PAPER I

Molecular Pharmacology: definition and determination of important pharmaco-kinetic parameters and pharmaco-dynamic parameters, pharmacokinetic basis of individual difference in response to drugs, pharmacokinetic properties, pharmacopore identification, influence of structural modifications on pharmacokinetic properties, mode of action of drugs, quantitative structure activity relationship, present and future aids to drug design, structure and confirmation of drugs and receptors, drug receptor binding forces, structural aspects of drug-nucleic acid interactions

Peptides-design, synthesis and applications: introduction to peptides, peptide design, synthesis of peptides (solution phase and solid phase), protection and deprotection of amino and carboxyl group, unnatural amino acids, conformation of peptides, purification and crystallization of peptides, determination of structure of small molecules (briefly), application of peptides

Biomechanics: Basic concepts of fluid dynamics, Bernoulli equation and its applications, streamline flow, Reynolds number, viscous flow, effects of gravity and external acceleration on circulation

Biostatistics: mean, median, mode, dispersion, standard deviation, correlation and regression, T-Test, chi-square test, F-test, ANOVA, how to enter data, edit and transform data, descriptive statistics ie. how to calculate mean, SD, range etc., frequency distribution, hypothesis tests for means and proportions, ANOVA, scatter plot, correlation matrix, regression, probability distribution.

Bioinformatics: Introduction, repositories, databases, pairwise sequence based alignment, relationship between sequence and structures, structural bioinformatics, genomics, proteomics, human genome project, software packages

Clinical proteomics

PAPER II

Spectroscopic techniques: Introduction to spectroscopy, basic principles, instrumentation and applications of UV-VIS absorption, infrared, Raman, atomic absorption, fluorescence, Circular dichroism, Laser spectroscopy, nuclear magnetic resonance, electron spin resonance, acoustic spectroscopy; solvent perturbation; difference spectroscopy; Fourier transform techniques; applications of Laser; mass spectroscopy.

Elementary crystallography: Introduction to crystallography, symmetry in crystals, lattices and unit cells, crystal systems, Bravais lattices, elements of symmetry- rotation axis, mirror planes and center of inversion, point group symmetry- monoaxial point groups, polyaxial point groups, translational symmetry- screw axis and glide planes, space group, equivalent points, X-ray diffraction and Bragg’s equation

X-ray diffraction methods: Scattering factor, structure factor expression, reciprocal lattice, Ewald’s sphere, electron density equation, phase problem, Patterson function, molecular replacement method, isomorphous replacement, refinement programs and interpretation of results, methods of data collection of crystal containing small molecule and large molecule, factors affecting the measurement of integrated intensities, photographic methods, diffractometers, area detectors and image plates.

Separation techniques: Basic principles and applications of electrophoresis-types of electrophoresis, estimation of molecular weight of proteins by logirthmic method; basic principles and applications of centrifugation-sedimentation, estimation of sedimentation rate by sedimentation velocity method and equilibrium method; basic principles and applications of chromatography-capacity factor of the gel, Kd value, α value.

Molecular modeling: Basic principle of modeling, modeling by energy minimization technique, concept of rotation about bonds, energy minimization by basic technique for small molecules, Ramachandran plot, torsional space minimization, energy minimization in cartesian space, molecular mechanics-basic principle, molecular dynamics basic principles

PAPER III

Cell biology: Organization and structure of prokaryotes and eukaryotes, nucleus, cytoplasm, plasma membrane, mitochondria-structure, function respiratory chain and ATP synthesis, endoplasmic reticulum, golgi apparatus, membranes, ribosomes, peroxisomes, lysozomes, transcription and translation, transport of proteins, cancer and its molecular genetics, oncogenes, tumor suppression gene

Molecular biology: central dogma, genetic code, gene and operon, structure of DNA and RNA, plasmids, selectable markers, agarose gel, PCR, Cloning PCR products, expression vectors, cell free translation, c- DNA libraries, genomic libraries, DNA micro arrays, DNA sequencing

