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B.Sc. Biotechnology and Bioinformatics Syllabus

Department of Bioinformatics, Faculty of Science and Humanities, SRM University, Kattankulathur 1

CELL BIOLOGY Semester : I Credits : 4

Category : Core Hrs/Wk : 4

Course Objective: To enable the students to learn the principles of structure and functions of cell and their organelles. Unit 1: Introduction 9 Cell as a basic unit of living systems – discovery of cell - the cell theory and pre-cellular evolution – diversity of cell size and shape – Classification of cells – Ultra structure of Prokaryotic cell and Eukaryotic cell and their differences. Plant cell and animal cell similarities and dissimilarities – Microscope – a short history and its importance in cell biology – Light microscope - Components and applications – handling. Unit 2: Cell Membrane and Cell wall 8 Plasma membrane – structure (fluid mosaic model) and function, transport of small molecules, channels, carriers, receptors, endocytosis, potentials. Cell wall: prokaryotic (bacteria) and eukaryotic (plant) – their structure and function. Unit 3: Cellular Organelles 9 Structure, function and biogenesis of cellular organelles - Mitochondria, chloroplasts, endoplasmic reticulum (rough and smooth), golgi bodies, lysosomes, peroxisomes, ribosomes - cytoskeletal structures (actin, myosin, microtubules etc.). Basic information on organelle genomes. Unit 4: Nucleus and Chromosomes 9 Nucleus (nuclear membrane, nucleoplasm, nucleolus) Chromatin reticulum, chromosome morphology, fine structure, chemical organizations - Organization of DNA- nucleoproteins - Histones and non-histones; Special types of chromosomes - salivary gland chromosomes and lamp brush chromosomes. Unit 5: Cell Division and Cellular Interactions 10 Cell division and cell cycle (including cell synchrony and its applications) – events during mitosis and meiosis and their significance. Cell cycle regulation. Cell-cell interactions and signal transduction - intercellular junctions, signaling by hormones and neurotransmitters; receptors, G-proteins, protein kinases and secondary messengers. Cell locomotion (amoeboid, flagellar and ciliar) - muscle and nerve cells - Cell senescence and death, Cell differentiation in plants and animals. RECOMMENDED TEXTS:

1. Verma P.S. & V.K. Agarwal, “Cell Biology, Genetics and Molecular Biology”, 2000, S. Chand. 2. Cohn, N.S., “Elements of Cytology”, 1979, Freeman Publishers. 3. Darnell, J., Lodish, KL and Baltimore, D., “Molecular Cell biology”, 2008, W. H. Freeman

Publishers. 4. De Robertis, E.D.P. and Robertis, E.M.F., “Cell and Molecular biology”, 1991, Lea and

Febiger, Washington. 5. J Roy, S.C. & Kalyan Kumar De, “Cell Biology”, 1997, New Central Book Agency, Calcutta



CHEMISTRY Semester : I Credits : 5

Category : Allied Hrs/Wk : 4

Course Objective: To review the concepts of chemistry relevant to biology. Unit 1: Atoms 9 Structure of atoms: Dalton’s atomic theory – subatomic particles – concepts of atoms and molecules – symbols for elements – electronic configuration of atoms – isotopes – shapes of atomic orbitals – periodical table – periodic classification – periodicity – valency – chemical bond. Unit 2: Properties 9 Materials on earth: Properties of gas, liquid, solid, compound, mixtures, solutions, colloids, suspension- acids, bases and salts – conductors and non-conductors. Unit 3: Exothermic Reactions 9 Changes around us: slow and fast changes – reversible and irreversible reactions – exothermic and endothermic reactions – condition of chemical reactions – types of chemical reactions – mole concept and stoichiometry in chemical reaction – technique used to determine chemical reactions. Unit 4: Classification of organic compounds 9 Organic chemistry and energy: organic compounds – classification – functional groups – aromatic, aliphatic, heterocyclic compounds – alkanes in gasoline – fuel from biogas, coal, hydrogen. Unit 5: Physical and Chemical Properties 9 Chemistry in living world: physical and chemical properties of amino acids and proteins – properties and kinetics of enzymes – bioenergetics – thermodynamics. RECOMMENDED TEXTS:

1. Lee, J.D., “Concise Inorganic Chemistry”, 2009, 5th Ed., Blackwell Science.

2. Negi A.S & Anand S.C., “A textbook of physical chemistry”, 2007, 2nd

Ed., New Age International Publishers. 3. Soni, P.L & Mohan Katyal, “A Textbook Inorganic Chemistry”, 2007, Sultan Chand & Sons. 4. Mathews, P., “Advanced Chemistry”, 1996, Cambridge University Press 5. Voet, D. and Voet, JG., ”Biochemistry”, 2010, 4

th Edition, John Wiley & Sons.



INTRODUCTION TO COMPUTERS AND PROGRAMMING Semester: I Credits: 3

Category: Hrs/Wk: 4

Course Objective: To equip students with fundamental knowledge and concepts of computers and basic programming skills. Unit 1: Introduction to Computers 10 Overview and function of computers - Characteristics of computers – History of Computers: Evolution, Generations of modern computers (I, II, III, IV and V), Classification of computers - micro computers, mini computers, mainframe, super computers, special purpose (comparison of their memory, power, cost, size) – PC types: Tower, Desktop, Notebook, Laptop, Handheld, Palmtop, PDA, Types of modern computers: Workstations, Servers. Unit 2: Computer Components and Number Systems 10 Components of a computer – input device (keyboard, mouse), output devices (monitors and printers), central processing unit, memory (RAM and ROM), secondary storage devices – Hard disk, magnetic tape, zip drives, digital tape, CD-ROM, DVD, BluRay. Number system: introduction, types - Decimal number system, Binary number system, Octal, Hexadecimal and their conversions using simple examples – Binary Codes: Introduction, types: Gray, Alphanumeric, ASCII, EBCDIC. Unit 3: Operating System (OS) and Software Development 8 Hardware and Software definition - Introduction to Operating systems- functions, classification: real time, single user single task, single user multi task, multitask, Basic description about DOS, Windows 98/XP, Windows server NT/2000,UNIX/LINUX, MVS, MacOS. Overview of Software Development - Software Development Phases – problem definition, analysis, algorithm design and representation, coding and debugging (simple description about each phase). Unit 4: Flow charts, Pseudocodes and Programming Languages 9 Basic Flowchart symbols and their meaning – Pseudocode – definition and importance – Syntax and Semantics - Programming approaches – Procedural, object oriented –. Programming languages – definition, categories – low level languages: Machine languages, assembly languages - advantages and disadvantages - High-level languages - advantages and disadvantages - interpreters, compilers and translators – overview of compilation process - types of high level languages. Unit 5: Multimedia and Internet 8 Multimedia: Introduction, Characteristics, Elements and Applications. The Internet and its Resources, World Wide Web (WWW): Associated tools, services, resources and various terminologies - An overview of computer viruses: virus definition, symptoms, transmission, dangers and general precautions. RECOMMENDED TEXTS:

1. Glenn Brookshear J, “Computer Science: An Overview”, 2011, 11th ed., Addison Wesley

Publishers. 2. Alexis Leon & Mathews Leon, “Fundamentals of Information Technology”, 2009, 2

nd Ed.,

Vikas Publishing House Pvt. Ltd. 3. Rajaraman. V, “Fundamentals of Computers”, 2004, 4

th Ed., Prentice Hall India Pvt. Ltd.

4. Francis Glasborrow & Roberta Allen, “A Beginner’s Introduction to Computer Programming”, 2003, John Wiley and Sons.

5. Anurag Seetha, “Introduction to Computers and Information Technology”, 2005, Ram Prasad & Sons, Bhopal.

6. Basandra S.K., “Computers Today”, 2011, 1st Edition, Galgotia Publications.



CELL BIOLOGY LAB Semester : I Credits : 2

Category : Core Practical Hrs/Wk : 4

Good Laboratory Practices

Components of Microscope

Handling of Microscope

Principle & operation of Centrifuge

Principle & operation of pH meter

Principle & operation of Colorimeter

Principle & operation of Spectrophotometer

Preparation of Molar solutions, Normal solutions, stock solutions and buffers

Microscopic Observation of plant cells / tissues after staining.

Microscopical Identification of Cells in Permanent Fixed Slides.

Differentiation of Blood Cells using Giemsa Staining / Leishman staining

Separation of Peripheral Blood Mononuclear Cells and Trypan Blue Assay for Live Cells

Osmosis and Tonicity Studies using Red Blood Corpuscles

Differential fractionation of cellular organelles using centrifugation technique.

Staining of Various Stages of Mitosis in Allium cepa (Onion)



CHEMISTRY LAB Semester : I Credits : 2

Category : Allied Practical Hrs/Wk : 4

Volumetric analysis:

acidimetry alkalimetry permanganametry Dichlorometry Iodimetry Complexmetry

Analysis of organic compounds with one functional group:

aldehyde Ketone Carboxylic acid Aromatic primary and secondary amine Phenol aromatic ester alcohol nitrocompound carbohydrates.



