PERIYAR UNIVERSITY

PERIYAR PALKALAI NAGAR

SALEM – 636 011

DEGREE OF BACHELOR OF
SCIENCE

CHOICE BASED CREDIT SYSTEM

SYLLABUS FOR B.Sc. BIOINFORMATICS

FOR THE STUDENTS ADMITTED FROM THE

ACADEMIC YEAR 2012 – 2013 ONWARDS

 REGULATIONS

1. ELIGIBILITY FOR ADMISSION

A candidate who has passed in Higher Secondary Examination with

Biology or Pure Science (Academic stream or Vocational stream) as
one of the subject under Higher Secondary Board of Examination,
Tamilnadu as per norms set by the Government of Tamilnadu or an
Examination accepted as equivalent thereto by the syndicate, subject
to such conditions as may be prescribed thereto are permitted to
appear and qualify for the Bachelor of Bioinformatics degree
examination of this university after a course of study of three
academic years.

2. DURATION OF THE COURSE

The course shall extend over a period of three years comprising of six
semesters with two semesters in one academic year. There shall not
be less than 90 working days for each semester. Examination shall be
conducted at the end of every semester for the respective subjects.

3. COURSE OF STUDY

The course of study shall comprise instruction in the following

subjects according to the syllabus and books prescribed from time to
time. The syllabus for various subjects shall be clearly demarcated
into five viable units in each paper/subject. Part -I, Part-II, Part – III
and Part – IV subjects are as prescribed in the scheme of examination.

4. EXAMINATIONS

The theory examination shall be three hours duration to each

paper at the end of each semester. The candidate failing in any
subject(s) will be permitted to appear for each failed subject(s) in the
subsequent examination. The practical examinations for UG course
should be conducted at the end of the even semester.
4.(a) Submission of record note books for practical examinations

Candidates appearing for practical examinations should submit bonafide

Record Note Books prescribed for practical examinations, otherwise the
candidates will not be permitted to appear for the practical examinations.
However, in genuine cases where the students, who could not submit the
record note books, they may be permitted to appear for the practical
examinations, provided the concerned Head of the department from the
institution of the candidate certified that the candidate has performed
the experiments prescribed for the course. For such candidates who do
not submit Record Books, zero (0) marks will be awarded for record note
books.

5. Revision of Regulations and Curriculum

The University may revise /amend/ change the Regulations and Scheme
of Examinations, if found necessary.

6(a). Passing Minimum – Theory

The candidate shall be declared to have passed the examination if the

candidate secure not less than 40 marks out of 100 (CIA – 10 marks out
of 25 and EA – 30 marks out of 75) in the University examination in
each theory paper.

6(b). Passing Minimum – Practical

The candidate shall be declared to have passed the examination if the

candidate secure not less than 40 marks put together out of 100 (CIA –
16 marks out of 40 and EA – 24 marks out of 60) in the University
examination in each practical paper.

7. Question Paper Pattern

7.1 (a). THEORY - Question Paper Pattern [EA] (Total Marks: 75)

PART – A (10 x 2 = 20 Marks)

(Answer ALL questions), (Two questions from each unit)

PART – B (5 x 5 = 25 Marks)

(Answer ALL questions) & (One question from each unit with
Internal Choice)

PART – C (3 x 10 = 30 Marks)
 (Answer ANY THREE questions) & (Open Choice – 3 out of 5
questions)

7.1(b). THEORY - Internal Marks Distribution[CIA] (Total Marks: 25)

 Attendance :5 Marks
 Assignment :5 Marks
 Internal Examinations :15 Marks

7.2(a). PRACTICAL – Marks Distribution & Question paper Pattern

(Max. Marks: 100)

[External [EA]: 60 Marks & Internal [CIA]: 40 Marks]

8. Commencement of this Regulation

These regulations shall take effect from the academic year 2012-2013,
i.e, for students who are to be admitted to the first year of the course
during the academic year 2012-2013 and thereafter.
 SEMESTER – I

Sem Part Sub Subject Marks

Code Credit
CIA EA Total

I Tamil - I 3 25 75 100

II English – I 3 25 75 100

4 25 75 100
Cell Biology
I Practical - I (Cell Biology &
III - - - -
Biophysics)

Allied I : Basic Mathematics 4 25 75 100

Value Education 2 25 75 100

Total 16 125 375 500

SEMESTER – II

Sub Marks
Sem Part Subject Credit
Code CIA EA Total

I Tamil - II 3 25 75 100

II English – II 3 25 75 100

Biophysics 4 25 75 100

Major Practical - I (Cell

6 40 60 100
Biology & Biophysics )

