TRIPURA UNIVRERSITY

SURYAMANINAGAR: 799022
CHOICE BASED CREDIT SYSTEM (CBCS)

Name of the Department: Department of Molecular Biology and Bioinformatics

Name of the Course Curriculum: M.Sc in Molecular Biology and Bioinformatics

CORE COURSES

Sl Course code Subject Name of the Course with Course Coordinator Credit Semester
No. number
1. MBB701C Fundamentals of Cell Biology 2 I
2. MBB702C Biomolecular Interactions 2 I
3. MBB703C Bioinformatics: Sequence Analysis 2 I
4. MBB704C Laboratory Exercise- Biochemistry and sequence analysis 4 I
6. MBB801C Genetics 2 II
7. MBB802C Recombinant DNA Technology 2 II
8. MBB803C Enzymes, Metabolism and Bioenergetics 2 II
9. MBB804C Genomics and Proteomics 2 II
10. MBB805C Laboratory Exercise-rDNA and Genomics, Proteomics 4 II
11. MBB901C Cell Communication, developmental biology and Cancer 2 III
12. MBB902C Immunology 2 III
13. MBB903C Structural Bioinformatics 2 III
14. MBB904C Laboratory Exercise on Structural Bioinformatics & Tissue Culture 4 III
15. MBB905C Review on a recent advancement on Biology 2 III
16. MBB1001C Dissertation and Presentation 14 IV

ELECTIVE COURSES

Sl Course Code Subject Name of the Course Credit Semester

No. Number
1. MBB706E Bio-Molecules 2 I
2. MBB806E Fundamentals of Recombinant DNA technology 4 II
3. MBB906E Stem cell biology 2 III
4. MBB1002E Animal cloning, Animal and Plant Tissue Culture 4 IV
5. MBB1003E Fundamentals of Bioinformatics 2 IV
6. MBB1004E Advancement in Bioinformatics 2 IV
Semester-I

Core Course: MBB701C

Fundamentals of Cell Biology Number of Credits – 2

Virus, Prokaryotic (Archaea and Eubacteria) and Eukaryote (Algae, Protozoa, Fungi, Plants and
Animals) cells and organelles: cell wall, nucleus, mitochondria, Golgi bodies, lysosomes,
endoplasmic reticulum, peroxisomes, plastids, vacuoles, structure and function of cytoskeleton.

Biological membranes- their structure, function and chemistry, diffusion, osmosis, ion channels,
active transport, ion pumps, mechanism of sorting and regulation of intracellular transport, electrical
properties of membranes.

Mitosis, Meiosis, Cell cycle and its regulation.

Organization of genes and Chromosomes: Gene families, structure of chromatin and chromosomes,
interrupted genes, unique and repetitive DNA, heterochromatin, euchromatin, insertion elements and
transposons.

Core Course: MBB702C

Bio-Molecular Interactions Number of Credit – 2

Chemistry of life: Importance of Carbon, water, polymerization, permeability and self assembly,
energy and coordination of anabolism and catabolism.

Biomolecules: Carbohydrates, Proteins and lipids.

Vitamins and their biological roles.

Proteins- primary, secondary, tertiary and quaternary structure, motifs, folds and stability, Structure of
DNA and RNA. Thermal Melting and cot curves, semi crystalline, cruciform, palindromes and i-
motifs of DNA.

Allosteric interaction, Cooperative ligandbinding in haemoglobin, Hill equation.

Core Course: MBB703C

Sequence Analysis Number of Credit – 2

Sequence Analysis: Sequence similarity, identity and homology, definations of homologous,

orthologous and paralogous.

Scoring Matrices: Matrices for nucleic acid and protein sequences, PAM and BLOSSUM.

Pairwise sequence alignment: Needleman and Wunsch, Smith and Waterman algorithms for pairwise
alignments, gap penalties.

Multiple sequence alignments (MSA): The need for MSA, basic concepts of various approaches for
MSA (e.g. progressive, hierarchical etc.). Algorith of CLUSTAL W.

