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Syllabus for 4-Year Bachelor of Science

Biochemistry and Molecular Biology

University of Dhaka

Session : 2010 – ‘11, 2011 – ‘12, 2012 –’13 and 2013 - 2014

· Each 4-credit theory course will be of 100 marks, comprising 60 lecturer- hours, 3-credit theory course of 75 marks comprising 45 lecture-hours and 2-credit theory course will be of 50 marks comprising 30 lecture-hours.

· Each 4-credit practical course will be of 100 marks comprising 180 hours of lab work, with 60% marks for continuous assessment and 40% marks for final examination.

· Examination (assessment & final) rules, allotment of marks etc. are given in the Letter Grading Booklet, with some modifications as per requirement of the Department of Biochemistry and Molecular Biology.

· As per university rules a student will have to earn 128 credits out of 132 credits for 4-year B.S. (Hons.) degree.

Back to Syllabus Index

1^st Year B.S. (Honors)

Departmental Courses:

BMB 101 Biophysical Chemistry 2 Credits

BMB 102 Bioorganic Chemistry 4 Credits

BMB 103 Cells and Biomolecules-I 2 Credits

BMB 104 Biomolecule-II 2 Credits

BMB 105 Introductory Molecular Biology 2 Credits

BMB 106 Introduction to applied Biochemistry 2 Credits

BMB 107 Laboratory works 4 Credits

BMB 108 Oral Examination 2 Credits

Extra-departmental Courses:

BMB 151 Foundation Course in English 4 Credits

BMB 152 Basic Microbiology 4 Credits

Total Credits in 1^st Years B.S. Hons = 28 Credits

2^nd Year B.S.(Hons.)

BMB-201 Enzyme 4 credits

BMB-202 Carbohydrate metabolism 4 credits

BMB-203 Biological membrane & lipid metabolism 2 credits

BMB-204 Endocrinology 2 credits

BMB-205 Molecular biology-I 4 credits

BMB-206 practical works 4 credits

BMB-209 Oral exam 2 credits

Extra-departmental courses

(For Biochemistry & Mol.Biol.students)

BMB-251 Human Physiology 4 credits

BMB-252 Botany 2 credits

BMB-253 Biostatistics 4 credits

BMB-254 Zoology 2 credits

Total credits in 2^nd Year B.B. (Hons.) = 34 credits

3^rd YEAR B.S. (Hons.)

BMB-301 Metabolism of nitrogenous compounds 3 credits

BMB-302 Molecular biology-II 2 credits

BMB-303 Molecular genetics 3 credits

BMB-304 Plant Biochemistry 2 credits

BMB-305 Basic immunology 2 credits

BMB-306 Human Nutrition 4 credits

BMB-307 Biochemistry & molecular biology of diseases 2 credits

BMB-308 Clinical biochemistry 2 credits

BMB-309 Practical works 8 credits

BMB-310 Oral examination 2 credits

Extra-departmental courses

BMB-351 Computer basics and data analysis 4 credits

Total credits in 3^rd Year B.S. (Hons.) = 34 credits

4^th YEAR B.S. (Hons.)

BMB-401 Cell biology 4 credits

BMB-402 Biochemistry of natural products 2 credits

BMB-403` Industrial biotechnology 4 credits

BMB-404 Molecular biology-III 2 credits

BMB-405 Biochemistry of Cancer 2 credits

BMB-406 Virology 2 credits

BMB-407 Immunology 4 credits

BMB-408 Biochemistry of drugs 2 credits

BMB-409 Neurobiochemistry 2 credits

BMB-410 Plant biotechnology 2 credits

BMB-411 Practical works 8 credits

BMB-412 Oral examination 2 credits

Total credits in 4^th Year B.S. (Hons.) = 36 credits

Grand total for B.S.(Hons) programme = 132 credits

of which students must earn 128 credits

BMB 101 : Bioph.ysical Chemistry 2 credits

1. Thermodynamics:

(a) First law of thermodynamics: Introduction, definitions, nature of heat

and work, PV work, maximum work, first law of thermodynamics - internal

energy, enthalpy, molar heat capacities, isothermal and adiabatic expansion.

(b) Thermochemistry: Exothermic and endothermic reactions, standard enthalpy

of formation, thermochemical equations, reaction enthalpy - dependence on

temperature, bond energies.

(c) Second law of thermodynamics: Thermodynamics - reversibility and

irreversibility, spontaneous processes, entropy, thermodynamic efficiency and

Carnot’s theorem, statements of second law, entropy changes - phase transition,

heating, irreversible processes. Third law of thermodynamics.

Free energy - variation with temperature and pressure, Gibbs-Helmholtz equation, applications of thermodynamics in biochemistry, biochemical relevance of classical thermodynamics, open systems.

2. Chemical equilibrium: Nature of chemical equilibrium, law of mass action,

equilibrium constant, relationship between DG and Keq, effect of temperature and

pressure, Le Chattelier principle, equilibrium reaction involving protons, coupling

of reactions. Applications in living systems.

3. Chemical Kinetics: Definition, reaction rate, rate laws, zero-, first- and second-

order reactions, molecularity of a reaction, pseudo-first order reaction, half-life,

determination of order and rate constant, effect of temperature on reaction rates.

Theories of reaction rates - the collision theory, the activated complex theory.

Catalysis : Definition, types, characteristics of catalysts, activation energy and catalysis.

4. Acids and bases: Bronsted-Lowry concept, Lewis concept, strengths of acids,

strong & weak acids and bases, pH, buffer solutions. Henderson-Hasselbalch

equation, buffering against pH changes in biological systems, Maintaining the pH

of blood, acid-base indicators, acid base titration, choice of a suitable indicator.

5. Properties of liquids (brief treatment): Introduction – the kinetic molecular

description, intermolecular forces in liquids, dielectric constant, surface tension,

viscosity, diffusion, osmotic pressure, phase rule, phase diagram of water,

ionization of water, water as a reactant.

6. Spectrophotometry: Beer-Lambert law, standard curves, working principle of a

spectrophotometer.

BMB 102 : Bioorganic Chemistry 4 credits

1.	Physico- chemical parameters for biomolecules: Inter- and Intra-molecular interaction: covalent, ionic bond, hybrid orbitals, polarity of bonds, electronegativity, dipole, hydrogen bonding, dihydrogen bonding, hydrophobic interactions, van der waals interaction.
2.	Nature of Bonding in Organic Molecules and in relation to biomolecules: Delocalized chemical bonding-conjugation, cross conjugation, resonance, hyperconjugation, bonding in fullerenes, tautomerism.
3.	Reaction Intermediates: Formation, structure, stability and reactions of Carbocation, Carbanions, Free radicals, Nitrenes, Carbenes, Benzynes.
4.	Reaction Mechanism: Structure and Reactivity Types of mechanisms, types of reactions, thermodynamic and kinetic requirements, kinetic and thermodynamic control, Hammond’s postulate, Curtin-Hammett principle. Potential energy diagrams. Effect of structure on reactivity-resonance and field effects, steric effect, quantitative treatment. The Hammett equation and linear free energy relationship, substituent and reaction constants. Taft equation.
5.	Aliphatic Nucleophilic Substitution The S_N2, S_N1, mixed S_N1 and S_N2 and SET mechanism (single electron transfer).
6.	Aromatic Nucleophilic Substitution The ArS_N1ArS_N2, benzyne and S_RN1 mechanism. Reactivity-effect of substrate structure, leaving group and attacking nucleophile.
7.	Organic Synthetic techniques involved in bioactive Drug Research Protection Deprotection of functional groups, Introduction to asymmetric synthesis.
8.	Stereochemistry and stereoisomerism: Enantiomers and chiral molecules, biological importance of chirality, polarimeter, plane polarised light and optical activity, diastereoisomers, racemic modification, meso structures, the (R-S) system, synthesis of chiral molecules, chiral drugs.
9.	Alcohols, ethers, epoxides and diols: Occurrence, nomenclature, structure, synthesis, physical and chemical properties and uses.
10.	Dienes: Structure and properties of 1, 3-butadiene, addition reactions, polymerisation, Diels-Alder and other reactions of dienes.
11.	Aromaticity: Structure of benzene, sources of aromatic hydrocarbons, industrially important aromatic compounds, nomenclature of benzene derivatives, electrophilic and nucleophilic aromatic substitution, chemistry of aromatic aliphatic compounds.
12.	Aldehydes and ketones: Nomenclature, synthesis, nucleophilic addition, elimination reaction, oxidation and reduction of carbonyl compounds, haloform reaction, enolisation in biological system, a-halocarbonyl compounds, aldol condensation, benzoin condensation, Claisen condensation, crossed aldol and crossed Claisen condensation, Perkin condensation. Wittig reaction, Reformatsky reaction, synthesis of a,b-unsaturated carbonyl compounds
13.	Carboxylic acids and their derivatives: Nomenclature, synthesis, classification, properties, reactions, uses, decarboxylation reactions, dicarboxylic acids, esters.
14.	Nitro-compounds and amines: Occurrence, nomenclature, synthesis, classification, properties, reactions, uses, diazonium compounds.
15.	Phenols: Occurrence, nomenclature, synthesis, properties and reactions, polyhydric phenols.
16.	Heterocyclic compounds: Chemical nature classification and synthesis, with special reference to pyrroles, purines and pyrimidines.

