BIOCHEMISTRY AND MOLECULAR BIOLOGY

UNIVERSITY OF DHAKA

SYLLABUS FOR M.S.

SESSION: 2011 - 2012 and onwards

BIOCHEMISTRY AND MOLECULAR BIOLOGY

UNIVERSITY OF DHAKA

The total number of earned credits for M.S. degree is 30, these the number credits on theory courses to be taken is 20, and for Practical/Thesis works will be 6 credits. 2 credits has been allocated for Seminar/Paper Presentation, while 2 credits have been earmarked for oral examination. No course will be offered to M.S. students if the number of students is less than 20% of the total students enrolled.

M.S. Courses

BMB 501 : Advanced Molecular Biology                                          4 Credits

BMB 502 : Bioinformatics                                                           2 Credits

1.      Introduction to bioinformatics database:

·        Organization of the databases  ●Accessing Bioinformatics database

·        Retrieval of desired data            ●Types of Biological data

·        Familiarization with databases (NCBI, ENSEMBL ect)

2.  Example and use of Bioinformatics in molecular biology and biotechnology

a)      BLAST : Application and interpretation of BLAST program for homology  

         searching

b)      Clustal W: Application of Multiple sequence alignment via clustal W program

c)      Codon optimization: Codon usage pattern in different species, Relative  

         Condon frequencies, Codon usage barriers, Condon optimization for the  

         synthesis of recombinant proteins.

3.   Basic algorithms and their uses in bioinformatics: Application of hidden

         markov model  

         (HMM) in designing various bioinformatics tools

4.   Evolutionary Bioinformatics

a)  Building and interpretation of Phylogenetic trees, b) Calculating Substitution rate (Jukes Cantor model and Kimura’s two parameter model)  c)Construction of distance matrix from the pairwise evolutionary distances  d) Non-synonimous vs synonymous substitution ratio (Ka/Ks)  in Protein/Gene evolution e)Identification of horizontally transferred genes in bacterial genomes  f) Use of Mega4 package for detail evolutionary analysis

g) Molecular Clock hypothesis

5.    Structural bioinformatics

a)      Importance of the structures of biomolecules in biological functions

b)      Analyzing RNA secondary structures: Basic concept of stem loop RNA  

         secondary structure, minimum free energy (MFE) calculation.  

c)      Analyzing protein secondary and tertiary structures: Concept of protein

          folding, Prediction of protein 3-d structure via homology modelling and de-

         novo modelling, Prediction of conserved domains via structure-function

         analysis.

d)      Identification of hydrophobic regions in proteins: Concept of hydrophobicity  

         idex of amino acids, Prediction of hydrophobic trans-membrane domain via

         sliding window algorithm

6.    Immunoinformatics:

a)      Basic mechanism of antigen presentation b) Familiarization with immunoinformatics websites and tools c) Identification of immunogenic epitopes by computational methods for designing vaccines

d) Identification of the proteasomal cleavage sites e) Analysis of HLA-epitope interaction

7.    Analysis of microarray data

a)   Microarray: Basic principle  b) Gene chips c) Handling processed microarray data  d) Clustering of genes based on their expression level

b)    Pathway analysis and building gene/protein regulatory network

8.   Computational proteomics

a)      Overview on LC-MS/MS  b) Peptide mass finger printing

b)      Application of Stable isotope labelling of amino acid in cell culture (SILAC)  

           technology for quantitative proteomics

BMB 503 :    Biochemistry of Drugs                                            4 Credits

1.          Introduction

(a)Drugs – basic features  (b) Broad classification with specific examples

2.         Some selected groups of drugs

(a)Cardiovascular drugs  (b)Immunosuppresive drugs & Immunotherapy

(c)Antimicrobials e.g. Penicillin-Cephalospirin groups, Aminoglycosides,

            Tetracylines etc.(d)Locally acting drugs e.g. Gastric antacids, Antiseptics, 

            Disinfectants. (e) Enzymes inhibitors that act as drugs

3.         Pharmacokinetics

(a)Drug absorption (b) Drug distribution, bio-availability, half-life.

(c)Drug metabolism and its various aspects, factors affecting drug metabolism, 

 methods of studying drug metabolism.(d) Drug excretion

4.         Molecular mechanism of drug action

(a) Basic aspects (b) Structure – activity relationship of drugs like, Antihistamines, Sulfa drugs and Psychiatric & antidepressants.

