1. Online Counseling Resource YCMOU ELearning Drive… School of Architecture, Science and Technology Yashwantrao Chavan Maharashtra Open University, Nashik – 422222, India

2. SEP-SBI074-CP3-01 Introduction Programmes and Courses SEP-SBI074-CP3- U03

3. School of Science and Technology, Online Counseling Resource… Credits  Academic Inputs by Sonali Alkari Faculty YCMOU Nagpur Centre, Faculty LAD college P.G. D of Biotechnology Research officer Ankur Seeds Pvt Ltd sonalisa_alkari@yahoo.co.in Sonalisaal@rediffmail.com 3© 2008, YCMOU. All Rights Reserved.

4. School of Science and Technology, Online Counseling Resource… © 2008, YCMOU. All Rights Reserved.4 How to Use This Resource  Counselor at each study center should use this presentation to deliver lecture of 40-60 minutes during Face-To-Face counseling.  Discussion about students difficulties or tutorial with assignments should follow the lecture for about 40-60 minutes.  Handouts (with 6 slides on each A4 size page) of this presentation should be provided to each student.  Each student should discuss on the discussion forum all the terms which could not be understood. This will improve his writing skills and enhance knowledge level about topics, which shall be immensely useful for end exam.  Appear several times, for all the Self-Tests, available for this course.  Student can use handouts for last minutes preparation just before end exam.

5. School of Science and Technology, Online Counseling Resource… © 2008, YCMOU. All Rights Reserved.5 Learning Objectives  After studying this module, you should be able to: Describe bond length and bond angle. Discuss molecular geometry. Describe dihedral angle. Discuss Ramchandran plot

6. School of Science and Technology, Online Counseling Resource… Bonds and Bonds Angle  Molecular geometry or molecular structure is the three-dimensional arrangement of the atoms that constitute a molecule.  Molecules, are most often held together with Covalent bond involving single, double, and/or triple bonds.  where a "bond" is a shared pair of electrons.  The method of bonding between atoms is called ionic bonding and involves a positive cation and a negative anion. 6© 2008, YCMOU. All Rights Reserved.

7. School of Science and Technology, Online Counseling Resource…  Molecular geometries can be specified in terms of bond lengths, bond angles and torsional angles.  The bond length is defined to be the average distance between the centers of two atoms bonded together in any given molecule.  A bond angle is the angle formed by three atoms bonded together.  The angle between two planes is called their dihedral or torsion angle. Molecular Geometries-1 7© 2008, YCMOU. All Rights Reserved.

8. School of Science and Technology, Online Counseling Resource… Molecular Geometries-2  The position of each atom is determined by the nature of the chemical bonds by which it is connected to its neighboring atoms.  The molecular geometry can be described by the positions of these atoms in space, evoking bond lengths of two joined atoms, bond angles of three connected atoms, and torsion angles of three consecutive bonds.  Dihedral angles have been defined by the IUPAC for molecules, such as the nucleic acids (DNA and RNA) and for polysaccharides. 8© 2008, YCMOU. All Rights Reserved.

9. School of Science and Technology, Online Counseling Resource… Dihedral Angle-1  The dihedral angle of two planes can be seen by looking at the planes "edge on", i.e., along their line of intersection.  In the illustration, A and B are two separate planes lying perpendicular to another plane C. The dihedral angle equals zero between planes A and B and t  A and  B equal 90 degrees. 9© 2008, YCMOU. All Rights Reserved.

10. School of Science and Technology, Online Counseling Resource… Dihedral Angle-2  We can increase dihedral angle between A and B greater than zero. Plane B can be rotate around the line where plane B and C intersect while letting plane A remain perpendicular to C.  For example, let  B (the angle where plane B intersects plane C) equal 60 degrees  The dihedral angle (represented by the symbol ) between A and B now equals 30 degrees 10© 2008, YCMOU. All Rights Reserved.

11. School of Science and Technology, Online Counseling Resource… Dihedral Angles of Protein Molecules-1 11© 2008, YCMOU. All Rights Reserved.

12. School of Science and Technology, Online Counseling Resource… Dihedral Angles of Protein Molecules-2 The rigid peptide dihedral angle, ω (involving the backbone atoms C α -C'-N- C α ). The bond between C1 and N is always close to 180 degrees. The dihedral angles φ (involving the backbone atoms C'-N-C α -C'). psi ψ (involving the backbone atoms N-C α -C'-N 12© 2008, YCMOU. All Rights Reserved.

13. School of Science and Technology, Online Counseling Resource… Dihedral Angles of Protein Molecules-3  φ controls the C'-C' distance.  ψ controls the N-N distance.  ω controls the C α -C α distance.  The planarity of the peptide bond usually restricts ω to be 180° (the typical trans case) or 0° (the rare cis case).  The distance between the C α atoms in the trans and cis isomers is approximately 3.8 and 2.9 Å, respectively.  The cis isomer is mainly observed in Xaa-Pro peptide bonds (where Xaa is any amino acid). 13© 2008, YCMOU. All Rights Reserved.

