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MSc Biophysics Syllabus Mumbai University by munotes
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UNIVERSITY OF MUMBAI
Syllabus for the M.Sc. Part - I
Program: M.Sc.
Course: Biophysics
(Chose Based credit System with effect from the
academic year 2016–2017)
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Preamble
The subject of Biophysics is one of the important interdisciplinary areas in teaching, training and learning
which is considered to be important in terms of human resource development and National development.
Biophysics is the physics of life phenomenon studied at all level, from molecules and cell to the biosphe re as
whole. It is the branch of knowledge that applies the principles of physics and chemistry and the methods of
mathematical analysis and computer modeling to understand how biological systems work.
The main emphasis of biophysics is on the quantitative analysis of the physical and chemical aspects of the
functions of biological molecules, organisms and entities. The techniques and methodologies that biophysics
relies on are closer to Physics and Chemistry, but areas of application are in the biological, medical and
related sciences
Biophysicists use mainly that technique includes UV visible spect roscopy, Gel electrophoresis, X-ray
crystallogr aphy, macrocalorimetry, Atomic F orce Microscopey , FTIR , Raman, SPR, NMR, Fluorescence
spectroscopy, Fluorescence Microscopy & spectroscopy , hydrodynamics techniques etc., are used to study
problem in exciting areas in biophysics ranging from structure aided drug design to cell signalling and transcriptional silencing etc. Biophysicist’s are employed in Universities, R & D industry, Medical
centres/Colleges, Rese arch Inst itutes and Government Organisation etc.
The two year programme of M.Sc. (Biophysics) is prescribed according to the choice based credit system of
the University of Mu mbai from the academic year 2016 -17. The course has been divided in to four
seme sters. The program has a total of 14 core papers, 14 number of laboratory courses , research project s,
review of literature and elective papers like Virology, Bacteriology, Medicine chemistry & drug design,
Ethics and IPR etc. Invited lectures by subject exper t in various areas as well as seminars and workshops
add value to the course and enhance their potential. In addition the students are encouraged to attend
seminars outside the department as well as attend summer internship in prestigious lab oratories in India as
well as abroad.
The programme endeavours to provide students a broad based training in Biophysics with strong background
of basic concepts as well as exposing them to recent advances in the field. The programme is focussed on
recent development s in the areas of biophysics. In addition, the oretical knowledge, significant emphasis has
been given to provide hands on experience to the students in the frontier areas of Biophysics. A
multidisciplinary approach has been employed to provide best leverag e to students to enable them to move
into advance d and frontier areas of biological research in future. Another important feature of course is that
a sufficient number of electi ve papers have been introduced as results student may particular subject of their
interest. Hence, apart from the core and elective papers an additional paper is introduced on soft skill as per
the guideline given by U niversity of Mumbai. This will enable the addition of new dimension in learning
and research skill of stud ents.
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Revised syllabus of M.Sc. Biophysics
(Choice Based Credit system )
Semester I
Paper code Paper nomenclature Lectur
es Credit Practical /Labor
atory course Hrs Credit Total
Credit
BP-CCT 101 General physic o-chemical
Principles 60 04 Lab course
(BP-LBC )
101 60 02 06
BP-CCT 102 Biomathematics &
Biostatistics 60 04 Lab course
(BP-LBC )
102 60 02 06
BP-CCT 103 Cellular Biophysics 60 04 Lab course
