Quick Review of Biochemistry For PDF

Quick Review of
Biochemistry
for Undergraduates
Questions and Answers
https://kat.cr/user/Blink99/
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Quick Review of
Biochemistry
for Undergraduates
Questions and Answers
Krishnananda Prabhu md
Associate Professor
Department of Biochemistry
Kasturba Medical College
Manipal University
Manipal, Karnataka, India
Jeevan K Shetty md
Associate Professor
Department of Biochemistry
RAK College of Medical Sciences
Ras Al Khaimah, UAE-SAS
The Health Sciences Publishers

New Delhi | London | Philadelphia | Panama
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Quick Review of Biochemistry for Undergraduates—Questions and Answers
First Edition: 2014
ISBN 978-93-5152-209-6
Printed at
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Preface
This book is specifically designed for a quick revision prior to examinations. Emphasis has
been on examination-oriented topics and clinical applications, wherever relevant. The content
has been designed for:
• Quick examination revision

• Easy and better recollection

For better focused study by the students, in each chapter, specific importance has been given to:
• Frequently asked questions in examinations

• Clinical applications

• Flow charts and concept maps

• Frequently asked viva questions

• Mnemonic (MN) created for better recollection.

Each topic is in the ‘question and answer’ format. At the end of each chapter, clinical

applications and key points, which are important for viva and MCQs, have been mentioned.
This book can also be used by the Nursing, MSc and Allied Health Science students.

Krishnananda Prabhu
krishnananda.prabhu@manipal.edu
Jeevan K Shetty
drjkshetty1978@gmail.com
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Contents
1. Cell and Plasma Membrane 1–8

2. Enzymes 9–24

3. Chemistry of Carbohydrates 25–31

4. Digestion, Absorption and Metabolism of Carbohydrates 32–56

5. Chemistry of Lipids 57–63

6. Digestion, Absorption and Metabolism of Lipids 64–89

7. Amino Acid and Protein Chemistry 90–103

8. Digestion, Absorption and Metabolism of Proteins 104–134

• Glycine 113

• Phenylalanine 116

• Tryptophan 121

• Methionine 123

• Cysteine 126

• Histidine 128

• Branched Chain Amino Acids 129

• Aspartate and Asparagine 131

• Glutamate 131

9. Biological Oxidation 135–140

10. Vitamins 141–157

• Fat-soluble Vitamins 142

• Water-soluble Vitamins 149

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viii
viii Quick Review of Biochemistry for Undergraduates
11. Minerals 158–165

• Macrominerals 158
• Microminerals 162
12. Nutrition 166–173
13. Nucleic Acid Chemistry 174–180
• Chemistry of Nucleotides 174
• Structure and Functions of Nucleic Acids 176
14. Nucleic Acid Metabolism 181–189
15. Molecular Biology-I 190–206
• Replication 190
• Transcription 194
• Translation 199
Contents
16. Molecular Biology-II 207–232

• DNA Repair and Mutations 207
• Regulation of Gene Expression 212
• Cancer Genetics 215
• Molecular Biology Techniques 220
• Acquired Immunodeficiency Syndrome 228
17. Acid-Base Balance and Disorders 233–241

18. Organ Function Tests 242–253
• Liver Function Tests 242
• Renal Function Tests 245
• Thyroid Function Tests 248
• Gastric Function Tests 250
• Pancreatic Function Tests 252
• Biochemical Tests for Cardiac Diseases 253
19. Radioisotopes 254–259

20. Metabolism of Xenobiotics (Detoxification) 260–263
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Quick Review of Biochemistry for Undergraduates ix xi

21. Miscellaneous 264–279

• Hormones 264

• Feed-Fast Cycle 267

• Free Radical Metabolism 271

• Techniques 273

• Electrolytes 275

22. Hemoglobin Metabolism 280–293

Index 295

Contents
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1 Cell and Plasma Membrane
1. Name all cellular organelles with one function for each.

The function of different cellular organelles is given in Table 1.1.
Table 1.1: Different cellular organelles and their functions
Organelle Functions
Plasma membrane Protection, selective barrier and maintains shape of the cell
Endoplasmic reticulum Translation and folding of new proteins (rough endoplasmic reticulum),
synthesis of lipids (smooth endoplasmic reticulum) and metabolism of drugs
Golgi apparatus Sorting and modification of proteins
Mitochondria Energy production—ATP—from the oxidation of food substances
Nucleus Maintenance of genetic material, deoxyribonucleic acid (DNA); controls all
activities of the cell, ribonucleic acid (RNA) transcription
Nucleolus Ribosome production
Lysosome Breakdown of large molecules—carbohydrates, lipids, proteins, etc.
Peroxisome Breakdown of peroxides
Ribosome Translation of RNA into proteins
2. Compare and contrast prokaryotic cell with eukaryotic cell.
The comparison between prokaryotic cell and eukaryotic cell is given in Table 1.2.
Table 1.2: Comparison of prokaryotic and eukaryotic cells
Property Prokaryotic cell Eukaryotic cell
Size Small Large
Cell membrane Rigid Flexible
Nucleus Not well-defined Well-defined with nucleolus
Subcellular organelles Absent Present
Cytoplasm Organelles and cytoskeleton absent Organelles and cytoskeleton present
Cell division Binary fission Mitosis and meiosis
Transport system Absent Present
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2 2 Quick Review of Biochemistry for Undergraduates

3. Draw a neat and labeled diagram of eukaryotic cell.

The structure of eukaryotic cell is shown in Figure 1.1.

Cell and Plasma Membrane
Fig. 1.1: Eukaryotic cell
4. Write short notes on fluid mosaic model of membrane.

As proposed by Singer and Nicolson in 1972, membrane is made up of lipid bilayer with

embedded proteins (enzymes, transporters and receptors). Membrane lipids are amphip-
athic in nature, so they spontaneously form a bilayer in aqueous medium, by arranging
their hydrophilic ends exposed to water and hydrophobic tails away from water (Fig. 1.2).
Membrane lipids are mainly phospholipids, glycolipids and cholesterol.
• Phospholipids: Glycerophospholipids and sphingomyelin

• Glycolipids: Cerebrosides and gangliosides, present on the outer surface of the membrane

• Cholesterol: Provides fluidity to membrane.
Membrane lipids show lateral movements and flip-flop movements. Hence, membrane is
fluid in nature. Hydrophobic interaction between the hydrocarbon tails in the phospholipids
keeps the bilayer intact.
Factors Affecting Membrane Fluidity

• Amount of unsaturated fatty acids: More the unsaturated fatty acids, more will be the fluidity
• Saturated fatty acids: Decreases the membrane fluidity
• Cholesterol: Increases the membrane fluidity at low temperatures.
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Quick Review of Biochemistry for Undergraduates 3 3

Fig. 1.2: Fluid mosaic model of membrane structure
Membrane Proteins
Peripheral membrane proteins: Are attached loosely to the surface of membrane bilayer.
Integral membrane proteins: Are deeply embedded in bilayer structure (proteins that extend
all along the membrane bilayer are called transmembrane proteins).
Functions of Membrane Proteins

• Transport of molecules across the membrane
• Act as receptors
• Function as enzymes
• Components of respiratory chain.
Asymmetry in Membranes
The protein to lipid ratio varies in different membranes to suit their functions. For example, inner
mitochondrial membrane, which has electron transport chain, is rich in proteins with protein and
lipid ratio of 3.2, whereas in myelin sheath, which is designed to insulate the nerve fibers, this
ratio is 0.23. Also, there is asymmetry with respect to distribution of phospholipids. For example,
phosphatidylcholine, sphingomyelin are predominantly on the outer leaflet and phosphatidylser-
ine, phosphatidylinositol, phosphatidylethanolamine are predominantly on the inner leaflet.
5. Write the functions of plasma membrane.
Plasma membrane is a barrier with selective permeability. It is made up of lipids and
proteins. It separates the cell from external environment and divides the interior of cell
into different compartments. Fluid outside the membrane is called extracellular fluid and
inside the cell is intracellular fluid.
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Functions of Plasma Membrane
• Protects cytoplasm and organelles
• Maintains shape and size of the cell
• Selective barrier—permits transport of required substances in either direction
• Cell-cell interaction
• Signal transmission.
6. Describe the characteristics of facilitated diffusion. Mention two examples of transport

by facilitated diffusion.
Definition: Movement of particles along the concentration gradient with the help of

transport proteins. Facilitated diffusion does not require energy, e.g. transport of glucose,
galactose, leucine and other amino acids.
Mechanism: Ping-pong Model

Carrier protein has two conformations—ping and pong conformation: Pong conformation of the car-
rier protein exposes it to higher concentration of molecules (solute) to be transported. Binding
of molecules induces conformational change in the carrier protein to ping state, which exposes
it to lower concentration of the molecules resulting in their release. Once the molecules are
released, the conformation of the carrier protein reverts back to pong form (Fig. 1.3).
Fig. 1.3: Facilitated diffusion
7. Explain active transport with suitable examples.

Definition: Carrier-mediated transfer of molecules against the concentration gradient

(from lower concentration to higher concentration) with the help of energy [adenosine
triphosphate (ATP)]. Substances that are actively transported through cell membranes
include Na+, K+, Ca2+, Fe2+, H+, Cl–, I–. Active transport is susceptible to inhibition and
this property is used for designing of drugs in some diseases.
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Classification
i. Primary active transport: Transport of substrate against its concentration gradient with
utilization of energy directly. For example, Na+-K+ ATPase, Ca2+-pump, H+-pump.
ii. Secondary active transport: ATP is used indirectly for transport.
For example,
Symport: Glucose-sodium cotransport, amino acid-sodium cotransport; two different sub-
stances are carried across the membrane in the same direction.
Antiport: Sodium-calcium cotransport, sodium-hydrogen pump; two different substances
are carried across the membrane in the opposite direction.

Primary Active Transport
Na+-K+ ATPase: It pumps 3 Na+ from inside to outside of the cell and brings in 2 K + from
outside to inside of the cell against their concentration gradient, using energy provided by
hydrolysis of one ATP molecule (Fig. 1.4).
Inhibitor of Na+-K+ ATPase and its significance:
Digoxin: Used in the treatment of congestive cardiac failure (CCF).
Fig. 1.4: Na+-K+ antiport (ECF, extracellular fluid; Na+, sodium ion; K+, potassium ion;
ADP, adenosine diphosphate; ICF, intracellular fluid)
Secondary Active Transport

For example, Na+-glucose cotransport (Fig. 1.5). The Na+- K+ ATPase in the basolateral membrane
of the cell transports Na+ out of the cell with the help of energy (ATP hydrolysis) creating
a Na+ gradient. This Na+ gradient is used by sodium-glucose cotransporter—sodium moves
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along its concentration gradient into the cell pulling glucose along with it against its gradient.
Hence, energy is utilized indirectly.
Fig. 1.5: Sodium-glucose cotransport
8. Describe transport processes across the membrane.

Membrane is a selectively permeable barrier. Non-polar substances gain easy access because

of solubility in lipid bilayer, but polar substances cross the membrane selectively.
Selectivity of membrane transport depends upon:

i. Size of molecules: Small solutes pass through easily than larger ones.

ii. Charge of the molecule: Molecules with less charge pass through the membrane easily than

one with more charges.
iii. Transport proteins: Specific proteins transport specific molecules.

iv. Type of molecules: Water readily traverses through the membrane.

Classification of transport mechanisms across the membrane:
i. Passive transport.

ii. Active transport.

iii. Endocytosis/exocytosis.

iv. Ionophores.

Passive transport: Simple diffusion, facilitated diffusion and transport through ion channels.

Simple diffusion

Definition: Movement of the particles across the membrane, along the concentration gradient,
without any involvement of carrier proteins. Energy is not required for simple diffusion.
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For example, small and lipophilic molecules like O2, CO2, N2 and H2O are transported
by this process.
Facilitated diffusion (Refer question number 6)
Definition: Movement of the particles with the help of transport proteins along the concen-
tration gradient. Facilitated diffusion does not require energy and is carried out by Ping-
Pong mechanism (refer Fig. 1.3), e.g. glucose, galactose, leucine and other amino acids.
Ion channels
Ions pass through the ion channels, which open or close in response to a signal. Ion
channels are:

i. Voltage gated: Open due to changes in membrane potential, e.g. Ca2+, Na+ and K+ channels.
ii. Ligand gated: Binding of ligand to receptor site results in opening and closing of the chan-
nel, e.g. acetylcholine receptor.
Active transport (Refer question number 7)
Endocytosis and exocytosis
Endocytosis
Uptake of macromolecules into the cells. For example, uptake of low-density lipoproteins
(LDL), polysaccharides, proteins and polynucleotides.
Two types:
i. Pinocytosis: Uptake of fluid and fluid contents by cell (cellular drinking).
ii. Phagocytosis: Ingestion of larger particles like bacterial cells and tissue debris by mac-
rophages, which are further hydrolyzed by lysosome.
Exocytosis
Release of macromolecules from the cell to outside. For example, calcium-dependent secre-
tion from vesicles (secretion of hormones).
Ionophores
Ionophores are the molecules that facilitate transport of ions across membranes.
Two types:
i. Carrier ionophores: They increase permeability for a particular ion, e.g. valinomycin trans-
ports K+ and inhibits oxidative phosphorylation.
ii. Channel-forming ionophores: They facilitate passage of ions by forming channels, e.g. grami-
cidin A inhibits oxidative phosphorylation by facilitating movement of Na+ and K+ across
the membrane.
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Key Points
Hartnup disease: Defect in absorption of neutral amino acids in intestine and their defective reab-

sorption in kidney.
Cystinuria: Defect in reabsorption of cysteine in kidney.

Vitamin D-resistant rickets: Defective renal reabsorption of phosphate from kidney.

Myasthenia gravis: Defect in acetylcholine receptors (ligand-gated channels).

Cystic fibrosis: Due to mutation in chloride channels.

Digoxin: Inhibitor of sodium-potassium ATPase. Inhibition of this pump by digoxin will increase in-

tracellular calcium concentration and myocardial contractility. So, digoxin is useful in the treatment
of congestive cardiac failure.
Omeprazole: Inhibitor of hydrogen-potassium ATPase. Omeprazole inhibits gastric acid secretion,

hence is used in the treatment of peptic ulcer.
Facilitated transporters: It can be classified with regard to direction of solute movement as:

• Uniport: Movement of one molecule at a time (bidirectional) by transporter, e.g. transport of

fructose in intestine
• Symport: Movement of two different molecules simultaneously in the same direction, e.g. sodium-

glucose transport in the intestine
• Antiport: Movement of two different molecules simultaneously in the opposite direction, e.g.

chloride-bicarbonate transport in the red blood cell (RBC).
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2 Enzymes
1. What are coenzymes? Explain with two examples.

Definition: The non-protein, organic, low-molecular weight substances associated with
enzymes and required for their biological activity are called coenzymes.
For example,
Pyruvate dehydrogenase complex
Pyruvate Acetyl-CoA
NAD +
, TPP, FAD, CoASH, lipoic acid
a-ketoglutarate dehydrogenase complex
α-ketoglutarate Succinyl-CoA
TPP, NAD+, FAD, CoASH, lipoic acid
Nicotinamide adenine dinucleotide ( NAD +), thiamine pyrophosphate (TPP), flavin
adenine dinucleotide (FAD), CoASH and lipoic acid are coenzymes.
2. What are cofactors? Explain with two examples.

Definition: Inorganic groups that bind in a transient, dissociable manner either to the
enzyme or to a substrate are called cofactors (Table 2.1).
Table 2.1: Enzymes and their cofactors
Enzyme Cofactor required
Carbonic anhydrase, alcohol dehydrogenase Zinc
Enolase Manganese
Cytochrome oxidase, catalase, peroxidase Iron
Xanthine oxidase Molybdenum
Salivary amylase Chloride
Kinase Magnesium
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1010 Quick Review of Biochemistry for Undergraduates

3. Explain enzyme specificity with suitable examples.
Definition : Enzyme specificity is defined as the ability of an enzyme to bind to just

one substrate from a group of similar compounds. Because of specificity for a substrate,
more than one enzyme can exist in a cell without affecting the function of the other
(Table 2.2).
Table 2.2: Types of specificity of enzymes
Classification Definition and properties Example
Absolute specificity Act on only one substrate Glucokinase

and catalyze one reaction Glucose Glucose-6-phosphate
Lactase

Lactose Glucose + Galactose
Group specificity Act on specific bond or Phosphatase: Hydrolyze organic phosphates
group of substrates Exopeptidase: Hydrolyze terminal peptide
bonds
Enzymes
Reaction specificity Enzymes are specific for 1 2

a particular reaction even Acetyl-CoA Pyruvate Lactate

though the substrate is 3 4
same for each reaction
Oxaloacetate Alanine

Stereospecificity Act on only one type of L-amino acid oxidase

stereoisomer L-amino acid Keto acid

D-amino acid oxidase

D-amino acid
Keto acid

1, pyruvate dehydrogenase complex; 2, lactate dehydrogenase; 3, pyruvate carboxylase; 4, alanine transaminase.
4. Define and classify enzymes with suitable examples.

Definition: Enzymes are colloidal, thermolabile, biological catalysts, which are protein in na-

ture. They are classified into six classes [Mnemonic (MN): OTH LIL = On The Heaven Life Is
Luxurious].
i. Oxidoreductases: They catalyze oxidation-reduction reactions.

For example,

Alcohol dehydrogenase

Ethanol + NAD+ Acetaldehyde + NADH + H+

Lactate dehydrogenase

Lactate + NAD+ Pyruvate + NADH + H+

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Quick Review of Biochemistry for Undergraduates 1111
ii. Transferases: A group, other than hydrogen, is transferred from one substrate to other by
transferases.
For example,
Hexokinase
Glucose + ATP Glucose-6-phosphate + ADP
Fructokinase
Fructose + ATP Fructose-1-phosphate + ADP
iii. Hydrolases: Catalyze hydrolysis of ester, ether, peptide, glycosidic bonds by addition
of water.
For example,
Lactase
Lactose + H2O Glucose + Galactose
Maltase
Maltose + H2O Glucose + Glucose
Enzymes
iv. Lyases: Catalyze removal of groups or break bonds (without hydrolysis).
For example,
Aldolase A Glyceraldehyde-3-phosphate +
Fructose-1,6-bisphosphate
Dihydroxyacetone phosphate
Enolase
2-phosphoglycerate Phosphoenolpyruvate (PEP)
v. Isomerases: Catalyze optical, positional, geometrical isomerization of substrates.
For example,
Phosphohexose isomerase
Glucose-6-phosphate Fructose-6-phosphate
Epimerase
Glucose Galactose
vi. Ligases: Catalyze binding of two substrates by using energy (usually, hydrolysis of ATP).
For example,
Acetyl-CoA carboxylase Malonyl-CoA
Acetyl-CoA + ATP + Biotin + CO2 + ADP + Pi + Biotin

Pyruvate carboxylase Oxaloacetate
Pyruvate + ATP + Biotin + CO2
+ ADP + Pi + Biotin
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5. Write briefly on active site of an enzyme.
Definition: The active site of an enzyme is a three-dimensional structure that has amino

acids or groups and occupies a small portion of the enzyme. It has substrate binding site
(binds substrate non-covalently) and a catalytic site. It makes the reaction possible by:
• Bringing the reactive groups of substrate together (catalysis by proximity)

• Expelling water

• Stabilizing the transition state

• Lowering the activation energy.

Its specific interaction with substrate is explained by two theories:

i. Active site has a structure complementary to substrate (lock and key theory).

ii. After binding to a substrate, the active site and enzyme undergo conformational change,

which further facilitates the interaction (induced fit theory).
Substrate Binding Site
Enzymes

Substrate binding site on the enzyme consists of certain groups (such as –OH, –SH, –COO –),
which recognize and bind to substrate to form enzyme-substrate (ES) complex.
Catalytic Site
Catalytic site enhances reaction rate by lowering energy of activation and converts the ES
complex to enzyme + product (Fig. 2.1).
Fig. 2.1: Components of active site
6. Explain the models proposed for interaction of substrate with active site of an enzyme.
Lock and Key Model

Lock and key model was proposed by Emil Fisher in 1980. According to this model, the active
site of an enzyme has a structure complementary to that of substrate (Fig. 2.2). The substrate
binding site recognizes and binds the substrate through hydrophobic/electrostatic interactions
or hydrogen bonds.
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In this model, the interaction between substrate and the binding site is compared to a key
fitting into a rigid lock. For example, most enzymes in carbohydrate metabolism can bind to
D-isomers of hexoses, not L-isomers. This model does not explain interaction of the enzyme
with allosteric modulators.
Fig. 2.2: Lock and key model (E, enzyme; S, substrate; P, product)
Induced Fit Model or Hand in Glove Model of Daniel E Koshland

According to this model, the shape of active site undergoes a change following binding of the
Enzymes
substrate. Once the substrate binds to an enzyme, rapid conformational change occurs in the
enzyme, which strengthens its interaction with the substrate (Fig. 2.3).
Fig. 2.3: Induced fit model (E, enzyme; S, substrate; P, product)
7. What are the various factors affecting enzyme activity? Explain with suitable diagrams.
Substrate Concentration
At low substrate concentration [S], most of the enzymes will be in unbound form (active site
is free), so rate of reaction will be proportional (first-order kinetics) to (S). This reaches a point
beyond which, any increase in substrate concentration causes a minimal increase in V; plateau/
steady state is reached. This is called zero-order kinetics. At Vmax, most of the enzymes will
be in bound form (ES) and enzymes available for binding is very few or zero. In this state, a
further increase in [S] does not have any effect on the rate of the reaction (Fig. 2.4).
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Fig. 2.4: Effect of substrate concentration on velocity of a reaction (A, first order; B, mixed order; C, zero-order kinetics;
[S], substrate concentration; V, velocity of reaction)
Enzymes
Enzyme Concentration
When saturating amount of substrate is present, the velocity of a reaction is directly propor-
tional to the amount of enzyme (Fig. 2.5).
Fig. 2.5: Effect of enzyme concentration on velocity of reaction
Effect of pH on Enzyme Activity

Every enzyme has an optimum pH and activity of enzyme is highest at this pH. Above and
below optimum pH, enzyme activity is decreased. Optimum pH varies from enzyme-to-enzyme.
For example, optimum pH of pepsin is 2 and that of trypsin is 8. A bell curve is obtained on
plotting enzyme activity against pHhttps://kat.cr/user/Blink99/
(Figs 2.6 and 2.7).
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Fig. 2.6: Effect of pH on velocity of reaction Fig. 2.7: Effect of pH on enzyme substrate interaction
(↑, increase; ↓, decrease)
Enzymes
Effect of Temperature on Enzyme Activity
At extreme temperature, enzyme activity is lost. All human enzymes have maximum activity
at body temperature (Figs 2.8 and 2.9).
Fig. 2.8: Effect of temperature on velocity of reaction Fig. 2.9: Schematic diagram showing the effect of
temperature on velocity of reaction
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8. What is Michaelis-Menten equation? What is its significance?
Definition: It is an equation showing relationship between initial reaction velocity V i and

substrate concentration [S].
Vmax [S]

Vi = ;V = Maximum velocity, Km = Michaelis constant.
max

Km + [S]

It can be used to calculate Km or Vmax of a reaction.

9. What is Michaelis constant? What does it signify?
Definition: Michaelis constant, denoted as Km, is equal to the substrate concentration at half
the maximal velocity of a reaction. It is inversely proportional to affinity of the enzyme for its
substrate. This means higher is the Km, lower is the affinity of the enzyme for the substrate
(refer Fig. 2.4).
Enzymes
10. What is enzyme inhibition? What is its significance?

Definition: Enzyme inhibitors are molecules that interact with enzymes, thus decreasing
the rate of enzymatic reaction. They can be substrate analogs, drugs, toxins or metal
complexes.
The study of enzyme inhibition is important for understanding enzyme regulation, ac-

tion of drugs and toxic agents on biological system.
Significance [MN: MATS]

• To elucidate the Metabolic pathways in cells

• To understand the nature of functional group at Active site of an enzyme and its mecha-

nism of catalysis
• Therapeutic applications: Antibiotics like penicillins, sulfonamides, antiviral drugs like acy-

clovir, anticancer drugs like 5-fluorouracil and methotrexate act by inhibiting enzymes
• To understand Substrate specificity of enzymes.

Types of Enzyme Inhibition
Enzyme inhibition is of different types as shown in Figure 2.10.
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Fig. 2.10: Types of enzyme inhibition
Reversible Inhibition
Reversible inhibitors bind to enzyme through non-covalent bonds or by weak interaction.
Activity of enzyme is restored when more substrate is added.
Enzymes
Irreversible Inhibition
Irreversible inhibitors bind to enzyme covalently or by strong interactions and inhibit the
activity of enzyme, which cannot be restored.
11. Enlist the features of competitive inhibition. Give two clinically relevant examples.
Competitive inhibition
• Competitive inhibitor is similar to substrate in structure
• It binds to active site of the enzyme
• It competes with substrate for the active site of the enzyme
• Inhibition is reversible: Inhibition can be overcome by increasing substrate concentration
• During competitive inhibition, Km is increased (affinity for substrate decreases as some
active sites are occupied by the inhibitor), but Vmax remains same.
For example,
HMG-CoA reductase
HMG-CoA Cholesterol
This enzyme is competitively inhibited by Lovastatin, a drug used to treat hypercho-
lesterolemia.
Folate reductase
Folic acid Tetrahydrofolic acid
This enzyme is competitively inhibited by methotrexate, an anticancer drug.
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12. Enlist the features of non-competitive inhibition. Give two examples.
Non-competitive inhibition

• The inhibitor is not similar to substrate in structure

• It does not bind to active site; it does not compete with substrate for binding to enzyme

• Inhibition is usually irreversible: Inhibition cannot be overcome by increasing substrate

concentration
• During non-competitive inhibition, Km is not altered (no change in substrate affinity), but

Vmax is reduced.
For example,
Enolase

2-phosphoglycerate Phosphoenolpyruvate

Fluoride is a non-competitive inhibitor of enolase.

Acetylcholinesterase

Acetylcholine Acetate + Choline
Enzymes

Acetylcholinesterase is inhibited by diisopropyl fluorophosphate (DIFP).

13. What is suicide inhibition? Explain with two examples.
Definition: It is a type of irreversible inhibition of an enzyme. After binding with active site

of the enzyme, the inhibitor is converted to a more potent compound resulting in irreversible
inhibition of the enzyme. This is also called mechanism-based inactivation (Table 2.3).
Table 2.3: Examples for suicide inhibition
Inhibitor Target enzyme Application
5-fluorouracil Thymidylate synthase Cancer treatment
Aspirin Cyclooxygenase Anti-inflammatory agent
Penicillin Bacterial transpeptidase Antibacterial agent
Deprenyl Monoamine oxidase Antidepressant, Parkinson's disease
Disulfiram Aldehyde dehydrogenase Alcohol de-addiction
14. Explain enzyme regulation.
Short-term Regulation

Short-term regulation is a quick regulation mechanism, which is based on altering the activities
of existing enzymes. It is of two types (Fig. 2.11):
a. Allosteric regulation.

b. Covalent modification.

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Allosteric Regulation
In allosteric regulation, the inhibitor is not a structural analog of substrate. Inhibition is
partially reversible when concentration of substrate is increased. The inhibitor causes an
increase in Km and a decrease in Vmax. This can be further subdivided into feedback inhibition
and feedforward regulation.
Enzymes
Fig. 2.11: Types of enzyme regulation
• Feedback allosteric inhibition: In multienzyme system, the first enzyme of the sequence of
reactions can be inhibited by the end product (Fig. 2.12).
Fig. 2.12: Schematic diagram of feedback inhibition (E, enzyme)
For example,
i. In heme synthesis, end product heme inhibits first enzyme (ALA synthase).
ii. Cholesterol inhibits its own synthesis by blocking HMG-CoA reductase (Table 2.4).
Table 2.4: Allosteric enzymes and their modulators
Pathway Enzyme Inhibitor Activator
Glycolysis Phosphofructokinase-1 ATP and citrate AMP
TCA cycle Isocitrate dehydrogenase ATP ADP
Glycogenolysis Glycogen phosphorylase ATP AMP
Gluconeogenesis Pyruvate carboxylase AMP ATP, citrate, acetyl-CoA
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• Feedforward regulation: Initial reactants in a reaction enhance their own metabolism by

inducing downstream enzymes. Usually associated with metabolism of drugs, alcohol,
poisons, etc.
For example, alcohol intake induction of cytochrome P4502E1 increased me-

tabolism of alcohol tolerance to alcohol.
Covalent Modification
Covalent modification is the regulation of enzyme activity by addition of phosphate groups to
specific serine, threonine or tyrosine residues of the enzyme or removal of attached phosphate
from the above residues. Depending on specific enzyme, phosphorylation/dephosphorylation
may lead to its activation/inactivation. For example, phosphorylation of glycogen phospho-
rylase increases its activity, whereas addition of phosphate to glycogen synthase decreases its
activity (Fig. 2.13).
Enzymes
Fig. 2.13: Reversible covalent modification
Long-term Regulation
Long-term regulation involves altering concentration of enzyme by increasing (induction) or
decreasing (repression) enzyme synthesis at genetic level.
Induction (Derepression)
Here, enzyme activity is increased by 1,000 or million times by increasing synthesis of the
enzyme. For example, induction of lactose operon in Escherichia coli by lactose.
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Other examples:
• Glucose: (+) Glucokinase
• Barbiturates: (+) ALA synthase
• Glucocorticoids: (+) Transaminase.
Note: (+) = Induction.
Repression
Here, enzyme activity is decreased by 1,000 to million times by stopping translation of enzyme
at genetic level. For example,
• Heme: (−) ALA synthase
• Cholesterol: (−) HMG-CoA reductase.
Note: (−) = Repression.
15. What are isoenzymes? Explain their clinical importance with an example.
Enzymes
Definition: Different molecular forms of an enzyme synthesized from different organs and
catalyzing the same reaction are called isoenzymes, e.g. isoenzymes of lactate dehydroge-
nase and creatine phosphokinase.
Lactate Dehydrogenase
Normal serum level is 100–200 U/L. LDH is a tetramer containing two types of polypeptide
chains—M (muscle) type and H (heart) type. It has five isoenzymes (Table 2.5).
Table 2.5: Various isoenzymes of lactate dehydrogenase
Type Composition Location Concentration Electrophoretic Elevated in
as % of total mobility
LDH1 HHHH Heart 30 Fast moving Myocardial infarction
LDH2 HHHM RBC, kidneys 35 – Anemia, renal disease
LDH3 HHMM Brain 20 – Leukemia
LDH4 HMMM Lungs, spleen 10 – Pulmonary infarction
LDH5 MMMM Liver, muscle 5 Slowest Liver/muscle disease
Creatine Phosphokinase
Normal serum level is 15–100 IU/L. Creatine kinase is a dimer and is made up of two types
of polypeptide chains—M (muscle) type and B (brain) type. It exists as three different isoen-
zymes (Table 2.6).
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Table 2.6: Various isoenzymes of creatine kinase
Type Composition % of total Location Electrophoretic Elevated in
mobility
CK1 BB 1 Brain Fast moving –
CK2 MB 5 Heart – Myocardial infarction
CK3 MM 80 Skeletal muscle Slow moving Muscular dystrophy
16. Explain the role of enzymes in diagnosis of acute myocardial infarction.

Serum enzyme levels during acute myocardial infarction is shown in Figure 2.14. The role

of isoenzymes in diagnosis of acute myocardial infarction is given in Table 2.7.
Enzymes
Fig. 2.14: Serum enzymes during acute myocardial infarction
Table 2.7: Serum enzymes in acute myocardial infarction

Enzyme Starts increasing (after onset of chest pain) Peak level Normalizes by
CPK Within 3–6 hour 12–24 hour 3rd day
AST Within 6–12 hour 48 hour 4th–5th day
LDH After 2nd day 3rd–4th day 10th day
17. Enlist some enzymes and conditions where they are elevated.
The enzymes in various clinical conditions is given in Table 2.8.

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Table 2.8: Enzymes in clinical diagnosis

Enzyme Condition where it is elevated
Amylase Acute pancreatitis
AST* Myocardial infarction, hepatitis
ALT †
Hepatitis
ALP‡ Obstructive jaundice, bone disease
ACP§ Prostate cancer
LDH ||
Myocardial infarction, liver/muscle disease
CPK¶ Myocardial infarction, muscle disease
5'-nucleotidase Obstructive jaundice
GGT** Alcoholic liver disease
Lipase Acute pancreatitis
AST, aspartate transaminase; †ALT, alanine transaminase; ‡ALP, alkaline phosphatase; §ACP, acid phosphatase; ||LDH, lactate
*
Enzymes
dehydrogenase; ¶CPK, creatinine phosphokinase; **GGT, γ-glutamyl transferase.
Key Points
Q10: Q10 or temperature coefficient is the factor, by which the rate of a biologic process increases

for a 10°C increase in temperature. For temperature range over which enzymes are stable, the rates
of most biologic processes typically double for a 10°C rise in temperature (Q 10 = 2).
Substrate: The molecule acted upon by the enzyme to form product.

Apoenzyme: It is the protein part of the enzyme without any prosthetic groups.

Prosthetic group: It is non-protein part of an enzyme bound to an apoenzyme.

Holoenzyme: Cofactor or prosthetic group + apoenzyme.

Maturity onset diabetes of the young (MODY): Occurs due to decreased glucokinase activity that

results in lower insulin secretion for a given blood glucose level.
Febuxostat: It is a non-purine substrate analogue of xanthine oxidase, which is used in the treat-

ment of gout.
Fluoride: Non-competitively inhibits enolase of glycolysis in RBC and is used as an additive when

collecting blood for glucose estimation.
Organophosphorus compounds: Accidental or suicidal ingestion of DIFP, nerve gases (sarin, tabun)

and insecticides act like poison and non-competitively inhibit acetylcholinesterase →↑ acetylcholine →↑
bronchosecretion, intestinal motility and salivation; bradycardia, hypotension, constriction of pupil, etc.
Methanol poisoning: Methanol is a common adulterant in spurious liquor. This can lead to blind-

ness, organ failure, acidosis and finally death. Methanol gets metabolized to formic acid, which is
very toxic. This can be prevented by administering ethanol to the patient which competitively blocks
methanol metabolism.
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Alcohol de-addiction: Disulfiram is a suicide inhibitor of aldehyde dehydrogenase. It blocks conversion

of acetaldehyde to acetic acid. Whenever a person on such a drug consumes alcohol, acetaldehyde
accumulates, which causes lot of unpleasant side effects like vomiting, hypotension, headache, flush-
ing (aldehyde syndrome). This makes the person abstain from alcohol.
People from Asian origin are more sensitive to alcohol as compared to people from West:

Asians have decreased activity of mitochondrial acetaldehyde dehydrogenase as compared to Western
population → slow metabolism of acetaldehyde → dizziness, headache, flushing.
Streptokinase and urokinase (tissue plasminogen activator): Cleave Arg-Val bond in plasminogen

to form active plasmin. They are useful for the treatment of myocardial infarction.
Uncompetitive inhibition: Inhibitor binds only to enzyme substrate complex. It decreases both V max

and Km. For example, placental alkaline phosphatase is inhibited by phenylalanine.
Competitive inhibition: Km is increased and Vmax is unaltered in competitive inhibition (Table 2.9).

Table 2.9: Examples for competitive inhibitors
Inhibitor (analog) Natural substrate Target enzyme Application
Malonate Succinate Succinate dehydrogenase –
Enzymes
Sulfonamides PABA Pteroid synthetase Antimicrobial agent

Dicumarol Vitamin K Epoxide reductase Anticoagulant
Allopurinol Xanthine Xanthine oxidase Gout
Methanol Ethanol Alcohol dehydrogenase Methanol poisoning
Enalapril, captopril Angiotensin I Angiotensin-converting enzyme Hypertension
Neostigmine Acetylcholine Acetylcholinesterase Myasthenia gravis
Non-competitive inhibition: K m is unaltered and V max decreases in non-competitive inhibition

(Table 2.10).
Table 2.10: Non-competitive inhibitors
Inhibitor Enzyme
Arsenite Glyceraldehyde-3-phosphate dehydrogenase
Fluoride Enolase
Omeprazole H+-K+ ATPase
Cyanide Cytochrome oxidase
Diisopropyl fluorophosphate (DIFP) Acetylcholinesterase
Specific proteolytic cleavage: Type of enzyme regulation in which enzymes are synthesized as

zymogens and are subsequently activated by cleavage of one or few specific peptide bonds (ir-
reversible covalent modification). For example, formation of pepsin from pepsinogen; chymotrypsin
from chymotrypsinogen.
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3 Chemistry of Carbohydrates
1. Define and classify carbohydrates with suitable examples.

Definition: Carbohydrates are polyhydroxy aldehydes (HC=O) or ketones (C=O) with an
empirical formula Cn(H2O)n (Fig. 3.1).
Exceptions: Deoxy sugars, e.g. deoxyribose—formula is C5H10O4.
Fig. 3.1: Carbohydrates: Aldose (glyceraldehyde) and ketose (dihydroxyacetone)
Classification
i. Monosaccharides: Are simplest sugars, which cannot be hydrolyzed further to a simpler
form of sugar, e.g. glucose, fructose.
ii. Disaccharides: Made up of two monosaccharide units joined by a glycosidic bond, e.g.
sucrose, trehalose, lactose, maltose.
iii. Oligosaccharides: Made up of 3–10 monosaccharide units joined by glycosidic bonds, e.g.
raffinose (glucose + galactose + fructose), stachyose (2 galactose + glucose + fructose),
verbascose (3 galactose + glucose + fructose).
iv. Polysaccharides: Made up of more than 10 monosaccharide units joined by glycosidic
bonds (Table 3.1). They are of two types.
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a. Homopolysaccharides: Made up of same monosaccharide units joined by glycosidic

bonds, e.g. starch, cellulose, glycogen, dextrin, inulin.
b. Heteropolysaccharides (glycosaminoglycan): Made up of different monosaccharide units

joined by glycosidic bonds, e.g. heparin, chondroitin sulfate, dextran.
Table 3.1: Composition and importance of some polysaccharides
Sugar Composition and importance
Inulin Homopolysaccharide; used for measuring glomerular filtration rate
Hyaluronic acid N-acetylglucosamine + glucuronic acid, not covalently attached to protein; lubricant,
shock absorber—present in synovial fluid, vitreous humor, umbilical cord, loose con-
Chemistry of Carbohydrates
nective tissue
Chondroitin sulfate N-acetylgalactosamine + glucuronic acid; present in cartilage, tendons, ligaments
Dextran Heteropolysaccharide; used as plasma volume expander
Dermatan sulfate N-acetylgalactosamine + L-iduronic acid; present in skin, blood vessels, heart valves
Heparin Glucosamine + glucuronic acid or iduronic acid; present in liver, lung, spleen;
anticoagulant
Keratan sulfate N-acetylglucosamine + galactose; present in cartilage, cornea; only glycosaminoglycan
not having uronic acid
2. What are the various functions of carbohydrates?

[MN: TERN]
• Part of connective Tissue, e.g. hyaluronic acid in joints

• Source of Energy: 65% of the calorie requirement comes from carbohydrates

• Fiber (Roughage): Relieves constipation, e.g. cellulose

• Part of Nucleic acids: Ribose in deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

3. Explain different types of carbohydrate isomers with examples.

Definition: Compounds, which have same molecular formula, but:

i. Have different structures are called structural isomers (Fig. 3.2).

For example, glucose, galactose and fructose.

ii. Have different spatial configuration are called stereoisomers (refer Fig. 3.2).

a. Epimers: Stereoisomers, which differ in orientation of H and OH around only one carbon.

For example, glucose and galactose (4 epimer of glucose).
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Fig. 3.2: Isomers of glucose
b. Enantiomers: Stereoisomers, which are mirror images of each other. For example,
D- and L-glucose (Fig. 3.3).
Fig. 3.3: Enantiomers
c. Anomers: Stereoisomers which differ in orientation of H and OH around anomeric carbon

(Fig. 3.4, p. 28). For example, α-glucose and β-glucose.
iii. Have different optical rotation are called optical isomers: dextro (d or +) and levo
(l or −).
• The rotation of polarized light either to the right or left determines whether an isomer is
dextro (d) or levorotatory (l) respectively (Fig. 3.5).
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Fig. 3.4: Anomers [MN: Alpha-OH is not Above, Beta-OH is not Below]
Fig. 3.5: Optical isomers
4. What are the modified sugars encountered in our metabolism?

Modified sugars are formed when the primary or secondary alcohol groups of sugars

get oxidized/reduced or replaced by amino group to form sugar acids/sugar alcohols or
amino sugars respectively. Some are often seen in our body tissues and genetic materials
(Table 3.2 and Fig. 3.6).
Table 3.2: Modified sugars
Name Modification Examples
Deoxy sugars OH group is reduced to H Deoxyribonucleic acid (DNA)
Amino sugars OH group replaced with amino group Glucosamine, galactosamine
Sugar acid Alcohol group of first carbon of glucose is oxidized to Gluconic acid
COOH
Contd...
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Contd...
Name Modification Examples

Uronic acid Last carbon of glucose is oxidized to COOH Glucuronic acid
Saccharic acid Alcohol groups of first and last carbon atoms of glucose –
are oxidized to COOH
Sugar alcohol Reactive aldehyde group of sugar is reduced to alcohol Sorbitol, mannitol, glycerol
Fig. 3.6: Modified sugars
5. What is mutarotation? Explain with an example.

Definition: Mutarotation is defined as the change in specific optical rotation, with time, of
a sugar in solution to reach an equilibrium mixture.
For example, glucose in solution has two forms α (+ 112.2°) and β (+ 18.7°); with time,
an equilibrium mixture of the two is formed with net rotation of (+ 52.7°).
6. What is a glycoside? Give some examples.
Definition: Glycoside is a molecule formed when the hemiacetal or hemiketal hydroxyl
group of anomeric carbon of a monosaccharide reacts with hydroxyl/amine group of ano-
ther carbohydrate or a non-carbohydrate (methanol, phenol, glycerol, sterol) with removal of
water. The non-carbohydrate moiety in a glycoside is referred to as aglycone (Table 3.3).
For example, streptomycin, erythromycin, ouabain, digitalis are glycosides.
Table 3.3: Glycoside and its components
Glycoside Carbohydrate Aglycone
Phlorizin (rose bark) Glucose Phloretin
Digitonin (foxglove) Galactose/xylose Digitogenin
Indican (stain) Glucose Indoxyl
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7.
Compare the structure of starch and glycogen.
The comparison between starch and glycogen is given in Table 3.4.

Table 3.4: Starch and glycogen—structural features
Starch Glycogen
Reserve carbohydrate of plant kingdom Reserve carbohydrate of animal kingdom
10%–20% amylose and 80% amylopectin Predominantly amylopectin-like structure
15–18 glucose residues/branch 6–7 glucose residues/branch
Branch every 8–9 residue Branch every 3–4 residues
Gives blue color with iodine Red-brown/violet color with iodine
8. What are glycoproteins? Give some examples.

Definition: These are proteins to which short chain of oligosaccharides are attached. Unlike

glycosaminoglycans, they lack uronic acids. They have comparatively less carbohydrates
(protein > carbohydrate) than glycosaminoglycans.
For example,

• Structural glycoproteins: Collagen

• Enzymes: Ribonuclease, prothrombin

• Glycoproteins in transport: Ceruloplasmin, transferrin

• Hormone: Thyroid stimulating hormone (TSH)

• Glycoproteins in immune system: Blood group antigen, immunoglobulins

• Membrane glycoprotein: Glycophorin of red blood cells (RBCs)

• Glycoprotein as lubricant: Mucin

• Receptor: Hormone receptors and receptors on surface of viruses.

Key Points
Lactose: Lactose is a milk sugar, which is digested by the enzyme lactase. A deficiency of this

enzyme can lead to lactose intolerance where the person cannot tolerate lactose in the diet.
Sucrose and trehalose: They are non-reducing sugars because anomeric hydroxyl group of indi-

vidual subunits in both of them are involved in formation of glycosidic bonds. Non-reducing sugars
will not answer Benedict's test, Barfoed's test and osazone test.
Inulin: It is a homopolysaccharide used for measuring glomerular filtration rate.

Hyaluronic acid: It is a heteropolysaccharide that is not covalently attached to protein. Hyaluronidase

enzyme is present in sperm head—it breaks this sugar (present on the outer layer of human egg)
and helps in entry of sperm. Absence of this enzyme on sperm head can lead to infertility.
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Keratan: It is the only glycosaminoglycan not having uronic acid.

Dextran: It is a heteropolysaccharide used as plasma expander.

Sorbitol: It accumulates in lens in diabetics resulting in cataract.

Mannitol: It is an osmotic diuretic, which can be used to treat cerebral edema.

Olestra: It is an artificially synthesized glycoside using sucrose + fatty acids. It can be used as a

fat substitute that adds no fat or calories.
Digitalis: It is a glycoside used to treat congestive cardiac failure.

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Digestion, Absorption and
4 Metabolism of Carbohydrates
1. Explain digestion and absorption of carbohydrates.

Digestion of Carbohydrates
Digestion of carbohydrate occurs in three phases: salivary phase, pancreatic phase and intes-
tinal phase (Figs 4.1 and 4.2).
Fig. 4.1: Digestion of carbohydrates

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Digestion, Absorption and Metabolism of Carbohydrates

Fig. 4.2: Intestinal brush border disaccharidases
Absorption
All carbohydrates, except cellulose, are digested to respective monosaccharides.
Glucose, galactose and fructose (monosaccharides formed as end products of digestion)
are initially absorbed by a common transporter GLUT-5 (passive facilitated diffusion) from
luminal side into the intestinal cell.
Glucose and galactose are also absorbed by sodium-dependent glucose transporter-1
(SGLUT-1) (Fig. 4.3). Cellulose cannot be digested and absorbed and acts as a dietary fiber.
Fig. 4.3: Absorption of carbohydrates in the intestine (Na+, sodium ion; K+, potassium ion;
ATPase, adenosine triphosphatase)
2. Write the individual reactions of glycolysis. Add a note on its energetics.

Glycolysis (Embden-Meyerhof pathway)
Definition: Glycolysis is a major pathway for glucose metabolism—glucose is converted
to pyruvate or lactate.
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Significance of Glycolysis
• Principal route for metabolism of glucose, fructose, galactose and other carbohydrates

• Operates in both aerobic and anaerobic conditions

• Lactate generated in anaerobic glycolysis is used for gluconeogenesis in the liver

• Anaerobic glycolysis is a major pathway that provides energy for skeletal muscles during

strenuous exercise
• Hexokinase is allosterically inhibited by product glucose-6-phosphate, which favors storage

of glucose in the liver as glycogen
• Deficiency of glycolytic enzymes (e.g. pyruvate kinase) results in hemolytic anemia

• Anaerobic glycolysis is the only pathway that provides energy for mature red blood cells

(RBCs).
Requirements for Glycolysis

• Site: All the cells in the body

• Subcellular site: Cytosol

• Starting material: Glucose

• End product: Pyruvate in aerobic and lactate in anaerobic glycolysis

• Coenzymes: Nicotinamide adenine dinucleotide hydrogen (NADH), adenosine triphos-

phate (ATP)
• Steps: Divided into two phases (Fig. 4.4, p. 35)

– Energy investment phase: Chemical priming phase requiring energy in the form of ATP

– Energy yielding phase: Energy is generated in the form of ATP.

Anaerobic Glycolysis

For steps refer Figure 4.4 + conversion of pyruvate to lactate shown below:
In anaerobic conditions, NADH generated is not used for ATP generation in electron

transport chain. NADH is used for conversion of pyruvate to lactate. This results in regen-
eration of nicotinamide adenine dinucleotide (NAD+), which is required for continuation
of glycolysis. So, in anaerobic glycolysis 4 ATPs are generated, while 2 ATPs are used
up—hence, net yield is 2 ATPs. https://kat.cr/user/Blink99/
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Fig. 4.4: Glycolysis (ATP, adenosine triphosphate; ADP, adenosine diphosphate; NAD, nicotinamide adenine dinucleotide;
NADH, reduced nicotinamide adenine dinucleotide; H+, hydrogen ion)
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Energetics of glycolysis: The number of ATPs generated per molecule of glucose in aerobic

glycolysis is given in Table 4.1.
Table 4.1: Energetics of glycolysis (aerobic conditions)
Reaction Enzyme ATP formed (+) or utilized (–)

Glucose → Glucose- Hexokinase/glucokinase (–) 1 ATP
6-phosphate
Fructose-6-phosphate → Phosphofructokinase (–) 1 ATP
Fructose-1,6-bisphosphate
Glyceraldehyde-3-phosphate → Glyceraldehyde-3-phosphate dehy- (+) 5 ATP
1,3-bisphosphoglycerate drogenase
1,3-bisphosphoglycerate → 1,3-bisphosphoglycerate kinase (+) 2 ATP
3-phosphoglycerate
Phosphoenolpyruvate → Pyruvate kinase (+) 2 ATP
Pyruvate
Total 7 ATPs
(+) ATP, ATP yielding phase; (−) ATP, ATP investment phase.
3. Briefly write about the regulation of glycolysis.

Regulation of glycolysis is given in Table 4.2.

Table 4.2: Regulation of glycolysis
Key enzymes Activated by (+) Inhibited by (–)
Hexokinase Insulin, Glucagon,
Glucokinase AMP*, cAMP†, ATP,
Phosphofructokinase NAD+, NADH + H+,
Pyruvate kinase CoASH Acetyl-CoA,
Pyruvate dehydrogenase Citrate
*
AMP, adenosine monophosphate; cAMP, cyclic adenosine monophosphate.
†
4. What is substrate level phosphorylation? Give any three examples for it.

Substrate level phosphorylation is a process by which ATPs are formed directly without

going through electron transport chain. Examples for substrate level phosphorylation is
given in Table 4.3.
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Table 4.3: Substrate level phosphorylation

Reaction Enzyme ATP yield
1,3-bisphosphoglycerate → 3-phosphoglycerate 1,3-bisphosphoglycerate kinase 1 ATP

Phosphoenolpyruvate → pyruvate Pyruvate kinase 1 ATP
Succinyl-CoA → Succinate Succinate thiokinase 1 ATP
5. Enlist inhibitors of glycolysis.

Inhibitors of glycolysis is given in Table 4.4.
Table 4.4: Inhibitors of glycolysis
Inhibitor Enzyme inhibited Outcome
Fluoride Enolase Prevents glycolysis in RBCs—used during
blood collection for glucose estimation
Arsenic Pyruvate dehydrogenase Lactic acidosis
Iodoacetate Glyceraldehyde-3-phosphate dehydrogenase Block in glycolysis and ATP formation
6. Explain metabolic disorders associated with glycolysis.

Metabolic disorders and its causes are given in Table 4.5.
Table 4.5: Disorders of glycolysis
Disorders Causes
Lactic acidosis Diabetes mellitus, alcoholism, hypoxia, strenuous exercise, deficiency of pyruvate
dehydrogenase/pyruvate carboxylase/thiamine
Hemolytic anemia Deficiency of pyruvate kinase, hexokinase and aldolase A
Muscular hypotonia Deficiency of pyruvate dehydrogenase complex/muscle phosphofructokinase
Neuronal loss, fatigue –
7. What is BPG shunt (Rapoport-Luebering shunt)? What is its significance?