II III Allied II: Fundamentals of

computer and office 4 25 75 100
automation

Allied Practical - I
6 25 75 100
(Computer lab)

IV Env. Studies 2 25 75 100

Total 28 190 510 700

 SEMESTER – III

Sem Part Sub Subject

Credit Marks
Code

CIA EA Total

I Tamil - III 3 25 75 100

II English – III 3 25 75 100

Microbiology 4 25 75 100
III NME-1 Fundamentals
2 25 75 100
III of Bioinformatics

Allied III: Chemistry 4 25 75 100

Total 16 125 375 600

SEMESTER – IV

Sub Marks
Sem Part Subject Credit
Code CIA EA Total

I Tamil - IV 3 25 75 100

II English – IV 3 25 75 100

Biostatics 4 25 75 100

Allied IV : Biochemistry 4 25 75 100

NME –2 Applications of
IV 2 25 75 100
Bioinformatics
III
Major practical –II
6 40 60 100
(Microbiology)

Allied Practical – II
6 40 60 100
(Biochemistry)

Total 28 205 495 700

 SEMESTER – V

Sub Marks
Sem Part Subject Credit
Code CIA EA Total

Molecular Biology 4 25 75 100

Biological Data bank and

4 25 75 100
their analysis

Immunology 4 25 75 100
III
V Plant & Animal
4 25 75 100
Biotechnology

Relational Data Bases

Management Systems 4 25 75 100
(RDBMS)

Total 20 125 375 500

SEMESTER – VI

Sub Marks
Sem Part Subject Credit
Code CIA EA Total

Systemic evolution and

4 25 75 100
Environmental Biology

Drug and Molecular

4 25 75 100
modelling

III Proteomics and Genomics 4 25 75 100

Data mining and

4 25 75 100
Warehousing

VI Object oriented programming

4 25 75 100
and C++

Major Practical III: Lab in

Molecular Biology and Plant 6 40 60 100
Biotechnology

Major Practical IV: Lab in

Data base analysis,
6 40 60 100
programming in PERL, C++
and molecular modelling

Total 32 205 495 700

Total Credits: 140

Total Marks: 3600

 SEMESTER – I

UBI 111- MAJOR PAPER- I

CELL BIOLOGY

UNIT I

Cell as a basic unit, classification of cell types, cell theory, organization

of plant and animal cells, comparison of microbial, plant and animal cell.

UNIT II

Ultrastructure of cells, Biochemical composition of cells (nucleic acid,

carbohydrate, protein and lipids).

UNIT III

Subcellular organization, cytosol, endoplasmic reticulum, nucleus,

cytoskeleton, ribosomes, mitochondria, chloroplast, vacuoles,
peroxisomes, lysosomes and cell wall.

UNIT IV

structure and function of cell membranes, Cell division ( eukaryotic and

prokaryotic), mitosis, meiosis and cell cycle.

UNIT V

Specialized cell, motile cells, nerve cells, muscle cells, cell death and
apoptosis .

Recommended Books:

De Robertis and De Robertis. 2005. 8th Eds. Cell and Molecular

Biology. Lippincott Williams & Wilkins

Lodish, Berk, Baltimore et al. 2000. 6th Eds Molecular Cell Biology.
W.H. Freeman & Co.

Gerald Karp, 2008. Cell and Molecular Biology: Concepts and

Experiments, 5th Eds. Wiley

Geoffrey Cooper, 2000. The Cell: A molecular approach. 2nd Eds.

Sinauer Associates Inc.
 SEMESTER II

UBI121-MAJOR PAPER-II

BIOPHYSICS

UNIT I

Energetics of a living body, sources of heat limits to temperature (

qualitative treatment), heat dissipation to conservation, laws of
thermodynamics. Nature of chemicsl bonds, intra and intermolecular
interaction in biological systems.

UNIT II

Absorption spectroscopy- Beer-Lambert’s law, Colorimetry to

Spectrophotometry( single and double beam spectrophotometer), primary
biophysical events in photosynthesis.

UNIT III

Spectroscopic techniques to find out molecular structure (quantitative

techniques), general spectroscopy (UV, Visible, Fluorescence, Atomic
absorption, IR to Raman spectra).