(BP-LBC )
103 60 02 06
BP-CCT 104 Methods in Biophysics 60 04 Lab course
(BP-LBC )
104 60 02 06
Total 24
Semester II
BP-CCT 201 Membrane Biophysics &
Ion channels 60 04 Lab course
(BP-LBC )
201 60 02 06
BP-CCT 202 Molecular Biophysics 60 04 Lab course
(BP-LBC )
202 60 02 06
BP-CCT 203 Biochemistry 60 04 Lab course
(BP-LBC )
203 60 02 06
BP-CCT 204 Recombinant DNA
Technology & Protein
Engineering 60 04 Lab course
(BP-LBC )
204 60 02 06
Total 24
Semester III
Paper code Paper nomenclature Lectur
es Credit Practical
Paper Hrs Credi
t Total Credit
BP-CCT 3 01 Core Core theory 60 04 Lab course
(BP-LBC )
301 60 02 06
BP-CCT 3 02 Core Core theory 60 04 Lab course
(BP-LBC ) 60 02 06
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302
BP-CCT 3 03 Core Core theory 60 04 Lab course
(BP-LBC )
303 60 02 06
Literature
review /
research
project 60 02 02
BP-ELC 301 Elective -1 30
02
BP-ECL 302 Elective -2 30 02
BP-ELC 302
Elective -3, 4.........n 30 02
Total 20+4* =24
(*electives)
Seme ster IV
BP-CCT 201 Core Core theory 60 04 Lab course
401 60 02 06
BP-CCT 202 Core Core theory 60 04 Lab course
402 60 02 06
BP-CCT 203 Core Core theory 60 04 Lab course
403 60 02 06
Research
project 02 02
BP-ELC 401 Elective -1 30
02
BP-ELC402
Elective -2 30 02
BP-ECL 403 Elective -3 ,4.....n 30 02
20+ 04* =24
(*electives)
No of credit: M.Sc. I ( Sem I & II) = 48
No of credit MSc II ( Sem III & IV) = 40
No of credit for electives ( Sem III & IV) = 08
Total credits: = 96
BP-CCT: Biophysics core course theory
BP-ELC: Biophysics elective course
BP-LBC : Biophysics Lab course
Evaluation : The students will be evaluated internally and externally. The intern al evaluation is done by
teacher s and external evaluation done by the committee appointed by the Universit y norms. Standard
passing and scale as per the university norms.
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Syllabus details Semester I
Course Code Title Credits
BP-CCT 101 General Physico -chemical Principles
Total lectures: 60 04
Unit I: Structure and Bonding
The electronic structure of atom, Ionic bond, Covalent bonds, Hydrogen bonds Van
der Waal s forces, Electric dipoles, Polarization and induced Dipoles, Casimir
interactions. General understanding of Quantum mechanics, Pauli Exclusion
Principle, Ionization energy, Electron affinity and Chemical bonding,
Electronegativity and strong bond, Secondar y bonds.
Interatomic potentials for strong bonds, Interatomic potential for weak b onds, Non-
central forces, Bond energies, Spring constants. ( 15L)
Unit II: Thermodynamics & Princ iples of kinetics and Molecules
Thermodynamic equilibrium, laws of thermodynamics and living system, Entropy,
Enthalpy and free energy, Internal energy, Carnot cycle, Chemical potential,
Oxidation reduction potential. 0th, Ist, 2nd& 3rd order reaction, Activation energy and
Rate constant, Diffusion, Osmosis, Osmotic pressure, Osmoregulation, Surface
tension, Dialysis, Adsorption, Viscosity, Thermal conduction, Sedimentation
filtration of biological fluid, Hydropathy, Biological importance o f hydropathies.
Precipitation, B iological significance of precipitation, Colloids & their types, Kine tic
& electrical properties of c olloids, Stability of c olloids, Gibbs Donnan Equilibrium in
living systems. 15L
Unit III: Solvent, Solute & Solution in Biological S ystem
Liquids, Solvents, Solubility, Saturated and unsaturated Solutions, Super saturated
solutions, D ilute and c oncentrated solution, types of solutions, Methods of expression
of concentration of solution, Molality, Mole fraction.
Hydrogen ion concentration, Dissociation of water, (water as electrolyte ),
concentration of equilibrium, Mechanisms of Ionization and Characterization, Acid
& Basic solutions, pH and its biological importance, General concept of acid, bases
and their dissociation constant, Bronsted -Lowry theor y, Inductive effect of groups on
acid strength, (Carboxyl group, Carbonyl group). Salts & their characteristics &
importance in biological system.