Bisphosphoglycerate (BPG) shunt pathway is shown in Figure 4.5.
• Site: Red blood cells (RBCs)
• Significance: Important regulator of oxygen affinity of hemoglobin. The levels of 2,3 BPG in
RBC is increased during hypoxia. It helps to release oxygen from hemoglobin especially
in cases of hypoxia or at high altitude, where oxygen saturation is less.
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Fig. 4.5: Bisphosphoglycerate (BPG) shunt
8. Write the reactions of tricarboxylic acid (TCA) cycle (Krebs cycle). Explain its energetics.

Definition: It is the final common pathway for the oxidation of carbohydrates, lipids and

proteins. It is the major pathway, which provides energy (Figs 4.6A and B).
• Site: All cells with mitochondria (except RBC)

• Subcellular site: Mitochondria

• Starting material: Acetyl-coenzyme A + Oxaloacetate

• End product: CO2 + H2O + ATP

• Coenzymes: NAD+, flavin adenine dinucleotide (FAD), guanosine diphosphate (GDP),

CoASH.
Fig. 4.6A: TCA cycle final common pathway
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Fig. 4.6B: Tricarboxylic acid cycle (TCA cycle)
• Energetics of TCA cycle is given in the Table 4.6.

Table 4.6: Energetics of TCA cycle
Reaction Enzyme ATP formed (+)
Isocitrate → α-ketoglutarate Isocitrate dehydrogenase (+) 2.5 ATPs
α-ketoglutarate → Succinyl-CoA α-ketoglutarate dehydrogenase (+) 2.5 ATPs
Contd...
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Contd...
Reaction Enzyme ATP formed (+)

Succinyl-CoA → Succinate Succinate thiokinase (+) 1 ATP
Succinate → Fumarate Succinate dehydrogenase (+) 1.5 ATPs

Malate → oxaloacetate Malate dehydrogenase (+) 2.5 ATPs
Total *10 ATPs
*Per molecule of acetyl-CoA
9. Write a short note on the regulation of TCA cycle.

Regulation of TCA cycle is given in Table 4.7.

Table 4.7: Regulation of TCA cycle
Key enzymes Inhibited by (–) Activated by (+)
Pyruvate dehydrogenase complex ATP, AMP, ADP,
Citrate synthase Citrate, CoASH,
Isocitrate dehydrogenase NADH + H+, NAD+,
α-ketoglutarate dehydrogenase Succinyl-CoA Ca2+
10. Enlist the inhibitors of TCA cycle.

List of inhibitors of TCA cycle are given in Table 4.8.

Table 4.8: Inhibitors of TCA cycle
Inhibitor Enzyme inhibited Type of inhibition
Fluoroacetate Aconitase Suicide inhibition
Arsenite α-ketoglutarate dehydrogenase Non-competitive inhibition
Malonate Succinate dehydrogenase Competitive inhibition
11. Explain the amphibolic role of TCA cycle.

Amphibolic means both anabolic and catabolic. TCA cycle, other than energy production

(catabolic), is also involved in providing raw materials for biosynthesis of various com-
pounds (anabolic). Examples are given in the Table 4.9.
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Table 4.9: Anabolic reactions of TCA cycle

Anabolic reactions Enzyme Use
Pyruvate → Oxaloacetate Pyruvate carboxylase Gluconeogenesis

Citrate → Acetyl-CoA → Malonyl-CoA Citrate lyase and acetyl-CoA carboxylase Fatty acid biosynthesis
α-ketoglutarate → Glutamate AST* and ALT †
Purine synthesis
Succinyl-CoA + glycine → ALA‡ ALA synthase Heme synthesis
Oxaloacetate → Aspartate AST Pyrimidine synthesis
*AST, aspartate aminotransferase; †ALT, alanine aminotransferase; ‡ALA, aminolevulinic acid.
12. What are the anaplerotic reactions of TCA cycle?

Since TCA cycle is both anabolic and catabolic, the intermediates of this cycle are used up
continuously. The reactions that can replenish these intermediates of TCA cycle are called
anaplerotic reactions (Table 4.10).
Table 4.10: Anaplerotic reactions of TCA cycle
Anaplerotic reactions Enzyme
Pyruvate + CO2 + ATP → Oxaloacetate Pyruvate carboxylase
Pyruvate + CO2 + NADPH → Malate Malic enzyme
Aspartate → Oxaloacetate Aspartate transaminase (AST)
Glutamate → α-ketoglutarate AST and alanine transaminase
13. Define gluconeogenesis. Write the reactions of this pathway.

Gluconeogenesis (Fig. 4.7) is the formation of glucose or glycogen from non-carbohydrate
precursors.
• Site: Liver, kidneys
• Subcellular site: Mitochondria and cytosol
• Starting material: Lactate, pyruvate, glucogenic amino acids, glycerol, propionyl-CoA
• End product: Glucose
• Coenzymes: Guanosine triphosphate (GTP), NADH, NAD+
• Energy requirement: To generate one molecule of glucose, 6 ATPs are required.
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Fig. 4.7: Gluconeogenesis (First reaction occurs in mitochondria and rest in the cytosol. Oxaloacetate formed inside the
mitochondria is transported to cytosol by malate shuttle) (PEPCK, phosphoenolpyruvate carboxykinase). Encircled are the
substrates for gluconeogenesis.
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Key Enzymes in Gluconeogenesis

• Pyruvate carboxylase: Pyruvate Oxaloacetate
• Phosphoenolpyruvate carboxykinase (PEPCK): Oxaloacetate Phosphoenol-

pyruvate (PEP)
• Fructose-1,6-bisphosphatase: Fructose-1,6-biphosphate Fructose-6-phosphate
• Glucose-6-phosphatase: Glucose-6-phosphate Glucose.
14. What is Cori cycle?
The process of conversion of lactate formed in the muscles (under anaerobic conditions) to
glucose in the liver, which is then converted to lactate in the muscle is called Cori cycle
(Fig. 4.8).
Fig. 4.8: Cori cycle
15. Explain the regulation of gluconeogenesis.

i. Allosteric regulation (Table 4.11).
Table 4.11: Allosteric regulation of gluconeogenesis
Key enzyme Inhibited by (−) Activated by (+)
Pyruvate carboxylase ADP, AMP, Citrate,
Phosphoenolpyruvate carboxykinase CoASH, Acetyl-CoA,
Fructose-1,6-bisphosphatase NAD+, insulin, NADH + H+,
Glucose-6-phosphatase Fructose-2,6-bisphosphate Anti-insulin hormones
ii. Regulation by compartmentalization.

First step of gluconeogenesis is inside mitochondria and rest of the steps are in cytosol.
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16. Mention the non-carbohydrate substrates for gluconeogenesis.
Non-carbohydrate substrates of gluconeogenesis is given in Table 4.12.

Table 4.12: Substrates of gluconeogenesis
Substrate Comment
Pyruvate and lactate They are the primary substrates for gluconeogenesis
Amino acids All except leucine and lysine
Propionate From odd chain fatty acids and amino acids like methionine, isoleucine, valine
Alanine During starvation, alanine released from muscles gets transaminated to pyruvate
Glycerol From triacylglycerol breakdown in adipose tissue
17. Write the reactions of glycogenolysis.

Definition: Breakdown of glycogen into glucose-1-phosphate (Figs 4.9 and 4.10).

Requirements
• Site: Liver, muscle, kidney, intestine, brain


• Starting material: Glycogen

• End product: Glucose-1-phosphate (liver, muscle) and glucose (liver)

• Key enzyme: Glycogen phosphorylase.

Fig. 4.9: Glycogenolysis
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Fig. 4.10: Steps in glycogenolysis
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18. Write the reactions of glycogenesis. Add a note on regulation of glycogen metabolism.

Definition: Synthesis of glycogen from glucose for storage in liver and muscle (Figs 4.11

and 4.12) is glycogenesis.
• Site: Liver, muscle

• Subcellular site: Cytosol—smooth endoplasmic reticulum


• End product: Glycogen

• Requirements: Glycogenin, glycogen primer, uridine triphosphate (UTP)

• Key enzyme: Glycogen synthase.

Glucose has to be converted to UDP-glucose. Glycogen is formed by addition of glucose

molecules on existing glycogenin to form a glycogen primer.
Fig. 4.11: Formation of UDP-glucose (UTP, uridine triphosphate; UDP, uridine diphosphate)
Regulation of glycogen metabolism: Hormones like glucagon, epinephrine and insulin

affect glycogen metabolism (Table 4.13, Figs 4.13A and B, p. 48).
• Regulatory enzyme in glycogenolysis: Glycogen phosphorylase

• Regulatory enzyme in glycogenesis: Glycogen synthase.

Table 4.13: Allosteric regulation of glycogen metabolism
Enzyme Activator Inhibitor
Glycogen synthase Glucose-6-phosphate –
Glycogen phosphorylase AMP (muscle isoform) Glucose-6-phosphate, ATP (mus-
cle and liver isoform)
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Fig. 4.12: Glycogen synthesis
19. Enlist the types of glycogen storage disorders with respective metabolic defects.
The types of glycogen storage disorders with respective metabolic defects are given in
Table 4.14.
Table 4.14: Glycogen storage disorders
Disorder Enzyme defect Clinical features
Von Gierke (type I) Glucose-6-phosphatase Hepatomegaly, fasting hypoglycemia, lactic
acidosis, hyperuricemia, ketosis
Pompe's disease (type II) 1,4-glucosidase Cardiomegaly and early death
Cori's disease (type III) Debranching enzyme Hepatomegaly, hypoglycemia
Anderson's disease (type IV) Branching enzyme Hepatomegaly, cirrhosis of liver, early death due
to liver and heart failure
McArdle's disease (type V) Muscle phosphorylase Muscle glycogen is high, exercise intolerance
Hers' disease (type VI) Liver phosphorylase Hepatomegaly, hypoglycemia
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Fig. 4.13A: Regulation of glycogenolysis
Fig. 4.13B: Regulation of glycogenesis
20. Write the reactions of pentose phosphate pathway (HMP shunt/direct oxidative pathway).

Add a note on its significance.
Definition: Alternative pathway for glucose metabolism with production of NADPH and

pentose sugars (Fig. 4.14). https://kat.cr/user/Blink99/
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Fig. 4.14: Hexose monophosphate shunt
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• Site: RBC, liver, intestine, lens, adrenal cortex, adipose tissue, gonads



• End products: Pentose sugar and NADPH

• Coenzymes: NADP, thiamine pyrophosphate (TPP)

• Cofactor: Magnesium ion (Mg2+)

• Regulatory enzyme: Glucose-6-phosphate dehydrogenase.

i. Allosteric regulation (Table 4.15).

ii. Hormonal regulation: Insulin induces glucose-6-phosphate dehydrogenase.

Table 4.15: Allosteric mode of regulation
Enzyme Activator Inhibitor
Glucose-6-phosphate dehydrogenase NADP+ NADPH
Significance:

• NADPH generated is required for synthesis of fatty acids, cholesterol, steroid hormones

• It also helps to maintain glutathione in reduced state, which is required for integrity of

RBC membrane
• NADPH also helps in detoxification of drugs (CYP450 of liver)

• WBC depends on NADPH (NADPH oxidase) for killing of bacteria

• Ribose-5-phosphate is required for synthesis of nucleotides and nucleic acids.

21. Discuss the metabolic defects of HMP shunt.
Glucose-6-phosphate Dehydrogenase (G6PD) Deficiency

• Defect: X-linked recessive disorder characterized by hemolytic anemia (Fig. 4.15)

• Clinical features: Hemolytic anemia, jaundice.

Precipitating Conditions
• Drugs [MN: AAA]: Antimalarial—primaquine, Antibiotic—sulfonamides and Antipyret-

ic—paracetamol
• Fava beans (favism): When a patient with G6PD deficiency consumes fava beans, he/she

develops hemolysis, jaundice, hemoglobinuria, pallor, etc.
• Infections.

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Fig. 4.15: Mechanism of hemolysis in G6PD deficiency
Thiamine Deficiency (Beriberi)

Thiamine deficiency results in decreased RBC transketolase activity leading to decreased NADPH
production.
• Clinical features: Hemolytic anemia and features of beriberi
• Treatment: Supplementation of thiamine.
Wernicke-Korsakoff Syndrome
Wernicke-Korsakoff syndrome occurs due to deficiency of thiamine (required for transketolase)
in alcoholics or decreased affinity of enzyme transketolase (of HMP pathway) for thiamine.
• Clinical features: Psychosis (encephalopathy), ataxia, ophthalmoplegia, nystagmus, etc.
• Treatment: Supplementation of thiamine.
22. Enlist the metabolic disorders associated with fructose and galactose metabolism.
Metabolic disorders associated with fructose and galactose metabolism are listed in
Table 4.16.
Table 4.16: Metabolic disorders of fructose and galactose
Name of disorder Enzyme defect Comment
Essential fructosuria Fructokinase Benign metabolic disorder, no treatment required
Hereditary fructose in- Aldolase B Lethal disorder associated with hypoglycemia, vomiting,
tolerance hepatomegaly, hyperlipidemia, etc.
Avoidance of fructose in diet
Contd...
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Contd...
Name of disorder Enzyme defect Comment

Galactosemia Galactose-1-phosphate Lethal; symptoms same as above, there will be associ-
uridyltransferase ated mental retardation and congenital cataract; avoid-
(classical)
ance of lactose in diet till age of 5 years
Galactosemia Galactokinase Benign disorder; does not require any treatment
(non-classical)
23. What is the significance of uronic acid pathway? What is the metabolic disorder associ-

ated with glucuronic acid pathway.
Definition: Alternative pathway for glucose oxidation.

Significance:

• Synthesis of UDP-glucuronic acid: For detoxification; synthesis of glycosaminoglycans

(heparin, hyaluronic acid, dermatan sulfate)
• Synthesis of UDP-glucose: For synthesis of glycogen, lactose and galactose

• Synthesis of ascorbic acid: In lower animals. Ascorbic acid is not synthesized in humans

due to lack of enzyme L-gulonolactone oxidase.
Metabolic Disorder
Essential Pentosuria
Benign disorder in glucuronic acid pathway due to deficiency of enzyme xylitol dehydrogenase.
24. Explain regulation of blood glucose level.

Regulation of blood glucose level is given in Table 4.17.

Net effect of insulin is decrease in blood glucose level; glucagon and anti-insulin hor-

mones increase blood glucose level.
Table 4.17: Regulation of blood glucose
Biochemical pathway Stimulated by (+) Inhibited by (–)
• Glycolysis Insulin Glucagon,
• Glycogenesis Adrenal hormones,
• Lipogenesis Thyroid hormones,
• Protein biosynthesis Anterior pituitary hormones
• Ketogenesis Glucagon, Insulin
• Lipolysis Adrenal hormones,
• Gluconeogenesis Thyroid hormones,
• Glycogenolysis Anterior pituitary hormones
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25. List the actions of insulin and glucagon.
Actions of Insulin (Fig. 4.16)

Fig. 4.16: Actions of insulin [(+), stimulates]
Actions of Glucagon (Fig. 4.17)
Fig. 4.17: Actions of glucagon [↓, decrease; (+), stimulates]
26. Define hypoglycemia and hyperglycemia. Mention some causes for the same.
Hypoglycemia
When plasma glucose level is less than 40 mg/dL.
Causes
• Prolonged fasting
• Alcoholism
• Overdose of insulin
• Insulinoma (insulin-secreting tumor)
• Hypoactivity of anti-insulin hormones.
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Hyperglycemia
When a person's fasting glucose is greater than 100 mg/dL and postprandial glucose greater
than 140 mg/dL, then it is called hyperglycemia.
Causes
• Diabetes mellitus: Decreased insulin production/action [fasting plasma glucose (FPG) >

126 mg/dL or postprandial plasma glucose (PPG) > 200 mg/dL or random plasma glucose
(RPG) > 200 mg/dL with signs and symptoms of hyperglycemia]
• Hyperactivity of anti-insulin hormones

• Glucagonoma

• Prolonged treatment with steroid hormones.

27. Define diabetes mellitus. Add a note on types and clinical features of the same.
Definition: It is a metabolic disease leading to hyperglycemia due to absolute or relative

insulin deficiency. The classification of diabetes is given in Table 4.18.
Table 4.18: Classification of diabetes mellitus
Type I Type II
Juvenile diabetes Adult onset diabetes
Due to lack of insulin Due to insulin resistance or relative deficiency of insulin
5%–10% of all diabetics fall under this category 90%–95% of all diabetics fall under this category
Common complications: Ketosis Common complications: Non-ketotic hyperosmolar coma
Clinical Features
• Excessive thirst (polydipsia)

• Frequent urination (polyuria)

• Extreme hunger or constant eating (polyphagia)

• Unexplained weight loss

• Presence of glucose in urine (glycosuria)

• Tiredness or fatigue.

Diagnosis (WHO Criteria)
• Fasting plasma glucose > 126 mg/dL OR

• Postprandial plasma glucose > 200 mg/dL OR

• Random plasma glucose > 200 mg/dL with signs and symptoms of hyperglycemia.

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Complications
• Diabetic retinopathy
• Diabetic neuropathy

• Diabetic nephropathy
• Atherosclerosis and coronary artery disease
• Gangrene of foot
• Ketoacidosis.
Treatment
• Diet regulation
• Exercise
• Antidiabetic agents: Insulin, sulfonylureas, biguanides, etc.
Key Points
Reducing substances in urine: Glucose, fructose, lactose, galactose, pentose, homogentisic acid,
salicylates, ascorbic acid and glucuronides of drugs.
Maturity-onset diabetes of young (MODY): There is a mutation in pancreatic glucokinase, which
has decreased Km and Vmax for glucose. This results in decreased release of insulin from pan-
creas. Interestingly, however, these patients are somewhat resistant to long-term complications
of chronic hyperglycemia.
Fructose intake can lead to obesity: Fructose enters glycolysis by phosphorylation to fructose-
1-phosphate and it bypasses the main regulatory step (hexokinase), resulting in formation of more
pyruvate (and acetyl-CoA) than is required for ATP formation. Also, there is increased availability
of dihydroxyacetone phosphate (DHAP), which generates glycerol-3-phosphate, a starting material
for triacylglycerol formation in the liver and adipose tissue, leading to increased lipogenesis.
Aldolase A: Present in most tissues, but aldolase B is present in liver and kidney.
2,3-BPG: Its concentration decreases in stored blood in blood bank and such blood may become
unsuitable for transfusion. This can be prevented by adding inosine to the blood.
Arsenate will not block glycolysis: It can substitute phosphate in the reaction by glyceraldehyde-
3-phosphate dehydrogenase forming highly unstable 1-arseno-3-phosphoglycerate, which readily
hydrolyses to form 3-phosphoglycerate.
Arsenite (trivalent): Works by forming a stable complex with enzyme-bound lipoic acid. Thus, it
can inhibit pyruvate dehydrogenase, α-ketoglutarate dehydrogenase and branched chain α-ketoacid
dehydrogenase. Arsenic was commonly used as a homicidal poison as it is a colorless, odorless
and tasteless compound. Chronic arsenic poisoning can be diagnosed by finding the compound in
hairs and finger nails of the victim.
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Enolase is inhibited by fluoride: When blood samples are taken for measurement of glucose, it is

collected in tubes containing fluoride to inhibit glycolysis. Fluoride binds with Pi to form fluorophos-
phates, which binds with Mg2+ bound enzyme and prevents the formation of metal bridge enzyme-
substrate-complex (E-M-S).
Iodoacetate: Is an alkylating agent, which acts on cysteine residues in proteins. It is often used to

modify SH-groups to prevent the reformation of disulfide bonds. It binds covalently and alkylates SH
groups of enzymes and prevents enzyme-substrate complex formation (irreversible).
Benefit of G6PD deficiency: It protects the person against falciparum malaria. Malaria parasite

requires reduced glutathione (GSH) and the products of the pentose phosphate pathway for survival,
and is unable to complete the life cycle due to early lysis of RBCs.
Succinate thiokinase (succinyl-CoA synthetase): This is the only example of substrate level

phosphorylation in the citric acid cycle.
Succinate dehydrogenase: This is bound to the inner surface of the inner mitochondrial membrane.

Alcohol ingestion can lead to hypoglycemia: Alcohol metabolism generates NADH, which converts

oxaloacetate to malate. So, oxaloacetate (an initial raw material required for gluconeogenesis) is
depleted leading to hypoglycemia.
Cancer cachexia: Conversion of lactate (formed in large amount in cancer cells) to glucose in the

liver requires 6 ATPs, which is responsible for much of the hypermetabolism and weight loss seen
in cancer cachexia.
Hereditary fructose intolerance (HFI): The most common defect is a single missense mutation

in exon 5 (G → C), resulting in an amino acid substitution (alanine → proline). As a result of this
substitution, a catalytically impaired aldolase B is synthesized.
Secondary diabetes: May be due to endocrinopathies, Cushing's syndrome, thyrotoxicosis, acro-

megaly or drug induced (steroids), pancreatitis.
Glycated Hb (HbA1c): For every 60 mg/dL rise in blood glucose level, approximately there is a rise

of HbA1c by 2%. Glycated Hb levels indicate average blood glucose levels during past 1–4 months
period. 4%–7% is considered as normal range for this parameter.
Fructosamine (glycated albumin): Provide average blood glucose levels during past 1–3 weeks.

Neotame: Is an artificial sweetener that is between 8,000 and 13,000 times sweeter than sucrose.

Sucralose: Is an artificial sweetener that is approximately 600 times sweeter than sucrose.

Glycogen has highly branched structure: It provides a large number of sites (non-reducing ends)

for glycogenolysis (glycogen phosphorylase), permitting rapid release of glucose.
Diabetic Prone States

Gestational diabetes mellitus (GDM): Pregnant woman having abnormal glucose tolerance, which

resolves after delivery. These patients are at high risk of developing frank diabetes.
Impaired glucose tolerance (IGT): In this condition, fasting blood glucose is more than 100 and

less than 126 mg/dL; postprandial blood glucose is more than 140 and less than 200 mg/dL.
Impaired fasting glycemia (IFG): In this condition, fasting glucose is more than 100 and less than

126 mg/dL, but postprandial sugar is within normal limits (< 140 mg/dL).

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5 Chemistry of Lipids
1. Define and classify lipids with suitable examples.

Definition: Lipids are organic substances, relatively insoluble in water and soluble in
organic solvents like alcohol, ether, etc. They are mainly compounds of C, H and O, but
also carry P, N and S in some cases.
Classification
Lipids are classified (Fig. 5.1) as following.
Fig. 5.1: Classification of lipids
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a. Simple lipids: Esters of fatty acid with alcohol.

• Fats or oils (triacylglycerol): Esters of fatty acids with glycerol

• Waxes: Esters of fatty acids with long-chain aliphatic alcohols other than glycerol, e.g.

cetyl alcohol. These are solid at room temperature.
b. Compound lipids: Esters of fatty acids with alcohol, carrying additional groups such as

phosphate and nitrogenous group or carbohydrate. Compound lipids are of two types:
• Phospholipids: For example, glycerophospholipids, sphingophospholipids

• Glycolipids: For example, cerebrosides, sulfatides, gangliosides, globosides.

c. Complex lipids: For example, lipoproteins—very low density lipoprotein (VLDL), low

density lipoprotein (LDL), high density lipoprotein (HDL) and chylomicrons.
d. Derived lipids: Obtained by hydrolysis of simple or compound lipids. For example, steroids

(cholesterol), prostaglandins, leukotrienes, etc.
Chemistry of Lipids
2. Give a brief account of functions of lipids.

• Source of energy

• Concentrated fuel reserve (adipose tissue)

• Constituent of membranes and regulate membrane permeability. For example, phospho-

lipids, glycolipids, lipoproteins and sterols
• As compounds of inner mitochondrial membrane, lipids participate in electron transport chain

• Phospholipids, glycolipids and sterols are constituents of plasma lipoprotein, which trans-

port fat
• Source of fat-soluble vitamins and bile acids

• Metabolic regulators—steroid hormones and prostaglandins

• Protect internal organs, serve as insulating materials.

3. Define and classify fatty acids.
Definition: Fatty acids are monocarboxylic acids with hydrocarbon side chain. They are
simplest form of lipids.
C
lassification
a. Depending on nature of hydrocarbon chain

• Saturated fatty acids: Do not contain double bonds in their hydrocarbon chain, e.g. palmitic

and stearic acid
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• Unsaturated fatty acids: Contain one (monounsaturated) or more (polyunsaturated) double bonds
in their hydrocarbon chain, e.g. oleic acid, linoleic acid, linolenic acid, arachidonic acid.
b. Depending on number of carbon atoms
• Even-chain fatty acids: Natural lipids with even number of carbon atoms in their chain,
e.g. palmitic acid (16), stearic acid (18)
• Odd-chain fatty acids: Propionic acid (3C) and valeric acid (5C).
c. Depending upon length of hydrocarbon chain of fatty acid
• Short-chain fatty acids: Chain contains six or less than six carbons, e.g. propionic acid,
butyric acid, etc.
• Medium-chain fatty acids: Chain contains 8–14 carbons, e.g. caprylic acid, myristic acid, etc.
• Long-chain fatty acids: Chain contains 16–22 carbons, e.g. palmitic acid, stearic acid, etc.
Chemistry of Lipids
d. Depending upon nutritional importance
• Essential fatty acids: Not synthesized in the body, therefore should be taken in the diet,
e.g. linoleic acid, linolenic acid and arachidonic acid
• Non-essential fatty acids: These can be synthesized in the body, e.g. palmitic acid, stearic
acid, etc.
4. Write a short note on essential fatty acids.
The essential fatty acids (EFA) are those which cannot be synthesized by the body, hence they
should be supplied in the diet. Chemically, they are polyunsaturated fatty acids (PUFA).
Biochemical basis for essentiality: Linoleic and linolenic acids are essential fatty acids—
humans lack the enzymes that can introduce double bonds beyond carbon 9 of fatty acids.
Functions of essential fatty acids: It is required for the following:
• Membrane structure and function
• Transport of cholesterol
• Formation of lipoproteins
• Synthesis of eicosanoids—prostaglandins, thromboxane, leukotrienes
• Protective effect against fatty liver.
Deficiency of EFA: The deficiency of EFA results in phrynoderma, hair loss and poor
wound healing.
5. What are the types of rancidity? How can it be prevented?
Definition of rancidity: It is the deterioration of fats and oils resulting in unpleasant taste
and smell.
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Types of rancidity

• Hydrolytic rancidity: Due to bacterial hydrolytic enzymes, which results in the formation of short-

chain fatty acids. It can be prevented by heat deactivation, proper handling and storage
• Oxidative rancidity: It is due to oxidation of fat by free radicals resulting in formation of
compounds such as dicarboxylic acids, aldehydes, ketones, etc.
Prevention: By antioxidants, e.g. tocopherol, hydroquinone, gallic acid and food preserva-

tives like butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), etc.
6. Define iodine number. Mention its significance.
Definition: Iodine number is defined as number of grams of iodine absorbed by 100 g of
fat. A higher iodine number indicates greater number of double bonds.
Significance: It measures average degree of unsaturation, so it is useful in detecting adul-
Chemistry of Lipids

teration of polyunsaturated fatty acid (PUFA) with saturated fatty acid. For example, iodine
number of coconut oil is 6–10 and sunflower oil is 141–155.
7. Define and write the significance of saponification number.
Definition: The number of milligrams (mg) of potassium hydroxide (KOH) required to

saponify 1 g of fat is saponification number.
Significance: It measures the average molecular weight of fat.
8. Define and classify phospholipids. Write its compositions and one example for each class.
Definition: Phospholipids are lipids containing phosphoric acid + fatty acids + alcohol

± nitrogenous base. They contain both polar and non-polar groups and are called am-
phipathic lipids.
Classification
Glycerophospholipids: Contain glycerol as alcohol (Table 5.1).
Table 5.1: Composition of individual phospholipids
Name Composition Function
Lecithin Glycerol + fatty acids + phosphoric • Membrane component, nerve transmission
acid + choline • Source of choline and methyl group
Dipalmitoyl lecithin Glycerol + palmitic acid (2) + phos- • Lung surfactant
phoric acid + choline • Deficiency causes respiratory distress
syndrome
Contd...
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Contd...
Name Composition Function

Cephalin Glycerol + fatty acids + phosphoric acid • Structural component of membranes
+ ethanolamine
Plasmalogens Alcohol + fatty acids + phosphoric acid • Structural component of membranes in
+ nitrogenous base + glycerol brain and muscle
Platelet-activating Contains alkyl linkage in first carbon of • Mediator of hypersensitivity, acute inflam-
factor glycerol. Second carbon contains acetyl matory reactions and anaphylactic shock
group. Third carbon is attached with
phosphate group to choline.
Cardiolipin Phosphatidic acid + glycerol + phos- • Component of inner mitochondrial mem-
phatidic acid brane has antigenic properties
Chemistry of Lipids
Phosphatidylinositol Glycerol + fatty acids + phosphate + • Phosphatidylinositol 4, 5-bisphosphate is
inositol second messenger for hormone action
• Anchors the glycoproteins to membranes
Sphingophospholipids: Contain sphingosine as alcohol.
• For example, sphingomyelins—major component of membranes of nervous tissue
• Composition: Ceramide (sphingosine + fatty acid) + phosphoric acid + choline
• Niemann-Pick disease: Due to excessive accumulation of sphingomyelin as a result of
deficiency of enzyme sphingomyelinase.
Functions of Phospholipids
• Constituent of cell membrane, myelin sheath
• Constituent of surfactant (dipalmitoyl lecithin) in lungs
• Second messenger (phosphatidylinositol)
• Source of arachidonic acid—for prostaglandin synthesis
• Components of lipoproteins (transport of lipids)
• Absorption of fat from the intestine (micelles and chylomicrons)
• Acts as lipotropic factor and prevents fatty liver
• Responsible for maintaining the conformation of electron transport chain in mitochondria.
9. Mention the composition of glycolipids and give examples.
Definition: Glycolipids are carbohydrates—lipid complexes having amphipathic nature.
They are the important components of cell membrane and nervous tissue.
Composition: Ceramide (sphingosine + fatty acid) + carbohydrate. Do not have phos-
phoric acid.
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Classification: Depending on the nature of attached carbohydrate chain.
Cerebrosides: Galactocerebroside (ceramide + galactose).

Sulfatides: Ceramide + galactose + sulfate.

Globosides: Ceramide + more than one hexose or hexosamine.

Gangliosides: Ceramide + oligosaccharides + NANA (N-acetylneuraminic acid).
10. What are prostaglandins? Mention their functions.

Definition: Unsaturated hydroxyl and ketosubstituted C20 fatty acids (Table 5.2).

Synthesis: Formed from arachidonic acid by cyclooxygenase pathway.
Significance: Act as local hormones and mediators of inflammation. Non-steroidal anti-
inflammatory drugs (NSAIDs) like aspirin, are the inhibitors of cyclooxygenase.
Chemistry of Lipids
Table 5.2: Functions of prostaglandins

Compounds Functions
PGE2 • Mediator of pain and fever

• Vasodilatation, relaxation of smooth muscle

PGF2α • Used for induction of labor

• Vasoconstriction

• Contraction of uterine smooth muscle

PGE1 • Decreases gastric acid secretion

PGI2 • Produced by endothelium of vessels

• Vasodilatation

• Inhibits platelet aggregation

TXA2 • Produced by platelets

• Platelet aggregation

• Vasoconstriction

PG, prostaglandin; PGI, prostacyclin; TX, thromboxane.
11. Mention four biological functions of cholesterol.

Functions
• Constituent of cell membrane

• Formation of bile salts (liver)

• Synthesis of steroid hormones (cortisol, aldosterone, testosterone, estrogen, progesterone)

• Precursor of vitamin D.

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12. What is the name of cholesterol ring? Mention the compounds derived from cholesterol.
• Name of the ring: Cyclopentanoperhydrophenanthrene ring
• Compounds derived from cholesterol: Vitamin D3, bile acids, testosterone, estrogens,
cortisol and aldosterone.
Key Points
Essential fatty acids: Linoleic, linolenic, arachidonic acid.

Trans fatty acids: They are found in partially hydrogenated vegetable oils and increase the risk of

atherosclerosis and cancer.
Omega-6 fatty acids: Linoleic and arachidonic acid.

Omega-3 fatty acids: Linolenic acid. High levels of omega-6 fatty acids and low omega-3 fatty acids

can lead to atherosclerosis and cancer.
Chemistry of Lipids
Iodine number: Used for detection of adulteration of unsaturated fat with saturated fat.

Saponification number: Used for measure of average molecular weight of fat.

Palmitic acid: Most common saturated fatty acid in diet; metabolized in the body.

Rancidity: Deterioration of oils and fat resulting in an unpleasant smell.

Food preservatives: Butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT).

Dipalmitoyl lecithin: Lung surfactant. Deficiency causes respiratory distress syndrome.

Phosphatidylinositol 4, 5 bisphosphate: Acts as a second messenger in hormone action.

Niemann-Pick disease: Due to deficiency of sphingomyelinase.

Arachidonic acid: Acts as a source for synthesis of prostaglandins.

Choline: Lipotropic factor and prevents fatty liver.

PGE2: Used for dilatation of cervix during labor.

PGF2α: Induction of labor by uterine contraction.

Aspirin and NSAIDs: Inhibitors of cyclooxygenase; used as anti-inflammatory and analgesic agents.

Steroids: Block the enzyme phospholipase A2—prevent the release of arachidonic acid, hence act

as anti-inflammatory agents.
LDL: Increases the risk of atherosclerosis.

HDL: Decreases the risk of atherosclerosis.

Cholesterol: Normal serum level is 140–200 mg/dL. Vitamin D3, bile acid, steroid hormone (cortisol,

testosterone and estrogens) are derived from cholesterol.
Leukotrienes: Formed from arachidonic acid by lipo-oxygenase pathway. They mediate chemotaxis,

allergy and inflammation. They are components of slow reacting substance of anaphylaxis.
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6 Metabolism of Lipids
1. How are lipids in our diet digested and absorbed in gastrointestinal tract?

Digestion of lipids is a process by which there is breakdown of large and complex lipid

molecules into smaller and relatively water-soluble molecules, which can be easily absorbed
by the gastrointestinal (GI) tract.

Sources of lipids in diet: Meat, animal fat, butter, milk, cheese, egg yolk, cooking oil and

ghee. About 20%–30% of total energy is obtained in the form of lipids.
Starting materials and end products of lipid digestion are given in Table 6.1.

Table 6.1: Starting materials and end products of lipid digestion
Starting material End product
Triglycerides Free fatty acids + 2-monoacylglycerols
Cholesterol esters Free cholesterol + free fatty acids
Phospholipids Free fatty acids + lysophospholipid
Digestion and Absorption of Lipids

In the mouth: Due to lack of favorable conditions, minimal digestion of lipid occurs in the
mouth. Lingual lipase acts on short-chain triglycerides.
In the stomach: In humans, initiation of fat digestion occurs in stomach with mechanical emul-
sification followed by the action of gastric lipase. Gastric lipase hydrolyzes dietary triglycerides
containing medium- and short-chain fatty acids (SCFAs) into diacylglycerol and free fatty acids.
In infants and patients with pancreatic insufficiency, gastric lipases play an important role in
fat digestion. Lingual lipase also acts in the stomach on short-chain triglycerides.
In the intestine: Bile salts (sodium and potassium salts of glycocholic and taurocholic acids)
form emulsions with lipids by reducing the surface tension.
Digestion, absorption, transport of lipids in small intestine: Small intestine is the major site of lipid
digestion due to pancreatic lipase—ithttps://kat.cr/user/Blink99/
requires colipase and bile salts for its activity (Fig. 6.1).

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Digestion, Absorption and Metabolism of Lipids

Fig. 6.1: Digestion, absorption and transport of lipids (FA, fatty acid)
Long-chain fatty acids are re-esterified in the intestinal cell to triglycerides. Short-chain fatty
acids directly enter into the blood vessels.
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Hormonal Control of Lipid Digestion
Cholecystokinin: It is a peptide secreted by duodenal and jejunal mucosal cells; secreted in re-
sponse to lipids in duodenum. It acts on gallbladder to release bile and on pancreas to release
pancreatic lipase and other enzymes.
Secretin: It stimulates pancreas to release bicarbonate, thereby helps to neutralize acidic pH.
Utilization of Lipids
• Chylomicrons in the circulation is acted upon by lipoprotein lipase and forms free fatty

acids, glycerol + chylomicron remnants
• Free fatty acids are taken up by tissues for energy or stored in the adipose tissue

• Glycerol is converted to glycerol phosphate in liver and used for lipid storage or it can

enter into glycolysis or gluconeogenesis
• Chylomicron remnants are taken up by liver and metabolized.

2. Explain β-oxidation of saturated fatty acids (or palmitic acid) under following headings:

a. Oxidation. b. Energetics.
Definition: b-oxidation is defined as oxidation of fatty acids in which two carbon fragments

are successively removed at 'b' position from the carboxyl end.
Requirements for β-oxidation

Site: Mitochondria of all cells in the body.
Starting material: Fatty acids, mobilized from adipose tissues (lipolysis) by glucagon-mediated
activation of enzyme hormone sensitive lipase. Activated lipase converts the triacylglycerol
into free fatty acids and glycerol. Glycerol enters into gluconeogenesis.
End products: Acetyl-CoA, NADH and FADH2.
Coenzymes: NAD+ and FAD.
Steps in β-oxidation
a. Activation of fatty acids into fatty acyl-CoA in the cytosol of cell.

Thiokinase

Fatty acid + ATP + CoA Fatty acyl-CoA + PPi + AMP

b. Transport of fatty acyl-CoA from cytosol to mitochondria is carried out by carnitine shuttle.

Long-chain fatty acids (LCFA) cannot cross mitochondrial membrane, hence they need
transport system. Carnitine transports LCFA through inner mitochondrial membrane.
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c. β-oxidation involves four steps (Fig. 6.2):

• Oxidation
• Hydration
• Oxidation
• Cleavage.

Fig. 6.2: β-oxidation of fatty acids
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Energetics in β-oxidation
Palmitic acid (16C) undergoes seven cycles of -oxidation to produce:
β
8 acetyl-CoA → TCA cycle → 10 ATP × 8 = +80 ATP
7 FADH2 → ETC → 1.5 ATP × 7 = +10.5 ATP
7 NADH → ETC → 2.5 ATP × 7 = +17.5 ATP.
Total = 108 ATPs.

Activation of fatty acid = -2 ATP.
Net ATP yield = 108 - 2 = 106.
Net ATP production on complete oxidation of palmitic acid is 106 ATP.
Regulation of β-oxidation

Energy status: In well-fed state, β-oxidation is blocked and fatty acid synthesis is active. Dur-
ing starvation, β-oxidation is active and fatty acid synthesis is blocked.
Hormones: Insulin stimulates lipogenesis and blocks lipolysis, whereas glucagon stimulates
lipolysis and blocks lipogenesis.
Malonyl-CoA (precursor for fatty acid synthesis): It blocks the entry of fatty acids from cytosol
to mitochondria by inhibiting carnitine palmitoyltransferase I.
3. Write briefly on oxidation of odd-chain fatty acids.
Oxidation of odd-chain fatty acid: It gives acetyl-CoA (depending on number of carbons

in the fatty acid), one propionyl-CoA, NADH and FADH2 as end products. Propionyl-CoA
enters into tricarboxylic acid (TCA) cycle after being converted into succinyl-CoA.
For example: Valeric acid is a fatty acid containing 5 carbons. It undergoes 1 cycle of

β-oxidation producing 1 acetyl-CoA + 1 propionyl-CoA.
Fate of acetyl-CoA: Enters into TCA cycle and generates 10 ATPs.

Fate of propionyl-CoA: Enters into TCA cycle as a precursor for gluconeogenesis after

getting converted into succinyl-CoA (Fig. 6.3).
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Fig. 6.3: Fate of propionyl-coenzyme A (TCA, tricarboxylic acid)
4. Briefly mention the disorders associated with oxidation of fatty acids.

Disorders associated with oxidation of fatty acids and their clinical features are given in
Table 6.2.
Table 6.2: Disorders of fatty acid oxidation
Disorder Defect Clinical features
Carnitine deficiency CPT-I and CPT-II deficiency • Severe hypoglycemia
• If not treated, coma and death
Zellweger's syndrome Deficiency of peroxisomes • Severe neurological symptoms
Dicarboxylic aciduria Medium-chain acyl-CoA dehydro- • Hypoglycemia, acidosis
genase
Jamaican vomiting sick- Consumption of unripe ackee fruit, • Hypoglycemia and excretion of medi-
ness which contain toxin hypoglycin that um- and short-chain dicarboxylic acids
inhibits acyl-CoA dehydrogenase in urine
CPT, carnitine palmitoyltransferase
5. Describe the de novo synthesis of fatty acids. Add a note on role of citrate in this process.
Definition: Defined as synthesis of palmitate from acetyl-CoA in the cytosol.
Site: Liver, kidney, brain, mammary gland, adipose tissue.
Cellular site: Cytosol.
Coenzymes/cofactors: NADPH (from HMP shunt), ATP, manganese, biotin, HCO3-.
Starting material: Acetyl-CoA.
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End product: Palmitate.

Enzyme: Fatty acid synthase complex (Fig. 6.4), which is a dimer with seven enzymes and

acyl carrier protein on each subunit.
Fig. 6.4: Fatty acid synthase complex (A = condensing unit; B = reduction unit; C = releasing unit; oblique line shows
arbitrary division between individual units of the dimer; ACP, acyl carrier protein).
Steps in the synthesis of fatty acids (Figs 6.5 and 6.6)

• Transport of acetyl-CoA from mitochondria to cytosol (as citrate)

Role of citrate: cetyl-CoA is formed by pyruvate in the mitochondria and transferred to

a
the site of synthesis (cytosol) after getting converted into citrate (Fig. 6.5).
Fig. 6.5: Transport of acetyl-CoA from mitochondria to cytosol (1 = pyruvate dehydrogenase; 2 = citrate synthase)
• Formation of malonyl-CoA

Acetyl-CoA carboxylase

Acetyl-CoA Malonyl-CoA
CO2, biotin, ATP


Ch-06.indd 70 21-06-2014 11:50:00

Fig. 6.6: Synthesis of fatty acid
To synthesize one molecule of palmitate: 1 acetyl-CoA + 7 malonyl-CoA + 14 NADPH +

14 H+ is required. Regulation of fatty acid synthesis is given in Table 6.3.
Table 6.3: Regulation of fatty acid synthesis
Enzymes Activator Inhibitor
Acetyl-CoA carboxylase Citrate, insulin Acyl-CoA, glucagon
Carnitine palmitoyltransferase I – Malonyl-CoA
6. How are ketone bodies formed and utilized in our body? Add a note on ketosis.
Definition: Ketone body metabolism occurs during the high rates of fatty acid oxidation,
primarily in the liver. The large amount of acetyl-CoA generated, which exceeds the capacity
of the TCA cycle, results in the synthesis of ketone bodies (ketogenesis). Ketone bodies are
acetoacetate, β-hydroxybutyrate and acetone (Fig. 6.7).
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Site: Liver.

Subcellular site: Mitochondria.


End products: Acetoacetate, -hydroxybutyrate and acetone.

β
Coenzymes: NADH, Coenzyme A (CoASH).

Fig. 6.7: Ketogenesis (ATP, adenosine triphosphate; CoA, coenzyme A)
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Transport: Ketone bodies are transported through the blood into peripheral tissues and
metabolized.
Utilization of ketone bodies (ketolysis): Enzyme thiophorase is present in all tissues
except the liver, so liver cannot utilize ketone bodies. Utilization of ketone bodies is
shown in Figure 6.8 and regulation of ketogenesis is given in Table 6.4.

Fig. 6.8: Utilization of ketone bodies (NADH, nicotinamide adenine dinucleotide (reduced); TCA, tricarboxylic acid)
Table 6.4: Regulation of ketogenesis

Inhibitor Stimulator
Acyl-CoA, malonyl-CoA Glucagon
Insulin
Ketosis: Elevated ketone bodies in the blood (ketonemia), which gets excreted in urine
(ketonuria).
Causes: The following are the causes of ketosis:
a. Diabetic ketoacidosis.
b. Prolonged starvation.
Mechanism of ketosis: The mechanism of ketosis is shown in Figure 6.9.
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Fig. 6.9: Mechanism of ketosis
7. Outline the pathway for synthesis of cholesterol. What is its importance?

Definition: Cholesterol is an animal sterol present in tissues and lipoproteins in either

esterified or free form. Cholesterol is a 27 carbon compound having cyclopentanoperhy-
drophenanthrene ring.

End product: Cholesterol.

Site: Liver, adrenal gland and gonads.

Subcellular site: Cytosol.

Coenzymes: NADPH and ATP.

Steps in cholesterol synthesis

Biosynthesis of cholesterol is shown in Figure 6.10.

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Fig. 6.10: Biosynthesis of cholesterol (- = inhibition)
Regulation of cholesterol synthesis

HMG-CoA reductase: It is rate limiting enzyme, which is inhibited by high cholesterol levels
and stimulated by low cholesterol levels (at gene level).
Hormonal regulation: Insulin and thyroxine increase cholesterol synthesis. Glucagon and
glucocorticoids decrease cholesterol synthesis.
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Drugs: Statins, competitive inhibitors of HMG-CoA reductase, are used in the treatment of

hypercholesterolemia, e.g. Lovastatin, simvastatin, atorvastatin.
Bile acids: Inhibit HMG-CoA reductase.

8. How are bile acids synthesized? What are their functions?

Bile acids: These are 24 carbon compounds essential for lipid digestion. Bile acid is the

route of excretion of cholesterol.
Classification
• Primary: Cholic acid and chenodeoxycholic acid
• Secondary: Deoxycholic acid and lithocholic acid.
Synthesis of Bile Acids (Fig. 6.11, P. 77)

Site: Liver.
Starting material: Cholesterol.
End product: Bile acids.
Coenzymes: NADPH.
Steps: Process involves following modifications in cholesterol structure (Fig. 6.11):
• Insertion of hydroxyl groups in specific positions

• Saturation of double bond in the B ring of cholesterol

• Hydrocarbon chain is shortened by 3 carbons and introduction of carboxyl group.

Regulation: The rate limiting enzyme is 7α-hydroxylase, which is inhibited by bile acids (feedback
inhibition).
Functions: Bile salts decrease the surface tension and cause emulsification of fat. They also
help to form micelles, which are important for fat absorption. They help in absorption of fat-
soluble vitamins A, D, E and K.
9. Write a note on enterohepatic circulation of bile salts.

Definition: Process involving secretion of bile acids from liver → intestine → reabsorp-

tion of secreted bile acids and salts from intestine → transport to liver → re-excretion in
bile. About 98%–99% of bile acids secreted are reabsorbed and this process is known as
enterohepatic circulation (Fig. 6.12, p. 77).
About 15–30 g of bile salt is secreted from liver to intestine per day. About 0.5 g is lost

per day and remaining reabsorbed by enterohepatic circulation. Approximately 0.5 g of
cholesterol is synthesized per day to replace the loss.
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Fig. 6.11: Synthesis of bile acids (NADPH, reduced nicotinamide adenine dinucleotide phosphate)
Fig. 6.12: Enterohepatic circulation of bile salts
10. Classify lipoproteins with their composition and functions.

Lipoproteins: These are complex lipids having lipids and specific proteins (apoproteins).
Lipoproteins are helpful in transport of lipids in plasma.
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Structure: Neutral lipid core (containing triacylglycerol and cholesterol ester) surrounded

by a shell of amphipathic apolipoproteins, phospholipids and non-esterified cholesterol
(Fig. 6.13).
Fig. 6.13: Structure of lipoproteins
Classification and functions: Depending on the electrophoretic mobility and density, lipids
are classified as given in Table 6.5.
Table 6.5: Classification of lipoproteins
Class Diameter (nm) Source and functions Major apolipoproteins
Chylomicrons 500 • Intestine: Transport of dietary tria- A, B-48, C-II, E

cylglycerol (TAG) to tissues.
Very-low-density lipo- 43 • Liver: Transport of TAG from liver B-100, C-II, E

proteins (VLDL) to peripheral tissues.
Low-density lipopro- 22 • IDL: Transport of cholesterol from B-100

teins (LDL) liver to peripheral tissues.
High-density lipopro- 8 • Transport of cholesterol from pe- A, C (I, II, III), E

teins (HDL) ripheral tissues to liver (reverse
cholesterol transport).
Donates apolipoproteins to chylomi-

crons and VLDL.
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11. What is the normal serum cholesterol levels? Briefly describe the metabolism of very-
low-density lipoproteins (VLDL) and low-density lipoproteins (LDL).
Normal serum cholesterol level is 140–200 mg/dL.
Metabolism of very-low-density lipoproteins (Fig. 6.14)

Fig. 6.14: Metabolism of very-low-density lipoproteins (VLDL) and low-density lipoproteins (LDL)
• Step 1: Very-low-density lipoprotein (VLDL) is synthesized in the liver as nascent VLDL;

Nascent VLDL will transport endogenous triacylglycerol and cholesterol
• Step 2: In the circulation, it acquires apolipoproteins (C and E) from HDL and becomes
mature VLDL
• Step 3: Lipoprotein lipase (on endothelium of capillaries) metabolizes triacylglycerol of
VLDL releasing free fatty acids (FFA) and glycerol. VLDL is converted to IDL
• Step 4: FFA released is taken up by extrahepatic tissues (adipose tissue and muscle)
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• Step 5: Intermediate density lipoproteins (IDL) lose triglycerides to form LDL
• Step 6: LDL, apo B-100 containing lipoprotein, is responsible for transport of cholesterol
from liver to peripheral tissues. Most of the LDL is formed from VLDL in the circulation.
From the circulation, cholesterol rich LDL is taken up by liver via apo B-100 mediated
uptake through LDL receptor
• Step 7: In the liver, LDL is hydrolyzed; cholesterol is secreted into intestine either directly
or after getting converted into bile acids.
12. Give an account of metabolism of chylomicrons.

Metabolism of chylomicrons

Chylomicrons are synthesized in the intestine; they transport dietary lipids from intestine

to peripheral tissues (Fig. 6.15).
Fig. 6.15: Metabolism of chylomicrons (HDL, high-density lipoproteins; FFA, free fatty acid)
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• Step 1: Nascent chylomicrons are synthesized in the intestinal cells, which take up dietary
triacylglycerol, cholesterol and transport them into circulation via lymphatics
• Step 2: In the circulation, it acquires apolipoproteins (C and E) from HDL and becomes
mature chylomicron
• Step 3: Lipoprotein lipase will act on chylomicrons to release free fatty acids and glycerol;
chylomicron is converted to chylomicron remnants

• Step 4: FFA released from chylomicrons is taken up by peripheral tissues
• Step 5: Chylomicron remnants are taken up by apo E-mediated uptake by liver
• Step 6: Cholesterol from chylomicron remnants is secreted into bile either directly or after
getting converted into bile acids.
13. How is HDL metabolized?
High-density lipoprotein (HDL) is responsible for transport of cholesterol from peripheral
tissues to liver and this process is termed as reverse cholesterol transport. Low HDL levels
are associated with increased incidence of atherosclerosis and coronary artery disease.
Metabolism of high-density lipoprotein (Fig. 6.16)
• Step 1 and 2: Synthesis of nascent HDL occurs in the intestine and liver—it is then released
into circulation; it is discoidal in shape
• Step 3: Nascent HDL takes up cholesterol from peripheral tissue
Fig. 6.16: Metabolism of high-density lipoprotein (CETP, cholesterol ester transfer protein; CE, cholesterol ester)
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• Step 4: Lecithin cholesterol acyl transferase (LCAT) binds to discoidal HDL and esterifies
free cholesterol → formation of spherical HDL3
• Step 5: HDL3 accepts more cholesterol (from tissues), which is esterified by LCAT→ forma-
tion of larger HDL2
• Step 6: Cholesterol ester transfer protein (CETP): Transfers the cholesterol esters from
HDL2 to VLDL in exchange for triacylglycerol from VLDL. HDL is taken up by liver and
degraded by hepatic lipase.
14. Enlist the functions of important apolipoproteins.