Proteins, purification, structure and function: twenty amino acids: structure and function, the peptide bond, primary structure of a protein: methods of sequence determination, forces determining protein structure, secondary structure of a protein: β strands, β sheets (parallel and anti parallel), β turns, α helix, 3₁₀ helix and π helix (differences), tertiary structure of a protein: protein folds-all α helix motifs (Lone helix, helix-turn-helix, four helix bundle and eight helix bundle), protein folds-all β sheet motifs (β sandwich, β barrel, greek Key topology and β propellars), protein folds- α / β motifs (Tim barrel, Rosman fold, α/β horseshoe), quaternary structure of a protein: macromolecular assemblies, domains and domain swapping, membrane proteins, purification methods, studies of proteins with MALDI-TOF, enzymes and enzyme kinetics, G-proteins and G-protein coupled receptors(GPCRs), proteins as targets for rational structure based drug design

Principles of nucleic acid structure: nucleotide structure and properties: introduction to DNA, RNA, bases, sugars, phosphates, structure of nucleotide, nucleosides and polynucleotides and their nomenclature scheme. tautomerisation and ionization. genetic code. stereochemistry: nucleoside, torsion angles, sugar conformation, NMR study, DNA structure: different types of DNA and their structure, DNA motifs, DNA repeats and their significance, function and stability, spectroscpic study of DNA: dye binding, interaction, denaturation, and renaturation of DNA, thermal denaturation and Tm value, RNA: structure and properties, different forms of RNA and their significance, alkaline hydrolysis of RNA, how it differs from DNA, role of 2’OH group, structure of phenylalanine tRNA, enzymes involved in molecular biology: DNA polymerase, RNA polymerase, reverse transcriptase, restriction endonuclease. DNA interaction: protein, dye, drugs and carcinogens, DNA replication: DNA polymerization, mutation, and DNA repair, DNA transcription: RNA synthesis, types of RNA polymerase, DNA polymorphism: repeats of DNA and their significance, single nucleotide polymorphism, c-DNA, cloning and expression and purification

Membrane biology: Lipid structure and their organization, comparison of different membrane models, diffusions and permeability, different types of transport system across membranes, liposome and its applications

PAPER IV

Imaging techniques: Ultrasound, nuclear magnetic resonance, positron emission topography, computer axial tomography, whole body scanner, dose calibrators, gamma scintillation camera, digital imaging techniques, acquisition, analysis and processing of data from gamma camera, enhancement, topographic reconstruction, display and recording of image

Radiation biophysics: production and types of radiations, radiation measurement units, interaction of radiation with matter, detection of radiation by ionization chamber, G.M counter, proportional counter, liquid scintillation counter, radiation protection, molecular effects of radiation on membranes, cytoplasmic organelles, macromolecules, factors modifying effects of radiation, repairs of radiation induced damage

Radio pharmaceuticals: Production of radionuclides by reactors, cyclotrons and particle accelerators, use of radionuclide generators, elements of radiochemistry

Diagnostic use of radionuclides: In vivo imaging and functional studiesof brain, thyroid, heart, biliary tract, liver, kidney, spleen, tumors, bones and abscesses, use of imaging devices and external detectors for organ imaging, time dependent and differential functional studies, use of physiological gating techniques for functional studies, methodology and quality control of competitive binding and radio immunoassay, procedures for the measurement of peptide hormones, drugs and other biological substances, basic principles of radionuclide therapy in thyrotoxicosis and carcinoma thyroid

Bioelectric potentials: Principles and interpretations of electro-encephalogram, electro-cardiogram and electro-retionogram

Dynamics of non-linear Processes: Physico-mathematical foundations of the dynamics of non-linear processes, phase plane method, different modes of excitations, nearly sinusoidal oscillations, building up of oscillations, effect of third harmonic distortion, Liapounov criteria of stability, limit cycles

