Bangladesh Agricultural University (BAU)

Course No. & Title	BMB 1105 Biochemistry and Molecular Biology
Level & Semester	L-1, S-1 (January-June)
Pre-requisite Course	Nil
Student	Compulsory for B. sc. In Bioinformatics Engineering
Number of Credit	02
Contact hours	02 hours per week,16 weeks
Total Mark	100

Rationale

The students need to have a proper Knowledge on the physical, chemical and molecular aspects of biomolecules for understanding molecular interplays in living systems.

Course Learning Outcome (CLO)

Upon completion of this course, the student will be able to:

CLO 1	Describe scope and importance of biochemistry and molecular biology in bioinformatics engineering.
CLO 2	Explain biological functions, physical and chemical properties of biomolecules.
CLO 3	Compare, contrast and interaction among various biomolecules in living system.
CLO 4	Construct the structures of various biomolecules.
CLO 5	Construct recombinant DNA and clones for development of new variety.

Mapping CLO with PLO

PLO CLO	PLO 1	PLO 2	PLO 3	PLO 4	PLO 5	PLO 6	PLO 7	PLO 8	PLO 9	PLO 10
CLO 1		√					√
CLO 2		√					√
CLO 3		√					√
CLO 4		√					√
CLO 5		√					√

SUMMARY OF COURSE CONTENT

COURSE CONTENT	Aligened Clo	No.of lectures
Cell & Tissue: Cell: Cell theory, prokaryotic cells & Eukaryotic cells, structure and functions of subcellular organelles. Membrane phenomena. Tissue: Types, structure and functions of animal tissues (Connective tissue, Muscle tissue, Nervous tissue, epithelial tissue, Mineralized tissue), plant tissue (Meristematic tissues & permanent tissues).	Clo 1	2
Carbohydrates & Nucleic acids: Carbohydrates: Definition, classification, structure, properties, occurrence and biological importance of Monosaccharides, Disaccharides, Oligosaccharides, and Polysaccharides. Nucleic acids: Types, structure properties, and function of nucleic acids, Deviation from Watson-Crick model, DNA as genetic material. Concept of r DNA technology	CLO 2 CLO 3 CLO 4 CLO 5	8
Proteins & Amino Acids: Amino acids: Definition, composition, structure, properties, stability and biological importance of Amino Acid, Formation of peptide bond, Identification of C and N terminal residues of amino acids Protein: Definition, classification, composition, structure, properties, occurrence and biological importance of protein. Techniques for separation, isolation and characterization of proteins: Electrophoresis- Basic techniques of Electrophoresis, Types, Working & Application, Advantages and disadvantages. Centrifugation- Basic principles, Types, Molecular weight determination & Application, Advantages and disadvantages. Chromatography- Overview of Centrifugation, Types, Principles, Working & Application, Advantages and disadvantages.	CLO 2, CLO 3, CLO 4	6
Lipids: Classification and function. Lipids as membrane constituents.	CLO 2, CLO 3, CLO 4	6
Vitamins and Minerals: Source, Classification and biochemical function	CLO 2, CLO 3, CLO 4	4

Teaching Strategy

Lectures and discussion, Demonstration by video, self-study, Case studies, practice, and Group studies.

Assessment Strategy

Question & answer (QA), Assignment, Quiz, and Observation

Recommended Books

Albert, a Johnson, J. Lewis, M. Raff, D. Bray, K. Hopkin, k. Roberts and P. Walter (2003): Essential Cell Biology”, 2^ndedition or later. Taylor & Francis Group, USA.
M. Devlin (2002): Textbook of Biochemistry, 5^th edition or later. John Wiley and Sons, Inc.USA.
Lodish, A. Berk, C.A. Kaiser, M. Krieger, A. Bretscher, H. Ploegh and K C. Martin (2016): Molecular Cell Biology, 8^th edition or later. W. H. Freeman and company, New York.
L. Nelson and M.M. Michael (2017): Lehninger Principles of Biochemistry, 7^th edition or later. Freeman and company, New York.
Stryer (1995): Biochemistry, 4^th edition or later. Freeman and company, New York.
Voet and J. G. Voet and J. G. (1995): Biochemistry, 2^ndedition or later. John Wiley and Sons, New York.