BMB 103 : Cells and Biomolecules-I 2 credits

1.	History, scope and future of biochemistry.

2.	Cells and organelles and their composition– isolation, identification & functional characteristics of organelles.

3.	Carbohydrates: Monosaccharides and their biological properties; colour test of reducing sugars, important derivatives of monosaccharides, sugar acids. Disaccharides and oligosaccharides of biological importance: maltose, lactose, sucrose and other disaccharides. Polysaccharides – storage and structural polysaccharides, structures and function of starch, glycogen and cellulose, other polysaccharides of biological interests, biological degradation, artificial sweeteners, dextrans. Glucosamines: structures and functions.
4.	Lipid as biomolecule: Chemical nature, classification with representative examples; fatty acids-nomenclature, saturated & unsaturated fatty acids and fats; triacylglycerol; phospholipids; sphingolipids; cerebrosides; gangliosides; saponification value, iodine number, acid number, rancidity etc. with their significance, steroids and their importance (in brief); very brief idea about prostaglandin, prostacyclines, thromboxane & leukotriene along with their physiological importance.

5.	Chemistry of amino acids– Classification, Physico-chemical properties, involving titration, buffering nutrition, optical behaviour, syn. of important biomolecules.

BMB 104 : Biomolecules-II 2 credits

1.	Peptides: Characteristics, peptides of biological importance.

2.	General Introduction to proteins, classification of proteins based on biological functions and nutritional values.
3.	Protein structure:
	(i)	Primary structure of proteins: sequencing of proteins, sequence homology.

	(ii)	Fibrous proteins: Secondary structure of proteins, protein conformation, a-keratins, planar peptide bonds, a-helix, helix forming and destablizing amino acids, the insolubility of a-keratins, b-keratins – conformation and structure, structures of collagen and elastin, filamentous proteins – actin, myosin and microtubules.
	(iii)	Globular proteins: Tertiary structures of proteins, distinctive tertiary structures of myoglobin and ribonuclease, renaturation of unfolded and denatured ribonuclease, factors maintaining the tertiary structure of globular proteins, oxygen-binding curves of hemoglobin and myoglobin, the cooperative binding of oxygen by hemoglobin, factors contributing to oxygen saturation curve of hemoglobin, sickle-cell anemia and its relation to hemoglobin.
	(iv)	Protein denaturation.
4.	Exploring proteins: Protein isolation, purification and characterization

	(i)	Salting-in and salting out, isoelectric precipitation, dialysis, gel filtration, chromatography: ion-exchange and affinity chromatography, HPLC, electrophoresis, SDS-polyacrylamide gel electrophoresis, isoelectric focusing.
	(ii)	Molecular weight determination by ultracentrifugation, SDS-PAGE, 2-D gel electrophoresis.

BMB 105 : Introductory Molecular Biology 2 credits

1.	Heredity: Mendel’s laws of inheritance, gene concept, conceptual relationship between gene and chromosomes, and gene and enzymes.
2.	DNA as genetic material.
3.	Chemistry of nucleic acids: Classification and composition of nucleic acids, bases, sugars, nucleosides, nucleotides and polynucleotides.

4.	DNA structure: Watson and Crick model and its characteristics, isolation of DNA from natural sources, its physicochemical properties.
5.	Gene expression:
	(i) Replication as continuity of transfer of genetic information. (ii) Transcription, types of RNAs, their characteristics and function. (iii) Translation leading to functional protein synthesis, colinearity of genes and proteins.
6.	Application of Molecular Biology: Concept: (i) Recombinant DNA technology – isolation of genes, restriction endonuclease, vectors, cloning and expression of cloned genes. (ii) Agricultural and industrial applications, with examples. (iii) Application in medical and related fields – forensic studies, detection of molecular diseases, pharmaceutical production, gene therapy. (iv) Some Molecular Biology techniques – Polymerase chain reaction, DNA fingerprinting, DNA mapping, use of genetic markers, DNA sequencing.

7.	Recombinant DNA technology – friend or foe: Concept and controversies of Genetically Modified Organisms (GMO).

BMB 106 : Introduction to applied Biochemistry 2 credits

1.	Health and diseases: disease, classification of human diseases, infectious and non infectious diseases; detection strategies of common pathogens like bacteria, fungi, protozoa and viruses; strategy for combating the diseases, protection against diseases, personal hygiene; immunity against diseases, vaccinations, nutrition in the prevention of diseases.
2.	Agriculture: Impact of urbanization & natural calamities on agriculture; major agro-crops; green revolution, cash crops and food crops; agro-fuels and wastes, fertilizer; animals- their feed, diseases, maintenance and health, biotechnology for improvement of crops and animals; control of insects and pests in prevention and control of diseases; biological control of pests.
3.	Drugs: Introduction, sources, uses of drugs under prescription; abuses of drugs and its impact on human health; search for new medicines and drugs; development of new vaccines and therapeutics; artificial blood development.
4.	Ecology & Environment: Geochemical cycles: water, carbon, oxygen, nitrogen, sulfar; food chains, food web & pyramids of biomas and energy; environmental pollution: air, water, thermal, sound; biochemical and molecular approach to control environmental pollution: bioremediation, waste management, biofuel; genetic arrangement clean up environment.
5.	Industries: Application microbes & enzymes in food, pharmaceutical, textile and tannery industries.

BMB 107 : Practical: 4 credits

1.	Use of electronic balances.
2.	Preparation of standard solutions.
3.	Standardization of HCl.
4.	Estimation of acetic acid content of vinegar.
5.	Estimation of calcium from milk.
6.	Estimation of iron from blood.
7.	Estimation of ascorbic acid content of biological samples.
8.	Identification of organic compounds and colour tests for biomolecules.
9.	Determination of saponification number of fat or oil.
10.	Determination of iodine number of fat or oil.
11.	Determination of lactose content of milk.
12.	Proteins from natural sources and their partial purification by dialysis.
13.	Hydrolysis of proteins and isolation and identification of amino acids by paper chromatography.
14.	Preparation of buffer and determination of pK of acetic acid.
15.	Separation of pigments from plants by adsorption chromatography and determination of Dmax.
16.	Determination of serum protein content by the biuret method.
17.	Determination of glucose content of serum by method.
18.	Determination of creatinine content of a urine samp.le.
19.	Isolation of DNA.

BMB 108: Viva-voce 2 Credits

EXTRA-DEPARTMENTAL COURSES:

BMB 151 Fundamental Course in English 4 Credits

SPEAKING

The segment is aimed at improving students’ speaking ability so that they can communicate freely in a good range of situations. This course will also help students reduce their shyness, nervousness and inhibition in speaking.

This segment will include, but will not be limited to, the following functions/items:

Introducing yourself and others
Expressing likes & dislikes, personal experiences, past habits, requests & offers, apologies & excuses, inviting, comparison & contrast
Describing people/place/things, narrating action & events, saying numbers & time
Giving & following instructions, asking for & giving direction
Reporting, complaining, suggesting
Role-plays in various authentic situations
Participating in debates, making extempore speech
Seminar presentations & interviews
Phonetics (IPA symbols; Using a dictionary for pronunciation; Phonetic transcriptions; Intonation and stress)

READING

This segment is mainly designed to provide the students an opportunity for reading, and understanding variety of texts and improving their communications skills and analytical capability, especially through effective reading. Reading should also involve activities and discussions that finally lead to effective writing.

Strategies of Reading: Predicting, skimming, scanning, inferencing, and analyzing

Selected Texts: 1. Variety of texts reflecting common interests

2. Special texts related to students’ major courses

WRITING

Students will learn the principles of and practice effective writing of different lengths. They should be able to write well-organized paragraphs and essays along with other types. They are expected to gain an understanding of the underlying principles of effective writing styles, to gain an understanding of the importance of the organization techniques of writing adapting to a variety of audiences and occasions and to demonstrate an ability to prepare and deliver effective written responses.

Items/Activities

Teaching the writing Process: Brainstorming, outlining, drafting and editing/ proofreading.
Paragraph Development: Paragraph structure, transitional devices/ connectives
Paragraph Types: Descriptive, narrative, process analysis, cause & effect, argumentative etc.
Essay Writing: Essay structure, thesis statement, introduction & conclusion, and different essay types.
Writing Formal letters.
Report Writing: Academic reports, newspaper reports, lab reports etc.
Miscellaneous: Combining sentences, summary/paraphrase writing.

LISTENING

This segment will introduce students to diverse speakers and types of English. Listening comprehensions focusing on varying elements of vocabulary and structures will be practiced. Students will be taught how to be an active listener to obtain information and understand the key ideas.

Class practice will include listening to tapes suitable for students’ needs.

GRAMMAR

Grammar teaching will involve remedial work. Much of the language will be contextualized and will encourage students to study meaning as well as form.