Biological Importance of Acids & Bases , Biological & buffering system, Buffer
solution, mechanism of buffer a ction, Factors influencing buffer capacity and pH,
Henderson and Hasselbad ch equation, Buffer system s in the body. (Bicarbonate,
Phosphate, Protein buffer, Ammonia buffer, etc.) 15L
Unit IV: Radioactivity
Energy of Radiation, Radioactive emission, α -ray, β -ray, ϒ-ray, and their properties,
detection of nuclear radiation, Geiger -Muller counter, Proportional counter,
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Course Code Title Credits
BP-CCT 102 Biomathematics & Biostatistics
Total lectures: 60 04
Unit I: Biomathematics
Limits of functions, derivatives of functions. Probability Calculation , Differential and
integral calculus , Derivative and its physical significance, basic rules for
differentiation (Without d erivation) Maximum and Minimum their application in
chemistry , Geometric meaning of integration, application in biology and chemistry .
(15L )
Unit II: Biostatistics I
1. Introduction, scope, application and use of statistics, collection and classification
Of data, census and sampling, graphs and diagrams, arithmetic mean, med ian standard
Deviation.
2.Correlation and regression for ungrouped data, scatter diagram, calculation and
interpretation of correlation coefficient, linear regression coefficients and equation of
the Lines of regression, nonlinear relationship transforma ble to liner form (Y=Abx,
Yaxb)
3. Probability, definition, addition and multiplicative laws (without proof). Random
variable and its distribution, binominal probability distr ibution, examples and
condition s means and variances, continuous variable, norm al distribution, use of
normal probability table for finding probabilities. (15L)
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Unit III: Biostatistics II:
1. Population parameter and sample statistics, sampling techniques, simple random
sampling stratified random sampling, systematic sampling standard error of mean.
2. Estimation, Point & interval, confidence interval for proportion. Scintillation counter, Liquid Scintillation counter, Crystal counter, Radioactive
decay, (α, β,decay), Half -life, Units of measurements of radioactivity, types of
radioactivity, Isotopes, Isobar, Isotones and their characteristics. Radioactive
equilibrium, Variety of isotopes, Radioactive isotopes, Nuclear reaction and
production of artificial ra dioactivity, Autoradiography. 15L
References:
1. Physical Chemistry for Life Sciences,Peter Atkins and Julio de Paula, 2006, Oxford
Press
2. Introduction to Biophysics by Cortell
3. Molecular and Cellular Biophysics, Meyer B Jackson (2006), Cambridge)
4. Tex Book of Biophysics , R N Roy, New Central Agency (P) Ltd, Culcutta
5. Physical Chemistry for the Biosciences, Raymond Chang,(2004), University book
Science Biological Thermodyanamics, Donald, T Hayine, (2007), Cambridge
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3.Hypothesis attesting, Type I and Type II errors levels of significance, one -tailed and
two tailed test, application to single proportion, equality of the population
means and two population proportions.
4. Chi -square test for independent attributes in r x c table, special case of 2 x 2 tables.
5. Students test for significance of correlation coefficient y for p=0 (small sample test)
( 15L)
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Unit IV: Biostatistics III
1.Fishers z transformation coefficient for getting yp -0 in large samples test of
significance for y (p=0)
2..Design of experiment: Principle and concepts of completely randomized design,
randomized block design and Latin square design,
3.variance ratio F -test-Analysis of variance in one -way classification .
4.Non -parametric test: Distribution -free method, sign test for method pairs, Wilcoxon
test for unpaired data Run test. (15L)
References :
1. Biostastistics:A foundation for analysis in the Health Sciences, 7th Ed.(1998) Wayne D,
Wiley
2. DNA Microarrays, David Bowtell & J Sambrook (2002), CSHL Press
3. Principles of Statistics, 2nd Ed. M Pagano & K Gauvreau (2007), Thomson Publ
Course Code Title Credits
BP-CCT 103 Cellular Biophysics
Total lectures: 60 04
Unit I : General organization of cells
Origin a nd evolution of cell, shape and size of cell; General organization of
prokaryotic and eukaryotic organism s basic concepts and their detailed structure and
functions, Prokaryotic cell wall, Eukaryotic cell wall, their functions, ribosomes,
physical and bi ological properties of protoplasm. Cytoskeleton – basic components,
properties and functions in prokaryotic and eukaryotic cells.
