Unit I

 

Carbohydrates: Classification, Structures-open chain forms, cyclic forms, glycosidic linkages, glycoprotein’s-structures and physiological functions. Amino acids: Classification (based on nature and metabolism), Zwitter-ion, optical activity and chelate formation. Stereochemistry of amino acids. Classification structure and functions of lipids.

 

Unit II

 

Protein Chemistry: Peptide bond-formation and geometry; Classification of proteins based on shape, composition, function and stability; Denaturation of proteins, Cleavage of disulfide bonds and separation of polypeptide chains, complete hydrolysis of poly peptide chains, identification of C and N terminal residues, partial hydrolysis, Ordering of peptide fragments,  assignment of the positions disulfide linkages. Protein folding pathways, Ramachandran Diagram.

 

Unit III

 

Enzymes- Active site, cofactors, Enzyme specificity, factors affecting enzyme activity. Enzyme kinetics- Michaelis – Menten equation, LB plot, Determination of Km,  Inhibitors, Allosteric enzymes, General mechanisms of action of  enzymes, Regulation of enzyme activity, Enzymes on solid support- methods of enzyme immobilization,  properties of immobilized Enzymes

 

Unit IV

 

Metabolic Pathways: Metabolism of glucose – glycolysis, TCA cycle, glycogenesis, glycogenolysis and gluconeogenesis, Pentose phosphate shunt, Protein metabolism- transamination, oxidative deamination and urea cycle. Interconnection of pathways, metabolic regulation

 

 

Unit V

 

Separation and Purification of Macromolecules-Extraction and purification of proteins and enzymes.

Centrifugation – differential, isopycnic and ultra centrifugation.

Chromatography-Gel filtration, ion-exchange chromatography, Affinity chromatography.

Electrophoresis-Principles, SDS-PAGE, Agarose Gel Electrophoresis, Capillary electrophoresis, 2D gel electrophoresis, isoelectric focusing.

 

 

 

RECOMMENDED TEXTS:

 

1.   Lehninger, AL, Nelson, DL, Cox, M, M M (2004), “Principles of Biochemistry”, 4^th edition, W.H. Freeman & Co., New York.

 

2.   Berg, JM, Stryer, L, Tymocozko, JL (2002), “Biochemistry” 5^th edition, W.H. Freeman & Co., New York.

 

3.   Voet, D, Voet, JG, Pratt, C.W. (2005) “Fundamentals of Biochemistry” 2^nd edition, John Wiley & Sons, USA.

 

 

REFERENCE BOOKS:

 

1.   Voet, D (2004), “Biochemistry”, 3^rd edition, Wiley, USA.

 

2.   Horton, R, Moran, L, Scrinmgeour, G, Perry, M, Ravon, D (2005) “Principles of Biocehmistry”, 4^th edition, Prentice-Hall of India, Kolkata.

 

3.   Satyanarayana, U (2005) ”Biochemistry”,  Books Allied (P) Ltd, Kolkata.

 

 

4.   Talwar, GP, Srivastava LM, (Editor) (2003) “Textbook of Biochemistry and Human Biology”, 3^rd edition, Prentice-Hall of India Pvt Ltd, New Delhi.

 

5.   Palmer, T (2004)”Enzyme: Biochemistry, Biotechnology, Clinical Chemistry” Affiliated-East-West Press, India.

Unit I

 

Classical and quantum mechanics: Elementary introduction to Lagrangian and Hamiltonian formulation of mechanics – breakdown of classical mechanics – Planck theory of blackbody radiation – photoelectric effect – Bohr model of the atom – atomic spectra – De Broglie theory of matter waves – Schrodinger wave equation – interpretation of wave function – atomic orbitals – molecular orbitals – hybrid orbitals –valency of carbon atom – covalent bond – bond order – resonance structure of benzene – partial double bond character of peptide bond.

