Skip to main content

6••Fourth Semester MSC BOTANY SYLLABUS

 FOURTH SEMESTER MSC BOTANY SYLLABUS & NOTES  

(KERALA UNIVERSITY) 

Click on each text, you will gets Notes 





SEMESTER IV

BO 541: SPECIAL PAPER-I BIOINFORMATICS AND BIOPHYSICS 


 

A. BIOINFORMATICS

1.Introduction to Bioinformatics: Definition and History of Bioinformatics Internet.

 Computational Biology and Bioinformatics.


2. Biological databases - Types of data and databases,

 Nucleotide sequence database 

(EMBL, GENBANK,    DDBJ) 


Protein sequence database (PIR, SWISS - PROT, TREMBEL),

 Secondary Databases (PROSITE, PRINTS, BLOCKS), 


Protein Structure Database (PDB)


3. Information retrieval from databases - search concepts, Tools for searching, homology searching, finding Domain and Functional site homologies.


4. Structural Bioinformatics - Molecular Structure viewing tool - Rasmol, Protein Structure Prediction - Secondary Structure prediction (Chou Fasman method and other Bioinformatics tools for secondary structure prediction) and Tertiary structure prediction (Comparative modeling, Abinitio prediction, Homology modeling)

-

5. Genomics Types (Structural and Functional), Genome Annotation, Gene Finding, Comparative genomics, Single nucleotide Polymorphism Gen - SNIP 


6.Proteomics Protein expression analysis, Mass spectrometry in protein identification, Protein Sorting, Metabolomics, KEGG, Systems Biology - an introduction


7. Sequence Analysis - Global Alignment, pairwise analysis, Scoring Matrices (anintroduction), Multiple Sequence Analysis


8. plecular Phylogeny - Gene and Species tree. Molecular evolution and Kimuras (12 hrs) theory, Phylogenetic Trees, Terminology in Phylogenetic tree. Cladogram and Phylogram, Significance of Molecular Phylogeny.

9. Computer Aided Drug Design and Molecular Docking, Breif study about Docking tools, AutoDock, molegro virtual docker, GOLD


10. Tools (Softwares) used in Bioinformatics - BLAST (including ALGORITHM of BLAST), Sequin, ClustalX, Clustal W, RasMol, Treeview, Phylip, GRAIL, GENSCAN, BIO - PERL.


11. Applications of  Bioinformatics

Transcriptomics, Metabolomics,

Pharmocogenomics, combinational synthesis (Brief Accounts).


B. BIOPHYSICS


1. Chemical bonds   :    

Ionic bond,   Covalent bond,   Vander Vaal's forces,    hydrogen bonding and hydrophobic interactions. 


Bonding in organic molecules. Effect of bonding on reactivity. Polarity of bonds. Bond length. Bond angle. Dissociation and association constant.

2. Bioenergetics: Concepts of free energy, Thermodynamic principles in Biology. Energy rich bonds. Coupled reactions and group transfers. Biological energy transducers.

3. Principles and applications of light and electron microscopy, resolving power, (10 hrs) depth of field. bright field and dark field, phase contrast (negative and positive phase contrast), fluorescence, fluorescence resonance energy transfer (FRET), differential interference contrast (DIC) microscopy, scanning and transmission electron microscopy. different fixation and staining techniques for EM, freeze fracture methods for EM, atomic force microscopy (AFM). Flow cytometry, confocal microscopy - different types, FISH, GISH.

4. Chromatography: Planar and column chromatography, Adsorption and partition chromatography, partition coefficient, Principle and applications of Gel filtration, Ion exchange and affinity chromatography, Thin layer chromatography, gas chromatography, 

HPLC,     HPTLC      , LCMS, GCMS.



 5. Electrophoresis. Horizontal and vertical gel electrophoresis, PAGE, SDS - PAGE, DIGE (Differential gel electrophoresis), PFGE (Pulsed field gel electrophoresis), Immuno electrophoresis. Enzyme localization by electrophoresis. Zymogram and isozyme analysis. ELISA. Isoelectric focusing.