The functions of important apolipoproteins are listed in Table 6.6.

Table 6.6: Functions of apolipoproteins
Apolipoprotein Functions
Apo A-I Structural component of HDL; activates LCAT
Apo B-100 Structural component of VLDL and LDL; ligand for LDL receptor
Apo C-II Activates lipoprotein lipase
Apo E Ligand for hepatic receptors—promotes uptake of chylomicron rem-
nants
Lp(a) Inhibits fibrinolysis; elevated Lp(a) levels increases the risk for ath-
erosclerosis
15. Name the tests done under lipid profile and give their normal values.
Lipid profile tests and their normal values are given in Table 6.7.

Table 6.7: Normal lipid profile (as per ATP III guidelines)
Test Normal values Method
Total cholesterol 140–200 mg/dL Cholesterol oxidase
Triglycerides 60–150 mg/dL Enzymatic
LDL cholesterol 50–130 mg/dL Total cholesterol—(HDL + TG/5)
HDL cholesterol 40–65 mg/dL Enzymatic after precipitation of other
lipoproteins
Total cholesterol/HDL cholesterol ratio < 5 (Calculation)
16. Classify hyperlipidemia with suitable examples.

Definition: Increase in serum lipids either due to genetic defect or due to underlying

diseases. https://kat.cr/user/Blink99/
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Classification
a. Primary hyperlipidemia (Frederickson's classification): It is due to genetic defect in me-
tabolism or clearance of lipoproteins (Table 6.8).
Table 6.8: Primary hyperlipidemia

Type Defect Clinical features
Type I Lipoprotein lipase deficiency • Increased chylomicrons, creamy plasma with elevated
triglycerides; xanthomas and pancreatitis are the char-
acteristic features
Type IIa LDL receptor defect • Increased cholesterol rich LDL with high risk for coronary
artery disease
Type IIb Apo B overproduction • Increased VLDL and LDL with high risk for coronary artery
disease
Type III Abnormality in Apo E • Increased chylomicrons and VLDL with xanthomas and
high risk for coronary artery disease
Type IV Overproduction of VLDL • Increased VLDL usually associated with diabetes and
hyperinsulinemia
Type V Secondary to disorders • Increased chylomicrons and VLDL with increased risk for
coronary artery disease
b. Secondary hyperlipidemia: It is characterized by elevated cholesterol or triglycerides

or both. It is due to underlying diseases:
• Nephrotic syndrome
• Obstructive jaundice
• Hypothyroidism
• Diabetes mellitus.
General Principles of Treatment in Hyperlipidemia

• Diet: Balanced diet with low cholesterol, supplementation of poly- and mono-unsaturated
fatty acids and fiber rich diet
• Exercise: Increased physical activity in the form of exercise
• Drugs: Hypolipidemic drugs like statins, fibrates, bile acid binding resins, niacin, etc.
17. Explain lipotropic factors with examples.
Lipotropic factors: These are compounds, which prevent fatty liver by proper mobilization
and utilization of fat reaching/produced in the liver.
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For example: Choline, betaine, inositol and methionine (vitamin B12, glycine and serine are

required for synthesis of lipotropic factors).
Functions

• Choline is required for synthesis of phospholipid lecithin and prevents accumulation of

excessive amount of fat, thereby protects against fatty liver
• Betaine and methionine contribute methyl group for synthesis of choline and carnitine. Car-

nitine favors increased movement of fatty acids into the mitochondria during β-oxidation,
thus prevents accumulation of fat.
18. Write a note on fatty liver.

Definition: Excessive accumulation of triacylglycerol in the liver either due to increased
production or due to decreased clearance of fat. In untreated cases, chronic accumulation
of fat in the liver can cause fibrotic changes, which can progress to cirrhosis.
Causes

• Starvation, high fat diet or uncontrolled diabetes mellitus: All these conditions lead to increased
plasma free fatty acids (from adipose tissue or extrahepatic tissues), which are taken up
by liver and esterified. Entry of free fatty acids to the liver exceeds the capacity of VLDL
to secrete fat from liver leading to fatty liver.
• Deficiency of lipotropic factors like choline, betaine, methionine, etc. leads to decreased synthesis
of phospholipids in lipoproteins, causing decreased clearance of fat from liver.
• Chronic alcoholism: Alcohol metabolism causes increased NADH/NAD+ ratio, which blocks
TCA cycle and β-oxidation. Also, alcohol provides acetyl-CoA, which stimulates lipogenesis
and cholesterol synthesis.
• Carbon tetrachloride, chloroform, lead and arsenic: Chronic exposure to these compounds,
which are hepatotoxic, can impair lipoprotein synthesis and secretion of fat from liver
leading to fatty liver.
• Essential fatty acid deficiency: They can contribute to development of fatty liver, as they are
components of phospholipids.
19. Explain lipid storage disorders or sphingolipidoses.

Sphingolipidoses: Group of inherited lipid storage disorders due to gene mutations leading

to defective synthesis of specific lysosomal hydrolytic enzymes responsible for breakdown
of lipids (Table 6.9).
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Table 6.9: Sphingolipidoses
Disease Defective enzyme Clinical features

Tay-Sachs disease Hexosaminidase A • Spot in macula (Blindness)
Ashkenazic jews
CNS degeneration (mental retardation)

Hexosaminidase A deficiency. Storage
disease (GM2 gangliosidosis) [MN: Sachs]
Sandhoff disease Hexosaminidase A and B • Mental retardation, blindness, muscle weakness
Fabry disease α-galactosidase • Renal failure; death at young age
Gaucher's disease β-glucosidase • Hepatosplenomegaly, long bone erosion, mental
retardation
Krabbe disease β-galactosidase • Mental retardation
Niemann-Pick disease Sphingomyelinase • Hepatosplenomegaly, mental retardation
20. Explain briefly about alcohol metabolism.

Metabolism of alcohol
Alcohol metabolism (Fig. 6.17, p. 86) generates NADH, which inhibits TCA cycle. Increased
NADH also converts oxaloacetate to malate (inhibits gluconeogenesis and causes hypoglyce-
mia). Acetyl-CoA generated is the raw material for lipogenesis and cholesterol synthesis.
21. What is the significance of brown adipose tissue?
Brown adipose tissue metabolism generates heat rather than ATP due to presence of natural
uncoupler of oxidative phosphorylation (thermogenin). Thermogenin can act as a proton
conductance pathway through the inner mitochondrial membrane and thereby uncouples
oxidation from phosphorylation, which generates heat.
Significance
People with significant amount of brown adipose tissue have less chance to develop obesity.
Brown adipose tissue is very active in hibernating animals and in newborn.
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Fig. 6.17: Metabolism of alcohol
22. What is atherosclerosis? Mention the causes for it.

Definition: Atherosclerosis is a complex disease characterized by thickening or hard-

ening of arteries due to accumulation of lipids. Events in atherosclerosis are given in
Figure 6.18.
Predisposing Causes of Atherosclerosis and Coronary Artery Disease

• Diabetes mellitus

• Hyperlipoproteinemias

• Nephrotic syndrome

• Hypothyroidism

• Obesity, smoking, hypertension.

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Fig. 6.18: Events in atherosclerosis
Key Points
Lipases: Pancreatic lipase, gastric lipase, lipoprotein lipase and hormone sensitive lipase.
End products of lipid digestion: Free fatty acids, 2-monoacylglycerol, 1-monoacylglycerol and
cholesterol.
Steatorrhea: When a person is unable to digest fat, his stool becomes bulky, glistening, yellow
brown and foul smelling and floats on the surface of the water. Seen in pancreatic insufficiency,
obstructive jaundice (defective bile salts secretion), cystic fibrosis, shortened bowel and colipase
deficiency (> 6 g of fat excreted in stool/day).
Chyluria: Characterized by excretion of milky urine due to abnormal connection between urinary
tract and lymphatics.
Chylothorax: Characterized by milky pleural fluid in pleural space due to abnormal connection
between pleural space of lungs and lymphatics of small intestine.
Congenital abetalipoproteinemia: Characterized by accumulation of triglycerides in the intestinal
cells due to lack of apo B-48 required for lipoprotein formation (chylomicrons).
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Gastric lipase: Digests triacylglycerol containing medium- and short-chain fatty acids. This has an

important role in digestion of lipids in infants and also in patients with pancreatic insufficiency. This
is the basis for treatment of such patients with triacylglycerol containing medium- and short-chain
fatty acids.
Enterohepatic circulation of bile salts: Reabsorption of bile salts from the intestine into liver,

followed by resecretion into intestine.
Gallstones: Formed due to increased cholesterol levels in bile, which reduces its ability to solubilize

in bile. This can be treated with chenodeoxycholic acid, an inhibitor of HMG CoA reductase.
Medium-chain fatty acids: These are absorbed into portal circulation as free fatty acids.

Orlistat: It is a drug, which inhibits pancreatic lipase—used in the treatment of obesity.

Cholecystokinin and secretin: These are hormones which stimulate secretion of enzymes of diges-

tion and HCO3- (neutralizes the acidic chyme) respectively.
Glycerol is not utilized by adipocytes: Due to lack of glycerol kinase, it enters into liver and is con-

verted into dihydroxyacetone phosphate (DHAP), which may enter into gluconeogenesis or glycolysis.
Carnitine (made up of lysine and methionine): Transports the long-chain fatty acids from cytosol to

mitochondria for -oxidation. It has three enzymes, carnitine palmitoyltransferase I (CPT I), carnitine
β
palmitoyltransferase II (CPT II), translocase. Patients undergoing dialysis can lose carnitine, which
may predispose to fatty liver.
Malonyl-CoA: Inhibits CPT I.

Number of ATPs generated after complete oxidation of palmitic acid (16C): 106.

β-oxidation of odd-chain fatty acid (valeric acid): Gives rise to acetyl-CoA and propionyl-CoA.

Propionyl-CoA is converted into succinyl-CoA and enters into TCA cycle.
Methyl-malonic acidemia: Due to deficiency of enzyme methyl malonyl-CoA mutase or vitamin B 12,

which is a coenzyme for conversion of L-methyl malonyl-CoA to succinyl-CoA.
Zellweger's syndrome: Lack of peroxisomes leading to accumulation of very long-chain fatty acids.

Refsum's disease: Autosomal recessive disorder characterized by accumulation of phytanic acid

due to deficiency of α-oxidase (enzyme for α-oxidation).
Jamaican vomiting sickness: Due to consumption of akee fruit (containing hypoglycin A), which

inhibits medium-chain fatty acyl-CoA dehydrogenase.
Omega oxidation: Minor pathway for oxidation of fatty acids, catalyzed by hydroxylase enzymes

involving cytochrome P450. The –CH3 in omega position is converted to –CH2OH and then oxidized
to –COOH thus forming dicarboxylic acid, which further undergoes β-oxidation.
Dicarboxylic aciduria: In deficiency of acyl-CoA dehydrogenase, fatty acids undergo omega oxida-

tion and produce large amounts of dicarboxylic acids, which are excreted in urine.
Lipotropic factors: Choline, betaine, methionine (prevent fatty liver).

Sources of NADPH: HMP shunt and malic enzyme.

Thiophorase: Is absent in liver, so it cannot utilize ketone bodies.

Rothera’s test: Acetone and acetoacetic acid can form purple color complex with sodium nitroprus-

side in the presence of ammonia.
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Ferric chloride test: Less commonly done test for ketone body detection. It can be used for detec-
tion of phenylpyruvic acid in case of phenylketonuria.
Causes for ketoacidosis (> 0.2 mmol/L): Uncontrolled diabetes and prolonged starvation.
Tay-Sach's disease: Due to deficiency of β-hexosaminidase A leading to accumulation of gan
gliosides (GM2) and neurological manifestations.
Niemann-Pick disease: Due to deficiency of sphingomyelinase and characterized by accumulation

of sphingomyelin, hepatosplenomegaly and neurological manifestations.
Gaucher's disease: Deficiency of β-glucosidase leading to accumulation of glucocerebrosides, he-
patosplenomegaly and neurological manifestations.
Statins (atorvastatin, lovastatin): Drugs, which reduce the serum cholesterol levels by inhibiting
HMG CoA reductase (rate limiting enzyme).
Bile acids: Cholic acid, chenodeoxycholic acid, deoxycholic acid and lithocholic acid.
7α-hydroxylase: Is rate limiting enzyme in bile acid synthesis.
Cholestyramine: Is a drug, which binds to bile acids and prevents their reabsorption (treatment of

hypercholesterolemia).
Fibrate: Is a drug, which increases the lipoprotein lipase activity and thereby reduces the triglyceride

levels in blood.
Abetalipoproteinemia: Hypolipoproteinemia due to defect in triglyceride transfer protein, leading to

an inability to load apo B with lipid. As a result, chylomicrons or VLDL are not formed and triacyl-
glycerol accumulates in liver and intestine.
Type IIa hyperlipoproteinemia: Due to LDL receptor defect—increased risk for coronary artery

disease.
Lipoprotein (a): Structurally similar to LDL particle with apoprotein a (apo a). Increased lipoprotein

(a) can inhibit fibrinolysis and increase risk for development of atherosclerosis.
Free radicals: Can cause oxidation of LDL particles, which triggers the formation of foam cells and

atherosclerotic plaque.
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Amino cid and protein
7
a
chemistry
1. Classify amino acids with examples.

Based on nature of side chain

Non-polar amino acids: Alanine, Phenylalanine, Valine ('al' is common to them).

Uncharged (neutral), polar amino acids: Serine, Threonine, Tyrosine (OH containing).

Acidic amino acids: Aspartic acid, Glutamic acid.

Basic amino acids: Arginine, Lysine, Histidine.

Based on nutritional requirement

Essential amino acids: Methionine, Arginine, Threonine, Tryptophan, Valine, Isoleucine,

Leucine, Phenylalanine, Histidine, Lysine [MN: MATT VIL PHLy].
Non-essential amino acids: Glutamic acid, Aspartic acid, Glutamine, Asparagine, Glycine,

Alanine [MN: GA GA GA].
Based on metabolic fate

Glucogenic amino acids: Glutamic acid, Aspartic acid, Glutamine, Asparagine, Glycine, Ala-

nine [MN: GA GA GA].
Ketogenic amino acids: Leucine.

Both glucogenic and ketogenic: Phenylalanine, Lysine, Isoleucine, Tyrosine and Tryptophan

[MN: SPLITT].
2. Define various orders of protein structures by giving examples.
Primary structure: It is defined as the number and sequence of amino acids in a protein.

It also includes the position of disulfide bonds.
Secondary structure: Local folding (regular/irregular) of short segments of polypeptides

results in secondary structure. For example, α-helices, β-pleated sheets and random coils.
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Tertiary structure: It is the folding and linking between secondary structural elements of a
protein to give it a three-dimensional structure. For example, β-barrel in pyruvate kinase,
four-helix bundle in cytochromes.
Quaternary structure: It refers to the regular association of two or more polypeptide chains
to form a complex. It is stabilized by weak interactions. Each polypeptide is called subunit.
For example, hemoglobin and immunoglobulin.
3. Explain secondary structures of proteins with examples.
Definition: Local folding (regular/irregular) of short segments of polypeptides results in
Amino Acid and Protein Chemistry

secondary structure. For example, α-helices, β-pleated sheets and random coils.
Alpha-helix
Structure: It is formed by regular folding of polypeptide chain to give a right-handed helical
conformation having 3.6 amino acids per turn with a pitch of 5.4 Å and distance between
adjacent amino acid is 1.5 Å (Fig. 7.1). For example, α-helix is present in hemoglobin and
myoglobin.
Fig. 7.1: α-helix formed by coiling of polypeptide chain
Common amino acids in α-helix: Methionine ALanine and Leucine [MN: MALL].
Amino acid disrupting α-helix: Proline, Arginine, Glutamic acid, Aspartic acid, Lysine
[MN: PAGAL].
Bonds stabilizing α-helix: Hydrogen bonds between adjacent amino acids.
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Beta-pleated sheet

Structure: It is a regular folding of polypeptide chain to give a pleated-sheet like app earance.

It is fully extended polypeptide chain with 3.5 Å distance per amino acid. For example,
carbonic anhydrase and silk fibroin.
Bonds stabilizing β-pleated sheet: Interchain or intrachain hydrogen bonds stabilize β-pleated

sheets. Disulfide bonds play a key role in U bends.
Direction of β-pleated sheet: Strands may be parallel (N-termini of both strands at the same

end) or antiparallel (Figs 7.2a and b).

Fig. 7.2a: Parallel β-pleated sheet Fig. 7.2b: Antiparallel β-pleated sheet

4. Explain various bonds seen in protein structure.
Six kinds of bonds are seen in a protein structure. They are peptide bonds, hydrogen

bonds, van der Waals interactions, hydrophobic interactions, ionic interactions and dis-
ulfide linkages.
Hydrogen bonds: It is formed by sharing of hydrogen between two electron donors. H is

donated by: -OH, -NH, -NH2; H-acceptors: COO-, C = O, -S-S-.
Electrostatic (ionic) bonds: It is formed by attraction between two oppositely charged

amino acids. Positively charged amino acids—lysine, arginine. Negatively charged amino
acids—aspartic acid and glutamic acid.
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Hydrophobic bonds: It is formed by interaction between the side chains of non-polar

amino acids. They are seen in the core of proteins.
van der Waals forces: These are attraction-repulsion forces between all atoms due to oscil-
lating dipoles.
Disulfide bonds: These are covalent linkages that may form when the thiol groups of two
cysteine residues are oxidized to a disulfide: 2 R-SH → R-S-S-R.
Peptide bonds: It is a covalent bond formed between α-carboxyl group of one amino acid
with α-amino group of the succeeding amino acid.

5. What is isoelectric pH? Mention its significance.
Definition: The pH at which a protein possesses equal number of positive and negative
charges (net charge is zero) is called isoelectric pH with respect to that protein (Table 7.1).
Significance: At this pH, proteins have least solubility and they precipitate in solution.
Table 7.1: Isoelectric pH of different proteins

Proteins Isoelectric pH
Pepsin 1.1
Casein 4.6
Albumin 4.7
6. What is denaturation of proteins?

Definition: Denaturation of proteins is an irreversible disruption of secondary, tertiary and
quaternary structure of proteins leading to loss of their physical, chemical and biological
properties.
Denaturing agents
• Physical agents: Heat, vigorous mixing, X-rays, ultraviolet (UV) radiation, etc.
• Chemical agents: Acids, alkali, organic solvents, salts of heavy metals, high concentration
of urea, etc.
7. Name some biologically important peptides giving their significance.
Definition: Peptides with few amino acids (4–10) are generally termed as oligopeptides
(Table 7.2).
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Table 7.2: Biologically important peptides
Name Property
Carnosine ( -alanyl-L-histidine) These two peptides are found in muscle. They activate myosin
b
Anserine (N-methyl-carnosine) adenosine triphosphatase (ATPase) activity
Glutathione (GSH tripeptide: γ-glutamyl- It is an important component of cellular antioxidant defense system.
cysteinyl-glycine) It participates as a cofactor in many reactions
Two molecules of GSH can donate a pair of hydrogen to reduce
a substrate
Glutathione peroxidase
H2O2 + 2GSH 2H2O + GS-SG
Thyrotropin-releasing hormone (TRH) Secreted by hypothalamus. It stimulates the release of thyroid-

(contain 3 amino acids) stimulating hormone (TSH) from anterior pituitary
Vasopressin (antidiuretic hormone: con- Secreted by posterior pituitary gland. It regulates water excre-
tains 9 amino acids) tion by kidney
Enkephalin (pentapeptide) Peptide found in brain, which inhibits the sense of pain
Angiotensin II A peptide with 8 amino acids, which stimulates release of aldos-
terone from adrenal cortex
Bradykinin (contains 9 amino acids) Vasodilator peptide
8. Enumerate different functions of proteins with suitable examples.

Function of proteins are shown in Table 7.3.

Table 7.3: Functions of proteins [MN: C TRENDS]
Functions Examples
Structural proteins Keratin of hair and nails, collagen (bones, cartilage and connective tissue)
Contractile proteins Actin, myosin
Transport proteins Hemoglobin, serum albumin, transferrin
Regulatory proteins Hormones (insulin, glucagon, growth hormone)
Enzymes Pepsin, trypsin, hexokinase
Defense proteins Immunoglobulin, fibrinogen
Storage proteins Ferritin, hemosiderin
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9. Classify proteins based on nutritional value.

Based on nutritional value, proteins are classified as:
a. Complete proteins (first class proteins): These are rich in all essential amino acids. For
example, egg albumin.
b. Incomplete proteins: They lack one or more essential amino acids. For example, pulse proteins
are poor in methionine and cereal proteins are poor in lysine (the essential amino acid that
is missing in a given protein is called limiting amino acid with respect to that protein).
10. Explain methods for separation of plasma proteins.

a. Salt fractionation: In concentrated salt solutions like ammonium sulfate, proteins precipitate
because of decreased availability of water molecules that keep them in solution. This is uti-
lized to isolate the protein of interest. For example, globulins are precipitated by 21%–28%
ammonium sulfate and albumin is precipitated by saturated ammonium sulfate.
b. Precipitation by organic solvents: Solvents like methanol, ethanol, acetone, etc. are dehy-
drating agents, which remove water needed to keep the proteins in solution resulting in
their precipitation.
c. Gel filtration: Columns packed with gels of various porosity are used to separate proteins
depending on molecular weight, size and shape. Here, proteins with higher molecular weight
pass through the column faster than smaller ones, which get trapped in the gel matrix.
d. Electrophoresis: It is separation of proteins based on migration of the charged molecule
in an electric field.
• In alkaline pH, proteins have more negative charge and move towards anode; rate of
migration is directly proportional to the charge on the protein and inversely proportional
to molecular weight
• In a normal pattern, albumin moves fastest followed by α1, α2, β and γ-globulin.
γ-globulins move very slowly and they remain near the point of application (Fig. 7.3).
Fig. 7.3: Normal serum electrophoresis
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• Relative percentage of various plasma proteins:

Albumin: 55%–60%

α1: 2%–4% (retinol binding globulin, cortisol binding globulin, thyroxine binding globulin)

α2: 6%–12% (haptoglobin, ceruloplasmin)

β: 12%–14% (transferrin, hemopexin)

γ: 12%–24% (immunoglobulin).

11. Write short notes on albumin.
Albumin is a major plasma protein with molecular weight of 69,000 Daltons, having 585

amino acids.
Synthesis: It is synthesized in the liver (12 g/day) and has a half-life of 20 days.

Normal serum level: 3.5–5 g/dL.

Significance: Serum albumin level reflects liver function.

Functions of albumin: [MN: NOT B].

Nutritive function: It serves as a source of amino acids for tissue protein synthesis.

Osmotic function: Contributes to 80% of total plasma oncotic pressure (25 mm Hg), maintains

blood volume and body fluid distribution.
Transport: Albumin transports many hydrophobic substances like bilirubin, heavy metals,

calcium, copper, free fatty acids, drugs, thyroxine, etc.
Buffering action: Since it is present in high concentration, it shows maximum buffering capacity.

Histidine residues (pK = 6.1) present on albumin are responsible for its buffering action.

Hypoalbuminemia: Albumin level (< 2 g/dL) leads to enhanced fluid retention in tissue

spaces leading to edema.
Causes of hypoalbuminemia [MN: BURP Him]

• Burns and trauma

• Undernutrition (malnutrition)

• Renal diseases

• Pancreatitis—leads to malabsorption

• Hepatic diseases.

12. Write short notes on insulin.
Synthesis: Insulin is a polypeptide hormone produced in pancreas by β-cells of islets of

Langerhans. It is released from β-cells as proinsulin, which undergoes proteolytic cleavage
and forms C-peptide and mature insulin (Fig. 7.4).
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Fig. 7.4: Structure of insulin
Structure: Consists of two chains, A and B chain linked by two interchain disulfide bonds.
Function: Insulin decreases blood glucose by activating glycolysis, protein synthesis, li-
pogenesis, glycogenesis, ketogenesis and inhibiting gluconeogenesis, lipolysis, proteolysis
and ketolysis.
13. Write short notes on immunoglobulins.
Definition: Immunoglobulins (Ig) are the defense proteins in plasma produced by B-
lymphocytes in response to a foreign antigen. They bind to antigens and destroy them.
Classification [MN: GAMED]: Five different types of immunoglobulins depending on the
type of heavy chain (Table 7.4).
Table 7.4: Types of immunoglobulins
Immunoglobulin Heavy chain
IgG Gamma (γ)
IgA Alpha (α)
IgM Mu (µ)
IgE Epsilon (ε)
IgD Delta (δ)
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Functions of immunoglobulins are given in Table 7.5.
Table 7.5: Functions of immunoglobulins
Type Properties Functions
IgG Major immunoglobulin present in highest Protects the body against various infections. It can
amount in plasma (75%–80%). cross placenta and provide immunity to fetus.
IgA Occurs as a monomer or dimer held by J It provides local immunity.

chain. Produced by secretory cells of respi-
ratory, digestive and urinary tracts, lacrimal

and salivary glands.
IgM Largest lg composed of 5 Y-shaped units It is the first antibody produced when bacteria/
held by J chains. virus enters the body. It cannot cross the blood
vessel wall.
IgE Contains a single Y-shaped monomer. It binds tightly with mast cells releasing histamine
It is produced by plasma cells. and causing allergy. It increases during allergy.
IgD Present on the surface of B cells. Functions as B cell receptor.
General structure of immunoglobulin (Fig. 7.5)

Variable and constant region: Each chain (L or H) has an amino terminal (variable region)

and carboxyl terminal (constant region).

Fig. 7.5: Structure of immunoglobulin (Unshaded portion = variable region; shaded portion = constant region)
Ch-07.indd 98 21-06-2014 11:50:13

Antigen-binding site: Two antigen-binding sites on the two arms of the Y formed by amino
terminal half of light chain and one fourth of heavy chain.
Fc segment: C-terminal half of the heavy chain forms the Fc segment.
Bonds which stabilize immunoglobulin structure: Interchain and intrachain disulfide bonds.
14. Write a note on structure of collagen.

Collagen: It is the most abundant fibrous protein forming structural component in hu-
man body.

Structure (triple helix): It has three polypeptides that are wound around each other to
form a rope-like structure.
Bonds stabilize triple helix: Hydrogen bonds between adjacent polypeptides.
Amino acid sequence: Collagen is rich in glycine and proline. Glycine is found as every
third amino acid and represented by Gly-X-Y, where X is frequently proline and Y is often
hydroxyproline or hydroxylysine. Vitamin C is required for maturation of collagen.
Defects in formation and maturation of collagen
Scurvy: Deficiency of vitamin C (required for hydroxylation of proline and lysine) leads to
poor maturation of collagen. Patient presents with bleeding of gums, poor wound healing
and easy bruisability.
Ehlers-Danlos syndrome: Stretchy skin and loose joints with poor strength of connective
tissue is due to a defect in collagen processing.
Osteogenesis imperfecta or brittle bone syndrome is a disorder with brittle bone, poor
healing of wounds and twisted spine.
15. Explain the structure and functions of hemoglobin.

Types of hemoglobin (in adult blood)
• HbA (97%)—2 α and 2 β chains
• HbA2 (3%)—2 α and 2 δ chains
• HbF—2 α and 2 γ chains.
Structure of adult hemoglobin (Fig 7.6): It is a tetramer protein made up of two types of
polypeptide chains. Almost 80% of hemoglobin structure is α-helix, which is divided into
eight segments (A to H). Heme group occupies a crevice lined by non-polar residues and
two histidines (E-7 and F-8).
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100

Fig. 7.6: Structure of hemoglobin
Bonds between two polypeptides in each of dimer (α1β1) and (α2β2): Interchain interactions,

ionic bonds and hydrogen bonds.
Relative position of dimers results in two forms of Hb: T-form (taut or tense) and R-

form (relaxed). T-form has low affinity for oxygen. R-form has high affinity for oxygen.
Hemoglobin can bind four oxygen molecules, one each at four heme groups.
Factors affecting binding of O2 to Hb: Partial pressure of O2, pH, partial pressure of CO2

and the presence of 2,3-bisphosphoglycerate.
Cooperativity: Binding of O2 to one heme increases the affinity of other hemes for oxygen.

Functions of hemoglobin
1. Transport of oxygen from lungs to peripheral tissues and CO2 from periphery to lungs.

2. Acts as buffer to maintain the pH of the blood.

16. Write briefly on oxygen transport by hemoglobin.
a. Binding of oxygen to hemoglobin:

Binding of first oxygen molecule to deoxyhemoglobin
Movement of heme iron into plane of heme
Rupture of salt bridges between subunits
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101
Transition of hemoglobin from low affinity T (taut) state to high affinity R (relaxed state)
Rupture of remaining few salt bridges

Progressive increase in affinity of remaining heme of unoxygenated subunits for oxygen
(cooperativity)

Binding of oxygen to remaining subunits
b. Release of oxygen from hemoglobin:

Decrease in pH/increase in pCO2 (peripheral tissues)
Decrease affinity of hemoglobin for oxygen; hemoglobin stabilized in the T state (Bohr effect)
Release of oxygen to peripheral tissues

17. What are hemoglobinopathies?
Hemoglobinopathies are group of disorders characterized by production of abnormal Hb
molecules. For example, sickle cell disease, hemoglobin C disease, methemoglobinemia and
thalassemia (Table 7.6).
Table 7.6: Hemoglobinopathies
Disease Defect Symptoms
Sickle cell Autosomal recessive disorder. Here, glutamate at In deoxygenated state, HbS polymerizes
anemia 6th position of b-chain is replaced by non-polar into long fibrous aggregates → blocks
(homozygous) valine (it moves slower than HbA towards anode capillaries → tissue anoxia → pain and
in electrophoresis). death of cells.
Sickle cell trait Same as above. Does not show symptoms.
(heterozygous)
Hemoglobin C Lysine substituting glutamate at 6th position of Mild disease, with chronic hemolytic
disease b-globin chain (it moves slower than HbS in elec- anemia.
trophoresis).
Contd...
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102

Contd...
Disease Defect Symptoms

HbM Replacements of -58 histidine or -92 histidine Oxidation of Fe2+ of heme to Fe3+ forms
a
b
by tyrosine. → fails to bind oxygen.
Thalassemias Imbalance in the synthesis of globin chains. Hereditary hemolytic diseases.

Caused by variety of gene mutations.
-thalassemias Synthesis of -chain is decreased or absent. Moderately severe hemolytic anemia
a
a
one gene is defective → silent carrier; Defect in all four -globin gene causes
a
two genes are defective → -thalassemia trait; fetal death.
a
three -globin genes are defective → hemoglobin
a
H disease.
-thalassemias -globin chain is decreased or absent; Increased HbF ( 2, 2 and 4 occurs)
b
b
a
g
g
one gene is defective → -thalassemia minor; Severe → require regular major
b
two genes are defective → -thalassemia major. blood transfusions.
b
Key Points
Acute phase proteins: Levels of certain plasma proteins are increased by several thousand folds

in inflammatory and neoplastic conditions. They are called acute phase proteins, e.g. α-1-antitrypsin,
haptoglobin, ceruloplasmin, C-reactive protein, etc.
Globulins: Different types of globulins present are α1, α2, β1, β2 and γ. The α- and β-globulins trans-

port hormones, minerals, lipids, vitamins, etc. The γ-globulins provide immunity against infections.
Fibrinogen: It is an acute phase protein synthesized by liver; required for blood coagulation.

α 1-antitrypsin: It protects the elastic tissues of the lung from destructive action of elastase.

Inherited deficiency of this protein is associated with emphysema and cirrhosis. It is a positive acute
phase protein.
α2-macroglobulin: It is an α2-globulin and it inactivates all proteinases; its concentration is markedly

increased in nephrotic syndrome.
C-reactive protein: It is synthesized in liver. Its levels are highly elevated in inflammation (acute phase

protein). Normal plasma range is 0.5–1 mg/dL. Used in predicting the risk of cardiovascular disease.
Haptoglobin: It is an α-2-globulin capable of binding hemoglobin. Low level indicates hemolysis.

Ceruloplasmin: Normal serum level of ceruloplasmin is 25–50 mg/dL. 90% of serum copper is bound

to this protein. It is elevated in infections and malignant condition. It has oxidase activity and is involved
in iron metabolism. Decreased ceruloplasmin concentration is associated with Wilson disease.
Transferrin: Normal serum level of transferrin is 200–300 mg/dL. It transports iron. Increased in iron

deficiency. Usually one third of its capacity is saturated with iron (TIBC—total iron binding capacity).
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103
Multiple myeloma: Malignancy of a clone of plasma cells. Usually occurs above the age of 45.

Here, large amount of immunoglobulin light chains are excreted in urine, which is called Bence
Jones proteins. Serum electrophoresis shows a classical distinct band (M-band) between β and
γ regions.
Liver diseases: Since albumin is synthesized in liver, its level decreases in chronic liver failure and

cirrhosis. As the half-life of albumin is 20 days, acute liver diseases will not show any change in
albumin concentration.
Renal diseases: Albumin may be excreted in urine because of defect in glomerular filtration (albu-

minuria). In nephrotic syndrome, large amount of albumin is lost in urine.

Microalbuminuria: Small amounts of albumin are lost in acute nephritis and urinary tract infection

(30–300 mg/L). Microalbuminuria is an early predictor of future renal disease (normal range of al-
bumin in urine is 0–30 mg/L).
Amyloidosis: Due to accumulation of misfolded proteins, this results in a neurodegenerative disorder,

Alzheimer disease.
Prion diseases (Creutzfeldt-Jakob disease): These are a group of neurodegenerative disorders

caused due to accumulation of prions (infectious misfolded proteins).
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8 Metabolism of Proteins
1. Explain the digestion and absorption of proteins.

Protein digestion can be divided into gastric, pancreatic and intestinal phases.

Gastric phase: Food in stomach → (+) gastrin → (+) hydrochloric acid (HCl) secretion

(Figs 8.1 and 8.2).
Rennin: Secreted from stomach of infant; helps in conversion of casein into calcium para-

caseinate, which can be acted upon further by pepsin.
Pepsin: The chief cells of stomach secrete inactive pepsinogen, which is activated by HCl.

Fig. 8.1: Effect of food on acid secretion (+ = stimulates)
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105
Digestion, Absorption and Metabolism of Proteins

Fig. 8.2: Gastric phase of protein digestion
Rennin Pepsin
Casein Calcium paracaseinate Small peptides and amino acids
Pancreatic phase (Fig. 8.3):
Fig. 8.3: Events leading to release of pancreatic enzymes (+ = stimulates secretion)
Enterokinase
Trypsinogen Trypsin Cleaves peptides at carboxyl group of lysine
and arginine (basic amino acids)
Trypsin
Chymotrypsinogen Chymotrypsin Cleaves at carboxyl group of aro-
matic amino acids
Trypsin
Proelastase Elastase Cleaves the carboxyl group of Glycine, Arginine
and Serine [MN: GAS]
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106

Trypsin

Procarboxypeptidase A and B Carboxypeptidase A and B Cleave one

amino acid at a time from carboxyl end of peptides

Intestinal phase: Digested products of gastric and pancreatic phase (oligopeptides, tri-

peptides and dipeptides) enter into intestinal phase of digestion. Aminopeptidase is an

exopeptidase that cleaves one amino acid at a time from amino terminals of peptides.
Dipeptidases and tripeptidases are endopeptidases. These enzymes convert peptides to
amino acids.
Dipeptidase
Dipeptides Amino acids

Tripeptidase
Tripeptides Amino acids

Aminopeptidase
Oligopeptides Amino acids

Absorption of amino acids: It occurs from upper small intestine (duodenum and proximal

jejunum). Amino acids are absorbed along with sodium (secondary active transport, an en-
ergy dependent process (Fig. 8.4, p. 107). There are five transport systems for various types
of amino acids (Table 8.1). Any defect in these transport system can cause disorders.
Table 8.1: Amino acid transport systems
Transport system Amino acids transported Disorders
Small and neutral AA Ala, Ser, Thr Hartnup disease
Large and neutral AA ILe, Leu, Val, Tyr, Trp, Phe Hartnup disease
Basic AA and cysteine [MN: COAL] Cys, Orn, Arg, Lys Cystinuria
Acidic AA Glu and Asp No disorder
Imino acid and Gly Pro, Hydroxy Pro, Gly Glycinuria
AA, amino acid; Ala, alanine; Ser, serine; Thr, threonine; ILe, isoleucine; Leu, leucine; Val, valine; Tyr, tyrosine; Trp, tryptophan;
Phe, phenylalanine; Cys, cysteine; Orn, ornithine; Arg, arginine; Lys, lysine; Glu, glutamic acid; Asp, aspartic acid; Pro, proline; Hy-
droxy Pro, hydroxy proline; Gly, glycine.
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107

Fig. 8.4: Mechanism of absorption of amino acids (Na+, sodium ion; AA, amino acid; K+, potassium ion;
ATPase, adenosine triphosphatase).
2. What is amino acid pool?

Amino acid pool is the total pool of amino acids available in blood at any given time for
various anabolic and catabolic activities. It is influenced by the type of diet, nutritional
status, metabolism, health condition, age, etc. (Fig. 8.5).
Fig. 8.5: Amino acid (AA) pool (NPN, non-protein nitrogenous)
3. What are transaminases? What are their significance?

Definition: These are enzymes that catalyze the reversible transfer of an amino group
between one 'α' amino acid and an 'α' keto acid (Fig. 8.6).
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108

Fig. 8.6: Transamination (PLP, pyridoxal phosphate)
Features of transaminases

• Catalyze reversible reaction

• Require pyridoxal phosphate (PLP) as coenzyme

• Except lysine, threonine, proline and hydroxyproline, all amino acids undergo this reaction

• Transaminase levels will be increased in hepatitis, myocardial infarction, etc.—useful in

diagnosis
• Transaminases funnel amino groups from excess dietary amino acids to those amino acids

(e.g. glutamate) that can be deaminated.
Functions of transamination

• Degradation of surplus amino acids

• Synthesis of essential amino acids

• Gluconeogenesis.

4. What are deamination reactions? What is its significance?
Definition: These reactions cause removal of amino group from an amino acid.
Classification
a. Oxidative deamination

• Glutamate dehydrogenase (major pathway of oxidative deamination): Catalyzes removal

of nitrogen group from amino acid pool (Fig. 8.7).
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109

Fig. 8.7: Oxidative deamination (+ = stimulation; – = inhibition)
• L and D-amino acid oxidase (minor pathway): Catalyzes removal of nitrogen from amino
acids in peroxisomes of liver cells.
b. Non-oxidative deamination: Following are the examples for non-oxidative deamination.

• Dehydration
Serine dehydratase
Serine Pyruvate + NH3
Threonine dehydratase
Threonine α-ketobutyrate + NH3
• Desulfhydration
Desulfhydrase
Cysteine Pyruvate + NH3 + hydrogen sulfide (H2S)
• Straight deaminations
Histidase
Histidine Urocanic acid + NH3
5. Explain the formation and metabolism of ammonia. Add a note on regulation of urea cycle.
Reactions, which generate ammonia in the body:
Transamination: Glutamate α-ketoglutarate + NH3
Deamination (oxidative): Glutamate α-ketoglutarate + NH3
Dehydration: Serine Pyruvate + NH3
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110

Desulfhydration: Cysteine Pyruvate + NH3

Direct deamination: Histidine Urocanic acid + NH3

Intestinal putrefaction: Urea NH3 (bacterial urease enzyme)

Purine and pyrimidine catabolism NH3

Transport: Ammonia is very toxic, so it is transported in blood as glutamate (by transami-
nation of amino acids), glutamine (from brain to liver) and alanine (from muscle).
Fate of ammonia (Fig. 8.8)

Fig. 8.8: Metabolism of amino group
Urea cycle: Converts the toxic ammonia into less toxic and more soluble urea, which is

excreted in the urine (Fig. 8.9).
Requirements

• Starting material: CO2 and NH3

• Site: Liver

• Subcellular site: Partly mitochondrial and partly cytosolic

• Nitrogen atom donors in cycle: Ammonia and aspartate (amino group)

• Energy (ATP): Three ATPs are used.

Regulation of urea cycle: At the level of key enzyme carbamoyl phosphate synthetase-1

(CPS-1).
Short-term regulation: N-acetyl glutamate is positive allosteric effector of CPS-1.

Long-term regulation: By induction of enzymes of urea cycle at the gene level.

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Fig. 8.9: Urea cycle (reactions in the box occur in mitochondria) (CO2, carbon dioxide; NH3, ammonia; Mg, magnesium;
ATP, adenosine triphosphate; ADP, adenosine diphosphate; Pi, inorganic phosphate; AMP, adenosine monophosphate;
H2O, water).
6. Compare the enzymes carbamoyl phosphate synthetase I and II.

Comparison of the enzymes is shown in Table 8.2.
Table 8.2: Comparison of carbamoyl phosphate synthetase I and II
Carbamoyl phosphate synthetase I Carbamoyl phosphate synthetase II
Site Mitochondria Cytosol
Substrate Ammonia Amide group of glutamine
Pathway Urea synthesis Pyrimidine synthesis
Activator N-acetylglutamate Phosphoribosyl pyrophosphate (PRPP)
Inhibitor – Uridine triphosphate (UTP)
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7. Explain urea cycle defects.

Urea cycle defects: are due to deficiency or lack of any enzyme in urea cycle (Table 8.3).

Table 8.3: Urea cycle disorders
Disorder Enzyme deficiency Features
Hyperammonemia type I Carbamoyl phosphate synthetase I Fatal or death occurs few days after birth
Hyperammonemia type II Ornithine transcarbamoylase X-linked; increased glutamine in blood and
CSF*
Citrullinemia Argininosuccinate synthetase Autosomal recessive; increased citrulline
excretion in urine; CSF citrulline levels are
elevated
Argininosuccinic aciduria Argininosuccinase Elevated argininosuccinic acid levels in blood,
CSF and urine
Hyperargininemia Arginase Elevated arginine levels in blood, CSF
*
CSF, cerebrospinal fluid
General clinical features: Ammonia intoxication causes vomiting, mental retardation,

convulsions, slurring of speech and blurring of vision.
Mechanism for toxicity

↑ NH3 → ↑conversion of α-ketoglutarate to glutamate/glutamine → ↓ activity of Krebs

cycle and decreased ATP formation

↑ Glutamate → ↑ γ-aminobutyric acid (GABA) = an inhibitory neurotransmitter in brain

↑ Glutamine → ↑ osmotic effect → cerebral edema

Biochemical picture in urea cycle defects: ↑ glutamine, citrulline or arginine (blood and

urine); ↑ ammonia, ↓ urea in blood and respiratory alkalosis.
Treatment of urea cycle defects

Hemodialysis: Removes ammonia from blood.

Low-protein diet: For less ammonia formation.

Arginine supplementation (in certain defects of urea cycle): Activates N-acetylglutamate synthase

and gives ornithine, which is required for first reaction of urea cycle.
Citrulline supplementation (in certain defects of urea cycle): Helps to generate ornithine (as

mentioned in above sentence).
Sodium benzoate and sodium phenylbutyrate: Covalently bind glycine (forming hippurate) and

glutamine (forming phenylacetylglutamine) respectively, which are excreted.
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GLYCINE
8. Explain glycine metabolism (anabolism + catabolism).

Glycine is the simplest aliphatic amino acid without asymmetric carbon atom and nutri-
tionally non-essential.

Glycine biosynthesis: Glycine can be synthesized from serine, threonine, ammonia, gly-
oxylate [MN: STAG] and choline.
a. Serine
b. Glycine synthase: substrates—CO2 and NH3
c. Choline
d. Glyoxylate
e. Threonine
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Degradation of glycine
a. Reversal of glycine synthase reaction: Glycine is broken down to NH3 and CO2.

b. Glycine transaminase: Converts glycine to glyoxylate.

9. Explain the metabolic disorders of glycine.

Metabolic disorders of glycine are shown in Table 8.4.

Table 8.4: Metabolic disorders of glycine
Disease Defect Clinical features
Primary hyperoxaluria Defect in transamination of glyoxylate to ↑ oxalic acid in blood and urine.
glycine (type I). Defect in D-glyceric acid Renal stones—oxalate + calcium =
dehydrogenase. Defect in decarboxylation calcium oxalate stones, which de-
of glyoxylate to formate. posit in renal/extrarenal tissues.
Hyperglycinemia Glycine cleavage system. Elevated glycine in blood and urine.
Mental retardation.
Glycinuria Defect in reabsorption of glycine/proline in Benign: Increased excretion of gly-
renal tubules. cine and proline in urine.
10. Explain the formation of specialized products of glycine and their significance.
List of specialized products from glycine: Glutathione, Creatine, heme and purine ring

(MN: GLyCIN; I = Iron containing heme; N = Nitrogenous base purine).
a. Creatine

• Phosphorylated (creatine phosphate) form is required for muscle contraction

• The amount of creatinine produced is related to muscle mass of a person and is constant

• Kidney function—serum creatinine and creatinine clearance is used to assess the kidney

function.
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b. Glutathione
• Serves as a reductant [maintains red blood cell (RBC) membrane integrity]
• Plays a role in the detoxification of drugs to render them more water soluble
• Helps in the transport of amino acids across cell membranes (the γ-glutamyl cycle)
• Serves as a cofactor for some enzymatic reactions.
c. Heme synthesis
• Glycine is starting material for heme synthesis.
d. Purine ring
• Carbons 4, 5 and 7th nitrogen atoms in the purine ring are donated by glycine
(Fig. 8.10).
Fig. 8.10: Glycine contribution in purine ring
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PHENYLALANINE
11. Explain the metabolism of phenylalanine. Substantiate why phenylalanine is both gluco-

genic and ketogenic.
• Metabolism of phenylalanine is same as that of tyrosine since phenylalanine is converted

to tyrosine (refer Q No: 12)
• Phenylalanine is both glucogenic and ketogenic amino acid: because after getting con-

verted into tyrosine, it is catabolized to fumarate and acetyl-CoA, which produce glucose
and ketone bodies respectively (Fig. 8.11).
Fig. 8.11: Metabolism of phenylalanine
12. Discuss the metabolism of tyrosine. Add a note on disorders associated with tyrosine

metabolism.
Synthesis: It is formed from essential amino acid phenylalanine in the presence of enzyme

phenylalanine hydroxylase.
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Catabolism: It generates fumarate (glucogenic) and acetyl-CoA (ketogenic) as shown in

Figure 8.12.

Fig. 8.12: Catabolism of tyrosine (PLP, pyridoxal phosphate)
13. Explain the formation of specialized products from tyrosine.

List of specialized products from tyrosine
• Dopamine, norepinephrine, epinephrine (catecholamines)
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• Thyroid hormones—T3 and T4

• Melanin.

a. Synthesis of catecholamines: Dopamine, norepinephrine and epinephrine (Fig. 8.13).

Fig. 8.13: Synthesis of catecholamines (DOPA, dihydroxyphenylalanine)
b. Synthesis of melanin

c. Thyroid hormones: Triiodothyronine (T3), thyroxine (T4) (Fig. 8.14).

Fig. 8.14: Synthesis of thyroid hormones (TG, thyroglobulin)
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14. Explain the causes and features of phenylketonuria.

Phenylketonuria (PKU): Is due to deficiency of phenylalanine hydroxylase (PAH) or
dihydrobiopterin reductase. The types of PKU are explained in Table 8.5.
Table 8.5: Classification of phenylketonuria

Type Defect Clinical features and treatment
Type I phenylketonuria Lack of phenylalanine hydroxylase Hyperphenylalaninemia (> 20 mg/dL): mental
(PKU) (PAH), also called classical PKU retardation, convulsions, mousy odor in urine
Treatment: phenylalanine free diet
Type II Deficiency of dihydrobiopterin re- Mild disease, diet therapy
ductase
Type III Deficiency of dihydrobiopterin re- Mild disease, diet therapy
ductase
Type IV Defective synthesis of dihydrobiop- Tetrahydrobiopterin therapy
terin
Type V – Tetrahydrobiopterin therapy
Consequences of PKU (Fig. 8.15)

• Cancer—increased risk of skin cancers due to photosensitivity.
Fig. 8.15: Consequences of phenylketonuria
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Biochemical tests for diagnosis and screening of PKU

Elevated blood phenylalanine may not be detectable until 3–4 days postpartum, so these

tests are done 2–3 days after birth.
• Ferric chloride test in urine—blue-green color

• Guthrie test

• Prenatal screening—by deoxyribonucleic acid (DNA) analysis of amniotic cells.

Treatment of PKU

Phenylalanine free diet—to prevent early mental retardation.

15. Write a short note on alkaptonuria.

Cause: It is due to deficiency of homogentisic acid oxidase leading to excretion of ho-

mogentisic acid in urine.
Clinical features

• It is a relatively benign disorder

• Dark urine: On exposure to air, urine becomes dark

• Arthritis: Binding of homogentisic acid to cartilage induces inflammation of joints

• Ochronosis: Pigmentation of cartilage (often seen on the ear lobules).

Diagnosis

• Ferric chloride test—urine shows green color

• High performance liquid chromatography—to demonstrate elevated homogentisic acid.

16. Write short notes on tyrosinemia and albinism.

a. Tyrosinemia (Table 8.6).

Table 8.6: Types of tyrosinemia
Tyrosinemia type I Fumarylacetoacetate hydrolase Hepatic failure, hypoglycemia
Tyrosinemia type II Tyrosine transaminase Photophobia, corneal erosion, keratosis
b. Albinism: It is due to deficiency of enzyme tyrosinase in the melanocytes leading to de-

creased melanin synthesis.
Clinical features

• Hypopigmentation of hair, skin and fundus.

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TRYPTOPHAN
17. Explain how tryptophan is both glucogenic and ketogenic.

Catabolism: Tryptophan catabolism generates alanine and acetyl CoA, which form glucose
and ketone bodies respectively (Fig. 8.16).

Fig. 8.16: Catabolism of tryptophan
18. Explain formation of specialized products from tryptophan.

List of specialized products from tryptophan:
a. Serotonin.
b. Melatonin.
c. Nicotinamide adenine dinucleotide (NAD).
a. Serotonin (Fig. 8.17)
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Functions

• Neurotransmitter

• Sleep inducer

• Vasoconstriction and smooth muscle contraction

• Platelet aggregation.

Fig. 8.17: Serotonin synthesis (H2-biopterin, dihydrobiopterin; H4-biopterin, tetrahydrobiopterin)
b. Melatonin: Secreted by pineal gland (Fig. 8.18).

Function: Neurotransmission and maintenance of circadian rhythm (sleep-wake cycle).

Fig. 8.18: Melatonin synthesis
c. Nicotinamide (NAD): Coenzyme for oxidation reduction reactions (refer vitamin niacin

for more details).
19. Write a note on disorders of tryptophan metabolism.

Disorders of tryptophan metabolism are shown in Table 8.7.

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Table 8.7: Disorders of tryptophan metabolism

Name Defect Clinical features
Hartnup disease Defect in intestinal/renal absorption of Pellagra-like features—dementia, dermatitis,
tryptophan and other neutral amino ac- diarrhea, increased excretion of indican in
ids—valine, alanine, serine, threonine urine and stool (Fig. 8.19a).