Database Searches: BLAST & FASTA; Use of these methods for sequence analysis including the on-
line usage. Taxonomy and phylogeny: Definition and description of phylogenetic trees and various
types of trees, phylogenetic analysis algorithms: Maximum Parsimony, UPGMA, Neighbourhood-
Joining, Bootstrapping.
Core Couse: MBB704C

Laboratory Exercise- Biochemistry and Sequence Analysis Number of Credit – 4

Biochemistry:

Clearing and autoclaving of glasswares. Preparation of buffers, reagents, media etc. Measurement of
Ph of a solution, Titration of Polybasic/Amino acids andevaluation of pKa’s. Estimation of nucleic
acids, protein, carbohydrate and lipid from given samples. Estimation of microbial load by total
microbial plate count and bacterial growth curve. Estimation of amylase activity (I.U.) and calculation
of specific enzyme activity, determination of Ph optima, Kinetics.

Sequence Analysis:

Bioinformatics resourses: NCBI, EBI, DDBJ, RCSB, ExPASY.

Sequence databases: Nucleic acid sequence databases: GenBank, EMBL, DDBJ; Protein sequence
databases: Uniprot- KB: SWISS-PROT, Tr-EMBL, Uniprot; Genome Databeses at NCBI, EBI, TIGR.
Structure Databases: PDB.

Sequences file formats: GenBank, FASTA.

Pairwise alignment, BLAST

Multiple sequence alignment: Clustal

Sequence patterns and Profiles: Generation of sequence profiles PSI- BLAST

Protein motif and domain analysis: Prosite, prodom, pfam

Phylogenetic analysis- Mega.

Semester – II

Core Course: MBB801C

Genetics Number of Credit - 2

Genetics of viruses and bacteria, introduction to human Genome, Mendelian inheritance, sex linked
inheritance, pedigree analysis, chromosomes, linkage maps and recombination.

Mutations- molecular (gene/point) and chromosomal, factors affecting gene frequencies, phenotype
and genotype relationships.

Chromosome and banding analysis, chromosome painting, FISH, comparative genome hybridization,
functional and positional cloning.

Genetic markers, microsatellite , single nucleotide polymorphism, copy number variations, population
genetics rinciples, gene mapping, marker assisted selection in palnt and animal.

Genetics and evolution, epigenetics.

Core Course: MBB802C

Recombinant Technology Number of Credit – 2

Protein sequencing methods.

DNA sequencing methods, Whole genome sequencing strategies.

Microarray based techniques for analyzing DNA, RNA & Proteins.

SI mapping, RNase protection assay, reporter assays.

Studying gene function through protein interactions: Two hybrid screening and phage display
libraries.

Synthetic genes and protein engineering.

DNA in disease diagnosis and medical forensic, Methods in DNA assay, Infectious disease, genetic
disease and its detection.

Core Course: MBB803C

Enzymes, Metabolism and Bioenergetics Number of Credit – 2

Enzymology: Enzymes- nature, classification, Enzymes-substrate reaction kinetics, Enzyme inhibition

kinetics, Enzyme specificity and diversity, Isoenzymes, Multienzyme complexes, Enzyme regulation-
allosteric modifications, feedback inhibition, covalent modification, proteolytic activation, Ribozyme,
Abzyme.

The ATP Cycle and glycolysis, Pentose Phosphate Pathway, Enter-Doudoroff Pathway, citric acid
cycle, electron transport chain, oxidative phosphorylation and regulation of ATP generation,
Respiration (Aerobic and Anaerobic) and fermentation, oxidative degradation of fatty acids and amino
acids, nitrogen fixation, CO2 fixation, chemolithotrophy and phototrophy.

