Biology of Cells: Prokaryotic and Eukaryotic cells E. coli and Yeast; Cell organelles and




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CORE COURSE - I

Biological Systems

UNIT-I

Biology of Cells: Prokaryotic and Eukaryotic cells - E. coli and Yeast; Cell organelles and

their functions, Differences and similarities in plant and animal cells, Principles of Membrane

organization, Membrane proteins, Cell transport, Cell division - mitosis, meiosis- cell cycle;

Enzymes- classification, structure, Mechanism of action.

UNIT-II

Cell Energetics and respiration: Energy - life's driving force; energy capture –

photosynthesis; role of ATP in energy cycle -Glycolysis, TCA cycle, Oxidative

phosphorylation; Fats and protein as alternate energy sources, Key Biomolecules - lipids,

polysaccharides, proteins, nucleic acids.

UNIT-III

Chromosome structure in Prokaryotes and Eukaryotes, Structures of DNA - Watson and

Crick model, Different conformations, Replication; RNA secondary structure; Central dogma

of molecular biology-Transcription, Post – transcriptional modifications, codon and anticodon

concepts, Translation and Post–translational modifications; Mutation-Types, Molecular

mechanism- DNA repair mechanism- Gene regulation- operon concept - lac, trp.

UNIT IV

Basics of recombinant DNA technology - Introduction to cloning, gene selection, restriction

enzymes-a brief account; cloning vectors – plasmid, phage vectors, cosmids, shuttle

vectors; DNA transformation; methods of clone selection and screening. Hybridization


Techniques-Southern-Northern-Western blots analysis and their applications.

Hrs 6

Credit 4

Code 07PBI 1401

Marks 75

Semester I

UNIT-V

DNA sequencing- Maxam-Gilbert, Sanger methods, automated DNA sequencing. PCR, RFLP

and RAPD techniques, bio-chips and DNA finger printing, Applications of recombinant DNA

technology - commercial aspects of recombinant proteins.

Text Books :

Freifelder D. Molecular Biology, Jones and Bartlett Publishers Inc. 1987.

Lehninger A.L., Principles of Biochemistry, CBS Publishers and Distributors, New Delhi,

1984.

Berg, J. M. , J.L. Tymoczko and L. Stryer, Biochemistry, 5th Edition W.H. Freeman, 2002.

Reference Books :

Benjamin Lewin, Genes VIII, Pearson - Prentice Hall International Edition, New Delhi. 2004.

Watson, J.D., et al., Recombinant DNA, 2nd ed. Scientific American Books, New York, 1992.

Winnacker E. L. From Genes to Clones, VCH Weinhem, Germany, 1987.

Prokop, Ales, Bajpai, Rakesh K., and Ho, Chester S., Recombinant DNA Technology and

Applications, McGraw-Hill, New York, 1991.

CORE COURSE II

COMPUTER PROGRAMMING - I

Unit I

Computer Introduction : Overview and functions of a computer System. Input and output

devices. Storage devices: Hard Disk, Diskette, Magnetic Tape, CD-ROM, DVD, Main Board :

Chips, Ports, Expansion Slots. Memory: Register, buffer, RAM / ROM, Concepts of flowchart,

algorithm;

Cprogramming: Data types, operators and expressions, Hierarchy of operators

Unit II

Declaring Variable and constants, Control statements including decision (if, if-else), loops

(while, do-while, for), branching (switch, break, continue), Iterative statements, Functions –

Simple, recursive functions, library functions – arguments.

Unit III

Arrays, Pointers, array of pointers, Structures , unions, storage classes dynamic memory

allocation, macros and preprocessor directives, command line arguments, file Operations in

C – read, write, append operations.

Unit IV

Perl – Introduction, Basic Concepts, data types, variables, scalar values, Operators :

Binding, bitwise, relational , conditional, additive, multiplicative, shift and range operators,

simple and compound statements, loop statements.

Unit V

Regular Expressions : Concepts, Uses , Patterns, Matching, Character classes, quantifiers,

Subroutines: semantics, passing references, prototypes

Declarations – Global, scoped declarations, Pragmas

Hrs 6

Credit 4

Code 07PBI 1402

Marks 75

Semester I

Reference Books:

Gary Bronson J., A First book of ANSI C, 3rd edition, Thomson Asia pvt. Ltd., Bangalore,

2001.