GENERAL MICROBIOLOGY

Semester : II Credits : 4


Course Objective: To provide the students basic knowledge on microbes and techniques to handle. Unit 1: History and Taxonomy 9

Brief History of Microbiology - Major contribution of scientists– Leeuwenhoeck, Edward Jenner,

Alexander Fleming, Joseph Lister, Robert Koch, Louis Pasteur, Hargobind Khorana. - Scope of

Microbiology. Classification of microorganisms- viruses, bacteria, fungi, algae and protozoans E. H.

Haekel’s classification, Whittaker’s five– kingdom concept of living organism – microbial taxonomy,

criteria used including molecular approaches, Microbial phylogeny and current classification of

bacteria, Bergey’s Manual of Systematic Bacteriology – Microbial Nomenclature.

Unit 2: Morphology of Microbes 9

Basic Morphology of Bacteria and algae – cell wall, peptidoglycan, difference between gram positive

and gram negative cell wall, cell membrane and their special structures, bacteriochlorophyll,

endospores, flagella, cilia, pilus, Bacterial DNA – chromosome and plasmids. Introduction to Fungal

morphology – yeasts and molds (hyphal filaments). Composition and structure of Virus - their

different forms.

Unit 3: Microscopy and Staining 9

Microscopy - Principles and applications, dark field, bright field, resolving power, magnification,

numerical aperture, chromatic aberration, phase contrast microscopy, fluorescent microscopy,

inverted microscopy, stereo microscopy, electron microscopy, TEM and SEM. Principles of staining,

simple staining, negative staining, differential staining, gram and acid fast staining, flagella staining,

capsule and endospore staining.

UNIT 4: Microbial Growth and Nutrition 9

Microbial growth, Growth curve, generation time, Synchronous, batch and continuous culture,

measurement of growth and factors effecting growth. Cultivation and maintenance of microorganisms,

nutritional categories of microorganisms, methods of isolation, purification & preservation of pure

culture.

Unit 5: Life Cycle and Control of microbes 9

Life cycle pattern of microbes: Viruses (Lytic and Lysogenic), bacteria, fungi-yeast and Neurospora.

Sterilisation, disinfection, antiseptic, tyndallisation, pasteurization: Physical- dry heat, moist heat, UV

light, ionizing radiation, filtration, HEPA filter, Chemical-phenol and phenolic compounds, (halogen

aliphatic alcohol, formaldehyde, ethylene oxide, heavy metals) anionic and cationic detergents.

RECOMMENDED TEXTS:

1. Pelczar MJ, E.C.S. Chan and Noel R. Krieg, “Microbiology”, 2004, 5th Ed., Tata McGraw Hill. 2. Prescott, Harley and Klein, “Microbiology”, 2010, 8

th Ed., McGraw Hill.

3. Powar, C.B. & Daginawala, H.F., “General Microbiology”, 2005, Himalaya Publishing House. 4. Atlas RM, “Principles of Microbiology”, 1997, WCB Publishers. 5. Davis BD, Dulbecco R, Eisen HN, Gihsbercs HS, “Microbiology”, 1990, Lippincott Williams and Wilkins publishers.



MATHEMATICS FOR BIOLOGICAL SCIENCES



Course Objective: To review the basic concepts of mathematics relevant to biology. Unit 1: Vectors and Matrices 10

Properties of determinants, minors, co –factors, inverse of a matrix,matrix method, cramers rule -

Vectors - Addition and subraction, dot product, cross product, gradient, divergence,curl

Unit 2: Basic Calculus 9

Differentiation and Integration - Concept of limit, continuity, differentiation, maxima and minima,

introduction to partial differentiation, Integral calculus, definite integral

Unit 3: Numerical Computation 9

Errors in Computer Arithmetic, Normalization Polynomial Interpolation, Solution of Non-linear

Equations, Errors, Convergence of Solutions, IterativeMethods for System of Linear Equations, Matrix

Inversion, Numerical Differentiation and Integration

Unit 4: Discrete Structures 10

Formal grammars, Chomsky Hierarchy, Permutation, Combination, Recurrence Relations, Principle of

Inclusion and Exclusion; Basic Concepts of Graphs and Trees, Adjacency and Incidence Matrices,

Spanning Tree, Transitive Closure, Shortest Path, Planar Graphs, Graph Coloring, Applications of

Graph, Theoretic concepts to Biology

Unit 5: Trigonometry and Analytical Geometry 7

Trigonometric ratios, De Moivre’s theorem, the general equation of a Straight line, slope of a line,

intercepts of a line, Angle between two lines, Intersection of two lines, the general equation of a

Circle.

RECOMMENDED TEXTS:

1. Boas, M.L., “Mathematical Methods in the Physical Sciences”, 2005, 3rd

Ed., Wiley Publication

2. Prasad, G., “Textbook on Differential Calculus”, 2003, 4th Ed., Poothisala Publications.

3. Prasad, G., “Textbook of Integral Calculus”, 2003, 3rd

Ed., Poothisala Publications.

4. Ayers, F. “Matrices and Vectors”, 1962, 1st Ed., Schaum Outline Series Publishing Co.

5. Schwartz, J.T., “Introduction to Matrices and Vectors”, 2001, Courier Dover Publications



PROGRAMMING IN C



Course Objective: To introduce students to C Programming Language and expose students to programming paradigms in a generic manner. Unit 1: Introduction to ‘C’ Language 9

Historical background of ‘C’: Character set, Constants, Variables, Keywords and Comments,

Instructions: Type declaration instruction, Arithmetic instruction, Integer and float conversion,

Hierarchy of operations, Control instructions.

Unit 2: Control Structures 9

Control Structure Definition, Various types of control structure used in ‘C ’ and its various applications

Decision control structure: The if statement, if-else statement, Nested if-else and forms of if. Case

control structure: Decision using switch, the goto statement

Unit 3: Operators and Looping Constructs 9

Operators: Arithmetic, Logical, Relational, Bitwise, Increment, Decrement, Conditional operators.

Loop Control structure: The while loop, for loop: Nesting of loops and multiple initializations in for loop,

Odd loop: break statement, continue statement, do-while loop.

Unit 4: Functions and Pointers 9

Introduction to Function: Application of function, Passing Values, Scope and rule of functions,

advanced features of function, Function declaration and prototype, call by values and call by

reference, Pointer: Introduction, Pointer notation and Back to function call, Recursion.

Unit 5: Arrays and Strings 9

Importance of arrays in ‘C’, Array initialization, Bounds checking, passing array element to a function,

Pointer and arrays – multidimensional arrays. Strings: Basic concept of strings, Standard library

function of string: strlen(), strcply(), srcat(), strcmp(), Two dimensional array of characters, Array of

pointer to strings, Limitation of array of pointer to strings.

RECOMMENDED TEXTS:

1) Balaguruswamy, E., “Programming in Ansi C”, 2011, 5th Edition, Tata McGraw Hill Publications

2) Yashvant P. Kanetkar, “Let us C”, 2008, 8th Ed., Infinity Science Press.

3) Brian W. Kernighan & Dennis Ritchie, “The ‘C’ Programming Language”, 2006, 2nd

Ed., Prentice

Hall Publications.

4) Gottfried, B., “Programming with C”, 1996, 2nd

Ed., Schaum’s Publishing Series.

5) Dilip Mali & Pramod Vasambekar, “C Application Program Project”, 2007, Penram International

Publication (India) Pvt. Ltd.



MICROBIOLOGY LAB



Sterilization techniques

Wet preparation – Hay infusion broth – hanging drop

Media preparation

o Liquid

o Solid

Simple staining

Differential staining

Inoculation techniques – pour plate – spread plate

Dilution techniques – serial and doubling

Colony morphology of bacterial cells on media.

Biochemical tests for bacterial identification

o Catalase test

o Oxidase test

o IMVIC test

o TSI test

o Carbohydrate fermentation

Enumeration of viable bacteria using haemocytometer

Morphological Identification of Molds

Morphological Identification of Yeasts



C LAB


Category : Hrs/Wk : 4

Basic C program parts

Expressions

Control Statements

Looping Constructs

Operators

Arrays

Pointers

Strings

Functions

File I/O operations



APPLIED MICROBIOLOGY

Semester : III Credits : 4


Course Objective: To enable students to understand and appreciate role of microbes in wide variety of areas.

Unit 1: Microbes and Human Disease 11 Microbiology of human diseases- Epidemiology, pathogenesis, diagnosis, prevention and control. Bacteria - Staphylococcus, Streptococcus, Enterobacteriaceae, Pseudomonas, Vibrio cholerae, Salmonella, Viruses - Poxs, Adeno, HIV virus, Fungi - Aspergillus, Candida. Protozoa - Amoeba, Plasmodia. Food borne diseases caused by different organisms. Role of antibiotics in treating microbial diseases. Unit 2: Industrial Uses of microbes: 8 Production and applications of Microbial Enzymes - amylase, protease, Polysaccharide – Xanthan gum, Solvents – Ethanol, Organic acid – Citric acid. UNIT 3: Metabolites from microbes: 8 Microbial Production of Amino acids, Antibiotics - Streptomycin, Penicillin, Cephalosporins and other secondary metabolites Unit 4: Environmental Role of Microbes 9 Environmental Biotechnology and Microbes in Bioleaching, Microbial Degradation of Xenobiotics, Sewage biodegradation. Microbial population of air, water and soil. Biogeochemical cycle: Nitrogen, carbon, sulphur cycles. Unit 5: SCPs and Biofertilisers 9 Microorganism in production of Biomass: Single cell protein, Mushroom cultivation. Biofertilizers, Biopesticides. RECOMMENDED TEXTS:

1. Tortora G J., Berdell R. Funke, Christine & L. Case, “Microbiology – An Introduction”, 2010, 10

th Ed., Benjamin Cummings.

