Syllabus for
Master of Science (Biotechnology)
Academic Year  (2021)

Biotechnology is a fundamental area of applied science that utilizes living cells and cellular materials to create pharmaceutical, diagnostic, agricultural, environmental, and other products to benefit society. The Master of Science in Biotechnology is designed to provide specialized scientific learning along with skills training to help students explore various career paths in agriculture, health care, forensics, industrial processing, and environmental management. Students will be provided hands on learning into the functioning of the biotechnology industry. Students will have to undertake an Industry Project in their second year of the programme.

Programme Outcome/Programme Learning Goals/Programme Learning Outcome:

PO 2: Appreciate the techniques applied in biotechnology and advanced research

PO 3: Acquire and critically appraise new data arising from the use of these techniques and to interpret the implications of such data

PO 4: Exhibit understanding of the commercial, financial and regulatory context in which the biotechnology sector operates.

PO 5: Exhibit skills in doing research in Universities and R&D Centres

The evaluation scheme for each course shall contain two parts; (a) internal evaluation and (b) external evaluation. 50% weightage shall be given to internal evaluation and the remaining 50% to external evaluation and the ratio and weightage between internal and external is 1:1.  (a) Internal evaluation: The internal evaluation shall be based on predetermined transparent system involving periodic written tests, assignments, seminars and attendance in respect of theory courses and based on written tests, lab skill/records/viva and attendance in respect of practical courses.

Microbes play a very significant role in the lives of higher organisms. The paper surveys the features of microbes like bacteria, viruses, fungi, algae and protozoa in order to make the students understand their biology so as to manipulate them. This course fulfils the basic knowledge in microbiology for those students who wish to pursue career in allied health fields and other technical programs.

History of Microbiology, Microscopy – Light, Phase contrast, Fluorescence & Electron microscopy – TEM and SEM, Physical and Chemical control of microorganisms, Classification and nomenclature of microorganisms, Bergey’s manual, Staining techniques - Gram’s, acid fast, capsular, flagellar and endospore staining. Microbial Taxonomy: Pure culture techniques (Streaking, spread plate, pour plate, serial dilution), Identification of microorganisms – Morphological, Biochemical, serological and molecular techniques.

Bacterial cell structure, classification based on shape and arrangement of cells, cell wall, flagella, pili and capsule – structure & functions, endospore formation, features of mycoplasma, Rickettsia, Prions and diseases caused. 

Microbial metabolism: Aerobic, anaerobic respiration, fermentation, Catabolism of carbohydrates, lipids and proteins. Bacterial photosynthesis, oxidation of inorganic molecules. Growth curve, factors affecting growth, Nutritional classification, Microbial associations (Mutualism, Syntrophism, Proto-cooperation, Commensalism, Ammensalism, Predation, Parasitism, Saprophytism, Satellitism and Endozoic microbes), Stress physiology: effect of oxygen toxicity, pH, osmotic pressure, heat shock on bacteria, HSPs, thermophiles, halophiles, alkaliphiles, acidophiles, psychrophiles and barophiles and their adaptations and significance,  Nitrogen fixation mechanisms and genes involved.

Hepatitis B virus. RNA viruses: HIV, bacteriophages-. Lifecycle of Lambda phage. Evolution and mutation of viruses. Cultivation and assay of viruses: Cultivation of viruses in embryonated eggs, experimental animals and cell cultures

Fungi:- Structural features, Ainsworth’s system of classification, salient features of division, reproduction of fungi, fungi as food, as plant pathogens, control measures of fungi, Mycorrhizae- ecto and endomycorrhizae, significance, Algae:- Salient features, classification (Fritsch’s) and reproduction, measurement of algal growth, strain selection and large scale cultivation, Symbiotic algae, use as biofuel.

Major Bacterial diseases – Typhoid, Tetanus, Tuberculosis, Pneumonia and Cholera, Viral diseases - Dengue, Chikungunya, Rabies. Emerging viruses – H1N1, Ebola, Zika. Major parasitic diseases –Malaria, Amoebiasis, Giardiasis- pathogen, lifecycle and treatment measures. Etiology, symptoms and control measures of some plant diseases - Bacterial blight of rice, Late blight of potato, Coconut Root wilt, Ginger Soft Rot, Downy Mildew of Grapes, Rust of Wheat, Red Rot of Sugarcane.

Concepts of pathogenesis, virulence and epidemiology, Disease classification - Epidemic, endemic and pandemics, CDC and its role, normal human microflora, gut microbiota and its relevance. Diagnosis and control of infections, Antibiotic – types and mechanism of action, biomedical waste management, nosocomial infections, Drug resistance in bacteria – causes and consequences, super bugs.