Gottfried, B. S., Programming With C, Tata Mc Graw Hill

Lorry Wall, Tom Cheristiansan, Joe Orwant. Programming Perl, Shroff Publishers, Mumbai,

2005

Tisdall, J., Beginning Perl for bioinformatics, Shroff publishing, Mumbai, 2006

CORE COURSE III

C Programming – Lab Exercises :

1. C Basic Input / Output Functions

2. Arrays Concepts

3. Example for Structure

4. Sample program for Pointers

5. Illustration of Conditional Statements

6. Explaining Looping Statements

7. Functions – recursive, library functions

8. Dynamic memory Allocation

9. Data Structure operations like stacks and queues

10. File Operations including read, write and appending records

Perl Programming – Lab Exercises :

1. Program to convert DNA to RNA.

2. Program to convert DNA to RNA using subroutines.

3. Program to calculate reverse complement of DNA sequence.

4. Program to read Protein Sequence Data from a file.

5. Program to. Extract Annotation and sequence from Genbank file.

6. Program to Determining Frequency of Nucleotides.

7. Program to Reading and Translating a FASTA file.

8. Program to Searching for Motif.

9. Program to Translation of DNA to Protein.

10. Program to Translation of DNA sequence in all six reading frames.

Hrs 6

Credit 4

Code 07PBI 1403P

Marks 75

Semester I

CORE COURSE – IV

BIOSTATISTICAL AND MATHEMATICAL TECHNIQUES

UNIT I

BIOSTATISTICS – Introduction – Applications, Collection of Data: Sampling techniques,

Graphical and diagrammatic representation.

CENTRAL TENDENCY – Arithmetic Mean, Geometric Mean, Harmonic Mean, Median, Mode

DISPERSION – Importance, range, Mean Deviation, Variance, Standard Deviation

UNIT II

CORRELATION – types & measures, Karl Pearson, Scatter Diagram, Rank Correlation,

Correlation for bivariate frequency distribution, REGRESSION - types, measures, Testing of

hypothesis, ANOVA – One way, Two way, STUDENT ‘t’ tests for mean and difference of

mean, CHI SQUARE distribution: independent of attributes, goodness of fit.

UNIT III

PROBABILITY – Basic Laws: Events, Sample Space, Addition Rule, multiplication Rule,

Random Variable, Probability Distribution, NORMAL Distribution, BINOMIAL Distribution,

Poisson distribution, Introduction to Hidden Markov model

UNIT IV

CALCULUS – Basics, Differentiation of algebraic functions, Trigonometric functions,

Integrations – simple problems, properties of definite integrals , Uses of table of Integrals,

Numerical differentiations – Euler’s method, R-K second order method, Numerical

integration: Trapezoidal and Simpson 1/3 rule.

UNIT V

MATRIX – Types, Inverse, Algebra, Simultaneous Equations, Determinant, Eigen Values ,

Rank of a matrix. VECTORS – Operations, Scalar, Vector Product, Vector Calculus, Scalar

Triple Product, Divergence, Curl of Vector

Hrs 6

Credit 4

Code 07PBI 1404

Marks 75

Semester I

Reference Books :

Veer Bala Restogi, Fundamental of Biostatistics, Ane Books, New Delhi, 2006

Jorden D. W. , Smith P., Mathematical Techniques, 3 rd Edition, Oxford University Press,

New Delhi, 2004

Pillai RSM, Bagavathi,V., Chand .S “Statistics”

Ronald N.Forthofer Einsun, “Introduction to Biostatistics” Elsevier, 2006

CORE COURSE V

Computational Biology

UNIT-I

Analysis of DNA and Protein Sequences - distributions, frequency statistics; Protein and

Nucleic Acid Sequence Databases - PIR, Swiss-prot, GenBank; pattern and motif searches -

BLOCKS, PRINTS, PFAM; Structure Databases – PDB; Structure Classification, alignment

and analysis - SCOP, CATH, FSSP.

UNIT-II

Sequence alignment: Scoring matrices- PAM and BLOSUM; Local and Global alignment

concepts; dynamic programming Algorithms, Needleman and Wunsch, Smith-Waterman;

Pairwise and multiple sequence alignments - Progressive alignment – Different Database

searches for homologous sequences - FASTA and BLAST.

UNIT-III

Protein Secondary structure prediction - Chou-Fasmann rules, Gamier-Osguthorpe-Robson

(GOR) methods; Predicting 3D structure – homology modeling, threading - fold recognition

and ab initio methods - Rosetta - CASP - Molecular visualization tools - RasMol, SPDBV.

UNIT-IV

Fragment assembly - Genome sequence assembly, Gene finding methods: content and

signal methods, Background of transform techniques - Fourier Transformation analysis;

pattern recognition and gene prediction - Analysis and prediction of regulatory regions -

Neural network concepts and secondary structure prediction - RNA structure prediction.