Course No. & Title	BMB 1106 Biochemistry and Molecular Biology
Level & Semester	L-1, S-1 (January-June)
Pre-requisite Course	Nil
Student	Compulsory for B. sc. In Bioinformatics Engineering
Number of Credit	01
Contact hours	02 hours per week,16 weeks
Total Mark	100

Rationale

This course will develop the practical skill on various biochemical methods so that the students can use their acquired lab skill for various biochemical researches.

Course Learning Outcome (CLO)

Upon completion of this course, the student will be able to:

CLO 1	Prepare various types of solutions
CLO 2	Identify biomolecules from biological samples
CLO 3	Analyze moisture, fat, crude fiber and ash from biological samples
CLO 4	Extract and estimate starch vitamin, and DNA
CLO 5	Explore sophisticated biochemical techniques in different laboratories.

Mapping CLO with PLO

PLO CLO	PLO 1	PLO 2	PLO 3	PLO 4	PLO 5	PLO 6	PLO 7	PLO 8	PLO 9	PLO 10
CLO 1		√					√
CLO 2		√					√
CLO 3		√					√
CLO 4		√					√
CLO 5		√					√

SUMMARY OF COURSE CONTENT

COURSE CONTENT	Aligened Clo	No.of lectures
Preparation of solutions and their standardization	CLO 1	1
Qualitative analysis of carbohydrates and proteins	CLO 1	4
Quantification of carbohydrates and protein	CLO 2	3
Quantitative analysis of enzymatic and non-enzymatic antioxidants	CLO 4	2
Extraction and estimation of DNA	CLO 4	1
Proximate analysis: Moisture, fat, crude fibre and ash	CLO 3	1
Biochemical and molecular laboratory visit	CLO 5	1

Teaching Strategy

Lectures and discussion, Demonstration by video, self-study, Case studies, practice, and Group studies.

Assessment Strategy

Question & answer (QA), Assignment, Quiz, and Observation

Recommended Books

An introduction to practical Biochemistry. Davit T. Plummer. Tata McGraw-Hill Publishing Company Limited, New Delhi, 1995.
Biochemistry Laboratory Manual F. M. strong. WM.C. Brown Company Publishers, USA, 1965.
Biochemistry Laboratory Techniques. Sterling Chaykin. Wiley Eastern private Limited, New Delhi, 1970
Biochemical Calculations. How to Solve Mathematical Problem in General Biochemistry. Irwin H. Segel. John Wiley and Sons, Inc. New York, 1968.
Experimental Biochemistry. A Laboratory Manual. Gerald Litwack. John Liley and Sons.Inc, New York,1960
Official Methods of Analysis. Association of official Analytical Chemists (AOAC), Washington D. C, 1990.

Course No. & Title	BMB 3203 Biological Informatics
Level & Semester	L-3, S-2 (July-December)
Pre-requisite Course	Nil
Student	Compulsory for B. sc. In Bioinformatics Engineering
Number of Credit	02
Contact hours	02 hours per week,16 weeks
Total Mark	100

Rationale

This course will introduce fundamental concepts of bioinformatics, biopolymer, Sequence, Protein Structure, and Sequence alignment, DNA Coding and Structural analysis for living things,

Course Learning Outcome (CLO)

Upon completion of this course, the student will be able to:

CLO 1	Acquire fundamental knowledge about bioinformatics.
CLO 2	Understand biological database and biopolymers.
CLO 3	Create database for Protein, DNA, and RNA.
CLO 4	Analyze Protein and nucleic acid sequences.
CLO 5	Describe fundamentals of proteomics