UNIT IV

Physical methods of imaging, intact biological structures (X-ray, CAT-

Scan, ECG, EEG, NMR) and radioactive pollution- GM counter.

UNIT V

Structure of proteins – primary, secondary, tertiary and quaternary. X-

ray crystallography

Physical methods for determining size and shape of macromolecules –

diffusion to sedimentation, reverse osmosis, ultracentrifugation

Recommended Books:

Volkones, HV, General biophysics Vol I&II.

Pullman, B and M.Voino. Molecular biophysics.

 SEMESTER –II

UBIP121- MAJOR PRACTICAL-I

CELL BIOLOGY & BIOPHYSICS

1. Cell types – Microbial, animal and plant morphometric

measurements.
2. Fractionation of cellular components.
3. Cell membrane, separation and analysis of membrane
components.
4. Cell staining: Cyto chemical methods for demonstration of cellular
and sub cellular components. Protein, carbohydrate and lipids.
5. Enzymes: Assay of urease, demonstration catalytic activity.
6. Titration curve of amino acids.
7. Selection of complementary filters.
8. Beer- Lambert’s law verification.
 Allied paper - II (Semster – II)

FUNDAMENTALS OF COMPUTER AND OFFICE AUTOMATION

(This paper is introduced instead of Allied paper - II: Computer

Fundamentals and Basic programming)

UNIT I

Introduction to Computers: – Characteristics of Computers.

Classification of Computers – Programming Languages : Machine
Language – Assembly Language – Input Devices- Keyboard – Mouse -
Trackball – Out put Devices – Dot Matrix Printer – Inkjet – Laser Printer –
LCD & LED Printers: Hard Disk – CD –DVD – primary memory

UNIT – II

Getting Started: Starting a Program – Identifying Common Screen

Elements – Choosing Commands – Finding Common Ways to Work –
Getting Help with Office.

UNIT – III

MS-WORD: Learning Word Basics – Formatting a Word Document –

Working with Longer Document.

UNIT – IV

MS-EXCEL: Creating a Simple Spreadsheet – Editing a Spreadsheet –

Working with Functions and Formula – Formatting Worksheets –
Completing Your Spreadsheet – Creating Charts

UNIT – V

MS-POWERPOINT: Creating and Viewing Presentations – Editing a

Presentation – Working with Presentation Special Effects

TEXT BOOKS

1. Fundamentals of computers science and Communication

Engineering. Alexis Leon & Mathews Leon, Vikas Publishing
House Pvt. Ltd., New Delhi (Unit-I)
2. Microsoft Office XP – fast & easy (UNIT II, III, IV & V),DIANE
KOERS
Prentice Hall of India Private Limited, New Delhi, 2001
 Allied Practical –I: Computer lab

(This practical lab is introduced instead of Allied Practical -I: Computer

fundamentals and Basic programming)

Semester II: Lab exercise

MS Office

1. Create a document with tables, and do the following

Formatting, tab setting, page setting for printing, and Header & Footer
setting

2. Drawing flow chart using drawing toolbar, inserting picture and

setting frames

3. Mail Merge in word (Creating main document, data source, inserting

merge fields and

viewing merge data, viewing and printing merged letter, using main
merge to print envelope creating mailing labels)

4.. Create a document, Format the document and edit the document as
follows:
(i). Find and Replace options
(ii). Cut, Copy and Paste options
(iii). Undo and Redo options
(iv). Using Bold, Underline and Italic.
(v). Chance Character size using the font dialog box.
(vi). Formatting paragraph: Center, Left aligns & Right aligns
(vii). Changing paragraph and line spacing Using Bullets and Numbering
in paragraphs
(viii). Creating Hanging paragraphs

MS – EXCEL

1. Create a work sheet, moving / copying / inserting / deleting rows and

Columns. (Usage of cut, paste commands, copying a single cell, copying a
range of data, filling up a cell. Undo command, Inserting a row, column
Deleting rows and columns.)

2.Create a worksheet and perform to date, time ,Math functions, and

Logical and financial functions

3.a. Data base concept: Data base, Record field and field name – creating
and sorting a data base and maintaining a data base (date form)
b. Using auto filter, advanced filter
c. Creating subtotals and grand totals – Using database functions
4. Creating charts (pie, Bar, Line)
a. Using chart wizard (five steps)
b. Changing the chart type (pie, Bar, Line)
c. Inserting titles for the Axes x, y
d. Changing colors
e. Printing charts

MS – POWER POINT
1.Creating a presentation using auto content wizard
2.Different views in power point presentation
3.Setting animation effects / grouping / ungrouping / cropping power/
point objects

4.Design to presentation to market the product using animation

effects/ buttons/links
 SEMESTER – II

Non Major Elective Courses

NME –I

Fundamentals of Bioinformatics

Unit –I

Bioinformatics-Definition, History, Scope and Applications.

