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

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OC-SBI074-CP1-03 Introduction Programmes and Courses SEP – SBI074-CPO1_U01

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School of Science and Technology, Online Counseling Resource… Credits Academic Inputs by Sonali Alkari MSc (Botany), P.G. D.C. Bio-Informatics sonalisa_alkari@yahoo.com

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School of Science and Technology, Online Counseling Resource… © 2007, 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.

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School of Science and Technology, Online Counseling Resource… © 2007, YCMOU. All Rights Reserved.5 Learning Objectives After studying this module, you should be able to: Describe Fiber diffraction. Discuss Diffraction Pattern of a [Alpha]- helix. Describe Bessel functions. Discuss continuous and Discontinuous helix and their diffraction pattern. Discuss Watson-Crick model of double- stranded DNA.DNA

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School of Science and Technology, Online Counseling Resource… Introduction - 1 Many biological macromolecules cannot crystallize. fibrous macromolecules are the macromolecules in which the axes of the long polymeric structures are parallel to each other. Fibers show helical symmetry rather than the three-dimensional symmetry taken on by crystals.

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School of Science and Technology, Online Counseling Resource… Introduction - 2 By analyzing the diffraction from orientated fibers one can deduce the helical symmetry of the molecule and in favorable cases one can deduce the structure Fiber diffraction data led to several important advances in the development of structural biology, e.g., the original models of the α-helix and the Watson- Crick model of double-stranded DNA.structural biologyα-helixDNA

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School of Science and Technology, Online Counseling Resource… Fiber Diffraction - 1 Fiber diffraction is a scattering technique.scattering In Fiber diffraction molecular structure is determined from scattering data (usually of X- rays or electrons). Fibers composed of a regular array of molecules distinguished by a single direction (the fiber axis). The resulting diffraction patterns show layer lines, each with Bessel function intensities.Bessel function In non-crystalline fibers (e.g. B-form of DNA) the long fibrous molecules are arranged parallel to each other but each molecule takes on a random orientation around the c-axis.

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School of Science and Technology, Online Counseling Resource… Fiber Diffraction - 2 The resulting diffraction pattern of non crystalline fiber (right of figure h1) is based on layer-lines, which reflect the periodic repeat of the fibrous molecule. The intensity along the layer-lines is continuous intensity can be calculated via a "Fourier- Bessel Transform" The Fourier-Bessel transform arises because of the cylindrical symmetry. figure h1

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School of Science and Technology, Online Counseling Resource… [Alpha]-helix - 1 Calculating the x-ray diffraction pattern from a helix was of central significance in the development of molecular biology. It was first described by Francis Crick in his doctoral thesis. He wished to understand the diffraction to be expected from an [alpha]-helix.

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School of Science and Technology, Online Counseling Resource… [Alpha]-helix - 2 Crick showed that the diffraction from a helix occurs along a series of equidistant lines rather than the Bragg spots obtains from a three dimensional crystal. These lines (known as layer-lines) are at right angles to the axis of the fiber and the scattering along each layer-line is made up from Bessel functions

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School of Science and Technology, Online Counseling Resource… Bessel Functions - 1 Bessel was a German astronomer who calculated accurately the orbits of the planets. Fourier used Bessel functions to calculate the flow of heat in cylindrical objects. In helical diffraction Bessel functions take the place of sines and cosines one uses for crystals. Bessel functions (written J n (x), where n is called the order and x the argument) are the form that waves take in situations of cylindrical symmetry. e.g. the waves you get if you throw a pebble into the middle of a pond).

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School of Science and Technology, Online Counseling Resource… Bessel Functions - 2 Bessel functions characteristically begin with a strong peak and then oscillate like a damped sine wave as x increases. The position of the first strong peak depends on the order n of the Bessel function. A Bessel function of order zero begins in the middle of the pattern. A Bessel function of order 10 does everything roughly twice as far out.

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School of Science and Technology, Online Counseling Resource… A Continuous Helix -1 In Fig h3 we show a continuous helix and its diffraction pattern. Crick showed that for a continuous helix the order of Bessel function n occurring on a certain layer line is the same as the layer line number l (counted from the middle of the diffraction pattern). Because the order of Bessel function increases with layer line number so does the position of the first strong peak. which then form the characteristic "helix cross". Fig h3

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School of Science and Technology, Online Counseling Resource… A Continuous Helix - 2 The position of the first strong peak is also inversely proportional to the radius of the helix. The spacing of the layer-lines is reciprocal to the pitch (P) of the helix. There is a reciprocal relationship between the layer line separation and the pitch- small separation large P, large separation small P.