(15L)
Unit II: Cell Differentiation
Cell differentiation, localization of cytoplasm determinants in eggs, localization of
yolk and cytoplasm in different types of cells, Nucleocytoplasmic interaction and cell
function, Extracellular matrix – its development, mechanism of alpha adrenergic and
related response, modulation of extracellular m atrix by tumor cells – Fibroblast
interactions, growth factors in culture d cells – early cytoplasm , single and
cytoskeleton response; Role of cytoskeleton in maintaining cell -shape, contraction,
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behavior, apoptosis and mortality, impact of xenobiotic on th e components of
cytoskeleton. (15L)
Unit III: Cell growth and cell d ivision
Kinetics o f cell growth, role of protein kinase in cell growth, cell cycle, cell cycle
events G 1, S, G 2, cytokines, control of cell cycle in dividing and non- dividing cells,
synchronization of cell growth, cell transformation, malignant tumor growth,
apoptosis. In tra and extracellular factors and signals affecting cell growth, cell
division, cellular behavior during cytokinesis, chemotaxis and asymmetrical cell
division. ( 15L)
Unit IV : Cell -Cell Communication
Strategies of chemical signaling: endocrine, paracrine and synaptic. Signaling
mediated by intracellular receptors: mechanism of transduction by cell surface
receptor protein, role of calmodulin, Ca lcium and cyclic nucleotides, phosphoinositol
cycle, sodi um proton exchanger, molecular events involved during sperm -ovum (egg)
interaction, implications and the mechanisms of sperm -zone interaction, role of
soluble factors produced by follicle somatic cells on gamete interactions, factors
influencing sperm –ovu m (egg) recognition and binding, m orphological intercellular
connections in different types of cell and tissues. (15L)
References :
1. Molecular Biology of the Cell , Bruce Albert, Alexander Jhonson et al (2002),
Taylor & Francis Group.
2. The Cell Molecular Approach, G Cooper & R Hausman (2007) ASM Press
3. Molecular Biology , D Roberties, 8th Ed. SAE
4. Biochemistry by Strayer
5. Introduction to Biological Membrane, D Chapman
6. Molecular Cell Biology, Lodish
7. Molecular and Cellular Biophysics, Meyer B Jackson (2006), C ambridge)
Course Code Title Credits
BP-CCT 104 Methods in Biophysics
Total lectures: 60 4
Unit I: Spectroscopy
Principle, instruments and application of spectroscopic instruments: UV Visible: absorption
of light, radiation sources, sample holders, monochroamtors, radiation detectors, singl e and
double beam instruments, c olorimeter. IR spectroscopy: Rotational and vibration spectra,
Instrumental features, applications. Raman effect, strokes and anti -strokes lines, advantages,
applications. CD ORD principles and applications. Fluorescence: Fluorescence and
phosphorescence , bioluminescence and chemiluminiscence phenomenon, quenching, energy
transfer, and applications. Atomic absorption spectroscopy: Principle and instrumentations.
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(15L)
Unit II: Microscopy
Principle, instrumentation and application of m icroscopy, image formation,
magnification, resolving power. optimum resolution, image defects, d ifferent types
of Micr oscopy: Dark field ,Phase contrast, polarization microscopy, Interference
microscopy, Fluorescence microscopy, Electron m icroscopy: Electron guns, Electron
lens, electrostatic focussing, magnetic focussing, SEM, STEM, Atomic force
microscopy. (15L)
Unit III: Separation techniques I
Electrokinetics methods: electrophoresis, electrophoretic mobility (EPM), factors
affecting EPM, Paper, PAGE, SDS-PAGE, Disc gel, gradient gel, electrophoresis of
nucleic acid and its application, Pulse field electrophoresis, singl e cell gel
electrophoresis, Isolectrophoresis, preparative electrophoresis, 2- D gel
electrophoresis, Capillary, Iso -Electric focusing, applications in biology and
medicine. Chromatography, TLC, adsorption, partition, ion exchange , gel filtration,
affinity and FPLC, GLC
(15L)
Unit I V: Separation techniques II
HPLC: mobile phase systems, modes of operations, app lication, Hydrodynamics
method :fundamental principles’ Centrifugation: principle , preparative centrifuge,
analytical, ultracentrifuge, sedimentation and diffusion, Ultracentrifugation and their