Microbes in food manufacture (Yeast, Lactobacillus etc), food spoilage (Brucella, Bacillus, Clostridium, Escherichia etc, mycotoxins - aflatoxins, ochratoxins, ergot alkaloids), agriculture (Rhizobium, Trichoderma etc), environmental management, Biodegradation of Xenobiotics - hydrocarbons, pesticides and plastics, Bioleaching of Copper, Iron , Uranium, Gold.

CIA1: Assignment/test/poster preparation/review writing etc. for 20 marks

CIA2: MID SEMESTER EXAMINATION for 50 marks

CIA3: Assignment/test/poster preparation/review writing etc. for 20 marks

Attendance in class: 10 marks

END SEMSTER EXAMINATION: Consist of 2 sections. Section A consist of 10 questions carrying 5 marks each out of which students need to attempt 8 questions (8 X 5marks = 40 marks). Section B consists of 7 questions, carrying 12 marks each, out of which students need to attempt 5 questions (5 X 12 marks = 60 marks).

The paper is intended to develop understanding and provide scientific basis of the inanimate molecules that constitute living organisms. It also gives a thorough knowledge about the structure and function of biological macromolecules (proteins, carbohydrates, lipids, and nucleic acids), and the metabolic and bioenergetic pathways within the cell. Students learn to interpret and solve clinical problems.

Forces and interactions of biomolecules; chemical bonds – Covalent and Ionic bond (bond energy), Stabilizing interactions (Van der Waals, electrostatic, hydrogen bonding, hydrophobic interaction.), high energy molecules in living system (ATP, ADP, NAD, NADH, NADPH, FAD, FADH₂), Laws of thermodynamics, Concept of free energy, enthalpy, entropy, Coupled reactions, group transfer, biological energy transducers, redox potential.Buffers and Solutions: Concept of pH, pKa, titration curve, acids, bases and buffers, Henderson-Hasselbalch Equation, biological buffer solutions.Principles of thermodynamics; Kinetics, dissociation and association constants; energy rich bonds and weak interactions; Bioenergetics.

Classification, structure and Properties of mono, oligo and polysaccharides. Chirality and optical activity, stereoisomerism, cyclic structure of monosaccharide, (pyranoses and furanoses), structures of glucose. Absolute and relative configuration (D & L and R & S nomenclature). Disaccharides-structures of Maltose, Lactose, Sucrose, Trehalose, Raffinose. Polysaccharides. Structure and properties of homo and hetero polysaccharides. Storage polysaccharides. (Starch, Glycogen, cellulose, hemicellulose, and chitin) Derived sugars- Sugar acids (Aldonic, Aldaric and Saccharic acids), amino sugars. Derivatives of carbohydrates (Glycosaminoglycans, glycolipids, Proteoglycan and glycoproteins).

Carbohydrate metabolism: Glycogenolysis, Glycogenesis, Glycolysis- Energetics and Regulation, Fermentation reactions (Lactic acid and alcoholic fermentation), Gluconeogenesis, Reciprocal regulation of Glycolysis and Gluconeogenesis, Citric acid cycle- Energetics and regulation, Glyoxylate cycle. Pentose phosphate pathway.

Electron transport chain, Electron transfer reactions in mitochondria, Electron carriers, Ubiquinone, Cytochromes, Iron sulfur centers, Methods to determine sequence of electron carriers, Fractionation of Multi enzyme complexes I, II, III, IV of Mitochondria and their inhibitors, Oxidative phosphorylation, ATP synthesis, Chemiosmotic model, Proton gradient, Structure of ATP synthetase, Mechanism of ATP synthesis, Brown fat, Regulation of Oxidative phosphorylation.

Amino acids: Structure, properties, classification and functions, reactions of amino acids, modifications of amino acids in proteins, non-protein amino acids.

Proteins- peptide bond, psi and phi angle, Ramachandran's plot, Structural organizations of proteins (primary, secondary, tertiary and quaternary, Domains, Motifs & Folds), conformational analysis. Structure and functional classification of proteins. Structure- function relationship. Thermodynamics of protein folding, chaperones and chaperonins, Stability of Protein Structures, examples of  specific proteins; Keratin, Silk fibroin, collagen triple helix and hemoglobin; Denaturation and renaturation of proteins; neurotransmitters, Peptide hormones .

Amino acid and Protein metabolism: Transamination, Deamination, Decarboxylation, basic glutamine and glutamic acid pathways, urea cycle and its regulation, formation of uric acid.