 

Unit II

 

Thermodynamics and energetics: Thermodynamics systems – laws of thermodynamics – statement and applications – concepts of entropy and enthalpy – chemical potentials – free energy – Gibb and Helmholtz free energy – ATP as energy currency in biological systems – free energy of hydrolysis of ATP and otherorganophosphates.

 

Unit III

 

Molecular mechanics and dynamics: Basic principles – molecular representations – force fields – atom-atom pair potentials – bond length and bond angle and torsion angle potential – van der Waals and electrostatic potential – hydrogen bonding terms – MM3, AMBER, GROMOS, ECEPP/3 force fields – minimization techniques – line search and elementary introduction to gradient techniques – concepts of molecular dynamics – introduction to time-step integration algorithms – dynamics protocols – equilibration and data collection – trajectories and their analyses – graphical representations of trajectories of geometrical parameters.

 

Unit IV

 

Protein and nucleic acid structure: Levels of protein structure – primary, secondary, tertiary and quaternary with examples – alpha helix, beta sheet and beta turn – domains and structural kmotifs – Rossmann fold, Immunoglobulin fold – Double helical structure of DNA – DNA polymorphism – RNA secondary and tertiary structure, with  particular reference to tRNA and ribosomal RNA – Structure of macromolecular complexes – ribosome, viruses – TMV, TBSV and HIV

 

Unit V

 

X-ray crystallography and spectroscopy: Elementary description of crystallography – crystal growth, data collection, structure solution, refinement and interpretation – concept of resolution – IR spectroscopy – UV-Visible spectroscopy – hyperchromism and hypochromism – Raman spectroscopy –‘fingerprinting’ using Raman spectra – complementarity of Raman and IR spectroscopy Fluorescence spectroscopy – NMR spectroscopy – chemical shift – NOW – Fourier transform NMR spectroscopy - elementary introduction to COSY and NOESY – protein structure determination using NMR.

 

RECOMMENDED TEXTS:

 

1.   Vasantha Pattabhi and N.Gautham (2001) ‘Biophysics’ Narosa Publishing Company, New Delhi.

 

2.   P.Narayanan (1999) ‘Introductory Biophysics’ New Age Publishing Co., Mumbai, India.

 

 

REFERENCE BOOKS:

 

1.   C.R.Cantor and P.Schimmel (1985) ‘Biophysical Chemistry, Vol.I, II and III’ W.H.Freeman and Company, New York, USA.

 

2.   D.Freifelder (1982) ‘Physical Biochemistry’ W.H.Freeman and Company, New York, USA.

 

3.   E.Ackerman, L.B.M.Ellis and L.E.Williams (1979) ‘Biophysical Science’ Prentice Hall Inc., New Jersey, USA.

 

4.   F.W.Sears, M.W.Zemansky and H.D.Young (1985). ‘College Physics’ Addison Wesley Publishing Company, Massachusetts, USA.

 

5.   C.N.Banwell (1983) ‘Fundamentals of Molecular Spectroscopy’ Tata McGraw-Hill Publishing Company Lt., New Delhi, India.

 

6.   G.M.Barrow (1962) ‘Molecular Spectroscopy’ McGraw-Hill Book Company Inc., New York, USA.

 

7.   D.Sherwood (1976) ‘Crystals, X-rays and Proteins’ Longman Group Lts., London, UK.

 

8.   A.R.Leach (1996) ‘Molecular Dynamics Simulation’ John Wiley and Sons, New York, USA.

9.   J.M.Haile (1992) ‘Molecular Dynamics Simulation’ John Wiley and Sons, New York, USA.

 

10.        C.Branden and J.Tooze (1991) ‘Introduction to Protein Structure’ Garland Publishing Company, New York, USA.

Unit I

 

Statistics – Scope –collection, classification, tabulation of Statistical Data – Diagrammatic representation – graphs – graph drawing – graph paper – plotted curve –Sampling method and standard errors –random sampling –use of random numbers –expectation of sample estimates – means – confidence limits – standard errors – variance.