Mapping CLO with PLO

PLO CLO	PLO 1	PLO 2	PLO 3	PLO 4	PLO 5	PLO 6	PLO 7	PLO 8	PLO 9	PLO 10
CLO 1		√	√	√			√
CLO 2		√	√	√			√
CLO 3		√	√	√			√
CLO 4		√	√	√			√
CLO 5		√	√	√			√

SUMMARY OF COURSE CONTENT

COURSE CONTENT

Aligned CLO

No.of lectures

Introduction TO Bioinformatics: Bioinformatics, Introductory Biology, Scales of life, Animal Cell, Molecular Biology Information, Macromolecular Structure, Genes and Proteins, Gene Expression Datasets, Human Genome, APPlication domains.

CLO 1

Introduction to Biological Databases: Introduction to Nucleic Acid Data Bank, Introduction to protein Sequence Data Bank; Nucleotide Databases , Nucleic Acids Research Database Issue, Access, Species-Specific Databases Protein Databases (Swiss-prot, Tr-EMBL, PIR-PSD, Expasy); Derived Databases sequence Submission Methods and Tools (Sequin, sakura,Bankit); Sequence Retrieval Systems (Entrez &SRS).

CLO 2

CLO 3

Biopolymers: Introduction to biopolymers, Synthetic Polymer, Biopolymers vs Synthetic Polymers conventions and nomenclature, Structural Characterization, Biopolymers as materials Internal and External co-ordinate System, Genome Anatomy, prokaryotic genomes Structures, Eukaryotic genomes Structures.

CLO 3

Sequence Analysis: Introduction to Sequence analysis, History, Sequence Alignment, Profile comparison, Analysis of protein and nucleic acid sequences, multiple alignment programs, Development of programs for analysis of nucleic acid sequences, pairwise Sequence Alignment-Similarity, Identity and Homology, Global Alignment, Local Alignment, Sequence assembly, gene prediction, protein Structure Prediction, Methodology

CLO 4

Structural Analysis: Structures and Loads- classification of Structures & Loads, Analytical Methods- Limitations. Strength of Materials Methods (Classical Methods), Example- Method of Section, Elasticity Methods, Methods Using Numerical Approximation, Timeline, Analysis of Structures And Correctness of Structures, Submission of Data TO PDB Atomic coordinates And Electron Density Maps; Methods for prediction of Secondary And Tertiary Structures Of proteins.

CLO 5

Teaching Strategy

Lectures and discussion, Demonstration by video, self-study, Case studies, practice, and Group studies.

Assessment Strategy

Question & answer (QA), Assignment, Quiz, and Observation

Recommended Books

Baxevanis, D.B. Davison, R. D. M. Page and G. A. Petsko (2004); Current Protocols in Bioinformatics. New York, John Wiley & Sons Inc.
David w Mount (2004) Bioinformatics: Sequence and Genome Analysis. CSHL Press.
Harisha and S. Harisha (2007); Fundamentals of Bioinformatics. I. k. International Publishing House Pvt. Lit. Mumbai-110016 (India).
Gu Jenny, Philip E. Bourne (2011): Structural Bioinformatics, 2^nd John Wiley & Sons
Jonathan Pevsner (2009); Bioinformatics Functional Genomics, 2^nd John Wiley & Sons
Lesk (1999): Introduction to Bioinformatics, 1st edition. Oxford University Press.
Gautham (2006): Bioinformatics, Narosa Publishing Company, New Delhi.

Course No. & Title	BMB 3204 Biological Informatics
Level & Semester	L-3, S-2 (July-December)
Pre-requisite Course	Nil
Student	Compulsory for B. sc. In Bioinformatics Engineering
Number of Credit	01
Contact hours	02 hours per week,16 weeks
Total Mark	100

Rationale

This course will introduce fundamental concepts of bioinformatics, biopolymer, Sequence, Protein Structure, and Sequence alignment, DNA Coding and Structural analysis for living things,

Course Learning Outcome (CLO)

Upon completion of this course, the student will be able to:

CLO 1	Acquire skills to use different approaches for Retrieval of DNA Sequence
CLO 2	Develop the skills to Retrieval of protein Sequence from the protein databases.
CLO 3	Determine the three-dimensional structure of protein.
CLO 4	Develop the Knowledge to retrieve the particular information from the specialized databases.
CLO 5	Explore sophisticated biochemical techniques in different laboratories.

