Biophysical and Bioorganic Chemistry - Syllabus
Paper Code
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212901
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Marks: 100
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Credits: 4
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Class Hours: 60
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Paper Title:
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Biophysical
and Bioorganic Chemistry
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Part A: 50 marks
1.
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Thermodynamics:
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(a)
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First law of thermodynamics: Introduction, definitions, nature of heat and work, PV work,
maximum work, first law of thermodynamics - internal energy, enthalpy, molar
heat capacities, isothermal and adiabatic expansion.
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(b)
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Thermochemistry
: Exothermic and endothermic reactions, standard enthalpy
of formation,
thermochemical equations, reaction
enthalpy - dependence on temperature, bond energies.
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(c)
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Second law of thermodynamics:
Thermodynamics -
reversibility and irreversibility, spontaneous processes, entropy,
thermodynamic efficiency and Carnot’s theorem, statements of second law,
entropy changes - phase transition, heating, irreversible processes. Third
law of thermodynamics. Free energy - variation with temperature and pressure,
Gibbs-Helmholtz
equation, applications of thermodynamics in biochemistry,
biochemical relevance of classical thermodynamics, open systems.
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2.
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Chemical equilibrium :
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The nature of chemical equilibrium, law of mass action,
equilibrium constant, relationship between DG and Keq, effect of temperature and
pressure, Le Chattelier principle, equilibrium reaction involving protons,
coupling of reactions. Applications in living systems.
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3.
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Chemical Kinetics : Definition, reaction rate, rate laws,
zero-, first- and second-order reactions, molecularity of a reaction, pseudo
first order reaction, half-life, determination of order and rate constant,
effect of temperature on reaction rates. Theories of reaction rates - the
collision theory, the activated complex theory. Catalysis : Definition,
types, characteristics of catalysts, activation energy and catalysis.
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4.
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Acids and
bases : Bronsted-Lowry concept, Lewis concept,
strengths of acids, weak acids and bases, pH, buffer solutions.
Henderson-Hasselbalch equation, buffering against pH changes in biological
systems, maintaining the pH of blood, acid-base indicators, acid base
titration, choice of a suitable indicator.
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5.
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Properties
of liquids (brief treatment): Introduction – the kinetic molecular description, intermolecular
forces in liquids, dielectric constant, surface tension, viscosity,
diffusion, osmotic pressure, phase rule, phase diagram of water, ionization
of water, water as a reactant.
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6.
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Spectrophotometry
: Beer-Lambert law, standard curves, working principle of a
spectrophotometer.
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Part B : 50
marks
1.
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Physico-chemical
parameters for biomolecules:
Inter
and Intramolecular interaction: covalent, ionic bond, hybrid orbitals,
polarity of bonds, electronegativity, dipole, hydrogen bonding, dihydrogen
bonding, hydrophobic interactions, Van der waals interaction.
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2.
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Nature of bonding in
organic molecules and in relation to biomolecules: Delocalized chemical
bonding-conjugation, cross conjugation, resonance, hyperconjugation, bonding
in fluorescences, tautomerism.
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3.
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Reaction intermediates:
Formation, structure,
stability and reactions of Carbocation, Carbanions, free radicals, Nitrenes,
Carbenes, Benzynes.
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4.
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Alcohols,
ethers, epoxides and di-ols: Occurrence,
nomenclature, structure,
synthesis, physical and chemical properties
and uses.
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5.
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Dienes: Structure and properties of 1, 3-butadiene, addition
reactions, polymerisation, Diels-Alder and other reactions of dienes.
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6.
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Aromaticity:
Structure of benzene, sources of aromatic hydrocarbons,
industrially important aromatic compounds, nomenclature of benzene
derivatives, electrophilic and
nucleophilic aromatic substitution, chemistry of aromatic
aliphatic compounds.
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7.
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Aldehydes
and ketones:
Nomenclature, synthesis, nucleophilic addition, elimination reaction, oxidation and
reduction of carbonyl compounds, haloform reaction, enolisation in biological
system, a-halocarbonyl compounds,
aldol condensation, benzoin condensation, Claisen condensation, crossed aldol
and crossed Claisen condensation, perkin condensation. Witting reaction,
Reformatsky reaction, a,b-unsaturated carbonyl compounds
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8.
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Carboxylic acids and their derivatives: Nomenclature, synthesis, classification, properties,
reactions, uses, decarboxylation reactions, dicarboxylic acids, esters.
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9.
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Nitro-compounds
and amines: Occurrence, nomenclature,
synthesis, classification, properties, reactions, uses, diazonium compounds.
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10.
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Phenols:
Occurrence, nomenclature, synthesis,
properties and reactions, polyhydric phenols.
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11.
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Heterocyclic
Compounds: reactions, classification and
synthesis of heterocyclic compounds with special reference to – pyrroles,
purines and pyrimidines.
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Books Recommended:
1) Essentials of
Physical Chemistry
a.
By :
B.S. Bahl G.D. Tuli and A. Bahl
b.
Publisher
: S. Chand & Company Ltd.
2) Physical
Chemistry with Application in Biological Systems
a.
By :
Ramond Chang
b.
Publisher
: Macmillan Publishers Co.
3) Text Book of
Physical Chemistry
a.
By :
S. Glasstone
b.
Publisher
: D. Van Nostrand Company
4) Elements of
Physical Chemistry
a.
By.
S. Glasstone and D. Lewis
b.
Publisher
: The Macmillan Press
5) Organic
Chemistry
a.
By : R.T. Morrison and R.N. Boyd
b.
Publisher: Allyn and Bacon Inc.
6) Organic
Chemistry
a.
By : I.L. Finar Vol. 1 and
Vol. 2
b.
Publisher : English Language Book
c.
Society and Longman Group. Ltd.
7) Organic
Chemistry
a.
By: H. Hart and R.d. Schuetz
b.
Publisher: Houghton Mifflin Company
8) Contemporary
Organic Chemistry
a.
By: A. L. Ternay
b.
Publisher: W.B. Sanders Company
9) Concepts
In Modern Chemistry
a.
By: P. Kavanah, J. Robbins and J. Oberkrieser
b.
Publisher: Cambridge Book