# VTU Syllabus Biotechnology Engineering 4th Semester

**BIOSTATISTICS AND BIOMODELING Sem IV**

Module-1

BASIC STATISTICS Histogram, Ogive curve, Pie Diagram. Measure of dispersion (range, quartile deviation, mean deviation and standard deviation, coefficient of variation), Skewness & kurtosis.

Module-2

BI-VARIATE DISTRIBUTION Correlation, rank correlation and regression analysis (simple and linear) curve fitting (linear, non-linear and exponential).

Module-3

PROBABILITY Axioms, conditional probability, Bayes rule, Genetic Applications of Probability, Hardy – Weinberg law, Wahlund’s Principle, Forensic probability determination, Likelihood of paternity, Estimation of probabilities for multi-locus/ allele finger print systems. Random variables- Discrete and Continuous Probability distribution, Mathematical expectations.

Module-4

PROBABILITY DISTRIBUTIONS Discrete probability distributions- Binomial, Poisson, normal, exponential derivations. Central limit theorem. T distributions.

Module-5

STATISTICAL INFERENCE Estimation theory and testing of hypothesis, point estimation, interval estimation, sample size determination, parametric and non-parametric distributions -F-test, Chi Squared distribution, and goodness of fit test analysis of variance (one-way classifications). Randomization, random assignments, single and double blind experiments. Case studies of statistical designs of biological experiments. Microbial Growth in a Chemostat, Growth Equations of Microbial populations, Models of Commensalisms, Mutualism, Predation and Mutation. Volterra’s Model for n Interacting Species. Cigarette smoking, Lung cancer, epidemics.

Text Books :

- Principles of Biostatistics by Marcello Pagano & Kimberlee G, Thompson Learning.
- Introduction to Biostatistics by Ronadd N Forthofer and EunSul Lee, Academic Press.
- Mathematical Models in Biology and Medicine by J.N.Kapur New Age International.
- Introduction to Biostatistics by Ipsen, Feigl & Bancroft, Harper & Row, Publishers,NY.
- Basic Biostatistics & its Applications by Animesh K Datta , New Central Book Agency.
- Fundamentals of Biostatistics by P Hanumanth Rao and K Janardhan, IK Intl. Publishers.
- Biostatistics by Rastogi V.B. Medtec 3rded , 2015

Reference Books :

- Statistical methods in Bioinformatics by Warren J. Ewens, Gregory R. Grant, Springer 2nd edition, 2006.
- An Introduction to Biostatistics by P. S. S. Sundar Rao and J. Richard, Prentice Hall of India, publications, 4th edition, 2006.
- Biostatistics: A foundation for Analysis in the Health sciences by Wayne W. Daniel, John 7th edition, 2000.
- Fundamentals of Biostatistics by Veer BalaRastogi, Ane Books India.

**BIOCHEMICAL THERMODYNAMICS Sem IV**

Module-1

BASIC CONCEPTS & LAWS OF THERMODYNAMICS System, Surrounding & Processes, Closed and Open systems, State Properties, Intensive & Extensive Properties, State and Path functions, Equilibrium state, enthalpy, specific heat, Reversible and Irreversible processes.

Zeroth law of Thermodynamics, General statement of First law of Thermodynamics, First law for Cyclic Process, Non- Flow Process, Flow process, Heat capacity. Heat reservoir and Heat engines. General statements of the second law, Concept of entropy, Carnot principle, Calculation of entropy changes, Clausius inequality, Entropy and Irreversibility, Third law of Thermodynamics. Numericals.

Module-2

PVT BEHAVIOUR AND COMPRESSIBILITY CHARTS

PVT Behavior of pure fluids, equations of state & ideal gas law, Processes involving ideal gas law: Constant volume, constant pressure, constant temperature, adiabatic & polytrophic processes, Equations of state for real gases: Vander Waals equation, Redlich-Kwong equation, Peng- Robinson equation, virial equation. Numericals. Principles of corresponding states, generalized compressibility charts, Heat effects accompanying chemical reactions, Standard heat of reaction, formation, combustion, Hess’s law of constant heat summation, effect of temperature on standard heat of reaction.

Module-3

PROPERTIES OF PURE FLUIDS & THERMODYNAMIC DIAGRAMS

Reference properties, energy properties, derived properties, work function, Helmholtz free energy, Gibbs free energy, Relationships among thermodynamic Properties: Exact differential equations, fundamental property relations, Maxwell’s equations, Clapeyron equations, modified equations for internal energy (U) & enthalpy (H), Effect of temperature on U, H & Entropy (S). Gibbs- Helmholtz equation. Concept of Fugacity, Fugacity coefficient, effect of temperature and pressure on fugacity, Determination of fugacity of pure gases, solids and liquids, Activity: Effect of temperature and pressure on activity. Numericals. Thermodynamic diagrams – types of diagrams and construction of thermodynamic diagrams. Numericals.

