## Thursday, November 15, 2007

### M.SC BIOPHYSICS

BIOPHYSICS — M Sc

I. Molecular Biology, Radiation Biophysics, Electronics and Dynamics of Nonlinear Processes

II. Molecular Biophysics: X-ray Crystallography, Spectroscopy, Proteins, Viruses, Nucleic Acids And

Membranes.

III. Mathematical Methods, Quantum Chemistry, Theoretical Modeling And Microsocopy.

IV. Laboratory Experiments.

PAPER – I

MOLECULAR BIOLOGY, RADIATION BIOPHYSICS, ELECTRONICS AND

DYNAMICS OF NONLINEAR PROCESSES

CELL AND MOLECULAR BIOLOGY

Central Dogma, Genetic code, gene and operon, Structure of DNA and RNA, extrachromal elements,

plasmids, selectable markers, gel electrophoresis, polymerase chain reaction (PCR), cloning PCR products,

expression vectors, DNA sequence analysis, cDNA libraries, genomic libraries, applications of molecular

biology methods, using internet resources in molecular biology

RADIATION BIOPHYSICS

Interaction of radiation with matter, ionizing radiation,nonionizing radiation, free radicals, ion pairs,

radiation units and dosimetry, dose effect graphs and target theory, direct and indirect radiation action,

radiation on proteins, nucleic acids, carbohydrates, cell and whole organism, genetic effects of radiation,

repair of radiation induced damage, radiation in diagnosis and therapeutics, protection from radiation.

ELECTRONICS

Passive circuit components, series and parallel circuits, circuit theory, power supplies, amplifiers, emitter

followers, oscillators and basic digital circuits.

10 Syllabus M Sc / M Biotech — AIIMS

DYNAMICS OF NONLINEAR PROCESSES

Physico-mathematical foundations of the dynamics of nonlinear 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

MOLECULAR BIOPHYSICS (X-RAY CRYSTALLOGRAPHY,

SPECTROSCOPY, PROTEINS, VIRUSES, NUCLEIC ACIDS AND

MEMBRANES)

X-RAY CRYSTALLOGRAPHY

X-ray Diffraction

Structure factor expression, electron density equation, phase problems, Patterson function, molecular

replacement method, heavy atom method, isomorphous replacement method, refinement procedure and

interpretation of results.

Data Collection

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.

SPECTROSCOPY

UV, IR, Raman ORD and CD, spectroscopy, basic principles, instrumenation and use. NMR/ESR:

classical description of magnetic resonance in terms of precession moments, relaxation process, Bloch

equation for line width and shape, spin Hamiltonian, ESR spectrometer, spin labelling in biological

molecules, NMR: spectrometer instrumentation, pulsed and Fourier transformed NMR, scalar and dipolar

broadening, line multiplicity, ring current shifts factors affecting relaxation time, Karplus equation and

use of NMR for conformational study, MÃ¶ssbauer spectroscopy, resonance absorption in biological

samples. Line shape, line width, chemical shifts, quardruple and magnetic splitting in MÃ¶ssbauer spectra

of biological molecules.

PROTEINS

Stability of protein structures: flexibility, reversible folding and unfolding, pH titration, chemical

denaturation, thermal denaturation solvent perturbation and chemical modification

Prediction of protein structures: circular dichroism, NMR Methods, Structure-function relationship,

catalysis, Study of three dimensional structures of Trypsin, Trypsinogen, Antibody molecules.

NUCLEIC ACIDS

Introduction of nucleic acids, definition of terms for nucleic acids, old nomenclature, IUPAC-IUB

nomenclature. Basis of Watson Cricks original model Different, base- pairing schemes Unsatisfactory

Course and Curriculum of Biophysics 11

nature of Hoogsteen and other base pairing schemes, biological implication of Watson Crick base pairing

scheme refinement of Watson-Crick model by linked- atom least squares, fiber X- ray diffraction studies,

single crystal X-ray diffraction, and NMR studies on mono- and oligo- nucleotides, DNA polymorphism,

parameters for A-, B-, C-, D- and Z-DNA, definitions of roll, tilt and propeller twist, spectroscopic

study of DNA polymorphism, interaction of DNA with proteins, drugs, dyes and carcinogens, experimental

and theoretical studies on base stacking, hydrogen bonding interactions, structure of RNA, basic

differences between DNA and RNA structures, structure of yeast phenylalanine tRNA.

