IISER Pune semester II

8/20/2019 IISER Pune semester II

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Semester II – SPRING 2016

Details of courses

1 Course code BIO102

2 Course Title Introduction to Biology II: Cellular and Molecular Biology

3 Credits 3

4 Course Coordinator Sudha Rajamani (Coordinator), Nagaraj Balasubramanian

5 Nature of Course

(Please mark the appropriate

one)

L- lectures alone

L&T- Lectures & Tutorials

P-Lab sessions alone

L&P- Lectures& Lab sessions

6 Pre requisites Compulsory course

7 Objectives (goals, type of

students for whom useful,

outcome etc)

This course aims to introduce second semester BS-MS students to

several fundamental facts and concepts in biology. It is aimed to give a

insight on how organisms work at the single and multicellular levels. Thi

course, more than anything, hopes to spark your imagination and

thinking about how biological systems function and are regulated.

8 Course contents

(details of topics with no of

lectures for each)

Basic Biochemistry:

1. Water and pH (2)

2.

Proteins (3)3. Carbohydrates (3)

4. Nucleic acids (3)

5. Lipids (3)

Basic Cell Biology:

1. Prokaryots vs eukaryotes (introduction to microscopy and cellula

organization) (2)

2. Cell wall and cell membrane (2)

3. Cytoskeletal network, motor proteins, endomembrane system

and nucleus (4)

4. Interaction of cells with each and the environment (2)

5. The central dogma (2)

6. Cellular ageing (2)



9 Evaluation /assessment

(evaluation components

with weightage, Pl keepequal

weightage for end sem& mid

sem exams)

a. End-sem examination- 30

b. Mid-sem examination- 30

c. Quiz I and II - 20

d. Assignments- 20

10 Suggested readings

(with full list of authors,

publisher, year, edn etc.)

Text Book(s)

1) Voet, D., Voet, J.G (2010). Biochemistry, 4th

2) Harper’s Illustrated Biochemistry (2009), 28

edition, Wileyth

3) Campbell and Reece (2005). Biology, 7th edition, Pearson Publishing.

edition, McGraw Hill.

4) Raven, Johnson, Losos and Singer (2005). Biology, 7th edition, McGraw

Hill.

5) Alberts, Bray, Hopkin, Johnson, Lewis, Raff, Roberts and Walters

(2003). Essential cell biology, 2nd edition, Garland Science.

6) Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith

Roberts, Peter Walter (2007). Molecular Biology of the Cell, 5th

Edition,

Garland Science.

1 Course code BIO 122

2 Course Title Biology Lab II

3 Credits 3

4 Course Coordinator Neelesh Dahanukar (coordinator), Krishanpal Karmodiya, Nishad

Matange, Jeet Kalia, Sonam Mehrotra, Tressa Jacob

5 Nature of Course

(Please mark the appropriateone)

L- lectures alone

L&T- Lectures & TutorialsP-Lab sessions alone


6 Pre requisites None



outcome etc)

This practical will cover biochemical, genetic and molecular basis of life.

8 Course contents

(details of topics with no of

lectures for each)

1. Sugar estimation (Colorimetry)

2. Lipid estimation (Titrimetry)

3.

Amino acid and chlorophyll (paper chromatography)4. Protein estimation (spectrophotometry)

5. Enzyme assay and kinetics

6. Human genetic traits and blood grouping

7. Drosophila genetics

8. DNA isolation



9. Plasmid DNA isolation

10. Restriction digestion

11. Transformation

12. Protein expression

13. Polymerase Chain Reaction

14. Electrophoresis


(evaluation components with

weightage, Pl keep equal

weightage for end sem and

mid sem exams)

Evaluation will be done on a continuous basis based on the performance

of students and it will be reflected in the viva and lab-diary evaluations.

Students will have to write a lab-diary with detailed account of work

done in the lab. Two viva will be conducted for each student, one before

the mid-sem exam and one before the end-sem exam. A test will be

conducted at the end of the semester to evaluate basic understanding o

the topic.

1. Viva I and lab diary = 30%

2. Viva II and lab diary = 30%

3. Test = 40%




Text Book(s)

1.

Plummer, D.T. (1988) An introduction to practical biochemistry. 3rd

2. Primrose, S.B., Twyman, R.M. and Old, R. W. (1994) Principles of Gen

Manipulation. 5

edition. Tata McGraw-Hill, New Delhi.

th

3. Strickberger, M.W. (2005) Genetics. Edition 3. Prentice Hall:New

Delhi.

