First Semester

POKHARA UNIVERSITY

B.Sc. Biochemistry (Revised Syllabus)

CHEM 111 (Physical Chemistry I) 

Section I
Gaseous State: Distribution of molecular velocities, Boltzmann equation, Types of average velocities, Derivation of the equation of state of an ideal gas, Critical temperature and pressure, Vander Walls equation, Departure from ideal gas laws.
Colloids:  Sols and their preparation, properties, Electrical properties of sols, Gels, Determination of molecular weight by osmometry and viscosity.

Section II
Conductance: Transport number and its determination, Hittorfs Rule, Oswald dilution law, Equivalent conductance, Ionic mobility, Interionic theory of conductance, Activity and Activity coefficients and its determination, Debye huckel theory of activity coefficients.

Section III
Kinetics: Rate of reaction, Experimental measurement of reaction rates, Order and Molecularity, Rate equation for zero, first, second and third order reactions. Opposing, Consecutive and Parallel reaction, Energy of activation, Collision theory of uni-molecular and bimolecular reactions, Transition state theory, Chain reactions, Catalysis.

Section IV
Thermodynamics: Entropy, Second law of thermodynamics, Entropy change in ideal gases, Entropy of mixing, Entropy change in physical and chemical transformations, Free energy, Calculation of free energy change, Criteria of equilibrium, Classius – claperyon equation, Chemical potential, Third law of thermodynamics.

Text Book:
1. Daniels F. and Alberty R.A. "Physical Chemistry" John Wiley and Sons Inc. (latest edition)
2. Maron S.H. and Prutton C.F. "Principles of Physical Chemistry" 4^th Edition, Oxford and IBH Pub. Co., 1992.

                                                                                                                                                             July 2003

CHEM 112 (Organic Chemistry I) 

Section I
Reaction Mechanism and Kinetics: Homolytic and heterolytic fission of covalent bonds, Functional groups, Nucleophiles and Electrophiles, Organic acids and bases, Types of organic reactions, Organic reaction mechanism, Energetics of reaction, Kinetic and non kinetic methods of determining reaction mechanism.
Reactive Intermediates:  Introductory treatment of structure, Generation and Reactions of organic intermediates such as carbocation, carbanion, free radical, carbenes, nitrene and benzyne.

Section II
Stereochemistry: Stereochemistry and stereoisomerisms, Tetrahedral carbon, Optical activity, Polarimeter, Specific rotation, Enantiomerism, Prediction of enantiomerism, The Chiral center, Enantiomers, The racemic modification, Configuration, Specification of configuration: R and S, Sequence rule, Diastereomers, Meso compounds, Specification of configuration: more than one chiral center, Geometrical isomerism, Cis and trans isomers, Z and E specification
Conformational analysis: Open chain and cyclic compounds, Baeyer strain theory, Heats of combustion and relative stabilities of cycloalkanes, Orbital picture of angle strain, Conformations and factor affecting stability of conformations, Conformations of cycloalkanes, Equatorial and axial bonds, Stereochemistry of cyclic compounds: cis and trans isomers, Stereochemistry of cyclic compounds: conformational analysis.

Section III 
Alkane: Preparation, Grignard reagent, Coupling of alkyl halide with organometallic compounds, Mechanism and orientation of halogenation, Relative reactivity of alkanes towards halogenation, Ease of abstraction of hydrogen atom, Stability of free radicals, Transition state for halogenation,   Pyrolysis.
Alcohols and ethers: Physical properties of alcohols, Industrial source, Fuel from carbohydrates, Ethanol, Preparation of alcohols, Alcohols as acids and bases, Reaction of alcohols with hydrogen halides, Formation of alkyl sulfonates, Oxidation of alcohols, Physical properties of ethers, Industrial source of ether, Preparation of ethers, Reaction of ethers.
Alkyl halide: Preparation, Nucleophilic aliphatic substitution, Rate of reaction, SN² reaction (mechanism, kinetics, stereochemistry and reactivity), SN1reaction (mechanism, kinetics, stereochemistry, and reactivity).

Section IV
Alkenes: Structure of ethylene, Hybridization, Physical Properties, Industrial source, Preparation, Dehydrohalogenation and its mechanism, The E2 mechanism, E2 reaction (orientation and reactivity), E1 reaction (mechanism and orientation) Dehydration of alcohols, Reaction of alkenes, Reactions at carbon-carbon double bond, Hydrogenation, Addition of hydrogen halide, Markounikoffs rule, Addition of hydrogen bromide, Peroxide effect, Addition of hydrogen halide, Markounikoffs rule, Addition of hydrogen bromide, Peroxide effect, Addition of Sulphuric acid, Addition of water, Electrophilic addition(mechanism, orientation and reactivity), Addition of halogens and its mechanism, Halohydrin formation, Oxymercuration demercuration, Hydroboration reaction(mechanism and orientation), Mechanism of free radical addition, Orientation of free radical addition, Hydroxylation, Ozonolysis.