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School of Science and Technology, Online Counseling Resource… Discontinuous Helix - 1 Real helicies are not continuous, rather they consist of repeating groups of atoms or molecules. The diffraction pattern of a discontinous helix (with 10 subunits in one turn) is shown in Fig h4. For a simple helix which repeats in one turn the fundamental layer line repeat is 1/P. Fig h4.

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School of Science and Technology, Online Counseling Resource… Discontinuous Helix - 2 The distance out along the meridian of the first meridional layer-line (not counting the origin) gives 1/p. The symmetry of a discontinuous helix can be defined in a number of ways: 1.how far one goes along the axis from one repeating subunit to the next in the macromolecule (the rise per residue p) 2.and by what angle you turn ([phi]) between one subunit and the next. The layer-lines can be grouped into two kinds: those which are strong on the meridian of the fiber diffraction pattern (meridional) and those which have no intensity on the meridian (non-meridional).

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School of Science and Technology, Online Counseling Resource… Watson-Crick Model - 1 DNA-B form is a simple helix which repeats in one turn. It has 10 base pairs per turn so that the angle turned ber base [phi] is 36°. The spacing between the bases is 3.4Å (i.e. p = 3.4 Å) and the pitch is ten times greater (i.e. P = 34Å. For low order layer lines the order of the Bessel function n which occurs on the l'th layer line is l. Because of their mass the phosphate groups are the dominant scatterers in a nucleic acids. Fig h5

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School of Science and Technology, Online Counseling Resource… Watson-Crick Model - 2 The phosphate oxygens show up as prominent white spheres in the atomic model (Fig h5). The spacing of the layer lines in Fig h1 corresponds to 34Å - the helix repeats in 34Å. In this case this is also the pitch P. From the helix cross in Rosalind Franklin's fiber diffraction patterns of DNA and Francis Crick's formula for the scattering of a helix, Jim Watson was able to glean the radius of the phosphate groups. These pieces of information went a long way towards defining the essential parameters of the Watson-Crick model.

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School of Science and Technology, Online Counseling Resource… Design of Fiber Diffraction Experiment In order to have interpretable data first order resolution or the highest resolution is needed. Highest resolution needed is achieved by using proper camera length and a beamstop size. The minimum beamstop size that is practical to use with the standard small- angle camera is 3.2 mm.

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School of Science and Technology, Online Counseling Resource… Software for Fiber Diffraction WCENWCEN is a preliminary fiber diffraction data processing program. The main features of the program include displaying fiber diffraction images, determining diffraction parameters, correcting systematic effects and mapping diffraction data into reciprocal space RADFN *RADFN is an angular deconvolution program designed for measuring intensity data from partially oriented specimens to the highest possible resolution FX-PLOR *FX-PLOR is a fiber diffraction extension to Axel Brunger's molecular dynamics program for atomic model refinement, X-PLOR CCP13CCP13 (Collaborative Computational Project 13) is a project located in the CCLRC Daresbury Laboratory, U.K. that develops software for use in fibre diffraction studies

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School of Science and Technology, Online Counseling Resource… What You Learn… You have learnt : What is fiber diffraction Diffraction pattern of alpha helix Diffraction pattern of continuous and discontinuous helix Bessel functions

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School of Science and Technology, Online Counseling Resource… Critical Thinking Questions 1.How to detrmine molecular structure of a non crystalline molecule. 2.State the difference between continuous and non-continuous helix and its diffraction pattern. © 2007, YCMOU. All Rights Reserved.23

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School of Science and Technology, Online Counseling Resource… Hints For Critical Thinking Question 1.Describe Fiber diffraction. 2.Discuss continuous and Discontinuous helix and their diffraction pattern. © 2007, YCMOU. All Rights Reserved.24

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School of Science and Technology, Online Counseling Resource… Study Tips Book Title:Fiber Diffraction — an introductionFiber Diffraction Author:Prof. K.C. Holmes www.en.wikipedia.org Microsoft Encarta Encyclopedia

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School of Science and Technology, Online Counseling Resource… End of the Presentation Thank You !

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

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

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