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Molecular Biophysics Biomolecular Physics I urge you to visit different web site - to study manuals and - to look at structures To Study Cells: many different aspects The histones (water insoluble proteins with basic character, isoelectric point at pH 8.5) are in connections with DNA of inactive genes in the nucleus. What subjects the course Molecular Biophysics ought to have to cover? Opportunities in Biology for Physicists While the number of physicists doing biology is still relatively small, it is one of the fastest growing fields in the discipline. The American Physical Society, the professional organization for physicists, is putting on a conference for young scientists titled ''Opportunities in Biology for Physicists.'' Biology is increasingly drawing in scientists from many disciplines beyond physics, including mathematics, computer science, and engineering. Indeed, some of science's most vibrant areas reside at the boundaries of the old disciplines -proof, some say, that the old ways of conceptualizing problems are holding back progress. ''Ask not what physics can do for biology,'‘ said Hans Frauenfelder, one of the field's pioneers, ''Ask what biology can do for physics.'' . (Adaptation of famous phrase from J.F. Kennedy) ''Biology has provided physics with its new frontier,'‘ said Robert Laughlin, who won the 1998 Nobel prize in physics (quantum Hall effect) and now devotes himself to theoretical problems in biology. ''The whole problem is that we are living in the 21st century with these 19th century guilds,'' said John Hopfield, a Princeton scientist, one of the first physicists to move into biology. Fundamental aspects of Physics •Systems with a large number of atoms •Molecular crystals: Repetitive structures •Importance of fluctuations •Difference between forces in biomolecules and forces in solids and liquids •Use of quantum physics (photosynthesis) •Complexity and hierarchy of structures •Order-disorder phenomena. Ising model •Dissipative processes. Origin of life •Information storage and transfer •Production, storage and transfer of energy Biomolecular Physics Determination of the structure x-ray, NMR, EPR, hydrodynamics, ε, χ, computational methods Equilibrium properties Thermodynamics and statistical mechanics Cooperative phenomena Kinetic properties Relaxation, chemical kinetics Fluctuations Biomolecules & Biopolymers Constituents :H, C, N, O, P, S, Ca, Cu, Mg, Fe, Zn, Mn Biomolecules --Atoms --Quantum Physics SOLIDS: strong forces LIQUIDS: weak forces BIOMOLECULES: strong + weak forces Determination of the structure Geometrical distribution of atoms within molecules, crystals and liquids Methods •x-ray diffraction •NMR •Electron microscopy The scattering of electrons and x-rays depends on interatomic distances. •Neutron diffraction is used for H-atoms . •Tunneling microscopy •Computational methods •Microwave spectroscopy gives information on vibrational levels, moment of inertia -- atomic distances Biomolecules → Life The interaction between biomolecules determines the development and evolution of living systems. Biomolecules contain a large number of atoms (102 to 1010) The hierarchy of living things Organism >1020 Cell 1010 Organelle 105–106 Biomolecule 103–104 Molecule 10 –100 Atom 1 Atom Physics Quantum mechanics Molecule Vibration-rotations, Chirality, Radiationless transitions Macromolecule Conformations, Phase transitions, Phonons, Solitons, Catalysis Macromolecular complex Collective modes, Cooperative phenomena, Multiple excitation Cell Metabolism, Signaling, Trafficking, Individuality, Differentiation Energy levels Energy landscape Information + Construction Instruction how to assemble Parts Assembler Self reproducing Information content Information capacity : Nbd= bd b = basis d = digits System basis 4 letter words 26 Protein 20 Nucleic acid 4 digits 4 100 107 N 264 20100 410000000 bits 18.8 432 2·107 SOLIDS PROTEINS Periodic Non-periodic Disorder ↔ Random Strong forces in all directions Strong + weak Local vibrations Large motions Energy levels Energy landscape Enormous number of states Profound difference in dynamic behavior Elastic motions Plastic motions Time scale Enormous number Proteins •20 building blocks, amino acids •100-200 amino acids per protein (range from 15 to 3000) •L-amino acids only!!! •Large number of possible sequences 20100 to 20200 (this is practically infinity) •For each sequence large number of conformations 2200 about 1060 •Instantaneous vs. average quantities Proteins Enzymes Storage Transport Protection Hormones Structure Light harvesting Light production Functions Lysozyme, Ribonuclease, LADH, Carbonic anhydrase Ferritin, Ovalbumen, Caseine Hemoglobin, Myoglobin Hemocyanine Antibodies, Fibrinogen, TrombinHSP Insulin, Growth factor Collagen, α-Keratin Rhodopsin, reaction centers Luciferase Packing Density of Proteins Spheres 0.74 Cylinders 0.91 Solid 1.0 To function, proteins must be flexible.