-

6. Centrifugation. Basic principles of centrifugation, RCF (relative centrifugal force), sedimentation coefficient, Ultra centrifugation Differential centrifugation, density gradient centrifugation (zonal and isopycnic).

7. Principles of biophysical methods used for analysis of biopolymers: X-ray diffraction Bragg equation, fluorescence, UV, visible, IR, NMR, ESR Spectroscopy, ORD/CD, Fourier transform techniques, hydrodynamic methods, plasma emission spectroscopy. Atomic absorption spectroscopy, Mass spectroscopy

8. Principles and applications of tracer techniques in biology. Radiation dosimetry. Radioactive isotopes. Autoradiography. Cerenkov radiation. Liquid scintillation.



BO 542a: SPECIAL PAPER - II (ELECTIVE)

BIOTECHNOLOGY

234 hrs (Theory 144 hrs; Practical 90 hrs)


Module I - Basics of Biotechnology

1. Genesis, projection of biotechnology as an interdisciplinary pursuit, prospects and bottlenecks.

2. Vectors, plasmids, bacteriophage and other viral vectors, cosmids, Ti plasmid, yeast artificial chromosome, BAC, Agrobacterium Ti and Ri plasmid, plant and animal viruses.

3. Enzymes used in genetic engineering, restriction enzymes - their types and target sites; Ligation - Enzymes and optimization

4. Impacts of biotechnology on agri - biodiversity, medicine, industry and environment Module II - Microbial Genetics and technology

1. Replication, regulation of bacterial gene expression.

2. Mutations, genetic transfer, manipulation of gene expression in prokaryotes.

(20 hrs)

3. Microbial production of amino acids, antibiotics, microbial enzymes, organic acids.

4. Methods for laboratory fermentations, isolation of fermentation products, Elementary principles of microbial reaction engineering.

5. Microbial culture selection, fermented foods, probiotics.

6. Applications in microbiology: biopolymers, biosurfactants and biopesticides. Probiotics, Prebiotics, Synbiotis & Problems of Antimicrobial resistance. Bioconversion processes Biosafety considerations

Module III - Genetic Engineering

(40 hrs)

1. Generation of Foreign DNA molecules, cutting and joining of DNA molecules - linkers, adapters, homopolymers.

2. Gene isolation, gene cloning, cDNA and genomic DNA library, expression of cloned genes.

3. Transposons and gene targeting

4. DNA labeling, DNA sequencing - Polymerase Chain Reactions (PCR), Various kinds of PCR, Real Time PCR, Ligation Chain Reaction, Applications of PCR, DNA finger printing.



5. Southern Blotting , Western Blotting 

 and   Northern blotting,   colony Blotting

 plaque Blotting   and Dot blots,  

 in situ hybridization.

 

6. Mapping of DNA: Restriction mapping, 

DNA foot - printing,  Gel retardation analysis,

 chromosome walking and jumping



7. Molecular marker techniques -  RFLP, 

 RAPD,     AFLP,   SCAR,    STR,     SSR,    SNPs. 


8. Site directed mutagenesis. 


9. Gene transfer technologies  : 

Agrobacterium and CaMV mediated gene transfer, 

Recombinant viral technique, 

DNA mediated gene transfer method,   

protoplast fusion, 

 microcell fusion technique, 

metaphase chromosome transfer, 

direct gene transfer using PEG, 

Micro injection,

 Electroporation,   biolistic method,      

      liposome mediated DNA delivery,    

gene therapy.


 

10. Transgenic organisms,   Social and ethical issues, 


        IPR,        Patents   and   Biopiracy. 


Module IV - Plant Tissue Culture Techniques.


1. Techniques and applications


callus culture and regeneration of plants,


 micropropagation for large scale production of

 crop plants,  

micropropagation for large scale production of 

medicinal plants, tree species and ornamentals



2. Suspension culture and development - methodology, kinetics of growth and production formation, elicitation methods, hairy root culture

3. Protoplast culture - isolation, fusion, generation of hybrids, cybrids, preferential elimination of chromosomes, role in cytoplasmic male sterility and genetic transformation.