Module-4

PROPERTIES OF SOLUTIONS & PHASE EQUILIBRIA

Partial molar properties of solution and its determination , chemical potential –effect of temperature and pressure , lewis –randall rule, Raoults law for ideal solutions, fugacity in solutions, Henry’s law and dilute solutions – ideal behavior of real solutions and Henry’s law, Activity in solutions, Activity coefficients effect of temperature and pressure, Gibbs – Duhem equation, calculation of activity coefficients using Gibbs-Duhem equation. Numericals. Criteria of phase Equilibria, criterion of stability, Duhem’s theorem, Vapour-Liquid Equilibria, VLE in ideal solutions, Non-Ideal solutions, Consistency test for VLE data, Azeotropes. Numericals.

Module-5

BIOCHEMICAL ENERGETICS

Coupled reactions and energy rise compounds, Reaction Stoichiometry, criteria of biochemical reaction equilibrium, equilibrium constant and standard free energy change, effect of temperature, pressure on equilibrium constants and other- factors affecting equilibrium conversion – Le – chatelier’s principle, liquid phase reactions, heterogeneous bioreaction equilibria, phase rule for reacting systems, Liquid-Liquid Equilibrium diagrams. Numericals.

Text Books :

- Introduction to Chemical Engineering thermodynamics, 6th Ed (2003) by J.M. Smith , H.C. Van Ness & M.M.Abbott. MGH.
- Biochemical Calculations, 2nd Ed,( 1976) by Irwin H.Segel, John Wiley & Sons.
- Engineering Thermodynamics by R K Singal, I K Intl.
- Engineering Thermodynamics by Spading and Cole, ELBS.
- Engineering Thermodynamics by Jones J.B. Hawkins, John Wiley.
- Principles of Biochemistry by Albert Lehninger, CBS publishers.
- Bioenergetics by L Eruster, Academic Press, New York

Reference Books :

- Chemical Engineering Thermodynamics by Y.V.C. Rao, New Age International.
- A Textbook of Chemical Engineering Thermodynamics, 1st Ed (2001) by K.V. Narayanan, PHI.
- Principles of Biochemistry by Lubert Stryer, Freeman Int. Edition.
- Biochemistry by Mathews, Vanholde & Arhen, Pearson Education.
- Biochemistry by Garett & Grisham, Thompson Learning.

**M****OLECULAR BIOLOGY Sem IV**

Module-1

INTRODUCTION & REPLICATION OF DNA

Chromosomal theory of heredity, genes and their location. Genetic code, Information flow in biological systems: central dogma, updated central dogma. Structures and forms of nucleic acids – DNA and RNA. Replication of DNA, structure and function of DNA polymerases, models of replications in prokaryotes, mechanism of DNA replication and enzymes involved.

Module-2

TRANSCRIPTION: Structure and function of RNA polymerases (prokaryotes & eukaryotes), mechanism of transcription in prokaryotes and eukaryotes, transcription factors, post-transcriptional processing (RNA editing, siRNA, splicing, poly A tail and 5’ capping), transcription inhibitors.

Module-3

TRANSLATION

Mechanism of translation, activation of amino acid initiation, elongation and termination of protein synthesis. Post translational modification and protein targeting, protein splicing. Differences between prokaryotic and eukaryotic protein synthesis, inhibitors of translation.

Module-4

GENE EXPRESSION IN PROKARYOTES & EUKARYOTES

Regulation of gene expression in prokaryotes: Operon model, gal, lac, trp Operons; positive versus negative

regulation. Regulation of eukaryotic gene expression, transcriptional control, homeobox in the control of developments in insects and vertebrates.

Module-5

GENETIC RECOMBINATION, MUTATION & GENE MAPPING

Genetic recombination in bacteria and viruses, site specific recombination, transposons and insertion sequences; Retroviruses. DNA damage & Repair, Mutation, Role of recombination and transposition in evolution; gene mapping techniques.

Text Books :

- Essentials of Molecular Biology by David Freifelder, Narosa Pub. House.
- Molecular Biology of the Cell by Alberts et al., Garland Publishing.
- Principles of Gene manipulation and Genomics by Primrose, Oxford University Press.
- Molecular Biology of the Gene by James D Watson et al., Pearson Education.