2. Satyanarayana. U, “Biotechnology”, 2008, 3

rd Ed., Books and Allied (P) Ltd.

3. Mark Wheelis, “Principles of Modern Microbiology”, 2007, 1

st Ed., Jones and Barlett

Publishers.

4. Madigan, M. T., John M. Martin & Jack Parker, “Brock’s Biology of Microorganisms”, 2010, 13

th Ed., Prentice Hall International, Inc., London.

5. Daniel Lim, “Microbiology”, 2002, 3

rd Ed., McGraw-Hill Company, New York.



GENERAL BIOCHEMISTRY

Semester : III Credits : 4


Course Objective: To acquire basic knowledge about molecules present in living systems and their importance.

UNIT 1: CARBOHYDRATES 9 Carbohydrates: Introduction, classification, monosaccharide-structure, Stereoisomers, structural isomers, mutarotation, and chemical reactions, Oligosaccharides, dissaccharides-structure and importance of sucrose, lactose and maltose - Polysaccharides - structure and importance of homopolysaccharides and heteropolysaccharides. UNIT 2: AMINO ACIDS 9 Amino acids: Classification, Essential & Non essential amino acids, structure and properties. Peptide bond and Polypeptides. Protein: Definition, classification and functions – structural levels of organization - difference between polypeptides and protein, UNIT 3: LIPIDS 9 Lipids: Classification, physical & chemical properties, saturated and unsaturated fatty acids, Structure of cell membrane & transport. UNIT 4: VITAMINS & HORMONES 9 Vitamins: Classification, occurrence, deficiency symptoms, and biochemical functions of fat-soluble and water soluble Vitamins. Hormones - Definition, Classification of Hormones, Secondary messengers (Cyclic AMP, IP3 and

DAG) Biological function and disorders of Pancreatic Hormones (Insulin & Glucagon), Brief

description on Thyroid hormone and its functions.

UNIT 5: ENZYMES 9 Enzymes – Definition, classification with example, active site, lock & key model, induced fit hypothesis. Enzyme units – kinetics - Michaelis-Menten’s Equation form and details significance of Vmax and Km- factors affecting enzyme activity – Enzyme inhibition – definition and types. RECOMMENDED TEXTS: 1. Voet, D., Voet, J.G., Pratt, W.C., “Fundamentals of Biochemistry”, 2011, 4

th Ed., John Wiley

Publications. 2. Rastogi, S.C., “Biochemistry”, 2010, 3

rd Ed., Tata Mc-Graw Hill Publications.

3. Agarwal, “Text Book of Biochemistry”, 2007, 14th Ed., Krishna Publishers.

4. Nelson L.D. & Cox, M. M, “Lehninger’s Principles of Biochemistry”, 2011, 5th Ed., W. H. Freeman

5. Jain, J. L., “Fundamentals of Biochemistry”, 2004, 6th Ed., S.Chand Publication.

6. Stryer, L., Berg, J.M. & Tymoczko, J. L., “Biochemistry”, 2010, 7th Ed., W. H. Freeman & Co. Ltd.

7. Sathyanarayana, U. & Chakrapani, “Biochemistry”, 2008, 3rd

Ed., Books and Allied (P) Ltd.



GENETICS Semester : III Credits : 4


Course Objective: To enable students understand the concepts of genetics and its importance in biotechnology and bioinformatics.

Unit 1: Mendelian Laws of Inheritance 9 Gene interactions - incomplete dominance - Mirabilis, co-dominance-coat colour in cattle, lethal genes-Albinism and coat colour in mice, complementary genes- flower colour in lathyrus, Epistasis- fruit colour in summer squashes, Duplicate genes with cumulative effect- fruit shape in summer squashes, Inhibitory factor- Leaf colour in Paddy, Pleiotropism Unit 2: Sex determination in Plants and Animals: 9 ex linkage ; non-disjunction as a proof of chromosomal theory of inheritance. Linkage and crossing over-mechanism of crossing overproof of crossing over-two point and three point test cross- interference and coincidence-Linkage maps, Sex linked inheritance - eye colour in Drosophila, Hemophilia in man-Holanclric inheritance- sex limited and sex influenced characters Unit 3: Quantitative Inheritance 9 General characters - skin colour in man, ear size in corntransgressive variation. Multiple alleles: Albino series in Rabbits- ABO blood group in man- self sterility in tobacco - Structural and Numerical Aberration Involving Chromosomes Hereditary defects-Kleinfelter, Turner and Down syndromes, Mutations- spontaneous and induced; chemical and physical mutagens; induced, mutation in plants, animals and microbes for economic benefit of man. Unit 4: Basic Microbial Genetics 9 Conjugation, transduction, transformation; isolation of auxotrophs, replica plating techniques, analysis of mutations in biochemical pathways, one gene one enzyme hypothesis Unit 5: Extra Chromosomal Inheritance 9 Mitochondrial and chloroplast genetic systems. Population genetics; Hardy-Weinberg equilibrium, gene and genotypic frequencies. RECOMMENDED TEXTS: 1. William Klug, “Essential of Genetics”, 2009, 7

th Ed., Pearson Educations

2. Griffiths A.J. F., Wessler, S.R., Lewontin, R.C. & Caroll, S.B., “Introduction to Genetic Analysis”,

2010, 10th Ed., W. H. Freeman Publishers

3. Hartwell, L, Leroy Hood, Michael Goldberg, Ann Reynolds, Lee Silver, Ruth Veres, “Genetics: From

Genes to Genomes”, 2010, 4th Ed., Mc-Graw Hill Series.

4. Krebs J.E., Goldstein, E.S., & Kilpatrick, S.T., “Lewin’s Genes X”, 2010, 10th Ed., Jones and Barlett

Publishers.

5. Sudbury, P. & Sudbury, I., “Human Molecular Genetics”, 2009, 3rd

Ed., Pearson Education.

6. Benjamin A. Pierce, “Genetics: A Conceptual Approach”, 2011, 4th Ed., W. H. Freeman Publishers



BIOSTATISTICS Semester : III Credits : 5

Category :Allied Hrs/Wk : 4

Course Objective: To review the basic concepts of statistics relevant to biology data handling.

Unit 1: Introduction 7

Biostatistics: Definition - Statistical terms: Population-sample - unit, variable, Parameters, Limitations and uses of statistics

Unit 2: Data collection 9

Data and its collection- Classification of Data: purpose of classification, advantages, types of classification. Tabulation of Data: Objectives of tabulation, rules of Tabulation, Difference between classification and Tabulation- Diagrammatic presentation of Data: Line Diagram Bar diagram percentage bardiagram-Pie diagram Graphical Representation of Data- Histogram. Frequency curve, frequency Polygon, Ogives.

Unit 3: Measures of central Tendency and Dispersion 9

Mean, Median, Mode, Quartiles, Deciles, and percentiles-merits and demarits of the above measures. Mean deviation measures of dispersion:- Range, mean deviation, standard deviation, and its relative measures- co-efficient of variation.

Unit 4: Correlation and regression analysis 10

Concepts of correlation-coefficient of correlation- Types of correlation-Scatter Diagram or Dot Diagram method- Karl Pearson’s co-efficient of correlation- Spearman’s Rank correlation coefficient probable error in correlation.

Regression - Meaning, Linear regression regression coefficient and its properties Regression equations, fitting, prediction-Difference between correlation and Regression.

Unit 5: Statistical Inference: 10

Tests of Significance Null hypothesis, alternative hypothesis, simple hypothesis and composite hypothesis, two types of errors- single tail and two tailed test. Large sample test: Test of Significance of a single mean and difference between two means- Student’s ‘t’ test: test of significance of a single mean and differences between means when n1=n2 and n1≠n2 Chi square test for goodness of fit- Analysis of variance-meaning, assumptions, one way classification and two way classification (simple problems). RECOMMENDED TEXTS:

1. Zar, J.H. “Biostatistical Methods”, 2009, 5th Ed., Prentice Hall Publications.

2. Gurumani. N, “Introduction to Biostatistics”, 2004, 1st Ed., MJP Publishers, Chennai.

3. Sundar Rao, P.S.S. & Richards, J. “An Introduction to Biostatistics”, 2003, 3rd

Ed., CMC.

4. Daniel W.W., “Biostatistics – A foundation for analysis in the Health Sciences”, 1999, 1st Ed.,

John Wiley and Sons.

5. Bishop, O.N, “Statistics for biology”, 1983, 3rd

Ed., Prentice Hall Press.



OBJECT ORIENTED PROGRAMMING WITH C++ Semester : III Credits : 4


Course Objective: To impart object oriented programming skills using C++ language and understand it’s importance in biological data management.