Opportunities in Bioinformatics. Emerging areas of Bioinformatics

Unit II

Computers and Programming Languages. Internet, World Wide Web,

Browsers, Search Engines – Google, Yahoo

Unit III

Cell Structures and Cell Organelles. Introduction to Macromolecules like

DNA, RNA and Proteins

Unit IV

Introduction to Molecular Biology and genetics. Central dogma of life:

DNA – RNA - Protein. Role of Bioinformatics in Human Genome Project

Unit –V

Biological databases, Importance of databases, Nucleic acid sequence

databases, Protein databases and Structure databases

References

1. Basic Bioinformatics – S.Ignacimuthu (2005). Narosa Publishing

House
2. Bioinformatics for Beginners – K.Mani and Vijayaraj (2002).
Kalaikathir Achagam
3. Fundamentals of Bioinformatics – Irfan Ali Khan, Atiya Khanum
(2003). Ukaaz publications.
 SEMESTER – III

UBI211 MAJOR PAPER - III

MICROBIOLOGY

UNIT 1

Microbial study: Types of Microscopes (Light, Phase-contrast and

Electron microscopy) –classification of microorganisms- viruses, bacteria,
fungi, algae and protozoans.

UNIT II

Microbial physiology: Microbial growth- medium, Environmental factors

affecting growth-nutritional classification of microbes. Microbial
metabolism: glycolysis, Aerobic process-Photosynthesis- cyclic and non-
cyclic Phosphorylation.

UNIT III

Viruses (Lytic and Lysogenic), Bacterial genetics: Plasmids and

conjugation, transduction and transformation. Mutations, mutagenesis
and recombination.

UNIT IV

Environmental & Agricultural microbiology: Biogeochemical cycle:

Biodegradation and bioremediation. Biofertilizers.

UNIT V

Microbiology of human diseases- Bacteria - Staphylococcus,

Vibriocholerae, Virus-Pox-virus, Adeno virus, Fungus-Aspergillus,
Candida. Medicine: Penicillin and Streptomycin.

Recommended Books

Michael T. Madigan John M. Martin & Jack Parker, 1984. Biology

of Microorganisms Prentice Hall International, Inc., London.
Edward A. Birge, 1992. Modern Microbiology. Principles and
application. W.M.C. Brown Publishers , Inc. U.S.A.
Gerard J. Tortora, Berdell R. Funke, Christine & L. Case, 2001.
Microbiology –An Introduction. Benjamin Cummings, U.S.A.
Danial Lim, 1998. Microbiology, McGraw-Hill company, New York.
 SEMESTER – III

UBIP221 MAJOR PRACTICAL - II

MICROBIOLOGY

1. Staining techniques - gram staining, negative staining, flagellar

staining and spore staining.
2. Microscopic slide preparation- bacterial and fungal strains.
3. Various sterilization techniques – surface, glassware, media, dry
heat, wet heat, radiation, chemicals and filtration.
4. Preparation of solid and liquid media.
5. Isolation of micro organisms from soil, air, plants and water by
streak plate, pour plate and spread plate methods
6. Maintenance of cultures – soil stock, glycerol stock and
lyophilisation
7. Biochemical test- starch hydrolysis, catalase production, milk
curdling, fluorescence, acid and gas production by Durham tube,
IMVIC.
 SEMESTER – III

NME –II

Applications of Bioinformatics

Unit –I

Protein Structure prediction, Gene and Protein expression data. Protein

interaction data, Similarity and database searching tools – FASTA,
BLAST

Unit II

Protein sequence data banks, NBRF, PIR, SWISSPROT, Nucleic Acid

Sequence Data Bank, EMBL & NCBI

Unit III

Sequence analysis and Phylogeny – sequence search alignment- spair

wise and multible sequence. Scoring matrices. Introduction to
Phylogenetic Trees.

Unit IV

Introduction to drug discovery. Structure based drug design. Docking.

Clasical SAR / QSAR.

Unit V

Structure of commonly used drugs in medical field. New drug design for
cancer. Identification of novel drug design with least side effect.