Reference Books:

- Statistical methods in Bioinformatics by Warren J. Ewens, Gregory R. Grant, Springer 2nd edition, 2006.
- An Introduction to Biostatistics by P. S. S. Sundar Rao and J. Richard, Prentice Hall of India, publications, 4th edition, 2006.
- Biostatistics: A foundation for Analysis in the Health sciences by Wayne W. Daniel, John 7th edition, 2000.
- A Textbook of Molecular Biology by S.M Gopinath, Archers & Elevators International Publishing House India. 1st Edition. 2014.
- Fundamentals of Biostatistics by Veer BalaRastogi, Ane Books India.

**B****I****O****P****R****O****CE****SS PRINCIPLES & CALCULATIONS Sem IV**

Module-1

BASIC CHEMICAL CALCULATIONS AND MATERIAL BALANCE

Concept of atom and mole, expressing composition of mixtures in Solids, liquids and gases. Expressing composition of mixtures and solutions – Percentage by weight percentage, mole percentage and Volume percentage; Normality, Morality, Molality. Generalized material balance equations for distillation, absorption, extraction, crystallization, mixing, drying & evaporation.

Module-2

MATERIAL BALANCE WITHOUT CHEMICAL REACTIONS AND FUELS

Material balances calculation in Distillation, Absorption, Extraction, Crystallization, Drying, Mixing and Evaporation Operations, Fuels – types of fuels, (solid, liquid and gaseous fuel), relevance to biofuels, characteristics of fuels, Ultimate and proximate analyses of fuels.

Module-3

MATERIAL BALANCE INVOLVING CHEMICAL REACTIONS

Material balances calculation involving bypass, recycle and operations. Generalized material balance equations, Principles of stoichiometry, Definitions of limiting and excess reactants, fractions and percentage conversion, yield and percentage yield, Selectivity, unit process – neutralization, oxidation, nitration, hydrolysis, and problems relating to these unit processes.

Module-4

ENERGY BALANCE

General energy balance equation for steady state. Heat capacity, estimation of heat capacity for solids, liquids, gases and their mixtures. Enthalpy, Standard Heat of formation, standard heat of reaction, Standard heat of combustion and calorific value, Calculation of heat of reaction at elevated temperature.

Module-5

BIOPROCESS PRINCIPLES & STOICHIOMETRY OF BIOPROCES

Historical development of bioprocess technology; Bioprocess principles and operations, generalized process flow sheets. General material balance equation for steady state (for manufacture of penicillin and ethanol) – outline of a bioprocess and the various (upstream and downstream) unit operations involved in bioprocesses. Stoichiometry of microbial growth and product formation.

**T****ext Books:**

- Principles of Biochemistry by David L. Nelson (Editors), W.H. freeman and company.
- Bioprocess Engineering Principles by Pauline Doran, Academic Press.
- Biochemical Engg. Fundamentals by J E Bailey & D. F. Ollis, McGraw Hill.
- Biochemical Calculations by I.H.Segel, John Wiley & Sons.

**R****e****f****erence Books:**

- Basic Principles and Calculations in Chemical Engineering by David Himmelblau, PHI
- Bioprocess Engineering by Shule and Kargi, Prentice Hall.
- Chemical Process Calculations by R. Asokan, University Press, 2011.

**STRUCTURAL BIOLOGY Sem IV**

Module-1

INTRODUCTION & PROTEIN STRUCTURE

Levels of molecular organization, Brief discussions on: Amino acids, Nucleic acids, Adenylates, Carbohydrates, Lipids, Cofactors, Vitamins, and Hormones. Composition and primary structures of proteins, Conformational analysis and forces that determine protein structures, geometries, phi, psi, omega angles, Ramachandran or steric contour diagram, allowed chi angles of side chains in proteins, hydrogen bonding, disulphide bonds, hydrophobic interactions, vanderwaals forces, potential energy calculations, alpha helices, beta sheets, helix to coil transition, general features and thermodynamic aspects of protein folding, folding kinetics, protein-ligand interactions, Scatchard plot, cooperative interactions, allosteric effects, Hill constant; Relationship between the primary, secondary, and tertiary structure of proteins. Structure of IgG, fibrous proteins (structure of collagen, keratin). Quaternary structures – dimers, homo & hetero dimers, trimers, tetramers; Protein folds, structural families and classes, multifunctional domains (qualitative examples).