The grammar exercises and editing works will help students overcome all sorts of grammatical problems.

BMB 152 Basic Microbiology 4 Credits

1. Overview of history of Microbiology - Biogenesis and abiogenesis; Contributions of Redi, Spallanzani, Needham, Pasteur, Tyndal, Joseph Lister, Koch [Germ Theory], Edward Jenner and Flemming [Penicillin] in Microbiology; Scope of Microbiology.

3. Classification and basic concepts of microbes - Systems of classification; general properties and principles of classification of microorganisms; general characteristics and functions of microbes; physical and chemical differences in the structural organization of different microbes.

2. Microscope: Microscopy and different types of microscope (light microscope, phase contrast microscope, fluorescence microscope, electron microscope).

4. Stains and staining techniques – Definition of auxochrome , chromophores, dyes; classification of stains; theories of staining; mechanism of gram staining, acid fast staining, negative staining, capsule staining, flagella staining, endospore staining.

5. Bacteria – Bacterial cell structure; General classification of bacteria; Nutritional aspects of bacterial cultivation media, composition; growth and reproduction; Male and female-ness in bacteria (F⁺, F' and Hfr); environmental factors affecting bacterial growth- temperature, pH, osmotic pressure; isolation of pure culture from natural sources, enumeration; steps to maintain microbial culture in an aseptic & sterile environment (how to inoculate, preserve & maintain).

7. Basic concepts of Virology - General characteristics of viruses; differences between bacteria and viruses; classification of viruses physical and chemical structures of different Viruses on the basis of capsid symmetry - enveloped (Herpes virus), helical (TMV) and icosahedral (Polyoma viruses), Viroids, prions, Virus of plants (TMV), HIV, H1N1 virus.

5. Bacteriophages: E.coli phage lambda; E. coli PhageT4; Stages in the Lytic Life Cycle of a typical phage; Properties of a phage infected bacterial culture; Specificity in phage infection; The lysogenic Cycle.

6. Beneficial Microbial Interaction with Human: Normal microbial population of healthy human body- skin, mouth, respiratory tract, urino-genital tract, eye.

7. Harmful Microbial Interactions with Human: Entry of pathogen into the host; Types of bacterial pathogens; Mechanism of bacterial pathogenicity; Colonization and growth; Virulence; Virulence factors- exotoxins, enterotoxins, endotoxins, neurotoxins- avoidance of host defense mechanisms, damage of host cell, Host factors for infection and innate resistance to infection.

8. Control of pathogens: Definition and classification of antibiotics on the basis of structure and mode of action, antibiotics produced by bacterial (bacteriocin, lantibiotic); Semi-synthetic antibiotic; Drug toxicity; Drug resistance.

9. Industrial Microbiology: Examples of industrially important microbes; their isolation from natural habitat; Basic concepts on fermentation technology; Bioconversion (Bio-gas, Bio-fuel); Microorganisms in Agriculture waste water treatment; Microbial pesticides; commercial products form microorganisms enymes, antibiotics); Bioremediation (chemical degradation, heavy metals).

10. Food microbiology: Microbiology of milk, Cheese, Yogurt; Spoilage of food; Pasteurization.

11. Agricultural Microbiology: Microbes in soil surface and different zones o f soil; nitrogenase & nitrogen fixation; Symbiosis; nitrosofying, nitrifying, ammonifying and photosynthetic bacteria.

Course BMB 201: Enzymes 4 credits

1.	Enzymes: basics concepts –characteristics, classification catalytic properties, lowering of activation energy, prosthetic group, coenzyme cofactor, concept of specificity of enzyme identification of residues at active sites & effect of substrate conc. temperature & pH on enzyme activity; activity unit, specific activity, turnover number.
2.	Enzyme kinetics: Michaelis – Menten equation, K_M & Vmax determination & their significance; enzyme inhibition – reversible & irreversible, determination of nature of enzyme inhibition, use of specific enzyme inhibitors as drugs.
3.	Enzyme regulation: Importance of enzyme regulation, covalent modification for enzyme regulation; de novo, synthesis & enzyme breakdown as regulatory means allosteric regulation showing concept of cooperativity; Hill equation, models of cooperation, isoenzymes, their distribution, regulatory role in metabolic flux, if any; zymogene, & their significance in metabolism, substrate cycles.
4.	Enzyme catalytic mechanisms: To understand that enzymes bind substrates at the active, site stabilize transition state and provide functional groups that make and break bonds required: specific examples: (a) ribonuclease, (c) carbonic anhydrase
5.	Novel enzymes: Ribozymes, abzymes.
6.	Membrane bound enzymes

BMB 202 Carbohydrate Metabolism 4 Credits

Bioenergetics: Bioenergetics & thermodynamic principle, high energy compounds; ATP cycle; ATP in metabolism.

General aspects of metabolism: Characteristics; study of metabolic intermediates to determine metabolic pathway.

Carbohydrate metabolism: overview; availability of glucose to cells; receptor mediated glucose entry & involvement of hormone in entry process; types of GLUTs.

Glycolysis: The pathway showing individual steps; aerobic and anaerobic aspects; energetics; regulation of glycolysis; anaerobic glycolysis and its physiological importance; glucose metabolism in premature babies; feeder pathways- entry of other mono- and di-saccharides in glycolysis; galactosemia; fructose intolerance; hypoglycemia; hyperglycemia & diabetes (brief outline).

TCA cycle: Overview of tricarboxylic acid cycle; the cyclic pathway and its regulation; energetics of the total oxidation of glucose; anapleorotic pathways; amphibolic nature of TCA cycle; futile cycle.

Glycogenolysis: Biological implication; enzymatic steps; regulation, glycogen storage diseases.

Biosynthesis of carbohydrates: Gluconeogenesis and its regulation; biosynthesis of di- and oligo- saccharides; glycogen biosynthesis and its regulation; role of insulin and glucagon in glycogen biosynthesis, biosynthesis of glycoproteins, proteoglycans; interconversion of saccharides (suggars)..

Electron transport & oxidative phosphorylation: Shuttles across mitochondrial membrane, mitochondrial structure and compartmentalization of respiratory metabolism; the evolution of electron transport chain; oxido-reduction & electron transport; oxidative phosphorylation; inhibitors & uncouplers of oxidative phosphorylation; disorders due to deficiencies of mitochondrial enzymes/proteins.

Pentose phosphate pathway: Glucuronic acid pathway; pathway for ascorbic acid biosynthesis; glyoxalate cycle.

BMB 203: Biological Membrane and Lipid Metabolism 2 credits

1. Biological Membranes: Membrane structure and membrane transport – chemical

composition of membranes, micelles, lipid bilayers and liposomes, structure of

biological membranes, movement of molecules through membranes, membrane

channels and transporters.

2. Lipid Metabolism: Brief overview of lipid metabolism, plasma lipoproteins

compositions and metabolism, fatty acid oxidation, ketone body formation and

utilization, fatty acid biosynthesis, regulation of fatty acid metabolism, storage of fatty

acids as triglycerides, utilization of fatty acids for energy production, metabolism and

functional role of polyunsaturated fatty acids, cholesterol metabolism, arachidonate

metabolism, prostagladins, prostacycline, thromboxane and leukotrienes, phospholipid

metabolism, sphingolipigs metabolism.bile acid metabolism.

3. Disorders of Lipid Metabolism: Stress, fatty acids and myocardial infarction, genetic

deficiencies in carnitine or carnitine palmitoyl transferase, sudden infant death

syndrome (SIDs), Refsum’s disease, respiratory distress syndrome, sphingolipidoses,

Gaucher’s disease, Diseases associated with lipoproteins and cholesterol metabolism.

BMB 204 : Endocrinology 2 credits

Characteristics of the hormone system : Introduction, function of hormones, endocrine glands, target gland concept, negative and positive feed back, hormone receptors and its abnormalities. Classification of hormones, intracellular messengers.

Pituitary and hypothalamic hormones, Thyroid and parathyroid hormones: Structure, synthesis, physiological and biochemical actions.

Hormones of the adrenal cortex adrenal medulla, gonads and Pancreas : Structure biosynthesis, regulation, transport, mechanism of action and pathophysiology.

Gastrointestinal hormones: Gastrin, cholecystokinin (CCK), secretin, glucagon, gastric inhibitory polypeptide (GIP), vasoactive intestinal polypepte (VIP), glicentin, neurotensin, substance P and somatostatin.

Hormone assay techniques: Assay of peptide and steroid hormones by radioimmunoassay (RIA) and enzyme-linked immunosorbent assay (ELISA).

BMB 205 Molecular Biology-I 4 credits

1.	Structure of DNA : Different physicochemical properties, such as Tm value, Cot values, hybridization kinetics, different conformations of DNA, sequence complexity, tandem sequence, palindromic sequence, cruciform structure, mention about DNA chips.

2.	DNA sequencing : Simple methods such as Sanger’s di deoxy method and Maxam and Gilberts method, next generation sequencing.