Edition. Blackwell Science, UK.

1 Course code CHM102

2 Course Title Chemical Principles II

3 Credits 3

4 Course Coordinator &

participating faculty(if any)

Dr. Aloke Das (Co-ordinator)

Dr. Arnab Mukherjee

Prof. K. N. Ganesh

5 Nature of Course


one)

L- lectures alone



L&P- Lectures& Lab sessions6 Pre requisites Core course



outcome etc)

The objective of this two-part course is to look at chemistry at the leve

of molecules and atoms, and make connections between the rule

governing such microscopic particles to what we observe in th

macroscopic world. In this second part, the focus is to introduce th



principles governing changes in matter.

Other goal is to introduce chemical principles to understand organi

reactions.

8 Course contents

(details of topics with no. of

lectures for each)

1.

What governs the changes in matter? (1 hr)

Thermodynamics in everyday life, System and surroundings,

macroscopic and microscopic systems

2. Probability, Distribution, and Equilibrium. (1 hr)

Probability – distribution of energy – equilibrium – Le Chatelier’s

principle from probability

3. Heat and Work (First Law of Thermodynamics) (1hr)

Macroscopic and microscopic understanding of temperature,

internal energy, heat and work, Conversion of internal energy into

work and heat

4. Entropy as the driving force of the change (Second law) (3 hrs)

Everything is about entropy --- Entropy as the arrow of time --

Entropy postulate – Microscopic definition of entropy --

Connection with thermodynamics – Thermodynamic postulates -

Maximization of Entropy – Boltzmann distribution -- Partition

Function – Average Property Measurement

5. Maximum Work and Engines (2 hrs)

Maximum Work – Carnot Cycle – Engine efficiency

6. Other thermodynamic potential (2 hrs)

Gibbs free energy, Helmholtz free energy, enthalpy, their

conversion, Maxwell relations – applications

7. Review on rates of chemical reactions: Rate of reaction, Order of

reaction, Molecularity of reaction, Basic laws of kinetics: Firstorder kinetics, second order kinetics, half life. (1 hr)

8. Experimental determination of reaction order and rate (1 hr)

9. Study of fast reactions: Flow process, Relaxation method. (1 hr

10. Simultaneous reactions: Opposing reactions, Consecutiv

reactions, Parallel reactions (2 hr)

11. Temperature dependence of reaction rate: Arrhenius equation (

hr)

12. Mechanism of chemical reactions: steady state approximation

and transition state theory (2 hr)13. Catalysis, enzyme catalysis (1 hr)

14. Unimolecular reaction: Lindemann mechanism (1 hr)

Introduction to Organic Chemistry



15. Carbon Compounds and Chemical Bonding: Valance bond theory

shapes of orbitals; Hybridization/LCAO, Molecular orbital theory

Hyperconjugation; Resonance; Tautomerism etc, (1 hr)

16. Conformations of acylic and cyclic systems: Deviations from bon

angles, cycloporane, cyclobutane, strain energy etc, High energ

materials from cyclic strained systems, propellanes, staffanes

cubanes etc. Natural product examples on cyclic small rings

(natural product drugs, thymine photodimerization, etc,

Renewable energy models from small strained cyclic system

(examples, photoirradiation of norbornadiene

tetramethyldioxetanes, light emitting examples etc

(3 hr)

17. Stereochemistry: Importance of stereochemistry, Chirality

Chirality in biomolecules (proteins, carbobydrates), drugs tha

interact with chiral biomolecules, assigning chirality

streochemical discriptors, R and S, E and Z notations, erythro

threo; syn, anti notations. Interaction of chiral molecules wit

light, optical activity. (3 hrs)

18. Organic Chemistry in day to day Life: For e.g. Cosmetics, Artificia

Sweeteners, Food additives, etc

(1 hr)


(evaluation components with



mid sem exams)

a. End-sem examination- (40)

b. Mid-sem examination- (30)

c. Quiz- (30)




Text Book(s)

1. Physical Chemistry: Peter Atkins and Julio de Paula

2. Chemical Principles: S.S. Zumdahl (2009) 6th

3. Organic chemistry by Jonathen Clayden, N. Greeves, S. Warren, P

Wothers Oxford University Press

edition, Houghton

Mifflin Company

4. Organic Chemistry by Solomon, John Wiley & Sons Inc; 2nd

5. Physical Chemistry, Donald A. McQuarrie and John D. Simon, Viv

Student Edition.