 

Unit II

 

Measures of central tendency – measures of dispersion – skewness, kurtosis, moments – Correlation and regression – correlation table – coefficient of correlation – Z transformation – regression – relation between regression and correlation

 

Unit III

 

Probability – Markov chains applications – Probability distributions – Binomial (Gaussian distribution) and negative binomial, compound and multinomial distributions – Poisson distribution – Normal distribution – graphic representation – frequency curve and its characteristics –measures of central value, dispersion, coefficient of variation and methods of computation – Basis of Statistical Inference –Sampling Distribution – Standard error – Testing of hypothesis – Null Hypothesis –Type I and Type II errors

 

Unit IV

 

Tests of significance for large and small samples based on Normal, t, z distributions with regard to mean, variance, proportions and correlation coefficient – chi-square test of goodness of fit – contingency tables – c² test for independence of two attributes – Fisher and Behrens ‘d’ test – 2×2 table – testing heterogeneity – r X c table – chi-square test in genetic experiments – partition X 2 – Emerson’s method – Tests of significance –t tests – F tests – Analysis of variance – one way classification – Two way classification, CRD, RBD, LSD.

 

Unit V

 

Spreadsheets – Data entry –mathematical functions – statistical function – Graphics display – printing spreadsheets – use as a database word processes – databases – statistical analysis packages graphics/presentation packages.

 

 

 

 

 

RECOMMENDED TEXTS:

 

 

1. Zar, J.H. (1984) “Bio Statistical Methods”,  Prentice Hall, International     

    Edition

 

2.   Sundar Rao P. S.S., Jesudian G. & Richard J. (1987), “An Introduction

      to   Biostatistics”, 2^nd edition,. Prestographik, Vellore, India.

 

1.   Warren,J; Gregory,E; Grant,R (2004), “Statistical Methods in Bioinformatics”,1^st edition,Springer

 

 

 

REFERENCE BOOKS:

 

1.   Milton,J.S.(1992),. “Statistical methods in the Biological and Health Sciences”, 2^nd edition ,Mc Graw Hill.

 

2.   Rosner,B (2005), “Fundamentals of Biostatistics”, Duxbury Press.

 

Unit I

 

Architecture of prokaryotic and eukaryotic cells and tissues. Biomembranes and the subcellular organization of eukaryotic cells. Cell motility and shape, Eukaryotic cytoskeleton- microfilaments-microtubules - intermediate filaments, Cell division-mitosis and meiosis, eukaryotic cell cycle and its regulation.

 

Unit II

 

The mitochondrion- structure, electron transport chain, oxidative phosphorylation, Chemiosmotic process. Chloroplasts-photosynthesis-photosystems, Calvin cycle, Dark reactions.

 

Unit III

 

Intracellular traffic- membrane transport-principles, active transport, ion channels. Protein sorting-an overview of targeting proteins to mitochondria, nucleus, endoplasmic reticulum, lysosomes and plasma membrane.

 

Unit IV

 

Cell signaling-Hormone-receptor interactions, G protein-coupled receptors and their effectors, Second messengers, Receptor tyrosine kinases, MAP kinase pathways. Cell-cell interactions in development.

 

Unit V

 

Basic immunology- Types of immunity-innate, acquired, active and passive, antigen-antibody reactions, elements of the immune system:

T cells, B cells, antigen presenting cells, helper and suppressor cells, natural killer cells, cell-mediated and humoral immunity.   

 

 

RECOMMENDED TEXTS:

 

1.   CGerald Karp (Editor) (2005) “Cell and Molecular Biology: Concepts and Experiments”, 4th edition, Wiley Publishing Co, USA.

 

2.   Lodish, H, Scott, M.P, Matsudaira P, Darnell, J, Zipursky, L, Kaiser, CA, Berk, A, Krieger, M, (2003) “Molecular Cell Biology”, 5^th edition, W.H. Freeman and Co, New York.

