Second Year

Course for 2nd Year B.S. (Honors) in Genetic Engineering & Biotechnology

Organic Chemistry

  1. Chemistry of:
  • Carboxylic acids
  • Amines
  • Diazonium salts
  • Azo dyes
  • Sulfadrugs
  • Phenols


  1. Alkaloids and Antibiotics:
  • Alkaloids and their classification
  • Extraction of important alkaloids and their biological roles
  • Chemistry of quinine, papavarine, morphine
  • Classification and general mode of action of antibiotics and chemistry of penicillin, chloramphenicol


  1. Polymers:
  • Definition and classification- natural and synthetic polymers
  • Mode of polymerization- addition and condensation.



Physical Chemistry:


  1. Kinetics and reaction mechanisms:
  • Nature and scope of chemical kinetics
  • Rate laws 
  • Rate of reaction: definition; factors influencing rate of reaction- temperature, concentration, pH, pressure, nature of the reactant and catalysts
  • The Arrhenius equation
  • Collision theory and transition state theory
  • Catalysts and catalysis
  • Concept of reaction order: first, second and pseudo-order reactions; determination of reaction order
  • The relationship between reaction order and stoichiometry
  • Molecularity of reactions 
  • Kinetics and reaction mechanism 
  • Concepts of elementary processes
  • The steady state approximation


  1. Electrochemical Cells:
  • Standard electrode potential 
  • Electromotive force of a cell 
  • Nernst equation 
  • Redox potential and biology


  1. Quantum Theory and Photochemistry:
  • Light energy and its interaction with matter 
  • Excitation and emission 
  • The Frank-Condon principle 
  • Nature of chromophores: d-d transitions, (n"π) and (π"π*) transition 
  • Fluorescence and Phosphorescence


  1. Spectroscopy and Quantification:
  • The nature of light and how it interacts with molecules
  • Vibrations of molecules (basic theory)
  • Infrared (IR) spectroscopy of organic molecules and functional groups
  • UV-visible spectroscopy and electronic structure, Beer-Lambert-Bouguer law
  • Nuclear magnetic resonance (NMR) spectroscopy (basic concepts); 13C spectra (shielding and chemical shifts); high-resolution 1H NMR spectra (coupling patterns); interpreting NMR spectra of organic molecule
  • Mass spectrometry (MS) and its use in the determination of structure of organic molecules

Recommended Readings:

  1. Atkins P, de Paula J. Physical Chemistry (9th Ed.). New York, WH Freeman (2009).
  2. Roussel MR. A Life Scientist's Guide to Physical Chemistry. London, Cambridge University Press (2012).
  3. Solomons TWG, Fryhle CB. Organic Chemistry (9th Ed.). New York, John Wiley (2007).
  4. Morrison RT, Boyd RN. Organic Chemistry (6th Ed.). Prentice Hall (1992).
  5. Van Holde KE, Johnson C, Ho PS. Principles of Physical Biochemistry (2nd Ed.). New York, Prentice Hall (2005).
  6. Fisher J, Arnold J. Instant Notes in Chemistry for Biologists (2nd Ed.). New York, Taylor & Francis (2012).
  7. Atkins RC, Carey FA. Organic Chemistry: A Short Course (3rd Ed.). New York, McGraw Hill (2001).


Additional reading materials may be suggested by the respective course instructor(s).

    1. Introduction:
    • A brief history
    • Enzymes as biological catalysts
    • Classification and nomenclature of enzymes
    • Cofactors and prosthetic groups
    • Units of enzyme activity (IU, Katal)
    • Specific activity of enzymes
    • Enzyme assay methods


    1. Enzyme Catalysis:
    • Role of enzymes in reducing activation energy
    • Factors affecting the rate of enzymatic reactions (substrate concentration, enzyme concentration, pH, temperature and the rate of mixing)
    • Factors affecting catalytic efficiency of enzymes (such as proximity, orientation-distortion or strain)
    • Covalent catalysis and general acid-base catalysis