[MN: VAST].
Carcinoid syndrome Tumor of argentaffin tissue. Increased Inceased excretion of 5-OH indole acetate
serotonin secretion. (5 HIAA) in urine. Associated with flushing,
hypertension, diarrhea, etc. (Fig. 8.19b).
Fig. 8.19a: Tryptophan degradation in intestine (PAPS, phosphoadenosylphosphosulfate)
Fig. 8.19b: Degradation of serotonin
METHIONINE
20. Discuss the metabolism of methionine.

• Methionine is a glucogenic, essential amino acid
• Products from methionine: S-adenosylmethionine (SAM), cysteine and the products of
transmethylation reactions.
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Catabolism (Fig. 8.20)

Fig. 8.20: Catabolism of methionine
21. Explain transmethylation reactions.

Methionine undergoes activation in the presence of ATP to produce SAM—methyl donor

for the transmethylation reactions [MN: SAM SAC].
Examples for transmethylation

• Guanidoacetate + SAM Creatine + S-adenosylhomocysteine (SAH)

• Norepinephrine + SAM Epinephrine + SAH

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• Nicotinic acid + SAM N-methylnicotinamide + SAH

• N-acetyl serotonin + SAM Melatonin + SAH
• Synthesis of polyamines from ornithine:

22. Name polyamines and mention their significance.
Polyamines: Putrescine, spermidine and spermine.
Synthesis: From ornithine and SAM.

Significance: Polyamines are essential for cell proliferation. In cancer, ornithine decar
boxylase activity and polyamine excretion in urine are increased.
23. Write a note on disorders of methionine metabolism.
Disorders of methionine metabolism are shown in Table 8.8.
Table 8.8: Disorders of methionine metabolism
Name Defect Clinical features
Hypermethioninemia Methionine adenosyltransferase Increased plasma methionine. Be-
nign condition
Cystathioninuria Cystathionase Mental retardation
Homocystinuria (autosomal re- Cystathionine b-synthase Dislocation of lens, osteoporosis,
cessive) cardiovascular disease
24. Explain the causes and features of homocystinuria.

Homocystinuria: Occurs due to defect in metabolism of homocysteine (Table 8.9) leading
to accumulation of homocysteine in blood (Fig. 8.21).
Table 8.9: Classification and clinical features of homocystinuria
Type I Cystathionine β-synthase deficiency ↑ homocysteine in blood and urine; mental retardation,
osteoporosis, dislocation of lens, thrombosis. (Homo-
cyteine interferes with collagen cross-linking; stimulates
platelet aggregation and vascular thrombosis by activating
Hageman factor)
Contd...
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Contd...

Type II Methylene tetrahydrofolate (THF) ↑ homocysteine in blood and urine + above features
reductase
Type III Defect in synthesis of active ↑ homocysteine in blood and urine + above features
methylcobalamin (vitamin B12)
Fig. 8.21: Causes of hemocystinuria
Biochemical tests for diagnosis of homocystinuria: Sodium nitroprusside test—detects

elevated homocysteine levels.
• Estimation of methionine levels in blood and urine

• Cystathionine b-synthase levels in fibroblast cultures.

CYSTEINE

It is a glucogenic and non-essential amino acid.
25. Explain the metabolism of cysteine (formation + degradation). Add a note on compounds

formed from cysteine.
Formation: Cysteine is formed during metabolism of methionine (refer Fig. 8.20).

Degradation: Transaminase converts cysteine into mercaptopyruvate and then into pyruvate

and hydrogen sulfide.
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Specialized products from cysteine

• Coenzyme A
• 4-phosphopantetheine
• Glutathione
• Taurine

• 3-phosphoadenosyl-5-phosphosulfate (PAPS).
a. Formation of coenzyme A
b. Glutathione
c. Taurine
d. 3-phosphoadenosyl-5-phosphosulfate (PAPS)
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26. Explain the metabolic defects of cysteine metabolism.

Metabolic defects of cysteine metabolism are shown in Table 8.10.

Table 8.10: Metabolic disorders of cysteine metabolism
Cystinuria Defect in cysteine transport system in kidney. In- Increased excretion of these amino acids
creased excretion of cysteine, ornithine, arginine, in urine

lysine [MN: COAL] in urine
Cystinosis Defective carrier-mediated transport of cysteine Cysteine gets deposited in soft tissues (kid-
ney, cornea, reticuloendothelial system)
HISTIDINE
27. Explain catabolism and specialized products from histidine.

Catabolism of Histidine
Histidine is a glucogenic and semi-essential amino acid (Fig. 8.22).
Fig. 8.22: Histidine catabolism (THFA, tetrahydrofolic acid)

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Specialized products from histidine

a. Histamine: Formed from histidine by decarboxylation reaction (Fig. 8.23).
b. Carnosine and anserine: These are formed from histidine and are required for muscle
contraction.

Fig. 8.23: Formation and effects of histamine
28. Explain the metabolic disorders of histidine

Metabolic disorders of histidine is shown in Table 8.11.
Table 8.11: Metabolic disorders of histidine
Histidinemia Enzyme histidase Mental retardation, increased urine and plasma histidine
Urocanic aciduria Enzyme urocanase Benign: Excretion of urocanic acid in urine
Folate deficiency Folate deficiency Formiminoglutamate (FIGLU) excretion, megaloblastic
anemia
BRANCHED CHAIN AMINO ACIDS
29. Discuss the catabolism of branched chain amino acids. Add a note on Maple syrup urine
disease (MSUD).
Catabolism: Refer Figure 8.24.
Maple syrup urine disease
Defect: Branched chain α-keto acid dehydrogenase deficiency.
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Fig. 8.24: Catabolism of branched chain amino acids; leucine (ketogenic); valine (glucogenic);
isoleucine (glucogenic + ketogenic).
Clinical features

• Vomiting

• Mental retardation (due to defective formation of myelin in CNS)

• Neurological manifestations (due to impairment in transport and meta bolism of other

amino acids)
• Acidosis (due to accumulation of corresponding keto acids)

• Urine has odor of burnt sugar (Maple syrup).

Biochemical tests for diagnosis and screening: Rothera's test is positive (urine), detection

of amino acids by chromatography or by enzyme analysis.
Treatment: Early detection and restriction of branched chain amino acids in the diet.

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ASPARTATE AND ASPARAGINE
30. Write the reaction by which aspartate and asparagine are formed. Name the compounds
derived from aspartate and asparagine.
Synthesis: Aspartate is a non-essential, glucogenic amino acid synthesized from oxaloacetate.

Compounds derived from aspartate and asparagine
• Urea synthesis
• N1 of purine ring
• Formation of ATP from IMP
• N1, C4, C5, C6 of pyrimidine ring
• Glucose (glucogenic) and protein synthesis.
GLUTAMATE
31. Explain how glutamate is synthesized and catabolized? Add a note on metabolic func-
tions of glutamate.
Synthesis
a. Glutamate is a non-essential amino acid synthesized from α-ketoglutarate by transamination

reaction.
b. From histidine—refer histidine metabolism.
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Glutaminase

c. Glutamine Glutamate + NH3

d. Glutamate is also formed during proline and arginine metabolism.

Catabolism

By glutamate dehydrogenase: Converted into -ketoglutarate and enters into tricarboxylic

a
acid (TCA) cycle.
Metabolic functions (significance) of glutamate

• Urea formation

• Glucose formation

• Formation of N-acetyl glutamate (NAG): This is a positive modifier of carbamoyl phosphate

synthetase I in urea cycle
• For trapping ammonia in non-toxic form—as glutamine

• Vitamin K-dependent activation of clotting factors requires glutamate for activation by

γ-carboxylation (refer vitamin K)
• It is an excitatory neurotransmitter in the brain

• It is required for formation of glutathione—intracellular antioxidant

• It is required for formation of γ-aminobutyric acid (GABA), an inhibitory neuro

transmitter.
32. What is the metabolic significance of glutamine?
• Ammonia is trapped in this form

• N3 and N9 of purine, amino group of GMP and N3 of pyrimidine comes from glutamine

• Maintenance of acid-base balance

• Takes part in conjugation reaction (phenylacetylglutamine)

• Required for synthesis of NAD and amino sugars.

33. Write a note on compounds formed from arginine.

List of compounds from arginine:

• Proteins—histones are rich in arginine

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• Creatine (glycine + arginine + SAM)

• Ornithine—used for urea cycle, polyamine and glutamate synthesis
• Glucose—arginine is glucogenic amino acid
• Nitric oxide (NO).

Functions of nitric oxide:
• Smooth muscle relaxation (BP regulation)
• Increases excretion of Na+ and H2O
• Inhibits platelet aggregation
• Neurotransmitter
• Increases host defence
• Glyceryl trinitrate—in treatment of angina pectoris.
Key Points
Hartnup disease: An autosomal recessive disorder with impairment of neutral amino acid transport

in renal tubules and small intestine leading to reduced intestinal absorption and increased renal loss
of tryptophan. This causes decreased availability of tryptophan and frequently pellagra-like rashes.
Some small peptides can be absorbed through the gaps between the intestinal cells and by γ-glutamyl
cycle. This kind of absorption of intact proteins may be beneficial [immunoglobulin A (IgA) by new-
born from colostrum] or harmful (gluten in non-tropical sprue).
Phenylalanine
Phenylalanine: Aromatic, essential, neutral, polar, glucogenic + ketogenic amino acid.
Pheochromocytoma: It is a neuroendocrine tumor of adrenal medulla (chromaffin cells), which se-
cretes excessive amount of catecholamines. It is diagnosed by estimation of urinary vanillylmandelic
acid (VMA) (normal 2–8 mg/day). Patient should avoid foods like chocolate, coffee, banana, vanilla
ice cream, citrus fruits before the test as they contain vanillin, which produces high VMA in urine.
Albinism: Defect in tyrosinase characterized by hypopigmentation.
Alkaptonuria: Defect in homogentisic acid oxidase, characterized by dark urine and arthritis.
Tyrosinemia: Defect in tyrosine transaminase.
α-methyl dopa: Is used in the treatment of hypertension. It inhibits DOPA decarboxylase and pre-
vents the formation of epinephrine.
Carbidopa is administered along with levodopa in Parkinson's disease: It will prevent peripheral
decarboxylation of levodopa → increased amount of levodopa reaches the brain.
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Tryptophan
Tryptophan is—polar, heterocyclic, aromatic, neutral, essential amino acid [MN: PHAN]

Tryptophan degradation in intestine: By bacteria to form indole and skatole (Fig. 8.19a).

Methionine
Methionine: Is sulfur containing essential glucogenic amino acid.

Folate-trap: To regenerate methionine from homocysteine, vitamin B12 and tetrahydrofolate are

essential. In vitamin B12 deficiency, conversion of homocysteine to methionine and regeneration of
active folate is blocked.
Difluoromethylornithine (DFMO): Suicide inhibitor of ornithine decarboxylase; used in the treatment

of Pneumocystis carinii, kala-azar and sleeping sickness.
Cysteine
Cysteine is a sulfur containing non-essential and glucogenic amino acid. Keratin is rich in

cysteine.
Histidine
Histidine is an essential basic glucogenic amino acid. It has an imidazole group, which has pKa of

6.8 and has maximum buffering capacity at physiological pH.
FIGLU test: After giving histidine load, FIGLU excretion in urine is measured. It is an indicator of

folate deficiency and can be used to differentiate megaloblastic anemia due to folate or B12 deficiency.
Branched Chain Amino Acids
Branched chain amino acids are transaminated and decarboxylated and finally converted into acetyl

-CoA or propionyl-CoA.
Aspartate and Asparagine
Asparaginase catalyzes cleavage of asparagine to aspartate and ammonia. Even though most

cells produce all the asparagine they need, some leukemia cells require exogenous asparagine. If
asparaginase is given to these patients, it can deprive the neoplastic cells of the asparagine that is
essential for their characteristic rapid growth. This can be exploited in treatment of cancer.
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9 Biological Oxidation
1. Define standard free energy change (∆G°) and energy coupling. Give some examples of
reactions with negative ∆G°. Add a note on energy coupling.
Definition: Standard free energy change is the energy change of a reaction during conver-
sion of 1 mole of each reactant to 1 mole of respective product at standard temperature
and pressure (∆G°). If the free energy change is negative, the reaction occurs spontaneously
and there is loss of free energy (exergonic). If the free energy change is positive, energy is
gained for the reaction to proceed (endergonic). Reactions having negative standard free
energy are given in Table 9.1.
Table 9.1: Reactions having negative standard free energy
Compound ∆G°l (kcal/mol)
Phosphoenolpyruvate → Pyruvate -14.8
1,3-bisphosphoglycerate → 3-phosphoglycerate + Pi -11.8
Creatine phosphate → Creatine + Pi -10.3
ATP → ADP + Pi -7.3
Glucose-1-phosphate → Glucose + Pi -5.0
Glucose-6-phosphate → Glucose + Pi -3.3
Glycerol-3-phosphate → Glycerol + Pi -2.2
Energy coupling: Free energy released during an exergonic reaction can be used for the
completion of another endergonic reaction.
For example:
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Phosphorylation of glucose is an endergonic reaction. For this reaction to occur, it is

coupled with hydrolysis of ATP (exergonic reaction).
2. Define and give examples of high-energy compounds.
Definition: Compounds, which have a high standard free energy (∆G°) of hydrolysis of
-7 kcal/mol or more are called high-energy compounds. These compounds release a
large quantity of free energy on hydrolysis (Table 9.2).
Table 9.2: High-energy compounds
Types of high-energy compound (~) Examples
Phosphates Adenosine triphosphate (ATP), adenosine diphosphate (ADP),
guanosine triphosphate (GTP), uridine triphosphate (UTP)
1,3-bisphosphoglycerate
Biological Oxidation
Creatine phosphate
Carbamoyl phosphate
Sulfur compounds S-adenosylmethionine (SAM)
Acetyl-CoA
3. Draw a neat diagram to show the flow of electrons in electron transport chain indicating
ATP producing sites.
Electron transport chain: It is involved in the transport of electrons and generation of
ATP from free energy released during the electron transport (oxidative phosphorylation).
Coenzymes, which can donate/accept electrons along with specialized electron carriers,
constitute the electron transport chain. The electrons are finally transported to oxygen to
reduce it to H2O (Fig. 9.1).
Fig. 9.1: Components of electron transport chain (FAD, flavin adenine dinucleotide; FMN, flavin mononucleotide; NADH,
nicotinamide adenine dinucleotide; FeS, iron-sulfur; ATP, adenosine triphosphate)
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Components of Electron Transport Chain

Location: Inner mitochondrial membrane
Protein complexes: I, II, III, IV
Complex I: NADH-Q oxidoreductase
Complex II: Succinate-Q reductase
Complex III: Cytochrome c oxidoreductase (Cyt b, Cyt c1, iron-sulfur protein)
Complex IV: Cytochrome c oxidase (Cyt a, Cyt a3 and Cu)
Mobile electron carriers: Coenzyme Q, cytochrome c.
Source of Electrons
• NADH: It is generated in the reactions catalyzed by pyruvate dehydrogenase, α-ketoglutarate
dehydrogenase, isocitrate dehydrogenase and malate dehydrogenase
• FADH2: It is generated in the reactions catalyzed by succinate dehydrogenase, fatty acyl-
CoA dehydrogenase.
4. Define chemiosmotic hypothesis with neat labeled diagram.
Chemiosmotic theory explains the process of oxidative phosphorylation. It states that free energy
liberated during the transport of electrons by electron transport chain is utilized in translocating
protons actively from matrix to intermembrane space of mitochondria. This generates a proton
gradient resulting in reentry of protons into matrix from intermembrane space, through ATP
synthase, leading to ATP synthesis (Fig. 9.2). Thus, oxidation is coupled to phosphorylation.
ATP synthase complex is located in the inner mitochondrial membrane and consists of Fo and
F1 subcomplexes. The protons reenter mitochondrial matrix by passing through Fo subcomplex
of ATP synthase, which results in conformational change in F1 leading to synthesis of ATP.
Fig. 9.2: Adenosine triphosphate (ATP) synthase complex
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Sites of Oxidative Phosphorylation

• Site 1: NADH and CoQ

• Site 2: Cyt b and Cyt c1

• Site 3: Cyt a, Cyt a3 and molecular oxygen:

– 2.5 ATP molecules are generated per molecule of NADH oxidized

– 1.5 ATP molecules are generated per molecule of FADH 2 oxidized.

5. Explain the shuttle mechanisms. What is their significance?
Definition: Shuttles are transport mechanisms that help to transport reducing equivalents

(NADH + H+) generated in cytosol during glycolysis to the matrix of mitochondria, where
they are processed to generate ATPs. Examples of shuttles:
i. Malate-aspartate shuttle (Fig. 9.3).

ii. Glycerophosphate shuttle (Fig. 9.4).

Fig. 9.3: Malate-aspartate shuttle
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Fig. 9.4: Glycerophosphate shuttle
Significance of shuttle mechanism is shown in Figure 9.5.
Fig. 9.5: Significance of shuttle mechanism
6. Enlist various inhibitors and uncouplers of electron transport chain indicating where
they act.
Inhibitors of electron transport chain are given in Table 9.3. In the presence of uncouplers,
oxidation occurs and energy released is not converted to ATP, but to heat.
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Table 9.3: Inhibitors and uncouplers of electron transport chain
Inhibitors Uncouplers
Complex l → Complex II Complex III b Complex IV ATP synthase Thyroxin* LCFA*

CoQ → CoQ → c1 → O2
Amobarbital Antimycin A Cyanide Oligomycin Thermogenin*
Rotenone Carboxin BAL Carbon monoxide Atractyloside Bilirubin*
Piericidin A Malonate 2,4-dinitrophenol
Hydrogen sulfide Dinitrocresol
Pentachlorophenol
BAL, British anti-Lewisite; LCFA, long-chain fatty acid; *Physiological uncouplers.
Key Points

British anti-Lewisite (BAL) or dimercaprol: It is used in the treatment of arsenic, mercury and

lead and other heavy metal poisoning. In addition, it used for the treatment of Wilson's disease, a
genetic disorder in which the body tends to retain copper.
Gibbs free energy (∆G): It is that part of the total energy change in a system that is available for

doing work.
First law of thermodynamics: During a reaction, total energy of a system remains constant; only

one form of energy is converted into another form.
Second law of thermodynamics: In spontaneous reactions, total entropy of a system increases.

Entropy (S): It is the extent of disorder of the system.

Redox potential (E0): It is a quantitative measure of tendency of oxidant to accept electrons or the

tendency of reductant to lose electrons.
Enzymes catalyzing redox reactions: Oxidases, dehydrogenases, hydroperoxidases, oxygenase,

superoxide dismutase.
Thermogenin: Physiological uncoupler found in brown adipose tissue. Thermogenin dissociates

oxidation from phosphorylation. Thus, it dissipates energy as heat.
Leber hereditary optic neuropathy (LHON), mitochondrial encephalomyopathy with lactic

acidosis and stroke-like episode (MELAS): Diseases due to mutations in mitochondrial DNA with
impaired ATP synthesis.
P/O ratio: Ratio between numbers of ADP converted to ATP per atom of oxygen. P/O ratio is 2.5 for

oxidation of substrate producing NADH (pyruvate, malate). P/O ratio is 1.5 for oxidation of substrate
producing FADH2 (succinate, fatty acyl-CoA).
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10 Vitamins
1. Define and classify vitamins with suitable examples.

Definition: Vitamins are organic substances, required in very small amounts, for optimum
growth and health, but cannot be synthesized in our body (except vitamin D and niacin).
Classification
i. Fat-soluble vitamins.
ii. Water-soluble vitamins (Fig. 10.1).
Fig. 10.1: Classification of vitamins with examples
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FAT-SOLUBLE VITAMINS
Vitamin A
2. Discuss vitamin A: a. forms, b. sources, c. RDA, d. functions, e. deficiency and toxic
manifestations.
Forms of vitamin A: Retinol, retinal, retinoic acid and beta carotene. The sources, RDA,

functions, deficiency and toxic manifestations are mentioned in Tables 10.1 and 10.2.
Table 10.1: Sources, RDA* and functions of vitamin A
RDA Sources Functions
750 µg of vitamin A Animal sources: liver, egg yolk, fish liver • Vision

oil, milk • Growth, development and tissue

Plant sources (carotene): carrot, differentiation

mango, papaya, green vegetables • For normal reproduction

• Maintain integrity of epithelial cells
Vitamins

• Synthesis of glycoproteins

• Antioxidant

*RDA, recommended daily allowance
• Visual cycle: Retinol is transported from liver to retina. In the retina, all-trans-retinol is

converted to 11-cis-retinol and then 11-cis-retinal, which combines with opsin to from
rhodopsin (visual pigment of the rods). When light falls on rhodopsin, conformational
changes occur resulting in the formation of metarhodopsin II, which activates transducin
leading to generation of nerve impulse. Finally, all-trans-retinal and opsin are released. The
all-trans-retinal is converted to 11-cis-retinal, which binds to opsin to regenerate rhodopsin
and the cycle is completed (Fig. 10.2, p. 143).
Table 10.2: Deficiency symptoms and toxic manifestations of vitamin A
Deficiency symptoms Toxic manifestations [MN: HALT]
Vision: Loss of sensitivity to green light, increased dark Headache, hepatomegaly, hypercalcemia
adaptation time, night blindness, xerophthalmia, Bitot's spots, Alopecia
keratomalacia, blindness
Others: Follicular hyperkeratosis, increased susceptibility Hyperlipidemia
to infection, anemia Teratogenicity
• Night blindness (nyctalopia): Vision is impaired in the dark.

• Xerophthalmia: Keratinization of conjunctiva and cornea → dryness of conjunctiva and cornea.

• Bitot’s spots: Grayish white plaques in conjunctiva due to conjunctival thickening.

• Keratomalacia: It is softening of the cornea. Infections can occur with perforation and blindness.

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Vitamins
Fig. 10.2: Wald's visual cycle
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Key Points

β-carotene dioxygenase: Cleaves β-carotene in the intestine to produce two retinal molecules.

Retinol: It is esterified with palmitic acid and stored as retinyl palmitate in the liver.

Retinol-binding protein (RBP): Transports retinol from liver to tissues. It is the earliest marker of pro-

tein energy malnutrition as its concentration in serum decreases early (half-life is only 10 hours).
Conopsin: Photosensitive protein present in cones. There are three types of conopsin—porphyropsin

(red), iodopsin (green), cyanopsin (blue).
Vitamin D
3. Discuss vitamin D: a. sources, b. RDA, c. synthesis and functions of calcitriol, d. defi-

ciency and toxic manifestations.
The sources, RDA and deficiency manifestations are mentioned in Tables 10.3 and 10.4.

Vitamins
Table 10.3: RDA* and sources of vitamin D

Vitamin D forms RDA and sources
Cholecalciferol/ergocalciferol/ 5–15 µg or 400 IU
calcitriol Fish liver oil, egg yolk
*
RDA, recommended daily allowance
Metabolic Functions of Vitamin D

Maintains serum calcium and phosphorus levels by acting on bone, kidney and intestine.
• Bone: Causes mobilization of calcium and phosphate from the bone and promotes bone
mineralization
• Kidney: Promotes reabsorption of calcium and phosphorus → decreases excretion of cal-

cium and phosphorus
• Intestine: Increases absorption of calcium (via calbindin) and phosphorus.
Causes of Deficiency
• Inadequate dietary intake

• Lack of exposure to sunlight

• Impaired absorption

• Liver and kidney diseases.

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Table 10.4: Deficiency manifestations of vitamin D

Deficiency diseases Signs and symptoms
Rickets: Improper mineralization resulting in soft Bow legs, forward projection of the breast one (pigeon
bones (occurs in children) chest), beading in the ribs (rachitic rosary), asym-
metrical or odd-shaped skull
Osteomalacia: Demineralization of previously formed Increased tendency of bone fractures, bone pain and
bone leading to increased susceptibility to fractures tenderness all over the body
(occurs in adults) Scoliosis: Lateral bending of spine
Kyphosis: Forward bending of spine
Toxic Manifestations of Vitamin D

Loss of appetite, nausea, thirst, calcium deposition in the heart, arteries and kidney (renal calculi).
4. Why is vitamin D called hormone?
• Synthesized inside the body, unlike a classical vitamin, which has to be supplied in the diet
Vitamins
• Synthesized as an inactive form and gets activated inside the body only when required
(Fig. 10.3)
• Like any hormone, it has a half-life (8 hours)
• It acts on distant target organs
Fig. 10.3: Calcitriol synthesis
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• It binds to a cytosolic receptor, which enters the nucleus and binds to a specific region on

genes and controls it. This action mimics that of a steroid hormone
• It is self-regulated, i.e. when its action is not required, it is converted into an inactive

metabolite 24,25-dihydroxycholecalciferol (Fig. 10.4).
Vitamins
Fig. 10.4: Autoregulation of calcitriol
5. Why does a person with chronic liver or chronic renal disease suffer from manifestations
of vitamin D deficiency?
In renal disease, 1-α-hydroxylation is impaired; in liver disease, 25-α-hydroxylation does not

occur. Thus, synthesis of calcitriol is impaired and the patient may present with symptoms
and signs of vitamin D deficiency.
Key Points
Transporter for vitamin D: Vitamin D2 and D3 are absorbed from the intestine and transported to

the liver bound to a specific vitamin D-binding protein.
1-α-hydroxylase: It is present in the proximal convoluted tubules of the kidneys, bone and placenta.

Mechanism of action of calcitriol is similar to steroid hormones: Upon entering the nucleus of

a cell, calcitriol functions as a steroid hormone and associates with the vitamin D receptor (VDR)
and promotes its association with the retinoic acid X receptor (RXR), which binds to the gene and
modulates transcription of calbindin in the intestine.
Hereditary rickets: It is an inherited form of the disease—the kidneys are unable to retain phosphate.

Fanconi syndrome: Disease of the proximal renal tubules of the kidney in which phosphate is

passed into urine, instead of being reabsorbed.
Anticonvulsants like phenobarbital: Can cause hypocalcemia, as it induces a microsomal enzyme

(cytochrome P450), which inactivates vitamin D.
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Vitamin K
6. What are the forms, sources, RDA, functions and deficiency manifestations of vitamin K?
Forms of vitamin K: Phylloquinone (K1), menaquinone (K2) and menadione (K3). Recom-
mended daily allowance (RDA) of vitamin K is 70–140 µg. The sources, functions, causes
and deficiency manifestations are mentioned in Tables 10.5 and 10.6.
Table 10.5: Sources and functions of vitamin K
Sources Functions
Green vegetables: cabbage, cauliflower, spinach (K 1); • Cofactor for synthesis of γ-carboxyglutamic
formed by intestinal bacteria, egg yolk, meat, liver (K2); acid (Gla) (Fig. 10.5)
water soluble, synthetic form (K3) • Formation of Gla is a post-translational modi-
fication required for activation of clotting fac-
tors II, VII, IX and X. Gla helps these proteins
to trap calcium
Vitamins
• Other Gla proteins: osteocalcin and matrix
Gla-protein (MGP) of bone
Fig. 10.5: Vitamin K cycle
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Table 10.6: Causes and deficiency manifestations of vitamin K
Causes for deficiency Manifestations
Prolonged antibiotic treatment: Kills intestinal flora (which forms • Easy bruising, ecchymosis, bleeding

vitamin K in adults) • Increased prothrombin time

Obstructive jaundice: No bile salt enters into the intestine, which
is necessary for absorption of fat-soluble vitamins
Malabsorption syndrome
Newborn (premature): Their gut is sterile and mother's milk is
not a good source of vitamin K
Anticonvulsant treatment: They interfere with absorption of
vitamin K
Key Points
Differentiating features of vitamin K and vitamin C deficiency: In contrast to vitamin K deficiency,

vitamin C deficiency will have increased bleeding time, but prothrombin time will be normal. Also,
Vitamins
there will be gum hyperplasia, inflammation, skeletal deformity and poor wound healing.
Warfarin and dicumarol: Structural analogues of vitamin K, competitively inhibit the enzyme epoxide

reductase and vitamin K quinone reductase. They are used as anticoagulants.
Toxic manifestations of vitamin K: In premature babies, menadione →↑ hemolysis →↑ serum

unconjugated bilirubin → kernicterus.
Vitamin E
7. Mention the sources, RDA and functions of vitamin E.

The RDA, sources and functions of vitamin E are mentioned in Table 10.7.

Table 10.7: RDA*, sources and functions of vitamin E
Active form RDA and sources Functions
α-tocopherol RDA: 8–10 mg • Antioxidant: Prevents peroxidation of

Wheat germ oil (richest source), polyunsaturated fatty acids and plasma lipoproteins

oils from nuts and seeds • Prevention of atherosclerosis, cancer and aging:

by reducing oxidative stress
• May have a role in cell signaling

*RDA, recommended daily allowance

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Key Points
Vitamin E deficiency: Deficiency in humans is very rare. The major symptoms are increased red

blood cell (RBC) fragility due to peroxidation.
WATER-SOLUBLE VITAMINS
Thiamine (Vitamin B1)
8. What are the sources, RDA, functions and deficiency manifestations of thiamine?
The sources, functions and deficiency manifestations are mentioned in Table 10.8 and
Box 10.1.
Table 10.8: Sources, RDA and functions of thiamine
Coenzyme form Sources and RDA Functions
Vitamins
Thiamine Unrefined grains, legumes (e.g. • Coenzyme for pyruvate dehydrogenase,
pyrophosphate (TPP) beans), nuts and yeast α-ketoglutarate dehydrogenase, branched chain
RDA: 1.0–1.5 mg (directly pro- α-ketoacid dehydrogenase and transketolase
portional to amount of carbohy- • Nerve conduction
drates in the diet)
Box 10.1: Deficiency manifestations of thiamine

Deficiency disease: (Fig. 10.6)
Dry beriberi (mainly neurological features)
• Peripheral neuropathy—diminished sensation and weakness in the legs and arms
• Muscle pain and tenderness, and difficulty in rising from a squatting position
Wet (cardiac) beriberi
• Edema, difficulty in breathing and ultimately congestive heart failure
Wernicke's encephalopathy and Korsakoff's psychosis: Seen in alcoholics and manifests as:
• Abnormal eye movements

• Abnormal gait
• Dementia
• Psychosis
Infantile beriberi: Occurs in children born to mother with thiamine deficiency. It presents with tachycardia,
convulsions, etc.
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Fig. 10.6: Consequences of thiamine deficiency (TPP, thiamine pyrophosphate; ATP, adenosine triphosphate;
LDH, lactate dehydrogenase; // = blocked)
Vitamins
Key Points
Requirement of B1 increases when a person is placed on high-carbohydrate diet: This is due

to increase in TPP-mediated reactions (e.g. pyruvate to acetyl-CoA, α-ketoglutarate to succinyl-CoA,
etc.) in carbohydrate metabolism.
Antithiamine factors: Certain raw freshwater fish, raw shellfish, ferns (they contain thiaminases,

which destroys thiamine).
Thiamine pyrophosphotransferase: Converts thiamine to its active form TPP in the brain and liver.

Transketolase activity: in RBCs is used to measure the thiamine status in an individual.

Riboflavin (Vitamin B2)
9. What are the sources, RDA and functions of riboflavin?

The sources, RDA and functions are mentioned in Table 10.9.

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Table 10.9: Sources, RDA and functions of riboflavin

Coenzyme forms RDA and sources Functions
Flavin mononucleotide RDA: 1.2–1.7 mg Flavin coenzymes are involved in mitochondrial respiratory
(FMN) Milk and dairy prod- chain, fatty acid and amino acid oxidation, and citric acid
Flavin adenine dinucle- ucts, egg, whole cere- cycle. They play a role in the metabolism of drugs and
otide (FAD) als, green leafy veg- toxins (cytochrome P450)
etables FMN-dependent enzymes
• L-amino acid oxidase
• NADH dehydrogenase (electron transport chain)
FAD-dependent enzymes
• Pyruvate dehydrogenase
• α-ketoglutarate dehydrogenase
• Glycerol-3-phosphate dehydrogenase (shuttle transport
in electron transport chain)
• Acyl-CoA dehydrogenase
• Xanthine oxidase
Vitamins
Key Points
Deficiency manifestations of riboflavin: Glossitis, angular stomatitis, cheilosis.

Niacin (Vitamin B3)
10. What are the sources, RDA, functions and deficiency manifestations of niacin?
The sources, functions and deficiency manifestations are mentioned in Tables 10.10 and 10.11.
Table 10.10: Sources, RDA and functions of niacin
Coenzyme form RDA and sources Functions
Nicotinamide adenine RDA: 10–15 mg Coenzyme in oxidation-reduction (redox) reactions
dinucleotide (NAD+) and Yeast, meat, poultry, • NAD+ is involved in the catabolism of
nicotinamide adenine fish, cereals, legumes carbohydrates, fats, proteins and alcohol to
dinucleotide phosphate produce energy
(NADP+) • For example: α-ketoglutarate → succinyl-CoA;
Succinate → fumarate
• NADP+ functions more often in biosynthetic
(anabolic) reactions, such as in the synthesis of
fatty acids and cholesterol
• NAD+ is source of ADP-ribose for ADP-ribosylation
of proteins
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Table 10.11: Causes and deficiency manifestations of niacin
Causes for deficiency Manifestations of niacin deficiency
Inadequate dietary intake, Pellagra (4D): Dermatitis, Diarrhea, Dementia, Death

Hartnup disease, carcinoid Dermatitis: Scaly, dark-pigmented rash, develops symmetrically
syndrome, pyridoxine (B6) in areas exposed to sunlight
deficiency Diarrhea: With blood and mucus in stools
Dementia: Loss of memory, inability to concentrate, irritability
Key Points

Carcinoid syndrome and pellagra: Normally 1%–2% of tryptophan is converted to serotonin in

argentaffin cells of gastrointestinal tract (GIT) and the rest is converted to niacin. But in carcinoid
syndrome (tumor of argentaffin cells), more than 60% of tryptophan is diverted for serotonin, so less
is available for niacin synthesis leading to pellagra.
Hartnup disease and pellagra: Tryptophan and other neutral amino acids are not absorbed from
Vitamins

intestine and also from kidneys, thus depleting amino acid tryptophan. This in turn leads to niacin
deficiency (pellagra).
Pyridoxine and pellagra: Synthesis of nicotinamide from tryptophan is pyridoxal phosphate (PLP)

dependent; so in its deficiency, this pathway will not proceed and may lead to pellagra.
Pharmacologic doses of nicotinic acid have been known to reduce serum cholesterol.

Pyridoxine (Vitamin B6)
11. What are the sources, RDA and functions of pyridoxine?

The RDA, sources and functions are mentioned in Table 10.12.

Table 10.12: RDA, sources and functions of pyridoxine
Pyridoxal RDA: 1.4–2.0 mg PLP acts as a coenzyme for:

phosphate (PLP) Whole grain cereals, • Transamination: Aspartate + -ketoglutarate → glutamate

a
eggs, legumes, milk + oxaloacetate
• Deamination: Serine → pyruvate

• Transsulfuration: Formation of cysteine from methionine

• Cystathionine synthase, cystathionase, kynureninase

• Heme synthesis: Aminolevulinic acid (ALA) synthase

• Decarboxylation reactions of amino acids

• Ceramide synthesis (palmitoyl-CoA + serine)

• Glycogenolysis

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Key Points
Tuberculosis: The antitubercular drug isoniazid, competes with pyridoxine kinase and blocks the forma-
tion of PLP. Thus, long-term treatment with isoniazid can result in pyridoxine deficiency, which manifests
as peripheral neuropathy; so pyridoxine is given along with isoniazid in tuberculosis patients.
Treatment of microcytic anemia: Along with iron and other supplements, pyridoxine is given, which
helps in heme synthesis [aminolevulinic acid (ALA) synthase reaction].
In infants, pyridoxine deficiency can predispose to seizures: This may be due to decreased
formation of γ-aminobutyric acid (GABA) from glutamic acid (decarboxylation reaction). GABA is an
inhibitory neurotransmitter, so its decreased concentration can lead to seizures.
Deficiency manifestations of B6: Irritability, depression, confusion, glossitis, stomatitis.
Cycloserine, penicillamine: Form complexes with vitamin B6, creating a functional deficiency.
Parkinsonism treated with levodopa: Administration of pyridoxine will facilitate the peripheral
decarboxylation of levodopa to dopamine; treatment becomes less effective as less of levodopa is
available to cross into the brain.
Dietary requirement of B6 increases when a person is placed on high-protein diet: Pyridoxine

Vitamins
has significant role in protein metabolism (transamination, decarboxylation, deamination and cond
ensation reactions). So, its requirement is directly proportional to protein intake.
Folic Acid (Vitamin B9)
12. What are the sources, RDA, functions and deficiency manifestations of folic acid?
The RDA, sources, functions and deficiency manifestations are mentioned in Tables
10.13 and 10.14.
Table 10.13: RDA, sources and functions of folic acid
Tetrahydrofolic acid RDA: 200 µg • Carry and transfer various forms of one carbon units
(THFA) Green leafy vegetables during biosynthetic reactions; one carbon donors
(foliage), legumes and are Glycine, Histidine, Odd chain fatty acids, Serine,
fortified cereals Tryptophan [MN: GHOST]
• Required for biosynthesis of serine, methionine,
glycine, choline, purine nucleotides and thymidylate
(dTMP)
• Conversion of homocysteine to methionine
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Table 10.14: Causes and deficiency manifestations of folate
Causes of deficiency Manifestations of folate deficiency
Dietary deficiency: alcoholics ↓ DNA synthesis during erythrocyte maturation → ↓ DNA replication + unin-
and overcooking of food hibited protein synthesis → bigger than normal RBCs (megaloblasts)
Impaired absorption: tropical Homocystinemia: Folic acid is required (with B12 and B6) for synthesis of
sprue, celiac disease methionine from homocysteine. So, folic acid deficiency leads to homo-
Increased demand: pregnan- cystinemia
cy, lactation Neural tube defect: Since folate is required for nucleic acid synthesis,
Anticancer drugs: lack of this vitamin leads to neural tube defects in newborn. Hence, every
methotrexate pregnant woman is administered folic acid in the first trimester
Predisposition to cancer
13. Mention folate antagonists and their uses.

The folate antagonists and their uses is given in Table 10.15.

Table 10.15: Folate antagonists
Vitamins
Names Uses
Methotrexate Inhibits dihydrofolate reductase. Used as an anticancer drug

Trimethoprim Inhibits bacterial dihydrofolate reductase. Used as an antimicrobial agent
Pyrimethamine Antimalarial agent
Sulfonamide Antibacterial agent
Key Points
Folinic acid (leucovorin or citrovorum factor): It is administered before giving methotrexate to

prevent its systemic toxicity; methotrexate blocks the conversion of dihydrofolate to THFA. Folinic
acid (N5 formyl-THFA) is the active coenzyme form and minimizes toxic effect of methotrexate on
normal cells; this is leucovorin rescue.
Formiminoglutamate (FIGLU) excretion test: It is done to detect folic acid deficiency. In folic acid

deficiency, increased excretion of FIGLU is observed after a load, due to impaired conversion of
FIGLU to glutamate.
Cobalamin (Vitamin B12)
14. What are the sources, RDA, functions and deficiency manifestations of cobalamin?
The RDA, sources, functions and deficiency manifestations of cobalamin (vitamin B 12) are

given in Tables 10.16 and 10.17.
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Table 10.16: RDA, sources and functions of cobalamin

5-deoxyadenosylcobalamin, RDA: 1 µg • Methylcobalamin: Required for enzyme
Methylcobalamin Only bacteria can synthesize methionine synthase (homocysteine →
vitamin B12 methionine)
Animal products such as meat, • 5-deoxyadenosylcobalamin: Required
eggs, fish for enzyme methylmalonyl-CoA mutase
No plant source (propionyl-CoA → succinyl-CoA)
Table 10.17: Causes and deficiency manifestations of cobalamin

Causes of deficiency Deficiency manifestations
Decreased intake: Strict vegetar- Megaloblastic anemia: Due to folate trap, folate is unavailable to par-
ians and alcoholics ticipate in DNA synthesis resulting in formation of megaloblasts leading
Impaired absorption: Due to lack to anemia
of intrinsic factor (pernicious ane- Homocysteinemia: Vitamin B12 is required (with folic acid and B6) for
Vitamins
mia); atrophic gastritis synthesis of methionine from homocysteine
Increased demand: Pregnancy ↓ Vitamin B12 → ↑ homocysteine → ↑ risk of cardiovascular disease
Methylmalonic acidemia: Due to block in the conversion of methyl
malonic acid to succinyl-CoA
Neurological symptoms: Demyelination due to vitamin B12 deficiency—
peripheral neuropathy, ataxia, both sensory and motor fibers are af-
fected
Key Points
Absorption of B12: Vitamin B12 binds to intrinsic factor (IF), a glycoprotein secreted by parietal cells
of stomach. Receptors on the surface of the ileum take up the IF-B12 complex in the presence of
calcium. It is bound to transcobalamin II and transported to the liver.
Vitamin B12: Only water-soluble vitamin stored in the liver (sufficient for upto 6 years).
Subacute combined degeneration of spinal cord (SACD): Group of neurologic symptoms—peripheral
neuropathy, tingling, numbness, weakness, mental disturbances and ataxia seen in cobalamin deficiency.
Folate trap: In vitamin B12 deficiency, conversion of methyltetrahydrofolate (methyl-FH4) to tetrahy-
drofolate (FH4) is affected and results in accumulation of methyl TH4. Thus, deficiency of vitamin
B12 can cause secondary folate deficiency.
Cyanocobalamin, mehylcobalamin (oral) and hydroxocobalamin (parenteral/injectable): Are
commercially available forms of cobalamin.
Schilling test: This is a test used to detect pernicious anemia (or to detect cause of megaloblas-

tic anemia). The patient is first given a saturating dose of vitamin B12 by injection and then given
radiolabeled B12 orally. If after sometime, there is no appearance of radioactivity in urine, it means
oral B12 is not absorbed. Then, oral radiolabeled vitamin B 12 is given along with intrinsic factor and
urine radioactivity is checked after some time. If it appears in urine, it indicates the person has per-
nicious anemia. If there is still no radioactivity in urine, the person has malabsorption syndrome.
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Biotin (Vitamin B7)
15. What are the sources, RDA, functions and deficiency manifestations of biotin?
The RDA, sources, functions and deficiency manifestations of biotin (vitamin B 7) is given

in Table 10.18.
Table 10.18: RDA, sources, functions and deficiency manifestations of biotin
RDA and sources Functions Deficiency manifestations
RDA: 30–100 µg Required for carboxylation reactions Dermatitis, hair loss (deficiency is rare)
Egg yolk, liver, yeast, in fatty acid synthesis and gluconeo-
intestinal flora genesis
• Acetyl-CoA carboxylase

• Pyruvate carboxylase

• Propionyl-CoA

carboxylase

Vitamins
Key Points
Biotinidase: Shown to catalyze the biotinylation of histones, suggesting that biotin may play a role

in DNA replication and transcription.
Consumption of raw egg white for a prolonged period may cause biotin deficiency as it contains

a protein avidin, which strongly binds biotin and prevents its absorption.
Pantothenic Acid (Vitamin B5)
16. What are the sources, RDA and functions of pantothenic acid?
The sources, RDA, functions and deficiency manifestations of pantothenic acid (vitamin

B5) are given in Table 10.19.
Table 10.19: RDA, sources, functions and deficiency manifestations of pantothenic acid
Coenzyme form RDA and Sources Functions Deficiency
manifestations
Coenzyme A (CoASH) RDA: 10 mg • Tricarboxylic acid (TCA) cycle and Deficiency is rare

Liver, yeast, egg yolk, gluconeogenesis • Burning foot

intestinal flora • For synthesis of fatty acid, choles- syndrome:

terol and steroid hormones Numbness and

• Acetylcholine, melatonin synthesis tingling of

• Heme synthesis hands and feet

• Ketone body synthesis and

utilization
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Ascorbic Acid (Vitamin C)
17. What are the sources, RDA, functions and deficiency manifestations of vitamin C?
The RDA, sources and functions of ascorbic acid (vitamin C) is given in Table 10.20.
Table 10.20: RDA, sources and functions of vitamin C
RDA and sources Functions
RDA: 75 mg • Hydroxylation of proline and lysine residues in collagen
Amla, guava, citrus fruits, green vegeta- • Antioxidant: protects proteins, lipids, carbohydrates and
bles nucleic acids from damage by free radicals
• Synthesis of norepinephrine, carnitine
• Involved in the conversion of cholesterol to bile acid
• Role in tryptophan and tyrosine metabolism
Scurvy
Deficiency of vitamin C leads to scurvy: There is poor hydroxylation of proline and lysine
Vitamins
residues of collagen.
Symptoms: Bleeding and easy bruising, hair and tooth loss, joint pain and swelling, poor
wound healing, etc.
Treatment: Vitamin C supplementation.
Key Points
High doses of vitamin C predisposes to renal stone: Vitamin C is metabolized to oxalic acid and

it is capable of precipitating calcium as calcium oxalate in the urine.
Vitamin C cannot be synthesized in humans: Because they lack the enzyme, L-gulonolactone

oxidase.
Lipoic acid: Acts as coenzyme for oxidation-reduction reactions (pyruvate dehydrogenase and
α-ketoglutarate dehydrogenase) and has antioxidant functions.
Choline: Lipotropic factor and prevents fatty liver.
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11 Minerals
MACROMINERALS
1. Classify minerals. Add a note on the sources, requirements and metabolic functions of

macrominerals.
The classification of minerals is given in Table 11.1.
Table 11.1: Classification of minerals
Macrominerals Microminerals (trace elements) Toxic minerals
Daily requirement > 100 mg, e.g. calcium, Daily requirement < 100 mg, e.g. Aluminum, lead, cadmium,
magnesium, sodium, potassium, phospho- iron, iodine, copper, zinc, manga- mercury
rus, chloride and sulfur nese, selenium, fluoride
The sources, requirements and metabolic functions of macrominerals are given in Table 11.2.
Table 11.2: Sources, requirements and metabolic functions of macrominerals
Mineral and serum Food sources Daily requirement Metabolic functions
levels
Calcium Milk and dairy prod- Adults: 500–800 mg • Muscle contraction

9–11 mg% ucts, cereals, fish, Children and lactat- • Secretion of hormones

egg, cabbage ing mother: 1,000– • Bone and teeth formation

1,300 mg • Second messenger

• Nerve transmission

• Activation of enzymes

• Blood coagulation

Phosphorus Milk, cereals, meat, 800–1,200 mg • Formation of bone and teeth

Adults: 2.5–4.5 mg/dL fish, nuts • Acid-base regulation—acts as

Children: 4–6 mg/dL a buffer
• Energy storage and transfer

• Regulation of enzyme activity

• Part of nucleic acids

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Mineral and Food sources Daily requirements Metabolic functions

serum levels
Magnesium Unrefined grains, nuts, 300–400 mg • Cofactor for enzymes hexoki-

1.8–2.2 mg/dL milk, green nase and fructokinase
leafy vegetables • Muscle and nerve function
Sodium Salt, nuts, whole grains, 1–5 g • Osmotic pressure and water
135–145 mEq/L butter, legumes balance; regulates plasma
volume
• Acid-base balance
• Cell membrane permeability
• Muscle and nerve function
Chloride Salt, leafy vegetables 1.5 g • Acid-base balance, fluid and
95–105 mEq/L electrolyte balance
• Acid secretion in the stomach
Minerals
Potassium Banana, tender coconut 2–5 g • Major cation in the intracellular
3.5–5 mEq/L water, apple, dates, fluid
legumes, meat • Maintenance of intracellular
osmotic pressure
• Normal muscle and nerve
function
• Acid secretion in the stomach
is by H+-K+-ATPase
2. Enlist the factors affecting calcium absorption.

The factors affecting calcium absorption are given in Table 11.3.
Table 11.3: Factors affecting calcium absorption
Facilitators of calcium absorption [MN: CLAAP] Inhibitors of calcium absorption
Calcitriol Phytic acid
Lysine Oxalates
Acidic pH Fatty acids
Arginine Phosphates
Parathyroid hormone (PTH)
3. Explain factors regulating serum calcium levels.

Calcium balance is regulated by calcitriol, calcitonin and parathyroid hormone (PTH)
through their actions on kidney, bone and intestine (Table 11.4).
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Table 11.4: Regulation of serum calcium
Organ Calcitriol (↑ plasma calcium) PTH (↑ plasma calcium) Calcitonin (↓ plasma calcium)
Intestine ↑ absorption of calcium and ↑ absorption of calcium _
phosphate (mediated by calcitriol)
Kidney ↑ reabsorption of calcium and ↑ reabsorption of calcium ↑ excretion of phosphate
phosphate and ↑ excretion of
phosphate
Bone ↑ bone resorption ↑ bone resorption ↓ bone resorption
↑ bone mineralization (↑ osteoclast activity)
↑, increase; ↓, decrease
4. Enlist the causes of hypercalcemia and hypocalcemia.

Hypercalcemia: Serum calcium > 11 mg/dL.
Hypocalcemia: Serum calcium < 8.5 mg/dL.
The causes of hypercalcemia and hypocalcemia are given in Table 11.5.
Minerals
Table 11.5: Causes of hypercalcemia and hypocalcemia

Hypercalcemia [MN: Hyper PTH] Hypocalcemia [MN: Hypo PARR]
Hyperparathyroidism Hypoparathyroidism
Multiple myeloma Pseudohypoparathyroidism
Milk-alkali syndrome Acute pancreatitis
Paget’s disease Dietary deficiency
Thiazide diuretics Renal tubular acidosis
Hypervitaminosis D Renal failure
5. Enlist the causes of hyperphosphatemia and hypophosphatemia.

The causes of hyperphosphatemia and hypophosphatemia are given in Table 11.6.
Table 11.6: Causes of hyperphosphatemia and hypophosphatemia
Hyperphosphatemia Hypophosphatemia
Renal failure Malnutrition
Hypoparathyroidism Hyperparathyroidism
High doses of calcitriol Fanconi syndrome
Aluminum-containing antacids
6. Enlist the causes and clinical manifestations of hypernatremia and hyponatremia.

Hypernatremia: ↑ sodium level in blood > 145 mEq/L.
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161
Hyponatremia: ↓ sodium level in blood < 135 mEq/L.

The causes and clinical manifestations of hyponatremia and hypernatremia are given in
Table 11.7.
Table 11.7: Causes and clinical manifestations of hypernatremia and hyponatremia
Causes of hyponatremia [MN: SIADH] Causes of hypernatremia
Sweating Dehydration
Inappropriate ADH secretion (SIADH) Diabetes insipidus
Addison's disease Steroids
Diuretics, Diarrhea Cushing's disease
Heart failure Primary hyperaldosteronism
Clinical manifestations of hyponatremia Clinical manifestations of hypernatremia
Minerals
Drowsiness Nausea
Confusion Vomiting
Decrease in BP Thirst
Tremors Restlessness
Coma Confusion
7. What are the causes and effects of hypokalemia?

The causes and effects of hypokalemia (serum K+ < 3.5 mEq/L) are given in Table 11.8.
Table 11.8: Causes and effects of hypokalemia

Causes Effects
Diarrhea Muscle weakness and cramps, abnormal heart
Conn's syndrome rhythm—arrhythmias, paralytic ileus, depressed reflexes
Insulin therapy of diabetic ketoacidosis
Alkalosis
Diuretics—thiazides, loop diuretics
8. What are the causes and effects of hyperkalemia?