Unit 1: Object Oriented Programming 9 Principles of object oriented programming (OOP): Software evolution-OOP paradigm basic concepts of OOP-object oriented languages-applications of OOP. Unit 2: Functions 9 Introduction to C++, Tokens, keywords, Identifiers, Variables, Operators, manipulators, Expressions and control structures in C++. Functions in C++-main function-function typing-call by reference-return by reference-function overloading-friend and virtual function. Unit 3: Classes and Objects 9 Classes and objects: constructors and destructors and operating overloading and type conversions. Unit 4: Inheritance 9 Inheritance: Types – single, multilevel, hierarchical and hybrid inheritance. Pointers, virtual functions and polymorphism. Managing console I/O operations. Unit 5: File Handling 9 Working with files: Classes for file stream operations-opening and closing a file-end of file (EOF), file detection-file pointers-updating a file-error handling during file operations-command line arguments. RECOMMENDED TEXTS:

1. Balagurusamy, E., “Object oriented programming with C++”, 2008, 4th Ed., Tata McGraw Hill.

2. Herbert Schildt, “C++ The complete Reference”, 2003, 4th Ed, Qinghua University Press.

3. Yashavant P. Kanetkar, “Let us C++”, 2003, BPB Publications. 4. Ray Lischner, “Exploring C++:The Programmer’s Introduction to C++”, 2009, Apress

Publishers. 5. Deitel, P & Deitel, H., “C++ How to Program”, 2011, 8

th Ed., Prentice Hall.



BIOCHEMISTRY LAB Semester : III Credits : 3


1. Buffer Preparation Procedure

2. Qualitative tests of glucose, fructose (Benedict’s test, Seliwanoff’s test)

3. Qualitative tests of sucrose (acid hydrolysis and benedict’s test)

4. Qualitative tests of proteins (peptone, egg albumin by biuret test, heat coagulation test),

5. Qualitative tests of amino acids (glycine by ninhydrin),

6. Qualitative tests of fats (coconut oil by saponification, emulsification)

7. Assay of enzyme activity

8. Kinetic studies on enzymes

9. Qualitative estimation of DNA

10. Extraction and separation of lipids

11. Paper Chromatography

12. TLC



C++ LAB Semester : III Credits : 2


1. Basic C++ program structure

2. Control structures

3. Looping Structures

4. cin and cout functions

5. Classes and Objects

6. Constructors

7. Destructors

8. Operator overloading

9. Friend functions

10. Single Inheritance

11. Multiple Inheritance



MOLECULAR BIOLOGY

Semester : IV Credits : 4


Course Objective: To expose students to molecular level details of the cell and their associated processes. UNIT 1: Central Dogma 9

Central dogma of Molecular Biology.DNA Replication. Prokaryotic and Eukaryotic DNA replication,

Mechanism of DNA replication, Enzymes and accessory proteins involved in DNA replication.DNA

Repair – light and dark mechanisms . Regulation of gene expression-lac and trp operons.

UNIT 2: Transcription 9

Transcription - Prokaryotic Transcription, Eukaryotic Transcription, RNA polymerase. Transcriptional

and post-transcriptional gene silencing.Modifications in RNA.5’ cap formation, 3’-end processing and

polyadenylation, splicing, Editing, Nuclear export of mRNA.

UNIT 3: Protein Synthesis 9

Translation - Prokaryotic and eukaryotic translation, the translation machinery, Mechanisms of

initiation, elongation and termination, co-and post-translational modifications of proteins. Import into

nucleus, mitochondria and chloroplast. Receptor mediated endocytosis.

UNIT 4: Oncogenes 9

Oncogenes and Tumor Suppressor Genes-Viral and cellular oncogenes,tumor suppressor genes from

humans, Structure, function and mechanisms p53 tumor suppressor proteins. Homologous

Recombination-Holliday junction model.

UNIT 5: Mapping Of Genome 9

Molecular Mapping of Genome - Genetic and physical maps. Southern and fluorescence in situ

hybridization in genome analysis – PCR and its types.

RECOMMENDED TEXTS:

1. Lodish, H., Berk, Matsudaira, Kaiser, Krieger, Scott, Zipursky, and Darnell, “Molecular Cell Biology”

2010, 6th Ed., W. H. Freeman Publishers.

2. Alberts, B., Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter, “Molecular

Biology of the Cell”, 2002, 4th Ed., Garland Science Publishers.

3. Watson, J.D., Baker, T.A., Bell, S.P., Gann, A., Levine, M. & Losick, R., “Molecular Biology of the

gene”, 2008, 6th Ed., Pearson Prentice Hall.

4. Karp, G., “Cell and Molecular Biology”, 2009, 6th

Ed., Wiley Publications.

5. Malacinki, G.M., “Essentials of Molecular Biology”, 2005, 4th Ed., Jones and Barlett publisher.



INTRODUCTION TO BIOINFORMATICS



Course Objective: To enable students to learn important databases and their associated tools commonly employed in bioinformatics UNIT 1: Introdution 9 Definition, role of computer in Bioinformatics, Branches of Bioinformatics, Aim of Bioinformatics, Scope and Research areas of Bioinformatics. Genome projects, human genome project, role of Bioinformatics in biological sequences. Biological data - DNA sequence protein sequence, macromolecular structure. UNIT 2: Introduction to Databases 9 Introduction to Genomic data and proteomic Data Organization-post genomic era- data acquisition- functions and purposes of biological databases- relational and object oriented concepts - Information retrieval concepts of digital libraries. Information Retrieval from Biological Databases:ENTREZ-SRS. UNIT 3: Introduction to Nucleic Acid Databases 9 Primary & Secondary database- Format vs content-INSDC- GenBank Flat File - EMBL nucleotide sequence data bank - DDBJ - RNA SEQUENCE DATABASES: 16S and 23S rRNA mutation databases- HIV sequence databases-NONCODE-sequence submission tools: sequin, webin, sakura, Bankit. UNIT 4: Introduction to Protein Sequence Databases 9 Protein sequence databases:PIR – SWISSPROT - Uniprot – TrEMBL – EXPASY - NCBI protein databases – PRF – Uniparc – MIPS - DIP.Protein sequence motif databases: Eblocks – emotif -PROSITE.PROTEIN DOMAIN DATABASES: ADDA, Interpro, Pfam - Prodom UNIT 5: Introduction to Structure Databases 9 PDB - PDBsum – SCOP - CATH - MMDB - EMSD - SWISS MODEL repository – ModBase - Protein Model Portal – EuroCarbDB – DIP – BIND - STRING. RECOMMENDED TEXTS:

1. Orpita Bosu & Simminder Kaur Thukral, “Bioinformatics: database, tools, algorithms”, 2007, Oxford University press. 2. Higgins, D. & Willie Taylor, “Bioinformatics: Sequence, Structure, and Databanks: A Practical Approach”, 2000, 1

st Ed., Oxford University Press.

3. Attwood, T. & David Parry-Smith, “Introduction to Bioinformatics”, 2008, Pearson Education (singapore) P Ltd. 4. Lesk A, M., “Introduction to Bioinformatics”, 2009, Oxford University Press. 5. Mount W. D., “Bioinformatics: Sequences and genome analysis”. 2004, 2

nd Ed., Cold Spring Harbor

Laboratory press.



BIOPHYSICS



Course Objective: To discuss the structural nature of biomolecules and their importance in living systems. Unit 1: Chemical & Physical basis of Biomolecules 11 Introduction to Biomolecules, Quantum Mechanics, Electronic structure of atoms, Molecular orbitals, Molecular interactions, Chemical structure of proteins, nucleic acids, carbohydrates and lipids The hydrophobic effect and its importance – acids, bases and pH-pK, pI and buffering.

Unit 2: Thermodynamics 10 Thermodynamics of biological systems-importance of Gibbs free energy, G-free in terms of enthalpy and entropy – dependence of G on temperature and pressure - chemical potential - chemical equilibrium.

Unit 3: Structure and Dynamics of Biomolecules 6 Introduction, Nucleic Acid Structure, Chemical Structure, Conformational possibilities of monomers and polymers, polymorphism of DNA, DNA supercoiling and unusual DNA structure, RNA structure, Protein structure-peptide bond-primary structure-secondary structure-alpha helix-beta sheet-tertiary structure-quaternary structure.

Unit 4: Enzyme Kinetics 8 Reaction kinetics - transition state theory - enzyme catalysis in terms of Gibb’s free energy - structure and function of chymotrypsin - charge relay system - activation of chymotrypsin - trypsin and elastase - convergent and divergent evolution – enzyme efficiency in terms of entropy and effective concentration.

Unit 5: Protein Structure – Methods 10

Protein crystallography - the phase problem-Patterson function - isomorphous replacement - anomalous scattering – refinement - comparison between x ray and neutron diffraction. NMR-Nuclear spin and splitting of energy levels in magnetic spin, the absorption of radiation by nucleus in a magnetic field, relaxation processes, chemical shift, spin-spin coupling. Fluorescence, UV, CD, IR-principles and application.