Mapping CLO with PLO

PLO CLO	PLO 1	PLO 2	PLO 3	PLO 4	PLO 5	PLO 6	PLO 7	PLO 8	PLO 9	PLO 10
CLO 1		√	√	√			√
CLO 2		√	√	√			√
CLO 3		√	√	√			√
CLO 4		√	√	√			√
CLO 5		√	√	√			√

SUMMARY OF COURSE CONTENT

COURSE CONTENT	Aligened Clo	No.of lectures
Retrieval of protein Sequence using Sequence databases: UNIPROT, Tr- EMBL. DNA Sequence using Sequence databases: NCBI, DDBJ, Genbank.	CLO 1	2
Retrieval of protein Structural information using Structure databases: SCOP, CATH. Retrieval of 3D protein Structure using protein Data Bank.	CLO 1 CLO 2	2
Specialized Databases: BEST (Database for Expressed Sequence Tags), DBSTS (Database of Sequence Tagged Sites).	CLO 3	2
Biological data retrieval system using Entrez. Retrieval the file formats of Sequence: Fasta Format, GCG Format.	CLO 4	2
Molecular visualization of protein Structure using Pymol, Rasmol. Protein function prediction Tools. Gene prediction using GenScan tool. Accessing Genome databases.	CLO 5	4
Bioinformatics Lab visit	CLO 1	4

Teaching Strategy

Lectures and discussion, Demonstration by video, self-study, Case studies, practice, and Group studies.

Assessment Strategy

Question & answer (QA), Assignment, Quiz, and Observation

Recommended Books

Baxevanis, D.B. Davison, R. D. M. Page and G. A. petsko (2004); Current Protocols in Bioinformatics. New York, John Wiley & Sons Inc.
Lesk (1999): Introduction to Bioinformatics, 1st edition. Oxford University Press.
Gautham (2006): Bioinformatics, Narosa Publishing Company, New Delhi.
R. Srinivas (2005): Bioinformatics: Sequences and genomics analysis, cold Spring Harbor Laboratory, press, Cold Spring harbor, USA.

Course No. & Title	BMB 3201 Enzymes and Metabolism
Level & Semester	L-3, S-2 (July-December)
Pre-requisite Course	Nil
Student	Elective for B. sc. In Bioinformatics Engineering
Number of Credit	02
Contact hours	02
Total Mark	100

Rationale

This course covers the mechanism of enzyme action and their impact on metabolic processes and their impact on human nutrition under normal and adverse condition.

Course Learning Outcome (CLO)

Upon completion of this course, the student will be able to:

CLO 1	Describe various terms of enzymes, enzymes activity, enzymes kinetics and regulation.
CLO 2	Explain various metabolic processes (pathways/cycles) with their relationships.
CLO 3	Calculate energy kinetics in various metabolic processes.
CLO 4	Construct the relationship between the metabolic processes.

Mapping CLO with PLO

PLO CLO	PLO 1	PLO 2	PLO 3	PLO 4	PLO 5	PLO 6	PLO 7	PLO 8	PLO 9	PLO 10
CLO 1		√	√				√
CLO 2		√	√				√
CLO 3		√	√	√			√
CLO 4		√	√				√