The causes and effects of hyperkalemia (serum K+ > 5 mEq/L) are given in Table 11.9.
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Table 11.9: Causes and effects of hyperkalemia
Causes Effects
Renal failure Bradycardia, cardiac arrhythmias, cardiac
Addison's disease arrest in diastole
Potassium-sparing diuretics
Hemolysis
Tissue damage*
Metabolic acidosis*
*
Due to redistribution of potassium to extracellular fluid.
Key points
Acidosis and hypercalcemia: Acidosis causes release of calcium bound to albumin leading to an

increase in plasma ionizable calcium. Reverse occurs in alkalosis.
Toxicity of magnesium: Diarrhea, lethargy, CNS depression, cardiac arrhythmia.

Calcium toxicity: Loss of appetite, nausea, vomiting, constipation and renal stones.

Minerals
Tetany: Caused due to extensive spasm of skeletal muscle in persons with hypocalcemia.

MICROMINERALS

9. Enlist the sources, daily requirements and metabolic functions of microminerals.

The sources, daily requirements and metabolic functions of microminerals are given in
Table 11.10.
Table 11.10: Sources, daily requirements and metabolic functions of microminerals
Mineral RDA and sources Metabolic functions
Iron Recommended daily allowance • Oxygen transport and storage

(RDA) • Electron transport and energy metabolism

Men: 10 mg • Component of enzymes: Xanthine oxidase, cyto-

Women: 20 mg chrome P450, tryptophan pyrrolase, ribonucleotide
Pregnancy: 40 mg reductase
Liver, meat, poultry, fish, leafy veg-
etables, dairy products, dry fruits,
jaggery
Copper RDA: 2–3 mg • Oxidation-reduction reactions: Cytochrome c oxi-

Meat, shellfish, cereals dase, lysyl oxidase, dopamine-b-monooxygenase,
monoamine oxidase, tyrosinase, extracellular su-
peroxide dismutase
• Scavenging of free radicals: ceruloplasmin

• Iron absorption

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Mineral RDA and sources Metabolic functions

Iodine RDA: adults: 100–150 mg • Formation of thyroid hormones-thyroxine (T4) and
Pregnant women: 200 mg triiodothyronine (T3)
Seafood, iodized salt
Zinc RDA: 10–20 mg • Cofactor for superoxide dismutase (cytosolic), car-
Shellfish, meat, nuts and legumes bonic anhydrase, carboxypeptidase A, DNA and
RNA polymerase, alcohol dehydrogenase
• Required for secretion and storage of insulin
• Protein structure and regulation of gene expression:
zinc finger motif
• Maintain the taste: Gusten, a protein containing zinc,
helps in taste sensation
• Has a role in apoptosis, hair growth, sperm matura-
tion and wound healing
Manganese RDA: 5 mg • Cofactor for superoxide dismutase
Nuts, tea leaves (of mitochondria), pyruvate carboxylase, phospho-
Minerals
enolpyruvate carboxykinase (PEPCK)
Fluoride RDA: 1 ppm in drinking water; • It forms fluorapatite layer on the tooth enamel and
Marine fish, fluoridated toothpastes protects the tooth against decay
Selenium RDA: 50–100 µg • Enzymes requiring selenium: Glutathione peroxi-
Meat, seafood dase, iodothyronine deiodinase
• Antioxidant
10. Enumerate iron absorption and factors affecting it.

The absorption of iron is shown in Figure 11.1 and factors affecting iron absorption are
given in Table 11.11.
Fig. 11.1: Iron absorption
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164

Regulation of Iron Absorption
i. Mucosal block theory: Iron metabolism is regulated at the level of absorption. If there is

excess of ferritin in mucosal cells, iron absorption is blocked. If the ferritin content in the
mucosal cell is less, more iron is absorbed. This mechanism of regulation of iron absorp-
tion, when iron is in excess in mucosal cells is called mucosal block theory.
ii. Anemia: There is increased iron absorption in anemia.
Table 11.11: Factors affecting iron absorption
Enhancers of iron absorption* Inhibitors of iron absorption* (form insoluble
(facilitate conversion of ferric to ferrous form) complexes with iron)
Vitamin C Phytic acid
Citric acid Calcium
Acidic pH Polyphenols
Lactic acid Phosphates, oxalates, antacids
*
Only non-heme iron in the diet is influenced by factors mentioned.
Minerals
11. What are the causes and manifestations of iron deficiency?
Causes

Nutritional deficiency, menstruation, repeated pregnancy, chronic blood loss (piles), hookworm
infestation.
Manifestations

• Fatigue, tachycardia and palpitations. In severe iron deficiency, brittle and spoon-shaped
nails, sores at the corners of the mouth and atrophy of taste buds can occur
• Difficulty in swallowing due to the formation of webs of tissue in the throat and esophagus
(Plummer-Vinson syndrome)
• Pica: A behavioral disturbance characterized by the consumption of non-food items
• Peripheral smear shows: Microcytic, hypochromic anemia.
12. What are the causes of iron overload?

• Hemochromatosis: An increase in total body iron (> 15 g) with tissue damage. Iron over-
load could be hereditary or secondary
Hereditary hemochromatosis: It is due to gene mutation. There is increased absorption of iron

from the small intestine
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165
Secondary iron overload is due to ineffective erythropoiesis, repeated blood transfusions,

excess of iron intake (bantu siderosis), etc. This may predispose to bronze diabetes (skin
pigmentation along with diabetes mellitus due to pancreatic damage).
Key Points
Goiter: Iodine deficiency in adults leads to enlargement of thyroid glands (goiter) and hypothy-
roidism.
Congenital hypothyroidism (cretinism): Due to iodine deficiency in pregnant mother causing
irreversible mental retardation in newborn (thyroid hormone is required for the myelination of
the CNS).
Menkes disease: It is due to defect in transport of copper from intestinal cell to blood. It is char-
acterized by mental retardation, impaired growth and kinky hair.
Wilson's disease (hepatolenticular degeneration): It is due to defect in transport of copper and
secretion of ceruloplasmin from the liver. There is accumulation of copper in liver, basal ganglia,
cerebral cortex, cornea (Kayser-Fleischer ring) and kidney.
Minerals
Acrodermatitis enteropathica: Genetic disorder resulting from impaired uptake and transport of
zinc; patient presents with perioral, genital, anal dermatitis, hair loss, growth retardation, diarrhea
and decreased cell-mediated immunity.
Keshan disease: Seen among young women and children in a selenium deficient region of China.
It is characterized by the sudden onset of cardiac insufficiency.
Kashin-Beck disease: It is due to selenium deficiency characterized by the degeneration of the
articular cartilage between joints.
Dental fluorosis: It is a result of excess fluoride intake prior to the eruption of the first permanent
teeth characterized by small opaque white flecks or spots on the enamel of the teeth. Severe dental
fluorosis results in marked staining and pitting of the teeth.
Skeletal fluorosis: It is a toxic manifestation of fluoride excess characterized by increased bone
mass. This may progress to calcification of ligaments, immobility, muscle wasting and neurological
problems.
Iron is stored in reticuloendothelial system (RES): Bone marrow, liver and intestinal mucosal
cells as ferritin.
Copper: Has a role in iron metabolism.
Antacids: H2 receptor antagonists and proton pump inhibitors may impair iron absorption.
Goitrogens: Some foods (cabbage, cauliflower) contain substances that interfere with iodine utiliza-
tion or thyroid hormone production. They are called as goitrogens.
Molybdenum: Required for action of enzyme xanthine oxidase.
Cobalt: It is constituent of vitamin B12 and is also used in treatment of cancer (radioactive cobalt).
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12 Nutrition
1. Define calorific value of food with examples.

Definition: Calorific value is defined as the amount of energy obtained from 1 g of food-

stuff (Table 12.1).
Table 12.1: Calorific values of different foods
Name of the foodstuff Calorific value (cal/g)
Carbohydrates 4
Proteins 4
Lipids 9
Alcohol 7
2. Define respiratory quotient with examples.

Definition: Respiratory quotient (RQ) is defined as the ratio of volume of carbon dioxide

generated to the oxygen used up during a given time (Table 12.2).
Table 12.2: Respiratory quotient of different foods
Type of food Respiratory quotient
Carbohydrates 1
Proteins 0.8
Fats 0.7
3. Define basal metabolic rate (BMR). What is the unit of expression of BMR? Add a note
on factors affecting the same.
Definition: Basal metabolic rate (BMR) may be defined as the energy required by an awake

individual in resting, postabsorptive state (12 hours after last meal).
Average BMR is 24 kcal/kg/day or 34 kcal/m2/h.
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Factors Affecting BMR

• Age: BMR of children is much higher than adults
• Sex: Women normally have lower BMR than men
• Surface area: BMR is directly proportional to the body surface area
• Climate: In colder climates, the BMR is high and in tropical climates it is proportionately low
• Fever: During febrile states, BMR is high
• Hormones: Thyroid hormones increase BMR.
4. Define specific dynamic action (thermogenic effect of food) with examples.
Definition: Specific dynamic action (SDA) may be defined as the extra heat produced other
than the energy normally generated from a particular amount of food. This 'extra heat' is
derived from energy reserves of the body. It is used for the metabolic interconversions of
food in the liver before it can be used by the body (Table 12.3).
Nutrition
Table 12.3: SDA of different foods
Type of diet Specific dynamic action (SDA)
Proteins 30%
Carbohydrates 15%
Fats 5%
Mixed diet 10%
5. What are dietary fibers? Why are they important?

Definition: Dietary fibers are non-digestible/non-absorbable carbohydrates in diet. Aver-
age intake of these should be 15–25 g/day. For example, cellulose, hemicellulose, lignin,
pectin, etc.
Functions of Dietary Fibers

• Increase peristalsis and prevent constipation
• Increase bile acid excretion
• Increase cholesterol excretion
• Prevent colon cancer
• Improve glucose tolerance
• Act as an antioxidant.
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Adverse Effects of Fiber

Consumption of large quantities of fiber can:
• Affect the absorption of certain nutrients
• Can cause flatulence and discomfort due to fermentation of some fibers by intestinal bacteria.
Sources of Dietary Fiber

The sources of dietary fibers are fruits, leafy vegetables, whole wheat legumes, rice bran, etc.
6. Define glycemic index with examples. What is its significance?
Definition: It is a measure of increase in blood glucose after consuming 50 grams of food as

compared to that seen after consuming 50 grams of glucose [glucose tolerance test (GTT)].
Area under GTT curve after 50 g of test meal

× 100
Area under GTT curve after 50 g of glucose

Nutrition

Significance: Diabetics should consume food with low glycemic index. Foods like ice cream,

milk, legumes, peas, beans, peanuts have low index; potato, bread, rice, fruits have high
glycemic index.
7. Write a note on nitrogen balance.
Definition: It is a state when a person's daily intake of nitrogen is equal to its daily excretion.

Classification
I = Intake, U = Urinary, F = Fecal, S = Sweat concentration of nitrogen.
i. Negative nitrogen balance: It occurs when a person's excretion of nitrogen exceeds his
daily intake and is often associated with muscle wasting (I < U + F + S). For example,
• Kwashiorkor and marasmus
• Corticosteroid therapy
• Cancer and uncontrolled diabetes.
ii. Positive nitrogen balance: It occurs when a person's nitrogen intake is more than excretion
(I > U + F + S). It is often associated with muscle growth. For example,
• Growing children
• Pregnant woman
• Recovery from illness.
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8. Write briefly on parameters used to assess nutritional value of proteins.

Parameters used to assess nutritional value of proteins are given in Table 12.4.
Table 12.4: Parameters to assess the nutritional value of proteins

Parameter Definition Significance
Biological value (BV) Percentage of absorbed protein retained in the body Index of quality of
Nitrogen retained protein
× 100 BV of egg—94
Nitrogen absorbed BV of milk—84
Net protein utilization Percentage of ingested nitrogen retained in the body Index of quality of
(NPU) protein
Nitrogen retained
× 100 NPU of egg—91
Nitrogen ingested NPU of milk—75
Protein efficiency ratio It is the gain in body weight in grams per gram of protein Index of quality of
Nutrition
(PER) ingested protein
Gain in body weight in gram PER of egg—4.5
× 100 PER of milk—3.0
Protein intake in gram
Chemical score (CS) Gives an idea about essential amino acid (AA) content of Index of quality of
a protein protein
mg of AA per gram of test protein CS of egg—100
× 100 CS of milk—65
mg of same AA per gram of reference protein

9. What is balanced diet? What are the factors to be considered, while prescribing a bal-
anced diet?
Definition: It is a diet, which contains different types of food in an amount that meets the
daily requirement for calories and nutrients for optimal growth and development.
Factors to be Considered, While Formulating the Balanced Diet

• Measure body weight
• Obtain BMR and add the extra requirement depending on physical activity
• Calculate total calorie requirement
• Add specific dynamic action—10% of total requirement
• Provide carbohydrate:protein:fat = 60:20:20.
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Calculation of Energy Requirement Depending on Physical Activity
• Calculate BMR
+ 30% of BMR for sedentary work
+ 40% of BMR for moderate work
+ 50% of BMR for heavy work
• Then add 10% of the above total as SDA
• Make it to nearest multiple of 50.
Example 1: Calculate the energy requirement (BMR = 34–37 kcal/m2/h) of a male sedentary
worker with a body surface area of 1.7 m2.
Energy requirement at basal level = 34 × 1.7 × 24 = 1,387.2 kcal
For sedentary work, 30% of above value = 416.16
Total = 1,387.2 + 416.16 = 1,803.36 kcal
SDA = 10% of the total calorie requirement = 180.34 kcal
Nutrition
Total energy requirement = 1,803.36 + 180.34 = 1,983.70 kcal/day = 2,000 kcal/day.

Example 2: Calculate the energy requirement of a 55 kg male doing moderate work
(BMR = 24 kcal/kg/day).
Energy requirement at basal level = 24 × 55 = 1,320 kcal/day.

For moderate activity, add 40% of above value = 528 kcal
Total = 1,320 + 528 = 1,848 kcal/day
SDA = 10% of the total calorie requirement = 184 kcal
Total energy requirement = 1,848 + 184 = 2,032 kcal/day = 2,050 kcal/day.
10. What is food guide pyramid?
Definition: It is a schematic representation of five food groups that provide all the neces-

sary nutrients in recommended quantities. Foods that are at the base of pyramid can be
taken more than those at the top (Fig. 12.1). The five basic food groups are:
i. Grains.
ii. Vegetables.
iii. Fruits.
iv. Meat and dairy products.
v. Sugar and fat.
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171
Fig. 12.1: Food guide pyramid
11. Define and classify protein energy malnutrition. Enlist the features of kwashiorkor and
marasmus.
Nutrition
Definition: Imbalance between the supply of nutrients and energy and the body's demand
for them to ensure growth and maintenance of specific functions.
The extreme forms of protein energy malnutrition (PEM) are kwashiorkor and marasmus
(Table 12.5).
Table 12.5: Features of marasmus and kwashiorkor
Sl No Features Kwashiorkor Marasmus
1. Age group affected Older children in 2nd or 3rd year of life Infants below 1 year of age
2. Defect Protein deficiency Decreased calorie intake

3. Muscle wasting Muscle wasting is masked by edema Emaciated child, with gross wasting
of muscle and subcutaneous tissue
4. Mental changes Child is listless, apathetic and lethargic Irritable
5. Edema Present Absent
6. Appetite Decreased Good
7. Serum albumin Markedly decreased Normal or mildly reduced serum pro-
teins
12. Write briefly about obesity.

Definition: It is a disorder characterized by accumulation of excess body fat. Overeating
and reduced physical activity can lead to sustained deposition of fat.
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Classification Based on BMI
Body mass index: It is defined as a ratio between weight in (kg) and square of the height in
meters (W/H2). It is used for identification and grading of obesity.
• Pre-obese: 25.00–29.99
• Obese class I: 30.00–34.99
• Obese class II: 35.00–39.99
• Obese class III: ≥ 40.
Causes of obesity

• Excess food intake: High-fat diet
• Sedentary lifestyle
• Genetic factors: Leptin (controls body fat) has got a role in development of obesity
• Environmental and endocrine factors.
Nutrition
Complications of obesity: Hypertension, diabetes mellitus, coronary artery disease, etc.

13. Write a note on total parenteral nutrition (TPN).
Definition: Administration of nutrients parenterally (bypass gastrointestinal tract) to meet
the nutritional requirement of a patient. TPN is given to prevent the risk of malnutrition
and its effects, like infection, weakness and immobility, which predispose to various diseases
and may delay recovery from the illness. The nutrients administered include carbohydrates,
proteins, lipids, electrolytes, vitamins and minerals.
Indications for TPN

• Preoperative nutrition to improve the outcome of surgery in severely malnourished
patients
• Critical illness, cancer cachexia
• Liver failure, renal failure
• Acute pancreatitis, inflammatory bowel disease
• HIV, hyperemesis gravidarum.
Complications of TPN
• Acid-base imbalance
• Fluid overload
• Electrolyte imbalance
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173
• Cardiovascular failure
• Hyperosmolar non-ketotic coma
• Infection.
Key Points
Lactulose (fructose + galactose): It is a synthetic sugar used in the treatment of constipation

(osmotic action) and hepatic encephalopathy.
Sucralose, aspartame, saccharin, neotame: These are artificial sweeteners used in food industry.

Trans-fatty acids: Are chemically classified as unsaturated fatty acids, but they increase the risk

of atherosclerosis. They are formed during the hydrogenation of vegetable oils.
Polyunsaturated fatty acids (linoleic acid, linolenic acid, arachidonic acid): Protect against

atherosclerosis and coronary artery disease.
Role of taurine in infant nutrition: Taurine has an important role in fat absorption in preterm and

possibly term infants (taurine-conjugated bile acids).
Nutrition
Mutual supplementation of proteins: To overcome limiting amino acids in a given type of food,

mixed diets are given so that deficiency of amino acid in one food will be supplemented from oth-
ers. For example, rice (lysine and threonine are limiting amino acids) + dal (lacking sulfur containing
amino acids).
Metabolic syndrome (syndrome X): It is a disorder characterized by abdominal obesity, glucose

intolerance, insulin resistance, hyperinsulinemia, dyslipidemia and hypertension.
Anorexia nervosa: It is a disorder associated with severe weight loss due to reduced intake of food

(fear of obesity).
Bulimia nervosa: Eating disorder characterized by episodes of overeating followed by induced

vomiting.
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13 Nucleic Acid Chemistry
CHEMISTRY OF NUCLEOTIDES
1. Explain purines and pyrimidines with suitable examples.

Purines and pyrimidines are heterocyclic compounds containing nitrogen, which form the

structure of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) (Figs 13.1, 13.2 and
Table 13.1).
Fig. 13.1: General structure of purine Fig. 13.2: General structure of pyrimidine

Table 13.1: Purines and pyrimidines
Base Purines Pyrimidines
Major bases in nucleic acids Adenine (A) Cytosine (C)
Guanine (G) Uracil (U)
Thymine (T)
Minor bases in nucleic acids 7-methyl guanine 5-methylcytosine
Dimethyl adenine 5-hydroxymethylcytosine
Metabolic intermediates and Hypoxanthine, xanthine, uric acid, caf- 5-fluorouracil
analogues feine, theophylline, allopurinol
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175
2. What are nucleosides?

Definition: Nucleosides are glycosides formed by combination of nitrogenous base with
pentose sugar (Fig. 13.3 and Table 13.2).
Composition: Base (purine or pyrimidine) + pentose sugar (ribose or deoxyribose). Ribo-
nucleoside has ribose and deoxyribonucleoside has deoxyribose.
For example: Adenine + ribose → Adenosine
Guanine + ribose → Guanosine
Uracil + ribose → Uridine
Cytosine + ribose → Cytidine
Thymine + ribose → Thymidine
Nucleic Acid Chemistry

Adenine + deoxyribose → Deoxyadenosine
Fig. 13.3: Structure of nucleoside
Table 13.2: Nucleosides

Name Examples
Nucleosides in DNA* • Deoxyadenosine, deoxyguanosine, deoxycytidine, deoxythymidine
Nucleosides in RNA† • Adenosine, guanosine, cytidine, uridine
Other nucleosides • Pseudouridine, thymidine, S-adenosyl methionine, 5-deoxyadenosyl
cobalamin
*
DNA, deoxyribonucleic acid; †RNA, ribonucleic acid.
3. What are nucleotides? Give some examples.

Definition: Nucleotides are phosphoric acid esters of nucleosides (nucleoside + phosphate).
They form the basic units of DNA and RNA (Fig. 13.4 and Table 13.3).
Composition: Base (purine or pyrimidine) + pentose sugar (ribose or deoxyribose) + phosphate.
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176

Fig. 13.4: Structure of nucleotide (AMP)
Table 13.3: Examples and functions of nucleotides

Examples Functions
Adenosine triphosphate (ATP) and guanosine triphos- • High-energy compounds
phate (GTP)
Cyclic adenosine monophosphate (cAMP) and cyclic • Second messenger
guanosine monophosphate (cGMP)
3’-phosphoadenosine-5’-phosphosulfate (PAPS) • Sulfate donor
Nicotinamide adenine dinucleotide (NAD), nicotinamide • Coenzymes
adenine dinucleotide phosphate (NADP), CoASH
Uridine diphosphate (UDP)-glucose • Glycogen and UDP-glucuronic acid synthesis
UDP-glucuronic acid • Detoxification
Cytidine diphosphate (CDP)-choline • Synthesis of lecithin and sphingomyelin
Deoxynucleotides: Nucleotides with 2’-deoxyribose. For example, deoxyadenosine triphos-

phate (dATP), deoxyguanosine triphosphate (dGTP).
STRUCTURE AND FUNCTIONS OF NUCLEIC ACIDS
4. Describe Watson-Crick model of DNA with a figure. What are the differences between
DNA and RNA?
i. In 1953, Watson and Crick proposed the DNA structure (Fig. 13.5).

ii. DNA consists of two polydeoxyribonucleotide strands coiled around the same axis to

form a right-handed helix. DNA is composed of deoxyribonucleotides (deoxyribose +
phosphate in diester linkage + bases like A, T, C, G).
iii. Polydeoxyribonucleotide strand is formed by phosphodiester bond between 3’-OH

group of one sugar and 5'-OH group of another sugar.
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177
iv. One strand is oriented in 5’ to 3’ direction; the other is oriented in 3’ to 5’ direction

(antiparallel).
v. The two strands are complementary to each other and are held together by hydrogen
bonds between the bases.
vi. Each strand acts as a template for synthesis of daughter DNA strand.
vii. Base pairing rule: Adenine pairs with thymine by two hydrogen bonds; guanine pairs
with cytosine by three hydrogen bonds. Four deoxyribonucleotides are deoxyadenylate,
deoxyguanylate, deoxycytidylate and thymidylate.

Fig. 13.5: Structure of DNA (G, guanine; C, cytosine; A, adenine; T, thymine)
viii. Chargaff’s rule: It states that, total amount of purines are equal to total amount of
pyrimidines in a DNA double helix (A + G = T + C).
ix. The backbone of DNA is made up of alternating deoxyribose and phosphate groups
(hydrophilic). The hydrophobic nitrogenous bases are towards the core of double helix.
The bases are arranged perpendicular to the axis of helix.
x. The spatial relationship between two strands creates two types of grooves (major and
minor grooves). These grooves are the sites of interaction of DNA regulatory proteins.
xi. The diameter of the helix is 2 nm (20 Å).
xii. Each turn of the helix has 10 base pairs with a pitch of 3.4 nm (34 Å) and the bases
are 0.34 nm (3.4 Å) apart from each other along the helix.
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Types of DNA
• B-form—DNA usually seen in human cells
• A-form—right-handed helix with 11 base pairs per turn
• Z-form—left-handed helix with 12 base pairs per turn.
Differences between DNA and RNA are given in Table 13.4.

Table 13.4: Differences between DNA and RNA
DNA RNA
Found in nucleus Found in nucleus and cytoplasm
Bases are A, T, G and C Bases are A, U, G and C
Deoxyribose is the sugar component Ribose is the sugar component

Double stranded Single stranded (usually)
Genetic information is transcribed to form different Genetic information is translated to form proteins
types of RNA
5. Describe the structure and functions of different types of RNAs.

Ribonucleic acid (RNA) is a single-stranded polymer of ribonucleotides linked by phos-

phodiester bond between 3’-OH of a preceding nucleotide and 5’-OH of next nucleotide.
Ribonucleotides contain three major components:

i. Ribose sugar.

ii. Nitrogenous bases—purines (adenine and guanine) or pyrimidines (cytosine and uracil).
iii. Phosphate.

Types
Messenger RNA
• Single-stranded polyribonucleotide strand formed by transcription. It carries genetic infor

mation from DNA for protein synthesis [heterogeneous RNA (hnRNA), the precursor form
of messenger RNA (mRNA), is processed to form mRNA]
• The mRNAs differ in size and sequences depending upon the protein that has to be syn-

thesized (heterogeneous)
• The coding region of mRNA is sandwiched between initiator codon (AUG) and terminator

codons (UGA, UAA, UAG)
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• 5’ cap: The eukaryotic mRNA is capped at the 5’ end by 7-methyl guanosine triphosphate,
which protects it from hydrolysis by 5’ exonuclease; it also helps in initiation of protein
synthesis
• Poly(A) tail: 3’ terminal contains a polymer of adenylate residues, which stabilizes the mRNA
• The mRNA is complementary to template strand of DNA.
Transfer RNA (Fig. 13.6)
i. Transfer RNA (tRNA) functions as an adapter, which brings a specific amino acid from
cytosol to the site of protein synthesis.
ii. It is small in size (75 nucleotides).
iii. Although there are 20 amino acids, around 32 tRNAs are found in humans.

iv. Intrastrand hydrogen bonds present in tRNA gives it a clover leaf shape.
v. A highly conserved sequence CCA is present towards the 3’ end (acceptor arm). The last
nucleotide, adenine at the 3’ end is involved in binding covalently to a specific amino acid.
vi. Three loops present in tRNA are:
• D arm: Formed by 2 or 3 dihydrouridine residues
• Anticodon arm: It has a triplet codon (complementary to the codon on mRNA molecule)
that specifically interacts with the codon on mRNA
• TΨC arm: T, Ψ and C stands for thymine, pseudouridine and cytosine.
Fig. 13.6: Structure of tRNA
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Ribosomal RNA
i. Ribosomal RNAs (rRNAs) are the most abundant forms of RNA, which are associated with

ribosomes.
ii. They have catalytic activity (like enzymes). They have a role in translation. Ribosomal

subunits are given in the Table 13.5.
Table 13.5: Subunits of ribosome
Subunits Prokaryotes Eukaryotes
Larger subunit 50S 60S
Smaller subunit 30S 40S
Key Points
Nucleoside: Base (purine or pyrimidine) + pentose sugar (ribose or deoxyribose).

Nucleotide: Base (purine or pyrimidine) + pentose sugar (ribose or deoxyribose) + phosphate.

Purine analogues: Allopurinol and 6-mercaptopurine used in the treatment of gout and cancer

respectively.
Pyrimidine analogues: 5’-fluorouracil (thymidylate synthase inhibitor) used in the treatment of cancer.

Nucleoside analogues: Arabinosylcytosine and 5’-iododeoxyuridine are used in the treatment of

cancer and herpetic keratitis respectively.
Base pairing rule: Adenine-thymine is linked by two hydrogen bonds and guanine-cytosine are held

together by three hydrogen bonds.
Chargaff's rule: Total amount of purines are equal to total amount of pyrimidines in double helix

(A + G = T + C).
Melting temperature (Tm) for DNA: At 90oC, half of double-stranded DNA denatures into single-

stranded DNA.
Small nuclear RNA (snRNA): The snRNAs U 1, U2, U4, U5, U6 are required for splicing of hetero-

geneous nuclear RNA.
Unusual bases and nucleosides in the tRNA: Thymidine, dihydrouracil, hypoxanthine, pseudouridine.

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14 Nucleic Acid Metabolism
1. Describe the sources of carbon and nitrogen atoms of purine nucleotide. Write the path-
way for de novo purine synthesis. Add a note on its regulation and inhibitors.
Definition: Purine synthesis involves sequential addition of carbon and nitrogen atoms
to ribose 5’-phosphate to generate nine-membered ring (Fig. 14.1). Sources of carbon and
nitrogen atoms of purine nucleotide are given in the Table 14.1.
Site: Liver.
Subcellular site: Cytosol.
Starting material: Ribose 5’-phosphate.
End product: Inosine monophosphate (IMP).
Table 14.1: Sources of different atoms of purine ring
Atoms Sources
N1 Aspartate
C 2, C 8 N10 tetrahydrofolate
N 3, N 9 Glutamine
C 4, C 5, N 7 Glycine
C6 CO2
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Nucleic Acid Metabolism
Fig. 14.1: Synthesis of purine ring
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Regulators and inhibitors of purine synthesis are explained in Tables 14.2 and 14.3
respectively.
Table 14.2: Regulation of purine synthesis
Enzyme Inhibitor Stimulator
PRPP* synthetase AMP‡, GMP§ –
Amidotransferase GMP, AMP –
Adenylosuccinate synthetase AMP GTP||
IMP† dehydrogenase GMP –
PRPP, phosphoribosyl pyrophosphate; †IMP, inosine monophosphate; ‡AMP, adenosine monophosphate; §GMP, guanosine mono-
*
phosphate; ||GTP, guanosine triphosphate.

Table 14.3: Inhibitors of purine synthesis
Inhibitor Mechanism of action
Sulfonamides PABA* analogues block folate synthesis in microbes
6-mercaptopurine Inhibits formation of AMP and GMP from IMP
Mycophenolic acid Inhibits IMP† dehydrogenase (used to prevent graft rejection)
Methotrexate Inhibits dihydrofolate reductase, reduces availability of active folate and
blocks purine synthesis; it is used as an anticancer agent
*
PABA, para-aminobenzoic acid; †IMP, inosine monophosphate.
2. How are purine bases salvaged? Add a note on Lesch-Nyhan syndrome.

Definition: It involves conversion of purines, purine ribonucleosides and purine deoxy
ribonucleosides to corresponding mononucleotides.
Reactions:
i. Phosphoribosylation of free purines.
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ii. Phosphorylation of purine ribonucleoside, e.g.

Adenosine kinase

Adenosine + ATP AMP + ADP

Significance: This pathway is the source of nucleotides for erythrocytes and brain. As they

lack amidotransferase, they cannot synthesize purines.
Lesch-Nyhan syndrome

Inheritance: X-linked.

Defect: Complete/partial absence of hypoxanthine-guanine phosphoribosyltransferase

(HGPRTase).
Consequences
• Poor salvage of hypoxanthine and guanine leads to excessive uric acid formation
• ↓ HGPRTase → ↑ phosphoribosyl pyrophosphate (PRPP), ↓ GMP and ↓ IMP → ↑ de novo
synthesis of purines; improper utilization + ↑ production of purines → ↑ degradation of
purines → ↑ uric acid.
Clinical Features
• Hyperuricemia and gouty arthritis
• Urate stones
• Self-mutilation
• Mental retardation.
Treatment
Allopurinol (refer Question 3).

3. How is uric acid formed in the body? Add a note on gout.

Uric acid: It is the end product of purine catabolism (excreted in urine) (Fig. 14.2, p. 185).
Starting material: Purines.
End product: Uric acid.
Gout: It is an acute inflammatory condition caused by increased production and deposition of
monosodium urate crystals in the joints and soft tissues.
Causes of Primary Gout [MN: GASP]

• Glucose-6-phosphatase deficiency (von Gierke disease)
• Amidotransferase not responding to feedback inhibition
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• Salvage pathway defect (Lesch-Nyhan syndrome)

• PRPP synthetase not under regulation.

Fig. 14.2: Steps of uric acid synthesis
Causes of Secondary Gout [MN: CRP]

• Cancer
• Renal failure
• Psoriasis.
Clinical Features
Red, tender, swollen joint in feet and hands; ↑ uric acid → sodium urate crystals deposited in
the joints → joint inflammation → gouty arthritis.
Treatment
• Allopurinol: Inhibits xanthine oxidase → ↓ uric acid production
• Probenecid → ↑ excretion of uric acid in the urine
• Non-steroidal anti-inflammatory drugs, steroids and colchicine: ↓ pain and inflammation.
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4. Describe the causes and features of hyperuricemia. How is it treated?

Definition: ↑ levels of uric acid in the blood (normal level: 4–7 mg/dL).
Causes, features and treatment (refer Question 3).

5. Describe the synthesis of pyrimidine ring. Add a note on its regulation and associated

disorders.
Definition: Sequential addition of nitrogen and carbon atoms to form a six-membered

pyrimidine ring (Table 14.4 and Fig. 14.3, p. 187).
14.4: Sources of different atoms of pyrimidine ring
Atoms Sources
N 3, C 2 Carbamoyl phosphate
C 4, C 5, C 6, N 1 Aspartic acid
Site: Cytosol and mitochondria.

Disorders of pyrimidine metabolism

Orotic aciduria: Refer Question 7.
6. Write a note on severe combined immunodeficiency (SCID).
Inheritance: Autosomal recessive.
Cause: Adenosine deaminase and purine nucleoside phosphorylase deficiency → ↑ dATP
and dGTP → (−) ribonucleotide reductase → ↓ DNA synthesis → decreased proliferation
of B and T lymphocytes → severe immune deficiency [(−) = inhibition].
Clinical features: Repeated life-threatening infections.
Treatment: Bone marrow transplantation and gene therapy.
7. Write briefly about orotic aciduria.
Definition: ↑ excretion of orotic acid in the urine.
Inheritance: Autosomal recessive.

Types and causes

• Type I orotic aciduria: Deficiency of enzyme orotate phosphoribosyltransferase and
orotidylate decarboxylase
• Type II orotic aciduria: Deficiency of orotidylate decarboxylase.
Clinical features: ↑ orotic acid in urine, megaloblastic anemia and failure to thrive.
Treatment: Oral uridine/cytidine → (−) enzymes in the pyrimidine synthesis pathway.
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Fig. 14.3: Pyrimidine synthesis (UMP, UDP, UTP, uridine mono, di and triphosphate respectively; CTP, cytidine
triphosphate; TMP, thymidine monophosphate; dUMP, dUDP, deoxyuridine mono and diphosphate respectively)
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• Urea cycle disorder: Ornithine transcarbamoylase deficiency (type II hyperammonemia) →
↑ carbamoyl phosphate → enters cytosol → ↑ orotic acid production
• Allopurinol: Competes with orotate phosphoribosyltransferase to inhibit the phospho

ribosylation of orotate, which may lead to orotic aciduria.
8. Explain the synthesis of deoxyribonucleotides.

Purine and pyrimidine ribonucleotides undergo reduction at the 2’ carbon to give rise to re-

spective deoxyribonucleotides in the presence of enzyme ribonucleotide reductase complex.
• Site: Actively dividing cells
• Requirements: Thioredoxin, thioredoxin reductase, NADPH
• General reaction:
Specific Reactions
CDP 2’dCDP 2’dCTP

UDP 2’dUDP 2’dTTP
GDP 2’dGDP 2’dGTP

ADP 2’dADP 2’dATP

Key Points
Folic acid: It is required for purine synthesis. Folate deficiency → impaired DNA synthesis →

megaloblastic anemia and neural tube defects.
Methotrexate: (−) dihydrofolate reductase → used as an anticancer agent.

5’-fluorouracil: (−) thymidylate synthase → anticancer agent.

Lesch-Nyhan syndrome: X-linked recessive disorder with defect in hypoxanthine-guanine phospho-

ribosyltransferase (HGPRTase). https://kat.cr/user/Blink99/
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Normal plasma uric acid level: 3–7 mg/dL.
Gout: It is an acute inflammatory condition caused by increased production and deposition of mono
sodium urate crystals in the joints and soft tissues.
Allopurinol (competitive and also suicide inhibitor): Inhibits xanthine oxidase, thereby decreases
the production of uric acid.
Severe combined immunodeficiency (SCID): Autosomal recessive disorder caused due to defi-
ciency of adenosine deaminase and purine nucleoside phosphorylase, leading to dysfunctional T
and B lymphocytes.
Carbamoyl phosphate synthetase II (CPS ll): It is a cytosolic enzyme required for pyrimidine synthesis.
Orotic aciduria: Autosomal recessive disorder → ↑ orotic acid in urine; due to deficiency of enzyme
orotate phosphoribosyltransferase and orotidylate decarboxylase.
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15 Molecular Biology-I
REPLICATION
1. Write an account on replication. Add a note on xeroderma pigmentosum.

Definition: It is the process in which two identical copies of daughter deoxyribonucleic
acid (DNA) molecules are formed from parent DNA during cell division.
Replication is semiconservative: Each daughter DNA gets one strand from parent DNA.
The other strand is newly synthesized.
Requirements for DNA replication

i. Double-stranded DNA.

ii. Deoxyadenosine triphosphate (dATP), deoxyguanosine triphosphate (dGTP), deoxythy-

midine triphosphate (dTTP) and deoxycytidine triphosphate (dCTP).
iii. Enzymes:

• DNA helicases: Unwind the double helix using energy (ATP)
• DNA topoisomerase I (nuclease and ligase activity): Relieves the supercoiling of DNA
by cutting and resealing one strand of DNA
• DNA topoisomerase II (nuclease and ligase activity): Relieves the supercoiling of DNA
by breaking and resealing both the strands of DNA
• DNA polymerase: It synthesizes a complementary strand of DNA from single strand
of DNA (template) by polymerization of deoxynucleotides
– DNA polymerase I: Required for proofreading and fills the gap between Okazaki frag-

ments of lagging strand; in proofreading, copying errors are identified and corrected
(5’-3’ polymerase activity, 3’-5’ and 5’-3’ exonuclease activity)
– DNA polymerase II: Required for proofreading and DNA repair

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191
– DNA polymerase III: It is the main replication enzyme, also required for proofreading
(5’-3’ polymerase activity and 3’-5’ exonuclease activity).
• DNA ligase: Seals the nick in single strand as well as in Okazaki fragments.
iv. Proteins:
• dnaA: Binds to AT-rich region → unwinding of DNA
• Single-stranded DNA-binding proteins (SSB proteins): Prevent annealing of separated
DNA strands
• Primase: Initiates synthesis of short segment of RNA (RNA primer).
Steps in DNA Replication

i. Identification of site of origin of replication (ori) by specific proteins: Origin of replica-
Molecular Biology-I
tion is a unique nucleotide sequence from where DNA replication begins. In prokaryotes,
there is a single ori, which consists of AT-rich region. In eukaryotes, multiple origins of
replication exist.
ii. Unwinding of double-stranded DNA to form 2 single-stranded DNA (ssDNA): dnaA
protein binds to AT-rich region in the origin of replication → local melting/unwinding
of dsDNA → short segment of ssDNA formed (required for initiation of DNA synthesis).
Single strand binding (SSB) proteins attach to each strand and prevent their annealing
(maintain DNA in single strand form). Separation of strands of DNA is required as DNA
polymerase binds to single strand of DNA.
iii. Formation of replication fork, synthesis of primer and initiation of DNA synthesis (Fig
15.1): Unwinding of DNA causes formation of replication fork → DNA helicase binds to the
fork → unwinding of adjacent double-stranded region → primase binds to DNA at 3’ end
of each strand → synthesis of short segment of RNA (RNA primer) → DNA polymerase
using RNA primer, initiates synthesis of daughter strand (complementary to template) in 5’
→ 3’ direction. Both parent strands are simultaneously replicated in the 5' → 3' direction.
The replication forks, thus, advance in opposite direction from their origin. This process
results in the formation of 'replication bubbles'.
Direction of DNA synthesis
a. Leading strand: DNA is synthesized continuously in 5’ → 3’ direction towards the
replication fork (Fig. 15.1) and it needs only one RNA primer.
b. Lagging strand: It is synthesized in short stretches in 5’ → 3’ direction, but away from
replication fork. These short stretches of discontinuous DNA are called Okazaki frag-
ments. It requires many RNA primers.
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Molecular Biology-I

Fig. 15.1: Replication fork (DNA, deoxyribonucleic acid; SSBs, single-stranded DNA-binding proteins;
RNA, ribonucleic acid).
Unwinding of DNA during replication creates supercoils, which are relieved by topoi-

somerase I and II.

iv. Elongation

a. It is the process where there is sequential addition of deoxynucleotides via phosphodiester

bonds. First phosphodiester bond is formed between 3’–OH group of RNA primer and 5’
phosphate group of first entering deoxynucleotide. DNA polymerase (DNA pol III) elon-
gates new DNA strand by adding deoxynucleotides (dATP, dGTP, dTTP, dCTP) one at a
time, to the 3’ end of growing chain, complementary to bases in the template strand.
b. Proofreading of newly formed DNA: Any errors due to mismatched nucleotides during

replication are immediately repaired to prevent lethal mutations. This is mainly done by
DNA polymerase III and DNA polymerase I.
c. Excision of RNA primer.

• DNA polymerase I, which removes the RNA primer (5’-3’ exonuclease activity) and
synthesizes DNA that replaces RNA using 5’-3’ polymerase activity; it also proofreads
the new chain using 3’-5’ exonuclease activity
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• DNA ligase: Catalyzes the formation of phosphodiester bond between DNA syn-
thesized by DNA polymerase III and that formed by DNA polymerase I using
energy (ATP).
v. In eukaryotes, an additional step occurs. The newly synthesized dsDNA reforms chromatin
structure.
Xeroderma Pigmentosum
Xeroderma pigmentosum is an autosomal recessive disorder with defective nucleotide ex-
cision repair due to deficiency of enzyme ultraviolet (UV) specific endonuclease. In this
condition, exposure to UV light can cause mutations in DNA (pyrimidine dimers), which may
lead to cancer.
Molecular Biology-I
2. What are Okazaki fragments?
Okazaki fragments are short segments of single-stranded DNA that are synthesized dis-
continuously on lagging strand during DNA replication (refer Fig. 15.1). DNA polymerase
I removes the RNA primers (5’-3’ exonuclease activity) between these fragments and syn-
thesize DNA that replaces RNA (5’-3’ polymerase activity). DNA ligase finally joins these
fragments (refer Elongation, p. 192).
3. Write a note on inhibitors of replication.
Inhibitors of replication, mechanism of action and therapeutic uses are given in Table 15.1.
Table 15.1: Inhibitors of replication
Inhibitor Mechanism of action Therapeutic use
Ciprofloxacin, novobiocin, nalidixic acid DNA gyrase inhibition Antibiotics
Etoposide, doxorubicin Inhibit topoisomerase II Anticancer agents
Cytosine arabinoside Prevents chain elongation Anticancer agent
Adenine arabinoside Prevents chain elongation Antiviral drug
Key Points
DNA replication occurs in S (synthetic) phase of cell cycle.
Proofreading: It is mainly done by DNA polymerase III and DNA polymerase I.
RNA primer (5–12 nucleotides long): Required for DNA synthesis; produced by primase.
Postreplicative modifications of DNA: These include methylation of DNA and mismatch repair.
Huntington's disease: Autosomal dominant disease with motor and cognitive dysfunction. This is
due to expansion of trinucleotide repeats (CAG), which codes for glutamate in huntingtin protein
(altering its function).
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194

Xeroderma pigmentosum: It is an autosomal recessive disorder with defective nucleotide excision

repair due to deficiency of enzyme UV-specific endonuclease.
Fanconi anemia: Due to defective repair of interstrand DNA cross-links presenting with micro cephaly,

mental retardation, anemia and leukopenia.
Telomeres: It is the 3' end of mammalian DNA with 5'-TTAGGG-3' repeats. The number of these

repeats decreases with each cell division and indicates normal aging of cells. In germ cells, the
enzyme telomerase maintains the length of telomere.
Cancer and telomerase: Telomerase activity is found to be high in cancer cells, which make them

immortal and replicate indefinitely. Telomerase inhibitors are under development as potential anti-
cancer agents.
TRANSCRIPTION
Molecular Biology-I
4. Write briefly about promoter regions.

Promoter region: These are highly conserved regions of DNA both in pro- and eu-karyotes,

which are recognized by RNA polymerases to initiate the process of transcription.
Prokaryotic Promoters (Fig. 15.2)

a. Pribnow box (TATA box): Stretch of 6 nucleotides (5’-TATAAT-3’) located about 10 nucle-

otides upstream from transcription start site. This has low melting temperature due to lack
of GC pairs. This will result in unwinding of DNA.
b. –35 sequence: It is a sequence of 8 nucleotides (5’-TGTTGACA-3’) located approximately

35 bp upstream from transcription start site.
Fig. 15.2: Prokaryotic promoter regions
Eukaryotic Promoters
About 25 nucleotides upstream of the transcription start site, similar to prokaryotes, a TATA
or Hogness box is present. Another consensus sequence CAAT box is present about 70–80
nucleotides upstream of transcription start site.
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All these promoters help in deciding the origin of transcription by facilitating effective
binding of RNA polymerase.
5. Describe transcription process. Add a note on inhibitors of transcription.
Definition: Transcription is the process of synthesizing RNA from a DNA template. It takes
place in the 5' → 3' direction. The newly synthesized mRNA [primary transcript, heteroge-
neous nuclear RNA (hnRNA)] is identical to the other DNA strand—the coding strand (except
having uracil in place of thymine).
Requirements
• DNA to be copied
• RNA polymerase, RNAP (holoenzyme): Core enzyme (2α, 1β, 1β') + σ (sigma) factor. It
Molecular Biology-I
is the enzyme that synthesizes mRNA
• Termination factor—ρ (rho): For termination of transcription
• ATP
• Helicase: Unwinding of DNA during transcription
• Topoisomerase I and II: Remove supercoiling.
Steps in Transcription
Steps in transcription include initiation, elongation and termination.
i. Binding of RNAP to the template strand of DNA and formation of preinitiation complex:
RNA polymerase (holoenzyme) binds to promoter region (-35 sequence) of DNA. It then
moves on and binds to TATA box → causes local unwinding of DNA.
ii. Initiation of chain synthesis: The first nucleotide of RNA binds to nucleotide binding site
of 'b' subunit of RNA polymerase to form 5’ end of RNA. RNA polymerase moves to next
base on the template strand. A corresponding nucleotide binds to RNA polymerase and
phosphodiester bond is formed between the two nucleotides (Fig. 15.3).
iii. Clearance of promoter: Nucleotides continue to be added. Once RNA has 10–20 nucle-
otides, RNA polymerase leaves the promoter site (promoter clearance) and moves along
template strand.
iv. Elongation: After promoter clearance, elongation phase starts. New nucleotides are added to
the nascent mRNA complementary to the template strand. RNA polymerase uses ribonucle-
otides ATP, GTP, CTP and UTP. For addition of each ribonucleotide, energy equivalent to
two ATP is used (Table 15.2). Elongation complex containing RNA polymerase moves along
DNA template → unwinding of DNA downstream by RNAP.
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Fig. 15.3: Transcription
Molecular Biology-I
Unwinding causes supercoils, which is relieved by topoisomerases.

Table 15.2: DNA template is copied in the following manner
DNA template Corresponding base on RNA strand
G C
C G
T A
A U
v. Termination: Process of transcription continues until termination signal sequence is reached

on the template strand of DNA.
Rho-dependent termination: Rho is a specific protein, which recognizes the termination signal

→ dissociation of RNAP from DNA and release of newly synthesized mRNA.
Rho-independent termination: Newly synthesized RNA forms hairpin structure. It also has

series of Us near the 3' end, which helps in release of newly synthesized mRNA.
The inhibitors of transcription are given in Table 15.3.

Table 15.3: Inhibitors of transcription
Drug Mechanism of action Application
Rifampicin Inhibits ' ' subunit of prokaryotic RNA poly- Treatment of tuberculosis
b
merase
Actinomycin D Binds to DNA template and interferes with move- Anticancer agent
ment of RNA polymerase
α-amanitin Inactivates RNA polymerase II Mushroom poison
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6. Write a note on histones.

• Histones are proteins, rich in lysine and arginine; they are associated with chromatin
• They form ionic bonds with DNA
• They are required for packaging of DNA into nucleosomes
• They play an important role in regulation of gene expression
• They are of five types namely H1, H2A, H2B, H3 and H4
• Histone acetylation/deacetylation can alter their interaction with DNA. This makes the
chromatin more/less accessible for transcription, respectively.
7. Write briefly on reverse transcriptase.
Definition: Reverse transcriptase is the RNA-dependent DNA polymerase. It synthesizes
Molecular Biology-I
DNA from RNA. It is present in retroviruses where it synthesizes viral DNA from viral
RNA (Fig. 15.4).
Fig. 15.4: Synthesis of viral proteins by reverse transcriptase
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Applications
• Preparing complementary DNA (cDNA) library

• RT-PCR (reverse transcriptase-polymerase chain reaction)
• Reverse transcriptase inhibitors: zidovudine, lamivudine, etc. are used in the treatment of
HIV infection.
8. Write a note on post-transcriptional modification.
Definition: Process by which newly synthesized RNA (primary transcript) is modified to

mature mRNAs, rRNAs and tRNAs. This type of modification is mainly seen in eukaryotic
mRNA, pro- and eukaryotic rRNA and tRNA.
Molecular Biology-I
Post-transcriptional Modifications of mRNA

a. 5’ capping: The primary RNA transcript is known as hnRNA. 7-methylguanosine triphos-

phate is attached to the 5’ end of this RNA (capping). S-adenosyl methionine is the methyl
donor. 5’ capping helps in stabilization of mRNA and initiation of translation.
b. Poly-A tail: A chain of 20–250 adenine nucleotides are attached to the 3’ end of mRNA.

Poly-A tail helps in stabilization of RNA and translation.
c. Removal of introns: The primary transcript has exons (coding region) and introns (non-

coding regions). Small nuclear RNAs (snRNAs) in association with some proteins form
small nuclear ribonucleoprotein particles (SnRNPs) → bind to RNA to form spliceosomes,
which remove the introns and join the exons (Fig. 15.5).
Fig. 15.5: Removal of introns of mRNA
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Post-transcriptional Modifications of tRNA (Pro- and Eu-karyotes)

• CCA tail added to 3’ end
• Some bases are modified by reduction, methylation, deamination, etc.
Post-transcriptional Modifications of rRNA (Prokaryotes)

• 23S rRNA + 5S rRNA + proteins → 50S subunit
• 16S rRNA + proteins → 30S subunit; 30S + 50S → 70S ribosome.
Post-transcriptional Modifications of rRNA (Eukaryotes)

• 28S rRNA + 5.85S rRNA + 5S rRNA + proteins → 60S subunit
Molecular Biology-I
• 18S rRNA + proteins → 40S subunit; 40S + 60S → 80S ribosome.
Key Points
RNA polymerase has no proofreading activity, so transcription is more error prone compared to
replication.
Mushroom poisoning (α-amanitin): Inhibits RNA polymerase II and prevents elongation.
Spliceosome: It removes the introns and joins the exons to form mature mRNA.
Reverse transcriptase: It is the RNA-dependent DNA polymerase present in retroviruses, where
they copy the viral RNA genome into DNA.
TRANSLATION
9. Describe the process of translation in a. Prokaryotes b. Eukaryotes.

Definition: Translation is the process by which mRNA is translated to produce a polypep-
tide sequence, also known as a protein (Fig. 15.6).
Fig. 15.6: Synthesis of proteins
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200

Requirements for Translation
a. Amino acids: For synthesis of polypeptide chain.

b. Transfer RNA: At least one tRNA per amino acid.

c. Aminoacyl-tRNA synthetase: Required for attachment of amino acids to the specific tRNAs.