Module-2

STRUCTURE OF NUCLEIC ACIDS AND BIOMEMBRANES

General characteristics of nucleic acid structures (A, T, G,C, U), forces and stabilizing geometries, glycosidic bond, rotational isomers. Stabilizing ordered forms of DNA (A, B and Z), base pairing types, base stacking, tertiary structure of DNA (Supercoiled DNA), Melting of the DNA double helix (Hyperchromicity), Interaction with small ions and small molecules. Ribose puckering and Tertiary structure of tRNA. Structure and conformational properties of cell membranes, Singer and Nicholson model, integral proteins in membranes, conformational variations during ion transport, Signal transduction and molecular reception (qualitative).

Module-3

BIOPHYSICAL TECHNIQUES

Rayleigh scattering, ultra-centrifugation, viscometry. Electron microscopy (SEM-TEM, AFM), luminescence (fluorescence & phosphorescence), Calorimetry, DSC, Mass spectrometry, LCMS, MALDI-TOF, Voltage Clamp and Patch Clamp (measurements of membrane potentials).

Module-4

SPECTROSCOPIC TECHNIQUES

X-ray diffraction: structure determination via single crystal diffraction, fibre diffraction; Neutron diffraction. XAFS. NMR spectroscopy (structure determination). ORD/CD, UV, IR, Laser Raman, ESR/EPR.

Module-5

BIOMOLECULAR INTERACTIONS & MOLECULAR DYNAMICS

Association of macromolecules, molecular conjugates, supramolecular interactions, protein-protein interactions, protein-nucleic acid interactions, lipid/membrane-protein interactions. Molecular mechanics and dynamics (Newtonian and Monte Carlo simulations), theoretical principles and its importance towards insilico simulations, results of molecular dynamics calculations and their implications to biological function.

**T****ext Books:**

- Biophysical Chemistry by Cantor R. and Schimmel P.R, W. H. Freeman.
- Physical Biochemistry by David Freifelder, W H Freeman and Company.
- Biophysical Principles of Structure & Function by Fred M. Snell & Sidney Shulman.
- Introduction to Protein Structure by Carl Branden and John Tooze, Garland Publishing.
- Proteins Structure – A Practical Approach by Creighton, Oxford University Press.
- Physical Chemistry: Principles and Applications in Biological Sciences by Tinoco and others, Prentice Hall.

**R****e****f****erence Books:**

- Biophysics – An Introduction by Cotterill, Wiley Student Edition.
- Foundations of Biophysics by A.L. Stanford, Academic Press.
- Principles of protein structure by G Schulz and R H Schrimer, Springer Verlag.
- Principles of nucleic acid structure by Sanger, Springer Verlag.
- Introduction to Protein Science by Arthur M Lesk, Oxford University Press.
- Biological Spectroscopy by J. D. Campbell and R. A.Dwek, Plenum Press.
- A Textbook of Biochemistry and Biophysics by S.M Gopinath, Archers & Elevators International Publishing House, India

**C****LI****N****I****CA****L BIOCHEMISTRY**

Module-1

DISORDERS OF CARBOHYDRATE METABOLISM Diabetes mellitus, glycohemoglobins, hypo-glycemias, galactosemia and ketone bodies. Various types of glucose tolerance tests. Glycogen storage diseases. Physiology of lipids/lipoproteins. Lipidosis. Clinical inter-relationships of lipids (sphingolipidosis and multiple sclerosis), lipoproteins and apolipoproteins. Diagnostic tests for HDL-cholesterol, LDL-cholesterol and triglyceride disorders.

Module-2

INBORN ERRORS OF METABOLISM

a) Disorders of amino acid metabolism – Phenylalanemia, homocystinuria, tyrosinemia, MSUD, phenylketonuria, alkaptonuria, albinism and animoacidurias. b) Disorders of nucleic acid metabolism- Disorders in purine/ pyrimidine metabolism.

Module-3

DISORDERS OF ACID-BASE BALANCE AND THEIR RESPIRATORY AND RENAL MECHANISMS.

Evaluation of organ function tests,Assessment and clinical manifestations of renal, hepatic, pancreatic, gastric and intestinal functions. Clinical importance of bilirubin. Diagnostic enzymes: Principles of diagnostic enzymology. Clinical significance of aspartate aminotransferase , alanine aminotransferase, creatine kinase, aldolase and lactate dehydrogenase. Enzyme tests in determination of myocardial infarction. Enzymes of pancreatic origin and biliary tract.

Module-4

HORMONAL DISTURBANCES

Protein hormones (anterior pituitary hormones, posterior pituitary hormones), steroid hormones, adrenocorticosteroids, and reproductive endocrinology. Disturbances in thyroid function. Disorders of mineral metabolism: Hypocalcaemia, hypocalcaemia, normocalcaemia, hypophosphatemia and hypophosphatemia.