RECOMMENDED TEXTS:

1. Pattabhi V. & N. Gautham, “Biophysics”, 2008, 2nd

Rev ed., Alpha Science International Ltd. 2. Bengt Nolting, “Methods in Modern Biophysics”, 2009, 3

rd Ed., Springer.

3. Cotterill, R., “Biophysics: An Introduction”, 2003, John Wiley & Sons. 4. Haynie, D.T., “Biological Thermodynamics”, 2008, Cambridge Press. 5. Daune M., “Molecular Biophysics: Structures in Motion”, 1999, Oxford University Press. 6. Glaser R., “Biophysics: An Introduction”, 2012, 2

nd Ed., Springer.

7. Roy, R. N., “A Text Book of Biophysics”, 2005, 6th Ed., New Central book agency Pvt. Ltd.

8. P. Narayanan, Essential of Biophysics, 2010, 2nd

Rev. Ed., Anshan Ltd.



METABOLISM AND BIOENERGETICS Semester : IV Credits : 4


Course Objective: To explain the fundamental knowledge and concepts of buffers, metabolism and energy management of the cell. Unit 1: Buffers 7

Definition and determination of pH, Henderson Hasselbalch Equation. Dialysis, Surface tension and

Viscosity. Principle and Applications of Colorimetry and Chromatography.

Unit 2: Carbohydrate Metabolism 11

Carbohydrate Metabolism – Introduction, importance - Glycolysis , Glycogenesis , Glycogenolysis,

Citric acid cycle & HMP shunt. Biosynthesis of nucleotides and bacterial cell wall.

Unit 3: Lipid Metabolism 8

Lipid Metabolism - Biosynthesis of Saturated &Unsaturated fattyacids. Beta & omega oxidation of

fatty acids and cholesterol Biosynthesis.

Unit 4: Protein Metabolism 9

Transamination, oxidative and non-oxidative deamination, decarboxylation - urea cycle.

Interrelationship of carbohydrates, proteins and fat metabolism

Unit 5: Bioenergetics 10

Laws of thermodynamics, Redox potential, Respiratory chain, Oxidative phosphorylation (Theories

and Mechanism), High energy compounds .

RECOMMENDED TEXTS:

1. Jain, J. L., “Fundamentals of Biochemistry”, 2004, 6th Ed., S.Chand Publication.

2. Rastogi, S.C., “Biochemistry”, 2010, 3rd

Ed., Tata Mc-Graw Hill Publications. 3. Agarwal, “Text Book of Biochemistry”, 2007, 14

th Ed., Krishna Publishers.

4. Nelson L.D. & Cox, M. M, “Lehninger’s Principles of Biochemistry”, 2011, 5th Ed., W. H. Freeman

5. Voet, D., Voet, J.G., Pratt, W.C., “Fundamentals of Biochemistry”, 2011, 4th Ed., John Wiley

Publications. 6. Stryer, L., Berg, J.M. & Tymoczko, J. L., “Biochemistry”, 2010, 7

th Ed., W. H. Freeman & Co. Ltd.

7. Sathyanarayana, U. & Chakrapani, “Biochemistry”, 2008, 3rd

Ed., Books and Allied (P) Ltd. .



DBMS AND WEB TECHNOLOGY



Course Objective: to enable students learn the concepts of databases and technologies employed in managing web. Unit 1: Database Concepts 9

Database – Definition and examples – computerized databases – advantages and disadvantages –

Characteristics of Database, Database System Applications, Database System Versus File Systems,

Concepts and Architecture

Unit 2: Database Model 8

Examples of logical models – hierarchial, network and relational models – RDBMS – object oriented

models. Database users and Administrators - Centralized and Client-Server Architecture, Distributed

DBMS, Data Integration, Data Warehousing.

Unit 3: Introduction to Database Management System (DBMS) 10

Advantages and Components of DBMS – Feasibility study – Class Diagrams – Data types – Events –

Normal Forms – Integrity – Converting Class Diagrams to normalized tables – Data Dictionary–

Structured Query Language Basic Structure, Set Operations, Aggregate Functions, Null Values,

Nested Sub queries, Views, Integrity: Domain constraints, Joined Relations, Data-Definition

Language, Embedded SQL, Dynamic SQL - Testing queries.

Unit 4: Basics of Network and Internet 9

Networking - LAN, WAN & MAN, Intranet - Internet, Web Services WWW, URL, DNS - Servers-E-mail

server, WEB servers, Browsers -IP Addressing - Structure of an IP address – Topologies - FTP and

Telnet

Unit 5: Markup language 9

How a Web Browser communicates with a web server, what is HTML and various standard HTML

tags, Introduction to CSS, Using external CSS files, Java Script, Basic Concepts, data types, control

structures, operators, basic scripting.

RECOMMENDED TEXTS:

1. Date, C.J., Kannan, A. & S. Swamynathan, “An introduction to Database systems”, 2006, 8th Ed.,

Pearson Education.

2. Elmasrim R & Navathe, S.B., “Fundamentals of Database Systems”, 2004, 4th Ed., Addison Wesley

Publishers.

3. Ullman, J. D. “Principles of Database systems”, 2008, 2nd

Edition, Galgotia Publications.

4. Dr.C.Xavier, ”WWW with HTML”, 2001, McGraw Hill Education.

5. Deitel and Deitel, “Internet and World Wide Web”, 2009, 2th Ed., Pearson Education International.



MOLECULAR BIOLOGY LAB



1. Isolation of Genomic DNA

2. Isolation of Plasmid DNA from E. coli cells

3. Isolation of extra cellular protein from prokaryotic cells

4. Isolation of intracellular protein from prokaryotic cells

5. Purification of proteins by ammonium sulfate precipitation

6. Purification of proteins by column chromatography

7. Agarose Gel electrophoresis

8. PAGE

9. PCR (Demonstration)



DBMS LAB



1. DDL

2. Simple Queries

3. DCL

4. DML

5. Built-in-functions

6. Group Functions

7. Multiple sub-queries



CONCEPTS IN BIOINFORMATICS

Semester : V Credits : 4

Category :Core Hrs/Wk : 4

Course Objective: To provide students with foundation in the important concepts associated with bioinformatics. Unit 1: Introduction to sequence alignment 9 Introduction. Sequence Alignment – Scoring matrix – PAM, BLOSUM, Gaps and Gap Penalities. Different gap weights, Biological significance of Gaps. Unit 2: Pairwise Sequence Alignment 9 DotPlot analysis, Dynamic programming, - Needleman – Wunch Algorithm, Smith-Watermann algorithm, Edit distance Dynamic Programming, Database similarity search – BLAST, FASTA. Unit 3: Multiple Sequence alignment 9 Sum of Pairs, Divide and Conquer, Progressive and Iterative alignment, ClustalW, TCOFFEE. Profile Methods – Gribskov profile, PSI-BLAST Unit 4: Phylogenetic Relationships 9 Clustering and Phylogeny; Methods for Phylogeny analysis: Distance and Character based methods; Motif detection; Protein family databases; Unit 5: Sequence analysis 9 Protein sequence: Compositional analysis ; Hydrophobicity profiles; Amphiphilicity; Nucleotide Sequences: Reading frames; Codon Usage analysis; Translational and transcriptional signals;

RECOMMENDED TEXTS: 1. Baxevanis A.D., “Current Protocols in Bioinformatics”, 2004, Wiley Publishers.

2. Mount, D.W., “Bioinformatics: Sequences and genome analysis”. 2004, 2nd

Ed., Cold Spring Harbor

Laboratory Press.

3. Pevzner P.A., “Computational Molecular Biology”, 2004, Prentice Hall of India Ltd.

4. Krane D.E. & M.L.Raymer, “Fundamental concepts of Bioinformatics”, 2003, Pearson Education

5. Gautham. N., “Bioinformatics: Databases and Algorithms”, 2006, Narosa publications.



IMMUNOLOGY



Course Objective: To expose students to the fundamental knowledge and concepts of immunity, immune system and it’s functioning. Unit 1: Introduction 9

Historical perspectives and overview of immune system, Types of immunity - innate and acquired immunity. Arms of acquired immunity - Immune system- Organs and Cells, Haematopoiesis.

Unit 2: Antigens and Immune Response 9

Antigen – Properties, Classes. Haptens, Adjuvants. Humoral response – B cell activation and proliferation. Cell mediated immunity – receptors and T cell activation. Major Histocompatability Complex – structure and its role in T-cell activation. Hypersensitive reactions (type I, type II, type III, type IV).

Unit 3: Immunoglobulins and Antigen – Antibody Interactions 9

Immunoglobulins – Structure and function., Monoclonal anti bodies. Organization and expression of immunoglobulin genes. Antigen – Antibody interaction – primary, secondary - agglutination reactions, precipitation reactions, tertiary reactions – solid phase immunoassays.

Unit 4: Cytokines 9

Cytokines: Types and function, Complement system – Classical pathway and Alternate pathway,

Unit 5: Infectious Diseases 9

Immune regulation and suppression, Autoimmunity, Vaccines and immune response to infections diseases, Immune deficiency diseases (AIDS).

RECOMMENDED TEXTS:

1. Roitt, L.M., J. Brestoff and D.K. Males, “Immunology”, 2006, 6th Ed., Freeman and company

Publications.