References

1. Introdcution to Bioinformatics - S.Sundararajan and Balaji

2. Instant notes – Bioinformatics – Westhead, Howard parish and
Twyman. Viva books Pvt. Limited. Chennai
3. Bioinformatics basic skills and applications - Rastogi
 SEMESTER – IV

UBI221 MAJOR PAPER - IV

BIO STATISTICS

UNIT 1

Biostatistics- definition- statistical methods- basic principles. Variables-

Measurements and functions. Limitations and uses of statistics.

UNIT II

Data - primary, secondary. Methods of data collection. Merits and

limitations. Classification, tabulation and presentation of data.

UNIT III

Measures of Central tendency- Mean, Median, Mode, – merits and

limitations. Measures of dispersion – range, standard deviation, mean
deviation.

UNIT IV

Correlation and regression, similarities and dissimilarities of correlation

and regression.

UNIT V

Statistical interference – hypothesis: simple hypothesis, Hypothesis

testing. Student’s t test, Chi-Square test, ANOVA.

Recommended Books

Daniel, W.W. 1987. Biostatistics, John Wiley Sons, New York.

Sundarrao, P.S.S. and Richards, J.2003. An Introduction to Biostatistics,

3rd Edition, CMC, Vellore.

Selvin, S. 1991. Statistical analysis of epidemiological data, University

press, NY.

Bishop, O.N, 1983. Statistics for biology, Hougtan, Boston.

Freedman, P, 1950.The principles of scientific research, Pergamon

press,NY.
 SEMESTER V

UBI311 MAJOR PAPER - V

MOLECULAR BIOLOGY

Unit I

Cell structure and function: Membrane architecture, membrane

associated process, ATP synthesis and photosynthesis, subcellular
organelles- mitochondria, chloroplast.

Unit II

Chromosomal structure: prokaryotes and eukaryotes. Gene transfer in

bacteria- genetic mapping and its uses.

Unit III

Prokaryotic and eukaryotic replication: Gene expression-transcriptional

and translational regulation in prokaryotes. Post translational
modification in eukaryotes.

Unit IV

Mutations and mutant, Biochemical basis of mutation, types of mutation

– spontaneous and conditional. Chemical and physical mutagens- point
mutation.

Unit V

Transposons and insertion sequences: Types of transposons –

prokaryotes and eukaryotes. DNA rearrangement mediated by
transposons.

Recommended Books

Lodish, Berk, Baltimore et al. 2000. Molecular Cell Biology. 6th

Edition. W.H. Freeman & Co
Twyman, R.M.2000. Advanced Molecular Biology. Garland/bios
Scientific Publishers.
Sandy B Primrose, 1991. Molecular Biotechnology. 2nd Edition..
Blackwell Scientific Publishers.
Brown, T.A, 2002.Genomes. 2nd Edition. Wiley-Liss (New York).
Larry Snyder, Wendy Champness, 2002. Molecular Genetics of
Bacteria . 2nd Edition. . American Society for Microbiology.
 SEMESTER V

UBI312 MAJOR PAPER - VI

BIOLOGICAL DATABANKS AND THEIR ANALYSIS

Unit I

DNA and protein sequence data banks, NCBI, EMBL, DDBJ, NBRF-PIR,
SWISSPROT, signal peptide databank.

Unit II

Analytical tools for sequences databanks: BLAST, FASTA, Pairwise

alignment- Multiple alignment- ClustalW, PRAS.

Unit III

Structural databanks: Protein databank (PDB), the Cambridge structural

database, Genome databank, metabolic pathway databanks- KEGG and
Meta Cyc.

Unit IV

Introduction to microbial strain data network, numerical coding system

of microbes, hybridoma data bank structure, virus and cell line
information system.

Unit V

Protein structure classification databases: SCOP and CATH, Human

genome and diseases database – OMIM.

Recommended Books

Adams, M. D., C. Fields, J. C. Venter. 1994. Automated DNA

sequencing and analysis. Academic press, London.
Bishop, M. J., C.J. Rawings. 1997. Nucleic acid and protein
sequencing, A practical approach, IRI press, Oxford.
Sushai, S, 1997. Theoretical and computational methods in genome
research. Plenum press, NY.
Hepsyba, S.G.H. and C.R. Hemalatha, 2009. Basic Bioinformatics,
MJP Publishers, Chennai.
 SEMESTER V

UBI313 MAJOR PAPER- VII

IMMUNOLOGY

UNIT I

Historical perspectives and overview of immune system: Innate and

acquired immunity. Cells and organs of immune system. Inflammation.