4. Exploitation of somaclonal and gametoclonal variations for plant improvement. 


Technique for detection and isolation of somaclonal variants, Factors affecting somoclonal variation


5. Production of virus free plants: different methods (brief account only)


6. Germplasm Storage and Cryopreservation - In vitro strategies, short, medium and long term (cryopreservation) 


preservation for germplasm conservation. Cryopreservation of vegetative propagated and recalcitrant seed species. 


Module V - Transgenic organisms

(20 hrs)

1. Microbes production of pharmaceuticals (somatostatin, humulin, interferons)  


Genetically modified microbes - biodegradation, biopesticides, bioremediation, mineral leaching and biofertilizers.

2. Plants insect resistance (Bt), virus resistance - coat protein, satellites, herbicide resistance. Increasing shelf life of foods flavr savr tomatoes, control of seed germination, genetically modified foods.


3. Animals production of vaccine and pharmaceuticals, hybridomas, monoclonal antibodies.

Module VI - Process Biotechnology


1. Bioprocess technology for the production of cell biomass and primary/secondary metabolites. 

  

2. Microbial production, purification and bioprocess applications of industrial enzymes and organic compounds.

3.Bioreactor designs for exploitation of microbial products, scaling up and downstream processing.

4. Chromatic and membrane based bioseparation methods, immobilization of enzymes and cells and their application for bioconversion processes.



ׂ╰┈➤        ׂ╰┈➤      ׂ╰┈➤     ׂ╰┈➤        ׂ╰┈➤






Comments

Post a Comment

Popular Posts

AFLP--Amplified Fragment Length Polymorphism

AFLP is a PCR-based DNA fingerprinting technique combining restriction digestion and selective PCR amplification of genomic DNA fragments. Developed by Vos et al., 1995. AFLP detects DNA polymorphisms at the genomic level and is highly reproducible and sensitive. Used in genetic mapping, diversity studies, phylogenetics, and marker-assisted selection. Principle AFLP relies on restriction digestion of genomic DNA, followed by ligation of adaptors and PCR amplification of a subset of fragments. Polymorphism arises due to variations in restriction sites, fragment length, insertions, or deletions. Key idea: Restriction digestion → Adaptor ligation → Selective amplification → Gel separation → Detection of polymorphic bands Materials Required Genomic DNA Restriction enzymes (usually EcoRI and MseI) Adaptors complementary to restriction sites PCR reagents: Taq polymerase, dNTPs, buffer, Mg²⁺ Primers complementary to adaptors with selective nucleotides Thermal cycler Polyacrylamide or agarose ...
Post a Comment
Read more

❥ Southern Blotting Notes

Southern Blotting  ❥ 𓆞❥ 𓆞❥ 𓆞❥ 𓆞❥ 𓆞❥ 𓆞❥ 𓆞❥ 𓆞❥ 𓆞❥  Introduction Southern blotting is a molecular biology technique used for the detection of specific DNA sequences in a complex mixture of DNA. It was developed by Edwin M. Southern in 1975. The method involves restriction digestion of DNA, separation by gel electrophoresis, transfer (blotting) onto a membrane, and hybridization with a labeled DNA probe. Principle of Southern Blotting The technique is based on the principle of complementary base pairing. A single-stranded labeled DNA probe hybridizes specifically with its complementary DNA sequence immobilized on a membrane. Detection of the label confirms the presence and size of the target DNA fragment. Steps Involved in Southern Blotting. 1. Isolation of DNA Genomic DNA is extracted from cells or tissues. DNA must be pure and intact to ensure accurate results. 2. Restriction Enzyme  Digestion DNA is digested using specific restriction endonucleases. Produces DNA f...
1 comment
Read more

Secondary Databases (PROSITE, PRINTS, BLOCKS)