PAPER I

Cell biology: Organization and structure of prokaryotes and eukaryotes, nucleus, cytoplasm, plasma membrane, mitochondria-structure, function respiratory chain and ATP synthesis, endoplasmic reticulum, golgi apparatus, membranes, ribosomes, peroxisomes, lysozomes, transcription and translation, transport of proteins, cancer and its molecular genetics, oncogenes, tumor suppression gene

Molecular biology: central dogma, genetic code, gene and operon, structure of DNA and RNA, plasmids, selectable markers, agarose gel, PCR, cloning PCR products, expression vectors, cell free translation, c- DNA libraries, genomic libraries, DNA micro arrays, DNA sequencing

Bioinformatics: Introduction, repositories, databases, pairwise sequence based alignment, relationship between sequence and structures, structural bioinformatics, genomics, proteomics, human genome project, software packages

Numerical methods: Introduction to numerical methods, solutions to non-linear algebraic equations by the method of iteration and Newton aphson method, numerical integration by trapezoidal rule and simpson’s rule, numerical solution of ordinary differential equations by picard’s method of successive approximation, Euler’s method and Runge-Kutta method

Dynamics of non-linear processes: Physico-mathematical foundations of the dynamics of non-linear processes, phase plane method, different modes of excitations, nearly sinusoidal oscillations, building up of oscillations, effect of third harmonic distortion, Liapounov criteria of stability, limit cycles

PAPER II

Elementary crystallography: Introduction, symmetry in crystals, lattices and unit cells, crystal systems, Bravais lattices, elements of symmetry- rotation axis, mirror planes and center of inversion, point group symmetry- monoaxial point groups, polyaxial point groups, translational symmetry- screw axis and glide planes, space group, equivalent points, X-ray diffraction and Bragg equation 

X-ray diffraction methods: scattering factor, structure factor expression, reciprocal lattice, Ewald’s sphere, electron density equation, phase problem, Patterson function, molecular replacement method, isomorphous replacement, refinement programs and interpretation of results, methods of data collection of crystal containing small molecule and large molecule, factors affecting the measurement of integrated intensities, photographic methods, diffractometers, area detectors and image plates.

Proteins : Purification, structure and function: twenty amino acids: structure and function, the peptide bond, primary structure of a protein: methods of sequence determination, forces determining protein structure, secondary structure of a protein: β strands, β sheets (parallel and anti parallel), β turns, α helix, 3.10 helix and π helix (differences), tertiary structure of a protein: protein folds-all alpha helix motifs (Lone helix, helix-turn-helix, four helix bundle and eight helix bundle), protein folds-all β sheet motifs (β sandwich, β barrel, greek Key topology and β propellars), protein folds- α / β motifs (Tim barrel, Rosman fold, α/β horseshoe), quaternary structure of a protein: macromolecular assemblies, domains and domain swapping, membrane proteins, purification methods, studies of proteins with MALDI-TOF, enzymes and enzyme kinetics, G-proteins and G-protein coupled receptors(GPCRs), proteins as targets for rational structure based drug design

Principles of nucleic acid structure: nucleotide structure and properties: Introduction to DNA, RNA, bases, sugars, phosphates, structure of nucleotide, nucleosides and polynucleotides and their nomenclature scheme. tautomerisation and ionization. genetic code. stereochemistry: nucleoside, torsion angles, sugar confirmation, NMR study, DNA structure: different types of DNA and their structure, DNA motifs, DNA repeats and their significance, function and stability, spectroscpic study of DNA: dye binding, interaction, denaturation, and renaturation of DNA, thermal denaturation and Tm value, RNA: structure and properties, different forms of RNA and their significance, alkaline hydrolysis of RNA, how it differs from DNA, role of 2’OH group, structure of phenylalanine tRNA, enzymes involved in molecular biology: DNA polymerase, RNA polymerase, reverse transcriptase, restriction endonuclease. DNA interaction: protein, dye, drugs and carcinogens, DNA replication: DNA polymerization, mutation, and DNA repair, DNA transcription: RNA synthesis, types of RNA polymerase, DNA polymorphism: repeats of DNA and their significance, single nucleotide polymorphism, c-DNA, cloning and expression and purification

