CHAROTAR UNIVERSITY OF SCIENCE & TECHNOLOGYcharusat.ac.in/Download/PDPIAS_Syllabus.pdf · Syllabus. CHAROTAR UNIVERSITY ... Introduction to microbiology and brief history, the nature

CHAROTAR UNIVERSITY OF SCIENCE & TECHNOLOGY

(CHARUSAT)

P D PATEL INSTITUTE OF APPLIED SCIENCES

(FACULTY OF BIOLOGICAL SCIENCES)

M. Sc. Biotechnology / Microbiology /

Biochemistry Syllabus


2

PDPIAS M. Sc. Syllabus 2009‐10

DEPARTMENT OF BIOLOGICAL SCIENCES (M.Sc. BIOCHEMISTRY)

BC 701 GENERAL BIOCHEMISTRY AND MICROBIOLOGY

CREDIT: 27

A. Objective of the course

The objective of the course is to introduce students to the world of basic biochemistry and

microbiology.

To explore the cellular organization and functional aspect of microbial organisms along with

their nutritional requirement, and control of growth.

This course also covers the details of physical and chemical basis of life biomolecules

involved in life processes and laws of energy transfer.

B. Outline of the Course

Sr No. Title of Unit Minimum No. of hrs

1. Introduction To Microorganisms And Their Diversity 9h

2. Microbial Nutrition, Growth And Control Of Microorganisms 9h

3. Physical And Chemical Basis Of Life 9h

4. Biomolecules 9h

5. Bioenergetics 9h

Total hrs(Theory) 45 Total hrs(lab) 75

Seminar, library 15 Total 135hrs/Sem


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C. Detailed syllabus

Sr

No.

Title of Unit Minimum

No. of hrs

weightage

1. INTRODUCTION TO MICROORGANISMS AND THEIR

DIVERSITY

9h 20%

Introduction to microbiology and brief history, the nature of the

microbial world, diverse groups of prokaryotic and eukaryotic

microorganisms, morphology and ultrastructure of prokaryotic cells,

early earth, origin of basic biological molecules, the evolutionary

time scale, major events in the evolutionary time scale, evolution of

prokaryotes and eukaryotes, principles of microbial diversity,

morphological, cultural and genomic methods for studying microbial

diversity, exploitation of microbial diversity, microorganisms and

environment

2. MICROBIAL NUTRITION, GROWTH AND CONTROL OF

MICROORGANISMS

9h 20%

Principles of microbial nutrition, nutritional categories of

microorganisms, culture media for the cultivation of

microorganisms, batch fed-batch, and continuous growth,

synchronous growth, mathematical nature and expression of

microbial growth, measurement of microbial growth, microbial

growth curve, effect of environment on microbial growth, control of

microorganisms


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3. PHYSICAL AND CHEMICAL BASIS OF LIFE 9h 20%

Early earth, Structure of atoms, molecules and chemical bonds,

stabilizing interactions, properties of water, ionization of water,

weak acids and weak base, pH, buffers, buffers in biological

systems, functional groups and general biochemical reactions,

reaction kinetics, colligative properties, and their influence on life

processes.

4. BIOMOLECULES 9h 20%

Structure, classification and functions of carbohydrates, lipids,

proteins and low molecular weight biomolecules

5. BIOENERGETICS 9h 20%

Concepts of bioenergetics, thermodynamics of biological processes,

free energy and free energy change, biological oxidations, enzymes

involved in biological oxidations, redox potentials, relation between

standard reduction potentials and free energy change, high energy

phosphate compounds, energy charge, modes of energy generation,

electron transport system, theories of energy coupling, ATP

synthase, uncouplers of electron transport chain

D. Instructional Methods and Pedagogy

The topics will be discussed in interactive class room sessions using classical black-board teaching

to power-point presentations. Practical sessions will be conducted in a highly equipped laboratory.

Experiments will be performed and analyzed by students individually. Special interactive problem

solving sessions will be also conducted by respective faculty members on weekly bases. Course

materials will be provided to the students from various primary and secondary sources of

information. Unit tests will be conducted regularly as a part of continuous evaluation and

suggestions will be given to student in order to improve their performance.


