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Second Semester

Second Semester

POKHARA UNIVERSITY

B.Sc. Biochemistry (Revised Syllabus)

 CHEM 121 (Physical chemistry II)

Section I
Surface Chemistry:
Adsorption, Adsorption of gases by solids, Types of adsorption, Adsorption isotherm, Determination of surface area of adsorbents, Adsorption of solutes by solids.
Photochemistry: Einstein law of photochemical equivalence, Consequences of light absorption by atoms and molecules, Phosphorescence, fluorescence.
Phase rule:
Gibbs phase rule, One and Two component systems.

Section II
Solid State:
  Crystalline and amorphous solids and their properties, Lattices and unit cell, Crystal systems, Designation of crystal planes, Diffraction method, Molecular crystals, Van der waal forces, Dispersion bond, Dipole bond, Hydrogen bonded crystals, Bonding and structure, Covalent crystals, Ionic crystals, Reciprocal and Bravais lattice, Miller indices and their calculation in simple crystal, Allotropy and polymorphism, Thermal and magnetic properties: Dulong’s petit law, Debye’s theory, Para magnetism and Diamagnetism
Solid-state reaction:
Wagner’s theory, oxidation of metals, kinetics of oxide film growth, sintering, photographic process.
Superconductivity:
Occurrence, mechanism and critical properties of superconductor, BCS theory of superconductor, High temperature superconductor, Application, Meissner’s effect and effect of magnetic field, Type I, II superconductor.

Section III
Electrochemistry:
Standard cells, Standard electrode potentials, Nernst equation, Calculation of single electrode potential and E.M.F.,  DS and DH ,Equilibrium constant, Types of electrode , Chemical cells with and without transference, Concentration cells with and without transference, Junction potential, Over voltage and its measurement , Commercial cells.

Section IV
Statistical Mechanics:
The thermodynamic probability of a system, The most probable distribution, The partition function, Systems of independent particles, The energy of a system, Separation of the partition function, The partition function for translation, The thermodynamic function for translation, rotation, vibration and electronic exitation, Mono atomic gases, Rotation, Vibration, The electronic partition function, Results of statistical calculation, Statistical calculation of equilibrium constants, Entropy and probability,Bose-Einstein and Fermi - Dirac statistics.

Text Book:

 Maron and Prutton“Principles of Physical chemistry” 4th Edition, Oxford and Ibh publisher.

CHEM 122 (Organic Chemistry II)

Section I 
Alkynes:
Structure of acetylene, Physical properties, Industrial source, Preparation and reactions of alkynes, Reduction of alkenes, Electrophilic addition to alkynes, Hydration of alkynes, Acidity of alkynes, Reactions of metal acetylides, Formation of carbon-carbon bonds.
Aromaticity:
  
Aliphatic and aromatic compounds, Structure of benzene, Kekule structure, Stability of the benzene ring, Heat of hydrogenation, Carbon-carbon bond lengths in benzene, Orbital picture, Representation of benzene ring, Huckel 4n + 2 rule, Polynuclear aromatics.
Electrophilic aromatic substitution:
Effect of substituent groups, Determination of orientation, Determination of relative reactivity, Classification of substituent groups, Orientation in disubstited benzenes, Mechanism of nitration, Sulphonation, Halogenation and Friedle crafts reactions, Reactivities and orientation, Theory of orientation, Electron release via resonance, Effect of halogenation on electrophilic aromatic substitution.

Section II
Aldehydes and Ketones:
Physical proporties, Preparation, Preparation of Ketones by friedel craft acylation and use of organo-copper compounds, Reactions: Oxidation, Reduction, Addition of cyanide, Alcohols and derivatives of ammonia, Cannizaro reaction, Addition of Grignard reagents, Products of Grignard synthesis, Limitations of Grignard synthesis, THP group as protecting group, Iodoform test.
Carboxylic Acids:
Physical properties, Salts of carboxylic acids, Industrial source, Preparation, Grignard and nitrile synthesis, Reactions, Structure of carboxylate ions, Effect of substituents on acidity, Conversion into acid chloride, Esters and amides, Reduction of acids into alcohols, Halogenation of aliphatic acids.

Section III
Amines: 
Preparation, Reduction of nitro compounds, Ammonolysis of halides, Reductive amination, Hoffmann rearrangement, Basicity of amines, Structure and basicity, Effect of substituents on basicity of aromatic amines, Ring substitutions in aromatic amines, Reactions of amines with nitrous acid, Diazonium salt, Sand Meyer reaction, Synthesis of phenol, Diazonium salt (replacement by – H), Synthesis using diazonium salts, Synthesis of azocompounds, Beckman rearrangement, Hoffmann rearrangement. 
Phenols:
Structure, Physical properties, Salts of phenols, Preparation, Reactions, Acidity of phenols, Fries rearrangement, Ring substitution, Kolbe's reaction, Riemer tiemann's    reaction, Formation of aryl ethers.