Enzyme nomenclature and classification, Isolation of enzymes. Extraction of soluble and membrane bound enzymes: Purification of enzymes-Criteria for purification; Assay of enzymes. Factors affecting enzyme activity, Isozymes, Coenzymes and cofactor, Metalloenzymes, membrane bound enzymes, Multienzyme complexes, Synthetic enzymes, Ribozymes. Mechanism of enzyme action, Active site and Specificity of enzyme. Theories on enzyme substrate complex. Free energy of enzyme reactions. Steady state kinetics. Michaelis-Menton, Lineweaver–Burk, Edde-Hofstee and Hanes-Woolf equations. Pre-steady state kinetics. Fast kinetics to elucidate the intermediates and rate limiting steps.

Enzyme inhibition: types of inhibitors; Mechanism of enzyme inhibition –competitive, non – competitive, uncompetitive, mixed and irreversible inhibition. Allosteric regulation in metabolic pathways. Applications of enzymes, enzyme engineering (Protein engineering). Immobilization of enzymes and their application.

Classification- Structure, properties, reactions and biological functions of lipids. Phospholipids, Sphingo and glyco lipids, Steroids-cholesterol-bile salts, steroid hormones,Cerebrosides, lipoamino acids, lipoproteins, lipopolysaccharides, eicosanoids (Prostaglandins, leucotrienes and thromboxane).Role of lipids in biomembranes.

Metabolism of Lipids: Biosynthesis of saturated and unsaturated fatty acids and cholesterol. Beta oxidation of Fatty acids: activation, transport to mitochondria, metabolic pathway. Oxidation of saturated and unsaturated fatty acids. Alpha and omega oxidation, metabolic disorders (Triglyceridemia, NaymanSacchs Disease).

Structure and properties- Bases, Nucleosides, Nucleotides, Polynucleotides.

Nucleic acid metabolism: Biosynthesis and regulation of purines and pyrimidines, Denovo and Salvage pathways, biodegradation of purines and pyrimidines.

Vitamins: Classification, Chemistry and Biological Functions, Fat and water soluble vitamins. Role in metabolism, Vitamins as co-enzymes. Metabolic Disorders –A, B, C, D, K.

Hormones:Autocrine, paracrine and endocrine action. Endocrine glands, Classification of hormones, basic mechanism of hormone action, importance of TSH,T3,T4, Estrogen, Testosterone, HCG, FSH, LH, Prolactin, Progesteron, adrenaline, insulin and glucagon. Hormone imbalance and disorders: hypothyroidism, hyperthyroidism, Polycystic Ovarian Disorder PCOD), Insulin Dependent Diabetes.

Plant Growth regulators: Biosynthesis, Physiological role and mechanism of action of plant growth hormones (Auxins, Gibberellins, Cytokinins, Ethylene, abscisic acid, Brassinosteroids), receptors and signal transduction (salicylic acid and jasmonic acid pathways).

Nelson, D. C. and Cox, M.M., Lehninger Principles of Biochemistry, 5th Edition, W. H. Freeman, 2010.

Voet D., Voet J.G, Biochemistry 4th Edition., John Wiley and Sons, 2011.

Elliott, W.H., Elliott, D.C. Biochemistry and Molecular Biology 3^rd Indian edition, Pub. Oxford.

Mathews, Van Holde and Ahern, Biochemistry by 3^rd edition, Pub Pearson education

Berg J.M., Tymoczko J.L. and Stryer L., Biochemistry. 7th edition, W.H. Freeman and Co. New York, 2011.

Kuchel, P.W., Ralston Schaums, G.B. Outlines of Biochemistry 2^nd edition Pub: Tata.

Devlin, T.M. (1997). Biochemistry with clinical correlations, Wiley-Liss Inc. NY

Zubey, G.L. Parson, W.W., Vance, D.E. (1994). Principles of Biochemistry WmC Brown publishers. Oxford.

Edwards and Hassall. Biochemistry and Physiology of the cell 2^ndEdn. McGraw Hill Co. UK. Ltd.

CIA1: Assignment/test/poster preparation/review writing etc. for 20 marks

CIA2: MID SEMESTER EXAMINATION for 50 marks

CIA3: Assignment/test/poster preparation/review writing etc. for 20 marks

Attendance in class: 10 marks

END SEMSTER EXAMINATION: Consist of 2 sections. Section A consist of 10 questions carrying 5 marks each out of which students need to attempt 8 questions (8 X 5marks = 40 marks). Section B consists of 7 questions, carrying 12 marks each, out of which students need to attempt 5 questions (5 X 12 marks = 60 marks).