5


E. Student Learning Outcomes / objectives

• The programme aims at providing students with the methodological concepts and tools needed to

acquire top-level skills in the field of biochemistry.

• Ensuring that students acquire an extensive and sound knowledge base for future research.

• At the end students would gain experience in how biologists design experiments and collect data,

and how this data are used in the formulation of theories; skills in observation, manipulation and

analysis.

F. Recommended Study Material

a) Text Books:

• Harper’s Biochemistry by Robert.KK.Murray 26/e, 2003.

• Fundamantals of Biochemistry by Debajyothi Das 11/e, 2002.

• Fundamentals of biochemistry- Life at the molecular level By: Voet, Voet and Pratt, 2nd edition,

2006.

• Prescott. Harley and Klien’s microbiology 7th ed 2008.

b) Reference books:

• Principles of Biochemistry by Albert Lehininger, 4/e, 2002.

• Human Biochemistry by James.M.Orten & Oho.W.Neuhaus, 10/e, 1983.

• Biochemistry by Lubert Stryer, 5/e, 2002.

• Brock biology of microorganism by MT Madigan and JM Martinko 11th ed, 2006.

c) Reading Materials, web materials with full citations:

d) Other materials (e.g. how to write journals, codes, software and Hardware, with specifics of what

is needed and how to obtain).


6


DEPARTMENT OF BIOLOGICAL SCIENCES (M.Sc. BIOTECHNOLOGY / MICROBIOLOGY)

BT701/MI701 GENERAL BIOCHEMISTRY AND MICROBIOLOGY

CREDIT: 27


The objective of the course is to introduce students to the world of basic biochemistry and

microbiology.

To explore the cellular organization and functional aspect of microbial organisms along with

their nutritional requirement, and control of growth.

This course also covers the details of physical and chemical basis of life biomolecules

involved in life processes and laws of energy transfer..


Sr No. Title of Unit Minimum No. of hrs

1. Introduction To Microorganisms And Their Diversity 9h

2. Microbial Nutrition, Growth And Control Of Microorganisms 9h

3. Physical And Chemical Basis Of Life 9h

4. Biomolecules 9h

5. Bioenergetics 9h




7



Sr

No.

Title of Unit Minimum

No. of hrs

weightage

1. INTRODUCTION TO MICROORGANISMS AND THEIR

DIVERSITY

9h 20%

Introduction to microbiology and brief history, the nature of the

microbial world, diverse groups of prokaryotic and eukaryotic

microorganisms, morphology and ultrastructure of prokaryotic cells,

early earth, origin of basic biological molecules, the evolutionary

time scale, major events in the evolutionary time scale, evolution of

prokaryotes and eukaryotes, principles of microbial diversity,

morphological, cultural and genomic methods for studying microbial

diversity, exploitation of microbial diversity, microorganisms and

environment

2. MICROBIAL NUTRITION, GROWTH AND CONTROL OF

MICROORGANISMS

9h 20%

Principles of microbial nutrition, nutritional categories of

microorganisms, culture media for the cultivation of microorganisms,

batch fed-batch, and continuous growth, synchronous growth,

mathematical nature and expression of microbial growth,

measurement of microbial growth, microbial growth curve, effect of

environment on microbial growth, control of microorganisms

3. PHYSICAL AND CHEMICAL BASIS OF LIFE 9h 20%

Early earth, Structure of atoms, molecules and chemical bonds,

stabilizing interactions, properties of water, ionization of water, weak

acids and weak base, pH, buffers, buffers in biological systems,

functional groups and general biochemical reactions, reaction

kinetics, colligative properties, and their influence on life processes.

4. BIOMOLECULES 9h 20%


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Structure, classification and functions of carbohydrates, lipids,

proteins and low molecular weight biomolecules

5. BIOENERGETICS 9h 20%

Concepts of bioenergetics, thermodynamics of biological processes,

free energy and free energy change, biological oxidations, enzymes

involved in biological oxidations, redox potentials, relation between

standard reduction potentials and free energy change, high energy

phosphate compounds, energy charge, modes of energy generation,

electron transport system, theories of energy coupling, ATP synthase,

uncouplers of electron transport chain




Experiments will be performed and analyzed by students individually. Special interactive problem

solving sessions will be also conducted by respective faculty members on weekly bases. Course

materials will be provided to the students from various primary and secondary sources of

information. Unit tests will be conducted regularly as a part of continuous evaluation and

suggestions will be given to student in order to improve their performance.