UNIT II

Antigens, antigenicity. Immunogenicity. Complement system. Antigen-

antibody interaction. Monoclonal antibodies.

UNIT III

Organization and expression of immunoglobulin genes. Major

Histocompatibility Complex (MHC) and antigen.

UNIT IV

Cytokines: Structure, function and receptors, Cell mediated immunity. T-

Cell maturation and activation. B-Cell activation and proliferation.
Hypersensitive reactions – Types I, II, III and IV.

UNIT V

Immune regulation, Vaccines, autoimmunity, immune response to

infectious and immuno-deficiency diseases.

Recommended Books

Thomas J. Kindt, Barbara A. Osborne, Janis Kuby, Richard A.

Goldsby, 2006. Immunology, Janis Kuby. W H Freeman & Co.
Charles Janeway, Paul Travers, Mark Walport, Mark Shlomchik,
Mark J. Shlomchik, 2004.Immunobiology: The Immune System in
Health and Disease . Garland Pub.
Abul K Abbas, Andrew K. Lichtman & Jordan S. Pober (Eds.),
1997. Cellular and Molecular Immunology, 3rd Edn. W.B.Saunders
Company.
 SEMESTER V

UBI314- MAJOR-PAPER-VIII

PLANT AND ANIMAL BIOTECHNOLOGY

UNIT I

Application of plant tissue culture, organogenesis and somatic

embryogenesis.Protoplast culture and fusion. Agrobacterium mediated
transformation in plants, production of secondary metabolites by cell
culture.

UNIT II

In-vitro conservation of germplasm. Synthetic seeds. Transgenic plant –

Bt, herbicides, resistance pests and pathogens .Biotic & Abiotic stresses.

UNIT III

Animal cell culture: historical perspectives and applications,

manipulation of animal cells (microinjection, electroporation, liposome
mediated transformation). Production of native and recombinant
proteins- animal viral vectors.

UNIT IV

Embryo transfer technology and animal breeding. Micromanipulation

and embryo splitting, In vitro fertilization- chromosome engineering. Stem
cells and its applications.

UNIT V

Transgenic animals: gene targeting ,types of vaccines recombinant and

DNA vaccines, production and its applications.

Re commended Books

Kalyan Kumar De, 1992. Plant Tissue Culture , New Central Book
Agency ,Calcutta
Robert N. Trigiano, Dennis J. Gray, 1996. Plant Tissue Culture
Concept and Laboratory Exercises, CRC Press, London.
P.S. Srivasta, 1998. Plant Tissue Culture and Molecular Biology ,
Narosa Publishing House ,New Delhi.
. R.Spier and J.Griffiths, 1994. Animal Cell Biotechnology.
Academic Press.
M .M. Ranga, 2000. Animal Biotechnology, Agrobios (India)
 SEMESTER V

UBI315 MAJOR PAPER – IX

RELATIONAL DATABASES MANAGEMENT SYSTEMS

Unit I

Purpose of database systems-Entity relationship model: mapping

constraints-primary keys-ER diagram.

Unit II

Relational model: Structure-formal query languages-relational Algebra-

relational calculus-commercial query language.

Unit III

Relational database design: Pitfalls-Normalization using functional

dependencies-Decomposition-Third and fourth normal form-
normalization. .

Unit IV

Hierarchial data model: Tree structure diagram-data retrieval, Networks

data model: Data structure diagram-DBTG CODASYL model, updating
and set processing.

Unit V

Interpretation-equivalence of expressions-Query processing cost- query

optimizer. Basic concepts of data base recovery-currency control,
database security and integrity-distributed database.

Recommended Books

Jeffery D. Ulman, 1998. Principles of database system, Galgotia

Publishers.
Jdate C.J., 1995. An Introduction to Database System, Third Ed.
Narosa Publishing company.
Henry F. Korth and Abraham Silberschatz, 2000. Database system
concepts, Mc Graw Hill International Publication.
 SEMESTER VI

UBI321- MAJOR PAPER – X

SYSTEMIC EVOLUTION AND ENVIRONMENTAL BIOLOGY

UNIT-I

Morphological classification of plants: Various systems, Binomial

nomenclature; Cyto and chemotaxonomy.

UNIT-II

Morphology and Whittaker’s five kingdom classification of animals,

animal diversity, classification of chordates and non-chordates up to
classes.