Section IV
Carbanions:
Acidity of µ- hydrogens, Reactions involving carbanions, Base-promoted halogenation of ketones, Acid-catalysed halogenation of ketone, Enolization, Aldol condensation, Dehydration of aldol products, Use of aldol condensation in synthesis, Crossed aldol condensation, Reactions related to the aldol condensation, The Wittig reaction, Claisen condensation, Formation of b-keto esters, Crossed Claisen condensation, Carbanions in organic synthesis, Malonic ester synthesis of carboxylic acid, Acetoacetic ester synthesis of ketones, Decarboxylation of b keto acids and malonic acids, Direct and indirect alkylation of esters and ketones, Synthesis of acids and esters via 2-oxozolines, Organoborate synthesis of acids and ketones,  Alkylation of carbonyl compound via enamines.

Text Book:

Morison R.T. and Boyd R.N. "Organic chemistry" 6th Edition, Prentice Hall of India Pvt. Ltd., 1994. 

CHEM 123 (Inorganic Chem. II)

Section I
Group 14 elements:
Introduction and uses of the elements (Carbon, Silicon, Germanium, Tin and Lead), Structure and allotropy of the elements, Differences between carbon, silicon and remaining elements, Carbon dating, Physical properties, Carbides, Oxygen compounds, Carbonates, the Carbon cycle, Sulphides, Oxides of Silicon, Silicates, Classification of Silicates, Silicates in technology, Organosilicon compounds and the Silicones, Hydrides, Cyanides, complexes, Internal π bonding using d orbitals, Tetra halides, Dihalides, Cluster compounds, Organic derivatives.
Group 15 elements:
Electronic structure and oxidation states, uses (Nitrogen, Phosphorous, Arsenic, antimony and bismuth), General properties, Bond type, Metallic and nonmetallic character, Reactivity, Hydride, Liquid ammonia as a solvent, Hydrogen azide and azide, Fertilizers, Nitrogen fixation, Urea, phosphate fertilizers, Halides, Oxides of nitrogen, Oxyacids of nitrogen, Oxides of phosphorous, Arsenic and bismuth, Oxoacids of phosphorous, The phosphoric acid series, The phosphorous acid series, major uses of phosphates.

Section II
Group 16 elements:
 General properties, Electronic structure and oxidation states, Uses of elements, Structure and allotropy of the elements, Chemistry of ozone, Oxidation states (+II), (+IV) and (+VI), Bond length and pπ-dπ bonding, Differences between oxygen and the other elements, General properties of oxides, Oxides of sulphur, selenium, tellurium and polonium, Oxoacids of sulphur, Hydrides, Halides, Compounds of sulphur and nitrogen.
Group 17 elements:
The halogens:
 Introduction and uses of the elements, Size of atoms and ions, Ionization energy, Types of bonds formed and oxidation states, Melting point and boiling points, Bond energy in X2 molecules, Oxidizing power, Reaction with water, Reactivity of the elements, Hydrogen halides, Halides, Bridging halides, Halogen oxides, Interhalogen compounds, Polyhalides, Basic properties of halogens, Pseudohalogens and pseudohalides.

Section III
Group 18 elements :
The noble gases:
Name of group and their electronic structure, Occurrence and recovery of the elements, Uses of elements, physical properties, Special properties of helium, Chemical properties of the noble gases, Chemistry of Xenon, Structure and bonding in Xenon compounds
Organometallic chemistry:
General methods of preparation, Bonding and structure of carbonyls and nitrosyls, 18e rule.
Non-transition organometallics
: general survey, types, Synthetic methods of metal alkyls of group I, II and III elements.
Transition metals:
transition metals to carbon pi bonds, Alkenes complexes, Alkynes complexes, Allyl complexes, Metallocenes (preparation, properties, structure and elementary approach of bonding).

Section IV
Coordination chemistry:
Double salts and coordination compounds, Werner's work, Recent methods of studying complexes, Effective atomic numbers, Shapes of d-orbitals, Bonding in transition metal complexes, Valence Bond theory, Ligand field theory, Crystal field theory, Octahedral complexes, Effects of crystal field splitting, Tetragonal distortion of octahedral complexes (Jahn-Teller distortion), Square planar complexes, Tetrahedral complexes, Chelates, Magnetism, Extension of the crystal field theory to allow for some covalency, Molecular orbital picture (π acceptors and π donors), Nomenclature of coordination compounds, Isomerism (Polymerization, Ionization, Hydrate, Linkage, Coordination, Coordination position, Geometrical, Optical).

Text Book:
 

Lee, J.D. "Concise Inorganic chemistry" 4th edition, ELBS with Chapman and Hall, 1991.

PHYS 124 (Physics II)

Section I
Relativity:
The postulates of relativity, Measurement of time, The relativity of time, Length contraction and its evidences, Doppler effect.
Relativistic Mechanics:
Introduction, Mass and force in relativity, Relativistic momentum and energy, Conversion of mass to energy, Massless particle.

Section II
Holography:
Synchronous detection, Hologram of a plane wave, Reconstruction of the image, and Hologram of a point object, Hologram of an arbitrary object, Quality of a photographic plate and the exposure time, Three-dimensional reproduction of the object, Thick holograms (Denisyuk's method), Bragg's law, Recording of holograms and reconstruction of a plane wave, Recording of holograms and reconstruction of a spherical wave, Holographic recording and reconstruction of the image of an arbitrary object, Three-dimensional colored image, Peculiarities of holograms as carries of information, Applications of holography,Polrization: Polarization of light and polarimetry.