E. Student Learning Outcomes / objectives

• The programme aims at providing students with the methodological concepts and tools needed to

acquire top-level skills in the field of biochemistry.

• Ensuring that students acquire an extensive and sound knowledge base for future research.

• At the end students would gain experience in how biologists design experiments and collect data,

and how this data are used in the formulation of theories; skills in observation, manipulation and

analysis.


a) Text Books:

• Harper’s Biochemistry by Robert.KK.Murray 26/e, 2003.


9


• Fundamantals of Biochemistry by Debajyothi Das 11/e, 2002.

• Fundamentals of biochemistry- Life at the molecular level By: Voet, Voet and Pratt, 2nd edition,

2006.

• Prescott. Harley and Klien’s microbiology 7th ed 2008.

b) Reference books:

• Principles of Biochemistry by Albert Lehininger, 4/e, 2002.

• Human Biochemistry by James.M.Orten & Oho.W.Neuhaus, 10/e, 1983.

• Biochemistry by Lubert Stryer, 5/e, 2002.

• Brock biology of microorganism by MT Madigan and JM Martinko 11th ed, 2006.

c) Reading Materials, web materials with full citations:

d) Other materials (e.g. how to write, journals, calculators, codes, software and hardware, with

specifics of what is needed and how to obtain).


10


DEPARTMENT OF BIOLOGICAL SCIENCES (M.Sc. BIOTECHNOLOGY / MICROBIOLOGY / BIOCHEMISTRY)

BT702/MI702/BC702 - CELL BIOLOGY

CREDIT: 27


Describe the structure and functions of biological molecules

Differentiate between prokaryotes and eukaryotes, and their cellular components

Clarify cell organelles, surface structures and their functions

Explain mitosis and meiosis

Awareness against cancer and cancer causing agents.


Sr.No Title of the units Minimum no of hours

1 Introduction to the Cell, Cellular Organization and Function 9h

2 Structural Organization and Function of Intracellular Organelles 9h

3 Cell Signaling 9h

4 Cellular Communication 9h

5 Cell Division and Cell Cycle 9h




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Sr.No Title of the units Min of hours Weightage

Unit 1 INTRODUCTION TO THE CELL, CELLULAR ORGANIZATION AND FUNCTION

9h 20%

Evolution and history of the cell, structure and organization

of prokaryotic and eukaryotic cells, shape and size of cells,

molecular organization and functions of biomembranes, cell

permeability, transport across membranes, passive

diffusion, facilitated diffusion, osmosis, ion channels, ion

pumps, active transport and receptor mediated endocytosis,

exocytosis, mechanism of sorting and regulation of

intracellular transport, membrane excitability, electrical

properties of membranes, techniques and methods used to

cells

Unit 2 STRUCTURAL ORGANIZATION AND FUNCTION OF INTRACELLULAR ORGANELLES

9h 20%

Structure and functions of cell wall, nucleus, mitochondria,

golgy bodies, lysosomes, endoplasmic reticulum,

peroxisomes, plastids, vacuoles, chloroplast, cytoskeleton

and its role in motility, special cellular structures in

prokaryotes, cell movement, vesicular transport and

membrane transport.

Unit 3 CELL SINGNALING 9h 20% Hormones and their receptors, cell surface receptor,

characteristics of receptors, signaling through G-protein

coupled receptors, signal transduction pathways, secondary

messengers, regulation of signaling pathways, bacterial and


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plant two component signaling systems, bacterial

chemotaxis and quorum sensing

Unit 4 CELLULAR COMMUNICATION 9h 20% Regulation of hematopoeisis, general principles of cell

communication, cell adhesion and roles of different

adhesion molecules, gap junctions, extracellular matrix,

integrins, neurotransmission and its regulation

Unit 5 CELL DIVISION AND CELL CYCLE 9h 20%

Mitosis and meiosis, regulation of mitosis and meiosis, cell

cycle and its control, cell death, introduction to cancer




Experiments will be carried out by students individually. Special interactive problem solving

sessions will be also conducted by respective faculty members on weekly bases. Course materials

will be provided to the students from various primary and secondary sources of information. Unit

tests will be conducted regularly as a part of continuous evaluation and suggestions will be given to

student in order to improve their performance.