14. School of Science and Technology, Online Counseling Resource… Dihedral Angles of Protein Molecules-4  These angles are the degrees of freedom of a protein, they control the protein's three dimensional structure.  They are restrained by geometry to allowed ranges typical for particular secondary structure elements, and represented in a Ramachandran plot.  The sidechain dihedral angles of proteins are denoted as χ 1 -χ 5, depending on the distance up the sidechain.  The χ 1 dihedral angle is defined by atoms N-C α -C β - C γ,.  The χ 2 dihedral angle is defined by atoms C α -C β -C γ - C δ, and so on. 14© 2008, YCMOU. All Rights Reserved.

15. School of Science and Technology, Online Counseling Resource… A Few Important Bond Lengths Peptide bond Average length Single bondAverage length Hydrogen bond Average (±30) Ca - C153 pmC - C154 pmO-H --- O-H280 pm C - N133 pmC - N148 pmN-H --- O=C290 pm N - Ca146 pmC - O143 pmO-H --- O=C280 pm 15© 2008, YCMOU. All Rights Reserved.

16. School of Science and Technology, Online Counseling Resource… Ramachandran Plot-1  A Ramachandran plot is also known as a Ramachandran map or a Ramachandran diagram.  It is developed by Gopalasamudram Naravana Ramachandran.  It is a way to visualize dihedral angles φ against ψ of amino acid residues in protein structure.  It shows the possible conformations of φ and ψ angles for a polypeptide.  The Ramachandran plot displays the psi and phi backbone conformational angles for each residue in a protein 16© 2008, YCMOU. All Rights Reserved.

17. School of Science and Technology, Online Counseling Resource… Ramachandran Plot-2 Figure shows a key to standard nomenclature for the atoms and the more important bond angles and dihedral angles along the polypeptide backbone. Atoms of the central residue are without subscripts. 17© 2008, YCMOU. All Rights Reserved.

18. School of Science and Technology, Online Counseling Resource… Ramachandran Plot-3 18© 2008, YCMOU. All Rights Reserved.

19. School of Science and Technology, Online Counseling Resource… Ramachandran Plot-4  The distance between two succession alpha carbon atoms in the backbone chain of a protein is approximately constant, as are the angles between the two bonds of such atoms.  The conformational angles show preferences for values that are expected based on simple energy considerations.  In a Ramachandran plot, the core or allowed regions are the areas in the plot show the preferred regions for psi/phi angle pairs for residues in a protein.  Mathematically, the Ramachandran plot is the visualization of a function f  [- ]* [- ] R +. 19© 2008, YCMOU. All Rights Reserved.

20. School of Science and Technology, Online Counseling Resource… Ramachandran Plot-5  The domain of this function is the torus. Hence, the conventional Ramachandran plot is a projection of the torus on the plane, resulting in a distorted view and the presence of discontinuities.  In a Ramachandran plot, the core or allowed regions are the areas in the plot show the preferred regions for psi/phi angle pairs for residues in a protein.  If the determination of protein structure is reliable, most pairs will be in the favored regions of the plot and only a few will be in "disallowed" regions. © 2008, YCMOU. All Rights Reserved.20

21. School of Science and Technology, Online Counseling Resource… Ramachandran Plot-6 A Ramachandran plot generated from the protein PCNA, a human DNA clamp protein that is composed of both beta sheets and alpha helices (PDB ID 1AXC). Points that lie on the axes indicate N- and C-terminall residues for each subunit.PCNA PDB-l 21© 2008, YCMOU. All Rights Reserved.

22. School of Science and Technology, Online Counseling Resource… What You Learn…  You have learnt :  Molecular geometry or molecular structure is the three-dimensional arrangement of the atoms that constitute a molecule.  Molecular geometries can be specified in terms of bond lengths, bond angles and torsional angles.  The Ramachandran plot displays the psi and phi backbone conformational angles for each residue in a protein 22© 2008, YCMOU. All Rights Reserved.

23. School of Science and Technology, Online Counseling Resource… Critical Thinking Questions 1.Describe in details molecular geometry of proteins. 2.Describe ramchandran plot. © 2008, YCMOU. All Rights Reserved.23

24. School of Science and Technology, Online Counseling Resource… Hints For Critical Thinking Question 1.Molecular geometry or molecular structure is the three-dimensional arrangement of the atoms that constitute a molecule. 2.The Ramachandran plot displays the psi and phi backbone conformational angles for each residue in a protein © 2008, YCMOU. All Rights Reserved.24

25. School of Science and Technology, Online Counseling Resource… Study Tips:1  Book1 Title: Molecular Cell Biology Author: Harvey Lodish, David Baltimore Publisher: W. H. Freeman and Company  Book2 Title: Principles of Biochemistry Author: AlbertL Lehninger Publisher: CBS Publishers & Distributors 25© 2008, YCMOU. All Rights Reserved.

26. School of Science and Technology, Online Counseling Resource… Study Tips:2  Book3 Title: Biochemistry Author: Lubert stryer Publishers: Freeman International  Book4 Title: Biochemistry Author: Keshav Trehan Publishers: Wiley Eastern 26© 2008, YCMOU. All Rights Reserved.

27. School of Science and Technology, Online Counseling Resource… Study Tips www.en.wikipedia.org Microsoft Encarta Encyclopedia http://en.wikipedia.org/wiki/ Wikipedia the free encyclopedia 27© 2008, YCMOU. All Rights Reserved.

28. School of Science and Technology, Online Counseling Resource… End of the Presentation Thank You 28© 2008, YCMOU. All Rights Reserved.