MEMBRANES

Lipid structure and their organization, phase transitions in lipids, polysaccharides, molecular shapes and

the conformation, comparison between different membrane models, diffusions and permeability, carrier

transport, ion transport, active and passive transport, ion pumps, water transport, use of liposomes for

membrane models and drug delivery systems.

PAPER III

MATHEMATICAL METHODS, QUANTUM BIOLOGY AND MICROSCOPY

MATHEMATICAL METHODS

Review of Fourier Series, Laplace transforms, transforms of derivatives, properties of Laplace transform,

solution of linear ordinary differential equation with Laplace transforms, Fourier transforms, solution of

partial differential equation with method of separation of variables.

QUANTUM CHEMISTRY

Atomic orbital models, the wave equation, molecular orbitals, the LCAO method the overlap, Coulomb

and resonance integrals, the hydrogen molecule, charge distributions, approximate methods.

Theoretical modeling

Basic principle of modeling, Modeling by energy minimization technique, Concept of rotation about

bonds, Energy minimization basic technique for small molecules. Ramachandran plot, Torsional space

minimization. Energy minimization in Cartesian space. Molecular mechanics basic principle. Molecular

dynamics basic principles.

MICROSCOPY

Optical Microscopy

Theory and use of light, fluorescence, phase and polarising microscopes, selection of suitable samples,

and observation in different optical systems, study of living cells, principle and techniques of

photomicroscopy, applications and limitations of optical microscopy.

Electron Microscopy

Principle of electron microscopes, preparation of samples, interpretation of ultrastructure and cell function,

confocal microscopy, atomic force microscopy.

12 Syllabus M Sc / M Biotech — AIIMS

LABORATORY EXPERIMENTS

1. Study of peptide/ligand DNA interaction

2. The determination of unit cell constants and space group of a given Crystal using Weissenberg

method.

3. The determination of unit cell constants and space group of given crystal by precession method

using a layer line screened photgraph.

4. Crystallization of Lysozyme and examination of its crystals in the polarizing microscope.

5. Urea Denaturation of protein

6. (a) Conformational energy plot for tripeptide or dinucleotide monophosphates and obtain lowest

energy conformation.

(b) Determine the geometric parameters for the obtained conformation.

7. Molecular weight determination by SDS PAGE.

8. Plasmid isolation.

9. DNA Electrophoresis

10. PCR

I. Molecular Biology, Radiation Biophysics, Electronics and Dynamics of Nonlinear Processes

II. Molecular Biophysics: X-ray Crystallography, Spectroscopy, Proteins, Viruses, Nucleic Acids And

Membranes.

III. Mathematical Methods, Quantum Chemistry, Theoretical Modeling And Microsocopy.

IV. Laboratory Experiments.

PAPER – I

MOLECULAR BIOLOGY, RADIATION BIOPHYSICS, ELECTRONICS AND

DYNAMICS OF NONLINEAR PROCESSES

CELL AND MOLECULAR BIOLOGY

Central Dogma, Genetic code, gene and operon, Structure of DNA and RNA, extrachromal elements,

plasmids, selectable markers, gel electrophoresis, polymerase chain reaction (PCR), cloning PCR products,

expression vectors, DNA sequence analysis, cDNA libraries, genomic libraries, applications of molecular

biology methods, using internet resources in molecular biology

RADIATION BIOPHYSICS

Interaction of radiation with matter, ionizing radiation,nonionizing radiation, free radicals, ion pairs,

radiation units and dosimetry, dose effect graphs and target theory, direct and indirect radiation action,

radiation on proteins, nucleic acids, carbohydrates, cell and whole organism, genetic effects of radiation,

repair of radiation induced damage, radiation in diagnosis and therapeutics, protection from radiation.

ELECTRONICS

Passive circuit components, series and parallel circuits, circuit theory, power supplies, amplifiers, emitter

followers, oscillators and basic digital circuits.

10 Syllabus M Sc / M Biotech — AIIMS

DYNAMICS OF NONLINEAR PROCESSES

Physico-mathematical foundations of the dynamics of nonlinear 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

MOLECULAR BIOPHYSICS (X-RAY CRYSTALLOGRAPHY,

SPECTROSCOPY, PROTEINS, VIRUSES, NUCLEIC ACIDS AND

MEMBRANES)

X-RAY CRYSTALLOGRAPHY

X-ray Diffraction

Structure factor expression, electron density equation, phase problems, Patterson function, molecular

replacement method, heavy atom method, isomorphous replacement method, refinement procedure and

interpretation of results.