E. Student learning outcome/objective

By the end of this course, students will be able to:

Describe various theoretical models of the creative process.

Apply a variety of creativity enhancing modes in a team setting.

Understanding in their own style of learning and how this relates to leadership.

Identify and interact with creative pockets in the community to continue to re-energize their skills.


13



1. Essentials of Cell and Molecular Biology: by de Robertis E. D. P. and E. M. F. , Holt Saunder's

International Edition (new edition)

2. Essentials of Molecular Biology, 4th edn., by Malacinski GM (2003) Jones & Batiett, London.

(ISBN: 0-7637- 2133-6)

3. Instant Notes : Immunology, by Ladyard, Whelan and Fanger (new edition), Viva books

4. Molecular Biotechnology –Glick

5. The Physiology and Biochemistry of Prokaryotes, by White, D (2000) Oxford University Press,

Oxford

6. The Biochemistry of Cell Signalling- Ernst J. M. Helmreich ( Indian Edition)-2005 Oxford

University Press

7. Molecular biology of the Cell by Bruce Alberts.

8. Molecular biology of the Cell by Lodish .

9. Immunology by kuby.willey and sons.

10. Immunobiology by Janeway.

11. The Microbial Cell Cycle. Gloover & Hopwood


14



BT703/MI703/BC703 - BIOINSTRUMENTATION AND BIOSTATISTICS

CREDIT: 27


This course is designed to cover the tools and techniques of modern statistics with specific

applications to biomedical and clinical research. Both parametric and nonparametric analysis will be

presented. Descriptive statistics will be discussed although emphasis is on inferential statistics and

experimental design.

The objective of the course is to equip students with research skills necessary for a successful career

in biomedical engineering. With this in mind, the course has been structured to provide students

experience at: i) applying engineering tools and concepts learned in class and in other courses to

realistic biological problems, ii) working in different teams to complete research projects, and iii)

collecting and presenting data in a meaningful and professional manner



1 Microscopic, Histochemical, Immunotechniques And

Imaging Techniques

9h

2 Biophysical Methods- I 9h

3 Biophysical Methods- Ii 9h

4 Molecular Biology Methods 9h

5 Biostatistics 9h




15



Sr.No Title of the units Min of hours

Weightage

Unit 1 MICROSCOPIC, HISTOCHEMICAL,

IMMUNOTECHNIQUES AND IMAGING

TECHNIQUES

9h 20%

Principle and applications of light, phase contrast,

fluorescent microscopy, scanning electron

microscopy (SEM), transmission electron

microscopy (TEM), scanning tunneling microscopy

(STM), atomic force microscopy (AFM), confocal

microscopy, cytophotometry and flow cytometry,

ELISA, RIA, western blot, immunoprecipitation, in

situ localization in cells by FISH and GISH, imaging

techniques- plasma emission tomography (PET),

MRI, FMRI, CAT

Unit 2 BIOPHYSICAL METHODS- I 9h 20%

UV/Vis, fluorescence, circular dichroism (CD),

NMR, ESR, X-ray diffraction, light scattering, mass

spectrometry, centrifugation, atomic absorption

spectroscopy, surface plasma emission spectroscopy,

IR and Raman spectroscopy, single neutron

recording, patch clamp recording, ECG

Unit 3 BIOPHYSICAL METHODS- II 9h 20%

Chromatography, electrophoresis, measurement of

viscosity, osmosis and pH, electrochemical

techniques, radioisotope techniques, safety

guidelines for use of radioisotopes, tracer techniques

in biological research


16


Unit 4 MOLECULAR BIOLOGY METHODS 9h 20%

Isolation, purification and analysis of RNA, DNA

(genomic and plasmid), proteins, isoelectric focusing

(IEF), PCR, detection of post translational

modification of proteins, DNA sequencing methods,

methods for analysis of gene expression at RNA and

protein level, isolation, separation and analysis of

lipid molecules, microarrays, SAGE, RFLP, RAPD

and AFLP techniques, protein sequencing

Unit 5 BIOSTATISTICS 9h 20%

Populations, samples and inference, variables, data

representation, measures of central tendency and

dispersion, probability distributions (binomial,

poisson and normal), sampling distribution,

hypothesis testing, confidence interval, analysis of

variance (ANOVA), regression and correlation, t-

test, F-test, χ2 test, introduction to experimental

designs .