SUMMARY OF COURSE CONTENT

COURSE CONTENT	Aligened Clo	No.of lectures
Introduction to Enzymes: Introduction to enzymes, nomenclature, classification, riboenzyme, general characteristics of theories of enzyme catalysis, substrate specificity, isozymes,coenzymes, cofactors, regulation of enzyme activity, chemical kinetics and enzyme kinetics, Michaelis- Menten equation,effect of various factors on rate of reactions, inhibition of enzymatic reactions and kinetics, multienzyme system and bisubstrate reactions, catalytic mechanisms, regulatory enzymes and immobilized enzyme.	CLO 1	5
Introduction to Metabolism: Introduction to Metabolism-Overview of anabolic and catabolic pathways of carbohydrates, proteins and lipids. Role of ATP, NAD, FAD and CoA in metabolism. Concept of Bioenergetics.	CLO 2	3
Carbohydrate Metabolism: Digestion and absorption of carbohydrates. Glycolysis and its significance, Fermentation, Fate of pyruvate, Citric acid cycle, Gluconeogenesis, Cori cycle, Glycogenesis, Glycogenolysis Glycogen storage diseases. HMP shunt, Uronic acid pathway, Metabolism of hexoses other than glucose, Regulation of glycogen metabolism, Glyoxylate pathway, Biosynthesis of oligosaccharides and glycoproteins.	CLO 2 CLO 3 CLO 4	8
Lipid Metabolism: Digestion and absorption of lipids. Introduction to lipids metabolism, B-Oxidation of fatty acids, Ketogenesis. Biosynthesis of fatty acids, Triacylglycerols and prostaglandins. Metabolism of phospholipids, glycolipids and cholesterol. Lipoproteins: Metabolism of HDL, Disorder of plasma Lipoproteins, Fatty liver, obesity, Atherosclerosis, Tay–sach disease, Gauchers disease, Niemann- pick disease.	CLO 2 CLO 3 CLO 4	6
Protein Metabolism: Digestion and absorption of proteins. General aspects of amino acids metabolism; deaminaton, transamination, transmethylation, transpeptidation, and decarboxylation. Metabolism of ammonia: urea cycle and its regulation, Nitrogen balance, biosynthesis of non-essential amino acids, Metabolic breakdown of individual amino acids.Clinical correlation of protein metabolism. Integration of metabolism.	CLO 2 CLO 4	6
Nucleic Acid Metabolism: Central dogma of life; replication, transcription and translation. Biosynthesis and degradation of purines and pyramidines, neucleosides and nucleotides. Clinical correlation of purine and pyrimidine metabolism. Nucleotides as coenzymes.	CLO 2 CLO 4	4

Teaching Strategy

Lectures and discussion, Demonstration by video, self-study, Case studies, practice, and Group studies.

Assessment Strategy

Question & answer (QA), Assignment, Quiz, and Observation

Recommended Books

Lehninger principles of Biochemistry by David L. Nelson, 2008. 5^th W. H. freeman and company. New York.
Textbook of Biochemistry by Thomas M. Devlin, 2002. 5^th edition John Wiley & Sons, Inc. printed in USA.
Biochemisstry by Donald voet, 1995. 2^nd edition, John Wiley and Sons, New York.
Outlines of Biochemisstry by Eric E. Conn and paul k. stumpf, 1987. 5^th John Wiley and Sons, New York.
Biochemisstry by Albert L Lehninger, 1982. 2^nd edition Kalyani publishers. Ludhiana, New York.
Harper’s Biochemisstry by Robert K Murry, 2002. 25^th McGraw Hill. Printed in Singapore.
Biochemisstry by Lubert Stryer, 1995.4^th W. H. freeman and company. New York.
Textbook of Biochemistry by Edward S. West, Wilber R. Todd, Haward S. Mason and T. van Bruggan. 4^th Edition, 1966The MaCmillan Company.Collier- MaCmillan Ltd. London.