Secondary Databases (PROSITE, PRINTS, BLOCKS  Secondary Databases Introduction Biological databases are broadly classified into primary and secondary databases. Primary databases store raw experimental data (e.g., nucleotide or protein sequences), whereas secondary databases contain derived information obtained by analyzing primary sequence data. Secondary databases are mainly used to: Identify protein families Detect conserved motifs, patterns, and domains Predict protein function Study structure–function relationships Examples of secondary databases include PROSITE, PRINTS, BLOCKS, Pfam, etc. 1. PROSITE Database Definition PROSITE is a secondary database that documents protein domains, families, and functional sites in the form of patterns and profiles. Developed by Swiss Institute of Bioinformatics (SIB) Maintained along with UniProt Principle PROSITE is based on the idea that functionally important regions of proteins are conserved during evolution. These conserved regions can ...
Post a Comment
Read more

DNA-Mediated Gene Transfer – Detailed Notes

DNA-Mediated Gene Transfer – Detailed Notes 1. Definition DNA-mediated gene transfer refers to the direct introduction of exogenous DNA into a host cell’s genome or cytoplasm without using viral or bacterial vectors. It is a physical or chemical approach to achieve gene delivery. Also called direct gene transfer. 2 . Principle Foreign DNA is delivered into host cells through physical or chemical methods. DNA may integrate into the host genome (stable transformation) or remain episomal (transient expression). Expression depends on: DNA sequence and promoter Type of host cell Delivery efficiency 3. Types of DNA-Mediated Gene Transfer A. Physical Methods These methods use physical forces to introduce DNA into cells. Microinjection DNA is injected directly into the nucleus or cytoplasm using a glass micropipette. Used in: animal embryos, oocytes, plant protoplasts Advantages: Precise, can deliver large DNA fragments Limitations: Labor-intensive, requires specialized equipment, low throughp...
Post a Comment
Read more

Single Nucleotide Polymorphisms (SNPs) – Detailed Notes

Single Nucleotide Polymorphisms (SNPs) – Detailed Notes 1. Definition SNPs are single base-pair variations in the DNA sequence that occur at a specific position in the genome among individuals of a species. Example: At a specific locus, one individual may have A while another has G: Copy code Individual 1: …A T C G A T…   Individual 2: …A T C G G T… SNPs are the most common type of genetic variation in most organisms. 2. Characteristics of SNPs Single base change: Involves substitution of one nucleotide for another (A↔G, C↔T). Biallelic nature: Most SNPs have only two alleles in a population. Widespread in the genome: Found in coding regions (exons), non-coding regions (introns, promoters, intergenic regions). Stable inheritance: Passed from generation to generation like other genetic markers. Frequency: Occur approximately every 100–300 bp in the human genome. 3 . Types of SNPs SNPs are categorized based on location or effect on gene function: A. Based on genomic location Cod...
Post a Comment
Read more

SSR (Simple Sequence Repeat) Marker

SSR (Simple Sequence Repeat) Markers – Detailed Notes Introduction SSR markers, also called microsatellites, are short tandem repeats (1–6 bp) of DNA sequences found throughout the genome. Examples: (A)n, (CA)n, (GATA)n, where n is the number of repeat units. SSRs are highly polymorphic, co-dominant, and locus-specific, widely used in genetic mapping, variety identification, population genetics, and marker-assisted selection (MAS). SSRs are similar to STRs; in plants and animals, the term SSR is more commonly used in molecular breeding, while STR is used more in forensics and human genetics. Structure of SSR Repeat motif: 1–6 bp Number of repeats: Variable among individuals → basis of polymorphism Flanking regions: Conserved sequences used to design specific PCR primers SSR loci are generally abundant in non-coding regions, though some occur in genes. Principle SSR markers exploit variation in the number of repeat units at a specific locus. PCR amplification using primers flanking the...
Post a Comment
Read more

Protein Structure Database (PDB)

