UNIVERSITY OF MADRAS
B.Sc. DEGREE COURSE IN Physics
SEMESTER SYSTEM WITH CREDITS
(Effective from the Academic Year 2003-2004)

SYLLABUS

Semester VI - Application Oriented Subject - Molecular Biophysics

Duration of Examination: 3 hrs
Maximum Marks: 100
Credits: 4

Unit I

Cellular Basis of Life:

Structure and constituents of animal cell - plant cell and bacterial cell - its organelles - Molecular constituents of cell (elementary ideas) - Structure of viruses - Types.

Stereo Chemistry and conformation: Asymmetric carbon - Isomerism - Types - Constitution, Configuration and Conformation - Chirality - Fisher convention - L and D system - R-S system - Torsion angle - Newman Projection - Conformation of ethane and n-butane - Barrier to rotation.

Unit II

Structure and Conformation of Proteins:

Amino acids - Structure - Peptide bond - Rigid planar peptide - Cis and Trans configuration - Torsion angles and - Steric hindrance - Hardsphere approximation - contact criteria - Ramachandran (diagram) map - Allowed conformations for a pair of linked peptide units - (map for glycine and alanine residues) - classification of proteins : based on functions - based on structure - globular - fibrous - Levels of structural organization - Types of secondary structure - Helix - Sheet - turns - super secondary and domains.

Unit III

Sturcture and Function of Carbohydrates:

Classification - Simple Mono saccharides - Glyceraldehyde - Fisher projection formulae - L and D and R and S notation - other monosaccharides - Pyranose form - Stereio isomerism of sugars - conformation of pyramid rings - Disaccharides - Structure of Cellobiose - Maltose - Lactose - Sucrose - Types of linkages in polysaccharides - Ramachandran map for Disaccharides - Polysaccharides - Classification - Structural-Storage - Functions of cellulose - Amylase - Chitin - Glycogen - Complex carbohydrates - Functions of glycoproteins - Proteoglycons - Structure of peptidoglycon - Lectins.

Unit IV

Structure and Function of Nucleic Acids:

Nucleosides and nucleotides - structure of oligonucleotides - Structure of DNA - Watson and Crick model - base pairing and base stacking - Variations in DNA structure - Polymorphism - A, B and Z DNA - Structure of RNA and tRNA - Genetic code - Protein biosynthesis - Reverse transcription - Basic ideas of Genetic engineering.

Unit V

Elementary Programs for: (Fortran and C+)

Internal Parameters - Bond Length - bond angle - torsion angle - calculation - Programs - coordinate generation - Fractional to orthogonal - Given and, generation of coordinates - GNR MAP for dipeptide - disaccharide - helical parameters - helix generation - Energy calculation - Energy map for : Ethane, dipeptide and disaccharide.

Books for Study and Reference:

1. Principles of Biochemistry by A.L. Lehninger, D.L. Nelson and M.M. Cox, CBS Publishers, New Delhi, 1993.

2. Biochemistry by L. Stryer, W.H. Freeman and Co., Newyork 1997.

3. Conformation of Carbohydrates by V.S.R. Rao, P.K. Qasba, P.V. Balaji and R. Chandrasekaran, Harwood Academic Publishers, 1998.

4. Steno Chemistry of Carbohydrates J.F. Stoddart , Wiley Interscience 1971.

5. Complex Carbohydrates their Chemistry by N. Sharon, Biosynthesis and Functions, Addison-Wesley, London, 1975.

6. Bio active carbohydrates in Chemistry, Biochemistry and Biology by J.F. Kennedy and C.A. White, Ellis Harwood, New York, 1983.

7. Principles of Protein Structure by G. Schulz and R.H. Schirmer, Springer - Verlag, 1984.

8. Introduction to Protein Structure by C. Branden and J. Tooze, Gar land Publishing, 1991.

9. Proteins Structure and Molecular Properties Thomas E. Creighton, W.H. freeman and Company, New York, 1993.

10. Principles of Nucleic acid Structure, W. Saenger, Springer verlag, 1984.

11. Biophysics by W. Hoppe. et. al., Springer - Verlag, 1989.

12.An Introduction to X-ray Crystallography by M.M. Woolfson, Cambridge University Press, UK, 1980.

13. Biophysics by Vasantha Pattabhi and N. Gautham, Narosa Publishmg House, New Delhi, 2002.

14. Essentials of Biophysics by P. Narayanan, New Age International (P) Ltd. Publishers, New Delhi 2000.