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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, Mössbauer spectroscopy, resonance absorption in biological
samples. Line shape, line width, chemical shifts, quardruple and magnetic splitting in Mössbauer 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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