    1. Specificity of Enzymes:
    • Absolute, broad and intermediate specificity
    • Stereospecificity
    • Active site: common features and determination


    1. Kinetics of Simple and Complex Reactions:
    • Thermodynamic aspects of reactions: reaction coordinates, activated complexes and transition states


    1. Enzyme Kinetics:
    • Introduction to kinetics: Steady state kinetics and pre-steady state kinetics
    • Enzyme-substrate complex formation and experimental evidences
    • Mono-substrate enzyme kinetics
    • Michaelis-Menten equation and its linear transformations: Lineweaver-Burk plot, Eadie-Hofstee plot, Hanes-Wolf plot, Cornish-Bowden plot and their limitations
    • Km, Vmax and Kcat/Km: definition, determination, significance
    • Bisubstrate enzyme kinetics: Single and double displacement reactions, random & ordered mechanism


    1. Enzyme Inhibition:
    • Reversible inhibition: competitive, noncompetitive and uncompetitive kinetics
    • Irreversible inhibition, specific examples


    1. Enzyme Regulation:
    • General mechanism of enzyme regulation
    • Reversible and irreversible covalent modification of enzymes
    • Protein-ligand binding
    • Cooperativity phenomenon, Hill and Scatchard plots
    • Allosteric enzymes, sigmoidal kinetics and their physiological significance, symmetric and sequential modes for action of allosteric enzymes and their significance
    • Feed Back inhibition and Feed Forward stimulation
    • Enzyme repression, induction and degradation
    • Control of enzymatic activity by products and substrates
    • Monocyclic and multicyclic cascade systems


    1. Mechanism of Enzyme Action:
    • Detailed mechanisms of Chymotrypsin, Lysozyme, RibonucleaseA, Carboxypeptidase


    1. Non-Protein Enzymes:
    • Abzymes, Ribozymes and DNA enzymes


    1. Industrial and Diagnostic Application of Enzymes:
    • Isoenzymes: characteristics and importance
    • Enzymes and isoenzymes in diagnosis (lactate dehydrogenase (LDH), creatine kinase (CK), transaminases, phosphatases, amylase and cholinesterase)
    • Serum enzymes in health and diseases
    • Normal and diagnostic value of enzymes
    • Industrial applications of proteins and enzymes
    • Biosensors and immobilized enzymes


    Recommended Readings:

    1. Palmer T, Bonner PL. Enzymes: Biochemistry, Biotechnology and Clinical Chemistry (2ndEd.).CambridgeWoodhead Publishing, Limited (2007).
    2. Polaina J, MacCabe P. Industrial Enzymes: Structure, Function and Applications. New York, Springer (2010).
    3. Methods in Enzymology (Book Series), selected volumes. New York, Academic Press (1955-2012).
    4. Lehninger A, Nelson DL, Cox MM. Lehninger Principles of Biochemistry (5th Ed.). New York, W H Freeman (2008).
    5. Fersht A. Enzyme Structure and Mechanisms. New York, WH Freeman, W. H. & Company (1998).
    6. Wiseman A. Handbook of Enzyme Biotechnology (2nd Ed.). New York, Ellis Horwood Publishers (1985).
    7. Berg JM, Tymoczko JL and Stryer L. Biochemistry (7th Ed.). W H Freeman & Company, New York (2010).
    8. Voet D, Voet JGBiochemistry (4th Ed.)John Wiley and Sons, Inc, New York (2010).
    9. Mckee T, Mckee JR.Biochemistry the Molecular basis of life (5th Ed.). Oxford University Press (2011).


    Additional reading materials may be suggested by the respective course instructor(s).