Core Course: MBB804C

Genomics and Proteomics Number of Credit – 2

Genomics: Large scale genome sequencing strategies. Basic principles of genome assembly and
annotation, prediction of genes, promoters. Identification of disease genes, role of bioinformatics –
OMIM database, identification of SNPs, use of SNPs for identification of genetic traits, SNP database
(dbSNP) and its use: Metagenomic approach towards genome analysis. DNA microarray:
Understanding of microarray data, normalizing amicroarray data, Gene Expression Omnibus (GEO),
Array Express, SAGE database. Comparative genomics: Basic concepts and applications, whole
genome alignments: Artemis, MuMmer. Synteny and gene order, Comparative genomics database,
COG. Proteomics: protein arrays: bioinformatics- based tools for analysis of proteomics data (Tools
available at ExPASY Proteomic server); databases (such as InterPro) and analysis tools. Gene/ protein
function prediction using machine learning tools. Protein- protein interactions: databases such as DIP,
PPI server and tools for analysis of protein- protein interactions.
Core Course: MBB805C

Laboratory Exercise-Rdna technology and Genomics, Proteomics Number of Credit - 4

Rdna technology:

Isolation and quantitaion of genomic DNA from E.coli, plant and animal cells

Cloning of DNA / gene

Preparation of vector for cloning, Dephosphorylation and ligation

Competent cell reparation by cacl2 and electroporation.

Transformation and preparation by glycerol stocks for long term maintenance of clones. Designing
primers using website

PCR, RT-PCR and cloning of amplified product

FLP, RAPD, AFLP

Southern and northern hybridization

Recombinant protein expression, Transformation of an expressing plasmid to a bacterial strain.

Induction of recombinant protein.

Genomics and Proteomics

Important databases: OMIM, dbSNP, GEO, SAGE, COG

Whole genome alignment using Artemis, MuMmer.

Protein- protein Interaction: DIP, PPI server and analysis of protein- protein interactions.

Viva- Voice for the course content of Ist and IInd semester.

Semester – III

Core Course: MBB901C

Cell Communication, developmental biology and Cancer Biology Number of Credit – 2

Cell signalling, hormones and their receptors, cell surface receptors, signalling through GPCR, signal
transduction pathways.

Cellular Communication, Cell adhesion and roles of different adhesion molecules, gap junctions,
extracellular matrix, integrins, neurotransmission and its regulation.

Developmental Biology: history, techniques and model organisms.

Fertilization: cellular and biochemical process and strategies for monospermy and species specificity.

Cleavage: Types of cleavage and blastulation in model organisms.

Gastrulation: Gastrulation in sea Urchin frog and chick, primary organizer and mesoderm induction,
Axis specification and embryonic patterning in Drosophila, HOX complex in vertebrates and
Drosophila, cell- cell interaction.

Basic biology of cancer: Genetic and molecular basis, mutations leading to abnormalities in
programmed cell death, cell proliferation and differentiation.

Core Course: MBB902C

Immunology Number of Credit – 2

Introduction to immune systems, organization and structure of lymphoid organs. Cells of the immune
system and differentiation. Immunoglobulin (antibody), class, sub-class and structure, antibody
diversity, class switching, nature and biology of antigens and super antigens, antigen-antibody
interaction, MHC, complement system. Components of Innate immunity, mechanisms of innate
immune response. Regulation of Immune response, antigen processing and presentation, The structure
and functions of T- cell receptors(TCR), generation of humoral and cell mediated immune response,
B and T- cell activation, cytokine and role in immune regulation, immunological tolerance, ADCC,
hypersensitivity, autoimmunity, transplantation and rejection.

Strategies of vaccine development, edible vaccines, hybridoma technology and monoclonal antibody
production, acatalytic antibodies (abzymes).

Core Course: MBB903C

Structural Bioinformatics Number of Credit – 2

Structure prediction strategies: Secondary structure prediction: Algorithm viz. Chou Fasman, GOR
methods; Databases of structure based classification: CATH and SCOP. Web sources for structure
prediction. Tertiary structure prediction: Homology Modelling, fold recognition, threading approaches
and ab-initio structure prediction methods. PHD and PSI-PRED methods. Itroduction to molecular
force fields. Molecular Energy mimization: steepest decent, conjugate gradient. Molecular
Simulation. Methods: Newtonian dynamics, Monte carlo, QSAR.