or 3 r

edition

1 Course code CHM121

2 Course Title Chemistry Lab I

3 Credits 3

4 Course Coordinator & Dr. Jeetender Chugh (Course Coordinator), Dr. B S M Rao, Dr. Pramod



participating faculty (if any) Pillai, Dr. M. Musthafa

5 Nature of Course


one)

L- lectures alone




√




outcome etc)

This course is designed to acquaint the students with the practice o

experimental physical chemistry. The goal of the labs is to provid

modest introductions to the core area of scientific activity, which woul

help the students to apply the principles of titrations, thermodynamics

kinetics and spectroscopy presented in the physical chemistry lectur

course, in some illustrative experiments. Students are encouraged to

understand the interconnection between the experimental foundatio

and the underlying theoretical principles and appreciate the limitation

inherent in both theoretical treatments and experimenta

measurements. Students will gain familiarity with a variety o

measurement techniques, which will help them to understand th

methods to develop the laboratory skills and the ability to wor

independently, instill good attitudes and habits towards knowing th

safe way of doing science.

8 Course contents

(details of topics with no. of

lectures for each)

1. Acid Base Titration using pH meter

2. Acid Base Titration using conductivity method

3. Depression in Freezing point

4.

Potentiometric titrations

5. Optical Activity by Polarimetry

6. Kinetic Study of Ester hydrolysis

7. UV - VIS Spectrophotometry

8.

Heat of Neutralization

9. Colligative properties of Solutions

10. Determine the radius from viscosity measurements


(Evaluation components with



The overall grade for the entire laboratory course is determined from th

continuous evaluation. REMEMBER there would not be any separat

examination for this course. The respective evaluation components wit

weightage are mentioned below:



mid sem exams)

Note Book Evaluation - 40 %

Daily Conduct - 10 %

Viva - 25 %

Exam - 25%




Lab Manual: The Laboratory manual is available from the chemistr

undergraduate laboratory from the respective instructor at the start o

the semester. This contains the details on the experiments including th

procedure, observation and the calculations of respective practical. If yo

find any errors or think something is not explained adequately or if you

feel there is a need for improvements, you can let the instructors know

Supplemental information may then be given to you and the manua

revised for the future use.

1 Course code MTH 102

2 Course Title Multivariable Calculus

3 Credits 3

4 Course Coordinator Diganta Borah

5 Nature of Course L & T


7 Objectives In this course, you will learn about the calculus of scalar/vecto

valued functions of several variables. You will study the generalizations o

the notions of continuity, differentiability and integration of real value

functions which you have learnt in MTH 101. You will get acquainted wit

the techniques of partial derivatives, integration along curves an

surfaces; and some of their applications.

There will be equal emphasis on theory and applications of the subjec

matter. The material covered in this course is very core to mathematic

and every science student must learn it.

8 Course contents 1. Differential Calculus: (14 lectures + 7 Tutorials approx..)

• Notion of distance and open sets in n-dimensional Euclidean

space R^n, Limits and continuity of functions from R^m to R^n

• Partial derivatives and directional derivatives, Gradient of scalar

fields, Divergence and curl of vector fields

• Total derivative, Chain rule

• Statements of Taylor’s theorem, implicit function theorem and



inverse function theorem

• Maxima and minima, Method of Lagrange multipliers for

extremum points with constraints

• Curves in R^3: Arclength and curvature

2. Integral Calculus: (12 lectures + 6 tutorials approx..)

•

Multiple integrals, Change of variables formula

• Line integrals, Statement of Green’s Theorem

• Surface integrals, Stoke’s Theorem and Divergence Theorem

• Applications to area and volume.

9 Evaluation /assessment a. End semester examination- 30%

b. Mid semester examination- 30%

c. Quizzes and homeworks- 40 %

10 Suggested readings •

The main textbook: Basic multivariable Calculus by J. Marsden, A

Tromba and A. Weinstein, Springer-Verlag 1993, Indian Reprin

2004.

• Other reference book: Calculus (Volume II) by Tom Apostol

(Second edition (2011), Wiley-India.)

1 Course code PHY102

2 Course Title World of Physics II - Waves and Matter

3 Credits 3


participating faculty

Bhas Bapat* and Sunil Mukhi

5 Nature of Course L&T- Lectures & Tutorials


7 Objectives To understand the fundamental aspects of wave phenomena an

properties of matter. This is part of an introduction to basics of world o

physics.