UNIT-V

Evolutionary analysis: Analogy versus homology; evolutionary distances – Dendrogramsclustering

methods - rooted and un-rooted tree representation - Bootstrapping strategies -

phylogenetic trees - PHYLIP.

Hrs 6

Credit 4

Code 07PBI 2405

Marks 75

Semester II

Reference Books:

Lesk, A. M. Introduction to Bioinformatics, Oxford University Press, New Delhi

(2003).

Higgins, D. and W. Taylor (Eds), Bioinformatics- Sequence, structure and databanks,

Oxford University Press, New Delhi (2000).

Durbin, R., S.R- Eddy, A. Krogh and G. Mitchison, Biological Sequence

Analysis, Cambridge Univ. Press, Cambridge, UK (1998).

Baxevanis, A. and B.F. Ouellette. Bioinformatics; A practical Guide to the Analysis of

Genes and Proteins, Wiley- Interscience, Hoboken, NJ (1998).

Michael, S. Waterman, Introduction to computational Biology, Chapman &

Hall, (1995).

Gibas, C. and P. Jambeck, Developing Bioinformatics Computer Skill, 1st

Edition, O'Reilly, 2001.

CORE COURSE VI

Computer Programming – II

Unit I

Client / Server: Introduction, methodology and uses. Visual Basic: Introduction to visual

basic , Data Types, Strings, Variants, Constants, Data Arrays, Looping and Iterative

Statements, Functions in Visual Basic

Unit II

Tools and Controls :Command Buttons, Text Boxes, Labels, Drive List Box, Directory List

Box, Combo Box, List Box, Check Button, Option Button and Timer Control. Introduction to

data connectivity, Menu Designer, Project – form operations

Unit III

Data base systems : Introduction to DBMS, DB architecture and design Data Models:

Introduction, architecture, Entity, relations, E–R Model : Components, E R diagram, Network

Model, Hierarchical Model – advantages and disadvantages, Normalization, Data abstraction,

Instances and Schemas , Introduction to Distributed Data bases

Unit IV

Oracle : Introduction to RDBMS, ORDBMS, Normal forms, oracle database architecture,

approaches, Data definition language, Data manipulation language, data types in Oracle,

Constraints, Operations, Queries and sub queries

Unit V

SQL : Structure, Operators, tables, views, indexes, aggregate functions, Insert, Update,

delete statements, introduction to PL/ SQL and simple PL/SQL programs

Hrs 6

Credit 4

Code 07PBI 2406

Marks 75

Semester II

Reference Books :

Leon, A., and M. Leon , Essentials of Database Management System , Vijay Nicole imprints,

Chennai, 2006

ISRD group, Introduction to Database Management Systems, Tata Mc Graw Hill Press Ltd,

New Delhi, 2006

Visual Basic 6 Complete, BPB publications, New Delhi, 1999.

Cornell, G., Visual Basic 6 from the ground up, Tata Mc Graw Hill, 8th Edition, New Delhi,

1999.

Vaswani, V., The complete reference My SQL, Tata Mc Graw Hill, New Delhi, 2002.

CORE COURSE VII

LabII for CC V, VI ( Bioinformatics and Computational Biology)

1. Study of Internet resources in Bioinformatics - E.g. NCBI, ICGEB, EMBL-EBI.

2. Searches on NCBI - PubMed bibliographic databases. Concept of boolean operators.

3. Multiple sequence alignment – CLUSTAL W

4. Phylogenetic Trees - PHYLIP

5. 5Multiple alignment - Domain / Motif databases - BLOCKS, PRINTS, - SBASE and

PFAM

6. Protein Structure and Classification databases - PDB, SCOP, CATH, FSSP, PDBSUM

7. Evaluation of protein structure by Swiss PDB viewer or by any other suitable

programs like Insight-II

8. Calculation of phi - psi angles and Ramachandran plot for a given protein structure.

9. Pairwise alignment - Global alignment using Needleman-Wunsch algorithm

10. Pairwise alignmen t- Local alignment using Smith-Waterman algorithm

11.BLAST, FASTA- algorithms to search and analyze sequence databank.

Hrs 6

Credit 4

Code 07 PBO 2407P

Marks 75

Semester II

Exercises : ( VB, SQL & Office)

1. Document Preparation, Presentation – MS Office

2. Mean, Median and Mode – Excel

3. Regression Analysis - Excel

4. Basic Input Output Inputbox, Msgbox Functions

5. Forms, MDI Forms - Operations

6. Text, Label Controls

7. Data Control – Operations

8. Conditional Statements, Looping Statements

9. Graphics Programs

10.Database – Creation, Update – SQL

CORE COURSE VIII
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