2. Thomas J. Kindt , Barbara A. Osborne, Richard Goldsby, “Kuby’s Immunology”, 2006, 6th Ed.,

Freeman and company

3. William E. Paul, “Fundamental Immunology”, 2003, 5th Ed., Lippincott Williams and Wilkins.

4. Rajasekara Pandian M and Senthil kumar, “Immunology and Immunotechnology”, 2007, Panima

publishing corporation, New Delhi.

5. Roitt. & Roitt, “Essential Immunology”, 2006, 11th Ed., Wiley Blackwell publishers.



PERL AND BIOPERL



Course Objective: To enable students learn the programming skills using PERL programming language as applicable to bioinformatics. Unit 1: Introduction To Perl 5 Introduction to PERL and data types – scalars – a functional approach – constructing atgc.pl. tr/// function – text formatting – formatting numerical output with printf – trapping errors at run time – the s/// operator – the chop and chomp operators. Unit 2: Introduction To Arrays And Hashes 10 Introduction to arrays and Hashes– split function – for each loop – advanced array operation – copying and creating arrays – populating arrays with sequential data – qw function – determination of the size of an array – counting arrays – accessing last element in an array – adding elements to the end of an array – adding elements – removing elements – altering elements – array slices – splicing array – sorting arrays – reversing arrays – arrays from strings. Creating Hashes-Adding elements to Hashes- printing hash elements. Unit 3: Regular Expressions 8 Perl regular expressions – special characters (+, *,?, [ ]) – regex operator – pattern modifier operator – conditional matching operator – range operator – match quantifiers – pattern comments. Unit 4: Control Statements And Modules 10 Perl control statements – control structures – if statements – if-else – if-elsif – if-elsif-else – while loop – until loop –unless for loop – foreach loop – scoping of variables. Introduction to Perl modules: Getopt: Long module and LWP:: Simple Module. Files – operating files – file modes – file test operators – accessing files with , @ ARGV variable – accessing file with perl modules – extracting files – deleting files – accessing directories – Cwd module – system function – perl subroutines and functions. Unit 5: Bioperl 12 General Bioperl Classes, Sequences, Sequence Manipulation, Features and Location Classes - Alignments: AlignIO - Analysis: Blast. Databases: Database Classes, Accessing a local database - Bioperl module - parsing blast reports – align sequences – clustalw.pm RECOMMENDED TEXTS: 1. Harshawardhan Bal, “PERL Programming For Bioinformatics”, 2002, 1

st Ed., Tata McGraw Hill

Publications. 2. Steven Holzner, “PERL, Black Book”, 2001, 2

nd Ed., Dreamtech Publications.

3. James D. Tisdall, “Beginning Perl for Bioinformatics”, 2001, O’Reilly Publications. 4. James D. Tisdall, “Mastering Perl for Bioinformatics”, 2003, O’Reilly Publications. 5. Cynthia Gibas & Per Jambeck, “Developing Bioinformatics Computer Skills”, 2001, O'Reilly Media. 6. Randal Schwartz and Tom Phoenix and brian d foy, “Learning Perl”, 2005, 4

th ed., O'Reilly &

Associates.



RECOMBINANT DNA TECHNOLOGY


Category : Application Oriented Hrs/Wk : 4

Course Objective: Explain the fundamental knowledge and concepts of computers; introduce the computer organization and its development; acquaint computer operations and develop basic programming skills Unit 1: Introduction 9

History and recent developments in rDNA Technology - Enzymes in rDNA Technology – Restriction Endonuclease – Ligases – Alkaline phospotase – Polynucleotide kinase - Terminal deoxynucleotidyl transferase - S1 nuclease - DNA polymerase - Rnases – Ribonuclease – Reverse transcriptase - Taq polymerase .

Unit 2: Vectors and Plasmids 9

Vectors- Plasmids - Size - Copy Number - Amplification- Types – Plasmid pBR322 - origin – advantage –pUC - Col E1 plasmid – Ti plasmid - F plasmid – R plasmid . Lamda phage vectors, cosmids and phagemid as vectors.

Unit 3: Viruses 9

Animal and Plant Viruses and their use as vectors, Shuttle vectors, Expression vectors. Screening and selection of recombinant clones.

Unit 4: Techniques 9

Gene transfer techniques. Molecular mechanism of antisense technology. PCR, RAPD, RFLP, Safety regulations in recombinant DNA.

Unit 5: Libraries 9

Construction of genomic and cDNA libraries, screening of libraries, Site directed mutagenesis, Ethical issue involving in rDNA Technology. rDNA Technology in solving human problems.

RECOMMENDED TEXTS

1. Lewin, B., Kreb’s, J.E., Goldstein, E.S., & Kilpatrick, S.T., “Lewin’s Gene X”, 2010, 10th Ed., Jones

and Barlett Publisher.

2. Primrose, S B and Twyman, R.M, “Principles of Gene Manipulation and Genomics”, 2006, 7th Ed.,

Blackwell Publishing Company.

3. Satyanarayana. U, “Biotechnology”, 2008, 3rd

Ed., Books and Allied (P) Ltd

4. Brown, T.A., “An Introduction to Gene Cloning”, 2003, 5th Ed., Willey Blackwell Publications.

5. Glick, B.R., Pasternak, J. J. & Patten, C.L., “Molecular Biotechnology: Principles and Applications of Recombinant DNA”, 2010, 4

th Ed., ASM Press.



IMMUNOLOGY LAB



1. Blood collection by vein puncture technique (demonstration)

2. Separation of serum / plasma from blood sample

3. Agglutination- Haem agglutination-ABO blood grouping

4. WIDAL test

5. ASO test

6. Immunodiffusion

7. Immunoelectrophoresis

8. ELISA



PERL LAB



1. Scalar variables

2. Array variable

3. Array functions

4. Hashes variable

5. Control structures

6. Looping Constructs

7. File input and output

8. Pattern matching

9. Subroutines



Elective I

NANOBIOTECHNOLOGY


Category : Elective I Hrs/Wk : 5

Course Objective: To enable students understand the concepts involved in biotechnological applications of nanoparticles. Unit 1: Introduction 9 Nanotechnology – definition and scope, nanobiotechnology- recent development and applications, Biocompatability and cytotoxicity studies of Nanomaterials, carbon nanotubes , Bioconjugation mediated drug delivery. General medicine is changing into personalized nanomedicine. Unit 2: Biopolymer 9

Biopolymer- polymer nanofibers - electrospinning method and their biomedical applications, polymer nanocomposite- bone and dental restorations, polymer controlled drug delivery for the treatment of cancer and other diseases. Biodegradable polymer derived from amino acid.

Unit 3: Biocompatible nano materials 9

PLA and PLGA Based nanoparticulate delivery system. Metal Microbes interaction, Biological metal nanoparticle synthesis and biomedical application – Dendrimers, Biodegradable optical nanoparticles for tumor diagnosis and treatment.

Unit 4: Liposphere in drug target and delivery 9

Liposome - liposomes in sensor technology, polymeric Micelles – Production of Lipospheres for Bioactive compound delivery – Melt dispersion technique, Solvent evaporation technique and InVitro drug release - Polymeric biodegradable liposphere for vaccine delivery.

Unit 5: Nucleic acid based nanomaterials 9

Nucleic acid engineered nanomateials and their applications. Protein patterning for applications in biomaterials. DNA lipoplexes – Lipofection efficiency In Vitro and In Vivo, Polymer controlled delivery of therapeutic nucleic acid.

RECOMMENDED TEXTS:

1. Challa S.S.R. Kumar, “Biological and Pharmaceutical nonmaterial’s”, 2006, Wiley-VCH Verlag

GmBH & Co.

2. Jain. K.K., “Nanobiotechnology in Molecular Diagnostics: Current Techniques and Application”,

2006, Horizon Biosciences.

3. Niemeyer, C.M. & Mirking C.A., “Nano biotechnology concepts. Applications and Perspectives”,

2004, Wiley- VCH, Weinheim

4. Claudio Nastruzzi, “Liposphere in drug targets and delivery”, 2005, CRC press.



ELECTIVE – I

PLANT AND ANIMAL BIOTECHNOLOGY



Course Objective: To provide overview on the importance of different concepts associated with Plant and Animal cells. Unit 1: Introduction 9

Introductory history - Laboratory organization - sterilization techniques – nutrition for plant cells, types

of media – MS – Nitsch & Nitsch media, Gamborg’s media, White’s Media. Structure and function of

Growth regulators – Auxins, Cytokinins and Gibberellins. Establishment and maintenance of callus

and suspension cultures. Somatic embryogenesis, cytology of callus. Green house effect.

Unit 2: Somatic Hybridization 9

Protoplast isolation, Culture regeneration, fusion. Somatic hybrids, cybrids, cryopreservation,

Synthetic seeds – Terminator seed concept. Gene transfer techniques in plants. Applications of

transgenic plants.

Unit 3: Plant micropropagation 9

Plant micro propagation – micro grafting – invitro clonal multiplication – clonal orchards – meristem

culture and virus elimination shoot tip culture. Edible vaccines from plants – Banana, Watermelon.