This requires energy (two ATP molecules).
d. Messenger RNA (mRNA): Has codons, which dictate synthesis of polypeptide chain.

e. Ribosomes (50S, 30S in prokaryotes; 40S, 60S in eukaryotes): Located in the cytosol as

free form or associated with endoplasmic reticulum.
• A, P and E sites on ribosome (p. 201) for binding tRNA
– A-site: For binding of incoming aminoacyl-tRNA as specified by codon at that site

Molecular Biology-I
– P-site: Has peptidyl tRNA (tRNA with newly synthesized chain of amino acids)

attached to it
– E-site: It is occupied by empty tRNA.

f. Initiation, elongation and termination factors.

g. Energy from:

• 2 ATP for binding of amino acids to specific tRNA
• 2 GTP for binding of aminoacyl-tRNA to A-site and translocation.
h. Binding between codon on mRNA and specific anticodon of tRNA: As per base pairing

rule (Fig. 15.7).

Fig. 15.7: Codon-anticodon interaction
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201
Steps of Translation in Prokaryotes
i. Initiation: Mechanism by which ribosome recognizes nucleotide sequence on mRNA to

initiate the translation.
• Shine-Dalgarno sequence (purine-rich region 5’-UAAAGGAGG-3’): Located 6–10 bases
upstream from AUG codon on the mRNA; this facilitates the binding of 30S ribosome
to mRNA
• Initiation codon AUG (Fig. 15.8): Located on mRNA; it is recognized by initiator tRNA
with N-formylmethionine.
Transformylase
tRNA-methionine + N10 formyl THF tRNA-N-formylmethionine
(fMet-tRNA) + THF
Molecular Biology-I
a. Formation of 30S initiation complex: 30S ribosome + mRNA + aminoacyl-tRNA
specified by start codon + initiation factors (IF 1, 2, 3) → 30S initiation complex is
formed (Fig. 15.8).
b. Formation of 70S initiation complex (Fig. 15.9):
IF 1, 2, 3
50S ribosome + 30S initiation complex + GTP 70S initiation complex
The fMet-tRNA is at the P-site.
Fig. 15.8: 30S initiation complex Fig. 15.9: 70S initiation complex
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202

ii. Elongation:

a. Binding of appropriate tRNA to empty A-site: Elongation factors (EF-Tu, EF-Ts), in the

presence of GTP, will help in binding of appropriate tRNA with an amino acid to next
codon in the empty A-site (Fig. 15.10).
Molecular Biology-I
Fig. 15.10: Binding of tRNA to A-site
b. Peptide bond formation: Peptidyl transferase transfers the amino acid/peptide from the

P-site on to amino acid at the A-site and catalyzes peptide bond formation between the
amino acids. The tRNA at the P-site now does not have an amino acid (empty tRNA).
c. Translocation: Ribosome moves a distance of three nucleotides along mRNA in the

5’-3’ direction in the presence of GTP and EF-G. Thus, the empty tRNA, which was
at the P-site, now lies at E-site; peptidyl tRNA at A-site is now at P-site; A-site is
empty (Fig. 15.11).

Fig. 15.11: Translocation
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203
A new aminoacyl-tRNA binds to corresponding codon on mRNA at A-site. These

steps for formation of required peptide are repeated until termination codon of mRNA
is at A-site.
iii. Termination: When termination codon (UAA, UGA, UAG) of mRNA is at A-site, it is rec-
ognized by release factor (RF). RF binds to this site and releases newly formed peptide in
the presence of GTP. The ribosome dissociates into its subunits.
Steps of Translation in Eukaryotes

i. Formation of aminoacyl-tRNA:
Aminoacyl-tRNA synthetase
Amino acid + ATP + tRNA Aminoacyl-tRNA + AMP
Molecular Biology-I
ii. Initiation of protein synthesis:
a. Dissociation of ribosome → 40S subunit + 60S subunit.
b. Formation of 43S preinitiation complex:
GTP + initiation factor 2 + Met-tRNA (methionine is the first amino acid to be incorpo-
rated in protein synthesis)

Complex formed

Binds to 40S ribosomal subunit

43S preinitiation complex formed
c. Formation of 48S initiation complex:
mRNA binds to 43S preinitiation complex

48S initiation complex
The initiation (start) codon AUG on mRNA is identified by Kozak sequence.
The anticodon of Met-tRNA binds to initiation codon AUG on mRNA.
d. Formation of 80S initiation complex:
48S initiation complex binds with 60S ribosomal subunit

80S initiation complex formed
Met-tRNA is attached to P-site of ribosome. The A and E sites are free.
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204

iii. Elongation: Addition of amino acids to the new growing peptide chain.

a. Binding of new, appropriate aminoacyl-tRNA to codon at acceptor A-site.

b. Formation of peptide bond by peptidyl transferase between new amino acid of tRNA

at A-site and amino acid attached to tRNA at P-site → transfer of amino acid/growing
peptide chain from P-site to amino acid at A-site. Thus, tRNA at P-site now does not
have any amino acid.
c. Translocation:

Ribosome moves along mRNA by 3 nucleotides (one codon) in the 5’ → 3’ direction

Movement of tRNA from P to E site from which it is released

Movement of peptidyl-tRNA from A to P site.

A-site is empty—a new aminoacyl-tRNA binds with codon of mRNA at this site.
Molecular Biology-I

iv. Termination:

Process of addition of amino acids continues till the termination (stop) codon on mRNA is

reached at the A-site. There is no tRNA with anticodon complementary to the stop codon
at A-site.
Releasing factor recognizes stop codon at A-site

Binds to A-site

Causes release of newly formed peptide chain, tRNA and mRNA from ribosomes

Dissociation of 80S ribosome → 60S + 40S subunits

10. Describe the properties of genetic code. Add a note on Wobble hypothesis.

• Genetic code is a sequence of 3 nucleotides (triplet code) in mRNA coding for an amino acid
• There are totally 64 different codons (43) from 4 nucleotides in different combinations
• AUG: Start codon, codes for methionine
• UAA, UAG, UGA: Stop codons, do not code for any amino acid—cause termination of
peptide synthesis.
Properties of Genetic Code

• Universal: Same codons code for same amino acids in all living organisms
• Specific: The specific codon always code for the same amino acid
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205
• Non-overlapping and comma less: Codons are read in a continuous manner without any
punctuation
• It is degenerate (redundant): An amino acid may have more than one codon coding for
it, since there are 61 codons for 20 amino acids, e.g. arginine has six codons.
Wobble Hypothesis
Pairing between the bases at third position (last nucleotide) of codon on mRNA and first
position of anticodon of tRNA is non-traditional (not always as per Watson-Crick rule). So,
a single tRNA anticodon can bind to more than one codon (refer Fig. 15.7). For example,
the codons for glycine GGU, GGC and GGA pair with a single anticodon CCI of tRNA. The
base I at third position of anticodon can pair with either U, C or A of mRNA codon (Table
15.4). This is 'Wobble' [Note: Pairing between bases at first and second position of codon and
Molecular Biology-I
that of anticodon (second and third position) is as per Watson-Crick rule].
Table 15.4: Non-traditional base pairing between codon and anticodon
mRNA codon (5' → 3') for glycine GGU GGC GGA
tRNA anticodon (3' → 5') for glycine CCI CCI CCI
11. Write a note on inhibitors of translation.

Inhibitors of translation and clinical significance are given in Table 15.5.
Table 15.5: Inhibitors of translation
Inhibitor Site of action Clinical significance
Streptomycin Binds to 30S subunit and interferes with ini- Antibacterial agent
tiation
Tetracycline Inhibits binding of aminoacyl-tRNA to m-RNA Antibacterial agent
ribosome complex
Chloramphenicol Inhibits peptidyl transferase Antibacterial agent
Erythromycin Inhibits translocation Antibacterial agent
Diphtheria toxin Inactivates elongation factor (eEF-2) and pre- Causes diphtheria
vents translocation
Puromycin Structural analogue of tyrosinyl-tRNA and binds Antibiotic used in cell cultures
to A-site causing premature release of poly-
peptide chain
12. Write a short note on post-translational modification.

Definition: Process by which newly synthesized polypeptide chain undergoes modifications
to produce biologically active protein.
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i. Trimming: Proteins are synthesized as functionally inactive large precursors. They undergo

trimming by proteases to produce functionally active protein. For example,
Proinsulin Insulin

Pepsinogen Pepsin

Trypsinogen Trypsin

ii. Covalent modification: Proteins may be activated or inactivated by covalent attachment

of variety of chemical groups.
a. Phosphorylation: Hydroxyl group of serine, threonine and tyrosine residues in protein

can undergo phosphorylation.
Phosphorylase kinase

Molecular Biology-I
Glycogen phosphorylase Glycogen phosphorylase (P)

(inactive) (active)

b. Glycosylation: Attachment of carbohydrate to hydroxyl groups of serine, threonine,

hydroxylysine (O-linked) and asparagine (N-linked).

Collagen synthesis: Hydroxylysine undergo glycosylation.

c. Hydroxylation: Proline and lysine undergo hydroxylation during collagen synthesis.

d. Carboxylation: Clotting factors undergo g-carboxylation of glutamic acid residues in the

presence of vitamin K during coagulation.
e. Farnesylation: For anchoring of proteins to membranes.

Key Points
Starting codon: AUG (methionine).

UAA, UAG, UGA: Stop codons, do not code for any amino acid.

Selenocysteine: It is considered as 21st amino acid, which is coded by UGA stop codon.

Protein farnesyltransferase inhibitors: Tipifarnib; anticancer agent used in the treatment of acute

myeloid leukemia.
Protein targeting: Is sorting of synthesized protein into required location.

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16 Molecular Biology-II
DNA REPAIR AND MUTATIONS
1. Explain causes and types of DNA damage.
Causes of DNA Damage

• Mismatch of bases during replication
• Spontaneous deamination: Changes the cytosine (C) to → uracil (U), adenine (A) → hypo
xanthine (H) and guanine (G) → xanthine (X)
• Physical agents: Ultraviolet (UV) light, X-ray, ionizing radiation
• Chemical agents (mutagens): For example, anticancer drugs like methotrexate, cyclophos
phamide, etc.
Types of DNA Damage

• Single base alteration: Nucleotide deletion/insertion, loss of amino groups from C, A, G,
alkylation of base, base analogue incorporation
• Two base alteration: Thymine dimer formation by cross-linkage between bases of same
strand (induced by UV radiation)
• DNA single/double strand breaks: Induced by ionizing radiation/reactive oxygen species.
2. Explain various DNA repair mechanisms and add a note on xeroderma pigmentosum.
In order to maintain the integrity of the genome, DNA undergoes repair.
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Nucleotide Excision Repair (NER)
For example, repair of pyrimidine dimers and base adducts (Fig. 16.1). UV specific endonu
-
clease recognizes and cleaves a piece of DNA on both ends of the dimer → DNA polymerase
and DNA ligase together will repair and replace the gap with proper nucleotides. Defects in
this type of repair mechanism can lead to xeroderma pigmentosum, Cockayne's syndrome,

ataxia telangiectasia, etc.
-

Molecular Biology-II
Fig. 16.1: Nucleotide excision repair
Xeroderma Pigmentosum
Refer to Chapter 15, question number 1.
Mismatch Repair
i. Replication errors (escaped from proofreading) → mismatch of one to several bases (e.g.
instead of thymine, cytosine may be incorporated opposite to adenine).
Base mismatch on the daughter strand is recognized by endonuclease → cleavage of

strand near the defect → mismatched bases are removed from the daughter strand by
exonucleases → DNA polymerase I and DNA ligase repair and replace the gap with
appropriate nucleotides (Fig. 16.2).
ii. Defect in mismatch repair: May lead to hereditary non polyposis colon cancer.
-
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209
Fig. 16.2: Mismatch repair
Base Excision Repair

Cytosine, adenine and guanine can undergo spon
taneous deamination to form uracil, hypoxanthine
and xanthine respectively. Abnormal bases are recog
nized by DNA glycosylases → hydrolytically remove
the abnormal base from their sugar → apyrimidinic
or apurinic site (AP site) → AP endonucleases →
produce break in the strand → deoxyribose phos
phate lyase → removes sugar phosphate residue
→ DNA polymerase I and ligase → regeneration of
strand (Fig. 16.3).
Double-strand Break Repair

Double-strand break repair is caused by ionizing
radiation, free radicals and chemotherapy.
Repair Mechanism
• Non-homologous end joining (NHEJ): Two non-
homologous ends of the broken DNA strand are
brought together by proteins with some loss of
DNA Fig. 16.3: Base excision repair
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210

• Homologous recombination: Two non homologous ends of the broken DNA strand are
-
brought together by proteins without loss of DNA.
3. Define and classify mutations with examples.
Definition: A mutation is a change in the sequence of nucleotides of DNA. It may or may

not alter the amino acid sequence of the protein encoded by that gene.
Chromosomal Mutations
• Philadelphia chromosome: Chromosomes 9–22 translocation → activation of c Abl; seen
-
in 80% of chronic myeloid leukemia cases
• Burkitt's lymphoma: 8–14 translocation → c Myc activation
-
• Non-Hodgkin's lymphoma: 14–18 translocation → activation of bcl 2 → suppression of
-
apoptosis.
Gene Mutation
• Point mutation
• Frameshift mutation
• Others.
Point mutation: Alteration in a single base is point mutation. This is of two types depend
ing on the type of base replaced.
a. Transition: Purine replaced by purine or pyrimidine replaced by pyrimidine.
For example, A ↔ G or C ↔ T.
b. Transversion: Purine replacing pyrimidine or pyrimidine replacing purine.
For example, A ↔ T or C ↔ G or A ↔ C or T ↔ G.
Effects of Point Mutation
a. Silent mutation: New codon formed after mutation codes for the same amino acid as

original codon. There is no change in the amino acid sequence and property of protein.
b. Missense mutation: New codon formed after mutation codes for a different amino acid.

This alters the amino acid sequence and may alter the function of protein. The effects
could be acceptable (function of protein not altered), partially acceptable (protein function
is partially affected) and non acceptable (non functional protein formed—could be fatal)
-
-
(Table 16.1).
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211
c. Nonsense mutation: New codon formed after mutation codes for terminator codon leading
to premature termination of protein synthesis (Fig. 16.4).
Fig. 16.4: Various consequences of point mutations
Table 16.1: Effects of missense mutations (A, B = 'α' helical segments of globin chain)
Effects Normal hemoglobin Mutated hemoglobin
Acceptable B 61: AAA (lysine) B 61: AAU (asparagine): Hb Hikari
Partially acceptable B 6: GAG (glutamic acid) B 6: GUG (valine): Hb S (sickle cell disease)
Non-acceptable A 58: CAC (histidine) A 58: UAC (tyrosine): Hb M
Frameshift mutations: It occurs due to insertion or deletion of nucleotides. It has more

serious consequences than point mutation as entire frame (sequence of codons for amino
acids) changes from the point of insertion or deletion. It can lead to formation of a non-
functional protein, premature termination of protein synthesis (Fig. 16.5, p. 212).
The amino acid sequence, distal to insertion or deletion of nucleotide, changes. For example,
frameshift mutation has been demonstrated in diseases like cystic fibrosis, thalassemia, etc.
Other Mutations
• Huntington's disease: CAG trinucleotide sequence is repeated many times → insertion of
many extra glutamine residues in the huntingtin protein → unstable proteins → accumula
tion of protein aggregates
• Fragile X syndrome and myotonic dystrophy: Trinucleotide expansion occurs in the un
translated portion of a gene → ↓ in the amount of protein produced
• Splice site mutation can affect removal of introns and protein formation. For example,
β-thalassemia (incorrect splicing of β-globin mRNA) and systemic lupus erythematosus
(SLE) (autoimmune antibodies against snRNP).
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212

Fig. 16.5: Frameshift mutation
REGULATION OF GENE EXPRESSION
4. Explain Lac operon model of gene expression.
Lac Operon Model

Operon: In prokaryotes, genes that code for proteins in a metabolic pathway are arranged
in a linear fashion along with a regulatory region (Fig. 16.6) [MN: RPOS = Regulation of
Prokaryotic Operon System].
In prokaryotic operon, genes are arranged in the following order from 5’ to 3’ on the
chromosome.
• Regulatory gene: Forms mRNA → forms a repressor protein → which binds operator gene
→ prevents translation of the protein (constitutive)
• Promoter gene: RNA polymerase binds to this region
• Operator gene: Site where repressor protein binds
• Structural gene: Responsible for formation of proteins.
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Lactose Operon or Lac Operon (Fig. 16.6)

Lac operon has three structural genes coding for different enzymes required for lactose
metabolism:
• Lac Z for β-galactosidase: Hydrolyzes lactose
• Lac Y for permease: Helps in movement of lactose into cell
• Lac A for thiogalactoside transacetylase: Function unknown.
There is an operator, promoter, CAP-binding site and a regulatory gene (Lac I).
a. When Escherichia coli is exposed to glucose only, repressor protein is formed → binds
operator gene → prevents the movement of RNA polymerase (RNAP) bound to promoter
→ no proteins (enzymes) formed (repression).
b. In the presence of lactose and absence of glucose (derepression).
• Small amounts of lactose enter E. coli → converted to allolactose (inducer) → binds to
repressor proteins and prevents its interaction with operator gene → no obstruction for
movement of RNAP → protein (enzyme) synthesis occurs
• Absence of glucose → (+) adenylyl cyclase → ↑ cyclic adenosine monophosphate (cAMP) →
cAMP-catabolite activator protein (CAP) complex → binds to CAP site → ↑ ability of bound
RNAP to initiate transcription of lac Z, lac Y and lac A genes to produce β-galactosidase,
permease and thiogalactoside transacetylase, respectively. These enzymes help E. coli
to metabolize lactose to produce energy.
Fig. 16.6: Regulation of prokaryotic Lac operon system [MN: RPOS] (RNAP, ribonucleic acid polymerase)
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214

c. When both glucose and lactose are available:
Operator site is free from inhibition as allolactose binds with repressor protein.
Glucose → ↓ cAMP → no CAP cAMP complex formation → RNAP cannot function
-
effectively → no protein (enzymes) formed → lactose cannot be utilized. Hence, glucose
is used first even though operator site is free. After all glucose is utilized by bacteria → ↑
cAMP → cAMP CAP complex formation → (+) RNAP → protein (enzyme) formation.
-
5. Briefly explain eukaryotic gene regulation.
Unlike prokaryotes, eukaryotic gene regulation is much complex. It can occur by six dif
ferent mechanisms.
a. Gene amplification: This occurs when a constant stimulus exists for a long time, e.g. dihydro
folate reductase gene gets amplified (increase in the number of DHFR genes) in a person on
antifolate drugs (for cancer).
b. Gene switching: When a person is exposed to a foreign antigen for the first time, immu
noglobulin M (IgM) is produced. Later, by gene switching for the same antigen, IgG is
produced.
c. Rearrangement of genes in DNA: Depending on the nature of antigens exposed, many types
of antibodies can be produced from a limited number of J, V and C segments. This is by
rearrangement of genes.
d. Control of transcription: This is done by cis and trans acting elements on DNA like enhanc
-
-
ers/silencers, hormones binding to hormone response elements, various proteins binding
to DNA, histone modifications, etc.
e. Post-transcriptional regulation: Post transcriptional modifications like 5’ capping, poly A tail,
-
splicing, etc. can regulate the stability of RNA. A transcribed monocistronic RNA can form
different proteins by RNA editing (alteration of a base in mRNA), e.g. apolipoproteins Apo
B100 and Apo B48 are formed from the same RNA.
f. Translational regulation: This is not a major mechanism in eukaryotes. For example, heme
can block its own synthesis by inhibiting the production of enzymes responsible for it.
Key Point
Cistron: Smallest unit of gene expression. It codes for one peptide or a subunit of protein.

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215
CANCER GENETICS
6. Explain cell cycle.

Cell cycle consists of mitosis phase and interphase. Interphase is the time between end of
previous mitosis and commencement of next (Fig. 16.7).
Fig. 16.7: Cell cycle
Interphase
Interphase consists of (G—gap; S—synthetic):
a. G1 phase.
b. S phase.
c. G2 phase.
G1 Phase
Longest phase and lasts for 10–12 hours. It is also called the growth phase. This phase is
marked by synthesis of various enzymes that are required in S phase, mainly those needed
for DNA replication.
S Phase
S phase is called synthetic phase (DNA synthesis) and usually lasts for 6–8 hours. Whenever
there is a mitogenic signal, DNA starts replicating and each chromatid forms its duplicate
sister chromatid.
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G2 Phase
G2 phase usually lasts for 4–6 hours. As DNA becomes tetraploid; cell volume, cytoplasm and
protein synthesis increases; cell prepares itself for division.
Mitosis Phase
Mitosis is the shortest phase of cell cycle lasting for about 1 hour. Chromosomes condense, nuclear
membrane dissolves, chromosomes pair and mitotic spindles are formed. Then chromosomes
separate and cytoplasmic division follows. Daughter cells may enter into G0 or G1 phase.
Cells may enter into G0 phase (resting phase)—this may occur due to lack of nutrients,
growth factor or contact. Some cells, after division, may enter into G0 phase for a long time/
lifelong. This occurs in those cells, which will not multiply rapidly like neurons, cardiac
muscles, skeletal muscles, etc. Cells can re enter G1 from G0 phase.
-
Regulation
Check point is at G1/S transition, G2 phase and G2/M transitions depending on the avail
ability of growth factors, mitogenic signals, cyclins and cyclin dependent protein kinases.
-
Cyclin dependent protein kinases phosphorylate specific proteins. This regulates the metabolic
-
activities of the cell.
7. Explain oncogenes and proto-oncogenes with examples.
• Oncogenes: These are cancer causing genes (Table 16.2)
• Proto-oncogenes: These genes are found in normal cells and code for growth stimulating
proteins.
Oncogenes were first discovered in viruses. They are named based on the type of cancer
they cause and their respective proto oncogenes are named after oncogenes with a prefix
-
c (c = cellular).
For example, Rous sarcoma virus contains src oncogene, which produces sarcoma. Normal
human cells also contain closely similar gene c-src.
Table 16.2: Oncogenes and proto-oncogenes
Proto-oncogene Protein formed Oncogene
c-sis B-chain of PDGF *
sis
c-erbB Receptor for EGF† erbB
Contd...
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217
Contd...
Proto-oncogene Protein formed Oncogene

c-myc Nuclear TF‡ myc
c-ras GTPase ras
c-abl Tyrosine kinase (signal transducer) abl
*
PDGF, platelet-derived growth factor; †EGF, epidermal growth factor; ‡TF, transcription factor.
8. Explain the mechanisms of conversion of proto-oncogene to oncogene.

There are different mechanisms by which proto-oncogene can become an oncogene.
i. Chromosomal translocation: A part of one chromosome is removed and attached to another
chromosome. For example, in Burkitt's lymphoma, 8–14 translocations occurs leading to
activation of inactive proto-oncogene (c-myc) on chromosome 14.
ii. Gene amplification: An increase in the number of a particular gene. For example, gene
amplification of dihydrofolate reductase (DHFR) gene in cancer makes it resistant to the
anticancer drug.
iii. Viral insertion: The terminals of retroviruses have enhancers. Here, integration of a retro
virus (with enhancers) close to a proto-oncogene activates the proto-oncogene to oncogene.
For example, a leukemia virus gets integrated near c-myc gene leading to its activation.
iv. Point mutation: For example, point mutation in ras oncogene results in decreased GTPase
activity that can lead to pancreatic, colon and lung cancer.
9. Define and classify tumor markers with suitable examples.
Definition: Tumor marker is a substance produced by tumor tissues that can be detected
and estimated in body fluids to detect presence of tumor/cancer.
General Uses of Tumor Markers
• Screening of cancer
• Diagnosis of cancer
• To decide prognosis of cancer
• To monitor cancer treatment
• To detect cancer recurrence.
For example, Bence Jones protein (light chain of immunoglobulin produced in excess
by the plasma cells) present in urine of patients with multiple myeloma was the first
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218

reported tumor marker. This precipitates between 45ºC and 60ºC; beyond 80ºC, it starts
to dissolve.
Types of Tumor Markers

Depending on their nature, tumor markers are divided into oncofetal products: α fetoprotein
-
(AFP); carcinoembryonic antigen (CEA); enzymes—alkaline phosphatase (ALP), acid phosphatase;
hormones—β human chorionic gonadotropin (β HCG), calcitonin and others (Table 16.3).
-
-
Table 16.3: Tumor markers
Tumor marker Associated cancer Family (type)
α-fetoprotein (AFP) Hepatoma, germ cell tumor Oncofetal antigen
Carcinoembryonic antigen (CEA) Colorectal, ovarian cancer Oncofetal antigen

Alkaline phosphatase (ALP) Bone cancer Enzymes
Prostate-specific antigen (PSA) Prostate cancer Enzymes
Acid phosphatase Prostate cancer Enzymes
'β'-human chorionic gonadotropin (β-HCG) Choriocarcinoma Hormones
Calcitonin Carcinoma of thyroid Hormones
Vanillylmandelic acid (VMA) Pheochromocytoma Hormone metabolite
Hydroxyindoleacetic acid (HIAA) Carcinoid syndrome Hormone metabolite
Bence-Jones protein Multiple myeloma Others
Cancer antigen (CA)-125 Ovarian cancer Others
Note: Some of the tumor markers may be elevated in non-cancerous conditions.
10. Define and classify carcinogens.

Definition: Carcinogen is a substance capable of inducing cancer in a normal person.

Classification
• Physical
• Chemical
• Biological
• Hormonal.
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219
Physical Agents
For example,
Chemical Agents
Indirect: Chemical (procarcinogen) is metabolically activated to a carcinogen, which causes
DNA damage. For example, tobacco smoke, smoked food, coal tar, etc.
Aflatoxin: It is produced by a fungus Aspergillus (in improperly stored nuts, wheat and rice). This
toxin is converted into a carcinogen by CYP450 microsomal enzymes in our body.
Direct: Chemical interacts directly with DNA to cause damage. For example, alkylating agents
like chlorambucil, cyclophosphamide, etc.
Chemical carcinogens can produce cancer at:
• Site of exposure, e.g. tobacco—buccal cancer
• Site of metabolism, e.g. aflatoxin—hepatoma
• Site of elimination, e.g. aromatic drugs—bladder cancer.
Biological Agents
For example, viruses:
a. DNA viruses: [MN: HEAP] = Hepatitis B/Epstein-Barr/Adenoma/Polyoma.
b. RNA viruses: [MN: RAIL] = Rous sarcoma/AIDS/Leukemia (sarcoma).
Hormonal Agents: [MN: CEA]
a. Contraceptives can cause breast cancer.
b. Estrogen can cause endometrial cancer.
c. Anabolic steroids can cause liver cancer.
Key Points
Cancer may be caused by inactivation (by mutation) of tumor suppressor gene. For example, RB
inactivation causes retinoblastoma; p53 inactivation causes breast cancer, lung cancer, etc.
Apoptosis: Programmed cell death in response to external and internal injury.
p53 gene: Codes for a nuclear protein. It is a transcriptional regulator. Whenever there is DNA
damage, it causes cell cycle arrest. If there is extensive DNA damage, it causes apoptosis.
Retinoblastoma (RB) gene: The protein formed from this is a nuclear regulator of cell cycle. It
inhibits E2F transcription factor. Inactivation of this gene causes retinoblastoma.
Cancer cells show different morphology and growth behavior. They have round shape, grow densely
due to loss of contact inhibition, loss of anchorage dependence and have ↓ requirement of growth
factors. Cancer is characterized by:
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1. Spread to other tissues (metastasis).

2. Invasion of local tissue.

3. Loss of control on cell division.

4. Loss of contact inhibition.

[MN: SPILL]

MOLECULAR BIOLOGY TECHNIQUES
11. Explain DNA cloning (recombinant DNA technology).

Definition: It is a laboratory method by which genetic material from different sources is

joined together. The hybrid genetic material is introduced into a replicating cell for am
plification (production of many copies) of genetic material of interest.
Requirements: Restriction endonucleases, vectors and host cell (E. coli).
Restriction endonucleases (REs): These are endonucleotidases, which recognize a palin
drome stretch of DNA sequences (restriction site) and cleaves it. The fragments produced
are restriction fragments. As shown below, palindrome is a sequence, which reads the
same on complementary strands when read from 5’ to 3’ direction.
5’—GAATTC—3’
3’—CTTAAG—5’
Vector: It is a DNA molecule to which DNA of interest is incorporated. It should be capable

of replication in a host cell and should have at least one restriction site and one marker
gene. For example, plasmids, phages (bacterial viruses), cosmids, etc.
Plasmids: These are small, circular, extrachromosomal, duplex DNA found in some bacte
ria, which carry genes for antibiotic resistance. These can replicate using host replication
system. A few kilobase pair length of foreign DNA can be inserted into them.
Steps in Recombinant DNA Technique

i. Human DNA of interest is isolated.
ii. A restriction endonuclease (RE) cleaves it.
iii. Vector DNA (plasmid carrying gene for antibiotic resistance) is cut with same RE;
the vector and human DNA fragments are joined by ligase to get recombinant DNA
(hybrid DNA).
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iv. Mix recombinant DNA + suspension of bacterial cells. This leads to entry of recombinant
DNA into bacteria (transformation) (Fig. 16.8, p. 222).
v. These bacteria are grown in a media containing antibiotics. Cells that have taken up plasmid
(containing DNA of interest) will survive as plasmid provides antibiotic resistance to bacteria.
vi. Surviving cells multiply to form a colony of cells called clone. These bacteria are lysed to
get many copies of recombinant plasmids. These plasmids are then lysed with the same
restriction enzymes to get copies of DNA of interest.
Uses of Recombinant DNA Technology [MN: PART]

• Prenatal diagnosis of genetic disorders
• Abundant production of proteins (insulin, growth hormone, clotting factors)
• Rape suspect identification (medicolegal)
• Transgenesis (Dolly), gene therapy.
12. Explain the types of DNA libraries.
Definition: It is a collection of restriction fragments of DNA of an organism.
• Genomic library: It is a collection of restriction fragments of entire genome of an organism
• Complementary deoxyribonucleic acid (cDNA) library: It is a collection of DNA produced
from mRNAs of an organism.
13. Explain gene therapy with its applications.
Definition: Gene therapy is a technique involving insertion of a gene for the missing en
zyme/protein resulting in production of correct protein.
Types (Depending on Cell Type)

i. Somatic cell gene therapy: Non-reproductive cells are used to insert normal functional gene.
ii. Germ cell gene therapy: Germ cells are taken and corrected by introducing normal func
tional gene.
Classification Depending on Method of Gene Therapy

i. Ex vivo gene therapy: Cells obtained from the patient → missing gene introduced into the
cell → corrected cells are reintroduced into the patient. This was tried in severe combined
immunodeficiency (SCID) caused due to deficiency of enzyme adenosine deaminase (ADA)
(Fig. 16.9, p. 223).
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ii. In vivo gene therapy has been tried: The normal gene is introduced into the cells directly

in vivo.
Fig. 16.8:https://kat.cr/user/Blink99/
Steps in recombinant DNA technique
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Steps in Ex Vivo Gene Therapy (Fig. 16.9)
Fig. 16.9: Steps in gene therapy
Diseases treated by gene therapy: Hemophilia A, cystic fibrosis, familial hypercholester

olemia, α-1 antitrypsin deficiency (emphysema).
14. Explain Southern blotting (steps) and its applications.
Definition: Process by which DNA of interest is identified in a cell.
Applications of Southern Blotting [MN: RFLP]
• Rape suspect identification (medicolegal, paternity disputes)
• Fingerprinting DNA
• Learn (identify) heterozygous carrier/defective gene (detect mutations—insertion/deletion
of nucleotides, point mutation)
• Prenatal screening of inherited disorders, sickle cell anemia.
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Steps in Southern Blotting (Fig. 16.10)
Fig. 16.10: Steps in Southern blotting (*DNA probe: short segment of single-stranded DNA labeled with radioisotope,
complementary to target DNA)
15. Explain restriction fragment length polymorphism (RFLP) and its applications.
Definition: Polymorphism is a variation in DNA sequence in a population. Often, they occur

in intervening sequences or non coding segments of DNA. RFLP is an inherited variation in
-
the length of restriction fragments between individuals. RFLP could be due to single base
changes or due to the presence of variable numbers of tandem repeats (VNTR). Tandem re
peats are short DNA sequences repeated several times at various regions in genome. Number
of repeat sequence varies from one to another. Accordingly, when sliced with a restriction
endonuclease, the fragment length may vary. It is identified by Southern blotting.
Applications of RFLP [MN: RFLP]

• Rape suspect identification, medicolegal, paternity disputes
• Fingerprinting DNA
• Learn (identify) heterozygous carrier/defective gene
• Prenatal screening of inherited disorders, sickle cell anemia.
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Restriction Fragment Length Polymorphism Analysis of Sickle Cell Anemia

Mutation abolishes recognition site of a restriction endonuclease, MstII. Normal DNA pro
duces 1.15 kb fragment, while βs gene (sickle cell gene) generates 1.35 kb fragment. This can
be detected by prenatal screening using fetal DNA.
16. Explain northern blotting and its applications.
Definition: Technique by which RNA of interest is identified. Mixture of mRNAs → elec
trophoresis → blot on a membrane → add radiolabeled probe → binds to target mRNA →
band formed → identified by autoradiography. There is no restriction digestion (as RNA
is short as compared to DNA) and no alkali denaturation (as RNA is single stranded).
Applications of Northern Blotting
• Detection/quantification of mRNA in tissues
• Detection of size variation in RNA from different tissues
• To study expression of mRNA in different tissues during development and during various
diseases.
17. Explain western blotting and its applications.
Definition: Western blotting is a technique to identify a protein of interest. Proteins are
separated by electrophoresis (on polyacrylamide gel) → blotted on to nitrocellulose sheet
→ labeled antibody added → reacts with antigen → produces a band. This is useful in
detection and quantification of minute amounts of protein.
Applications: Confirmatory test for AIDS, hepatitis.
18. Explain enzyme-linked immunosorbent assay (ELISA).

Refer Chapter 19, Radioisotopes.
19. Explain polymerase chain reaction (PCR) and its applications.

Definition: Polymerase chain reaction is a method to amplify a selected sequence of DNA.
It can produce millions of copies of a selected DNA sequence in few hours. It has high
sensitivity and speed. There is an increase in the number of copies of DNA of interest
with each cycle.
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Steps in PCR (Figs 16.11A and B)

Figs 16.11A and B: Steps in PCR (*flanking region: nucleotide sequence adjacent to target sequence in the DNA)
Applications [MN: PCR]
• Prenatal diagnosis of inherited diseases, e.g. cystic fibrosis

• Cancer detection—detect mutant gene
• Rape cases (forensics), analyze materials from crime scene
• Infectious diseases—detect HIV when small number of cells is infected.
20. Explain hybridoma technology and its applications.
Definition: Hybridoma technology is a method by which monoclonal antibodies are pro

duced from a single clone of plasma cells. Monoclonal antibodies are directed against one
epitope of an antigen.
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Steps in Hybridoma Technology (Fig. 16.12)
Fig. 16.12: Hybridoma technology
B cells from spleen produce antibody, but are not immortal. Myeloma cells grow permanently,
but do not produce antibodies. Fusion of these cells → hybridoma cells → produce antibody
and are immortal.
Applications [MN: HAT]

Monoclonal antibodies produced by this technique can be used for:
• Hormone detection
• Antigen detection: Protein, infections
• Tumor marker detection
• Drug delivery for treatment of various diseases.
Key Points
Antisense therapy: Based on the principle that microRNA (short RNA of 21–23 nucleotides) is used

for silencing (gene silencing) of undesired mRNA (prevents translation). This therapy has been tried
in acute leukemia and human immunodeficiency virus (HIV) infection. A short half-life and lack of
specificity of antisense RNA molecules are the limitations.
RNA interference: Small double-stranded RNA, when artificially introduced into a cell, can silence

mRNA. The presence of double-stranded RNA in a eukaryotic cell can trigger a process known as
RNA interference or RNAi (also known as RNA silencing or RNA inactivation).
Small nucleolar RNA: Involved in formation of ribosomes from precursor 28S, 18S and 5.8S; also

involved in telomere synthesis.
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X-inactive specific transcript (XIST) RNA: Responsible for inactivation of one of X chromosome

in females.
DNA probe: A fragment of DNA labeled with 32P used to identify a target DNA fragment.

Restriction endonucleases: Recognize and cleave specific sequence in a DNA. Used in recombi-

nant DNA technology, e.g. EcoR1.
Endonucleases: Cleave internal phosphodiester bonds.

Exonucleases: Hydrolyze terminal nucleotides.

Vectors: Carriers of DNA fragments to be inserted into the host cell. For example, plasmids, bac-

teriophages, cosmids, yeast artificial chromosomes.
DNA sequencing: Detection of base sequence in a DNA, which is done by Sanger method.

Molecular chaperones: They are proteins that facilitate the folding of proteins, e.g. heat shock

proteins.
Protein targeting: Directing a synthesized protein into its exact location.

Transgenic animal: It is an animal with inserted foreign gene in its genome. This is useful in the

production of proteins of interest.
ACQUIRED IMMUNODEFICIENCY SYNDROME
21. Explain acquired immunodeficiency syndrome (AIDS) and the tests available for its
diagnosis.
i. Acquired immunodeficiency syndrome (AIDS) is caused by a retrovirus having RNA ge
nome with reverse transcriptase. Its core is surrounded by membrane, which is studded
with spike like assembly of gp41 and gp120 viral proteins, which helps it to infect the host
-
cells. It infects CD4+ T cells, macrophages and dendritic cells.
ii. Transmission: Blood transfusion, semen, vaginal secretion or breast milk, contaminated

needles, mother to infant during pregnancy, childbirth, etc.
Phases of Infection
i. Window period: After the virus infection, initially for 2–12 weeks no antibodies will be

detected in the host. This is called 'window period' (seronegative period), but during this
phase, virus capsid antigen p24 may be detected in host.
ii. Intermediate phase (seropositive phase): Person looks normal, but can transmit the disease
to others; antibodies can be detected by ELISA; this period lasts for 5–10 years.
iii. AIDS: In this phase, CD4+ T cells count falls (< 400/mm3), which leads to decreased im
munity. Patient usually dies within 2 years in this phase without treatment.
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Laboratory Tests
• Enzyme-linked immunosorbent assay (ELISA): Antibodies to viral gp120 is detected by
this method; it is a screening test and may show false negative response
• Western blot: Six different viral components are detected with this test and is a confirma
tive test
• Polymerase chain reaction (PCR): This is the most sensitive test and can detect infection
in the seronegative phase as it detects the viral genome
• Treatment: Anti-HIV drugs
– Reverse transcriptase inhibitors: Azidothymidine (AZT), delavirdine, nevirapine
– Inhibitors of protease: Saquinavir, ritonavir
– Fusion inhibitors: Enfuvirtide.
22. Write briefly about fluorescent in situ hybridization (FISH) technique.
Definition: Fluorescent in situ hybridization (FISH) is a technique that can be used to
detect and localize specific DNA sequences on chromosomes (Fig. 16.13).
Requirements
• Fluorescent probes—fragments of DNA/RNA labeled with fluorescent molecule. They bind
complementarily to specific sequence of the chromosomes. Probe is constructed by cloning
techniques
• Target DNA of interest
• Fluorescence microscope—to detect the site of binding of fluorescent probe.
Applications: [MN: CLAM] for detection of:
i. Chromosomal aberrations (translocations).
ii. Localization of a specific gene on chromosome.
iii. Amplification of genes in cancer can be detected.
iv. mRNA expression.
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Steps of FISH (Fig. 16.13)
Fig. 16.13: Fluorescent in situ hybridization technique
23. Explain the principle and applications of microarray technique.

A DNA microarray consists of thousands of immobilized single stranded DNA fragments
-
of known nucleotide sequence organized on a small solid support like slide/membrane.
By this technique, thousands of genes can be studied at a given time. Analysis of activity
(active/inactive) of genes will help in understanding the normal functions of a cell and
how functions are affected following a change in the gene. With the help of microarray
technology, different diseases can be studied. An important area for the application of this
technique is cancer (Fig. 16.14). Cancers can be classified based on the gene activity in the
tumor cells. Treatment can thenhttps://kat.cr/user/Blink99/
be developed to target directly a specific type of cancer.
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Fig. 16.14: Microarray technique
Highly active gene → produces more mRNAs → more cDNA bind/hybridize to DNA
on microarray slide → generate bright fluorescence.
Inactive gene → no mRNAs → no cDNAs → no hybridization on the slide → no fluorescence.
i. Green spot: More mRNA produced from normal cell → the gene is highly expressed in
normal cells.
ii. Red spot: More mRNA produced from cancer cell → the gene is highly expressed in
cancer cells.
iii. Yellow spot: Both normal and cancer cells produce same amount of mRNA → the particular
gene is equally expressed in both types of cells.
iv. Black/dark spot: None of the cells produced the particular mRNA.
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Applications
• To analyze changes in gene expression (by collecting mRNA molecules from a particular cell)

• To observe mutations in the gene (genotyping)

• To observe genomic gains and losses

• Gene discovery

• Disease diagnosis: Classify the types of cancer on the basis of the patterns of gene activity

in the tumor cells
• Pharmacogenomics: To study the correlations between therapeutic responses and the genetic

profiles of the patients
• Toxicogenomics: Check the toxin induced changes in the cell.

-
24. Write briefly on human genome project (HGP).
The project of DNA sequencing was initiated in the United States. The International Hu
man Genome Sequencing Consortium and a private enterprise, Celera Genomics undertook
the project of sequencing of human genome. It was an international scientific project with
a primary goal of determining the sequence of human genome, identifying and mapping
approximately 25,000 genes. The sequence of the entire human genome (with the exception
of few gaps) was completed in 2003.
Goals were to
i. Identify all the 20,000–25,000 genes in human DNA.
ii. Determine the sequences of chemical base pairs that make up human DNA.
iii. Store this information in databases; develop tools for analysis of data.
iv. Address the ethical, legal and social issues (ELSI) that may arise from the project.
Techniques: Used for sequencing included mapping and shotgun sequencing.

Implications
• Isolation of almost any gene and study of its structure and function is possible
• Genes, which were previously unknown, were detected as a result of HGP
• Improvements in procedures for detecting disease causing genes—development in genetic,
immunologic and microbiological diagnostics
• Gene therapy
• Use of genetic information for drug development and treatment (pharmacogenomics)
• Use in forensic medicine, e.g. help to identify crime suspect
• Assessment of damage following exposure to carcinogens, radiation, etc.
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Acid-Base Balance and
17 Disorders
1. Write briefly on buffer systems in the body. Add a note on Henderson-Hasselbalch

equation.
Definition: Buffer is a solution of a mixture of weak acid with its conjugate base, or a
weak base with its conjugate acid, which resists change in pH on addition of alkali or
acid (Table 17.1).
Table 17.1: Buffer systems
Buffer systems Base/acid pKa
Bicarbonate HCO3– 6.1

H2CO3
Phosphate HPO42– 6.8
H2PO4–
Hemoglobin Hb
HHb
Protein Protein
H protein
pKa: Negative logarithm of dissociation constant K. Buffers are very effective within ±1 pH unit of their pKa.
Functions of buffer: Maintenance of intracellular and extracellular pH.

Henderson-Hasselbalch equation
(Base)
pH = pKa + log
(Acid)
Where,
• pH: Negative logarithm of hydrogen ion concentration
• pKa: Negative logarithm of dissociation constant.
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Significance of Henderson-Hasselbach equation
• To determine acid-base status of an individual

• To measure any one of the parameter in the equation, if others are known

• Preparation of buffers.
2. What is the normal pH of blood? Define and classify acid-base disorders.
Normal pH of arterial blood is 7.35–7.45.

Classification of acid-base disorders
Acid-Base Balance and Disorders
a. Acidosis: When arterial pH drops below 7.35.

• Metabolic acidosis
• Respiratory acidosis.
b. Alkalosis: When arterial blood pH rises above 7.45.

• Metabolic alkalosis
• Respiratory alkalosis.
c. Mixed: Presents with either acidosis or alkalosis in both systems together, e.g. metabolic

acidosis with respiratory acidosis.
3. What is anion gap?
Anion gap: It is a measure of unmeasured anions (e.g. lactic acid, ketone bodies, sulfate,

phosphate, etc.) in blood.
Normal range: 12 ± 5 mmol/L.

Formula: [Na+ + K+] − [Cl− + HCO3−].

Increased anion gap: It is seen in lactic acidosis, diabetic ketoacidosis.

4. What is metabolic acidosis? Mention some causes for it.
Definition: Metabolic acidosis is a decrease in pH due to a primary decrease in bicarbonate

(HCO3– < 22 mEq/L) concentration in blood.
Serum bicarbonate (normal range): 22–27 mEq/L.

Causes
• Increased acid production—lactic acidosis, ketoacidosis
• Decreased acid excretion—renal failure
• Bicarbonate is used up for buffering of accumulated acids
• Increased bicarbonate loss—diarrhea, gastroenteritis.
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Classification
a. High anion gap metabolic acidosis: Due to increased production/decreased excretion of unmea-
sured anions.
Causes [MN: U SLID]: Uremia, salicylate toxicity, lactic acidosis, ischemia, diabetes mel-
litus (uncontrolled).
b. Normal anion gap metabolic acidosis: There is metabolic acidosis, but anion gap is normal.
Causes: Diarrhea (severe), renal tubular acidosis, intestinal fistula.
Biochemical findings in metabolic acidosis are given in Table 17.2.

Table 17.2: Biochemical findings in metabolic acidosis (uncompensated)
Parameter Finding
pH Decreased
pCO2 Normal
Bicarbonate Decreased
5. What is respiratory acidosis? Mention the causes.

Definition: Decrease in pH due to primary increase in pCO2 (normal range: 35–45 mm Hg).
Respiratory acidosis occurs when pCO2 value is above 45 mm Hg. CO2 retention results
in increased carbonic acid in blood. Biochemical findings in respiratory acidosis is given
in Table 17.3.
Table 17.3: Biochemical findings in respiratory acidosis (uncompensated)
Parameter Finding
pH Decreased
pCO2 Increased
Bicarbonate Normal
Causes [MN: COPD]

• Cardiac arrest
• Obstructive airway disease
• Paralysis of respiratory muscles due to polio or central nervous system (CNS) injury
• Drugs: Opiates causing respiratory depression.
6. Define and mention the causes for metabolic and respiratory alkalosis.
The causes and features of alkalosis is mentioned in Table 17.4.
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Table 17.4: Causes and features of alkalosis
Respiratory alkalosis Metabolic alkalosis
Definition Increase in pH due to Increase in pH due to
primarily a decrease in CO2; primarily an ↑ in HCO3 ; this is due to ↑ reabsorption
-
↓ CO2 → ↓ carbonic acid of HCO3 or ↑ loss of H+
-
Causes Hyperventilation, Gastric Aspiration, vomiting
anemia, salicylate Iatrogenic—overuse of antacids
poisoning [MN: HAS] Diuretics
Steroid excess (Cushing's syndrome) [MN: AIDS]
Features
pH Increased Increased
pCO2 Decreased Normal
Bicarbonate Normal Increased
7. How is pH (hydrogen ion concentration) regulated in our body?

Concentration of hydrogen ion is regulated sequentially by:

• Blood buffer systems: act within seconds
• Respiratory center in the brainstem: acts within 1–3 minutes
• Renal mechanisms: require hours to days.
Buffers in Body Fluids

They can buffer excess acids or bases, but they cannot eliminate them from the body. Three
major chemical buffer systems in our body are:
a. Bicarbonate (HCO3 /H2CO3) buffer system (base to acid ratio 20:1): Important extracellular
-

buffer.
b. Phosphate buffer system (HPO42 /H2PO4 ): This system is an effective buffer in urine and
-
-

intracellular fluid. At physiologic pH, its base to acid ratio remains at 4:1.
c. Protein buffer system (protein/H protein): Histidine residue in proteins has pKa value of

6.1, which is close to normal pH and hence is most effective in buffering.
Respiratory System
There is a reversible equilibrium between:
• Dissolved carbon dioxide (H2CO3) and water
• Carbonic acid, hydrogen and bicarbonate ions.
CO2 + H2O ↔ H2CO3 ↔ H+ + HCO3−
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Mechanism of Regulation
• Decrease in plasma pH → stimulation of chemoreceptors in respiratory center → deeper
and more rapid breathing → expels more carbon dioxide (hyperventilation) → ↓ H2CO3
→ ↑ pH
• When ↑ plasma pH → slower, shallow breathing → ↑ H2CO3 → ↑ H+ → ↓ pH.
Where more carbon dioxide (CO2) is formed, there is an increase in hydrogen ion (H+)
and bicarbonate (HCO3–). H+ is bound by Hb to form HHb. Once this reaches lungs, H+ at-
tached to Hb is replaced by O2 forming HbO2. HCO3− reacts with H+ to form H2CO3. H2CO3

dissociates to CO2 and H2O. CO2 is expelled from the lungs. This mechanism effectively
converts the carbonic acid to CO2, which can be eliminated from the lungs.
Renal Mechanisms of Acid-base Balance

Acid-base balance occurs by:
a. Reabsorption of filtered bicarbonate.
b. Excretion of hydrogen ions with simultaneous regeneration of bicarbonate (in proximal
convoluted tubule).
c. Excretion of titratable acid as sodium dihydrogen phosphate (distal convoluted tubule).
d. Excretion of ammonium ions in distal tubule.
i. Reabsorption of filtered bicarbonate (Fig. 17.1)
H+ generated in tubular cell → lumen → reacts with HCO3− → H2CO3 → H2O + CO2. CO2
diffuses into the tubular cell → reacts with H2O → H2CO3 → H+ + HCO3−. Bicarbonate
is absorbed into plasma.
Fig. 17.1: Reabsorption of filtered bicarbonate (CA, carbonic anhydrase)
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ii. Excretion of hydrogen ions with simultaneous regeneration of bicarbonate and excretion

of titratable acid as sodium dihydrogen phosphate (Fig. 17.2).
Fig. 17.2: Excretion of H+ with simultaneous regeneration of bicarbonate and excretion of titratable acid as sodium dihy-
drogen phosphate (CA, carbonic anhydrase).
iii. Excretion of ammonium ions (Fig. 17.3)

Filtered H+ combines with NH3 to form ammonium ion (NH4) and is eliminated.

Fig. 17.3: Excretion of ammonium ions (CA, carbonic anhydrase)
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8. What is the relation between serum potassium and acid-base disorders?

• In metabolic acidosis: As there are more H+ ions in plasma, body tries to buffer it by
exchanging H+ with intracellular potassium ions leading to hyperkalemia, which mani-
fests as severe bradycardia, cardiac arrhythmias and cardiac arrest
• In metabolic alkalosis: Shift of extracellular K+ into the cells in exchange for H+, lead-
ing to hypokalemia. Also, the kidneys retain H+ in exchange for potassium, which also
leads to hypokalemia. Hypokalemia → tachycardia → cardiac arrhythmias.

Key Points
Compensatory changes
Compensation comes from the complementary system (other system) to aid the inadequacy of one
system. For example, the respiratory system will attempt to correct metabolic acid-base imbalances.
The kidneys will work to correct acid-base imbalance caused by respiratory disease.
Respiratory compensation
a. In metabolic acidosis: Increased rate of respiration removes carbon dioxide from the blood; pCO 2
falls bringing back the pH to normal.
b. In metabolic alkalosis: As a compensatory mechanism, there is slow, shallow breathing, allowing
carbon dioxide to accumulate in blood, which increases carbonic acid in blood and brings down the
pH to normal level.
Renal compensation
a. In respiratory acidosis: Kidneys try to retain bicarbonate to offset the acidosis.
b. In respiratory alkalosis: Kidneys eliminate bicarbonate from the body.
Calcium in acid-base disorders
a. In acidosis, because of increased H+ in serum, plasma proteins try to buffer them, which may displace
some protein bound calcium, so plasma calcium increases relatively in acidosis.
b. In alkalosis, because of high pH, proteins are negatively charged; they bind to positively charged
Ca2+. This may lead to relative hypocalcemia.
General instructions for identifying an acid-base disorder
Look at the pH value in the arterial blood gas (ABG) analysis report.
Is there an acid-base disorder present?
• If pH is less than 7.35, then it is acidosis; if pH is more than 7.45, then alkalosis
• If pH is within normal range then,
– Either acid-base disorder is not likely to be present (if other parameters of ABG analysis are
normal) or
– It is a fully compensated acid-base disorder (if other parameters of ABG are abnormal).
Look at pCO2 and HCO3– values to identify the primary change.
Initial change is the abnormal value that correlates with the abnormal pH.
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• If pH is low (acidosis); primary change is increased pCO2 or decreased HCO3−
– Low pH + increased pCO2 = respiratory acidosis

– Low pH + Low HCO3− = metabolic acidosis.