 

 

 

 

REFERENCE BOOKS:

 

1.   Alberts, B; Johnson, A; Lewis, J; Raff, M; Roberts, K; Walter, P (2002)

     “Molecular Biology of the Cell”, 4^th edition, Garland Science, Taylor        

      and Francis group, USA.

 

2.  Verma, PS; Agarwal,VS (2005) “Cell Biology, Genetics, Molecular

Biology,  Evolution and Ecology”,14^th edition, S.Chand & Company Ltd, New Delhi.

 

1.   Alberts, B; Johnson, A; Lewis, J; Raff, M; Bray,D; Hopkin,K; Roberts, K; Walter, P (2003), “Essential Cell Biology” ,2^nd edition, Garland Science, Taylor & Francis Group,USA.

 

2.   Becker, WM ;  Klein smith, LJ Hardin (2005),“World of the Cell”  6^Th edition, Benjamin Cummings

 

Unit I

 

Program structure-components of a program-program compilation and execution-flow charts-arrays (single and multi dimensional) and string functions-user defined functions and function categories-input/output devices

 

Unit II

 

Mathematical foundations-Data structures-reasoning about correctness-complexity analysis-implementation techniques

 

Unit III

 

Internet- communication types on the internet-hypertext, www, client programs-accessing internet resources via a web browser- static and dynamic web pages-wireless application protocol, network computing and grid computing-downloading using ftp-examples 

 

Unit IV

 

UNIX-understanding the UNIX system-fundamentals of using the UNIX system- mastering the special features of the UNIX system.

 

Text processing: commonly used UNIX commands-resources for users of the UNIX system-interacting with the UNIX system-essentials of system administration-octal equivalents to ASCII-different file editors-handling files-introduction to Linux

 

Unit V

 

C++ programming- introduction to programming in C++ - The ASCII code- C++ keywords-C++ operators-C++ types-conditional statements and integer types-interaction and floating types.

 

Functions-arrays-pointers and references-strings-classes-overloading-operators-A string class-composition and inheritance-stream I/O - simple programs which demonstrates inheritance, operator overloading and polymorphism

 

 

 

 

 

 

 

 

REFERENCE BOOKS:

 

 

1.   Hubbard, John (2000) “Programming with C++", Schaum’s outline series, Tata McGraw Hill International

 

2.   Thomas, Rebecca and Jean Yates (1987), “A user Guide to the UNIX system,” Tata McGraw Hill International

 

3. Arnold Robbins & Daniel Gilly, (1999) “Unix in a Nutshell”, O’Rielly and

    Associates

 

4. Kay. A Robbins, Steven Robbins, Kay. Ret. Robbins and Steve Robbins

    (1999) “The C programming language”, Prentice Hall.

 

 

Unit I

 

Basics of computing: Introduction to operating systems – WINDOWS, UNIX, LINUX; Advantages of security installation; Use of internet; Graphics – visualization techniques; softwares and hardwares; Computer networking – LAN, WAN, MODEM, Optical vs electronic networking, firewalls; Ethernet and TCP/IP family of protocols.

 

Unit II

 

Data warehousing, data capture, data analysis; Introduction to Nucleic Acid and Protein Sequence Data Banks; Nucleotide databases (Genbank, EMBL, DDBJ); Protein databases (Swiss-Prot, Tr-EMBL, PIR_PSD, Expasy); Derived Databases (Prosite, PRODOM, Pfam, PRINTS); Sequence submission Methods and tools (Sequin, Sakura, Bankit); Sequence retrieval systems (Entrez & SRS); Sequence File Formats and Conversion tools; Genome (NCBI, EBI, TIGR, SANGER), Metabolic Pathway database (KEGG, EMP, EcoCyc, BioCyc and MetaCyc); Specialized database (IMGT, Rebase, COG, LIGAND, BRENDA); Structural database.