The topics will be discussed in interactive class room sessions using classical black-board teaching to

power-point presentations. Practical sessions will be conducted in a highly equipped laboratory.

Experiments will be carried out by students individually. Special interactive problem solving sessions will

be also conducted by respective faculty members on weekly bases. Course materials will be provided to the

students from various primary and secondary sources of information. Unit tests will be conducted regularly

as a part of continuous evaluation and suggestions will be given to student in order to improve their

performance.




17


Describe various theoretical models of the creative process.

Apply a variety of creativity enhancing modes in a team setting.

Understanding in their own style of learning and how this relates to leadership.

Identify and interact with creative pockets in the community to continue to re-energize their skills.


1. An Introduction to Genetic Engineering By Desmond S. T. Nicholl

2. Biochemical Calculations by Segel. I. R. - 1995 - John Wiley and Sons.

3. From Genes to Genomes: Concepts and Applications of DNA Technology by Jeremy W. Dale

(2007).

4. Gene and Genome Technology: Principles and Applications of Recombinant DNA and Genomics by

Sandy Primrose

5. Methods in Biotechnology, by Schmauder, H.P, Schweizer, M and Schewizer, L.M (2003), Taylor

and Francis Ltd., London (ISBN: 0-7484-0430-9)

6. Microbial Genomes - D. A. Realman and E. Strauss - 2000 - American Academy Of Microbiology

(http:// WWW. ASMUSA.ORG / ACASRC / ACA1 .HTM


8. Spectrometric Identification of Organic compounds by R M Silverstein and F X Webster, (2002)

9. Spectroscopy: D.R.Browning

10. Validation Standard Operating Procedures, 2nd edn., by Haider, SI (2006) CRC Press Taylor and

Francis Group, NY (ISBN: 0-8493-9529

11. Elements of biostatistics by S. Prasad. C. Edwards

12. Genetics as a tool in Microbiology

13. Biostatistics by Lewis A.E.

14. Statistics and experimental design by G. M. Clarke

15. Gene cloning and manipulation Christopher Howe

16. Basic Biotechnology by Colin Ratledge and Bjor

17. Methods in Biotechnology by Hans-peter-schmauder

18. Recombinant DNA Principles and Methodology by James J Greene & Venigalla B. Rao

19. Molecular Bio methods Handbook by Rapley & Walker

20. Analytical biochemistry by Wilson and walker.

21. Biochemical Methods by Pingoud A. etl.


18



BT704/MI704/BC704 MOLECULAR BIOLOGY

CREDIT: 27


To gain a thorough understanding of the basic principles of molecular biology. To understand

the tools of DNA technology. To be able to read and interpret scientific papers. To design

approaches to addressing questions in molecular biology and to interpret experimental data in

molecular biology.

To become proficient with a number of advanced and basic tools in molecular biology. To

interpret and design experiments.

To keep a laboratory notebook, to gain the confidence and skills necessary to be able to attempt

new laboratory procedures and troubleshoot their implementation. To be competitive for

employment in an introductory laboratory research position.