applications in molecular weight, size determination. Viscosity and its application ,
dialysis, solvent fractionation, isoelectric precipitation,
( 15L)
References
1. Methods in Molecular Biophysics, Igor N S, N Zaccai & J Zaccai, (2007)
Cambridge
2. Principle of Biochemistry, D Voet, J Voet and CW Pratt, 3rd Ed,
3. DNA Clonning, Grover Vol. I, II, III
4. Advanced Methods in Protein Microsequencing, Witmann
5. Essential Biophysics, Narayanan, New Age Publ
6. Handbook of Molecular Biophysics (Methods & Application), 2009, HG Bohr,
Wiley
Syllabus details Semester II
Course Code Title Credits
BP-CCT 201 Membrane Biophysics & Ion channels
Total lectures: 60 4
Unit I :: Membrane structure and Models
Membrane architecture, Lipid vesicles and planar bilayer membrane, m embrane
permeability, transmembrane helices, hydropath Plot , Membrane asymmetry,
Membrane fluidity, Functiona l reconstitution of membranes. Models of membrane
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fusion: bilayer fusion, viral fusion, cellular fusion, SNAREs, cell -cell fusion, fusion
in mitochondria , Lipid bilayer and early models , Fluids mosaic model, Evidence from
model system and biomembranes. Membrane Channels, voltage gated channels,
ligand gated channels, channel conductance,
( 15L)
Unit II: Physic s of membrane
Membrane deformations: bending, sharing shape fluctuation etc, Differential
geometry of membranes, Elastic properties, Elastic constants, Charge -induced
microstructures and domain. Hysteresis of domain s formation , Lateral phase
separation, Critical c oncentration s fluctuation, selective lipid protein interactions,
Membrane melting. (15L)
Unit III: Membrane transport
Transport system with non- electrolytes and electrolytes. Transpor t with chemical
reaction system: Primary and secondary active transport. Transport s of molecules by
simple and facilitated diffusion , Transport by flux coupling. Transport by
phosphotransferase system, Transport by vesicle formation, Ionophores, epithelial
transport.
Electron T ransport & oxidative phosporylation: Reduction potential and free energy
changes in redox reaction, organization of electron treansport chain, chemiosmotic
coupling, proton gradient drive and synthesis of ATP, P/O ratio for oxidative
phosporylation, Cytosolic NADH electron feeding into electron transfer.
( 15L)
Unit IV : Electrical properties of membranes & Lipid Membrane Technology
Cell surface charge, Resting membrane potential, Action potential, properties of
action potential, Nernst equation, Goldman equation, Nernst -Plank equation,
Hodgkin- Huxely equation, Hodking- Kartz experiment, Voltage clamp, Na+, K+
conductance, Membrane impedance and capacitance, Transmembrane potential, Zeta,
stern and total electrochemical potential, Chemical synapse, post synaptic potential,
Historical perspective of lipid model systems lipid monolayer. Liposomes: small and
large unilamellar and multilamellar v esicles, planner lipid bilayer, Application of
liposomes in biology and medicine. ( 15L)
References :
1. Molecular & Cellular Biology, D Roberties,
2. Biophysical Aspects of Transmembrane signaling, Sandor D (2005), Springer
3. Biophysics, Vasant Pattabhi, Gautam (2002), Narosa
4. Biomembrane structure and Function, Chapman D.
5. Introduction to Biological Membrane, Jain R K
6. Biophysics, Hopp, Lohman, Mark and Ziegler
7. Advances in Biophysics, Vol 18, 15
8. Molecular and Cellular Biophysics, Meyer B Jackson (2006), Cambridge)
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9. Text Book of Physiology, Guyton & Hall, 11th Ed. 2006
Course Code Title Credits
BP-CCT 20 2 Molecular Biophysics
Total lectures: 60 4
Unit I: Principles of proteins structure and confo rmations
Basics aspects of protein structure, Polypeptide chain geometrics, estimates of
potential energy, results of potential energy calcul ations, hydrogen bonding,
hydrophobic & hydrophilic interactions and water as universal solvent in biological
systems, Disruption of hydr ophobic interactions by urea, ionic interactions,
hydrophobic versus ionic interactions, Disulfide bond, Ways of pairing N -half
cystine, formation of specific disulfide link, prediction of protein structure. ( 15L)
Unit II: Protein structure & stability
Principles of ionization equilibrium ionization of side chain, equilibria in proteins.