Unit 4: Animal Tissue Culture methods 9

Animal Tissue culture – Principles & practice, cleanliness, precautions, care to be taken. Nutrition &

Physiology media components – Serum, balanced salt solutions, washing, packing, sterilization

practices, instruments. Primary cell culture, establishing & maintenance of lymphocyte culture.

Unit 5: Characterization of Animal Cell lines 9

Cell lines – Insects & Animals cells, subculture. Organ & tissue culture. Karyotyping, biochemical &

genetic characterization of cell lines. Cell Repositories, their function. Application of Animal cell

cultures.

RECOMMENDED TEXTS:

1. Davis. M. J., “Animal Cell culture: Essential Methods”, 2011, Wiley Blackwell Publications

2. Satyanarayana, U., “Biotechnology”, 2008, 3rd

Ed., Books and Allied (P) Ltd.

3. Chawla, H.S., “Introduction to Plant Biotechnology”, 2009, 3rd

Ed., Oxford and IBH Publishing

4. Islan A.C., “Plant tissue culture”, 1996, Oxford& IBH Publishing Co.

5. Ramawath, “Plant biotechnology”, 2003, 2nd

Ed., S. Chand & co.



ELECTIVE – I

BIOPROCESS TECHNOLOGY Semester : V Credits : 5


Course Objective: To enable students to learn the principles of bioprocess technology

Unit I: Basic principle of Biochemical engineering 9 Isolation, screening and maintenance of industrially important microbes; Microbial growth and death kinetics (an example from each group, particularly with reference to industrially useful microorganisms); Strain improvement for increased yield and other desirable characteristics. Unit II: Concepts of fermentation processes 9 Bioreactor designs; Types of fermentation and fermenters; Upstream processing: Media formulation; Sterilization; Aeration and agitation in bioprocess; Measurement and control of bioprocess Parameters; Scale up and scale down process. Unit III: Downstream processing 9 Bioseparation; Filtration; Centrifugation; Sedimentation; Flocculation; Cell disruption; Liquid-liquid extraction; Purification by chromatographic techniques; Reverse osmosis and ultra filtration; Drying; Crystallization; Storage and packaging; Treatment of Effluent and its disposal. Unit IV: Industrial production of chemicals 9 Alcohol, acids, solvent, antibiotics, amino acids and single cell protein; Fermentation economics of Largescale production. Unit V: Enzyme production 9 Production, recovery and scaling up of enzymes and their role in food and other industries; Immobilization of enzymes and their industrial applications. Recommended Texts

1. Rajiv Dutta, “Fundamentals of Biochemical Engineering”, 2010, 1st Ed., Springer, Heidelberg.

2. Henry C. Voegel, “Fermentation and Biochemical Engineering Handbook”, 2007, 2nd

Ed., William

Andrew Publishers.

3. Jackson AT, “Bioprocess Engineering in Biotechnology”, 1990 (Digitized: 2007), Oxford University

Press.

4. P F Stanbury, S. Hall, “Principles of fermentation technology”, 1999, 2nd

Ed., Butterworth –

Heinmann Publishers.

5. Michael L. Shuler, “Bioprocess Engineering: Basic Concepts”, 2001, 2nd

Ed., Prentice Hall.



ALGORITHMS IN BIOINFORAMTICS

Semester : VI Credits : 4


Course Objective: To enable students understand the basic algorithms necessary for proper interpretation of results obtained by using several bioinformatics tools. Unit 1: Strings and trees: 9

Definitions – strings – substrings, superstrings, suffix and prefix strings – operations on strings – concatenation – delete operator – graphs – definitions – directed, connected, cyclic, complete graphs – trees and terminology – leaf, node, branch root – algorithms – big O notation – classification of algorithms – P, NP, NP-hard, NP – complete, with examples.

Unit 2: Sequence alignment: 9 Why align sequences – similarity v/s homology – heterologs, orthologs, paralogs, xenologs – Karlin – Altschul statistics to estimate significance of an alignment – expectation values and Z values – sequence comparisons using dot matrices with examples – dynamic programming – details of Needleman – Wunsch, and Smith – Waterman algorithms with worked out examples – BLAST and FASTA.

Unit 3: Alignment strategies: 9

Multiple sequence alignment, substitution matrices. Representing and scoring a multiple sequence alignment – progressive or hierarchical alignment with worked out examples – substitution matrices – evolutionary models – PAM substitution matrices – BLOSUM substitution matrices – gap penalties

Unit 4: Evolutionary Relationships 8

phylogenetic trees – distance matrix methods – UPGMA, neighbour joining, with worked out examples – maximum parsimony with worked out examples - maximum likelihood. and phylogenetic trees

Unit 5: Pattern matching: 10

Pattern discovery and characterization in protein and DNA sequences. Sequence pattern representations – deterministic patterns – regular expressions – probabilistic patterns – sequence logos – general methods of pattern classification – methods for proteins – hidden Markov models and application to analyses of protein sequences – general methods of gene discovery – using HMM, GenMark

RECOMMENDED TEXTS:

1. Mount D.W., “Bioinformatics: Sequences and genome analysis”. 2004, 2nd

Ed., Cold Spring

Harbor Laboratory Press.

2. Gautham. N., “Bioinformatics: Databases and Algorithms”, 2006, Narosa publications.

3. Srinivas V.R. “Bioinformatics: A Modern Approach”, 2009, Prentice-Hall.

4. Pevzner P.A., “Computational Molecular Biology”, 2004, Prentice Hall of India Ltd. 5. Gusfield D., “Algorithms on Strings, Trees and Sequences”, 1997, South Asian Edition,

Cambridge University Press, Cambridge, UK

6. Durbin R., S. Eddy, A.Krogh & G.Michison, “Biological Sequence Analysis”, 1999, Cambridge

University Press, Cambridge, UK

7. Baldi P. & S.Brunak “Bioinformatics”, 2003, Affiliated East-West Press, New Delhi, India



GENOMICS AND PROTEOMICS



Course Objective: To introduce the students to the concept of in silico and in vitro analysis of Genome and Proteome. Unit 1: Genome Organization 9 Organization of the prokaryotic and eukaryotic genomes; Genome maps and types; current sequencing technologies; partial sequencing; gene identification; gene prediction rules and softwares; Genome databases; Annotation of genome. Genome diversity: taxonomy and significance of genomes bacteria, yeast. Unit 2: Genomics: 9 Basic concepts and applications, whole genome alignments: understanding the significance; Artemis, BLAST2, MegaBlast algorithms, PipMaker, AVID, Vista, MUMmer, applications of suffix tree in comparative genomics, synteny and gene order comparisons Comparative genomics databases: COG. Unit 3: Human Genome 9 Mapping of Human Genome; Construction of physical maps; Basics of radiation hybrid maps; Sequencing of the entire human genome, annotation and analysis of genome sequences: sequence repeats, transposable elements, gene structure. Unit 4: Proteomics 9 Protein arrays: basic principles. Computational methods for identification of polypeptides from mass spectrometry. Protein arrays: bioinformatics-based tools for analysis of proteomics data (Tools available at ExPASy Proteomics server); databases (such as InterPro) and analysis tools. Unit 5: Proteome Technology 9 Introduction; Expression proteomics (express profile); Cell map proteomics; Protein separation technology - 2D-Gel Electrophoresis, liquid chromotagraphy, affinity chromatography (for cell map proteomics); mass spectroscopy and its uses in protein identification; Forward and Reverse Proteomics RECOMMENDED TEXTS: 1. Primrose, S.B. and Twyman, R.M., “Principles of Genome Analysis and Genomics “, 2003, 3

rd Ed.,

Blackwell Publishing Company, Oxford, UK. 2. Liebler, D.C. “Introduction to proteomics Tools for the new biology”, 2002, 1

st Ed., Human Press

Inc., NJ, USA. 3. Pevsner, J., “Bioinformatics and Functional Genomics”, 2003, John Wiley and Sons, NJ, USA. 4. Mount, D.W., “Bioinformatics: Sequence and Genome Analysis “, 2004, Cold Spring Harbor Laboratory Press, New York. 5. Lesk, A.M., “Introduction to Bioinformatics”, 2009, Oxford University Press, UK. 6. Rastogi, S.C., N. Mendrita P. Rastogi, “Bioinformatics Methods and Applications: Genomics Proteomics and Drug Discovery”, 2006, 2

nd Ed., Prentice Hall India



STRUCTURAL BIOINFORMATICS AND DRUG DESIGN



Course Objective: To develop students managing biomolecular structures and designing of effective drugs using in silico methods.