Text Book:
1. Morison R.T. and Boyd R.N. "Organic chemistry" 6^th Edition, Prentice Hall of India Pvt. Ltd., 1994.
2. March, J. "Advanced organic chemistry" 4^th edition, Wiley Eastern Ltd., India, 1999.

CHEM 113 (Inorganic Chemistry I)

The Covalent bond:The Lewis theory: the octet rule, Exceptions to the octet rule, Sidgwick-Powell theory, VSEPR theory:  Effect of lone pair, Effect of electro negativity, Isoelectronic principle, some examples using the VSEPR theory (BF₃, BF₄^-, NH₃, H₂O_, PCl₅, ClF₃, I₃^-, SF₆, IF₇), Valence bond theory, hybridization, Extent of d-orbital participation in molecular bonding, sigma and pi ponds, Molecular orbital method, LCAO method (s-s, s-p, p-p, p-d and d-d combination of orbitals), Nonbonding combination of orbitals, Molecular orbital treatment of homonuclear diatomic molecules (H₂, He₂, N₂, O₂, H₂⁺, O₂^- ion) and heteronuclear diatomic molecules (NO, CO and HCl).

Section II
Metallic bond:  General properties of metals: conductivity, Luster, Malleability and cohesive force, Crystal structure of metals, Bond lengths, Theory of bonding in metals: Valence bond theory, Molecular orbital or band theory, Conductors, Insulators and Semi conductors, Alloys: Ionic compounds, Interstitial alloys and related compounds, Substitutional alloys, Super conductivity.

Section III
Periodic Table: 
The s-Block elements: Electronic configuration, Size of atoms and ions, Density, Ionization energy, Electro negativity and bond type, Born-Haber cycle: energy changes in the formation of ionic compounds, Hardness and cohesive energy, Melting and boiling points, Flame colors and spectra, Color of compounds, Chemical properties: Reaction with water, air and dinitrogen, Organic and organometallic compounds, Complexes, Crowns and crypts, Biological importance.
The p-Block elements: General Introduction and Uses, Oxidation states and types of bond, (+III) – oxidation state, (+I) oxidation state, The inert pair effect, Melting point, Boiling point and structures, Size of atoms and ions, Electropositive character, Ionization energy.

Section IV
The d-Block elements:  Metallic character, Variable oxidation state, Stability of the various oxidation states, Complexes, Size of atoms and ions, Density, Melting an energy, Color: polarization, Incompletely filled d or f shell, Magnetic properties measurement of magnetic moments, Catalytic properties, Nonstoichiometry, Abundance, Differences between the first and other two rows: Metal - metal bonding and cluster compounds, Stability of oxidations states, Complexes, Sizes, Magnetism.

 
Text:
1.  Lee J.D. "Concise Inorganic Chemistry" 4^th edition, ELBS with Chapman and Hall, 1991.

PHYS 114 (Physics I)

Section I
Properties of matter: Free surface energy, Surface tension, The mechanism of emergence of surface tension, Direct manifestation of surface tension, Equilibrium conditions at the interface between two liquids, Equilibrium conditions for liquid solid interfaced, The pressure under a curved surface, Capillary effects, Surface active substances (surfactants). 

Section II
Structure of Liquids: Liquid crystals pair distribution function, Calculation of potential energy, Dependence of properties of a liquid on molecular, Structure of Liquid crystals, Types of liquid crystals: Smectics, Namatics, Cholesterics, Properties and applications of liquid crystals,
Chemical potential and phase equilibrium: Chemical potential, Equilibrium conditions, Chemical potential for a one-component system.