Predicting properties from amino acid composition, Usual amino acids. Primary
structure sequencing of polypeptide, hemoglobin, homologies in proteins, Secondary
structure alpha and beta conf ormation, collagen structure, stability of alpha helix,
Ramchandran plot, Tertiary structure, structure of myoglobin and hemoglobin,
Quaternary structure, symmetry consideration, Analysis of subunits and chain
arrangement of subunits, stability of globular quaternary structure. Protein foldi ng
rules, pathways and kinetics ( 15L)
Unit III: Enzyme structure & mechanisms
Enzymes, classification & structure, active site and its identification, mechanisms of
enzyme acti on with special reference to chymotrypsin, carboxypeptidase and
lysozyme, Enzyme kinetics, Michaelis -Menten equation, Inhibitors, kinetics of
competitive, non competitive and unc ompetitive inhibitors, Allosteric cooperative
behaviour, ligand protein interaction, Hill equation, Mettaloenzymes. Determination
Vmax, K m, various graphical plots. (15L )
Unit IV: Glycobiology & Lipids
carbohydrates, classification an d types, stereochemistry, mutarotation, glycoprotein
and proteoglycan, Biosynthesis of glycoprotein, structure and roles of
polysaccharides, lipids: types of lipids , classification and biological significance
(15L)
References:
1. Biophysical Chemistry, The Behaviour of biological macromolecules, Vol I,II, III,
Cantor and Schimmel, (2008), W H Freeman & Co
2. Applied Biophysics, A Molecualr Approach for Physical Scientist, Tom A Weigh,
(2007), Wiley
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3. Introduction to Protein Sciences, Arthur M Lesk (2004), Oxford Press
4. Molecular and Cellular Biophysics, Meyer B Jackson (2006), Cambridge)
5. Chemical Biophysics, Daniel A Beard and Hong Q (2008), Cambridge Univ Press
6. Proteins Structure & Function, David Whitford (2005), Wiley
7. Introduction to Protein Structure, Carl Brenden & Joh n Tooze (1999), Garland Publ,
NY
8. Essentials of Biophysics, P Narayanan (2005), New Age Publ.
9. Physical Chemistry for Biomedical Sciences, S R Logan, (1998), Taylor & Francis.
10. Handbook of Molecular Bi ophysics (Methods & Application), 2009, HG Bohr,
Wiley
11. Principal of Protein Structure, GE Schulz, RH Schirmer (2004), Springer
Course Code Title Credits
BP-CCT 203 Biochemistry
Total lectures: 60 4
Unit I: Hormones action
cAMP/cGMP, G protein and G protein family receptor, G protein cascades, c -AMP
and protein kinase, protein phosporylation, Inosit ol triphosphate and DAG signals
(15L)
Unit II : DNA structure, Replication and Repair
Nucleic acid composition, DNA, RNA base compositions, Chargaff’s rule, primary
and secondary structure of nucleic acids, sequence information, DNA motifs, DNA
repeats and their significance. A, B & Z DNA structure, major & minor groves in
DNA, Protein DNA interactions, supercoiling of DNA, Topoisomerase I and relaxed
DNA, DNA gyrase, eukaryotic gene.
Replication in vivo, semi -conservative mechanism of replication. Direction of
replication. Discovery of DNA polymerase I and its function. DNA synthesis in
vitro, other DNA polymerase s, role of various proteins/enzymes in DNA synthesis.
Model of DNA synthesis, molecula r basis of mutations, DNA repair mechanism s,
reverse transcription. (1 5L)
Unit III: RNA synthesis & Translation
RNA polymerase and its action, promoter sites of DNA template, sigma factor,
elongation and termination of RNA chain, processing of precursors -RNA,sn -RNA
and tRNA, mRNA. RNA polymerase I and transcription of mRNA in eukaryotic
cells. Transcription factors in eukaryotes. Ribozyme and self splicing, genetic code -
discovery and silent features.
Recent advances, amino acid activation, fidelity of aminoacyl, tRNA synthesis,
tyrosyl AMP complex, tRNA structure and function. Ribosomal RNA structure,
Architecture of E lectron Microscopy and neutron diffraction. Initiation of protein
synthesis, translocation and peptide bond formation, termination and stop codon,
protein synthesis in eukaryotes.