8 Course contents Oscillations in 1, 2, 3 dimensions, Damped and driven oscillations



Resonances. [7]

Oscillations of continuous string and Fourier analysis. [4]

Travelling waves, pulses and wave packets, phase and group velocity

reflection, refraction and transmission, [4]

Electromagnetic waves, polarisation, interference and diffraction. [4]

Properties of deformable media, Hooke's law, stress and strain. [4]

Torsion and bending of rods, deflections of rods. [5]

9 Evaluation /assessment • End-sem examination – 30%

• Mid-sem examination – 30%

• Quizzes/Assignments – 40%

10 Suggested readings 1. Waves, F. S. Crawford, (Berkeley Physics Course, Tata McGraw-

Hill Ltd, 2008)

2. Physics of Vibrations and Waves, H. J. Pain, (Wiley, 2005).

3. Vibrations and Waves, A. P. French, (MIT Press/CBS Publishers)

4.

Feynman Lectures on Physics Vol II (Addison-Wesley1963/Narosa 2011)

5. Mechanics (Lectures on Theoretical Physics Vol 1),

Arnold Sommerfeld (Levant Books, Kolkata 2006)

1 Course code PHY121

2 Course Title Physics Lab I

3 Credits 3


participating faculty

Surjeet Singh*, Arijit Bhattacharyay, Apratim Chatterji, Sulabha Kulkarn

5 Nature of Course P-Lab sessions alone



students for whom useful,outcome etc)

It’s a course on experimental learning where emphasis will be placed o

key learning tools including reproducibility in an experiment, variatioand control of experimental parameters, importance of observatio

data analysis, interpretation and case studies of over-analysis leading

misinterpretation of data. The instructors will also stress on th

importance of maintaining the lab journal.

8 Course contents Torsional pendulum, physical pendulum, Young's modulus, coefficient



friction, Euler's relation, Faraday's and Lenz's law of electromagne

induction, Biot-Savart's law, Stoke's law, numerical experiments.

9 Evaluation /assessment • End-sem examination: 30 %

• Mid-sem examination: 30 %

• Lab journal and periodic viva: 40 %

10 Suggested readings Text Book(s)

1. Handouts will be provided

2. Advanced Practical Physics: B.L. Worsnop and H.T. Flint, Asia

Publishing House

1 Course code IDC 102

2 Course Title Mathematical Methods

3 Credits 3

4 Course Coordinator Sudarshan Ananth

5 Nature of Course L- lectures alone




outcome etc)

Covers aspects of mathematical methods used in all the basic science

Should prove useful to all BS-MS students.

8 Course contents

(details of topics /sections

with no. of lectures for each)

1. Introduction to Vectors

2. Divergence, Gradient, Curl

3. Elements of Vector Calculus

4. Introduction to differential equations

5. Fourier Transforms and small oscillations

6. Sequences and Series

9 Evaluation /assessment a. End-sem examination- 35%

b.

Mid-sem examination- 35%

c. Assignments- 30%






Text Book(s)

1. Mathematical Methods in the Physical Sciences, Mary Boas,

Wiley, 3E, 2005

2. Mathematical methods for physicists, Arfken, Weber, and Harris

Elsevier Academic Press, 6E, 2005

1 Course code HSS 102

2 Course Title Critical Reading and Communication

3 Credits 02

4 Course Coordinators Aditi Deo, Pooja Sancheti*

5 Nature of Course L+ T (lectures and tutorials)

6 Prerequisites None



outcome etc)

1) To develop critical reading and thinking skills that will enable studen

to identify and evaluate arguments, evidence provided, steps of

reasoning, conclusions

2) To develop effective writing skills in terms of appropriate language,

organizational structure and sound content

3) To cultivate oral presentation skills applicable to a wide variety of

settings

4) To understand natural sciences as part of society and explore their

relationships with humanities and social sciences

8 Course contents The course involves extensive reading of assigned non-technical article

on a variety of topics related to science and society

1. History of science&technology

2.

Biographies of scientists

3. Interactions between sciences and humanities, particularly creative

art (e.g. science fiction; art-science creative collaborations)

4. Overlap of social sciences and natural sciences (e.g. economics and

evolutionary biology)

5. Social differences (e.g. class/ caste/ gender/ religion/ region/

language) and social institutions (e.g. nation/ politics/ religion) that

affect science

Students are expected to write short notes on a variety of topics and

participate in discussions and debates in the class room

9 Evaluation /assessment a. End-sem examination- 30%

b. Mid-sem examination- 30%

c.

Project work/term paper- 20%

d. Quiz - 10%

e. Assignment/s and participation- 10%



10 Suggested readings Assigned readings

IISER Pune semester II

Documents