3.	DNA replication : Basic mechanism of visualization of DNA replication by autoradiography. Basic mechanisms of DNA replication involving helicases, topoisomerases polymerases, ligases, methylases, nucleases, lebelling & modification. Semiconservative replication, semidiscontinuous replication, priming of DNA synthesis, bidirectional replication, unidirectional replication and roling circle replication, fiedility and regulation of replication. DNA replication: Speed of replication, initiation, priming in Eukaryotes, Elongation, termination, Disentangling daughter DNAs. Separate DNA polymerases for initiation and elongation, creating the replication fork at an origin, methylation and at the origin of replication and regulation of replication.
5.	Recombinant DNA: Vectors, plasmids;l-phage DNA, M13-based expression vectors for eukaryotic expression genomic and cDNA libraries, restriction enzymes & other enzymes involved in recombinant DNA technology, RTPCR DNA fragments screening and finding right colons. Characterization of coloned genes by DNA sequencing data bank entries and annotation analysis of sequence, sequence compression, protein structure & function.

BMB 206 Practical Works 4 credits

1. Determination of the rate of a chemical reaction: Iodination of

acetone.

2. Isolation and determination of cholesterol from egg.

3. Determination of distribution coefficient of iodine in aqueous and organic

layers.

4. Chemical synthesis of oil of wintergreen.

5. Chemical synthesis of aspirin.

6. Determination of Keq for the reaction KI + I₂= KI₃.

7. Determination of pH. of a solution.

8. Preparation of buffer and demonstration of buffer action.

9. Determination of pKa of a protein..

10. Determination of pI of glycine or alanine.

11. Determination of Km and Vmax of urease, glucose oxidase or alkaline

phosphatase.

12. Collection of serum and plasma from human peripheral blood.

13. Determination of serum triglycerides by the enzymatic colorimetric method.

14. Determination of serum total cholesterol by the cholesterol oxidase method.

15. Determination of serum HDL cholesterol by precipitation and the

cholesterol oxidase method.

16. Determination of serum alanine aminotransferase by the enzymatic method.

17. Determination of serum aspartate aminotransferase by the enzymatic

method.

18. Determination of serum total bilirubin by colorimetry.

19. Determination of serum alkaline phosphatase by colorimetry.

20. Determination of serum urea by the enzymatic method.

21. Determination of serum creatinine by colorimetry.

22. Determination of the total red blood cell count from a blood sample

23. Determination of hCG from urine.

24. Estimation of inorganic phosphate

BMB 207 Oral Examination 2 credits

Extra-departmental courses

(For Biochemistry & Molecular Biology Students)

BMB 251 Human Physiology 4 credits

BMB 252 Botany 2 credits

BMB 253 Biostatistics 4 credits

BMB 254 Zoology 2 credits

BMB 251 Human physiology 4 credits

1.	Circulatory System : Hemostasis, biochemistry of blood clotting, Blood, Blood cells, lymph, serum, plasma, total count (TC), differential count (DC), origin of the blood cells. Blood grouping: The ABO system, determination of blood group, Rh-factor. Heart, chambers of heart and its valves, their functions and locations, specialized cardiac tissues, sinoaortic node (SA node), atrioventricular node (AV node), bundle of His, Purkinjee’s fibers, pace maker, artificial and natural cardiac output, blood pressure, systemic, pulmonary and coronary blood circulation.
2.	Lymphatic and lymphoid system: Lymph and lymph vessels, lymphatic circulation, outline of primary and secondary lymphoid organs and their functions, structure and function of lymph nodes, spleen, thymus and bone marrow in immunity.
3.	Digestive system: The gastrointestinal tract, digestive enzymes, digestion of food components and absorption of digested products gut hormones
4.	Excretory system: role of kidney in water, electrolyte and acid-base balance of the body, buffers of the cells, regulation of extracellular fluid composition and formation and excretion of urine.
5.	Hepatobiliams system : Structural organization and function.
6.	Reproductive system:
7.	Nervous system: Nerve cells, ionic basis of excitation and conduction, synaptic transmission, the sense, sense receptors, hypothalamus and temperature regulation.
	Practical : (a) Total Blood Count (CBC), Differential Count (20 marks) (b) Blood Grouping (c) Hb estimation (d) Prothrombintime (e) ESR determination (f) Liver function test: assay of ALT, AST, Bil, ALP

BMB 252 : Botany 2 Credits

A. Theory (40 Marks):

1. Plants :

(i) Plant classification - systems of classification, characteristic features of plant

divisions, some typical examples.

(ii) Plant anatomy - primary tissues in plant-meristem, ground, dermal and vascular

tissues of plants.

2. Plant Pathology: Definition of disease in plants, causes of plant diseases, plant diseases caused by plant viruses, bacteria, fungi, Koch’s postulate in the diagnosis of plant diseases, plant disease control through cultural, biological and chemical methods.

3. Cytology, Genetics and Plant breeding : Reproductive biology of important crop plants, inbreeding and outbreeding methods of crop improvement, hybridization, mitosis and meiosis and their significance, Mendel’s experiments and achievements, monohybrid and dihybrid inheritance, idea about quantitative traits.

4. Ecology :

(i) Ecological features of hydrophytes, xerophytes and halophytes (mangrove)

(ii) Fresh water ecology, food chain and food web.

(iii) Green house gases, ozone depletion and CFC use in Bangladesh. consequence of

ozone layer depletion, acid rain causes & consequences.

B. Practical (10 Marks):

1. Plant diversity Practical

Study of angiosperms:

(a) Herbs, shrubs, trees, climbers, epiphytes sciophytes, halophytes.

(b) Differences between dicot and monocot leaves and flowers, stems and leaves.

2. Plant Pathology Practical

(a) Study of plant disease covered in the theory course, and fungi causing damage to food stuff, leather and cotton fabrics.

(b) To demonstrate the culturing of fungi and preparations of Bordeaux mixture.

3. Plant Breeding Practical

(a) Preparation of temporary slides to study mitosis in onion root tip cells.

(b) Hybridization technique.

BMB 253 : Biostatistics 4 Credits

1. Introduction: Research and experimentation, the role of statistics, the nature of

statistics, scope of biostatistics

2. Sampling techniques : Definition, sampling procedure (simple random sampling).

3. Basic statistical principles and terminology: Populations and parameters,

samples and statistics, variables, statistical characterization of samples, distributions,

statistical concepts pertaining to interpretation and decision.

4. Sample description : Estimation of uncertainty.

(i) Calculation of the mean, variance, and standard deviation

(ii) Machine method of calculating the variance and standard deviation

(iii) Estimation of the standard deviation from the range

(iv) Standard deviation of the mean

(v) Confidence limits of a mean

5. Test of significance:

(i) Measured data: The t test - the t test in paired experiments, the t test in non-

paired experiments, selection of the appropriate method of calculating, confidence

limits of a difference between means.

(ii) Analysis of variance : The F test - single classification data, single classification

data with subgroups, multiple classification data, Duncan’s multiple range test, least

significant difference test, relationship between t and

F, general remarks.

(iii) Enumeration data: The Chi-square ( X²) test - the 1 x n table, the 2 x n table,

the use of X² with occurrence-nonoccurrence data, X² analysis of a 2 X 2 or

four-fold table, alternate methods of calculating X²,tests of significance when

cell frequencies are small, general remarks.

6. Statistical methods: Binomial distribution, Poisson distribution, normal distribution.

(i) Confidence limits of the mean

(ii) Significance of a difference between rates

7. The relationship between variables: Correlation, linear regression.

(i) The “least squares” regression line

(ii) Test for linearity of a regression

(iii) Confidence limits of the regression coefficient

(iv) Significance of a difference between regression coefficients.

8.Dosage-response data:

(i) The estimation of 50 per cent endpoints - graphic approximation of an ED₅₀

value, the Reed-Muench method of estimating 50 per cent endpoints

(ii) The estimation of relative potency.

9. Nonparametric Tests

10. Statistical Package for Social Science (SPSS)

Practical works (20 marks):

Construction of frequency distribution; different types of graphical representation data ( Simple Bar Diagram, Histogram, Frequency Polygon, Frequency Curve, Pie-Chart, Line Graph, Less than Ogive & More than Ogive); different measures of central tendency(Arithmatic Mean, Geometric Mean,HJarmonic Mean, Median, Mode, Quartiles, Deciles & Percentiles); different measures of dispersion (Range, Quartile Deviation, Mean Deviation, Standard Deviation, Variance, Coefficient of Variation); Stem and Leaf lot; scatter diagram; simple correlation coefficient; Rank correlation coefficient; probable error; fitting of regression line; interpretation of regression coefficients; drawing a simple random sample; paired t-test; analysis of variance and test of independence in a contingency table.

BMB 254 : Zoology 2 Credits

A. Theory (40 marks):

1. Introducing nonchordates and chordates: Classification of all major phyla upto

classes, distinguishing features, distribution.

2. Ecosystem and habitats: The biospohere, terrestrial ecosystems, wetland ecosystems, food chain and energy flow in ecosystems.