Protein Structure Database (PDB) Introduction The Protein Structure Database (PDB) is the primary global repository for the three-dimensional (3D) structures of biological macromolecules such as proteins, nucleic acids, and protein–ligand complexes. These structures are determined experimentally using techniques like X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, and Cryo-Electron Microscopy (Cryo-EM). PDB plays a vital role in understanding: Protein structure and function Molecular interactions Drug discovery and design Structural biology and bioinformatics History and Development Established in 1971 Founded by Brookhaven National Laboratory (USA) Initially contained only 7 protein structures Now maintained by the Worldwide Protein Data Bank (wwPDB) Members of wwPDB RCSB PDB (USA) PDBe (Europe) PDBj (Japan) BMRB (Biological Magnetic Resonance Data Bank) Objectives of PDB To collect, store, and distribute 3D structural data of biomolecules To provide free and ope...
Post a Comment
Read more

GEL RETARDATION ANALYSIS

GEL RETARDATION ANALYSIS (EMSA – Electrophoretic Mobility Shift Assay) Introduction Gel retardation analysis, also known as Electrophoretic Mobility Shift Assay (EMSA), is a widely used in vitro technique for studying DNA–protein and RNA–protein interactions. The method is based on the observation that a DNA–protein complex migrates more slowly than free DNA during non-denaturing gel electrophoresis, resulting in a mobility shift or “retardation”. EMSA is extensively used to study transcription factor binding, regulatory DNA elements, and binding specificity. Definition Gel retardation analysis (EMSA) is a technique used to detect and analyze binding interactions between nucleic acids and proteins by observing the reduced electrophoretic mobility of nucleic acid–protein complexes compared to free nucleic acids. Principle A labeled DNA or RNA probe is incubated with a specific binding protein. When binding occurs, a nucleic acid–protein complex is formed. This complex has a larger size ...
Post a Comment
Read more

Agrobacterium & CaMV-Mediated Gene Transfer –

Agrobacterium and CaMV-Mediated Gene Transfer – Detailed Notes 1. Introduction Gene transfer in plants is often achieved by exploiting natural genetic mechanisms of Agrobacterium tumefaciens and Cauliflower Mosaic Virus (CaMV). These systems allow stable introduction of foreign genes into plant genomes for transgenic plant development. 2. Agrobacterium-Mediated Gene Transfer 2.1 Definition Agrobacterium-mediated gene transfer uses the natural ability of Agrobacterium tumefaciens, a soil bacterium, to transfer a part of its DNA (T-DNA) into plant cells. T-DNA integrates into the plant nuclear genome, enabling stable transformation. 2.2 Mechanism Recognition and attachment Agrobacterium detects phenolic compounds secreted by wounded plant cells. These compounds activate virulence (vir) genes on the Ti (tumor-inducing) plasmid. Activation of vir genes VirA (sensor kinase) and VirG (response regulator) induce expression of other vir genes (VirB, VirC, VirD, VirE). T-DNA processing and tran...
Post a Comment
Read more

SCAR (Sequence Characterized Amplified Region) Markers

SCAR (Sequence Characterized Amplified Region) Markers   Introduction SCAR markers are PCR-based DNA markers derived from RAPD, AFLP, or other random markers. Developed by Paran and Michelmore in 1993 to convert dominant, less reproducible markers into specific, reproducible, co-dominant markers. SCAR markers are locus-specific, reproducible, and sequence-characterized, making them ideal for marker-assisted selection (MAS). Principle SCAR markers are designed based on known DNA sequences obtained from cloned RAPD/AFLP fragments. Specific primers (18–24 bp) are synthesized to amplify a single, defined locus. The PCR amplification of this region generates a distinct band, which is highly reproducible and can distinguish homozygotes from heterozygotes if designed as co-dominant. Key idea: Random marker (e.g., RAPD) → Cloning & sequencing → Design specific primers → PCR → SCAR marker Materials Required Genomic DNA from the organism Specific primers (18–24 bp) designed from sequence...
Post a Comment
Read more