Unit 1: Structural Features of Biomolecules 9 Techniques used to determine the structure of biomolecules; Methods for single crystal X-ray Diffraction of macromolecules: molecular replacement method; analysis of structures and correctness of structures; submission of data to PDB: atomic coordinates and electron density maps. Unit 2: Structure Refinement 9 Ramachandran Plot Analysis, the structural formats - mmCIF formats and other data formats, The Nucleic Acid Database, Protein data Bank, other structure databases and Molecular visualization tools, Rasmol, SPDBV, Pymol Unit 3: Protein Modelling 9 Methods for prediction of secondary and tertiary structures of proteins knowledge-based structure prediction; fold recognition; ab initio methods for structure prediction, Comparative protein modeling. Unit 4: Structural Features 9 Protein structure evolution, the SCOP database, The CATH domain structure database, structure quality assurance, structure validation, structure comparison and alignment. Secondary structure assignment, Identifying structural domains in proteins, inferring protein function from structure. Unit 5: Drug Designing 9 Drug design: Drug discovery process. Target identification and validation, lead optimization and validation. Methods and Tools in Computer-aided molecular Design, Structure based drug design:- Docking, De Novo Drug Design (Fragment Placements, Connection Methods, Sequential Grow), Virtual screening. RECOMMENDED TEXTS: 1. Mount, D.W., “Bioinformatics: Sequence and Genome Analysis”, 2004, Cold Spring Harbor Laboratory Press, New York. 2. Lesk, A.M., “Introduction to Protein Architecture”, 2001, Oxford University Press, UK. 3. Mc Pherson, A, “Introduction of Molecular Crystallography”, 2003, John Wiley Publications, USA. 4. Leach, A.R., “Molecular Modeling Principles and Applications”, 2001, 2nd Ed., Prentice Hall, USA. 5. Pattabhi V. & N. Gautham, “Biophysics”, 2008, 2 Rev ed., Alpha Science International Ltd. 6. Philip E Bourne, “Structural Bioinformatics”, 2004, Wiley Publications.



BASIC BIOINFORMATICS LAB



1. Searching Genbank Database

2. Accessing EMBL Database

3. Searching Swiss Prot Database

4. Accessing PIR Database

5. Downloading Genbank format from Genbank

6. Downloading fasta format file from Genbank

7. Depositing sequence to public database

8. Searching and Downloading structure file from PDB

9. Searching and Downloading SCOP database

10. Searching and Downloading ProSite Database

11. Basic Sequence Analysis (Nucleic acid and Protein)

12. Pairwise Sequence Alignment



STRUCTURAL BIOINFORMATICS LAB



1. Multiple sequence alignment

2. Protein Families

3. Phylogenetic Analysis

4. Structural Classification

5. Sequence Format conversion

6. Modeling

7. Rasmol Command prompt Access

8. Structure Validation

9. Accessing Drug Molecule information from Pubchem, Drugbank

10. Docking by Arguslab - Demo

11. Chemical structure drawing by chemsketch

12. File format conversions.



Elective – II

SYSTEMS BIOLOGY Semester : VI Credits : 5

Category : Elective-II Hrs/Wk : 5

Course Objective: To enable students to obtain overview on in silico methods in managing metabolic pathways.

Unit 1 Introduction 9 Systems Biology- Networks.- basics of computer networks and Biological –uses and Integration. Micro array – definition, types of array, Micro array analysis: Hierarchical clustering, Applications of Micro Arrays in systems biology- Self-organizing maps- Connectivity maps- definition and its uses- Networks and Pathways – Types and methods. Metabolic networks, or network of metabolites and enzymes. Unit 2 : Simulation and pathways: 9 Objectives of Systems Biology, Strategies relating to In silico Modeling of biological processes, Metabolic Networks, Signal Transduction Pathways, Gene Expression Patterns. E-cell and V-cell Simulations and Applications. Unit 3 Biochemical Networks 9 Translating biochemical networks into linear algebra. Cellular models, ECELL Networks and Motifs – Gene Networks: basic concepts, computational model such transcription networks basic concepts .as Lambda receptor and lac operon as an example. – all types of networks.-uses. Unit 4 Design of Databases 9 Introduction- databases KEGG and EMP etc. Introduction- databases MetaCyc and AraCyc etc., Expression databases and various databases related to systems biology. Unit 5 Reconstruction of pathways and annotation 9 Reconstructing metabolic pathways from sequence and function information in microbial species; statistical profiling and function annotation of genomes with a microbial genome as an example. Recommended Texts 1. Hunt, S.P. and Livesey, F.J., “Functional Genomics a practical approach”, 2000, Oxford University Press, UK. 2. Wilkins, M.R., Wiliams, K.L., Appel, R.D. and Hochstrasser, D.F. “Proteome Research: New frontiers in Functional Genomics“, 1997, Springer Verlag, New York, USA. 3. Witten, I.H. and Frank, E., “Data mining: Practical Machine Learning Tools and Techniques”, 2005, Morgan Kauffman Publishers, USA. 4. Rastogi, S.C., N. Mendrita, P. Rastogi, “Bioinformatics Methods and Applications: Genomics Proteomics and Drug Discovery”, 2006, 2

nd Ed., Prentice Hall India



ELECTIVE – II

APPLICATIONS OF BIOINFORMATICS Semester : VI Credits : 5

Category : Elective II Hrs/Wk : 5

Course Objective: To expose students to important areas employing the concepts of bioinformatics. Unit 1: Microarray analysis and Bioinformatics 9 Systems Biology- Networks.- basics of computer networks and Biological –uses and Integration. Micro array – definition, types of array, Micro array analysis: Hierarchical clustering, Applications of Micro Arrays in systems biology- Self-organizing maps- Connectivity maps- definition and its uses- Networks and Pathways – Types and methods. Metabolic networks, or network of metabolites and enzymes. Unit 2: Pharmacogenomics 9 Pharmacogenomics of Cardiovascular Diseases, of Cancer treatment, of Neurodegenerative Diseases, in Depression, Respiratory diseases, in AIDS, in Antibiotics. Management Of Pharmacogenomic Information – The Pharmacokinetics and Pharmacogenomics knowledge Base, Systems for the Management of Pharmacogenomic Informations. Unit 3: Commercial Bioinformatics 9 Definition of Bioinformatics company. Genome technology: high throughput sequencing and assembly. Diagnostic drug discovery and genomics. Pharmacogenomics and its application. SNPs and their applications. Proteomics in medicine, Toxicology. Unit 4: Immunoinformatics 10

Definition of Immunoinformatics – overview of the Immune system- Bioinformatics strategies for better

understanding of immune function – structural features of MHC peptides-MHC peptide interaction

parameters: a) interface area between peptide and MHC, b) intermolecular hydrogen bonds,

Immunological databases – IMGT – IMGT-GENE-DB – IMGT-HLA IMGT/LIGM-DB – HaptenDB –

EPITOME – dbMHC – GenPep.

Unit 5: Nutrigenomics Nutritional genetics – nutritional genomics-genetic nutrition-gene directed nutrition with reference to diabetes, cardiovascular diseases and obesity and neurogenomics-short notes on herbal informatics (medicinal foods)

RECOMMENDED TEXTS: 1. Hunt, S.P. and Livesey, F.J., “Functional Genomics a practical approach”, 2000, Oxford University Press, UK. 2. Wilkins, M.R., Wiliams, K.L., Appel, R.D. and Hochstrasser, D.F. “Proteome Research: New frontiers in Functional Genomics“, 1997, Springer Verlag, New York, USA. 3. Zdanowicz, M.M., “ Concepts in Pharmacogenomics”, 2010, American Society of Health-System Pharmacists. 4. Darren. R. Flower, “Immunoinformatics”, 2007, Humana Press Inc.

5. Simopoulous, A.P. & Milner, J.A., “Personalized Nutrition”, 2010, Karger Press.



ELECTIVE – II

CHEMINFORMATICS Semester : VI Credits : 5

Category : Elective II Hrs/Wk : 5

Course Objective: To provide overview on role of computers in managing chemical data associated with biological systems.

UNIT 1: Introduction to Cheminformatics 9 Introduction to Cheminformatics - History and evolution of Cheminformatics - Chemical representation - Sequence, 2D, 3D structure, Types of chemical representation - linear notation, tabular storage, graphical representation – Chemical data management - Chemical mark up languages. UNIT 2: Chemical Databases 9 Chemical Databases - CHEMDB, KEGG LIGAND, CSD, CAS REGISTRY, BIOMETA DB, National Cancer Institute Database(NCI) - Chemical searching methods - exact searching, sub structure searching, similarity searching, reaction searching. UNIT 3: Combinatorial Chemistry 9 Combinatorial chemistry: Introduction, Liquid Phase synthesis, Solid phase synthesis, Designing combinatorial Synthesis, High through put screening. UNIT 4: Combinatorial Library Design 9 Combinatorial library design - Rational principles of compound selection for combinatorial library design and optimization approach, Descriptor Analysis, Modeling toxicity, Computer Assisted Synthesis design and structure based library design. UNIT 5: Application of Cheminformatics 9 Application of cheminformatics - QSPR Drug design - Target identification and Validation, lead finding and optimization - Pharmacophore-Based Drug Design - Structure-Based Drug design - Application of Cheminformatics in Drug Design. RECOMMENDED TEXTS: 1. Leach, A.R.& Gillet, V.J., “An Introduction to Cheminformatics”, 2007, Revised Edition, Springer Publication. 2. Gasteiger, J & Dr. Thomas Engel, “Cheminformatics”, 2003, Wiley-VCH Press. 3. Bajorath, J., “Cheminformatics: Concepts, Methods and Tools for Drug Discovery”, 2004, Humana Press. 4. Oprea, T. L., “Cheminformatics in Drug Discovery”, 2005, Wiley-VCH Press.

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