3. Biodiversity: Concept, Bangladesh fauna, beneficial and harmful insects, pest control methods, human parasites, fish and shellfish resources, major wild animals of Bangladesh, values and conservation of biodiversity.

4. Type study: Prawn, honey bee, rohu fish, pigeon.

B. Practicals (10 Marks):

Study of representative specimens of major classes.
Dissection of major system: Prawn, Pila, any fish, and Rat/Pigeon.
Laboratory culture: Culture and study of Ciliates, Hydra and Drosophila.
Study of permanent slides: Zooplanktons, parasites, histological slides.

BMB 301 : Metabolism of nitrogenous compounds 3 credits

1. Amino acid metabolism : Overview, general reactions of amino acids, glucogenic and ketogenic amino acids, oxidative degradation of amino acids to specialized products, amino acid biosynthesis, metabolism of branched chain amino acids, regulation of amino acid metabolism, propionate and methylmalonate metabolism, nitrogen fixation, folic acid and one-carbon metabolism, glutathione metabolism, clinical correlations: phenylketonuria, alkaptonuria, folic acid deficiency, hyperammonemia and hepatic coma, Urea cycle and deficiencies of the urea cycle enzymes.

2. Nucleotide metabolism : Overview, metabolic functions of nucleotides, synthesis of purine and pyrimidine nucleotides and deoxyribonucleotides, nucleotide degradation, uric acid formation biosynthesis of nucleotide coenzymes, nucleotide metabolizing enzymes as a function of cell cycle and rate of cell division, antimetabolities of purine and pyrimidine nucleotide metabolism. heme metabolism, regulation of nucleotide metabolism, Lesch-Nyhan syndrome, gout, orotic acidurea.

3. Metabolic interrelationships : Overview, starve-feed cycle, mechanisms involved in switching the metabolism of the liver between the well-fed state and the starved state, metabolic interrelationships of tissues in various nutritional and hormonal states.

BMB 302: Molecular Biology-II 2 credits

1.	DNA damage and repair: Damage by mutagens and repair by different enzymes
2.	Nucleic acid hybridization principles and application, Preparation of nucleic acid proves, Fluorescence labeling and detection system, standard and reverse nucleic acid hybridization assays. Southern blotting
3.	Genetic codes: Introduction, codons and triplet words, codon -anticodon interactions, sporadic alterations in the genetic code, nonsensecondon and their suppressors, recoding and changes of the meaning of codon. Codon redundancy.
4.	Transcription: Prokaryotic and eukaryotic transcriptions, RNA polymerases, regulation of transcription, eukaryotic transcription factors, Polysomes, transport of eukaryotic mRNA, UTRs, promoters, transcription activators and transcription factors enhancers and terminators, mechanism of RNA splicing and RNA processing, mRNA structure and its relation to stability, tissue specific gene expression. Transcriptional and posttranscriptional regulation. Introduction to protein –protein and other macromolecular interaction.
5.	Protein biosynthesis: Ribosome structure, active sites in each subunits, protein synthesis- initiation, elongation and termination; control of translation in both prokaryotes and eukaryotes, peptydal transferase activity of 23s rRNA.
6.	Application of DNA markers: RFLP, AFLP, SSR, RAPD & SNP (including assay)

BMB 303 : Molecular Genetics: 3 credits

1.	Principles of inheritance, allelic variation and genetic function, geneaction genotype and phenotype, chromosome and chromosomal basis of inheritance, chromosome structure and function.
2.	General nature of mutation: Types of mutation, mis sense, same sense and nonsense mutation, deletion and lethal mutation and frame shift mutations physicochemical mutagens, molecular mechanism of mutation, in vitro mutagenesis, site-directed mutagenesis, mutation by transposons and retroposons mutations induced by radiation repair mechanism in mutation, mutation rate and its measurement. Mutations in human, deleterious and recessive. Screening of carcinogens Ames Test.
3.	Recombination: Various models for recombination, Biochemistry of recombination system and site specific recombination.
4.	Genetics of viruses bacteria and fungi, Mechanisms of genetic exchange in bacteria conjugation, transduction, transformation and transfection, restriction mapping, chromosome walking, genetics of lambda phage, assembly of T phage.
5.	Linkage and chromosome mapping in higher organism: Recombination and crossing over, Exception to Mandelian principles of independent assorment, Frequency of recombination as a measure of linkage intensity, Crossing over as physical basis of recombination, chiasma and time of crossing over, Recombination with two and three point cross over recombination frequency and genetic map distance Linkage analysis in chromosome (human), Gene and pedigree patterns.
6.	Cytogenetics: Cytological techniques: Analysis of mitotic chromosome, the human karyotype, Cytogenetic variation an overview, polyploidy Aneuplody, Trisomy and monosomy and mosaisism, deletion and duplication of chromosome segments, Invesion translocation, compound chromosomes and Robertsonian chromosomes.
7.	Gene expression: Constitutive, inducible and responsible gene expression positive and negative control of gene expression, attenuation of trap operon, autogenous regulation of l operon. The lac and trp operons, control of gene expression for both prokaryotic and eukaryotic systems. Autogeneous regulation of gene expression.

BMB 304 : Plant Biochemistry 2 Credit

1. Plant cell and metabolism specialities, Cellular and sub-cellular compartmentation, .Plant Cell and organelle structure, role of compartmentation in regulation of metabolism, unique aspects of plant metabolism and their impact on metabolic flux, transporters in metabolic flux.

2. Photosynthesis. Light reaction, electron transport, dark reactions, Calvin Cycle and regulation, Photorespiration, C3, C4 and CAM metabolism and their comparison. Role of carbohydrate metabolism in plants in normal and stress conditions.

3. Plant respiration specialties : Cyanide insensitive respiration; Glyoxylate cycle.

4. Nitrogen and sulfur assimilation and metabolism. Role of transporters.

5. Plant hormones. Physiology and importance of auxins, cytokinins, gibberellins, abscises acid, ethylene, brassinsteroids and polyamines. Basic concepts of plant cell signaling and stress physiology. Role of jasmonic acid, salicylic acid, nitric oxide and phospholipids.

6. Secondary metabolites, Alkaloids and plant phenolics. Their production and commercial application. Medicinal plants and their uses.

BMB 305: Basic Immunology 2 Credits

Introduction to Immunology: Innate and adaptive immunity, features of adaptive immune responses; cells and soluble mediators of immunity: complement, cytokines and antibodies; antigens, phases of adaptive immune responses: recognition of antigens, clonal selection and activation of lymphocytes, effector phase of immune responses, homeostasis; inflammation, chemotaxis, phagocytosis, defenses against extracellular and intracellular pathogens, vaccination, immunopathology.

1. Cells of the Immune System:

(i) Cells of the innate immune system: Mononuclear phagocytes and polymorphonuclear granulocytes, development of phagocytes, neutrophils, eosinophils, basophils and mast cells, platelets, natural killer cells.

(ii) Cells of the adaptive immune system: Antigen presenting cells, lymphocytes, morphological heterogeneity of lymphocytes, resting blood T and B cells, characteristic surface markers of lymphocytes, cluster designation (CD), families of cell surface markers, T-cell antigen receptor complex, B-cell differentiation, lymphoid tissues.

2. 2. Immunoglobulins: Distribution of major human immunoglobulins, immunoglobulin classes and subclasses, physicochemical properties and functions of human immunoglobulin classes, general properties of immunoglobulins, molecular structure of antibodies: general feature, variable and constant regions, association between heavy and light chains; antibody effector functions; structure of immunoglobulin in relation to function: enzymatic cleavage of human IgG1, structure in relation to antigen binding, genetic basis of antibody diversity: isotype, allotype, idiotype.

3. 3. Antigens: Chemical basis of antigenicity, immunogenicity: epitopes; antigenic determinants, haptens, antigen-antibody binding, antibody affinity and avidity, antibody specificity and cross-reactivity; physiological significance of high and low affinity antibodies.

4. 4. The Complement System: Complement proteins; activation and regulation of complement pathways: classical, alternative and lectin pathways; membrane attack complex (MAC), biological effects of complement.

5. 5. Techniques in Antigen-Antibody Interactions: precipitation reactions, agglutination reactions, simple immunodiffusion, double immunodiffusion, immunoelectrophoresis, counterimmunoelectrophoresis, two-dimensional immunoelectrophoresis, complement fixation, radioimmunoassay(RIA), enzyme-linked immunosorbent assay (ELISA), immunofluorescence.

BMB 306 : Human Nutrition 4 credits

1. Overview of Nutrition: Definition of nutrients, Introducing the nutrients: carbohydrates, lipids, proteins, vitamins, minerals and water, nutrients and energy, balanced diet, dietary recommendation and reference standards.

2. Role of carbohydrates in human nutrition : Different forms of starch in food, their changes during food processing and cooking.

3. Role of proteins in human nutrition: Essential amino acids, limiting amino acids, mutual supplementation, protein quality and its evaluation, protein requirement, Protein energy malnutrition: Kwashiorkor, marasmus and their management.