  1. Peptides and Proteins:
  • Biologically active peptides
  • General functions of proteins
  • Protein classification


  1. Protein Composition and Structure:
  • An overview of protein structure and conformation
  • Peptide bonds to form polypeptide chains
  • Primary structure, secondary structure (α-helix, β-sheet, turn and loop)
  • Tertiary structure and quaternary structure
  • Structural function of fibrous proteins
  • Structural features of α-keratin, collagen and silk fibroin
  • Structure of globular proteins: myoglobin
  • Molecular chaperone
  • Methods for determining three dimensional structure of proteins
  • Protein denaturation and folding, protein misfolding
  • Prion diseases


  1. Protein Purification and Amino Acid Sequence Determination:
  • Purification according to size, charge and binding affinity
  • Salting in, salting out, and dialysis of proteins
  • Chromatography: gel-filtration, Ion-exchange, Affinity chromatography, HPLC
  • Gel electrophoresis, isoelectric focusing, 2D electrophoresis
  • Protein quantification and detection
  • Amino acid sequence determination by Edman degradation and other methods


  1. Protein Function:
  • Protein-ligand binding
  • Oxygen-binding proteins (myoglobin and hemoglobin)
  • Oxygen transport by hemoglobin; structural change on oxygen binding; cooperative binding of oxygen
  • Hill Equation and Hill Plot; models of cooperative binding
  • The Bohr Effect
  • Regulation of oxygen binding by 2,3-BPG; physiological consequences of 2,3-BPG binding to hemoglobin
  • Sickle-cell anemia and hemoglobin


Recommended Readings:

  1. Lehninger A, Nelson DL, Cox MM. Lehninger Principles of Biochemistry (5th Ed.). New York, W H Freeman (2008).
  2. Berg JM, Tymoczko JL and Stryer L. Biochemistry (7th Ed.). W H Freeman & Company, New York (2010).
  3. Lodish H, Berk E, Kaiser J et al. Molecular Cell Biology (7th Ed.), New York, WH Freeman (2012).
  4. Alerts B, Johnson A, Lewis J et al. Molecular Biology of the Cell (5th Ed.), New York, WH Freeman (2007)..
  5. Petsko GA, Ringe D. Protein Structure and Function, New Science Press (2008).


Additional reading materials may be suggested by the respective course instructor(s).

  1. Biological Membranes and Transport:
  • The composition and architecture of membranes
  • Membrane lipids and proteins
  • Membrane dynamics
  • Solute Transport across the membranes
  • Various types of membrane transporters, channels and pumps
  • Membrane integrated ATPases involved in ion pumping across the membrane


  1. Bioenergetics:
  • The second law of thermodynamics
  • The concept of free energy, entropy and enthalpy
  • The exergonic and endergonic reactions, high and low energy bonds and chemical compounds
  • Activation energy, enzyme catalysis
  • (Phosphoryl) group transfer in driving endothermic reactions
  • Biological oxidation and reduction reactions
  • Oxidation of the carbon fuels including sugars, amino acids and fatty acids
  • Roles of NAD, NADP and FADH, the electron transport system and ATP synthesis


  1. Carbohydrate Metabolism:
  • Glycolysis- the energy conversion pathway
  • Coordinated regulation of glycolysis and gluconeogenesis
  • Pentose Phosphate Pathway and NADPH generation
  • Coordinated regulation of glycogen synthesis and breakdown
  • Glycogen breakdown- the interplay of several enzymes: Phosphorylase, Epinephrine and Glucagon
  • The citric acid cycle- the reactions, its regulations and its role as a source of biosynthetic precursors
  • Anaplerotic reactions
  • Oxidative phosphorylation and its regulation: proton gradient powers the ATP synthesis
  • Glyoxylate cycle
  • Role of glucose-6-phosphate dehydrogenase in protecting against reactive oxygen species


  1. Fatty Acid Metabolism & Cholesterol Biosynthesis:
  • Digestion, mobilization and transport of lipids
  • Fatty acid biosynthesis
  • Oxidation of fatty acids
  • The role of ketone bodies
  • Cholesterol biosynthesis


  1. Amino Acid metabolism:
  • Transamination, deamination and decarboxylation of amino acid
  • Carbon atoms of degraded amino acids as major metabolic intermediates
  • Urea cycle
  • Inborn errors of amino acid metabolism


  1.  Nucleotide Biosynthesis and Metabolism
  • Biosynthesis of the purine and pyrimidine nucleotides
  • Formation of the deoxyribonucleotides
  • Biosynthesis of NAD+, FAD, and CoA
  • Catabolism and salvage of the purines and pyrimidines