Module-5

BIOCHEMICAL ASPECTS OF HEMATOLOGY

Disorders of erythrocyte metabolism, hemoglobinopathies, thalessemias thrombosis and anemias. Laboratory tests to measure coagulation and thrombolysis. Detoxification in the body: enzymes of detoxification, polymorphism in drug metabolizing enzymes. Mechanism of drug action and channels of its excretion, Disorders of vitamins and trace elements.

**Text Books:**

- Textbook of Medical Biochemistry by MN Chatterjea and Rana Shinde, Jaypee Brothers.
- Lehninger- Principles of Biochemistry by David L. Nelson and Michael M. Cox, 5th Edition, WH Freeman and Company.
- Medical Biochemistry (Paperback) By John W. Baynes and Marek Dominiczak. Publisher Mosby.
- Clinical Biochemistry: 3rd Ed By Allan Gaw, Michael Murphy, Robert Cowan, Denis O’Reilly, Michael Stewart and James Shepherd.

**R****e****ference Books:**

- Review of Medical Physiology (Lange Basic Science) (Paperback) By William F. Ganong. Publisher: McGraw-Hill Medical
- Harper’s Biochemistry (Lange Medical Books) (Paperback) By Robert K. Murray, Daryl K. Granner, Peter A. Mayes and Victor W.
- Clinical Biochemistry Paperbackby Nanda Maheshwari, 2008.
- Appreciate the biochemical aspects of hematology.

**CELL & MOLECULAR BIOLOGY LABORATORY Sem IV**

Experiments :

1. Study of divisional stages in Mitosis.

2. Study of divisional stages in Meiosis.

3. Study of Polytene and Lampbrush chromosomes using permanent slides.

4. Isolation and fusion of plant protoplasts.

5. Isolation of plasmid DNA from bacteria.

6. Isolation of genomic DNA (plant / microbial sources)

7. Agarose gel electrophoresis and quantification of nucleic acids (colorimetric, ethidium bromide dot blot and standard DNA marker)

8. Digestion and mapping of plasmid pUC18.

9. Competent cell preparations.

10. Transformation and selection of recombinants.

11. Study of conjugation in E.coli.

12. Amplification of DNA by PCR.

**R****e****ference Book**:

- Molecular Cell Biology by Darnell J Lodish& H Baltimore, Freeman Pub
- Biochemistry & Molecular Biology by William H Elliot and Daphane C Elliot, Oxford University Press
- Current protocols in molecular biology,edited by Frederick M. Ausubel et al., John Wiley & Sons
- Methods in enzymology by Berger S.L. & Kimmel A.R., Vol.152, Academic Press.
- Cellular & Biochemical Science by G. Tripathi, IK Intl.

**C****LI****N****I****CA****L ****BIOCHEMISTRY LABORATORY Sem IV**

Experiments :

1. pH measurements, volume / weight measurements, concentration units, sensitivity. Specificity, precision, accuracy, preparation of buffers of constant strength.

2. Titration of amino acids with acids & bases.

3. Qualitative tests for carbohydrate and lipids.

4. Qualitative tests for amino acids and proteins.

5. Estimation of blood sugar by Folin method and by O-toluene method.

6. Estimation of inorganic phosphate by Fiske-Subbarao method.

7. Estimation of amino acid by ninhydrin method.

8. Estimation of total cholesterol from Serum.

9. Determination of Saponification value and iodine value of lipids with error analysis.

10. Determination of acetyl value of a lipid with error analysis.

11. Estimation of urea by diacetyl monooxime method with error analysis.

12. Estimation of iron from hemoglobin with error analysis.

**R****e****ference Books:**

- Modern Experimental Biochemistry by Rodney Boyer, Pearson Education.
- Practical Biochemistry by Cole, Cambridge University Press.
- Practical Biochemistry by Keith Wilson, Cambridge University Press.
- An introduction to practical biochemistry by Plummer, Tata McGraw Hill.
- Experimental Biochemistry by Beedu Sashidhar Rao and Vijay Deshpande, I.K.Intl.
- Lab Math by Dany Spencer Adams, IK Intl. Pub. House.
- Lab Ref by Jaine Roskams & Linda Rodgers, IK Intl. Pub. House.
- Manual of Practical Biochemistry for medical students, 2nd edition, University Press.
- Practical Manual Of Biochemistry by Sharma S. Medtech ,2016