(15L)
Unit IV :Regulation of Gene expression in prokaryotes & Eukaryotes
Operator -operon concept, Negative and positive control of transcription with
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example of lac operon and Arbinose operon. Control of transcription, control of
regulatory protein, transcription termination, repressor, croprotein. Eukaryotic
RNA, role of histone, nuclosome, bidirectional replication , repetitiv e DNA,
transcription ; factor IIIA.
(15L)
Reference:
Molecular cloning by Maniatis Vol. I, II, III
DNA cloning by Glover vol. I, II, III
Genome analysis a practical approach by devis.
Protein engineering practical approach by Reas.
Advanced method in protein micro sequence by Witmannn.
Principles of Biochemistry, Leninger (2008(, Freeman Publ
Course Code Title Credits
BP-CTT 204 Recombinant DNA Technology & Protein Engineering
Total lectures: 60 4
Unit I: Preparation, DNA analysis & Enzymatic Manipulation of DNA &
RNA
Genomic DNA from mammalian tissue plant tissue and bacteria resolution
recovery of l arge and small fragments of DNA using various Electromagnetic
techniques , chemical synthesis of oligonuleotides , genes and their uses
analysis of D NA sequences by blotting and hybridization.
Restriction endonuclease and mapping enzymes for modification and
radioactive labeling of nucleic acids, construction of hybrid DNA molecules.
Polymerase chain reac tion (PCR) . Preparation and analysis of RNA .
(15L)
Unit II: a) Construction of Recombinant DNA libraries & In vitro Mutagensis
Genomic an d c-DNA libraries preparation, inserting DNA from genomic
DNA and RNA production of library and amplificat ion. Screening of
Recombinant D NA Libraries: Screening by DNA hybridization ,
Immunological assay and protein activity. Mutagenesiss with degenerate
oligonuleotides , region specifi c Mutagenesis , linker scanning
Mutagenesis.
b) Introduction of DNA into Mammalian cell and System for study of
cloned Genes : Transformation of DNA using calcium Phosphate , DEAE ,
Dextrin and Elecroporation and its optimization and uses. Bacterial Yeast
expression vectors gene transfer Into cultured cells. Development and use of
transgenic animals. Manipulation and gene
expression in prokaryotes, Heteroge nous protein production in eukaryotic
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cells. (15L)
Unit III: Micro sequencing Methods for proteins & Engineering proteins
for purification
Modern advancement such as Tar Sequencing Strategies. DABITC/ PITC
methods. Solid phase micros equencing; Fast atom Bombardment (FAB) mass
spectra in protein sequencing. Cho ice of purification tag, Enzyme purification
Tags. Affinity purification tag, ion exchange, hydrophane IC, covalent and
chelate. Purification tags; PEG enzyme and PEG enzyme conjugates.
(15L)
Unit IV: Chemical Approach to protein Engineering : & protein
engineering for thermo stability
Function al group modification chimeric Protein, protein engineering of Ab,
Directed Mutagenesis and P rotein Engineering. Directed Mutagenesis
procedure adding disulfide bonds , reducing number of free sulphydryl
residues , increasing /modifying Enzyme activity/specificity. Ch imeric
antibody , replacement of FC domains, C atalytic Antibodies (enzymes),
Idiotype vaccines. Hybridoma technology. stability estimates from
denaturation curve , Engineering physical and biology properties of protein
by chemical modification s. (15L)
Reference:
1. Molecular Clonning,Sambrook and Russell Vol 3, Cold Sprong Harbour lab press
2. Molecular and Cell biology, Lodish et al, (2004) Freeman
3. Electrophoresis in Practice, Reiner Westermeirer, (2005) Wiley
4. Methods in Molecular Biophysic s Igor N S et al (2007), Wiley
Molecular cloning by Maniatis Vol. I, II, III
DNA cloning by Glover vol. I, II, III
Genome analysis a practical approach by devis. Protein engineering practical approach by Reas.
Advanced method in protein micro sequence by Witmannn.