Course No. & Title	BMB 4103 Recombinant DNA Technology
Level & Semester	L-4, S-1 (January-June)
Pre-requisite Course	Nil
Student	Elective for B. sc. In Bioinformatics Engineering
Number of Credit	02
Contact hours	02
Total Mark	100

Rationale

This course will develop the practical skill on various biochemical methods and techniques to facilitate acquiring skill for carrying out various biochemical analyses

Course Learning Outcome (CLO)

Upon completion of this course, the student will be able to:

CLO 1	Acquire basic knowledge about the fundamentals and role of biomolecules in Recombinant DNA technology.
CLO 2	Enrich the quest on applications including gene cloning, cloning vectors and expression vectors.
CLO 3	Know about the concepts of cell transformation due to the chamges in genetic material, and cell cloning methods.
CLO 4	Learn about the advent of polymerase Chain Reaction and PCR based mutagenesis and gene silencing techniques its impact on molecular biology.

Mapping CLO with PLO

PLO CLO	PLO 1	PLO 2	PLO 3	PLO 4	PLO 5	PLO 6	PLO 7	PLO 8	PLO 9	PLO 10
CLO 1		√					√
CLO 2		√					√
CLO 3		√					√
CLO 4		√					√
CLO 5		√					√

SUMMARY OF COURSE CONTENT

COURSE CONTENT	Aligened Clo	No.of lectures
Cloning and rDNA Technology: Introduction to Cloning and rDNA Technology, Recombinant DNA, Cloning DNA, Cloning vector: Plasmids (pUC18 and Ti Plasmids), Bacteriophages, Plasmids, Cosmids, SV40, retrovirus and Artificial Chormosomes (BAC, YAC), Amplification of Recombinant DNA.	CLO 1 CLO 2	5
Gene cloning: Strategies in gene cloning: restriction enzymes, ligase, insertion into vector, cloning, transformation into host cell, Enzymology of Recombinant DNA. Screening for recombinant (Insertional inactivation, Colony/in situ hybridization, radioactive antibody test, xgal, complementation and physical methods)	CLO 2	6
Genome Sequencing: Methods of gene transfer and genone sequencing: CaPO4 mediated gene transfer, liposomes, electroporation, electro fusion, micro-injection, particle bombardment. DNA sequencing (Sanger and coulson method; maxam and Gilbert methods and Automated method)- Chromosomal walking, transposons, construction of genomic and cDNA libraries; molecular markers- RAPD, RFLP.	CLO 4	6
Transgenic Plants: Transgenic Plants: Definitions, types, benefits, public concern and future Genetically modified crops: High yielding, salt, draught, herbicide,disease resistant,Transgenic animals –for improved livestock production. Biosafety and ethical issues related to genetically modified organism.	CLO 3 CLO 5	6
rDNA in Medicine: rDNA in medicine: Recombinant DNA T herapy in Medicine, Vaccines, enzymes, blood factors, interferon, gene therapy.DNA fingerprinting and its application in forensic sciences, Application of Recombinant Technology- Gene mapping,Diagnosis of Molecular disease, Application in forensic medicine	CLO 5	6
Molecular Biology laboratory visit	CLO 4 CLO 5	1

Teaching Strategy

Lectures and discussion, Demonstration by video, self-study, Case studies, practice, and Group studies.

Assessment Strategy

Question & answer (QA), Assignment, Quiz, and Observation

Recommended Books

Primrose (2002): `` Principles of genetic manipulation, 6^th or later edition. Blackwell Science publication.
Keya Chaudhuri (2013): Recombinant DNA Technology, 1^st edition or later. The Energy and Resources institute (TERI)
A. Brown (1995):An introduction to Gene Cloning, 3^rd or later edition. Chapman and Hall publications.
Sardul Singh Sandu (2010): Recombinant DNA Technology 1^st edition or later. I. K. International pvt Ltd.
Monika Jain (2012): Recombinant DNA Techniques: A Textbook, 1^st Alpha Science international.
peter Snustad and Michael J. Simmons (2012): Principles of genetics, 6^th or later edition. John Wiley & Sons Inc
David Clark (2009): Molecular Biology, 2^nd Elsevier Academic press.

B.Sc. Bioinformatics Engineering