(c)Drug receptors (e.g. ion channel receptors, G-protein coupled receptors, etc.) & their characteristics. (d) Non-receptor mediated drugs. (e) Agonists-antagonists with emphasis on drug and receptor interaction,  drug-drug & drug-metabolite interaction.(f) Drug resistance and its implication

(g)Drug toxicity and its effect, evaluation in lower animals, drug allergy & tests for its prediction, design of toxicity tests, antidote.

 5.        Drug design

(a)Basic concepts;  physico-chemical factors in designing of a drug e.g. thermodynamic, electrostatic & stearic factors, topology, molecular interaction and kinetics (b) Molecular methods in drug design and development - targeting and pharmacogenomics.

BMB 504 : Molecular Diagnosis  & DNA Forensic Sciences                 4 Credits

A.        Molecular Diagnostics :

Introduction to Molecular Diagnosis (MD) and Molecular Diagnostic Laboratory (MDL)

Appropriate Clinical Specimen for MD

Isolation and characterization of DNA/RNA from different clinical specimens: basic principle of DNA extraction by Organic method, Chelex method, Spin columns, magnetic beads etc.

Overview of the application of molecular methods for diagnosis of genetic disorders, infectious diseases and cancer.

PCR in molecular diagnostics: Conventional PCR & real time PCR, qualitative and quantitative PCR, PCR-ELISA

Molecular Diagnosis : of Viral Disease e.g. HBV, HCV, HCMV, HIV and HPV;  Bacterial Disease e.g.  MTB and STDs; Cancer: 

Hematological cancer and solid cancer

Molecular HLA Typing: SSP, SSOP and SBT methods for typing HLA Class I & Class-II

B.       Pharmacogenomics

Introduction: Promises, opportunities and limitations of pharmacogenomics, pharmacology and toxicology in the genomics era, germ line genomics, evolving landscapes in pharmacogenomics and personalized medicine, genetic polymorphisms of metabolic reaction, role of single nucleotide polymorphisms in pharmacogenomics, variability of pharmacogenetics polymorphisms within a population.

Applications of pharmacogenomics in personalized medicine

Pharmacogenomics and the treatment of various diseases such as Alzheimer disease, cancer (eg., lung and breast cancer), asthma, alcoholism, cardiovascular diseases, pharmacogenomics and lipid-lowering agents, tobacco addiction, antibiotics.

Pharmacogenomics tests currently in clinical use

Genotypic techniques to identify new drugs, functional analysis to identify gene variants of UDP-glucuronosyltransferase, drug transporter genes eg, ABC genes, CYP450, CYP2D6, CYP2C19, CYP2C9, VK0RC1 and their role in drug metabolism.

 C.    DNA technology in forensic sciences 

DNA Polymorphism; Minisatellite sequences or Variable Number of Tandem Repeats (VNTRs); Microsatellite sequences or Short Tandem Repeats (STRs); Biology and nomenclature of STR markers; Single Nucleotide Polymorphism (SNPs),SINEs and LINEs; Mitochondrial DNA variations ; Y-Chromosome STRs; X-Chromosome STRs

Amelogenin: the sex typing marker

DNA typing methods

DNA profile: Definition (DNA fingerprinting/DNA testing); Restriction Fragment Length polymorphism (RFLP); Single locus and multi-locus DNA typing; Allele specific oligonucleotides (ASO); Polymerase Chain Reaction (PCR): overview

Analysis of minisatellites by PCR, STR analysis by PCR; DNA detection methods: Silver staining, Fluorescent dyes; Capillary electrophoresis, principles and

Instrument platform for capillary electrophoresis e.g. 310/3100 Genetic analyzer

DNA Extraction and quantitation from forensic samples

DNA Extraction from liquid blood, soft tissues, bone, teeth, buccal cells, semen, blood stains, and semen stains etc.  FTA Card, Differential extraction; DNA quantitation by: Spectrophotometry, Fluorometry, Slot-blot, Real-time PCR 

Applications of DNA Profiling

Identity test ; Parentage test;   Sib ship analysis ;   Kinship analysis ; Identification of dead bodies  ;  Resolving immigration and inheritance disputes

BMB. 505:  Agricultural Biochemistry                                          2 Credits

    Responses to plant pathogenesis

            (i)Ways in which plant pathogenesis cause disease.(ii) Plant defense

            systems, (iii)      Genetic basis of plant-pathogen interactions

            (iv)Biochemistry of plant defense reactions, (v)Systemic plant defense

             responses, (vi) Control of plant pathogen by genetic engineering

    Responses to Abiotic Stresses

            (i) Plant responses to abiotic stresses, (ii)Stresses involving water deficit

            (iii)Osmotic adjustment and its role in tolerance to drought and salinity.