 

Unit III

 

Internal and external co-ordinate system; Generation of co-ordinates of biopolymers in Cartesian and cylindrical polar co-ordinate system; Genome Anatomy, Prokaryotic genomes structures, Eukaryotic genomes structures,  Gene density, Gene Ontology, Gene Order (synteny), Plasticity zone, Gene Network, tandem repeats, Transposable elements, Pseudo genes, Gene Clusters, Segmental duplication, non-coding conservation, Comparative genomics, Importance of Full Genome Alignments, Concepts & applications of Suffix tree in comparative genomics, Algorithms for BLAST2, Mega Blast, Mummer.

 

Unit IV

 

Analysis of protein and nucleic acid sequences, multiple alignment programs, Development of programs for analysis of nucleic acid sequences, Pairwise Sequence Alignment - Similarity, Identity and Homology, Global Alignment, Local Alignment; database search methods and scoring matrics ; Dynamic Programming, Heuristic approach, Scoring Matrices and Affine Gap costs; Detailed method of derivation of the PAM & BLOSUM Matrices; Differences between Distance & Similarity Matrix; Assessing the Significance of Sequence Alignments.

 

Multiple Sequence Alignment - Multiple alignment programs, Development of programs for analysis of nucleic acid sequences, Conversion of various file formats; Phylogenetic Analysis - Concept of dendrograms; Strings and Evolutionary trees; Ultra metric trees and Ultra metric distances; Additive - Distance trees; Methods of Construction of Phylogenetic trees-Maximum Parsimony Method, Maximum likelihood method and Distance Methods, Reliability of trees.

 

Unit V

 

Analysis of structures and correctness of structures, Submission of data to PDB: atomic coordinates and electron density maps; Anatomy of Proteins - Ramachandran plot, Secondary structures, Motifs, Domains, Tertiary and quaternary structures; Calculation of conformational energy for bio-macromolecules; Methods for Prediction of Secondary and Tertiary structures of Proteins - Knowledge-based structure prediction, Fold recognition, Ab initio methods for structure prediction; Methods for comparison of 3D structures of proteins; Molecular interactions of - Protein – Protein, Protein – DNA, Protein – carbohydrate, DNA – small molecules etc.; Docking of Molecules; Molecular Design.

 

 

RECOMMENDED TEXTS:

 

1. Lesk, A.M. (2002) “Introduction to Bioinformatics”, 1^st Edition, Oxford University Press, Oxford, UK.

 

2. N. Gautham (2006) “Bioinformatics”, Narosa Publishing Company, New Delhi.

 

3. Westhead, D. R., Parish, J.H and Twyman, R.M (2003) “Instant Notes Series – Bioinformatics” 1^st Edition, Viva Books Private Limited, New Delhi, India.

 

4. Bernhard Haubold and Thomas Wiehe (2006) “Introduction to Computational Biology – An Evolutionary Approach” Birkhauser Verlag, Switzerland.

 

 

REFERENCE BOOKS:

 

1. Krane, DE; Raymer, ML (2003), “Fundamental concepts of Bioinformatics”, Benjamin Cummings

 

2. Ignacimuthu, S (2005) “Basic Bioinformatics”, 1^st Edition,  Narosa Publishing House, New Delhi, India

 

3. P. Baldi and S. Brunak (2003) “Bioinformatics” Affiliated East-West Press, New Delhi, India

 

Unit I

                                               

DNA is the genetic material-structure –DNA  polymerases-replication –telomerases, DNA repair mechanisms, genetic recombination –Holliday model, transposons and retroposons

 

Unit II

 

Gene expression;-Prokaryotic and Eukaryotic RNA polymerases, Initiation of transcription, termination of transcription, regulation of gene expression, lac operon and tryptophan operon, hormonal regulation of gene expression, translation-gene regulatory proteins, DNA methylation.