• If pH is increased (alkalosis); primary change is decreased pCO2 or increased HCO3−
– Increased pH + decreased pCO2 = respiratory alkalosis

– Increased pH + increased HCO3− = metabolic alkalosis.

Once the initial change (primary event) is identified, then the other abnormal parameter is the com-
pensatory response (Table 17.5); if its direction of change is the same as primary event then it is
simple acid-base disorder. Compensatory response indicates that the disorder is compensated.
Table 17.5: Primary and compensatory event

Acid-base disorder Initial chemical change Compensatory response
Respiratory acidosis ↑ pCO2 ↑ HCO3−
Respiratory alkalosis ↓ pCO2 ↓ HCO3−
Metabolic acidosis ↓ HCO3− ↓ pCO2
Metabolic alkalosis ↑ HCO3 − ↑ pCO2
Note: Both the primary event and compensatory response occur in the same direction, i.e. either both increase or both decrease.
Problem Solving Exercises

1. A 35-year-old man was admitted to hospital with an asthmatic attack. His ABG report

showed: pO 2 70 mm Hg, pCO 2 30 mm Hg, pH 7.50, HCO 3–: 23 mEq/L. Comment on
this.
a. Look at pH: It is increased—alkalosis.

b. Look at pCO2 and HCO3–: Low pCO2 is the primary change, hence it is respiratory alka-

losis. As HCO3– is within normal range, it is uncompensated respiratory alkalosis.
2. A 65-year-old chronic smoker was admitted with increasing breathlessness. History re-

vealed he is a patient of COPD. His ABG showed following: pO2 45 mm Hg, pCO2 53
mm Hg, pH 7.3, HCO3–: 35 mmol/L.
a. Look at pH: Slightly decreased.

b. Look at pCO2 and HCO3−: pCO2 is high and HCO3– is also high. The primary response

is increase in pCO2, so it is respiratory acidosis.
c. HCO3− is increased as compensatory mechanism to bring back the pH to normal (direc-

tion of change is same).
d. Impression: Respiratory acidosis (partially compensated as pH is not normal).

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3. A 50-year-old man came to the outpatient clinic with a history of intermittent profuse
vomiting and loss of weight. He had tachycardia and hypotension. History revealed
he is a case of pyloric stenosis. ABG report showed: blood pH 7.55, pCO2 48 mm Hg,
HCO3– 35 mmol/L, hyponatremia, hypokalemia. His urine pH was 3.5.
a. Look at pH: Increased, so alkalosis.
b. Look at pCO2 and HCO3−: HCO3– is high and pCO2 is slightly increased. The primary
response is increase in HCO3– (loss of hydrogen ions due to vomiting) and increase in
pCO2 is compensatory mechanism (direction of change is same as primary event).
c. Impression: Metabolic alkalosis (partially compensated).

d. Comment: This patient had depletion of chloride due to vomiting, which limited re-
absorption of sodium in the thick ascending limb of the loop of Henle. So, sodium is
exchanged for hydrogen and potassium ions in the distal nephron leading to hypokalemia
and acidic urine inspite of alkalosis. This is called paradoxical acid urine.
4. During resuscitation of a 60-year-old man from a cardiorespiratory arrest, the blood gas
analysis revealed: pH 7.00 (7.37–7.44), pCO2 52 (35–45 mm Hg), bicarbonate 11 (23–30
mEq/L), pO 2 91 mm Hg (during treatment with 48% oxygen), lactic acid 7 mmol/L
(0.7–1.8).
a. Look at pH: Decreased, so acidosis.
b. Look at pCO2 and HCO3–: Bicarbonate is low and pCO2 slightly increased. Both indicate
primary event.
c. pCO2 is increased and bicarbonate is decreased (opposite direction)—it indicates mixed
acid-base disorder.
d. Impression: Metabolic acidosis with respiratory acidosis (lack of ventilation).
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18 Organ Function Tests
LIVER FUNCTION TESTS
1. Write a short note on liver function tests.

Liver function tests: They are tests done to assess the functional capacity of liver (Tables

18.1 to 18.3).
Functions of liver

• Metabolism: Carbohydrates, lipids and proteins
• Excretion: Bilirubin, bile acids and bile salts
• Synthesis: Albumin, α- and β-globulins, clotting factors, cholesterol, lipoprotein
• Storage: Glycogen, vitamins (A, D, B12), etc.
• Detoxification and drug metabolism.
Liver function tests are used to

• Detect and diagnose liver disease
• Evaluate the severity of liver disease
• Monitor response to therapy
• Assess prognosis of liver disease.
Table 18.1: Liver function tests
Class Tests
Tests based on excretory function Estimation of serum/urine bilirubin, bromsulfthalein
Tests based on serum enzymes Estimation of serum alanine transaminase (ALT),
(indicator of liver damage/cholestasis) aspartate transaminase (AST), alkaline phosphatase (ALP),
γ-glutamyl transferase (GGT)
Tests based on synthetic functions Total proteins, serum albumin, globulin, albumin globulin ratio,
prothrombin time
Tests based on detoxification Hippuric acid test, blood ammonia
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Table 18.2: Important liver function tests

Tests Normal range Methods Clinical utility
Total bilirubin 0.2–0.8 mg/dL van den Bergh reaction Helps in diagnosis of jaundice
Direct bilirubin 0.1–0.2 mg/dL van den Bergh reaction ↑ in hepatic and obstructive jaundice
Indirect bilirubin 0.2–0.6 mg/dL Total bilirubin – direct bilirubin ↑ in hemolytic jaundice
ALT 5–40 U/L Enzymatic method ↑ in liver damage (e.g. hepatitis)
AST 5–40 U/L Enzymatic method ↑ in liver damage (e.g. hepatitis)
ALP 40–140 U/L Enzymatic method ↑ in obstructive jaundice
Total protein 6–8 g/dL Biuret ↓ in cirrhosis of liver
Albumin 3.5–5 g/dL Biuret ↓ in cirrhosis of liver
Organ Function Tests

Globulin 2–3.5 mg/dL Total protein – albumin ↑ in multiple myeloma, ↓ in HIV infection
HIV, human immunodeficiency virus; ALT, alanine transaminase; AST, aspartate transaminase; ALP, alkaline phosphatase;
↑ = increased; ↓ = decreased.
Table 18.3: Other tests with uses

Tests Normal range Clinical utility
γ-glutamyl transferase (GGT) 10–50 U/L ↑ in alcoholic hepatitis and obstructive jaundice
Prothrombin time < 14 second ↑ in hepatocellular disease
Plasma ammonia 25–94 µg/dL ↑ in severe hepatocellular disease
Alfa-fetoprotein (AFP) < 15 ng/mL ↑ in germ cell tumor, ↑ in maternal serum in neural
tube defect in fetus
↑ = increased; ↓ = decreased
2. Explain the principle and applications of van den Bergh reaction.

van den Bergh reaction: It is a test done to detect the presence of bilirubin in blood and
the type of jaundice (Table 18.4).
Principle: It is based on the formation of a purple-colored azobilirubin, when serum con-
taining bilirubin is allowed to react with freshly prepared diazo reagent.
Ehrlich’s Diazo reagent: It is prepared by mixing 10 mL of sulfanilic acid in HCl + 0.8 mL
of sodium nitrite in water.
Response obtained: Three types.
Direct positive: Conjugated bilirubin, if present in serum, reacts directly with diazo reagent
to give a purple color immediately.
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Indirect positive: Unconjugated bilirubin in serum reacts with diazo reagent only on addi-

tion of methanol to give a purple color.
Biphasic reaction: It is observed when both conjugated and unconjugated bilirubin is increased

in serum. Initially, a purple color is formed immediately (direct positive) on addition of
reagent. On addition of methanol, the color intensifies (indirect positive).
Normal levels in blood

• Total bilirubin: 0.2–0.8 mg/dL
• Unconjugated bilirubin: 0.2–0.6 mg/dL
• Conjugated bilirubin: 0.1–0.2 mg/dL.
Table 18.4: Pattern of van den Bergh reaction in different types of jaundice
Types of jaundice Causes Types of bilirubin in blood
Prehepatic Rh incompatibility Unconjugated ↑

Sickle cell anemia (indirect positive)
Hepatic Viral hepatitis—A, B, C Conjugated ↑
Toxic hepatitis—alcohol Unconjugated ↑
(biphasic reaction)
Posthepatic Gallstones Conjugated ↑
Pancreatic tumor (direct positive)
↑ = increased
3. Explain the principle and applications of Ehrlich’s test.

Principle: Urobilinogen in urine reacts with Ehrlich's reagent to form a red color, which

intensifies on addition of sodium acetate (Table 18.5).
Table 18.5: Ehrlich's test in different types of jaundice
Conditions Urine urobilinogen
Normal range 0–4 mg/24 hour
Prehepatic ↑
Hepatic ↓ if there is intrahepatic obstruction
Obstructive jaundice Absent
4. Write a note on hippuric acid test.

Indication: To assess the detoxifying capacity of liver.

Principle: Benzoic acid (sodium benzoate), administered orally or intravenously, combines

with glycine to form hippuric acid. Amount of hippuric acid excreted in urine in a fixed
time is determined. Thus, hippuric acid determines the conjugating capacity of the liver.
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Types
• Oral hippuric acid test: Normally, at least 3 g of hippuric acid should be excreted at the end
of 4 hours after ingestion of 6 g of sodium benzoate
• Intravenous hippuric acid test: It is done only if absorption is impaired or patient has nausea
and vomiting.
Interpretation: Decreased excretion means decreased conjugating capacity of the liver (due
to damage to hepatocytes).
5. Explain the biochemical findings in blood, urine and feces in different types of jaundice.
Refer Chapter 22, question number 3.
Key Points

van den Bergh test: This is done to detect serum bilirubin. Direct reaction detects the conjugated
bilirubin and indirect reaction detects unconjugated bilirubin.
Hemolytic jaundice (hemolysis): Elevated unconjugated bilirubin + absent urinary bilirubin + in-
creased urobilinogen in urine.
Hepatic jaundice (viral hepatitis): Elevated conjugated and unconjugated bilirubin + elevated as-
partate transaminase (AST) and alanine transaminase (ALT).
Obstructive jaundice (gallstones): Elevated conjugated bilirubin + increased urinary bilirubin +
absent urine urobilinogen.
γ-glutamyl transferase: It is used to detect alcoholic liver disease and obstructive jaundice.
Alkaline phosphatase: This is a canalicular enzyme; elevated in obstructive jaundice.
Hay’s sulfur test: For detection of bile salts in the urine.
Fouchet’s test: For detection of bile pigments in urine.
Ehrlich’s aldehyde test: For detection of urobilinogen in urine.
RENAL FUNCTION TESTS
6. Describe the renal function tests.

Renal function tests: Group of tests done to assess the functional capacity of kidneys.
Functions of kidney
• Elimination of metabolic end products and foreign compounds (drugs)
• Maintenance of water and electrolyte balance
• Maintenance of acid-base balance
• Endocrine functions—production of calcitriol, renin and erythropoietin.
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Renal function tests are used to (Tables 18.6 and 18.7)

• Identify renal dysfunction
• Diagnose renal disease
• Monitor progression of renal disease
• Monitor response to treatment.
Table 18.6: Renal function tests
Serum urea Creatinine clearance (glomerular function)
Serum creatinine Concentration/dilution test; acidification test (tubular function)
Serum uric acid Serum electrolytes—Na+, K+, Cl- HCO3-
Urine examination—physical, chemical Serum calcium and phosphorus
characteristics; microscopy
Table 18.7: Renal function tests with clinical utility

Tests Normal value Clinical utility
Blood urea 10–40 mg/dL ↑ in acute and chronic renal failure,
obstruction in the lower urinary tract
Serum creatinine 0.6–1.4 mg/dL ↑ in acute and chronic renal failure
Serum uric acid 3–7 mg/dL ↑ in acute and chronic renal failure
Serum electrolytes To assess the acid-base status and
Na+ 133–146 mEq/L electrolyte balance in renal disease and
K+ 3.5–5 mEq/L to monitor treatment
Cl– 96–106 mEq/L
HCO3– 22–26 mEq/L
Serum calcium 9–11 mg/dL ↓ in chronic renal failure
Serum phosphorus 2–4.5 mg/dL ↑ in chronic renal failure
Concentration and To diagnose tubular damage: abnormal response seen in
dilution tests chronic renal failure
Routine urine examination
Physical characteristics
Volume 1.5 L Altered in renal failure
Specific gravity 1.015–1.025 Altered in renal failure
Microscopy Absent Bacterial infections—pus cells present
Hematuria—RBC present
Protein Absent Present in nephrotic syndrome, acute
glomerulonephritis
Sugar Absent Present in diabetes mellitus
↑ = increased; ↓ = decreased https://kat.cr/user/Blink99/
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7. Define renal clearance. Write the formula for renal clearance. Name renal clearance tests
with normal values.
Renal clearance: It is defined as the volume of plasma from which a measured amount of
substance can be completely eliminated into urine per unit time. Renal clearance depends
on renal blood flow and glomerular filtration rate (Table 18.8).
UV
Clearance (mL/min) =
P
Where, U = concentration of cleared substance in urine (mg/dL).
V = volume of urine (mL/min).
P = plasma concentration of the substance (mg/dL).

Use: To measure the glomerular filtration rate (GFR). Normal GFR is 125 mL/min.
Table 18.8: Different renal clearance tests with normal values
Tests Normal value Significance
Urea clearance 75 mL/min Not suitable since urea is secreted as well
as reabsorbed. Value obtained is lower than
glomerular filtration rate (GFR).
Creatinine 90–120 mL/min Advantage: Creatinine is an endogenous sub-
clearance stance, it is not much affected by non-renal
factors. Hence, it is a better indicator of renal
function than urea.
Inulin clearance 125 mL/min Advantage: Gold standard. It is neither
reabsorbed nor secreted by renal tubules.
Measures exact GFR.
Disadvantage: Exogenous, can cause allergy in
some people.
8. Write short notes on creatinine clearance.

Creatinine clearance: It is defined as volume of plasma from which a measured amount
of creatinine could be completely eliminated into urine per unit time.
Advantages of creatinine clearance over other clearance tests
• Creatinine is an endogenous substance and easy to measure
• Creatinine excretion is constant
• Serum creatinine levels are not much affected by non-renal factors.
UV
Creatinine clearance (mL/min) =
P
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Where, U = concentration of creatinine in urine (mg/dL).
V = volume of urine (mL/min).
P = plasma concentration of creatinine (mg/dL).
Use: To measure the glomerular filtration rate. Creatinine clearance is decreased in renal failure.

Key Points

Normal specific gravity of urine (1.012–1.024): Specific gravity is increased in diabetes mellitus,

acute glomerulonephritis and decreased in diabetes insipidus.
Creatinine coefficient: It is defined as mg of creatinine excreted/kg/day. Normal range is 15–25.

Microalbuminuria: Excretion of albumin in urine in the range of 30–300 mg/24 hours. It is an early

indicator of diabetic nephropathy.

Proteinuria: Causes are nephrotic syndrome, acute glomerulonephritis and multiple myeloma.

Normal serum creatinine: 0.6–1.4 mg/dL.

Normal blood urea: 10–40 mg/dL.

Normal glomerular filtration rate (GFR): 125 mL/min.

Creatinine clearance (120 mL/min): It is defined as volume of plasma from which a measured

amount of creatinine could be completely eliminated into urine per unit time. Formula for creatinine
clearance (mL/min) = UV/P.
Cockcroft and Gault formula: Used to measure creatinine clearance.

(140–Age in year) × weight (Kg)

Creatinine clearance =
Creatinine (mg/dL) × 72

NPN: Non-protein nitrogen (NPN) includes urea, creatinine and uric acid. They are increased in

renal dysfunction.
BUN: Blood urea nitrogen (BUN). It is a measure of the amount of urea nitrogen in blood. Normal

value is 7–21 mg/dL. Urea nitrogen concentration can be converted to serum urea concentration
(mg/dL) by multiplying by 2.14.
Abnormal constituents of urine: Blood (acute glomerulonephritis), glucose (diabetes mellitus),

ketone bodies (diabetic ketoacidosis), bile salts and pigments (obstructive jaundice); some of the
abnormal constituents can be detected by dipstick strips.
THYROID FUNCTION TESTS

9. How do you biochemically investigate the thyroid function?

Thyroid function tests: Group of tests done to evaluate the functional capacity of thyroid

gland (Tables 18.9 and 18.10). https://kat.cr/user/Blink99/
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249
Thyroid function tests are used to

• Detect and diagnose thyroid disease
• Monitor response to treatment of thyroid disorders
• Evaluate the prognosis of thyroid cancer.
Table 18.9: Thyroid function tests
Routinely done tests Special tests
Triiodothyronine (T3) Free T3, free T4
Thyroxine (T4) Anti-thyroperoxidase antibodies
Thyroid-stimulating hormone (TSH) Anti-thyroglobulin antibodies
Iodine uptake studies

Thyroid scan
Stimulation and suppression tests
Table 18.10: Blood picture in thyroid function tests

Condition Clinical features T3 T4 TSH
Normal (euthyroid) Normal 1.8–3 nmol/L 65–150 nmol/L 0.5–5 µIU/mL
Hyperthyroidism Heat intolerance, increased pulse High High Low
rate, diarrhea, tremors, etc.
Hypothyroidism Cretinism (children)
Growth and mental retardation Low Low High
Myxedema (adults)
Cold intolerance, hoarseness of
voice, hypercholesterolemia, etc. Low Low High
Key Points
T3, T4, TSH: Routinely done thyroid function tests.
Deficiency of thyroxine causes myxedema and cretinism.
Excess of thyroxine: Seen in Graves' disease.
Goiter: Characterized by swelling of thyroid gland in response to increased stimulation by TSH,
whose secretion is increased due to reduced synthesis of thyroid hormones caused by deficiency
of iodine.
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GASTRIC FUNCTION TESTS
10. Write a note on functions of gastric juice.

Functions: The functions of gastric juice are given in Table 18.11.

Table 18.11: Constituents and functions of gastric juice
Components Functions
Hydrochloric acid (HCl) • Maintains acidic pH for activation of pepsinogen; germicidal
• Denatures proteins, thus helps in protein digestion
Pepsin • Digestion of protein into smaller components
• Activation of pepsinogen
Rennin (in infants) • Digestion of milk proteins in infants

Mucin • Protects gastric mucosa against corrosion by acids
Intrinsic factor • Absorption of vitamin B12
11. Write briefly about gastric function tests.

Gastric function tests: These are the tests done to assess gastric function by gastric juice

analysis (Table 18.12).
Indications

• Diagnosis of achlorhydria, peptic ulcer
• Diagnosis of Zollinger-Ellison syndrome
• To determine completeness of surgical vagotomy
• Diagnosis of pernicious anemia.
Table 18.12: Gastric function tests with their uses
Tests Significance
Free acidity Absent in gastric carcinoma
↑ in gastrinoma
Total acidity ↑ in pyloric obstruction
Starch Present: Due to delayed gastric emptying resulting from pyloric
obstruction in gastric carcinoma
Lactic acid Present: Due to delayed gastric emptying resulting from pyloric
obstruction in gastric carcinoma
Blood Present: Gastric ulcer, carcinoma
Bile salts and bile pigments Present: Regurgitation due to duodenal obstruction
Contd...
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Contd...
Tests Significance
Pentagastrin test Zollinger-Ellison syndrome: Increased basal secretion
Pernicious anemia: No acid secretion
Augmented histamine test Pernicious anemia: No increase in free acidity
Hollander test (insulin-induced To check completeness of vagotomy
secretion of gastric acid)
12. Write a note on free and total acidity of gastric juice.

• Normal volume of fasting gastric juice is about 20–50 mL
• Increase in volume is seen in
– Hypersecretion—duodenal ulcer

– Delayed emptying—pyloric stenosis or regurgitation.
Free acidity: It is due to HCl in gastric juice.
• Achlorhydria: Free acidity is low
• Peptic ulcer: Free acidity is high.
Total acidity: About 10–40 mEq/L; it is due to free HCl + lactic acid + other organic acids.
Combined acidity: Total acidity-free acidity. This is due to presence of acids other than
HCl. Combined acidity is increased in pyloric stenosis due to acids like lactic acid and
butyric acids generated from bacterial fermentation of retained food products.
13. Explain Schilling test and its applications.

Schilling test: It is done to check the absorption of vitamin B12. Radiolabeled vitamin B12
is ingested orally with and without intrinsic factor.
Pernicious anemia: Radiolabeled vitamin B12 starts appearing in urine only when given
along with intrinsic factor.
Ileal (malabsorption) disease: Radiolabeled B12 will not appear in urine even after giving
intrinsic factor.
14. Write a short note on fractional test meal.

Steps in fractional test meal
• Collection of gastric contents using Ryle's tube after overnight fasting, volume is noted
• Ingestion of test meal and time is noted
• Removal of 5–6 mL of gastric contents at every 15 min interval for 2–3 hours; basal, total
and free acidity is measured.
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Interpretation

Normal response: Free acidity levels are low initially, then steadily increase reaching a maxi-

mum at 60–90 min, thereafter the values return to basal levels in about 120–150 min. Total
acidity follows similar pattern, but the values are 8–12 units higher than free acidity.
Abnormal response

• Hyperchlorhydria: High free acidity values at fasting, reaches peak level and values remain
high throughout the test, e.g. duodenal ulcer, gastric ulcer
• Achlorhydria: Free acidity levels remain low or absent throughout the test, e.g. carcinoma
stomach.
PANCREATIC FUNCTION TESTS

15. Write briefly how to biochemically assess pancreatic functions.

Pancreatic function tests: These are done to assess the functional capacity of pancreas

(Table 18.13).
Indications

• To diagnose acute and chronic pancreatitis
• To diagnose cystic fibrosis
• Differential diagnosis of malabsorption syndromes.
Tests

• Serum amylase: Normal: 80–240 U/L
• Serum lipase: Normal: 5–80 U/L.
Table 18.13: Pancreatic function tests
Condition Causes Serum amylase Lipase
Acute pancreatitis Gallstone, alcohol consumption Elevated Elevated
Chronic pancreatitis Gallstone, alcohol consumption N/slight ↑ N/slight ↑
Cystic fibrosis Mutation in CFTR gene N/slight ↑ N/slight ↑
CFTR, cystic fibrosis transmembrane conductance regulator; N, normal.
Key Points
Serum amylase and lipase: Levels are elevated in acute pancreatitis.

Serum lipase: It is more specific for acute pancreatitis than amylase (amylase is also secreted from

salivary glands).
Serum amylase levels: These are also elevated in mumps.

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BIOCHEMICAL TESTS FOR CARDIAC DISEASES
16. Briefly discuss the biochemical tests for cardiac diseases.

Indications (Table 18.14)
• To diagnose acute myocardial infarction (AMI)
• To differentiate myocardial infarction from non-cardiac chest pain
• To monitor therapy
• To assess the severity of myocardial injury
• To diagnose cardiac failure—brain natriuretic peptide (BNP).
Non-enzyme markers—troponin T and troponin l, BNP, lipid profile.
Enzyme markers—CK, CK-MB isoform, AST, LDH, LDH1/LDH2 ratio.

Table 18.14: Cardiac function tests
Tests Normal levels Time of increase Significance
after MI
Total CK 15–100 IU/L 6–8 h Acute MI—non-specific
CK-MB isoform < 5% total CK 2–4 h Acute MI—specific
Troponin T < 0.1 mg/L 3–4 h Acute MI—specific
Troponin I < 1.5 mg/L 4–6 h Acute MI—specific
Total LDH 100–200 IU/L 12–24 h Acute MI—non-specific
LDH1/LDH2 ratio < 1 12–24 h Flipped ratio—acute MI
AST 4–40 IU/L 8 h Acute MI
Brain natriuretic peptide (BNP) 40–125 pg/mL Congestive cardiac failure
CK, creatinine kinase; LDH, lactate dehydrogenase; MI, myocardial infarction.
Key Points
Routinely done tests (cardiac specific markers) for diagnosis of acute myocardial infarction:
CK-MB, troponin T and troponin I.
LDH flip: Normally LDH 1/LDH2 ratio is less than 1. In acute myocardial infarction, LDH 1 activity
increases due to myocardial injury and ratio is reversed.
Brain natriuretic peptide: It is a useful marker in diagnosis of cardiac failure.
Lipid profile (total cholesterol, triglycerides, LDL and HDL cholesterol): Levels are measured
for early detection of risk in development of atherosclerosis and coronary artery diseases.
AST, LDH and CK: These are non-specific for detection of myocardial injury since their levels are
also elevated in liver injury, hemolytic anemia and muscle dystrophies, respectively.
Total LDH or LDH1: Useful for late detection (48 hour after chest pain) of myocardial infarction.
Myoglobin: It can also be used for diagnosis of AMI immediately (elevated early) after myocardial
infarction. Elevated myoglobin may be non-specific, since it is present in skeletal muscle.
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19 Radioisotopes
1. Define isotopes with examples.

Definition: Elements with the same atomic number (left subscript to the chemical symbol),

but different mass number (left superscript to the chemical symbol). Behave similarly in
chemical reactions (Table 19.1).
May be stable (nuclear composition does not change with time) or unstable (undergoes

spontaneous decay).
Table 19.1: Some examples for isotopes
Stable Unstable
2
H (deuterium), 11 H 3
H (tritium)

1 1

12
6
C 13
6
C 14
6
C

127
53
I 125
53
I 131
53
I

2. Define radioactivity. What are the units of measurement of radioactivity?
Definition: It is a property of unstable isotopes to undergo spontaneous degradation of

nucleus with emission of particles or rays to attain a stable conformation.
Units of radioactivity
a. The international system (SI) unit of radioactivity: Becqueral (Bq) = decay/second (dps).

b. Older unit of radioactivity: Curie (Ci) = 3.7 × 1010 dps.

3. Define radioactive decay and half-life.
Radioactive decay: It is a process by which an unstable (radioactive) nucleus can become

stable by emitting particles and energy. The radiation emitted can either be 'a' particles,
'b' particles or γ-rays. Radionuclides are isotopes that can undergo radioactive decay.
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255
Half-life of radioactive compound: Half-life is the time taken for a radioisotope to reach
half of its original radioactivity (Table 19.2).
Table 19.2: Examples for half-life of radioactive elements
Radionuclide Half-life
Iodine-131 8 days
Cobalt-60 5.26 years
Cesium-137 30 years
Carbon-14 5,730 years
Uranium-235 703,800,000 years
4. What are the forms of radiation? Give examples.

Non-ionizing radiation: It contains low energy electromagnetic waves. For example, ul-
Radioisotopes
traviolet, visible light, infrared, microwave and radio wave.
Ionizing radiation: This includes high speed particles and high energy electromagnetic
waves. Their energy is high enough to remove orbital electrons from atoms. They can
cause DNA damage, mutation and cancer. Their ability to destroy deoxyribonucleic acid
(DNA) has been exploited to kill cancer cells.
Forms of Radiation
a. Alpha (α) decay (2 protons + 2 neutrons): After emission of 'a' particles, there is a decrease
in atomic number by two and mass number by four (equivalent to helium nucleus). They
have maximum ionizing and minimum penetration power (stopped by a sheet of paper).
For example,
b. Beta (β) radiation: When neutron splits, it forms proton (+), β (−) particle (electron) and
neutrino. There is an increase in atomic number by one, but no change in mass number.
'β' radiation is negatively charged with negligible mass and has more penetration. It is
used widely in clinical medicine for diagnosis and treatment.
For example,
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256

c. Gamma (γ) radiation and X-rays: γ-rays are emitted, after emission of ' ' particle, when

β
neutron is converted to proton or during electron capture by proton to form neutron. γ
radiation are electromagnetic waves, have no charge or mass. It has maximum penetrating
power. For example,

5. What are the applications of radioisotopes?
Research

• Tracer technique: 14C can be used to study metabolic pathways
• 131I can be used to study half-life of immunoglobulins
• 131I-labeled albumin can be used to study blood volume.
Radioisotopes
Diagnosis
• 131I for thyroid scan: 'Cold nodule' (less/no uptake of radioactive isotope)
• 51Cr to study red blood cell (RBC) life
• 90Sr (strontium): Scan to detect osteoblastoma
• 125I-labeled antigen is used in radioimmunoassay (RIA).
Treatment
Radiotherapy

a. Liquid form of radioactive isotope is administered ('b' particles are emitted). For example,

131
I is administered orally in thyroid carcinoma.
b. 'γ' radiation can be used to treat cancer. It can be directly applied on the tissue (brachyther-

apy) or as needle. For example, cesium (137Cs) is useful for cervical carcinoma.
c. Teletherapy: Source kept at a distance in a thick-walled metal container with small aperture

and radiation is focused on cancer tissue. γ-rays are used for this. For example, 60Co/137Cs
for deep-seated cancers.
6. Write short notes on radioimmunoassay (RIA).
Principle
There is a competition between isotope-labeled antigen (fixed amount) and unlabeled

antigen (in patient's sample) for binding to a constant number of antibodies or binding
sites. As the amount of unlabeled antigen increases, more of it binds to the antibody by
displacing the labeled antigen (Fig. 19.1).
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Procedure
Radioactive isotope 125
I is often used.
Radioisotopes
Fig. 19.1: Radioimmunoassay
Interpretation
If patient's serum has no antigen or very low antigen concentration, then more labeled
antigens are bound to antibodies. At increasing concentrations of unlabeled antigens in
patient's serum, more amount of radioactive (labeled) antigen is displaced from the anti-
body molecules. So, the precipitate will have relatively less radioactivity as concentration of
labeled antigen-antibody complex in it decreases. Hence, the radioactivity of the precipitate
is inversely proportional to the unlabeled antigen concentration in serum (Fig. 19.2).
Advantages
Very small quantities (microgram or picogram) of substances can be analyzed, only mi-
crocuries of radioactivity are used and radiation hazard is minimal.
Disadvantages
Half-life of 125I is only 60 days; it can be carried out only in laboratories approved by
authorities. Also, radioactive materials are expensive.
Uses: To detect and quantify antigens, hormones, tumor markers, etc.
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258

Radioisotopes
Fig. 19.2: Bound radioactivity decreases as unlabeled antigen concentration in patient's serum increases
7. Write short notes on enzyme-linked immunosorbent assay (ELISA).

ELISA is a widely used method for measuring the concentration of a particular molecule

(e.g. hormone, drug, antigen, etc.) in biological fluids like serum, urine, etc. (Fig. 19.3).
Procedure of ELISA
Fig. 19.3:https://kat.cr/user/Blink99/
Enzyme-linked immunosorbent assay
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259
Applications
• To detect antigens, e.g. hepatitis B antigen
• To detect antibodies, e.g. HIV antibody
• To detect hormones, e.g. T4, TSH, HCG, etc.
Advantages
No radiation hazard as no radiolabeled material is used. Simple, less time consuming
and less expensive than RIA. Small quantities of hormones/antigen/antibodies can be
detected.
8. Write briefly on effects of radiation on our body (radiation hazard).
Radiotherapy can cause some unwanted effects on the body. This damage depends on the
system or organ exposed and dose of radiation.
a. Skin: Epilation (hair loss), dermatitis, hypopigmentation, loss of elasticity.
Radioisotopes
b. Mucous membrane: Nausea, vomiting, ulceration, bleeding, adhesion, fibrosis.
c. Blood cells: Thrombocytopenia, leukopenia, anemia.
d. Reproductive organs: Sterility, genetic alterations in offspring.
e. Can produce cancer.
Key Points
Radiosensitivity: Success of treatment depends upon how sensitive the tumor is to radiation.
Highly sensitive: Lymphoma, Hodgkin disease and neuroblastoma.
Moderately sensitive: Oral, cervical, breast cancer.
Poorly sensitive: Osteoblastoma, malignant melanoma.
Precautions to reduce hazards due to radiation
• Use lead shields, lead rubber gloves and aprons
• Radioactive substances should be properly stored and disposed.
Gray and rad: Units of absorbed dose of radiation by a tissue.
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Metabolism of Xenobiotics
20 (Detoxification)
1. Define xenobiotic.
Xenobiotic is a compound that is foreign to the body. It may include drugs, chemical

carcinogens, polychlorinated biphenyls (PCBs) and insecticides.
2. Explain the process of detoxification with examples.
Detoxification: It is a process by which toxic compounds are converted into less toxic
and easily excretable forms.
Sites of Xenobiotic Metabolism

i. Liver: It is a major site for detoxification.

ii. Non-hepatic sites: Intestinal mucosa, kidney, lung, gastrointestinal (GI) tract and placenta.

X
enobiotics are Detoxified in Two Phases
Phase 1
Attachment of new functional groups or transformation of existing functional groups by hy-
drolysis, oxidation, reduction, etc.
i. Oxidation: It is the removal of hydrogen or addition of oxygen. Oxidation is carried out by

CYP450 system, alcohol dehydrogenase, aldehyde dehydrogenase and monoamine oxidase.
For example,
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261
ii. Reduction: It is the removal of oxygen and addition of hydrogen or electrons.

For example,
iii. Hydrolysis: It is the breakdown of compounds by addition of water.

For example,
Metabolism of Xenobiotics (Detoxification)

Phase 2
Conjugation: The existing functional group of a compound is conjugated by glucuronidation,
acetylation, methylation, attachment of an amino acid or other mechanisms. Most of the con-
jugated compounds are water soluble and can be easily excreted.
i. Glucuronidation: The compound is conjugated with glucuronic acid.
For example,
ii. Conjugation with glycine.

For example,
iii. Acetylation.
For example,
iv. Methylation.
For example,
v. Sulfation.
For example,
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262

3. How are the following compounds detoxified?
i. Indole.

ii. Aspirin.

iii. Paracetamol.

iv. Cyanide.

v. Phenobarbital.

vi. Isoniazid.

i. Indole: Undergoes deamination and decarboxylation to produce indolepyruvate and finally

indoleacetate.
ii. Aspirin: It is detoxified by hydrolysis.

iii. Paracetamol (acetaminophen): It is detoxified by both glucuronidation and sulfation.

Paracetamol can also be detoxified by CYP2E1 to produce N-acetyl-p-benzoquinoneimine

(NAPQI), which conjugates with glutathione (GSH) to form inactive compound.
iv. Cyanide: Conjugates with thiosulfate to form less toxic thiocyanate.

v. Phenobarbital: Detoxified by hydroxylation by CYP450 group of monooxygenases in the

liver followed by glucuronidation.
vi. Isoniazid (antitubercular drug): Undergoes acetylation. Genetic variations in the enzymes

(acetyl transferases) lead to slow and fast acetylators.
4. Explain the role of glutathione in detoxification mechanism.
i. Glutathione (γ-glutamyl-cysteinylglycine) is a tripeptide consisting of glutamic acid, cysteine

and glycine.
ii. Carcinogens (R) are conjugated with GSH, a reaction catalyzed by glutathione S-transferase

to form glutathione conjugate, which is further metabolized and excreted as mercapturic
acid (Fig. 20.1).
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263

Fig. 20.1: Detoxification by glutathione
Key Points
N-acetyl-p-benzoquinoneimine (NAPQI): It is a metabolite (minor) of paracetamol. It is detoxified by
conjugation with glutathione. In paracetamol overdose, excess NAPQI is generated, which depletes
the hepatic glutathione stores and then causes damage to liver.
Most isoforms of CYP450 are induced by certain drugs: For example, administration of phe-
nobarbital causes hypertrophy of smooth ER 3–4 folds in 4–5 days. This can result in increased
metabolism of drugs.
Warfarin: Used to prevent blood clotting, is metabolized by CYP2C9, which is induced by
phenob arbital. Thus, when warfarin is coadministered with phenobarbital, warfarin is rapidly
metabolized.
Ethanol induces CYP2E1: Which increases the risk for carcinogenicity in alcoholics.
Certain isoforms of CYP450 (CYP1A1): Are involved in the metabolism of polycyclic aromatic
hydrocarbons (PAHs) and are also responsible for carcinogenesis produced by these agents. For
example, in the lung, it is involved in the conversion of inactive PAH inhaled by smoking to active
carcinogens by hydroxylation.
Certain CYP450 enzymes exhibit genetic polymorphism: Some of them show low catalytic activ-
ity. This explains variations in drug responses noted among patients.
Activity of CYP450 is also affected by tissue or organ disease (e.g. cirrhosis of liver).
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21 Miscellaneous
HORMONES
1. Define and classify hormones.

Definition: Hormones are chemical messengers, released from ductless glands into the
bloodstream and regulate the activity of other tissues.
Classification
Based on Chemical Nature
i. Peptide or protein hormones: For example, insulin, glucagon, antidiuretic hormone,

oxytocin.
ii. Steroid hormones: For example, glucocorticoids, mineralocorticoids, sex hormones.

iii. Amino acid derivatives: For example, epinephrine, norepinephrine, thyroxine (T 4), tri-

iodothyronine (T3).
Based on Mechanism of Action

i. Group I hormones: For example, glucocorticoids, estrogens, progesterone, mineralocorti-

coids, calcitriol, thyroxine.
a. Action is mediated via intracellular receptors.

ii. Group II hormones: Action is mediated via cell surface receptors and second messen-

gers. Hydrophilic in nature. They are divided into three categories depending on second
messengers:
a. Hormones using cyclic adenosine monophosphate (cAMP) as second messenger. For

example, adrenocorticotropic hormone (ACTH), follicle-stimulating hormone (FSH),
luteinizing hormone (LH), parathormone (PTH), adrenaline.
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265
b. Hormones using phosphatidylinositol/calcium as second messenger. For example,

thyrotropin-releasing hormone (TRH), gonadotropin-releasing hormone (GnRH), gastrin,
cholecystokinin (CCK).
c. Hormones using cyclic guanosine monophosphate (cGMP) as second messenger. For
example, atrial natriuretic peptide (ANP).
2. Explain the general mechanism of action of group I hormones.
The general mechanism of action of group I hormones is shown in Figure 21.1.
Hormones (e.g. glucocorticoids) pass through the plasma membrane
Bind to their specific, intracellular receptors in the cytoplasm of target cells
Form hormone-receptor complex
Miscellaneous
Undergoes conformational change
Activated hormone-cytoplasmic receptor complex moves into the nucleus and binds with
high affinity to a specific DNA sequence called hormone response element (HRE)
Production of messenger ribonucleic acids (mRNAs)
Production of specific protein, which influence metabolic processes
Fig. 21.1: Mechanism of action of group I hormones, e.g. glucocorticoids (H, hormone; R, receptor)
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266
Example of effect of glucocorticoids: Induction of synthesis of gluconeogenic enzymes.

• Thyroid hormones directly enter nucleus → bind to their receptor, which is already bound

to the response element on DNA → conformational changes in the receptor → gene
transcription
• The hormone action, mediated through intracellular receptors is not immediate, since suf-

ficient time is needed for transcription and translation.
3. Explain the mechanism of action of any one group II hormone (glucagon).
• Group II hormones bind to cell surface receptors resulting in the generation of certain

molecules, namely second messengers
• Group II hormones are divided into three categories depending on second messengers

(Refer question 1).
Miscellaneous
Mechanism
The mechanism of action of glucagon is shown in Figures 21.2 and 21.3.

Glucagon binds to G protein-coupled receptors and acts via cAMP as second messenger.
G protein is GTP-binding membrane protein. It consists of three subunits—a, b, g.
Fig. 21.2: Steps of glucagon action

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267
Miscellaneous
Fig. 21.3: Mechanism of action of glucagon (R, receptor; ATP, adenosine triphosphate; cAMP, cyclic adenosine mono-
phosphate; GDP, guanosine diphosphate)
FEED-FAST CYCLE
4. Explain the metabolic changes in the well-fed state.
Well-fed State (Fig. 21.4 and Table 21.1)

• Increase in levels of blood glucose, amino acids and chylomicrons
• Increased insulin secretion. Glucose uptake into tissues from blood is promoted by insulin
(except brain, RBCs)
• Glucose used as fuel by all tissues—brain utilizes glucose as fuel
• Energy stored as glycogen (liver, muscle) and triacylglycerol (adipose tissue)
• Amino acids from blood are taken up by tissues—protein synthesis occurs.
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268
Miscellaneous
Fig. 21.4: Metabolic changes in various organ systems during well-fed state (HMP, hexose monophosphate; TCA, tricar-
boxylic acid; VLDL, very-low-density lipoprotein)
5. Explain the metabolic changes seen during fasting.

Starvation results from:
• Inability to obtain food

• Desire to lose weight

• Trauma, surgery, neoplasms, burns.

Fasting state (Fig. 21.5 and Table 21.1)
• Decreased blood glucose, amino acids and triacylglycerol

• Increased secretion of epinephrine, glucagon and cortisol; decreased insulin secretion

• Liver maintains blood glucose levels by glycogenolysis and gluconeogenesis

• ↑ protein breakdown → amino acids → hepatic gluconeogenesis

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269
• Fatty acids (from hydrolysis of triacylglycerol in adipose tissue) is taken up by liver and
muscle
• Increased ketone body formation in the liver → used as fuel by other tissues
• Brain uses glucose as fuel. On prolonged fasting, it utilizes ketone bodies.
Miscellaneous

Fig. 21.5: Metabolic changes in various organ systems during starvation (TCA, tricarboxylic acid)
Table 21.1: Events during fast-feed cycle

Organ Fed state Fasting state
Liver ↑ glycogen synthesis ↑ glycogen breakdown
↑ glycolysis ↑ gluconeogenesis
↑ fatty acid synthesis ↑ utilization of fatty acids
↑ triacylglycerol formation ↑ formation of ketone bodies
↑ VLDL synthesis
Adipose tissue ↑ entry of glucose into adipose Hydrolysis of triacylglycerol to fatty acids
tissue (used as fuel by tissues) and glycerol
↑ synthesis of triacylglycerol (utilized in hepatic gluconeogenesis)
(↑ lipogenesis)
Contd...
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270
Contd...
Organ Fed state Fasting state

Skeletal muscle ↑ entry of glucose
↑ synthesis of glycogen ↑ utilization of fatty acids, ketones as fuel
↑ protein synthesis ↑ protein breakdown to amino acids →
hepatic gluconeogenesis
Brain Glucose used as fuel Glucose and ketones used as fuel
6. Mention the different sources and fate of acetyl-CoA.

Sources and fate of acetyl-CoA is given in Table 21.2.

Table 21.2: Sources and fate of acetyl-CoA
Sources of acetyl-CoA Fate of acetyl-CoA

Miscellaneous
Glycolysis Cholesterol synthesis

-oxidation of fatty acids Fatty acid synthesis
β
Catabolism of ketogenic amino acids Ketone body synthesis
Ketone bodies Oxidation in tricarboxylic acid (TCA) cycle
7. Discuss the significance of multienzyme complexes with two examples.

Multienzyme complex is a protein consisting

of more than one catalytic domains formed
by structurally distinct and ordered collec-
tion of enzymes, often catalyzing successive
steps in a metabolic pathway.
i. Pyruvate dehydrogenase complex: It is a com-

plex assembly of three enzymes—pyruvate
dehydrogenase (E1), dihydrolipoyl transacetylase (E2) and dihydrolipoyl dehydrogenase (E3)

and five coenzymes (lipoic acid, NAD+, FAD, TPP and pantothenic acid).
This complex coordinates the conversion of pyruvate to acetyl-CoA with liberation of CO2.

ii. Fatty acid synthase complex: It is a dimer with each unit having seven enzymes and one

acyl carrier protein (ACP) (Fig. 21.6).
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271
Miscellaneous
Fig. 21.6: Fatty acid synthase complex
For the synthesis of fatty acid, condensing unit of one monomer and reduction and releas-
ing unit of other monomer coordinate to synthesize fatty acid. Thus, only a dimer is active.
Key Points
Enzymes active in dephosphorylated state: Glycogen synthase, phosphofructokinase-2, pyruvate
kinase, pyruvate dehydrogenase, acetyl-CoA carboxylase.
Enzymes inactive in dephosphorylated state: Glycogen phosphorylase, fructose bisphosphate
phosphatase-2 and hormone-sensitive lipase.
Adipocytes lack glycerol kinase: Glycerol-3-phosphate for triacylglycerol synthesis is provided by
glycolysis.
Brain uses glucose and ketone bodies: Brain uses glucose (well-fed condition) and ketone bodies
(starvation) as major sources of energy.
FREE RADICAL METABOLISM
8. Define free radicals. How are they produced? Add a note on effects of free radicals on
our body.
Definition: Free radicals are highly reactive molecular species that contain one or more
unpaired electrons in the outermost shell. They can potentially damage proteins, carbohy-
drates, fats and nucleic acids.
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272
Generation of Free Radicals

They are produced endogenously:
• During metabolic reactions

• In electron transport chain

• During inflammation and infections

• By ionizing radiation.

Examples
Oxygen radicals also known as reactive oxygen species (ROS) include:
.

• Hydroxyl radical (OH )
.

• Nitric oxide (NO )
.

• Superoxide (O2 )
.

• Lipid peroxide radical (ROO )

Miscellaneous
• H2O2 is also considered as ROS, as it is highly reactive.

Other free radicals—methyl radical.

Effects of Free Radicals on Body
Free radicals damage DNA, proteins and lipids. They modify proteins and lipids in low-density
lipoprotein (LDL). Free radicals can cause peroxidation of lipids in membranes.
Free radicals are implicated in tissue damage that occur during:

• Autoimmune disease

• Myocardial infarction: Oxidation of LDL leading to atherosclerosis

• Cataract formation

• Aging

• Carcinogenesis: Mutation of genetic material.

9. What is lipid peroxidation?
Definition: It is the process by which unsaturated fatty acids interact with reactive oxygen
species (compounds having unpaired electrons in their outermost shell) leading to oxida-
tive degradation of lipid. It can be divided into three stages: initiation, propagation and
termination.
Steps in Lipid Peroxidation

The three steps are as follows:
i. Initiation: Hydroxyl radicals and singlet oxygen can react with polyunsaturated fatty acids

(PUFA) forming lipid peroxyl radicals.
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273
. .
PUFA-H + X PUFA + X-H
. . .
PUFA + O2 PUFA OO
ii. Propagation: Peroxyl radical formed is highly reactive and is able to propagate the chain
reaction by reacting with another molecule of PUFA.
.
PUFA-OO + PUFA-H PUFA-OOH (hydroperoxide) + PUFA
The lipid hydroperoxides produced (PUFA-OOH) can undergo reductive cleavage by re-
duced metals, such as Fe2+.
. .
Fe2+ + PUFA-OOH Fe3+ + OH + PUFA-O
iii. Termination: This involves reaction of two radicals to form an inactive compound result-
ing in the termination of the reaction.
. .
ROO + ROO RO – OR + O2
. .
ROO + R RO – OR
Miscellaneous
1 0. How are free radicals metabolized?
Substances, which protect against damage by reactive oxygen species, are antioxidants.
Antioxidants prevent lipid peroxidation by converting lipid hydroperoxide radicals into
stable compounds.
i. Endogenous antioxidants (preventive antioxidants): They include enzyme systems in the
body, which neutralize free radicals. For example, catalase, peroxidase, superoxide dismutase
(SOD), etc.
SOD Catalase
.
O2 O2 H 2O 2 H 2O + O 2
ii. Chain-breaking antioxidants: For example, β-carotene, vitamin C, vitamin E, glutathione.
Glutathione is a tripeptide present in all the cells of our body and is one of the main
antioxidant in our blood. Selenium acts as a cofactor for glutathione peroxidase and can
complement the requirements of exogenous antioxidant vitamins.
TECHNIQUES
1 1. Write a note on electrophoresis.

Definition: Electrophoresis is the migration of charged particles under the influence of
electric current. All biologically important molecules possess ionizable groups and exist as
charged species at any given pH, either as cations or anions. On application of electrical
field (direct current), charged particles move towards the electrode of opposite charge
(Fig. 21.7).
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274
Fig. 21.7: Normal pattern of serum electrophoresis
Albumin: 55%–65%.

1
: 2%–4% (retinol-binding protein, T4-binding globulin, cortisol-binding globulin).

α

2
: 6%–12% (haptoglobin, ceruloplasmin and prothrombin).

α
: 12%–14% (transferrin, hemopexin).

β

: 12%–22% [immunoglobulin G, E, M (IgG, IgE, IgM)].

γ

Miscellaneous
Applications
Separation of:

• Plasma proteins

• Lipoproteins To identify diseases states

• Hemoglobin.

1 2. Write a note on principle and application of chromatography.
Definition: Chromatography is separation of the analyte in the mixture based on differential

partitioning between the mobile and stationary phases.
Classification
• Paper chromatography

• Column chromatography

• Thin layer chromatography (TLC)

• High-performance liquid chromatography (HPLC).

Paper Chromatography
Involves placing a small amount of sample solution onto a strip of chromatography paper placed
in a jar containing a shallow layer of solvent. As the solvent rises/descends through the paper,
it meets the sample mixture, which starts to travel up/down the paper with the solvent. This
paper is made of cellulose, a polar substance; compounds within the mixture travel farther if
they are non-polar, while polar substances get bound to the cellulose paper and therefore do not
travel as far. Separation takes 14–16 https://kat.cr/user/Blink99/
hours. The ratio of fronts (Rf value) is calculated by:
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275
Distance moved by analyte

Rf =
Distance moved by solvent
TLC: Separation of biomolecules requires 2–4 hours.
HPLC: Separation is faster (within minutes) and better.
Application
• Separation of biomolecules (carbohydrates, amino acids, etc.).
1 3. Write the principle and applications of colorimetry.
Definition: Colorimetry is a technique used for quantitative estimation of color. Substances
to be estimated colorimetrically should either be colored or capable of forming colored
compounds on addition of reagents.
Miscellaneous
Principle
• Beer's law: The amount of light absorbed is directly proportional to the concentration of
colored substance
• Lambert's law: The absorbance is directly proportional to the path length of liquid through
which light passes.
A = εcl (A = absorbance, ε = extinction coefficient, c = concentration, l = path length).
Limitations
• Less sensitive at very low concentration of substance to be estimated
• Works within the range of Beer's law
• Volatile and thermally unstable compounds cannot be estimated.
Applications
Quantitative analysis is of compounds in pure state or in biological samples.
ELECTROLYTES
1 4. List important anions and cations of our body.

Important anions and cations are given in Table 21.3.
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276
Table 21.3: Important anions and cations in our body

Important cations Important anions
Sodium (Na ) +
Chloride (Cl–)
Potassium (K+) Bicarbonate (HCO3–)
Calcium (Ca ) 2+
Phosphate (H2PO4– and HPO42–)
Magnesium (Mg2+) Sulfate (SO42–)
1 5. What is Donnan membrane equilibrium?