            (iv)Impact of water deficit and salinity on transport across plant   

             membranes. (v) Additional genes induced by water stress.

            (vi)Freezing stress.(vii) Flooding and oxygen deficit (viii)            Oxidative

            stress, (ix)Heat stress

  Molecular Physiology of Mineral Nutrient Acquisition, Transport and    

  Utilization.

            (i)Overview of essential mineral elements (ii) Mechanisms and regulation of plant

             K^Å transport, (iii)Phosphorus nutrition and transport, (iv)          The molecular

             physiology of micronutrient acquisition (v) Plant responses to mineral toxicity.

             Plants as bioreactors.

Crop Improvement and yield enhancement

New edible uses of novel plant products :

            Uses and modifications of fatty acids & lipids, plants as sources of

biodegradable plastics, plants as factories for chemical drug.

BMB. 506:  Environmental Biochemistry                                 4 Credits

Introduction to ecology and ecosystem

Environmental pollution (water, soil and air), noise and thermal pollution, their sources and effects. Pollution due to arsenic, tannery, textile, lead and sulphur- rich coal.

Waste water (sewage and industrial effluents) treatments: anaerobic and aerobic treatment, conventional and advanced treatment technology, methanogenesis, methanogenic, acetogenic, and fermentative bacteria-technical process and conditions, emerging biotechnological processes in waste - water.

Solid waste management : landfills, composting, earthworm treatment, recycling and processing of organic residues.;

Treatment of heavy metal wastes

Development of Industrial Waste Treatment System.

Anaerobic digestion of agroindustrial byproducts & wastes

Bioremediations :  Biotransformation of toxic wastes to harmless products.

Wasteland :  Uses and management, bioremediation and biorestoration of contaminated lands.

Environmental genetics : degradative plasmids, release of genetically engineered microbes in environment.; Environmentally friendly biofertilizers & biopesticides

Biofuels & Biogas; Bioengineered foods : regulation and safety

Plant Environment & Agriculture

Responses to plant pathogenesis

(i)Ways in which plant pathogenesis cause disease;        (ii)Plant defense systems

(iii)Genetic basis of plant-pathogen interactions (iv)        Biochemistry of plant defense reactions; (v)Systemic plant defense responses; (vi)  Control of plant pathogen by genetic engineering

Responses to Abiotic Stresses

(i) Plant responses to abiotic stresses; (ii)Stresses involving water deficit ;           (iii)Osmotic adjustment and its role in tolerance to drought and salinity; (iv)Impact of water deficit and salinity on transport across plant membranes; (v)Additional genes induced by water stress; (vi)Freezing stress; (vii)Flooding and oxygen deficit ;(viii)Oxidative stress

(ix)Heat stress

 Molecular Physiology of Mineral Nutrient Acquisition, Transport, and Utilization.

(i)Overview of essential mineral elements; (ii)Mechanisms and regulation of plant K^Å transport; (iii)         Phosphorus nutrition and transport;(iv)The molecular physiology of micronutrient acquisition ; (v)Plant responses to mineral toxicity. Plants as bioreactors.

Crop Improvement and yield enhancement

New edible uses of novel plant products :

Uses and modifications of fatty acids & lipids, plants as sources of biodegradable plastics, plants as factories for chemical drug.

BMB 507: Clinical ImmunologyandImmunodiagnostics                               4 Credits

1.      Autoimmunity: Characteristics Pathogenesis and genetic susceptibility to autoimmunity; infection and autoimmunity pathogenic role of autoantibodies control mechanisms, treatment, effector cell assays, autoimmun diseases like; autoimmun diabetics, autoimmun hemolytic anemia, rhematoid arthrities, hereditary angioneurotic edema etc; diagnostic and prognostic value of autoantibodies.

2.       Allergy and Hypersensitivity: Coombs and Gell classification.

Type I -Immediate hypersensitivity: Induction and effector mechanisms; allergens, atopy, IgE involvement; control of IgE production; Immune  response to inhalent allergens; role of mast cells, mediators and the reactions involved; genetic susceptibility and immunopathology; diagnosis; skin prick test; immunotherapy and new approaches for treatment.

Type II- Antibody dependent cytotoxicity: Mechanism of tissue damage; reactions involving hemolytic diseases in newborn, autoimmune hemolytic anemia and hyper acute graft rejection; treatment.

Type III- Immune complex mediated hypersensitivity: Types of immunecom.plex diseases; inflammatory mechanisms involved; experimental models to study; persistence, deposition and detection of immune complexes.