Section III
Atomic physics:
Review of classical physics. Black body radiation, Atomic structure and radioactivity and X rays,
Radioactivity: Radioactive decay, Consequences of decay and units of radioactivity, Production of radio isotopes, Interaction of radiation with matter and the effect of ionizing radiation on biomolecules, Detection of radiation. GM and scintillation counter.
Plank's theory and birth of Quantum physics: Atomic spectra, Schrodinger wave equation, Molecular spectra

Section IV
Elementary particles:
Introduction, Antiparticles, pions and muons, The four fundamental forces, Leptons, Hadrons, Quark, Model of hadrons, Strong force and QCD, Electroweak interactions, The W and Z particles, High-energy accelerator.


CHEM 125 (Biomolecules I)

Section I
Amino acids, peptides and proteins:
Amino acids, Peptides and Proteins, Working with proteins, The Covalent Structure of Proteins, Protein sequences and evolution

Section II
Three Dimensional Structures of Protein:
  Protein Secondary Structure, Protein Tertiary Structure, Protein Quaternary Structure, Protein Denaturation and Folding

Section III

Carbohydrates and Glycobiology: Monosaccharides and Disaccharides, Polysaccharides, Glycoconjugates:  Proteoglycans,  Glycoproteins and Glycolipids, Carbohydrates as Informational Molecules: The Sugar Code, Working with Carbohydrates

Section IV
Nucleotides and Nucleic Acids: Some Basics, Nucleic Acid Structure, Nucleic Acid Chemistry, Other Functions of Nucleotides


Text book :

Nelson D.L. and Cox M.M. "Lehninger Principle of Biochemistry" 4th Edition, Worth Publishers, US
A                              

                 

PRACTICALS FOR SECOND SEMESTER

Chem121L

1.Study of the reaction between potassium persulphate and potassium iodide by Iodine clock method and determination of the activation energy.

2.Determination of the distribution coefficient of iodine between organic liquid and water.

3.Determination of the mutual solubility curve of phenol and water and hence determination of the upper consulate temperature.

4.Verification of the Ostwald’s dilution law by measuring the conductance of acetic acid at different concentration and determination of the ionization constant of the acid.

5.Determination of the equivalent conductance at infinite dilution of strong electrolyte by conductance measurment.

6.Study of the alkaline hydrolysis of ethyle acetate at two temperatures titrimetrically and hence determination of the energy of activation of the reaction.

7.Study of the adsorption of acetic acid from aqueous solution by activated charcoal and examination of the validity of Freundlich and Langmuir adsorption isotherm.

8.Determination of the concentration of halide mixture by potentiometric titration with silver nitrate.

9.Study of the kinetics of iodination of acetone.

10.Determination of the molecular weight of acetone.

11.Determination of the cell constant.

 

Chem. 122L

1.Preparation of acetanilide.

2.Preparation of p-nitro acetanilide.

3.Preparation of benzene azo beta-napthol.

4.Preparation of phenyl hydroxylamine.

5.Preparation of ethyl acetate.

6.Preparation of benzanilide.

7.Preparation of benzoic acid.

8.Distillation under reduced pressure.

9.Fitration under partial vacuum.

 

Chem. 123L

1.Quantitative estimation of sulphate ion as barium sulphate by gravimetry.

2.Preparation of Prussian blue from iron fillings.

3.Preparation of Cuprous chloride.

4.Preparation of Tetra-ammine copper (II) sulphate.

5.Preparation of Potassium trioxalato chromate.

6. Preparation of Chrome alum.

7. (a) Preparation of the standard deci normal solution of oxalic acid and standardization of the given potassium permanganate solution by it.

  (b) Estimation of the amount of Mohr’s salt and ferrous ion present in the given volume of Mohr’s salt solution permanganetometrically in terms of gram equivalent and number of moles.

 Phy 124L

1.To study the characteristics of a given transistor.

2.To use a potentiometer to find the internal resistance of a cell.

3.To use a potentiometer to calibrate a given ammeter and voltmeter.

4. To determine the ECE of given electrolytic surface.5. To use the earth inductor to find the horizontal component of the earth's field.

Chem/Biochem 125L

1.Estimation of carbohydrate by Anthrone’s method.

2.Determination of
alpha amylase activity of saliva by Caravel’s method.

3.Determination of reducing sugar by Benedict’s test.

4.Isolation of casein from milk biochemically.

5.Determination of the acid value of provided Vanaspati Ghee.

6.Determination of the validity of Beer’s law for the colorimetric estimation of creatinine.

7.Determination of the pka and ka value of p-nitrophenol by absorbance measurement.

8.Determination of pI value of glycine.

9.Quantitative estimation of blood sugar by enzymatic method.

10.Quantitative estimation of blood cholesterol by enzymatic method.

11.Determination of egg cholesterol.

12.Qualitative estimation of egg protein.

      July 2003
 

 

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