzymes of Riboflavin
Riboflavin exists in two active coenzyme forms
1. Flavin mononucleotide (FMN)
2. Flavin adenine dinucleotide (FAD)
Flavin coenzymes mostly occur as prosthetic groups of
oxidoreductase enzymes. These enzymes are known as
flavoproteins.

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CHAPTER 8
Structure of riboflavin and synthesis
of FMN and FAD

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Common reactions involving FMN and FAD as coenzymes in various
metabolisms
Riboflavin through its coenzyme forms participates in oxidation-
reduction reactions in various metabolic pathways and in the
respiratory chain

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CHAPTER 8

Milk and other dairy products, lean meat, fish, eggs
and legumes are good sources.

The recommended dietary allowance (RDA) for an
adult is about 1.5 mg, with slightly higher amounts
(by 0.2 to 0.5 mg/ day) recommended for pregnant
and lactating women.
Dietary Sources And Daily
Requirement

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
Its deficiency usually occurs in association with
deficiencies of other Bcomplex vitamins. It usually
affects the tongue and lips; characterised by
glossitis (magenta tongue), angular stomatitis,
cheilosis (fissure- like lesions at the corners of the
mouth), pharyngitis and genital dermatitis.

Laboratory diagnosis done by measurement of
FAD- dependent glutathione reductase activity in
RBC.

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Niacin
Coenzymes of niacin
1. Nicotinamide adenine dinucleotide (NAD+
)
2. Nicotinamide adenine dinucleotide phosphate
(NADP+
)

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CHAPTER 8
- NADH generated in various catabolic pathways is
oxidised in the respiratory chain to generate ATP.
NADH thus plays a vital role in cellular respiration.
- NADPH serves as a readily available reducing power
in biological systems. It is used as a reductant in
biosynthetic processes.

Several enzymes require either NAD+
or NADP+
in
oxidation–reduction reactions.

There is a fundamental distinction between NADH
and NADPH

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CHAPTER 8
Biosynthesis of nicotinamide nucleotides,
NAD+
and NADP+
(Continues…

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CHAPTER 8
…Continued)
Biosynthesis of nicotinamide nucleotides, NAD+
and NADP+

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CHAPTER 8
Selected list of enzymes
dependent on NAD+
/ NADH
(Continues…

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CHAPTER 8
…Continued
Selected list of enzymes dependent on NAD+
/ NADH

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Mechanism of oxidation and
reduction of NAD+

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CHAPTER 8
Pentose phosphate pathway of carbohydrates (HMP shunt) is the major
contributor of NADPH in cells
Generators and Consumers of
NADPH

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CHAPTER 8
Selected list of enzymes dependent on NAD+
(Continues…

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CHAPTER 8
…Continued

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CHAPTER 8
Pellagra
Pellagra is a classic disease caused by the deficiency
of niacin.
The disease is characterised by three D's –
dermatitis, diarrhea and dementia.

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CHAPTER 8
Pyridoxine (Vitamin B6)
(Continues…
Vitamin B6 and its coenzyme [PLP]

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…Continued) Vitamin B6 and its coenzyme [PLP]

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CHAPTER 8
• Transamination
Biochemical Functions of B6
Transamination reaction
(Continues…

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CHAPTER 8
Histamine
Serotonin (hydroxy tryptamine)
• Decarboxylation
(Continued…
…Continued)

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CHAPTER 8
Catecholamines
GABA (gamma amino butyric acid)
(Continues…
…Continued

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CHAPTER 8
• Production of niacin coenzymes
• Heme synthesis
• Metabolism of sulphur- containing amino acids
• Phosphorylase
• Deamination
…Continued)

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CHAPTER 8

Plants contain B6 as pyridoxine, whereas animal
tissues contain PLP and pyridoxamine phosphate.
Rich sources of B6 include wheatbran, rice bran,
dried yeast, legumes, nuts, meat, fish, milk, eggs
and leafy vegetables.

Requirements are related to protein intake as it is
chiefly concerned with amino acid metabolism. The
RDA for adults is 2 mg/ day. As usual, during
pregnancy and lactation it is slightly higher.
Dietary Sources and Daily
Requirement

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CHAPTER 8

Neurological symptoms include irritability,
generalised weakness, peripheral neuropathy,
personality changes including confusion and
depression.

Carpal tunnel syndrome
Hematological manifestations include microcytic,
hypochromic anemia due to diminished hemoglobin
synthesis. Platelet dysfunction may also occur.
Dermatological manifestations include seborrheic
dermatitis, stomatitis, glossitis and cheilosis.

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• Isonicotinic acid hydrazide (INH- isoniazid) inhibits
the enzyme pyridoxal kinase, thus affecting the
synthesis of PLP adversely.
• Women taking oral contraceptives are prone to
develop B6 deficiency as OCP are known to inhibit
enzymes dependent on PLP.
• Alcoholism may result in B6 deficiency, as
acetaldehyde which is formed from ethanol can
compete with PLP for protein binding.
Drug interactions

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CHAPTER 8
Biotin
Biotin is more popularly known as anti- egg white
injury factor.
Structure of
biotin

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CHAPTER 8

Role in gluconeogenesis and Krebs cycle
Conversion of pyruvate to oxaloacetate is catalysed
by biotin- dependent pyruvate carboxylase.

Role in fatty acid synthesis

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CHAPTER 8

Role in the metabolism of odd- numbered fatty acids
and branched- chain amino acids

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The conversion of pyruvate to oxaloacetate by pyruvate carboxylase is
shown.
Reaction mechanism of carboxylation by
biotin coenzyme

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CHAPTER 8

RDA of 200–300 mg/ day.