Recommended Readings:

  1. Lodish H, Berk E, Kaiser J et al. Molecular Cell Biology (7th Ed.), New York, WH Freeman (2012).
  2. Alerts B, Johnson A, Lewis J et al. Molecular Biology of the Cell (5th Ed.), New York, WH Freeman (2007).
  3. Berg J M, Tymoczko J L and Stryer L. Biochemistry (7th Ed.). W H Freeman & Company, New York (2010).
  4. Voet D, Voet J, Pratt C. Fundamentals of Biochemistry (4th Ed.). New York, John Wiley (2012).
  5. Lehninger A, Nelson DL, Cox MM. Lehninger Principles of Biochemistry (5th Ed.). New York, WH Freeman (2008).
  6. Pratt CW, Cornely K.  Essential Biochemistry (3rd Ed.). Wiley, John & Sons (2013).


Additional reading materials may be suggested by the respective course instructor(s).

  1. Tissues:
  • Types and functions of tissues (epithelial, connective, muscular and neuronal tissues)
  • The ultra structure of muscle, molecular mechanism of muscle contraction
  • The organs and the organ systems- lymph, lymphatic vessels and the primary, secondary and tertiary lymphatic tissues (bone marrow, thymus, lymph nodes, spleen, tonsils, and the Payer’s patches)
  • Control systems and maintenance of homeostasis


  1. Digestive Systems:
  • General anatomy
  • The digestive processes and functions
  • Digestive enzymes: composition, function and regulation of salivary, gastric, pancreatic, bile and intestinal juices
  • Chemical digestion and absorption of carbohydrates, lipids, proteins and nucleic acids
  • Balanced diet; importance of vitamins, minerals and trace elements


  1. Gastro-Intestinal (GI) System and Liver:
  • An overview of the GI system
  • Mouth, pharynx, esophagus, stomach, pancreas, small and large intestine
  • Gross anatomy, microscopic anatomy and functions of the liver


  1. Cardiovascular and the Circulatory System:
  • Anatomy of heart
  • Systemic, pulmonary and coronary blood circuits
  • Cardiac muscle and the conduction system 
  • The cardiac cycle (origin, conduction and regulation of heart beat)
  • Electrical and contractile activity of the heart and electrocardiogram
  • Circulatory system (general anatomy of blood vessels, arteries veins and capillaries)
  • Blood pressure, capillary pressure, regulation of blood pressure


  1. Respiratory System:
  • Introduction to cardiopulmonary anatomy and physiology
  • Mechanism and control of breathing (inspiration and expiration), control of respiration
  • Transport of oxygen and carbon dioxide; oxygen dissociation curve of hemoglobin and myoglobin
  • The Bohr effect; chloride shift
  • The effects of hydrogen ions
  • Respiratory system defense mechanisms


  1. Brain andNervous System:
  • Overview of the brain,
  • The hindbrain, midbrain and forebrain
  • Organization of cerebral cortex, brain stem, cerebellum and spinal cord
  • Structure and function of central nervous system (CNS) and peripheral nervous system (PNS)
  • Structure of the neurons
  • Nature of nerve impulse- its origin and propagation
  • Membrane potential and action potential
  • Synapse and myoneural junction
  • Different types of neurotransmitters
  • The neural circuits
  • Structure and function of sensory organs concerned with vision, sound perception, taste, smell and touch
  • Higher brain functions (brain waves and sleep, cognition, memory, emotion, sensation, motor control, speech and language)


  1. Renal System:
  • Micro-architecture and function of kidney
  • Nephron
  • Renal functions and glomerular filtration
  • Urine formation and its properties
  • Role of the kidney in the regulation of water, salt and acid base balance
  • The relationship between kidney function and blood pressure
  • Renal insufficiency and hemodialysis