1 Nucleic Acid Structure and Genome Organization 9h

2 DNA Replication, Recomibination and Repair 9h

3 RNA Synthesis and Processing 9h

4 Protein Synthesis and Processing 9h

5 Control of Gene Expression 9h




19



Sr.No Title of the units Min of hours

BC704 MOLECULAR BIOLOGY

Unit 1 NUCLEIC ACID STRUCTURE AND GENOME

ORGANIZATION

9h 20%

DNA as a genetic material, DNA structure, DNA

topology, supercoiling, topoisomerases I and II, C-

value paradox, structure of mRNA, rRNA and

tRNA; packaging in viruses, prokaryotes and

eukaryotes, structure of chromatin and

chromosomes, DNA-protein interactions, interrupted

genes, gene families, unique and repetitive DNA,

transposons

Unit 2 DNA REPLICATION, RECOMIBINATION

AND REPAIR

9h 20%

DNA replication in DNA viruses, prokaryotes and

eukaryotes; enzymes involved and mechanism of

replication, replication models, regulation of

replication, role of telomerases, DNA synthesis in

retroviruses, mechanism of recombination and

repair, inhibitors of replication, extrachromosomal

replicons

Unit 3 RNA SYNTHESIS AND PROCESSING 9h 20%

Organization of transcriptional units, transcription in

prokaryotes and eukaryotes, transcription factors,

transcription activators and repressors, RNA

polymerases, formation of initiation complex and its


20


regulation, RNA processing, RNA editing, splicing,

post transcriptional modifications, RNA transport,

catalytic RNA

Unit 4 PROTEIN SYNTHESIS AND PROCESSING 9h 20%

Ribosomes, genetic code, initiation, initiation factors

and their regulation, elongation and elongation

factors, translational proof reading, post translational

modification of proteins, translational inhibitors, role

of tRNA, aminoacylation of tRNA, aminoacyl tRNA

synthetase

Unit 5 CONTROL OF GENE EXPRESSION 9h 20%

Regulation of phages (T4, T7 and λ), plant and

animal viruses; operon concept, regulation of

prokaryotic and eukaryotic gene expression,

chromatin remodeling, regulation of lac, ara, his and

trp operons, gene silencing, regulatory circuits, role

of chromatin in gene expression


The topics will be discussed in interactive class room sessions using classical black-board teaching to

power-point presentations. Practical sessions will be conducted in a highly equipped laboratory.

Experiments will be carried out by students individually. Special interactive problem solving sessions will

be also conducted by respective faculty members on weekly bases. Course materials will be provided to the

students from various primary and secondary sources of information. Unit tests will be conducted regularly

as a part of continuous evaluation and suggestions will be given to student in order to improve their

performance.


21




Describe various theoretical models of the creative process. Apply a variety of creativity enhancing modes in a team setting. Understanding their own personal style of learning and how this relates to leadership. Identify and interact with creative pockets in the community to continue to re-energize their skills.

A. Recommended Study Material

Reference books:

1. An introduction to human molecular genetics: mechanisms of inherited diseases

2. Jack j. Pasternak 2000.

3. Computational biology and genome informatics jason t. L. Wang , cathy 2003 world scientific

4. Genome transcriptome and proteome analysis by alain bernot, james2004 john wiley and sons

5. Methods in biotechnology and bioengineeringby s. P. Vyas, d.2002cbs publishers .

6. Molecular genetics of bacteria jeremy dale, simon f 2004 john wiley and sons.

7. Practical handbook of biochem and mol.bio geralal .jasmen.

8. Molecular biology by David Freifelder

9. A genetic switch by Mark Pthasne.

10. Microbial genetics by David Freifelder

11. Essential of molecular biology by David Freifelder

12. Principles of Genome analysis

13. S.B.Primose

14. Bacteriophages by John Douglas

15. Biotechnology an Introdoction by Susan R. Barnum.

16. Biotechnology Volumes by H.J. Rehm & Reed

17. Genes IX by lewin

18. Molecular biology of the gene by J.D.Watson.

19. Gene cloning and DNA analysis by T.A.Brown.

20. From genes to Clone

21. Molecular Biology Lab fax I & II : T. A. Brown



22 PDPIAS M. Sc. Syllabus 2009‐10

23. Molecular Genetics of Bacteria 4th Edition by Dale, J.W., Park, S.F. (2005) Wiley and Sons Inc

24. Intellectual Property Rights on Biotechnology, by Sigh, KC BCIL, New Delhi

25. Introduction to Modern Virology 4th Edition by Dimmock N J, Primrose S. B. 1994. Blackwell

Scientific Publications. Oxford.

26. DNA Science by David .A.Micholas.

Documents

CHAROTAR UNIVERSITY OF SCIENCE & TECHNOLOGYcharusat.ac.in/Download/PDPIAS_Syllabus.pdf · Syllabus. CHAROTAR UNIVERSITY ... Introduction to microbiology and brief history, the nature