Liver, soyabean, yeast, egg yolk, peanut, grains are
all rich sources of biotin.
Deficiency manifestations

Biotin deficiency is uncommon since it is synthesised
by the intestinal microflora and its ubiquitous
occurence in nature.

However, prolonged use of antibiotics that kill the
gut bacteria and excess consumption of raw eggs
result in biotin deficiency.

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CHAPTER 8
Pantothenic Acid

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CHAPTER 8
Synthesis of Coenzyme A from Pantothenic Acid
(Continues…

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CHAPTER 8
Synthesis of coenzyme a from pantothenic acid
…Continued)

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Some Examples of Compounds Bound to
Coenzyme A

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CHAPTER 8

More than 70 enzymes have been identified till date that
are dependent on CoA making it the central molecule in
the metabolism of lipids, proteins and carbohydrates. A
few examples of enzymes involving coenzyme A are
given below.

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CHAPTER 8
Pantothenate is widely distributed in plants and
animals. Excellent food sources include egg yolk,
liver, yeast, legumes, whole grains and vegetables.
A daily intake of 10 mg is recommended for adults.
Dietary Sources and Daily Requirements

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CHAPTER 8
Formation and Fate of Acetyl CoA

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CHAPTER 8
Folic Acid
Folic acid reduced to tetrahydrofolic acid
(Continues…

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CHAPTER 8
Folic Acid
…Continued
Folic acid reduced to
tetrahydrofolic acid

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CHAPTER 8
• Role in DNA and RNA synthesis: The one- carbon
groups are utilisef for the synthesis of C2 and C8 of
purine ring.
• Role in amino acid metabolism: THF is involved in
the conversion of serine to glycine, catabolism of
histidine and synthesis of methionine.
• Role in protein biosynthesis: THF is required for
the formation of N- formylmethionine, which
initiates protein biosynthesis.

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CHAPTER 8
Different One- Carbon Units Carried by
THF

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CHAPTER 8

The RDA of folic acid in adults is about
200 g/ day.
μ

During pregnancy (400 g) and lactation
μ
(300 g).
μ

An additional supplement is recommended during
pregnancy because its deficiency is linked to neural
tube defects and other congenital malformations.
Daily Requirement

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CHAPTER 8

Folic acid is widely distributed in natural foods.
Green leafy vegetables, cereals, fruits, eggs and dairy
products are rich sources of folic acid.
Bananas, oranges, cauliflower and broccoli contain
high levels of folate.
Dietary Sources

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CHAPTER 8
• Macrocytic anemia
• Neural tube defects in the fetus
• Hyperhomocysteinemia
Histidine load test

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CHAPTER 8
Anticonvulsants and oral contraceptives interfere
with folate absorption and prolonged use of these
drugs may cause folate deficiency.
Folate Antagonists
• Aminopterin (4- amino folic acid) and amethopterin
(methotrexate) (4- amino, 10- methyl folic acid) are
structural analogues of folic acid. They competitively
inhibit the enzyme dihydrofolate reductase and block
the formation of THF.
• Trimethoprim inhibits folate reductase and blocks
the formation of THF. Sulphonamides are
compounds that are structurally similar to PABA.

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CHAPTER 8
Structure of vitamin B12
[R = substituted by
different groups]
Vitamin B12

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CHAPTER 8
Absorption, Transport And Storage of
Vitamin B12
HC – haptocorrin
IF – intrinsic factor
TC – transcobalamins

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CHAPTER 8
Represents blockage in B12 deficiency - - Folate trap).
(Continues

Synthesis of methionine from homocysteine

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CHAPTER 8

Conversion of methylmalonyl CoA to succinyl CoA
…Continued
Conversion of methylmalonyl CoA
to succinyl CoA involving vitamin
B12 as coenzyme
Blockage in B12 deficiency leads
to the formation of ethylmalonic
acid. The latter is excreted into
the urine.

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CHAPTER 8
Normal daily requirement is about 1 g.
μ
Vitamin B12 is also synthesised by bacteria in colon.
It is not found in foods of plant origin. Hence, strict
vegans who do not consume milk products are at risk
of developing B12 deficiency.
Liver, meat, fish, eggs, milk, curd and cheese are good
sources of vitamin B12.
Daily Requirement And Dietary
Sources

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CHAPTER 8
• Megaloblastic anemia
• Subacute combined degeneration
• Demyelination
• Pernicious anemia

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CHAPTER 9
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Section III
Physiological Biochemistry
Phone: 040-2766 5446/5447

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CHAPTER 9
Chapter 9
Biochemistry of Blood

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CHAPTER 9
Plasma Proteins
1. Albumin constitutes around 60%of all the plasma
proteins (3.5–5 g/ dl).
2. Globulins: Normal plasma concentration is
2–3 g/ dl. Globulins occur in different forms:
i) a- globulins
ii) b- globulins
iii) g- globulins
3. Fibrinogen (0.2–0.4 g/ dl)
Types of plasma proteins
The normal total plasma protein concentration is around
6 to 8 g/ dl of blood. The major forms of plasma
proteins are:

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1. Salting out technique
2. Electrophoresis
3. Ultracentrifugation technique
4. Cohn's fractionation
5. Gel filtration (molecular sieving)
Separation of Plasma Proteins

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CHAPTER 9
Electrophoretic
patterns: Normal
and abnormal

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CHAPTER 9
1. Maintains colloid osmotic pressure (COP) of plasma
2. Transport function
3. Buffering action
4. Nutritional function
Functions of Albumin

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