Core Course: MBB904C

Laboratory Exercise on Structural Bioinformatics & Tissue Culture Number of Credit-4

Secondary structure prediction, Tertiary structure prediction through homology modelling, Molecular
dynamics, energy minimization.

Basic methods of animal and plant tissue culture, sub culturing methods.

Plant tissue culture

Detection of antigen-antibody reaction, ELISA, Immuno-precipitation.

Core Course: MBB904C

Review work and Presentaion Number of Credit – 2

Review on a recent advancement of Biology, preparation and presentation of the review report.

Semester – IV

Core Course: MBB1001

Dissertation and Presentation Number of Credit - 14

Research work on a specific problem, paper presentation and preparation of project report

Elective Course

Semester – I

Elective Course: MBB706E Number of Credit – 2

Bio- Molecules

Importance of Carbon in life, water, polymerization, permeability and self assembly, energy and
coordination of anabolism and catabolism. Basic chemistry of carbohydrates, Proteins and lipids

Liposomes and their applications, vitamins and their significance, structure of macromolecules like
protein, DNA, RNA.

Semester – II

Elective Course: MBB806E Number of Credit – 4

Fundamentals of Recombinant DNA technology

Basics of nucleic acid hybridization: southern, northern, in situ hybridization and isolation of specific
nucleic acid sequences. RFLP, RAPD, AFLP and their usage, cloning of DNA fragments in bacterial
and eukaryotic systems, expression of recombinant proteins in bacteria and eukaryotes, vector
engineering and codon optimization, Construction oof genomic and cDNA libraries in suitable vectors
(plasmid, phage, cosmid, BAC and YAC), In vitro mutagenesis and deletion deletion techniques, gene
knock out in bacteria, transposon mutagenesis, taransposition in Drosophila, transport tagging.
Transgenic and gene knock out technology: Allelic replacement and complementation.

Semester – III

Elective Course: MBB906E Number of Credit – 2

Stem cell Biology

Stem cells, definations, classification and sourses.

Embronic stem cells, embryonic germ cells, fetal stem cells, umbilical cord stem cells, adult stem
cells, constitutive and facultative their developmental capacity- totipotent, pluripotent, bipotent and
unipotent, hematopoietic stem cell, mesenchymal stem cells.

Multipotent tissue stem cells and their plasticity, (gut & liver stem cells, bone & cartilage stem cell,
epidermal stem cell, neuronal stem cell, pancreatic stem cell, eye stem cell).
Primordial germ cells, developmental potential of the cells of early embryo, commitment and
pluripotency. Molecular control of pluripotency and developmental of stem cells from differentiated
adult tissue.

Stem cell therapies in animal models.

Semester – IV

Elective Course: MBB1002E

Animal Cloning, Animal and plant tissue culture Number of Credit – 4

Animal Cloning:

History, methodology to produce cloned animals and their utility in basic research and application.

Animal and Plant Tissue Culture:

History, methodology to set up primary culture, callus culture. Permanent cell line development and
charterization.

Semester – IV

Elective Course: MBB1003E

Fundamentals of Bioinformatics Number of Credit – 2

Submission and retrieval of data in GenBank. Basic principle of genome assembly and annotation.
Scoring matrices for nucleic acid and protein sequence analysis: PAM and BLOSSUM. Pairwise and
multiple sequence alignment. Gap penalties. Database searching using BLAST. Phylogenetic analysis.

Elective Course: MBB1004E

Advancement in Bioinformatics Number of Credit – 2

Large scale genome sequencing strategy. Concept of computational systems biology. Evolutionary
processes: Mutation, Natural selection. Rates of evolution. C/C++ programming for biological
sequence analysis.