 

Unit III

 

Post transcriptional modifications-RNA splicing and ribozymes, gene control in development

Translation-initiation, elongation and  termination, inhibitors, post   translational modifications

 

Unit IV

 

Cloning and expression vectors-plasmids-cosmids-phages-viruses-YAC, BAC-Molecular probes-gene library-restriction enzymes-restriction mapping-southern, northern, western blotting-screening of cDNA libraries

 

Unit V

 

Antisense RNA technology-DNA finger printing-foot printing-gene amplification-Basic PCR-its modifications-RT- PCR- applications-RAPD. Introduction to nano technology, commercial applications of nanotechnology. Immunotechnology- Hybridoma technology –production of  Interferon – vaccines –DNA vaccines.

 

RECOMMENDED TEXTS:

 

1. Benjamin Lewin  (2004) “Genes VIII” ,8th edition, Pearson Education      

    International

 

2. Glick,BR; Pasternak, JJ (2003), “ Molecular Biotechnology;Principles

    and Applications of Recombinant DNA”,3rd edition,American Society    

    of Microbiology

 

3. Satyanarayan,U (2005) “Biotechnology”, Books and Allied (Pvt) Ltd

    Calcutta.

 

 

 

REFERENCE BOOKS:

 

1. Watson, J; Zoller, M ;Gilman, M; Witkowski, J (1992), “Recombinant    

    DNA”,2nd edition,W.H. Freeman.

 

2. Old,RW ; Primrose, SB (1994), “ Principles of Gene Manipulation-An   

    Introduction to Genetic Engineering” 5th edition, Blackwell Science.

 

3.Brown ,TA (2001) “Gene Cloning and DNA analysis-an introduction”,4th edition,Blackwell Science.

 

4. Poole,C; Owens, FJ (2003) “Introduction to Nanotechnology”, John   

   Wiley and Sons.

 

Unit I

 

An introduction to JAVA programming – OOPS and JAVA - Java basics - Working with objects – creating classes and application in JAVA- More about methods

Conditionals and Loops

 

Unit II

 

Array and strings - Java applets Basics – Threads – Streams and I/O

 

Unit III

 

Graphics, fonts and color – Simple animation – More animation, Images and sound – Managing simple events and interactivity – creating user Interfaces with AWT Windows, Networking and other Tidbits – Modifiers, Access control and class Design.

 

UNIT IV

 

Packages and Interfaces – Exception and Managing errors – Multithreading.

 

UNIT V

 

Using Native Methods and Libraries – Under the Hood – Java programming tools – Working with Data structures and Java

 

RECOMMENDED TEXTS:

 

1.   Patrick Niemeyer, P;  Knudsen,J (2002) Learning JAVA, 2^nd edition,O’Reilly Publishers.

 

2.   Liang,YD (2002) “Introduction to JAVA Programming”,4^th edition,Prentice Hall.

 

Reference  Books:

 

1. Crawford,W; Farley,J (2005),  “Java in a nutshell” ,3^rd edition,O’reilly    

    Pubishers.

 

 

Unit 1

 

Drug Discovery: Introduction, Conventional drug design approaches, irrational vs. rational, various steps of drug design process-Lipinski rule-phramcophore kinetics and dynamics-ADME properties, Lipinski rule-Examples uses of computer based drug discovery-benefits

 

Unit 2

 

Introduction to Bioinformatics: What is bioinformatics-sequence database and their uses -analysis of sequence-multiple sequence analysis-secondary structure prediction-uses of different bioinformatics tools and applications

 

Unit 3

 

Biomacromoleclar structure and function: Various levels of protein structure, Ramachandran Plot, Protein folding, Structure of DNA-protein-protein interaction, protein-DNA interactions-enzyme kinetics-inhibitors

 

Unit 4

 

Introduction to molecular modeling: Molecular structure, bonding, Various types of Forces responsible for stabilization of biomolecules and their interaction- Potential energy surface-force field-molecular mechanics method –Structure activity relationship- de novo drug design pharmacophore-and docking- scoring

 

Unit 5

 

Quantitative structure activity relationship: QSAR, concept, and properties of organic molecules- various descriptors used in the QSAR,multiple linear regression, and its applications to drug design

 

 

 

 

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