This paper has been designed in a standard manner to impart knowledge of the cell and its various attributes among the post graduate students. The topics included in this paper gives not only the basic idea about the subject but also provides in-depth knowledge. Students get an idea about the cellular structures, as well as how these structures are helpful for the cell to communicate with its environment and transduction of various signals, whether intracellular or extra-cellular. Furthermore, students also learn the mechanism of mitotic and meiotic cell division as well as how the cell cycle is regulated. The course structure also fulfils the important criteria regarding the preparation of students for the competitive examinations, for e.g. National Eligibility Test (NET), conducted by Council of Scientific and Industrial Research (CSIR), as well as various other entrance examinations for pursuing doctoral research.

Introduction: Discovery of cells, basic properties and classes of cells. Study of cells: Microscopy: Brief overview of Light microscopy, phase contrast microscopy, electron microscopy, Confocal Microscopes, Scanning probe microscope, micrometry. Purification of cells and their parts: cells separation and culture, flow cytometry, fractionation of cell contents.

Structure: History of studies on plasma membrane structure, Singer-Nicolson Model, Chemical composition of plasma membrane: lipids, proteins and carbohydrates; Dynamic nature of plasma membrane: role of lipids in membrane fluidity, diffusion of proteins, restrictions of lipids and proteins mobility: fluorescence recovery after photobleaching (FRAP), single-particle tracking, membrane domains and cell polarity.

Functions: Movement of substance across the membrane: Energetics of movement of solute, partition coefficient, Simple diffusion: mechanism, ion channels and types (voltage, ligand and mechano-gated ion channels), Facilitated diffusion (Glucose transport, GLUT proteins) and active transport (structure and working of F0-F1 ATPase, Na+/K+ ATPase, Ca2+ ATPase, P and V-type ATPases, H+/K+ ATPase, ABC transporters); Cotransport(Uniport, Symport and Antiport); Membrane potentials and Nerve impulse: resting potential, action potential and its propagation as an impulse.

Cell wall: Primary wall, middle lamella and secondary wall; Lysosomes: structure and functions, autophagy; Endoplasmic reticulum: structure and functions of smooth endoplasmic reticulum and rough endoplasmic reticulum; Golgi complex: structure and function and movement of materials through Golgi apparatus. Structure and function of mitochondria: Structure of mitochondria: mitochondrial membranes, mitochondrial matrix; Structure and function of chloroplast: basic structure, photosynthetic units and reaction centers; Functions: photosynthetic pigments and absorption of light, photophosphorylation; carbon dioxide fixation: synthesis of carbohydrates in C3, C4 and CAM plants.

Principles and importance; Whole mount preparation; Types of microscopic slides; Types of microtome; Process: Killing and fixing, Types fixation & fixatives, Dehydration, Microtome sectioning, Stains and staining, Mounting and mountants; Histochemical techniques for starch, protein, lipid and lignin; Specimen preparation for electron microscopy: Material collection, fixing, dehydration, embedding, sectioning and staining.

Study of cytoskeleton:  Live cell fluorescence imaging, in vitro and in vivo single molecule assays; Microtubules: Structure, microtubule associated proteins, properties of microtubules with reference to the structures and functions of cilia and flagella; Intermediate filaments: structure and function; Microfilaments: basic Structure and function with reference to myosin.

Extra cellular matrix; Communication between cells and extracellular materials: roles of integrins, focal adhesions and hemidesmosomes; Communication between cells and other cells: roles of selectins, immunoglobulin superfamily, cadherins, adherens junctions and desmosomes; Tight Junctions; Gap Junctions; Plasmodesmata

Signaling mediated by G-protein coupled receptors, second messengers, enzyme tyrosine kinase, steroid receptors, role of calcium and NO as intracellular messenger, signaling via extrinsic and intrinsic pathways of apoptosis, two-component signaling in plants and bacteria; Quorum sensing.

Phases and progression of cell cycle; Control of cell cycle: Major events, cyclin dependent protein kinases (Cdks), suppression of Cdk by Cdk-Inhibirotry Proteins (CdI), dependence of Cdks on transcriptional regulation, biochemical switches in cell cycle, mitogen stimulated cell division: G1-Cdk and G1/S Cdk activities; Apoptosis: role of Caspases, Extrinsic and Intrinsic pathways, roles of Bcl2 and IAPs in apoptosis, inhibition of apoptosis by extracellular factors; Necrosis.

Cancer: Benign and Malignant tumors, metastasis, oncogenes (retinoblastoma) and tumor suppressor genes (p53).

G. Karp, Cell and Molecular Biology: Concepts and Experiments, 6^th ed. USA: Wiley and Sons, 2009.