Data Collection

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.

SPECTROSCOPY

UV, IR, Raman ORD and CD, spectroscopy, basic principles, instrumenation and use. NMR/ESR:

classical description of magnetic resonance in terms of precession moments, relaxation process, Bloch

equation for line width and shape, spin Hamiltonian, ESR spectrometer, spin labelling in biological

molecules, NMR: spectrometer instrumentation, pulsed and Fourier transformed NMR, scalar and dipolar

broadening, line multiplicity, ring current shifts factors affecting relaxation time, Karplus equation and

use of NMR for conformational study, MÃ¶ssbauer spectroscopy, resonance absorption in biological

samples. Line shape, line width, chemical shifts, quardruple and magnetic splitting in MÃ¶ssbauer spectra

of biological molecules.

PROTEINS

Stability of protein structures: flexibility, reversible folding and unfolding, pH titration, chemical

denaturation, thermal denaturation solvent perturbation and chemical modification

Prediction of protein structures: circular dichroism, NMR Methods, Structure-function relationship,

catalysis, Study of three dimensional structures of Trypsin, Trypsinogen, Antibody molecules.

NUCLEIC ACIDS

Introduction of nucleic acids, definition of terms for nucleic acids, old nomenclature, IUPAC-IUB

nomenclature. Basis of Watson Cricks original model Different, base- pairing schemes Unsatisfactory

Course and Curriculum of Biophysics 11

nature of Hoogsteen and other base pairing schemes, biological implication of Watson Crick base pairing

scheme refinement of Watson-Crick model by linked- atom least squares, fiber X- ray diffraction studies,

single crystal X-ray diffraction, and NMR studies on mono- and oligo- nucleotides, DNA polymorphism,

parameters for A-, B-, C-, D- and Z-DNA, definitions of roll, tilt and propeller twist, spectroscopic

study of DNA polymorphism, interaction of DNA with proteins, drugs, dyes and carcinogens, experimental

and theoretical studies on base stacking, hydrogen bonding interactions, structure of RNA, basic

differences between DNA and RNA structures, structure of yeast phenylalanine tRNA.

MEMBRANES

Lipid structure and their organization, phase transitions in lipids, polysaccharides, molecular shapes and

the conformation, comparison between different membrane models, diffusions and permeability, carrier

transport, ion transport, active and passive transport, ion pumps, water transport, use of liposomes for

membrane models and drug delivery systems.

PAPER III

MATHEMATICAL METHODS, QUANTUM BIOLOGY AND MICROSCOPY

MATHEMATICAL METHODS

Review of Fourier Series, Laplace transforms, transforms of derivatives, properties of Laplace transform,

solution of linear ordinary differential equation with Laplace transforms, Fourier transforms, solution of

partial differential equation with method of separation of variables.

QUANTUM CHEMISTRY

Atomic orbital models, the wave equation, molecular orbitals, the LCAO method the overlap, Coulomb

and resonance integrals, the hydrogen molecule, charge distributions, approximate methods.

Theoretical modeling

Basic principle of modeling, Modeling by energy minimization technique, Concept of rotation about

bonds, Energy minimization basic technique for small molecules. Ramachandran plot, Torsional space

minimization. Energy minimization in Cartesian space. Molecular mechanics basic principle. Molecular

dynamics basic principles.

MICROSCOPY

Optical Microscopy

Theory and use of light, fluorescence, phase and polarising microscopes, selection of suitable samples,

and observation in different optical systems, study of living cells, principle and techniques of

photomicroscopy, applications and limitations of optical microscopy.

Electron Microscopy

Principle of electron microscopes, preparation of samples, interpretation of ultrastructure and cell function,

confocal microscopy, atomic force microscopy.

12 Syllabus M Sc / M Biotech — AIIMS

LABORATORY EXPERIMENTS

1. Study of peptide/ligand DNA interaction

2. The determination of unit cell constants and space group of a given Crystal using Weissenberg

method.

3. The determination of unit cell constants and space group of given crystal by precession method

using a layer line screened photgraph.

4. Crystallization of Lysozyme and examination of its crystals in the polarizing microscope.

5. Urea Denaturation of protein

6. (a) Conformational energy plot for tripeptide or dinucleotide monophosphates and obtain lowest

energy conformation.

(b) Determine the geometric parameters for the obtained conformation.

7. Molecular weight determination by SDS PAGE.

8. Plasmid isolation.

9. DNA Electrophoresis

10. PCR

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