  1. Blood:
  • Composition and function of blood, plasma and serum
  • Erythrocytes and hemoglobin: formation, structure and function
  • Structure and properties of different types of leukocytes, abnormalities of leukocyte count,
  • Blood group (A, B, O and Rh) antigens, blood transfusion and cross-matching tests
  • Blood coagulation,
  • Erythrocyte disorders, erythroblastosis fetalis,
  • Significance of erythrocyte sedimentation rate (ESR)


  1. Endocrine System:
  • Hormones and other signaling molecules
  • Anatomy of the endocrine organs (hypothalamus, pituitary, thyroid, parathyroid, adrenal, pancreas, testes, ovary, pancreatic islets and other endocrine elements)
  • Local chemical mediators; prostaglandins
  • Consequence of endocrine malfunction


  1. Reproductive System:
  • Human reproduction and development
  • The male reproductive system: spermatogenesis and regulation of spermatogenesis
  • The female reproductive system: oogenesis and its regulation, puberty, menstruation, menstrual cycle and its regulation,
  • Male and female sterility and infertility
  • Birth control strategies, pregnancy & lactation




Recommended Readings:

  1. Barrett KE, Barman SM, Boitano S, Brooks H.Ganong’s Review of Medical Physiology (24th Ed.). New York,McGraw-Hill (2012).
  2. Sylvia SM, Boyd RN.Understanding Human Anatomy & Physiology (5th Ed.). New York, McGraw-Hill (2010).
  3. Saladin KS.Anatomy & Physiology: A Unity of Form and Function (6th Ed.). Boston, McGraw Hill (2012).
  4. Guyton C and Hall JE.Textbook of Medical Physiology (12th Ed.). Philadelphia, WB Saunders (2010).
  5. Marieb EN, Wilhelm PB, Mallat JB. Human Anatomy and Physiology (10th Ed.). New York, Benjamin Cummings (2011).
  6. Jenkins G, Kemnitz C, Tortora GJ.Anatomy and Physiology: From Science to Life (3rd Ed.). New York, John Wiley (2012).


Additional reading materials may be suggested by the respective course instructor(s).

  1. Fluid Mechanics:
  • Nature of fluids and types
  • Dimension and units
  • Force and kinematics
  • Friction and drag, Poiseuille’s equation, Viscosity, Strokes formula
  • Diffusion constant and Einstein Formulas
  • Laminar, turbulent and pulsatile flow
  • Blood velocity and turbulence


  1. Electricity and Magnetism:
  • The nature of electric charge, Coulomb force
  • Electrical potential, electric field, electric dipole, Ohm’s law; Kirchiff’s law
  • Capacitors and dielectrics, RC circuits, capacitor charging, discharging and its application in biology
  • EMF, electromagnetic oscillations, electromagnetic spectrum (radio, micro-waves, infra-red, optical, ultraviolet, X-rays, alpha, beta and gamma rays) including elementary facts about their properties, uses and propagation
  • Magnetic field, nuclear magnetic resonance (NMR)


  1.   Biophysical Phenomena of Light:
  • Polarimeter, photometer
  • Photochemistry and transmitter of vision
  • Light attenuation in vision
  • The eye as an optical instrument, illumination of retina; formation of image
  • Effects of long continued exposure of light
  • Light application in therapy
  • Biological light (bioluminescence) 


  1. Basic Electronics and Biosensors:
  • Solid state electronics devices and their applications
  • Diode, transistors and amplifiers
  • Oscillators, Integrated circuits
  • Electrical signal detection in biological systems: silicon, glass and metal electrodes
  • Bioelectronics device production: microelectronic fabrication methods as adapted to bioelectronics, hard and soft lithography
  • Biosensors: miniaturization, microsystems- sensing using optical techniques, field effect transistors, ion-selective and enzyme-sensitive electrodes and their monitoring, commercial biosensors (glucose monitoring and DNA analysis)


  1. Nuclonics and Nuclear Medicine:
  • Radioactivity and its detection
  • Radioactive decay
  • Isotopes
  • Biological effects of radiation, radiation hazard
  • Organ scan (liver, bone, brain etc.)
  • Positron emission tomography
  • X-ray
  • Magnetic resonance imaging
  • Radioiodine for diagnosis of disorder (thyroid disorder)
  • Laser beam in diagnosis and therapy
  • Nuclear medicine in therapy