Membrane Biology: Lipid structure and their organization, comparison of different membrane models, diffusion and permeability, different types of transport systems across membranes, liposome and its applications

Peptides-design, synthesis and applications: Introduction to peptides, peptide design, synthesis of peptides (solution phase and solid phase), protection and deprotection of amino and carboxyl group, unnatural amino acids, conformation of peptides, purification and crystallization of peptides, determination of structure of small molecules (briefly), application of peptides

PAPER III

Mathematical methods and their applications in biological systems: Ordinary differential equations of the first degree and first order (variable separable method, linear equation), linear differential equations of the second order with constant coefficients, the Laplace Transform, Inverse Laplace transform, application of Laplace transform to solutions of differential equations, Fourier series and their applications.

Quantum biology and its uses: Classical mechanics, Newton, Lagrange and Hamilton’s equations, Schrodinger’s equation and its complete solution for S.H.O, central force and angular momentum

Quantum chemistry: Atomic orbital models, the wave equation, molecular orbitals, the LCAO method, the overlap method, coulomb and resonance integrals, the hydrogen molecule, charge distributions, approximate methods.

Theoretical modeling of biomolecular systems: Basic principles of modeling, modeling by energy minimization technique, concept of rotation about bonds, energy minimization by basic technique for small molecules, Ramachandran plot, torsional space minimization, energy minimization in cartesian space, molecular mechanics-basic principle, molecular dynamics basic principles

Spectroscopic techniques: Introduction to spectroscopy, basic principles, instrumentation and applications of UV-VIS absorption, infrared, Raman, atomic absorption, fluorescence, circular dichroism, Laser spectroscopy, nuclear magnetic resonance, electron spin resonance, acoustic spectroscopy; solvent perturbation; difference spectroscopy; Fourier transform techniques; applications of Laser; mass spectroscopy.

PAPER I

Cell biology: Organization and structure of prokaryotes and eukaryotes, nucleus, cytoplasm, plasma membrane, mitochondria-structure, function respiratory chain and ATP synthesis, endoplasmic reticulum, golgi apparatus, membranes, ribosomes, peroxisomes, lysozomes, transcription and translation, transport of proteins, cancer and its molecular genetics, oncogenes, tumor suppression gene

Molecular biology: central dogma, genetic code, gene and operon, structure of DNA and RNA, plasmids, selectable markers, agarose gel, PCR, cloning PCR products, expression vectors, cell free translation, c- DNA libraries, genomic libraries, DNA micro arrays, DNA sequencing

Bioinformatics: Introduction, repositories, databases, pairwise sequence based alignment, relationship between sequence and structures, structural bioinformatics, genomics, proteomics, human genome project, software packages

Numerical methods: Introduction to numerical methods, solutions to non-linear algebraic equations by the method of iteration and Newton aphson method, numerical integration by trapezoidal rule and simpson’s rule, numerical solution of ordinary differential equations by picard’s method of successive approximation, Euler’s method and Runge-Kutta method

Dynamics of non-linear processes: Physico-mathematical foundations of the dynamics of non-linear processes, phase plane method, different modes of excitations, nearly sinusoidal oscillations, building up of oscillations, effect of third harmonic distortion, Liapounov criteria of stability, limit cycles

PAPER II

Elementary crystallography: Introduction, symmetry in crystals, lattices and unit cells, crystal systems, Bravais lattices, elements of symmetry- rotation axis, mirror planes and center of inversion, point group symmetry- monoaxial point groups, polyaxial point groups, translational symmetry- screw axis and glide planes, space group, equivalent points, X-ray diffraction and Bragg equation 

X-ray diffraction methods: scattering factor, structure factor expression, reciprocal lattice, Ewald’s sphere, electron density equation, phase problem, Patterson function, molecular replacement method, isomorphous replacement, refinement programs and interpretation of results, methods of data collection of crystal containing small molecule and large molecule, factors affecting the measurement of integrated intensities, photographic methods, diffractometers, area detectors and image plates.