4. Fats and oils in human nutrition: Saturated, monounsaturated and polyunsaturated fatty acids, omega-3 and omega-6 fatty acids in health, essential fatty acids.

5. Vitamins: Fat soluble and water soluble vitamins: sources, biological function, deficiency symptoms and RDA; coenzyme activities of vitamins (where known).

6. Mineral and trace elements: Functions and importance of minerals and trace elements in human body.

7. Energy metabolism: Energy requirement and energy expenditure, energy balance, basal metabolic rate, specific dynamic action of foods, measurement of energy metabolism, respiratory quotient.

8. Life cycle nutrition: Maternal and infant nutrition, nutrition during childhood, adolescence and elderly stages.

9. Planning a healthy diet: -tools for a healthful diet: Principles and guidelines, food groups and food guides, diet planning, My Pyramid: foods, serving sizes, food labels.

10. Complementary nutrition: functional foods and dietary supplements: Functional foods, claims for functional foods, strategies for functional food use, food additives and preservatives, natural toxins in foods, dietary supplements: vitamins and minerals, natural health products.

11. Dietary management of diseases: Such as diabetes mellitus, gout, atherosclerosis, jaundice and other liver diseases, obesity and cancer.

12. Assessment of nutritional status: Of a population, nutritional problems of Bangladesh and their possible remedies.

BMB 307 : Biochemistry and Molecular Biology of diseases 2 credit

1.	Diseases – interpretation, diagnosis of diseases using specific parameters true positive, false positive, true negative & false negative use of diff. approaches for disease diagnosis, like microbial, parasitic infection, reliability of diagnostic approach.
2.	Biochemistry of various diseases: biochemical interpretation of the causes & possible treatment options: Atherosclerosis, Major lipid metabolism in, vascular dysfunction and its contribution to, oxidative stress and platelet function in, lipoprotein influx and efflux in, protein oxidation in Atherosclerosis, and other diseases hepatitis, diabetis, obesity, gout, hepatitis, rheunatoid arthrities, malabsorption syndromes, acidosis & alkalosis. Thyroids dys-function, HRT
3.	Genetic basis of biochemical disorders.
	(a) Karyotyping for uneven chromosome distribution diseases like Down syndrome turner Syndrome, Kleinfelter syndrome etc. (b) Genetic basis of biochemical disorders autosomal & X-linked dominant & recessive disorders with possible modes of distribute, citing specific examples of each type.
4.	Microbial & viral diseases – introduction to bacterial and viral diseases - cholera, shigellosis, viral hepatitis, HIV, Influenza etc.
5.	Parasitic diseases their identification by using biochemical as well as molecular markers and immuno techniques.

BMB 308 : Clinical Biochemistry 2 credit

1. Hazards and Safety in clinical biochemistry laboratory: Hazards safety

methods and quality control.

Clinical application of enzymes and metabolites as diagnostic tools : Basic

approach to diagnosis involving handling and processing of samples, acquisition and interpretation of biochemical data, Reference value & its implications sensitivity & specificity of a test; general idea about the instruments used; investigation of CSF, Tumer markers, Biochemical aspects of mental handcrafts. enzymes in diagnosis, use of enzymes e.g. alanine aminotransferase (ALT), aspartate aminotransferase (AST), creatine kinase (CK), lactate dehydrogenase (LDH), amylase, acid phosphatase (ACP), Alkaline phosphatase (ALP), and metabolites e.g. bilirubin, Serum creatinine, uric acid, blood urea nitrogen (BUN), cholesterol and electrolytes in diagnosis, cancer marker, Pancreatitis.

3 Biochemical interpretation & certain genetic disorders –PKU, Fructose intolerance,

Glycogen storage diseases, sickle cell anemia, hemolytic anemia, thalassemia,

hypercholesterolemia, lipid storage disease, muscular dystrophy. Diagnosis of

genetic disorders – invasive & non-invasive pre. natal diagnosis; possible treatment

options..

4. Antioxidant intervention studies in human beings, anti-oxidents and co-

antioxidation.

5. Gene therapy.

BMB 309 : Practical 8 credits

Group A : General Biochemistry

(a) Isolation/separation and assay of biomolecules :
     1. Liver glycogen extraction and estimation.
     2. Thin layer chromatographic separation of amino acids.
     3. Estimation of acetoaminophen and salicylate in serum.

(b) Enzymology:

1. Determination of serum GOT and GPT activity.
2. Study on the activity of salivary amylase.
3. Assay of heart succinic dehydrogenase and cytochrome oxidase.
4. Determination of Km and Vmax of bovine kidney alkaline phosphatase.
5. Determination of serum acid phosphatase.
6. Assay of muscle lactate dehydrogenase and coenzyme NAD+

7. Assay of pancreatic lipase.

(c) Study on the solubility and precipitation of proteins:

      1. Effect of ionic strength on protein solubility.
      2. Determination of total globulin in serum by precipitation.
      3. Effect of pH on protein solubility (precipitation of serum albumin and

globulin at their respective pI).
4. Isolation of casein by precipitation at its isoelectric point.

(d) Study on the separation and determination of fatty acids/lipids:
1. Determination of nonesterified fatty acids from serum.

2. Determination of brain phospholipid.

3. Separation of components of a lipid mixture by TLC.

4. Determination of total fatty acids in a lipid extract.

5. Determination of unsaturated fatty acids in a lipid extract.

6. Determination of cholesterol in a lipid extract.

7. Isolation of cholesterol from gallstones.

8. Determination of serum cholesterol.

(e) Hormonal effect on biomolecules:

1. adrenal ascorbic acid

2. adrenal cholesterol

3. liver glycogen

4. blood sugar

Group B : Molecular Biology:

Isolation of plasmid DNA from E. coli.

Transformation of E. coli with plasmid DNA.

Agarose gel electrophoresis of DNA.

Isolation and assay of bacteriophage lamda, amplification of DNA by polymerase

chain reaction (PCR).

Part C : Assignment : Out of 200 marks of this course, 20 marks are allotted for

an assignment. In this, every student will be assigned a separate project

and will be asked to use library, INTERNET etc. to dig out information

and submit a short report on the project.

BMB 310 : Viva-Voce 2 credits

Extra-Departmental Course

BMB 351 : Computer basics and data analysis 4 Unit

(Theory: 2 credit like other theory courses:

Practical works: 2 credit lab works)

C. Programming

Introduction to programming languages:

Introduction to C: compilers; Basic data types: constants, variable types, key and reserve words;

Expression and operators: assignment statement, arithmetic operators, logical connectors;

Control statements: if-else statement, switch statement, different types of loops;

Functions in C: scope of function variables, modifying function arguments, pointers in C, arrays and pointers;

Input and output: input output file, character input/output, formatted input/out, strings;

R programming

Introduction and preliminaries;

Simple manipulations: numbers and vectors; Objects; Ordered

and unordered factors: Arrays and matrices; List and data frames; Reading data from files; Grouping, loops and conditions; Writing functions; Graphical procedures; Statistical methods using R: exploratory data analysis, one-sample and two-sample tests, regression and correlation, analysis of variance, nonlinear curve fitting:

Practical works: as per theory contents

Textbook:

W.N. Venables and D.M. Smith (2010). An introduction to R.

P. Dalgaard (2008), Introductory statistics with R, second edition.

BMB 401: Cell Biology 4 credits

1.	Techniques used in the study of cell biology: phase contrast microscopy, confocal microscopy, fluorescence microscopy, video-enhanced microscopy, atomic force microscopy, electron microscopy, immuno-electron microscopy, scanning electron microscopy, transmission electron microscopy and cryo-electron microscopy.
2.	Membranes and transport mechanisms: Ion channels and carriers, the membrane potential, K+, Na+ and Ca++ channels and their biological functions, aquaporins, uniporters, symporters and antiporters, specific transporters: the Na+ transporter, the Ca++-ATPase and the F1FO-ATPase.
3.	Membrane targeting of proteins: the secretory pathway, signal sequences to target for translocation, translocation of protein coupled to translation, post-translation translocation, transmembrane translocation, processing of proteins for translocation, the endoplasmic reticulum, the ER membrane, signal sequences associated with import into and out of mitochondria.
4.	Protein trafficking between membranes: exocytic and endocytic pathways, vesicle mediated protein transport, signal mediated and bulk flow transport, transport from ER to the Golgi apparatus and from Golgi apparatus to ER, Rab GTPases, tethers and SNARE proteins, clathrin coated vesicles.
5.	Microtubules and associated motor proteins: Functions of microtubules, structure of microtubules, assembly and disassembly of microtubules, dynamic instability of microtubules, regulation of the stability of microtubules, microtubules based motor proteins, interactions between microtubules and actin filaments, eukaryotic cilia and flagella, ciliary and flagellar movement.
6.	Actin filaments and associated myosin molecules: functions of microfilaments, structure of microfilaments, actin polymerization and depolymerisation, regulation of actin polymerization, actin bundles and networks, skeletal muscle and smooth muscle structure, structure of myosins, muscle contraction models, regulation of muscle contraction..
7.	Intermediate filaments: structure and assembly, keratins and lamins, diseases associated with intermediate filaments.
8.	Cell division: Mitosis, description of the stages of mitosis, role of microtubules in mitosis, meiosis, stages of meiosis, benefits of sex.
9.	Cell cycle and its regulation: the cell cycle, regulation of cell cycle by CDK and associated proteins, cell cycle check points, regulation of passage through check points, effects of cell cycle deregulation.
10.	Differentiated cells and the maintenance of tissues: maintenance of differentiated state, tissues with permanent cells, renewal by simple duplication, renewal by stem cells, epidermis, renewal by pluripotent stem cells, blood cell formation, quiescent stem cells, skeletal muscle, soft cells and tough matrix, growth turnover, repair skeletal connective tissue, territorial stability in the adult body.