UNIT-III

Evolution: Origin of life, fossils, Carbon dating in fossils, Geological time

scale. Palaeozoic, Mesozoic, Cenozoic life, Lamarkism, Neolamarkism,
living fossils, modern concepts of evolution and speciation, variations,
natural selection, isolation, mechanisms in evolution and speciation.

UNIT-IV

Environmental biology: Autoecology, synecology, ecosystem and its

components, energy flow, primary productivity, food chain. Wild life
preservation and management, water, air and noise pollution. Global
warming and Marine pollution (Oil spills).

UNIT-V

Function of ecosystems. Vegetation pattern in South India. Pollution and

soil conservation. Afforestation and social forestry. A general account of
renewable and non renewable resources.

Recommended Books

G.L.Chopra, 1976. Angiosperms. S.Nagin & Co, Delhi.

C.L.Porter, 1969. Taxonomy of flowering plants. Eurasia Pub.
house, Delhi.
Hans-Joachim Jördening, Josef Winter, 2005. Environmental
Biotechnology: Concepts and Applications. Wiley.
S.K. Dwivedi , M.C. Kalita , Padmanabh Dwivedi.2007.Biodiversity
and Environmental Biotechnology. (1st edition) Scientific
Publishers.
P.D.Sharma, 1994. Environmental Biology. Rastogi Publishers.
Gary K.Meffe & .Ronald Carroll, C, 1994. Principles of
Conservation Biology,
Sinauer Associates, Inc., Massachusetts.

SEMESTER VI

UBI322-MAJOR PAPER – XI

DRUG AND MOLECULAR MODELLING

UNIT I

Classification of drugs, routes of drug administration. Absorption

& Distribution of drugs. Role of kidney in drug interaction with
biomolecules. Binding of drugs to plasma proteins.

UNIT II

Drug receptors: Drug-receptor interaction, Drug action not

mediated by receptors. Structural based drug design, mechanism
of their action. Lipinski’s rule of 5, Clinical trials 1-4 phases.

UNIT III

Effect of drug doses on the rate of metabolism- mechanisms and

importance of Phase I and Phase II biotransformation. Role of
cytochrome p450. Enzyme inhibition strategies, enzyme induction
and pharmacological activity, LD50 and IC50.

UNIT IV

Principles & mode of action cancer and HIV chemotherapy agents

and target sites for cancer and HIV chemotherapeutic agents.
antimetabolites, antibodies, plantibodies, radiation therapy and
alkylating agents. PUBCHEM database.

UNIT V

Quantitative Structure Activity Relationship (QSAR). Types of

descriptors-constitutional, topological, charge, quantum chemical,
walk and path counts, geometric descriptors. Types of QSAR
methods-In static contour plot, in electro static contour plots, 3D-
QSAR.
Recommended Books

Singh.H and Kapoor. V.K, 2002. Organic pharmaceutical

chemistry. Vallabh prakashan publishers. New Delhi
Andrew, R., 1998. Molecular modeling: principles and
application. Leach. Harlow.
Andrew, R., 1997. Molecular modeling: Basic principles and
applications. Hans- X.

SEMESTER VI

UBI323-MAJOR PAPER-XII

PROTEOMICS AND GENOMICS

UNIT I

Algorithms and applications of proteomics: proteome mining,

protein expression profiling, protein-protein interaction, protein
modification and automation.

UNIT II

Protein digestion techniques, 2D Electrophoresis, Isoelectric

focusing(IEF), High Performance Liquid Chromatography- Mass
Spectroscopy (HPLC-MS).

UNIT III

Overview of genome, genome sequence acquisition and analysis,

comparative homologies, evolutionary changes, Single Nucleotide
Polymorphism (SNPs). Genetic analysis: linkage mapping and
analysis; physical mapping, Microarrays; sequence specific tags,
sequence tagged sites, ISH, FISH.

UNIT IV

DNA sequencing: Maxam and Gilbert method, Sanger method,

Ladder, Fluorescent, Shotgun, Automation DNA sequencing.
Implications of DNA sequencing.