Proteins : Purification, structure and function: twenty amino acids: structure and function, the peptide bond, primary structure of a protein: methods of sequence determination, forces determining protein structure, secondary structure of a protein: β strands, β sheets (parallel and anti parallel), β turns, α helix, 3.10 helix and π helix (differences), tertiary structure of a protein: protein folds-all alpha helix motifs (Lone helix, helix-turn-helix, four helix bundle and eight helix bundle), protein folds-all β sheet motifs (β sandwich, β barrel, greek Key topology and β propellars), protein folds- α / β motifs (Tim barrel, Rosman fold, α/β horseshoe), quaternary structure of a protein: macromolecular assemblies, domains and domain swapping, membrane proteins, purification methods, studies of proteins with MALDI-TOF, enzymes and enzyme kinetics, G-proteins and G-protein coupled receptors(GPCRs), proteins as targets for rational structure based drug design

Principles of nucleic acid structure: nucleotide structure and properties: Introduction to DNA, RNA, bases, sugars, phosphates, structure of nucleotide, nucleosides and polynucleotides and their nomenclature scheme. tautomerisation and ionization. genetic code. stereochemistry: nucleoside, torsion angles, sugar confirmation, NMR study, DNA structure: different types of DNA and their structure, DNA motifs, DNA repeats and their significance, function and stability, spectroscpic study of DNA: dye binding, interaction, denaturation, and renaturation of DNA, thermal denaturation and Tm value, RNA: structure and properties, different forms of RNA and their significance, alkaline hydrolysis of RNA, how it differs from DNA, role of 2’OH group, structure of phenylalanine tRNA, enzymes involved in molecular biology: DNA polymerase, RNA polymerase, reverse transcriptase, restriction endonuclease. DNA interaction: protein, dye, drugs and carcinogens, DNA replication: DNA polymerization, mutation, and DNA repair, DNA transcription: RNA synthesis, types of RNA polymerase, DNA polymorphism: repeats of DNA and their significance, single nucleotide polymorphism, c-DNA, cloning and expression and purification

Membrane Biology: Lipid structure and their organization, comparison of different membrane models, diffusion and permeability, different types of transport systems across membranes, liposome and its applications

Peptides-design, synthesis and applications: Introduction to peptides, peptide design, synthesis of peptides (solution phase and solid phase), protection and deprotection of amino and carboxyl group, unnatural amino acids, conformation of peptides, purification and crystallization of peptides, determination of structure of small molecules (briefly), application of peptides

PAPER III

Mathematical methods and their applications in biological systems: Ordinary differential equations of the first degree and first order (variable separable method, linear equation), linear differential equations of the second order with constant coefficients, the Laplace Transform, Inverse Laplace transform, application of Laplace transform to solutions of differential equations, Fourier series and their applications.

Quantum biology and its uses: Classical mechanics, Newton, Lagrange and Hamilton’s equations, Schrodinger’s equation and its complete solution for S.H.O, central force and angular momentum

Quantum chemistry: Atomic orbital models, the wave equation, molecular orbitals, the LCAO method, the overlap method, coulomb and resonance integrals, the hydrogen molecule, charge distributions, approximate methods.

Theoretical modeling of biomolecular systems: Basic principles of modeling, modeling by energy minimization technique, concept of rotation about bonds, energy minimization by basic technique for small molecules, Ramachandran plot, torsional space minimization, energy minimization in cartesian space, molecular mechanics-basic principle, molecular dynamics basic principles

Spectroscopic techniques: Introduction to spectroscopy, basic principles, instrumentation and applications of UV-VIS absorption, infrared, Raman, atomic absorption, fluorescence, circular dichroism, Laser spectroscopy, nuclear magnetic resonance, electron spin resonance, acoustic spectroscopy; solvent perturbation; difference spectroscopy; Fourier transform techniques; applications of Laser; mass spectroscopy.