Principles of Biochemistry, Leninger (2008(, Freeman Publ
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Semester I Lab course details
Paper code LAB COURSE -1 01 Credits
BP-LBC -101 1. PH Meter: Standardization of pH meter,
Preparation of Buffers,
2. pH titration curve of acid -base
3. Determination values of Iso -electric
point: Amino acids, proteins, phosphoric
acids.
4. Viscosity: Determination of viscosity of
biofluids and chemicals
5. Colorimeter: Verification of Beer’s-
Lambert law, determination of absorption
maxima of colo ured compounds,
determination of molar extinction
coefficient.
6. Estimation of percent purities of dyes and
inorganic compound
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LAB COURSE -102
BP-LBC -102 1. Calculation of measures of dispersion: a)
Mean deviation b) std deviation and
coefficient variation c) Quartile deviation
2. Test of significance: a) Chi -square test b)
t-test
3. To evaluate standard error and
interpretation of results of accuracy and
precision
02
LAB COURSE -103
BP -LBC -103 1. Microscopy: Familiarization with
bright field , phase contrast,
fluorescent, polarization microscopes.
2. Classification of gram – ve & +ve
ogananisms
3. Observe cell growth/ survival by
colony forming assay
4. Estimation of cell viability by dye exclusion and colony formation
assay .
5. Observe cel l death by physical and
chemical agents
6. Observe cell division and determine mitotic index ( Demonstration)
7. Observe RBC, WBC and DLC
8. Determination of cellular 02
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carbohydrates by Acid shifts (PAS)
reaction.
LAB COURSE -104 Credits
BP-LBC 104
1. Fractionation of proteins using: PAGE,
PAPER electrophoresis
2. TLC: Amino acids/ sugars/ fruit juice/oil
3. Column chromatography for protein
/pigment
4. To study of conformational changes in
biomolecules using os wall viscometer
5. Refractoemetry: study of sugars /
proteins/ amino acids
6. 2-D gel electrophoresis of protein & Iso -
electric focusing (Demonstration)
02
Semester II Lab courses
LAB COURSE -201 Credits
BP-LBC - 201
1. Study of thermal denaturation of
DNA and protein
2. Mutarotation of glucose and amino
acids
3. Study of DNA -Protein interaction
using fluouri metry
4. Study of fluorescence sensitivity and
quenching
5. Absorption spectra of Hb, DNA,RNA etc
6. Study of interaction of acridene
orange with DNA
7. Identification of C -terminal and N-
terminal amino acid 02
BP-LBC -202 LAB COURSE 202
1 Enzyme Assays (LKH, beta galacotsidase, acid
phopha tase, arginase, Succinic De –
hydrogenase): Time , Temp, enzyme
concentration, cofactors. LKH: Km & Vmax.
2. Estim ation of Protein by Lowery/Biuret/
Bradford methods
3. Isolation of casein protein from milk,
4.Assessment of antioxidants /Lipid peroxidation
from given samples
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LAB COURSE 203
BP-LBC 203 1. Isolation of DNA (Nuclear and
mitochondrial)
2. Detection of DNA modification
3. Determination of base composition of
Nucleic acids
4. Low prote in concentration detection by
Western blot & silver staining
5. Restriction endonuclase digestion and
separation of fragments by gel
electrophoresis
6. Gel filtrations chromatography
7. To find out capacity & nature of the given
ion exchange resin.
8. DEAE cellulose chromatography of DNA
9. Amplification of DNA by PCR (
Demonstration)
LAB COURSE 204 2
BP-LBC 204 1. Preparation of liposome’s / artificial
membrane: Lipid mixture/ BSA /
Ovalbumin (Demo)
2. Fluorescence anisotropy and polarization
measurement
3. Protein tryptophan fluorescent
measurement.
4. Study of membrane fluidity.
5. Effect of hypertonic/ hypotonic/isotonic
conditions on RBC membrane.
6. Purification of substances by dialysis
7. Study of volume regulation of erythrocyte
and osmotic fragility.
8. Ionophore effect on erythrocyte.
9. Osmolarity: Determination of osmotic
pressure of salts.
10. Study of diffusion of biomolecules/ions
(Fick’s Law)
11. Study of phase transition of membrane
phospholipid s
12. To study the membrane potential using
fluorescence spectroscopy 2
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