Section III
Astronomy: Universe, Theories of Universe, Solar system, Stars, Galaxies, Milky way, Cosmology (General introduction), Life in Universe. www.astronomy.com/home.asp

Section IV
Hysteresis: B-H Curve by ring method, Tuned circuits (parallel and series), Rotating magnetic field and induction motor, Electromagnetic wave. Rectifiers, Amplifier, Oscillators, Fermi energy  

   BIOCHEM 115 (Fundamentals of Biochemistry)

Section I
The Foundation of Biochemistry:

Cellular Foundations: Cells Are the Structural and Functional Units of All Living Organisms, Cellular Dimensions Are Limited by Oxygen Diffusion, There Are Three Distinct Domains of Life, Escherichia coli Is the Most-Studied Prokaryotic Cell, Eukaryotic Cells Have a Variety of Membranous Organelles, Which Can Be Isolated for Study, The Cytoplasm Is Organized by the Cytoskeleton and Is Highly Dynamic, Cells Build Supramolecular Structures, In Vitro Studies May Overlook Important Interactions among Molecules

Chemical Foundations: Biomolecules Are Compounds of Carbon with a Variety of Functional Groups, Cells Contain a Universal Set of Small Molecules, Macromolecules Are the Major Constituents of Cells, Three-Dimensional Structure Is Described by Configuration and Conformation, Interactions between Biomolecules Are Stereospecific

Section II
Physical Foundations: Living Organisms Exist in a Dynamic Steady State, Never at Equilibrium with Their Surroundings, Organisms Transform Energy and Matter from Their Surroundings, The Flow of Electrons Provides Energy for Organisms, Creating and Maintaining Order Requires Work and Energy, Energy Coupling Links Reactions in Biology, K_eq and G Are Measures of a Reaction’s Tendency to Proceed Spontaneously, Enzymes Promote Sequences of Chemical Reactions, Metabolism Is Regulated to Achieve Balance and Economy.

Genetic Foundations: Genetic Continuity Is Vested in Single DNA Molecules, The Structure of DNA Allows for Its Replication and Repair with Near-Perfect Fidelity, The Linear Sequence in DNA Encodes Proteins with Three-Dimensional Structures

Section III
Evolutionary Foundations: Changes in the Hereditary Instructions Allow Evolution, Biomolecules First Arose by Chemical Evolution, Chemical Evolution Can Be Simulated in the Laboratory, RNA or Related Precursors May Have Been the First Genes and Catalysts, Biological Evolution Began More Than Three and a Half Billion Years Ago, The First Cell Was Probably a Chemoheterotroph, Eukaryotic Cells Evolved from Prokaryotes in Several Stages, Molecular Anatomy Reveals Evolutionary Relationships, Functional Genomics Shows the Allocations of Genes to Specific Cellular Processes, Genomic Comparisons Will Have Increasing Importance in Human Biology and Medicine.

Section IV
Role of Water: Weak Interactions in Aqueous Systems, Ionization of Water, Weak Acids and Weak Bases, Buffering Against pH Changes in Biological Systems, Water as a Reactant, The fitness of the aqueous environment for the living organisms

Text Book:
Nelson, D.L. and Cox, M.M. "Lehninger Principle of Biochemistry" 4 ^th Edition, Worth Publishers, USA

PRACTICALS FOR FIRST SEMESTER

 CHEM 111L 

1.Determination of dissociation constant of acetic acid using pH meter.

2.Determination of rate constant and half-life of acid catalyzed hydrolysis of methyl acetate.

3.Determination of the concentration of a strong base by conductometric titration with a strong acid      and a weak base.

4.Determination of the concentration of the unknown solution by using viscometer.

5.Carrying out the conductometric titration of MOPS (0.1M) vs. and TRIS (0.1M) vs. and finding out the concentration of HCl.

6.Determination of viscosity of methanol, ethanol, n-propanol and n-butanol.

7.Determination of the pKa of MOPS and TRIS buffer by titrating it with HCl.

8.Determination of heat of neutralization of strong acid and strong base titration.

9.Determination of the surface tension of methyl acetate, ethyl alcohol and acetone. 

CHEM112L 

1.Detection of functional groups in the given organic compounds.

2.Purification of organic compounds by crystallization methods and to find out its melting point.

3.Purification of organic compounds by crystallization method and to check its purity by mixed melting point method.  

CHEM113L

1.Identification of two acid radicals present in the given salt mixture by dry and wet ways.

2.Identification of basic radicals present in the given salt by dry and wet ways.

3.Analyzing the salt completely by dry and wet ways.

PHYS114L

1.Determination of the surface tension of water by capillary tube method.

2.Determination of the viscosity of the liquid by using stoke's law.

3.Using of a potentiometer to find the internal resistance of a cell.

4.Using earth inductor to find the horizontal component of the earth magnetic field.

BIOCHEM115L

1.Preparation of phosphate buffers of different pH values.

2.Determination of Rf values of different amino acids by paper chromatography.

3.Estimation of non-reducing sugar from sugarcane. 

July 2003