Type IV-Delayed hypersensitivity: Contact hypersensitivity; tuberculin-type and granulomatous hypersensitivity; cellular reactions and disease manifestation in delayed hypersensitivity.

3.      Transplantation Immunology: Immunology of allogenic transplantation; recognition of alloantigens, activation of alloreactive T cells; effector mechanisms of allograft rejection: hyperacute acute and chronic rejection, prevention and treatment: immunosuppression, inducing donor-specific tolerance or suppression; Xenogeneic transplantation; blood transfusion; bone marrow transplantation: graft-versus-host disease.

4.      Tumor Immunology: Immune surveillance, tumor antigens, tumor associated antigens, immune responses to tumors, immune evasion by tumors, immunodiagnosis, immunotherapy for tumors.

5.       Immunodeficiencies: Primary (congenital) immunodeficiencies: B and T cell deficiencies- SCIDs, X-LA, selective IgA and IgG deficiencies, hyper IgM syndrome, common variable immunodeficiency, X-linked immunoproliferarive disease, defective class I and II MHC expression, Wiskott-Aldrich syndrome, ataxia-telangiectasia, chronic granulomatous disease, leukocyte adhesion deficiency, defects in complement proteins, defects in phagocytosis; therapeutic approaches Acquired (secondary) immunodeficiency: HIV and AIDS, treatment and prevention.

BMB 508 Applied Nutrition and Nutritional Biochemistry              4 Credits

1.  Malnutrition and Immunity

(a)Role of nutrition in immune response to infection; (b) Malnutrition and immunity

(c)Nutrition and immunodeficiency disorders; (d) Dietary modification in infection

2. Nutrition and Genomics

(a) Genetic and environmental variations and nutrient composition of foods.

(b)Role of nutrients in gene expression and regulation

3.  Nutrition – Drug Interaction

(a)Effect of Food on drug pharmacokinetics; (b) Effects of drugs on nutrition:  drugs which affect food intake, absorption, metabolism and excretion.

4.  Nutrition and IT

(a)Nutrition Information,  Education and communication  – IT offers a new approach

(b)IT & Nutritional support for patients with chronic illnesses

5. Malnutrition and Psychosocial Development

(a)Introduction : Definition and Terms; (b) Impact of PEM on brain development and  psychosocial development; (c) Nutritional rehabilitation and mental development

(d)Malnutrition and cognitive development: A multifaceted problem

6.  Current Topics in Nutrition

(a)Eating disorders ; Anorexia nervosa and Bulimia nervosa; (b)Total parenteral nutrition (TPN); {c}Sports nutrition; {d}Poverty and nutrition; (e) Nutrition in emergencies : famine, war, flood and natural disasters; (f) International nutrition : Nutrition in developing economics; (g) Globalization and Nutrition; (h) Nutritional enhancement of plant foods

7. Applied Nutrition

Diet, Nutrition – and lifestyle – related chronic non-communicable diseases (NCDS)

Low birth weight: increased risk of morbidity, mortality and retarded cognitive development; Nutrition and HIV/AIDS; Food and Nutrition Security in developing countries; Street food as meal of millions; Nutrition Interventions Programmes in Bangladesh.

BMB 509 Biochemistry of Natural Products                              2 Credits

NMR: Chemical shifts. Factors affecting the chemical shift, oupling constants: vicinal coupling, geminal coupling, long range coupling, use of coupling constant values in the determination of stereochemistry of some important natural and biochemical substances. AB and ABX system, Two dimensional NMR: NOE, COSY.

Use of NMR in Biochemistry and Molecular Biology: use of ¹³C NMR in the elucidation of Biochemical pathways including the biosynthesis of cephalosporin, bikaverin, penicillin, chlorophyll and Vitamin B₁₂; use of NMR in the determination of 3 dimensional structure of proteins, enzymes, DNA, RNA and protein signaling.

Use of NMR in Designing lead compounds (drugs): Use of NMR in drug screening. Clinical use of ³¹P NMR – Detection of abnormalities in different organs by the use of ³¹P NMR. Magnetic resonance tomography (MR) – use of MR to locates tumors, Vascular dilations and many other pathological abnormalities.

 Mass spectroscopy: Mass fragmentation of some important natural products.

(i) Structure determination of some medicinally important alkaloids; quinine, atrophine, morphine by synthetic and digradative methods. Biosynthesis of some complex alkaloids.

(ii)Molecular Mechanism of actions of some selective, antibiotics. prodrugs, Advantages of prodrugs, semesynthetic antibiotics, synthesis of antibiotics, mechanism of antibiotic action, Allergetic reactions, Chemical synthesis of some medicinal steroids: Progesterone, Cortisol, Vitamin D.