Definition: Donnan membrane equilibrium states that, in any given compartment of the

cell, the total number of anions should be equal to total number of cations (Table 21.4).
If one compartment has non-diffusible anions before equilibrium, then at equilibrium it
will have more diffusible cations. The products of diffusible electrolytes on both sides of
Miscellaneous
membrane after equilibrium will be the same (Table 21.5). The total number of a particular
ion before and after equilibrium is reached will be the same.
Table 21.4: Distribution of anions and cations in various body fluids

Solutes Plasma (mEq/L) Intracellular fluid (mEq/L)
Cations
Sodium 140 12
Potassium 4 160
Calcium 5 –
Magnesium 2 34
Total 151 206
Anions
Chloride 104 2
Bicarbonate 24 10
Sulfate 1 –
Phosphate 2 140
Protein 15 54
Other anions 5 –
Total 151 206
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277
Table 21.5: Distribution of diffusible electrolytes before and after equilibrium across
semipermeable membrane
Compartment l Compartment ll
Before equilibrium ••• •••••
•• •••••
∆∆ °°°°°
∆∆ °°°°°
∆
Positive charge = 5; Positive charge = 10;
negative charge = 5 negative charge = 10
After equilibrium °°°° ° °°°°°

∆∆∆∆∆ • •••••
•••••
••••
Miscellaneous
Positive charge = 9; Positive charge = 6;
negative charge = 9 negative charge = 6
Product of diffusible electrolytes 9 x 4 = 36 6 x 6 = 36
(sodium x chloride)
∆ = protein (negative charge); ° = chloride ion (Cl–); • = sodium ion (Na+); ( ) = Semipermeable membrane
1 6. Enlist the functions of sodium and potassium.

Refer Chapter 11, Question 1.
1 7. Enlist the causes and clinical manifestations of sodium imbalance.
18. Enlist the causes and clinical manifestations of potassium imbalance.
19. Explain the mechanism of water and electrolyte balance.

Water and electrolyte balance is maintained by renin-angiotensin-aldosterone system and
antidiuretic hormone (Figs 21.8 and 21.9).
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278
Miscellaneous
Fig. 21.8: Regulation of blood volume during hypovolemia (+ = stimulation)
Fig. 21.9: Regulation of blood volume during hypervolemia
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279
Key Points

Flame photometry: This technique is used for determination of sodium and potassium. Here,
sample is fed into non-luminous flame in the form of fine spray. Sodium gives yellow and potassium
gives violet color on ignition in flame, which is proportional to their respective concentrations.
Ion-selective electrodes: Used to measure sodium, potassium, chloride ions.
• Sodium: Accounts for 90%–95% of all solutes in the extracellular fluid (ECF). Contributes 280
mOsm of the total 300 mOsm of ECF. Reference range for serum sodium: 136–145 mEq/L
• Potassium: It is an important cation in the ICF. Reference range for the serum potassium is
3.5–5 mEq/L
• Chloride: It is a major ECF anion. Reference range for serum chloride: 94–111 mEq/L. CSF:
120–130 mEq/L.
Electrolyte concentration: Expressed in milliequivalents per liter (mEq/L). It is a measure of the
number of electrical charges in 1 liter of solution. For single charged ions, 1 mEq = 1 mOsm.
For bivalent ions, 1 mEq = 1/2 mOsm.
Miscellaneous
Osmotic concentration (Osm/L): Proportional to the number of osmotic particles formed,
which is calculated as moles x n (n = of particles in solution). For example, 1 mole of NaCl (n
= 2) forms a two osmolar solution in 1 L. 1 mole of CaCl 2 (n = 3) forms a 3 osmolar solution
in 1 L. For physiological concentrations, mOsm units are most appropriate (1 mOsm = 10 -3
osmoles/L). Plasma osmolarity measures ECF osmolarity. Plasma is dominated by [Na +] and
the associated anions. Under normal conditions, ECF osmolarity can be roughly estimated as:
2 [Na+] = 270–290 mOsm/L.
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22 Hemoglobin Metabolism
1. How is bilirubin formed and excreted?

Life span of mature red blood cells (RBCs) in bloodstream is around 60–120 days. In a 70

kg man, approximately 6 g/day of hemoglobin is liberated from breakdown of RBCs (Fig.
22.1) in the reticuloendothelial system. This hemoglobin is catabolized to form bilirubin.
Bilirubin is further conjugated and excreted through bile.
Fig. 22.1: Heme degradation
Steps in Bilirubin Metabolism (Fig. 22.2)

i. Breakdown of heme into bilirubin in reticuloendothelial cells.

ii. Transport of bilirubin (unconjugated) bound to albumin to liver.

iii. Uptake of bilirubin into liver cells.

iv. Conjugation of bilirubin with glucuronide by uridine diphosphate (UDP)-glucuronyl

transferase.
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281
v. Secretion of bilirubin into bile → intestine.

vi. Conversion of bilirubin to urobilinogen followed by reabsorption and excretion.
Hemoglobin Metabolism
Fig. 22.2: Bilirubin metabolism (NADP, nicotinamide adenine dinucleotide phosphate; UDP, uridine diphosphate)
2. Write the principle and applications of van den Bergh reaction.

Refer question number 2 in Chapter 18.
3. Define jaundice. How can it be classified? Describe the biochemical investigations to
differentiate different types of jaundice.
Definition: Jaundice is defined as yellowish discoloration of skin, nail beds and sclera. It
is caused by deposition of bilirubin, secondary to increased bilirubin levels in the blood.
When bilirubin concentration is more than 1 mg/dL, the condition is called hyperbiliru-
binemia. At a concentration of more than 2 mg/dL, bilirubin diffuses into tissues, which
then becomes yellow, leading to jaundice or icterus.
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282

Normal Levels in Blood
• Total bilirubin: 0.2–0.8 mg/dL

• Unconjugated bilirubin: 0.2–0.6 mg/dL

• Conjugated bilirubin: 0.1–0.2 mg/dL.

Classification
Jaundice is classified into three major types:
i. Prehepatic (hemolytic): Due to excessive hemolysis, bilirubin production exceeds the ca-

pacity of liver to conjugate it.
ii. Hepatic: Impaired uptake, conjugation or excretion of bilirubin.

iii. Posthepatic (obstructive): Caused by an obstruction in the biliary tract (Table 22.1).

Table 22.1: Classification and findings in jaundice
Type of Causes Serum Urine and feces Serum ALT Serum
jaundice bilirubin and AST ALP
Prehepatic Malaria ↑ unconjugated •• ↑ urobilinogen Normal or Normal or
[MN: Autoimmune bilirubin • Bilirubin negative
•
slight ↑ slight ↑
MARS] hemolytic anemia •• ↑ stercobilinogen
Rh incompatibility
Sickle cell anemia
Hepatic Hepatitis ↑ conjugated • Bilirubin present Markedly Normal or

•
and ↑ unconju- (if microobstruction) elevated slight ↑
gated bilirubin •• ↓ urobilinogen
(if microobstruction)
Post- Gallstones ↑ conjugated • Urobilinogen absent Normal or Markedly
•
hepatic Pancreatic tumor bilirubin slight ↑ elevated
Cholangiocarcinoma • Bilirubin present
•
• Clay-colored stool
•
4. Write a note on congenital hyperbilirubinemia.

Definition: A group of hereditary disorders of bilirubin metabolism due to defect in uptake,

conjugation or secretion of bilirubin (Table 22.2).
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Table 22.2: Congenital hyperbilirubinemia

Condition Defects Clinical features
Crigler-Najjar syndrome Severe deficiency of UDP-glucuronyl ↑↑↑ serum unconjugated bilirubin
Type I transferase Profound jaundice–does not respond
to phenobarbital; often fatal
Crigler-Najjar syndrome Mild deficiency of UDP-glucuronyl ↑ serum unconjugated bilirubin; mild
Type II transferase jaundice; responsive to phenobarbital
therapy
Gilbert syndrome Reduced activity of glucuronyl ↑ serum unconjugated bilirubin; mild
transferase jaundice
Dubin-Johnson Abnormality in secretion of ↑ serum conjugated bilirubin;
syndrome conjugated bilirubin into biliary moderate jaundice
system
Rotor syndrome Cause not known ↑ serum conjugated bilirubin; mild
jaundice
↑ = increased; ↑↑↑ = markedly increased
5. Describe heme synthesis. Add a note on its regulation.
Requirements
• Starting material: Glycine and succinyl-coenzyme A (CoA), Fe2+
• End product: Heme
• Site: RBC precursors (85%), liver (15%)
• Subcellular site: Mitochondria and cytosol
• Enzymes
• Coenzyme: Pyridoxal phosphate (PLP).
Regulation of Heme Synthesis

δ-aminolevulinic acid (ALA) synthase is inhibited by heme and hematin (Fe3+ form).
Heme
• Represses the synthesis of δ-ALA synthase by regulating gene transcription (negative
regulation)
• Diminishes the transport of δ-ALA synthase from cytoplasm to mitochondria.
Drugs: ALA synthase is upregulated by a large number of drugs including barbiturates,
testosterone and oral contraceptives. These drugs are metabolized by the microsomal
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cytochrome P450 monooxygenase system, which use up heme and decrease heme concen-
tration, which in turn stimulates enzyme synthesis (derepression).
Glucose: Prevents induction of ALA synthase.
Steps in Heme Synthesis (Fig. 22.3)

Fig. 22.3: Heme synthesis (ferrochelatase and ALA dehydratase are inhibited by lead)
6. What are porphyrias? How are they classified?

• Porphyrias are a group of disorders caused by deficiencies in enzymes of the heme bio-

synthetic pathway
• The majority of the porphyrias are inherited in an autosomal dominant manner except

congenital erythropoietic porphyria, which is autosomal recessive
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285
• Affected individuals have an accumulation of heme precursors that are toxic at high con-
centrations and can lead to abdominal pain or photosensitivity (due to porphyrins)
• Attacks of the disease are triggered by certain drugs, chemicals, foods and by exposure to
sunlight (UV radiation)
• Drugs (phenobarbital, steroids) are metabolized by the microsomal cytochrome P450
monooxygenase system, which in turn induces δ-ALA synthase, resulting in increased
levels of potentially harmful heme precursors prior to metabolic block
• Treatment involves administration of hematin, which provides negative feedback inhibition
of ALA synthase leading to decreased formation of heme precursors.
Classification (Table 22.3)
i. Erythropoietic: Enzyme deficiency occurs in RBCs, e.g. congenital erythropoietic porphyria,
protoporphyria.
ii. Hepatic: Enzyme defect occurs in liver, e.g. acute intermittent porphyria, porphyria cutanea
tarda, hereditary coproporphyria, variegate porphyria.
Table 22.3: Types of porphyria
Types Enzyme defects Clinical features Key findings
X-linked sideroblastic ALA synthase Anemia ↓ RBC count
anemia (erythropoietic) ↓ Hb%
ALA dehydratase ALA dehydratase Abdominal pain, ↑ Urine ALA (δ-amino-
deficiency (hepatic) neuropsychiatric symptoms levulinic acid)
Acute intermittent Uroporphyrinogen I Abdominal pain, ↑ Urinary ALA and
porphyria (hepatic) synthase neuropsychiatric symptoms porphobilinogen (PBG)
Congenital Uroporphyrinogen III Photosensitivity Uroporphyrin (+) and
erythropoietic synthase PBG (−) in urine
porphyria
(erythropoietic)
Porphyria cutanea Uroporphyrinogen Photosensitivity Uroporphyrin (+) and
tarda (hepatic) decarboxylase PBG (−) in urine
Hereditary Coproporphyrinogen Photosensitivity, abdominal Urinary PBG and
coproporphyria oxidase pain, neuropsychiatric coproporphyrin (+); fecal
(hepatic) symptoms coproporphyrin (+)
Variegate porphyria Protoporphyrinogen Photosensitivity, abdominal Urinary PBG and
(hepatic) oxidase pain, neuropsychiatric coproporphyrin (+)
symptoms
Protoporphyria Ferrochelatase Photosensitivity Fecal and red cell
(erythropoietic) protoporphyrin (+)
(+), present; (−), absent
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7. Write a note on acute intermittent porphyria.

Definition: It is a hepatic, autosomal dominant porphyria. It is caused by a deficiency

in uroporphyrinogen I synthase, which is involved in the conversion of porphobilinogen
(PBG) to hydroxymethylbilane.
Clinical Features
• Patients have neuropsychiatric symptoms and abdominal pain (neurovisceral) due to irritation

of abdominal nerves and central nervous system by toxic products like δ-ALA and PBG
• Symptoms become more severe after administration of drugs like barbiturates, which induce

cytochrome P450 and use up heme; this in turn stimulate key enzyme δ-ALA synthase and
results in production of toxic concentrations of products like PBG and ALA

• PBG and δ-ALA accumulate in plasma and are excreted in urine.

Treatment
• Symptomatic—analgesics

• Avoiding triggering factors, e.g. drugs like phenobarbitone

• Hematin administration to suppress heme synthesis.

8. Write briefly on porphobilinogen.
Porphobilinogen is an intermediate compound in the heme synthetic pathway (Fig. 22.4).

Fig. 22.4: Synthesis of porphobilinogen (PLP, pyridoxal phosphate)
• Fate: Four molecules of porphobilinogen condense in the presence of enzyme uropo

rphyrinogen I synthase to form hydroxymethylbilane
• Acute intermittent porphyria: It is due to deficiency of uroporphyrinogen I synthase. In
this condition, porphobilinogen https://kat.cr/user/Blink99/
is not metabolized leading to its accumulation in tissues.
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287
This in turn can cause irritation of abdominal nerves and nerve endings in central nervous
system causing abdominal pain and neuropsychiatric manifestations.
9. Write short notes on neonatal jaundice.
Neonatal jaundice is seen in newborn infants, due to accelerated hemolysis and an imma-
ture hepatic system for bilirubin uptake, conjugation and secretion. It is commonly seen
in premature infants and resolves within first 10 days of birth.
Causes
• Accelerated hemolysis
• Impaired glucuronyl transferase synthesis due to immaturity of liver
• Substrate UDP-glucuronic acid synthesis also may be inadequate.
Clinical Features
• Yellowish discoloration of skin and sclera due to elevated unconjugated bilirubin
• High levels (> 20 mg/dL) of unconjugated bilirubin are toxic to the newborn—due to its
hydrophobicity, it can cross the blood-brain barrier and cause kernicterus, which causes
mental retardation
• Mostly self-limiting; if serum bilirubin concentration exceeds 15 mg/dL for more than 15
days, it is usually pathological and needs to be further investigated.
Treatment
• If bilirubin levels are judged to be too high, then phototherapy is used to convert it to a
water-soluble, non-toxic form (maleimide and geometric isomers)
• Phenobarbital is useful in treatment—inducer of glucuronyl transferase
• If necessary, exchange blood transfusion—used to remove excess bilirubin.
1 0. Write briefly on thalassemias.
Definition: Thalassemias are a group of hereditary hemolytic diseases in which an imbalance
occurs in the synthesis of globin chains. They are the most common single gene diseases
in humans.
Classification
a. α-thalassemia—synthesis of α-chain of hemoglobin is decreased (Table 22.4).
b. β-thalassemia—synthesis of β-chain of hemoglobin is decreased (Table 22.5).
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288

Table 22.4: Classification and clinical features of α-thalassemia
Type Genotype Clinical features
Normal αα/αα Normal
Silent carrier 1 gene loss (-/α α/α) No signs and symptoms
α-thalassemia minor 2 genes loss (-/α -/α) Mild anemia
HbH disease (Bart) 3 genes loss (-/- -/α) Mild to moderately severe anemia
Due to absence of α-chain, γ-chain forms
tetramer, which is called Bart hemoglobin. These
tetramers have very high O2 affinity and fail to
deliver O2 to tissues.
Hydrops fetalis All 4 genes loss (-/- -/-) Abortion or fetal death
α-thalassemia

These are defects in which synthesis of α-globin chains are decreased or absent. Normally,

each individual has four copies of 'α' genes (two on each chromosome 16).
β-thalassemia

• Synthesis of β-globin chains is decreased or absent, whereas α-globin chain is normal;

normally, each individual has two copies of β-globin gene (one on each chromosome 11)
• α-globin chains cannot form stable tetramers and therefore, precipitate causing premature

death of cells initially destined to become mature red cells
• Accumulation of α2γ2 (fetal hemoglobin, HbF) and γ4 (Hb Barts) also occurs.

Table 22.5: Classification and clinical features of β-thalassemia
Type Genotype Clinical features
Normal (β/β) Normal
β-thalassemia minor 1 gene loss (β/β°) Mild anemia
β-thalassemia major 2 genes defective (β°/β°) β-globin gene is not expressed until late gestation;
so physical manifestations of β-thalassemias appear
only after birth. This leads to severe anemia requiring
regular blood transfusions. Repeated transfusion
though life saving, can cause iron overload (hemo si

derosis) and death around 15–25 years of life.
11. Describe the structure of hemoglobin and methemoglobin. Mention any two functions

of hemoglobin.
Structures of heme and hemoglobin are given in Figures 22.5 and 22.6 (refer Chapter 7,

question number 15).
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289
Fig. 22.5: Structure of heme (M, methyl; Fig. 22.6: Structure of hemoglobin
V, vinyl; P, propionyl)
1 2. Explain the causes and features of methemoglobinemia.
Oxidation of ferrous (Fe2+) component of heme to ferric (Fe3+) state forms methemoglobin,
which has poor affinity for oxygen → decreased oxygen transport.
Causes of Methemoglobinemia
• Drugs (nitrates) or reactive oxygen species (ROS) can transform hemoglobin to methemoglobin
• Inherited defect in NADH Cyt b5 reductase, which is responsible for the conversion of
methemoglobin (Fe3+) back to hemoglobin (Fe2+)
• Point mutation: Replacement of proximal/distal histidine of globin chains with tyrosine.
Clinical Features
• Symptoms are related to tissue hypoxia—anxiety, headache, dyspnea, etc.
• Chocolate cyanosis—dark-colored blood as a result of increase in methemoglobin.
13. Write a short note on sickle cell anemia.
Sickle Cell Disease (HbS Disease)

A genetic disorder of blood caused by a single nucleotide alteration in the β-globin gene
(point mutation). In the mutant β-chain, there will be substitution of glutamic acid by valine
at 6th position of β-chain; this will reduce the negative charge on the sickle cell hemoglobin,
hence it moves slower than HbA in electrophoresis.
Classification
• Homozygous (sickle cell disease): Inheritance of two mutant genes from each parent that
code for synthesis of β-globin chains of globin molecules, e.g. HbSS
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290

• Heterozygous (sickle cell trait): Inheritance of one normal and one sickle cell gene from
parents. Such heterozygotes contain both HbS and HbA.
Consequences of HbS
• Replacement of hydrophilic glutamic acid by hydrophobic valine on the surface creates

a sticky patch at low oxygen tension and leads to polymerization of hemoglobin inside
RBCs; this stiffens and distorts the RBCs producing sickled RBCs
• Such sickled cells frequently block the flow of blood in narrow capillaries, this leads to

localized anoxia in the tissue causing pain and eventually death of cell in the vicinity
of blockage
• Sickling is enhanced by increased pCO2, decreased pH and increased concentration of

2,3-bisphosphoglycerate (BPG).
Diagnosis: Hb Electrophoresis
Replacement of glutamate by valine in two β-chains reduces the negative charge on HbS—it
moves slower than HbA at alkaline pH during hemoglobin electrophoresis.
Complications of Sickle Cell Disease

Anemia: Due to accelerated hemolysis
•
Aplastic crisis: Temporary lack of production of RBCs and other cells in bone marrow
•
Bone necrosis: Degradation of bone tissue, which can lead to fracture in neck of femur
•
Hand and foot syndrome: Painful swelling in the hands and feet
•
Severe infections: Sepsis, meningitis and pneumonia; the risk of infection increases because
•
the spleen does not function properly
• Splenic sequestration crisis: The spleen is the organ that filters blood; rapid enlargement of
spleen can result due to entrapment of sickled cells and this condition can be life-threatening
• Stroke: Occurs when sickled cells block blood vessels within the brain.
Treatment of Sickle Cell Anemia

• Adequate hydration

• Analgesics

• Antibiotic therapy, if infection present

• Repeated transfusion

• Hydroxyurea—decreases the frequency of painful crises and reduces mortality.

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291
Partial Advantage of Sickle Cell Trait

• Frequency of sickle cell anemia is high in black Africans
• Heterozygote state makes them less susceptible to falciparum malaria. The malaria parasite
spends obligatory part of its life cycle in RBCs. In patients with sickle cell trait, RBCs with
HbS have a shorter life span than normal RBCs. Thus, the parasite cannot complete the in-
tracellular stage of development. This provides selective advantage to heterozygotes living
in these regions where malaria is major cause of death.
14. Write briefly on anemia.
Definition: Anemia is characterized by a decrease in the normal number of RBCs to below
normal levels or less than normal quantity of hemoglobin in the blood. This reduces the
oxygen-carrying capacity of blood resulting in various signs and symptoms.
Consequences of Anemia (Fig. 22.7)
Fig. 22.7: Consequences of anemia
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292

Classification of anemia is given in Table 22.6.

Table 22.6: Classification of anemia
Type Causes Consequences
Microcytic hypochromic • Deficiency of iron, copper, pyridoxine, • Decreased hemoglobin
•
•
anemia pantothenic acid and vitamin C; thalassemia, synthesis
lead poisoning • Leads to iron deficiency
•
• Chronic blood loss
•
Macrocytic anemia • Folic acid, vitamin B12 deficiency • Decreased maturation of
•
•
RBCs
Normocytic • Sickle cell disease, red cell metabolic defects, • Increased hemolysis
•
•
normochromic red cell membrane defects, niacin deficiency,
anemia riboflavin deficiency, G6PD deficiency
• Acute bleeding • Leads to loss of RBCs

•
•
Key Points
Heme-containing proteins: Hemoglobin, myoglobin, cytochromes, catalase, tryptophan pyrrolase.

Starting material for heme synthesis: Glycine + succinyl-CoA.

Number of glycine required to synthesize one molecule of heme: Eight.

Rate limiting enzyme in heme synthesis: α-aminolevulinate (ALA) synthase.

Mature RBCs cannot synthesize heme: Due to lack of mitochondria.

Lead poisoning: Lead inhibits ALA dehydratase and ferrochelatase.

Congenital erythropoietic porphyria: Only porphyria with autosomal recessive inheritance.

Acute intermittent porphyria: Is due to deficiency of uroporphyrinogen I synthase.

Precipitating factor for porphyrias: Barbiturates, alcohol consumption.

Enterohepatic circulation of bilirubin and bile salts: Small fraction of bilirubin and bile salts

reabsorbed from intestine into circulation and resecreted into intestine.
Hemolytic jaundice (hemolysis): Elevated unconjugated bilirubin + absent urinary bilirubin + in-

creased urobilinogen in urine.

Hepatic jaundice (viral hepatitis): Elevated conjugated and unconjugated bilirubin + elevated as-

partate transaminase (AST) and alanine transaminase (ALT).
Obstructive jaundice (gallstones): Elevated conjugated bilirubin + increased urinary bilirubin excre-

tion + urine urobilinogen absent.
Crigler-Najjar syndrome (type I): Due to complete absence of conjugating enzyme-UDP glucuronyl

transferase.
Neonatal jaundice: Caused by inability of liver to conjugate bilirubin due to immaturity of conjugat-

ing system.
van den Bergh test: Is done to detect bilirubin in serum. Direct reaction detects the conjugated

bilirubin and indirect reaction (adding methanol) measures total bilirubin.
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293
Kernicterus: In newborns, when unconjugated bilirubin level gets elevated to > 20 mg/dL, it crosses
the blood-brain barrier and damages the brain cells (mental retardation).
Adult hemoglobin: Is made of 2α and 2β chains (fetal Hb-2α and 2γ chains).
Myoglobin (heart and skeletal muscle): It is a hemoprotein with single polypeptide chain, which
is structurally similar to individual polypeptide chains of hemoglobin. Myoglobin acts as a reservoir
for oxygen.
α-thalassemia (4 genes for α-chain synthesis): Impaired synthesis of all α-chains results in HbH
and hydrops fetalis, which is a severe form of α-thalassemia.
β-thalassemia (2 genes for β-chain synthesis): β-chain synthesis is impaired, β-thalassemia major
is severe form in this group.
Manifestations of β-thalassemia appear only after birth: Because β-globin chain is not expressed
until late gestation (fetal Hb-2α and 2γ chains).
Sickle cell disease (HbS disease): A point mutation in β-chain, which leads to substitution of
glutamic acid by valine at 6th position. As a result of this, negative charge on the hemoglobin is
reduced, which introduces sticky patch in Hb structure and its polymerization (sickling of RBCs) in
venous blood.
Sickle cell trait individuals are less susceptible to Plasmodium falciparum malaria infection:
Due to reduced life span of RBCs in such individuals, parasite cannot complete its life cycle.
HbC disease: Substitution of glutamic acid by lysine at 6th position of β-chain, leading to mild
anemia.
HbSC disease: Compound heterozygote state with some β-chains having mutation found in HbS
and others have mutations found in HbC.
Methemoglobinemia: Characterized by elevated methemoglobin (hemoglobin with iron in the fer-
ric form), which may be due to nitrates, free radicals or congenital deficiency of enzyme NADH-
cytochrome b5 reductase and substitution of proximal/distal histidine with tyrosine. Methemoglobin
has low affinity for oxygen and causes cyanosis.
Hemoglobinopathy: Defect in the primary sequence of globin chain.
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Index
Page numbers followed by f refer to figure, t refer to table and b refer to box.
A Allopurinol 188, 189 Arachidonic acid 63

α1-antitrypsin 102 Arginine 159
Acetyl-CoA 66, 67f, 68 α2-macroglobulin 102 compounds 132

sources 270 α-amanitin 196t Arsenite 55

Acid-base balance Alpha-helix 91, 91f Ascorbic acid (vitamin C) 157
renal mechanisms 237 Amino acid pool 107 Asparagine 131, 134

Acid-base disorders 234, 239 Amino acid Aspartate 131, 134
calcium 239 absorption 106, 107f Aspirin 63, 262

Acidic pH 159t

branched chain 134 Atherosclerosis 86, 87f
Acidosis 162

classification 90 ATP synthesis 137, 137f
Acquired immunodeficiency

catabolism 129, 130f
syndrome 228

Aminoacyl-tRNA 203 B

Actinomycin D 196t
synthetase 200 Balanced diet 169
Active transport 4

Ammonia 109 Basal metabolic rate (BMR) 166
primary 5
Amyloidosis 103

secondary 5 Base excision repair 209
Anderson's disease (type IV) 47t

Acute myocardial infarction 22, Base pairing rule 180
22t, 22f Anemia Beriberi
consequences 291, 291f

Acute pancreatitis 23t dry 149b

Adenosine 175 Anion gap 234 infantile 149b

Albinism 120, 133 Anorexia nervosa 173 wet (cardiac) 149b

Albumin 96, 274 Anserine 129 Betaine 84
Alcohol de-addiction 24 Antioxidants β-oxidation 66, 67f, 88
Alcohol dehydrogenase 9t chain-breaking 273 Beta-pleated sheet 92

Alcohol metabolism 85, 86f endogenous 273 Bile acids 76

Alcoholic liver disease 23t Antisense therapy 227 functions 76

Aldolase A 55 Apoenzyme 23 synthesis 76, 77f

Alkaline phosphatase 245 Apolipoproteins 82 Bile salts 88
Alkaptonuria 120 Apoptosis 219 enterohepatic circulation 76

296
Bilirubin 244, 280 optical 27, 28f Chylomicrons 58, 66
conjugated 244, 282 stereoisomers 26, 27 metabolism 80, 80f
metabolism 280, 281f structural 26, 27 Chylothorax 87
total 282 Carbohydrates Chyluria 87
unconjugated 244, 282 Absorption 33, 33f Cistron 214
Biotin (vitamin B7) 156 digestion 32, 32f Clearance 247
Bitot’s spots 142 Carbonic anhydrase 9t Cobalamin 154
Blood glucose regulation Carboxylation 206 Cockcroft and gault formula 248
level 52 Carcinogens 218 Codon-anticodon interaction 200f
Blood pH 234 Carcinoid syndrome 123t, 152 Coenzymes 9
Blood urea nitrogen (BUN) 248 Cardiac function tests 253t Cofactors 9, 9t
Blood urea Carnitine 88 Collagen 99
normal 248 deficiency 69t formation and maturation
BMR 170 Carnosine 129 defects 99
Body mass index (BMI) 172 Catalase 9t
Bone disease 23t Congenital
Catecholamines 118 abetalipoproteinemia 87
Brain natriuretic peptide 253 dopamine 117
Index
Breast cancer 219, 259 Congenital erythropoietic

epinephrine 117
British anti-lewisite (BAL) 140 porphyria 284
norepinephrine 117
Brown adipose tissue 85 Congenital
Cell cycle 215
Buffer systems 233, 233t hyperbilirubinemia 282, 283t
Cell membrane
Buffers Cori cycle 43, 43f
fluid mosaic model 2, 3f
in body fluids 236 Cori's disease (type III) 47t
fluidity 2
bicarbonate 236 Covalent modification 206
proteins 3
phosphate buffer C-reactive protein 102
Cellular organelles 1
system 236 Creatine 114
Ceruloplasmin 102
protein buffer system 236 Creatine phosphokinase 21
Cervical cancer 259
Bulimia nervosa 173 Creatinine clearance 247, 248
Chargaff’s rule 177, 180
Chemiosmotic hypothesis 137 Creatinine coefficient 248
C Chloride 9t Cyanide 262
Cholecystokinin 66 Cyclopentanoperhydrophenan-
Calcitriol 159
Calcium Cholesterol 62, 63 threne See
absorption 159 ring 63 cholesterol ring 63
toxicity 162 synthesis 74, 75f Cystathioninuria 125
Calorific value 166 Choline 84 Cysteine 134
Cancer 168 Chromatography 274 metabolism 126
Carbamoyl phosphate column 274 Cystinosis 128t
synthetase 111, 189 high-performance liquid 274 Cystinuria 8, 106, 128t
Carbohydrate isomers 26 paper 274 Cytidine 175
anomers 27, 28f thin layer 274 Cytochrome oxidase 9t
297

D DNA polymerase 190, 192, 193 Energy coupling 135
DNA probe 228 Enolase 9
Deamination reactions 108 DNA repair and mutations 207 Enzyme activity
non-oxidative 109 DNA replication 190, 193 effect

oxidative 108, 109f elongation 192 pH 15, 15f

Dementia 152t inhibitors 193, 193t temperature 15, 15f

Deoxyadenosine 175 lagging strand 191 Enzyme concentration 14

Deoxyadenosine triphosphate steps 191 Enzyme inhibition 17

(dATP) 190 DNA sequencing 228 competitive 17, 24t

Deoxycytidine triphosphate DNA synthesis 191 non-competitive 18, 24t

(dCTP) 190 DNA topoisomerase I 190 suicide 18, 24

Deoxyguanosine triphosphate DNA topoisomerase II 190 Enzymes
(dGTP) 190 DNA viruses 219 active site 12

Deoxyribonucleic acid DNA activity 13

(DNA) 174 structure 177f classification 10

Deoxyribonucleotides types 178 inhibition 16

synthesis 188 Donnan membrane regulation 18
Index

Deoxythymidine triphosphate equilibrium 276 allosteric regulation 18,

(dTTP) 190 Double-strand break repair 209 19, 19t

Dephosphorylated state 271 covalent modification 18,

Dermatitis 152t E 20, 20f

Desulfhydration 109, 110 specificity 10, 10t
Ehlers-danlos syndrome 99

Detoxification 260 Enzyme-linked immunosorbent

Dextran 31 Ehrlich’s test 244, 244t, 245 assay (ELISA) 225, 258, 258f
Electrolyte concentration 279

Diabetes 168 Epimers 26
Diabetic ketoacidosis 73 Electrolytes 275 Escherichia coli 213
Diarrhea 152t Electron transport chain 136, 136f Essential fatty acids 59, 63
Dicarboxylic aciduria 69t, 88 components 137 deficiency 59

inhibitors 139, 140t

Dietary fibers 167 Ethanol induces CYP2E1 263

Digitalis 31 uncouplers 139, 140t Eukaryotic cell 1, 2

Digoxin 8 Electrophoresis 95, 95f, 273, 274f Eukaryotic gene regulation 214
Dihydrouracil 180 Electrostatic (ionic) bonds 92 Exocytosis 6, 7
Disaccharides 25 ELISA Exonucleases 228
Disulfide bonds 93 advantages 259

DNA 190 applications 259
F

DNA and RNA procedure 258

differences between 178t Embden-meyerhof pathway 33 Facilitated diffusion 4, 7

DNA cloning 220 Enantiomers 27 Fanconi anemia 194
DNA damage 207 Endocytosis 6, 7 Fanconi syndrome 146
DNA helicases 190 Endometrial cancer 219 Farnesylation 206
DNA libraries 221 Endonucleases 228 Fasting state 268, 269t
298
Fatty acid synthase complex 70, Gastric lipase 88 Glycogenesis
70f, 270, 271f Gene therapy 221, 223f reactions 46, 48f
Fatty acids 70, 70f, 71f germ cell 221 Glycogenolysis 44, 44f, 45f
de novo synthesis 69 somatic cell 221 Glycolipids 58, 61
disorders associated with Genetic code 204 Glycolysis 33, 34, 35f, 66
oxidation 69 Gestational diabetes mellitus Glycolysis
Fatty liver 84 (GDM) 56 anaerobic 34
Feed-fast cycle 267 Globulins 102 energetics 36
Fibrinogen 102 Glomerular filtration rate inhibitors 37, 37t
Flame photometry 279 metabolic disorders
normal 248
Fluorescent in situ hybridization associated 37
Glucagon 53, 53f
technique 230f regulation 36
Glucagon action
Fluoride 23 Glycoproteins 30
steps 266
Folate antagonists 154, 154t Glycoside 29, 29t
Glucocorticoids 266
Folate trap 155 Glycosylation 206
Folic acid 153 Gluconeogenesis 41, 42f, 66
key enzymes 43 Goiter 165
Folinic acid 154
Index
non-carbohydrate Gout 184, 189

Food guide pyramid 170, 171f
substrates 44, 44t primary 184
Formiminoglutamate (FIGLU)
regulation 43 secondary 185
excretion test 154
Gluconeogenic enzymes 266 Group I hormones
Fouchet’s test 245
Glucose-6-phosphate general mechanism 265
Fractional test meal 251
dehydrogenase (G6PD) Guanosine 175
Fragile x syndrome 211
Free fatty acids 66 deficiency 50, 56
Free radicals Glutamate H
effects 272 metabolic functions 132 Half-life 254
generation 272 synthesis 131 radioactive compound 255
metabolism 271, 273 Glutathione 115 Hand in glove model of daniel E
Fructose 55 Glutathione 262, 263f koshland 13f
Glycated Hb (HbA1c) 56 Haptoglobin 102
G Glycemic index 168 Hartnup disease 8, 106, 123t,
Gallstones 88 Glycerophosphate shuttle 138, 139f 133, 152
γ-glutamyl transferase 245 Glycine Hay’s sulfur test 245
Gastric function tests 250 degradation 114 Hb electrophoresis 290
indications 250 metabolic disorders 114 HDL 63, 81
Gastric juice specialized products 114 Heme degradation 280f
free acidity 251 Glycinuria 106t Heme synthesis 115
functions 250 Glycogen 30 regulation 283
total acidity 251 Glycogen phosphorylase 206 steps 284
299

Hemochromatosis 164 protein 264 Indole 262

Hemoglobin 99, 288 steroid 264 Induced fit model 13, 13f

functions 100 Human genome project Initiation codon AUG 201

oxygen transport 100 (HGP) 232 Initiation complex

structure 99, 100f Huntington's disease 193, 211 30S 201, 201f

types 99 Hyaluronic acid 30 48S 203

Hemoglobinopathies 101, 101t Hybridoma technology 226 70S 201, 201f

Henderson-Hasselbalch steps 227 80S 203

equation 233

Hydrogen bonds 92 Insulin 53, 53f, 96

Hepatitis 23t Hydrolases 11 function 97
Hereditary fructose intolerance Hydrophobic bonds 93

structure 97, 97f
(HFI) 56 Hydroxylation 206

Interphase 215

Hereditary rickets 146 Hypercalcemia 160 G1 phase 215
Hers' disease (type VI) 47t Hyperglycemia 53, 54

G2 phase 215, 216
Heteropolysaccharides 26 Hyperkalemia 161

S phase 215
High-density lipoprotein Hyperlipidemia 82

Introns 198
(HDL) 81t primary 83
Index
Inulin 30

High-energy compounds 136, 136t secondary 83
Iodine number 60, 63

Hippuric acid 244 Hypermethioninemia 125t
Hippuric acid test 244 Ion channels 7
Hypernatremia 160
intravenous 245 Iron 9t
Hyperphosphatemia 160
absorption 163, 163f

oral 245 Hyperuricemia 186

Histamine 129 deficiency 164
Hypoalbuminemia 96

Histidine catabolism 128, 128f Hypocalcemia 160 overload 164

Histidine Hypoglycemia 53, 69t Isoelectric pH 93
metabolic disorders 129 Hypokalemia 161 Isoenzymes 21

specialized products 129 Hyponatremia 160 Isomerases 11

Histones 197 Hypophosphatemia 160 Isoniazid 262
HMG-CoA reductase 75 Hypothyroidism Isotopes 254, 254t
HMP shunt/direct oxidative congenital 165
pathway See pentose

Hypoxanthine 180 J

phosphate pathway 48

Hodgkin disease 259 Jamaican vomiting
I sickness 69t, 88
Holoenzyme 23

Homocysteinemia 155t Immunoglobulins 97, 97t Jaundice 245, 281, 282
Homocystinuria 126f functions 98, 98t biochemical investigations 281

Homopolysaccharides 26 general structure 98, 98f hemolytic 245, 282

Hormones 264 Impaired fasting hepatic 245, 282

amino acid derivatives 264 glycemia (IFG) 56 neonatal 287

group I 264, 265f Impaired glucose obstructive 23t, 245

group II 264 tolerance (IGT) 56 posthepatic 282

300
K Lipid profile 82, 253 Melatonin 121, 122

Lipids Menkes disease 165
Kashin-beck disease 165 absorption 64, 65f Metabolic acidosis 234, 239
Keratan 31 classification 57, 57t Metabolic alkalosis 239
Keratomalacia 142 digestion 64, 65f Metabolic syndrome
Keshan disease 165 functions 58 (syndrome X) 173
Ketogenesis 71, 72f, 73 Lipogenesis 55 Metabolism
Ketolysis 73, 73f Lipoprotein (HDL) 58 glycine 113
Ketone bodies 71, 73 Lipoproteins 77, 78f Methanol poisoning 23
Ketosis 71, 73, 74f classification 78, 78t Methemoglobin 288
Kidney functions 78 Methemoglobinemia
functions 245 Lipotropic factors 83 causes 289
Kinase 9t Liver diseases 103 clinical features 289
Korsakoff's psychosis 149t Liver function tests 242, 243t Methionine 123, 134
Krebs cycle 38 uses 242 metabolism 125, 125t
Kwashiorkor 168, 171 Liver functions 242 Methotrexate 188
Lock and key model 12 Methylmalonic acidemia 155t
Index
L Low-density Michaelis-Menten equation 16

lipoproteins (LDL) 79 Microalbuminuria 103, 248
Lac A 213 Microarray technique 230, 231f
Lyases 11
Lac operon 213 Microcytic anemia 153
Lymphoma 259
Lac operon model 212 Microminerals 162, 162t
Lysine 159t
Lac Y 213 Mitosis phase 216
Lac Z 213 Modified sugars 28, 28t
Lactate dehydrogenase 21
M
Molecular chaperones 228
Lactose 30 Macrominerals 158 Molybdenum 9t
Lactulose 173 Magnesium 9t Monosaccharides 25
LDH flip 253 toxicity 162 Mucosal block theory 164
LDL 63 Malate-aspartate shuttle 138, 138f Multienzyme complexes 270
Leber hereditary optic Malignant melanoma 259 Multiple myeloma 103
neuropathy (LHON) 140 Malonyl-CoA 88 Muscle disease 23t
Lesch-nyhan Manganese 9t Mushroom poisoning 199
syndrome 183, 184, 188 Mannitol 31 Mutarotation 29
Leukotrienes 63 Maple syrup urine disease Mutations
Ligases 11 (MSUD) 129 chromosomal 210
Lipases 87 Marasmus 168, 171 frameshift 210, 211
Lipid peroxidation 272 Maturity onset diabetes of young gene 210
steps 272 (MODY) 55 missense 210, 211t
initiation 272 Mcardle's disease (type V) 47t nonsense 211
propagation 273 Megaloblastic anemia 155 point 210
termination 273 Melanin 118 silent 210
301

Myasthenia gravis 8 Oncogenes 216, 216t Pheochromocytoma 133
Myocardial infarction 23t Oral cancer 259 Phospholipids 58, 60
Myoglobin 253 Organophosphorus classification 60

Myotonic dystrophy 211 compounds 23 glycerophospholipids 60, 60t

Orlistat 88 sphingophospholipids 61

N Orotic acid 186 functions 61

Orotic aciduria 186, 189 Phosphorylation 36, 37t, 206
N-acetyl-p-benzoquinoneimine purine ribonucleoside 184
Osmotic concentration 279

(NAPQI) 263 Phrynoderma 59
Osteoblastoma 256, 259

NADPH 74, 76, 88 Ping-pong model 4
Osteogenesis imperfecta 99
Neotame 56 Pinocytosis 7
Osteomalacia 145t
Neural tube defect 154t Plasma proteins
Oxidative phosphorylation 138
Neuroblastoma 259 relative percentage 96
Oxidoreductases 10

Niacin 151 separation methods 95

Nicotinamide 122 Poly-A tail 198
Nicotinamide adenine P Polyamines 125
dinucleotide (NAD) 121 Paget’s disease 160t Polymerase chain
Index

Night blindness 142 Palmitic acid 63 reaction (PCR) 225, 226f

Nitric oxide 133 Pancreatic function tests 252 applications 226

Nitrogen balance 168 indications 252 steps 226

Non-protein nitrogen (NPN) 248 Polysaccharides 25, 26t

Pantothenic acid (vitamin B5) 156
Northern blotting Polyunsaturated fatty acids 173
Paracetamol 262
applications 225 Pompe's disease (type II) 47t
Parathyroid hormone (PTH) 159

Nucleic acids 176 Porphobilinogen 286, 286f
Parkinson's disease 133
Nucleoside 180 Porphyria 284
Pellagra (4D) 152t
Nucleoside analogues 180 classification 285, 285t
Pentose phosphate

Nucleosides 175, 175t, 175f clinical features 286
pathway 48

Nucleotide 180 intermittent 286

metabolic defects 50

structure 175, 176f Post-transcriptional

Pepsinogen 206

Nucleotide excision modification 198
Peptide bond 93

repair (NER) 208 Post-translational
Peptide bond formation 202

modification 205

Peptides 93, 94t Potassium 277
O Peroxidase 9t Potassium imbalance 277
Obesity 171 Phagocytosis Preinitiation complex 195
Okazaki fragments 193 carrier 7 Prion diseases 103

Olestra 31 channel-forming 7 Procarcinogen 219

Oligosaccharides 25 Phenobarbital 262 Proinsulin 206
Omega-3 fatty acids 63 Phenylalanine Prokaryotic cell 1
Omega-6 fatty acids 63 metabolism 116, 116f Promoters

Omeprazole 8 Phenylketonuria 119, 119f eukaryotic 194

302
prokaryotic 194, 194f R Respiratory quotient 166, 166t
Propionic acid 59 Restriction endonucleases 220
Propionyl-CoA 68 Radiation 255 Restriction fragment length
Prostaglandins 62 alpha (a) decay 255 polymorphism (RFLP) 224
Prostate cancer 23t beta (b) radiation 255 sickle cell anemia 225
Prosthetic group 23 forms 255 Retinoblastoma (RB) gene 219
Protein energy malnutrition 171, gamma (g) radiation and Reverse transcriptase 197, 197f, 199
171t X-rays 256 RHO-dependent termination 196
Protein farnesyltransferase Radiation hazard 259 RHO-independent termination 196
inhibitors 206 Radioactive decay 254 Riboflavin (vitamin B2) 150
Protein targeting 206, 228 Radioactivity 254 Ribonucleic acid (RNA) 174
Proteins Radioimmunoassay (RIA) 256, 257f Ribosomes 200
absorption 104 advantages 257 Rickets 145t
acute phase 102 disadvantages 257 Rifampicin 196t
complete 95 interpretation 257 RNA interference 227
denaturation 93 principle 256 RNA polymerases 194, 195,
denaturing agents 93 procedure 257 196t, 199
Index
digestion 104, 105f Radioisotopes 254 RNA primer 191, 192, 193
functions 94, 94t applications 256 RNA viruses 219
mutual supplementation 173 Radiosensitivity 259 RNAs 178
nutritional value 169, 169t Radiotherapy 256 messenger 178
structures 90 Rancidity 59, 63 ribosomal 180
synthesis 199f types 60 transfer 179, 179f
Proteinuria 248 Rapoport-luebering shunt See Rothera’s test 88, 130
Proto-oncogenes 216, 216t BPG shunt 37
Pseudouridine 180 Recombinant DNA technique
S
Purine analogues 180 steps 220, 222f
Purine ring 115f, 181 Red blood cell (RBC) life 256 Salivary amylase 9t
inhibitors 183, 183t Redox potential 140 Saponification number 60, 63
regulators 183, 183t Refsum's disease 88 Schilling test 155, 251
sources 181 Renal clearance 247 Scurvy 99, 157
synthesis 182f creatinine 247t, 248 Secondary diabetes 56
Purines 174, 174t, 174f, 178 inulin clearance 247t Selenocysteine 206
Pyridoxine 152 urea clearance 247t Serotonin 121, 122f
Pyrimidine analogues 180 Renal diseases 103 Serum amylase 252
Pyrimidine ring 131, 186 Renal function tests 245 Serum bicarbonate 234
Pyrimidines 174, 174t, 174f, 178 uses 246, 246t Serum calcium 159
synthesis 187f Replication fork 191, 192f Serum cholesterol 79
Pyruvate dehydrogenase Respiratory acidosis 235, 239 Serum creatinine 248
complex 270 Respiratory alkalosis 235, 235t, 239 Serum lipase 252
303

Serum potassium 239 energetics 39, 39t Tuberculosis 153

Severe combined inhibitors 40, 40t Tumor markers 217

immunodeficiency (SCID) regulation 40, 40t types 218, 218t

186, 189 TCA, tricarboxylic Tyrosine

Shine-dalgarno sequence 201 acid 73f, 269 metabolism 116, 117f

Sickle cell anemia Telomerase 194 Tyrosinemia 120, 120t
treatment 290 inhibitors 194

Sickle cell disease Telomeres 194
U
classification 289 Tetany 162
Thalassemias

complications 290 Urea cycle 110, 111f
α-thalassemia 287, 288, 288t

Sickle cell trait 291 defects 112

Simple diffusion 6 β-thalassemia 287, 288, 288t treatment 112

Thiamine 149 disorder 188
Single-stranded DNA-binding
Thiamine deficiency (beriberi) 51

proteins (SSB proteins) 191 regulation 110

Thiophorase 88

Sodium 277 Uric acid formation 184
Thymidine 175, 180 Uric acid level 189
Sodium imbalance 277
Thyroid function tests 248, 249t
Sodium-glucose cotransport 6, 6f Uric acid
Index
Thyroid hormones 118, 118f
Sorbitol 31 synthesis 185f
Thyroid scan 256

Southern blotting 223 Uridine 175
Total parenteral nutrition (TPN) 172
applications 223 Urine
Trans fatty acids 63

steps 224, 224f Transaminases 107 abnormal constituents 248

Specific dynamic action (SDA) Transcription 194, 195 normal specific gravity 248

167, 167t inhibitors 196t Uronic acid pathway

metabolic disorder

Sphingolipidoses 84, 85t steps 195

Spliceosome 199 Trans-fatty acids 173 associated 52

Steatorrhea 87 Transferases 11
Steroids 63 Transferrin 102 V
Stroke-like episode (melas) 140 Translation 199
Substrate 23 eukaryotes 203 Van den bergh reaction 243,
244t, 281

Substrate concentration 13 prokaryotes 201

Vectors 228

Succinate dehydrogenase 56 inhibitors 205, 205t

Succinate thiokinase 56 Translocation 202, 202f Very low density lipoprotein
Sucrose and trehalose 30 Transmethylation reactions 124 (VLDL) 58, 79

Tricarboxylic acid (TCA) cycle 68 Visual cycle 142, 143f
Trypsinogen 206 Vitamin
T
Tryptophan 134 A 142

TCA cycle catabolism 121 B1 see thiamine 149

amphibolic role 40, 41t metabolism disorders 122 B12 see cobalamin 154

anaplerotic reactions 41 specialized products 121 B3 see niacin 151

304
B6 see pyridoxine 152 Western blotting 225 methylation 261
B9 see folic acid 153 Wilson's disease 165 oxidation 260
D 144 Wobble hypothesis 204, 205 phase 1 260
transporter 146 phase 2 261
K 147 X reduction 261
toxic manifestations 148 sulfation 261
von gierke (type I) 47t Xanthine oxidase 9t Xeroderma pigmentosum 190,
Xenobiotic 260 193, 194, 207, 208
Xenobiotic metabolism Xerophthalmia 142
W
sites 260 X-inactive specific transcript
Warfarin 263 Xenobiotics detoxification 260 (XIST) RNA 228
Water and electrolyte balance 277 acetylation 261
Watson-crick model of DNA 176 conjugation 261
Z
Well-fed state 267, 268f conjugation with glycine 261
Wernicke-korsakoff syndrome 51 glucuronidation 261 Zellweger's syndrome 69t, 88
Wernicke's encephalopathy 149t hydrolysis 261 Zinc 9t
Index

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Questions and Answers

Prelims.indd 1 27-06-2014 14:46:04

The Health Sciences Publishers

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1. Cell and Plasma Membrane 1–8

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11. Minerals 158–165

16. Molecular Biology-II 207–232

17. Acid-Base Balance and Disorders 233–241

19. Radioisotopes 254–259

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1. Name all cellular organelles with one function for each.

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Fig. 1.1: Eukaryotic cell

4. Write short notes on fluid mosaic model of membrane.

Factors Affecting Membrane Fluidity

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Cell and Plasma Membrane

Functions of Membrane Proteins

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Mechanism: Ping-pong Model

Fig. 1.3: Facilitated diffusion

7. Explain active transport with suitable examples.

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Cell and Plasma Membrane

Secondary Active Transport

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Fig. 1.5: Sodium-glucose cotransport

8. Describe transport processes across the membrane.

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Cell and Plasma Membrane

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Omeprazole: Inhibitor of hydrogen-potassium ATPase. Omeprazole inhibits gastric acid secretion,

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1. What are coenzymes? Explain with two examples.

2. What are cofactors? Explain with two examples.

Ch-02.indd 9 21-06-2014 11:48:09

Reaction specificity Enzymes are specific for 1 2

4. Define and classify enzymes with suitable examples.

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Ch-02.indd 11 21-06-2014 11:48:10

Fig. 2.1: Components of active site

Lock and Key Model

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Induced Fit Model or Hand in Glove Model of Daniel E Koshland

Fig. 2.3: Induced fit model (E, enzyme; S, substrate; P, product)

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Fig. 2.5: Effect of enzyme concentration on velocity of reaction

Effect of pH on Enzyme Activity

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10. What is enzyme inhibition? What is its significance?

Significance [MN: MATS]

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Fig. 2.10: Types of enzyme inhibition