UNIT V

Construction of cDNA and genomic DNA libraries; Polymerase

Chain Reaction (PCR), Yeast two-hybrid system, SAGE Adaptation
for Downsized Extract (SADE), ESTs,
 Recommended Books

Leibler DC. 2002. Introduction to proteomics, tools for the

new biology. Humana press.
Hunt SP, Livesey FJ, 2000. Functional genomics, Oxford
University press.
Cantor CR, 1999. Genomics. John Wiley, NY.
Westermier R, Naven T, 2002. Proteomics in practice: A
laboratory manual of proteome analysis. John Wiley- VCH

SEMESTER VI

UBI324 MAJOR PAPER – XIII

DATA MINING AND WAREHOUSING

(This paper is introduced instead of Major Paper-XIII: Parallel Computing

and programming in PERL)

UNIT – I

Introduction: Data mining application – data mining techniques – data

mining case studies- the future of data mining – data mining software -
Association rules mining: Introduction- basics- task and a naïve
algorithm- apriori algorithm – improve the efficient of the apriori
algorithm – mining frequent pattern without candidate generation

UNIT – II

Classification : Introduction – decision tree – over fitting and pruning -

DT rules- estimation predictive accuracy of classification methods -
other evaluation criteria for classification method – classification software

UNIT – III

Cluster analysis: cluster analysis – types of data – computing distances-

types of cluster analysis methods - partitioned methods – hierarchical
methods – density based methods – dealing with large databases –
quality and validity of cluster analysis methods - cluster analysis
software.

UNIT – IV

Web data mining: Introduction- web terminology and characteristics-

locality and hierarchy in the web- web content mining-web usage mining-
web structure mining – web mining software - Search engines: Search
engines functionality- search engines architecture – ranking of web
pages.
UNIT – V

Data warehousing: Introduction – Operational data sources- data

warehousing - Data warehousing design – Guidelines for data
warehousing implementation - Data warehousing metadata - Online
analytical processing (OLAP): Introduction – OLAP characteristics of
OLAP system – Multidimensional view and data cube - Data cube
implementation - Data cube operations OLAP implementation guidelines

TEXT BOOK:

1. “Introduction to Data mining with case studies”, G.K. Gupta, PHI

Private limited, New Delhi, 2008.

BI324 MAJOR PAPER – XIV

OBJECT ORIENTED PROGRAMMING AND C++

Unit I

Principles of object oriented programming (OOP): Software evolution-OOP

paradigm-basic concepts of OOP-object oriented languages-applications
of OOP.

Unit II

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 III

Classes and objects: constructors and destructors and operating

overloading and type conversions.

Unit IV

Inheritance: Types – single, multilevel, hierarchical and hybrid

inheritance. Pointers, virtual functions and polymorphism. Managing
console I/O operations.
Unit V

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 Books

Balagurusamy, E. 1995.Object oriented programming with C++,

TMH.
Herbert Schidt, 1995. C++ The complete Reference, 2nd Edition,
Osborne, MGH.

SEMESTER-VI

UBIP321 – PRACTICAL III

LAB IN MOLECULAR BIOLOGY AND PLANT BIOTECHNOLOGY

1. Isolation of plasmid and analysis by Agarose gel electrophoresis

2. SDS-PAGE
3. Mutagenesis
4. Determination of molecular size of DNA
5. Restriction analysis of DNA
6. Ligation of DNA into vectors
7. Transformation
8. Preparation of culture medium and basic sterilization techniques
9. Organ culture
10. Callus induction
11. Shoot tip culture
12. Isolation of Plant DNA and analysis by Agarose gel electrophoresis
13. Biochemical test for identification of bacteria.
 SEMESTER-VI

UBIP322 – PRACTICAL IV

LAB IN DATABASE ANALYSIS, PROGRAMMING IN PERL, C++ AND

MOLECULAR MODELLING

1. PDB analysis of protein structure by RASMOL

2. NCBI, EMBL and DDBJ (accession of informations)
3. BLAST and FASTA search
4. Alignments – pair wise and multiple sequence alignment – Clustal
W and X
5. Program for function , operation overloading
6. program for multiple constructors in a class
7. program for multiple handling
8. program for error handling
9. program for friend and virtual functions
10. Molecular mechanics and dynamics of nucleotides and proteins.
11. Molecular modelling using HEX.
 SKILL BASED ELECTIVE COURSES

1. Microbial diversity

2. Medical Laboratory techniques

3. Recombinant DNA technology I

4. Recombinant DNA technology II

5. Microbial Biotechnology I

6. Microbial Biotechnology II

NON MAJOR ELECTIVE COURSES

1. Bioinstrumentation I

2. Bioinstrumentation II

PART IV

1. Environmental Studies

2. Value Education - Yoga

PART V

1. Extension Activities