(iii)Structure of Vitamin B₁₂, Biological reactions with participation of Vitamin  B₁₂ and coenzymes B₁₂. Chemical synthesis of vitamin E  a-tocopherol and b-tocopherol

BMB 510 Biotechnology Business Management                        2 Credits

 (i)Business management: The company, its environment, stakeholders; Corporate stretegies; Some basic economic principle (e.g. profit maximization, shareholder value); Business planning and decision making processes and supporting tools. Methods of business analysis. Introduction to :Technology development; Procurement; Operation management; Marketing and Sales.     

      (ii)Project management: Fundamentals of project management;Project life cycle   

      (definition, planning, execution and controlling; close out); Tools and methods of

       project management e.g. planning methods, problem solving methods; Social

       competence in project management (team work, communication).

(iii)Commercialization, Marketing and Management of Products:

      Fundamentals of marketing and sales of products; Creating and Marketing the

       image of the company; Positioning of the company name and products;The art

       of negociation;Workable marketing and the strength of distribution; Effective   

       advertizing and marketing; Opportunities of international marketing; Steps

        involved in commercialization of Biotechnology Products./

 (iv)Intellectual Property Rights:

        (a) Introduction: general introduction; Patent claims;Legal decision making

         process, Ownership of Intellectual property.(b) Basic requirements of

         patentability: Patentable subject matters, Novelty and the Public Domain.

        (c) Special issues in biotechnology patents: Disclosure quirements.Collaborative 

         research,Competitive research, Foreign patents. (d) Patent Litigation: Substa-

         ntive aspects and Procedural aspects of patent litigation,Recent development in

         Patent System and Patentability of Biotechnological invention.

BMB. 511 :  Thesis / Practical                                              6 Credits

Molecular Biology

1.                  Restriction mapping of DNA

2.                  Generation of nucleic acid probes by oligolabelling

3.                  Detection of nucleic acid sequences by hybridization

4.                  Southern blotting and dot blotting

5.                  DNA fingerprinting of bacterial strains.

6.                  Introduction of foreign DNA into tissue cultured cells

7.                  Isolation and analysis  of genomic DNA and RNA from tissue cultured cells.

8.                  Agarose gel electrophoresis of DNA and RNA

9.                  Polymerase chain reaction (PCR) of a specific target gene from genomic 

                     DNA

10.               Gel electrophoresis of proteins from normal & stressed plants.

Bioinformatics

1.         (a)       Retrieve at least 3 different types of gene sequences from database using

name/accession number of the genes 

(b)        Find ORFs, promoter sequences and transcription termination signals

(c)        Find restriction enzyme sites and construct restriction maps of the genes

(d)        Translate the nucleotide sequence into amino acid sequence. Analyze the 

            amino acid content in the protein sequence.

(e)       Do multiple alignment of the proteins and analyze their homology and conserved sequences. Prepare dendrograms of the homologus proteins.

(f)         Design primers in order to clone a gene through PCR amplification.

 Clinical Biochemistry

1.         Determination of creatine clearance rate (CCR)

2.         Determination of plasma lipid profile (total cholesterol, HDL- and LDL-cholesterol).

3.         Determination of cardiac enzymes (CPK, CK-MB and LDH).

4.         Determination of serum iron and iron binding capacity (TIBC).

Immunology 

1.                  Determination of serum immunoglobulin G by ELISA method.

2.                  Detection of HBsAG by ELISA method.

3.                  Determination of serum complement C3 by immunoturbidometric method.

4.                  Immunoelectrophoresis of major serum immunoglobulins.

Natural Products

1.                  Chemical synthesis of phenacetin

2.                  Clinical synthesis of benzocaine

3.                  Estimation of dichlofenac sodium from pharmaceutical preparation

4.                  Estimation of metronidazole from pharmaceutical preparation

5.                  Estimation of tolbutamide from pharmaceutical preparation

6.                  Estimation of acyclovir from pharmaceutical preparation

7.                  Estimation of AI₂O₃ and Mg(OH)₂ from pharmaceutical preparation

8.                 Extraction & Identification of alkaloids from Polyathia longifolia (Devdaru)  

                   leave or bark. 

Nutrition

1.                  Determination of toxin (ODAP) in Khesari seed

2.                    Field level estimation of blood hemoglobin

3.                  Determination of serum vitamin A and E by HPLC

BMB 512  Seminar / paper presentation                                     2 Credits

 BMB 513  Oral Examination                                                         2 Credits

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