  1. Biochemical Instruments:
  • Compound light microscope: phase contrast microscope, florescence microscope, UV- microscope, laser confocal microscope
  • Electron microscope
  • Ultramicroscope and micromanipulator



  1.   Acoustics:
  • Vibration
  • Sound, ultrasound, infra-sounds and their application
  • Hearing aids



Recommended Readings:

  1. Halliday D, Resnick R, Walker J. Fundamentals of Physics (9th Ed.). New York John Wiley (2010).
  2. Serway RA, Faughn JS. College Physics (8th Ed.). New York, Brooks Cole (2008).
  3. Raicu V, Popescu A. Integrated Molecular and Cellular Biophysics. New York, Springer (2010).
  4. Davidovits P. Physics in Biology and Medicine (3rd Ed.). New York, Academic Press (2007).
  5. Batchelor GK. An Introduction to Fluid Dynamics. London, Cambridge University Press (2000).
  6. Bar-Meir G. Basics of Fluid Mechanics. Orange Grove Texts Plus (2009).
  7. Serdyuk IN, Zaccai NR and Zaccai J. Methods in Molecular Biophysics: Structure, Dynamics, Function. London, Cambridge University Press (2007).
  8. Roy RN. A Text Book of Biophysics. New Central Book Agency Ltd. India (2009).


Additional reading materials may be suggested by the respective course instructor(s).


  1.   Introduction:
  • Brief history of computer
  • Basic organization, type
  • Overview of hardware and bios


  1. Operating Systems: 
  • Introduction to OSs (Windows, Linux, Mac OSx, Unix)
  • Tools/software installation in Linux environment
  • Basic Linux commands, command line arguments
  • Introduction to text editors: vim, Gedit
  • LINUX commands for batch file processing, data management and basic calculations (sum, subtract, multiplication, division, mean etc.)
  • Introductory regular expression


  1. Computer Networks and Internet Systems:
  • Basic concepts of networks, hubs, switches, gateways, and routers
  • Network security: basic concepts of public key and private key cryptography, digital signature firewalls,
  • Application layer protocols (icmp, dns, smtp, pop, ftp, http)


  1.   Databases and XML:
  • Introduction to flat files, DBMS and RDBMS, ER model
  • Database design (integrity constraints, normal forms)
  • Query languages (SQL)


  1.  Programming basics:
  • Introduction of C and C++ with fundamental object-oriented concepts


  1. Basic Perl:
  • Introduction to Perl and basic terminologies
  • Working with scalars, decisions, loops, lists, arrays, hashes, string operations, subroutines, control flow (if, else, elseif)
  • File handling, files and directories, and basic calculation using Perl script: read data from single and multiple files, manipulation, format conversion, sorting, concatenating; file parsing; pattern matching and regular expression
  • Mutation and randomization: Perl skills to acquire randomly select an index into an array and a position in a string




Recommended Readings:

  1. Peterson LL, Davie BS. Computer Networks: A Systems Approach (5th Ed.). New York, Morgan Kauffman Elsavier (2011).
  2. Kurose JF, Ross KW. Computer Networking: A Top-down Approach (5th Ed.). New York, Addison-Wesley (2009).
  3. Comer D, Stevens D. Internetworking with TCP-IP, vol. 1 and 2 (5th Ed.) New York, Prentice Hall (2005).
  4. Stevens WR, Fenner B, Rudoff AM. (2003). UNIX Network Programming, Vol. I: The Sockets Networking API. New York, Prentice Hall (2003).
  5. Silberschatz A, Korth HF, Sudarshan S. Database System Concepts. New York, McGraw-Hill (2002).
  6. Schneider MG, Gersting J. An Invitation to Computer Science (5th Ed.). Independence (KY), Cengage Learning Course Technology (2009).


Additional reading materials may be suggested by the respective course instructor(s).


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