BMB 402: Biochemistry of natural products 2 Credits

1.	Natural products: Sources (plant, animal, microbial, marine), classification on chemical basis, Role of natural products in development of medicinal chemistry.
2.	Spectroscopic techniques: UV, IR, Mass Spectroscopy: principle, Electron impact and chemical ionization, mass fragmentations of some natural products, interpretation of mass spectrum, McLaferty rearrangement. NMR: principle, instrumentation, solvents used, internal standard, Chemical shifts (position of signals), integration, multiplicity and intensity, deshielding and shielding effects, coupling constant, interpretation of NMR spectra of some important compounds and natural products.
3.	Alkaloids: Classification, Extraction, isolation and identification from plant sources, Structures of some medicinally important alkaloids: Ephedrine, atropine, morphine, quinine, vincristine and vinblastine. Taxol-anticancer agent. Mechanisms of alkaloid actions, Biosynthesis of some alkaloids.
4.	Antibiotics: Classification of antibiotics on the basis of sources, spectrum and structures, Structure determination of penicillins, chloramphenicol, tetracylines, streptomycin, erythromycin, Structure activity relationship, Semisynthetic antibiotics, Biosynthesis of penicillin & streptomycin.
5.	Steroids: Functions of steroids, structure determination of some important steroids: Cholesterol and Ergosterol.
6.	Flavonoids: Biological functions, classification, structure determination of flavones, flavonol and isoflavanol. Medicinal role of some important flavonoids as antioxidant, Biosynthesis of flavonoids.
7.	Bioactive compounds from marine sources (Curacin A) and from animal source-(epibatidine).

BMB 403: Industrial biotechnology 4 credits

1.	Fermentation Technology: Principles of Microbial growth, with merits & demerits different types of fermentation ; genetic enrichment of microbes for industrial use; different bioreactor designs and their operations, inoculums preparation; mode of fermentation; function process with specific control system; harvesting microbial cells, disrupting microbial cells, downstream processing or product extraction, fermentation technology for the production of single cell protein (SCP); biofuel: ethanol, methane.
2.	Immobilized Biocatalysts: Different types of biocatalysts, different immobilization processes of biocatalysts: adsorption, covalent binding, entrapment, encapsulation and covalent binding, applications of immobilized biocatalysts, multienzyme systems.
3.	Bioremediation and Biomass Utilization: Agro-industrial waste recycling, hydrocarbon and aromatic transformations, microbial degradation of xenobiotics. genetic engineering of bio-degradative .pathways.

4.	Animal Cell-culture: Animal cell culture, characteristics, culture design and significance, application in monoclonal antibody production: hybridoma cell lines, expression of engineered proteins in cell culture, application in introduction of a particular trait into an animal: embryo transfer technology, in vitro fertilization (IVF) technology, embryo cloning.
5.	Micerobial Toxins and Insecticides: Insecticidal toxin of B.thuringiensis, mode of action and use, engineering of B.thuringiensis toxin gene, baculoviruses as biocontrol agents.
6.	Traditional Application of Food Biotechnology: Fermented foods: e.g. dairy products, oriental fermentations, alcoholic beverages, food ingredients.
	Food Toxicology: Introduction to food toxicology; Toxicity testing, Natural toxicants present in foods (plants, animal, marine and microbial toxins).
	Food Processing and Control: Food preservation by heating, chilling, freezing, dehydration and ionising radiation, Packaging materials. Processing of selected food products, Food laws and standards, Concepts of food quality and safety. Factors which affect quality and safety, Food hazards, Process control, application of principles of food hygiene and relevant codes of practice/guidelines to ensure quality and safety. Product development and sensory perception. Food Flavors, additives and supplements.
7.	Ethical perspectives of food biotechnology: Environmental impact, safety, intellectual property rights, animal welfare, risk analysis, consumer perceptions, industry perspectives, producer perspectives around the world. Regulations of food biotechnology.

BMB 404: Molecular Biology III 2 Credits

1.	Gene Structure: Interrupted genes, organization of exons and introns, distribution of genes, organization of gene families variations in individual genomes, organization of genes in the orgelles. Repetitive genes, the special features of metaphase chromosome, DNA protein interaction in centromere and telomere
2.	DNA loss and amplification as a mechanism of gene regulation, DNA rearrangement and gene shuffling.
3.	Mobile genetic elements transposons, retroposons their chracteristics & function evolution of these elements.
4.	Gene expression: Tissue specific expression of proteins and messenger RNAs post transcriptional events.
5.	Regulation at the transcriptional level: Regulation of RNA splicing, RNA editing, Regulation of RNA transport, stability and translation.

6.	Transcriptional Control of DNA sequence elements: Short sequence elements located within or adjacent to the gene promoter, Enhancers, negative acting sequence elements locus control regions. Regulation lby RNA pol I & III, DNA binding by transcription factors.
7.	Transcription control of chromatin stracture: Changes in DNA methylation alteration in histones; changes in chromatin structure.
8.	Protein Localization: Introduction, passage across membrane, protein translocation, chaperons, signal sequences of translocation.
9.	Epigenetics: Epigenetics and Chromatin Dynamics, Silencing, transcriptional landscapes and genomes, Memory of transcriptional states, stem cells and reprogramming, Maintenance of (Epi) genome integrity. Epigenetics and Cancer.

BMB 405: Biochemistry of Cancer 2 Credits

1.	Introduction and Overview of Cancer: Oncogenes and Proto-Oncogenes, Tumor suppressor genes and hereditary cancer, Basic mechanisms of cell cycle regulation, Targeted ubiquitination, Mammalian Cell Cycle Regulation, Cyclins and cyclin-dependent kinases, Inhibitors of cyclin-dependent kinases.
2.	The Molecular Biology Cancer: The retinoblastoma tumor suppressor gene, Regulation of E2F transcription factors, Transcription regulation by RB/E2F, p⁵³ tumor suppressor gene, Regulation of p⁵³ response, DNA damage and cell cycle response, Apoptosis (programmed cell death), DNA tumor viruses, Growth Factors and Receptors, Non-receptor tyrosine kinases, Ras signalling and Adapter Proteins, Cancer Regression by Senescence.
3.	Cancer an Epigenetic Disease: DNA methylation in cancer, Gene silencing and cancer, Methyl CpG binding proteins and cancer.
4.	Cancer Treatment: Effective cancer therapy through immunomodulation: dynamics of treatment, Pharmacogenetics in cancer treatment, Cellular senescence in cancer treatment, Treating cancer’s kinase addiction.

BMB 406: Virology 2 Credits

Classification of viruses:
1.	Major groups of viruses: Bacterial, plant and animal viruses with their nomenclature and classification.
2.	Virus Cultivation: Detection and Genetics: Cultivation & virus: Cell culture,, Embryonated Eggs, laboratory animals. Dection of virus in hosts: Measurement of Infectious units, Measurement of virus particles and their components. Serological and molecular detection, plaque assay (PFU), infectious center assay, one-hit kinetic and two-hit kinetics of virus cultivations. Genetic Analysis of Virus: Classical genetic methods Engineering mutations into viruses engineering viral genomes: virul vectors.
3.	Host virus interaction: Attachment, entry and uncoating, replication, assembly and maturation, exit of virus from host cells: Mechanism of viral interation with cell. Mechanism of virus entry into cell.
4.	Animal virus: Classification based on gene expression, studies on virion structure, infectivity, mode of gene expression and virus assembly of representative member of each class – herpes virus, papovavirus, hepatitis virus (HBV and HCV), picornavirus, vesicular stomatitis virus (VSV), rabies virus, reovirus, retrovirus (HIV), white spot syndrome virus (WSSV) of shrimp., Birds flue, surneflu SARS, ROTA virus.
5.	Effect of animal viruses on host cells: Cytolytic effects, morphological and biochemical observations, inhibitions of proteins, RNA and DNA synthesis, pattern of viral infection- acute, chronic, persistent and latent viral infection.
6.	Plant virus: Structure genomic organization and molecular aspects of tobacco mosaic virus (TMV), cotton leaf curl Gemini virus (CLCuV) and potato virus Y.
7.	Prevention and control of viral infection: General prevention strategies.Immunization with vaccines and antiviral drugs, mechanisms of action and limitations of use of these drugs. Interferon and its modification.

BMB 407: Immunology 4 Credits

1.	Development of the Immune System: Development of immune cells in bone marrow, thymus, lymph nodes and spleen; development of memory B cells; cutaneous immune system; mucosal immune system; lymphocyte recirculation and homing.
2.	Cytokines: General properties of cytokines, cytokine receptors and signaling, functions of signature cytokines: cytokines in innate immunity - TNF, IL-6, IL-12, INF-a &-β, IL-10, chemokines; cytokines in adaptive immunity –IL-2, IL-4, IL-5, INF-γ, TGF-β, IL-13; cytokines of T_H-17 cells and Tregs; cytokines in pathogenesis; cytokine-based therapies.


3.	Innate and Cell-mediated Immunity: Components of innate immunity (brief treatment); antimicrobial peptides; toll-like receptors (TLR); TLR signaling pathways; connections between innate and adaptive immunity; effector mechanisms of cell-mediated immunity: T-cell mediated activation of macrophages and other leukocytes, CTL and NK cell-mediated killing of infected cells.
4.	Major Histocompatibility Complex (MHC): Production of inbred mouse strains, arrangement of H2 and HLA complexes, genetic map, structure of class I and II MHC molecules, peptide-MHC interactions, antigen processing and presentation, tissue typing, transplantation and rejection; association of MHCs with diseases.
5.	Activation of T and B Cells: Antigen receptors and accessory molecules of T cells, antigen recognition, MHC-restriction of T cells, cell cooperation in the antibody response, role of cytokines and costimulatory molecules in B and T cells activation; signaling pathways of T and B-cell activation.
6.	Immunogenetics: Immunoglobulin(lg) gene structure, mechanism and regulation of lg gene recombination and expression, generation of antibody diversity, class switching.
7.	Regulation of Immune Responses: Factors governing the outcome of immune responses; regulation by APCs, antigen and Ig; regulation by T cells; apoptosis, activation induced cell death (AICD), passive cell death (PCD), neuroendocrine regulation of immune responses; influence of genetic factors: MHC-linked and non-MHC linked immune response.
8.	Immunological Tolerance: General features and mechanisms of immunological tolerance, T and B cell tolerance to self antigens; tolerance of T and B cells; tolerance induced by Tregs; tolerance induced by foreign antigens; artificially induced tolerance; therapeutic applications of tolerance.
9.	Immunity to microbes: Innate, adaptive immune responses and immune evasion; immunity to extracellular bacteria, intracellular bacteria, viruses, fungi and parasites.
10.	Vaccination: Active and passive immunization; live attenuated vaccines; inactivated or killed vaccines; subunit vaccines; conjugate vaccines; DNA vaccines; recombinant vector vaccines; edible vaccines; prime-boost strategies.
11.	Immunotechniques: Surface Plasmon Resonance (SPR), production of monoclonal antibodies, antibody engineering: chimeric and humanized monoclonal antibodies, transgenic mice with human Ig loci, phage display libraries in the derivation of monoclonal antibodies; immunoblotting, immunohistochemistry; isolation of lymphocyte populations and subpopulations: Ficoll-Hypaque gradient, flow cytometry and FACS analysis, antibody-coated magnetic beads; ELISPOT assay; TUNEL assay; assay for cytotoxic T and CD4+ T cells, immunoelectron microscopy.

BMB 408: Biochemistry of Drugs 2 Credits

1.	Drugs: Definition, drugs against common diseases: Chemical synthesis, physicochemical properties such as ionization and absorption of drugs.
2.	Routes of administration: intravascular, intramascular and subcutaneous administration. Absorption of drugs through skin and inhalation of drugs.
3.	Drugs distribution: Binding of drugs with albumin passage of drugs through biological membrane, CNS & placenta.
4.	Major routes of elimination of drugs: Renal excretion of drugs and biliary excretion of drugs.
5.	Drug action: Rate of drug absorption and elimination zero order, first order elimination, plateau principle rate of equilibration of drugs in body fluids, influence of body fat on drug distribution.
6.	Drug metabolism biochemical pathways: Biochemical pathways of drug metabolism, inhibition of drug metabolic pathways.
7.	Drug resistance.
8.	Toxicology: Toxic substances & how they affected our health – characteristics, Exposure risks, Associated health effects.

BMB 409: Neurobiochemistry 2 Credits

1.

Brain as a specialized tissue: Structural, chemical and metabolic peculiarities; difference between growing and adult brain.

2.

Gross and fine structure of the brain:

(i) Gross structure – different parts of the brain, their functions and growth characteristics

                                    (brief treatment)

(ii) Fine structure -   cells of the brain, classification of neurons and glia, their structure,

                                   location and function.

3.

Synapse : Structure, their types – chemical and electrical, chemistry of neurotransmission (brief treatment).

4.

Nerve impulse : Action potential, its ionic basis, sodium channel.

5.

Conduction of nerve impulse: Mechanism of conduction along myelinated and unmyelinated neerve fibres, comparison of conduction velocity elong myelinated fibres.

6.

Neurotransmission : Neurotransmitters, their metabolism, storage and release, calcium channel, post synaptic receptors-their modulation with agonists and antagonists, neuropeptides.

7.

Brain growth and development : Species, structural and cell type differences, neurogenesis and gliogenesis, neuronal death and nervous system development.

8.

Myelination : Myelin composition and maturation.

9.

Metabolism of the developing brain: Energy metabolism, changes during development, susceptibility of developing and adult brain to energy supply.

10.

Brain development during malnutrition : Effect on cell proliferation, myelination and synaptogenesis.

11.

Malnutrition and brain metabolism : Energy metabolism, protein and lipid metabolism.

12.

Brain diseases: Parkinson’s Wilson’s Huntington’s chorea, Alzhemer’s disease.

13.

Biochemistry of memory : Short-term memory, long-term memory.

BMB 410: Plant Biotechnology 2 credits

1.	Plant cell culture and applications: Manipulation at cellular level, totipotency of plant cells, somatic embryogenesis, organogenesis, recalcitrant plants, micropropagation and applications, disease-free plants, protoplast culture and fusion with reference to cybrids and cytoplasmic male sterility, anther culture and applications for breeding, commercialization of tissue culture technology, plant tissue culture as a basis for genetic engineering.
2.	DNA markers and application for breeding: Fingerprinting for assessment of germplasm, concept of polymorphism, mapping and breeding populations, linkage of marker to trait of interest, marker-aided selection for breeding.
3.	Plant genetic transformation – prospects and potential: Current status, characters transformed, techniques for plant transformation such as agrobacterium-mediated and biolistics, use of constitutive, tissue-specific and stress-specific promoters for transformation, molecular assessment of transgenic status and inheritance of transgenes, gene silencing, current status of chloroplast transformation and advantages, plants as bioreactors and vaccine production systems, biosafety issues, GM crops.
4.	Discovery/cloning of plant genes: Probe-based-screening, genomic and proteomic approaches, map-based cloning, transposon tagging, isolation by T-DNA insertion, functional characterization by gene mutagenesis/silencing.

BMB 411: Practical Works 8 credits

Group A : Environment and Molecular Biology:

1.	Isolation of DNA from plant tissue.
2.	Isolation of plasmid DNA
3.	Agarose gel electrophoresis of DNA and RNA
4.	Isolation of bacteriophage.
5.	Isolation of microbes from natural habitats.

6.	Isolation of antibiotic resistant organisms from hospital effluents and study of their characteristics.
7.	Determination of biological and chemical oxygen demand (BOD, COD) of different water samples.
8.	Determination of bacterial load from different environmental samples
9.	Isolation of lactose fermenting bacteria.
10.	10.PCR/Restriction digestion of genomic DNA

Group B : Biochemical Techniques:

1. SDS polyacrylamide gel electrophoresis of rat liver proteins.

2. Thin layer chromatography (TLC) of fruit juices

3. Gel filtration chromatography for separation of known proteins.

4. Ion exchange chromatography of known proteins and checking for separation by gel electrophoresis.

Group C : Pharmaceutics:

1. Estimation of streptomycin.

2. Estimation of serum Vitamin A.

3.Analysis of food stuff: estimation of moisture, protein, fat and ash content.
4. Determination of antibacterial activity of plant extracts.

.
Group D : Cellular and Clinical Immunology:

1. Identification of blood groups.

2. Total and differential white cell counts.

3. Separation of blood leucocytes.

4. Determination of white cell viability.

5. Demonstration of phagocytosis by neutrophils.

6. Determination of ESR.

7. ELISA for detection of HBsAg.

8. Assay of human serum immunoglobulin,

Part E : Introduction to bioinformatics & its application in experimental biochemistry

1. Introduction

2. Application of pubmed

3. Familiarization with database

4. Exploring gene: Pairwise alignment techniques.

Part F : Assignment :

Out of 200 marks of this course, 20 marks are allotted for an assignment. In this, every student will be required to participate in two weeks practical training/orientation course during the summer vacation in pharmaceutical, clinical and research establishments and submit a short report.

BMB 412: Oral examination 2 credits