UČNI NAČRT PREDMETA / COURSE SYLLABUS Predmet: Course title: Molekularna biofizika Molceular biophysics Študijski program in stopnja Study programme and level Študijska smer Study field Letnik Academ ic year Semester Semester Univerzitetni študijski program 2.stopnje Fizika First cycle academic study program Physics Biofizika 2 tretji Biophysics 2 third Vrsta predmeta / Course type obvezni predmet /compulsory course Univerzitetna koda predmeta / University course code:??? Predavanj a Lectures Seminar Seminar Vaje Tutorial Klinične vaje work Druge oblike študija Samost. delo Individ. work 40 20 180 8 ECTS Nosilec predmeta / Lecturer: Prof. dr. Rudolf Podgornik, Prof. dr. Matej Praprotnik Jeziki / Languages: Predavanja / Lectures: Slovensko/Slovene Vaje / Tutorial: Slovensko/Slovene Pogoji za vključitev v delo oz. za opravljanje študijskih obveznosti: Prerequisits:! 1
Vpis v letnik študija. Pisni izpit (vmesni in zaključni) in opravljen seminar. Enrollment into the program. Written exam (midterm and final) and completed seminar. Vsebina: Content (Syllabus outline):! 2
Rentgensko in svetlobno sipanje: Opis in predstavitev osnovnih eksperimentov s sipanjem EM valovanja. Sipalna intenziteta pri rentgenskem in svetlobnem sipanju. Von Lauejeva in Braggova enačba. Cochran-Crick-Vand teorija sipanja na vijačnih molekulah in eksperiment Franklinove in Goslinga. Rentgensko sipanje na molekuli DNK in na molekuli kolagena. Peterlinova teorija svetlobnega sipanja na raztopini DNK in persistenčna dolžina DNK. Struktura DNK: Opis osnovnih strukturnih lastnosti DNK. Dvojna vijačnica: hidrofobne dušikove baze in nabita fosfatna hrbtenica DNK. Strukturni principi nastanka dvojne vijačnice in model Watsona in Cricka. Deformacija DNK in elastična energija DNK. Zlom kontinuumske slike elastičnosti DNK. Struktura kolagena: Opis osnovnih strukturnih lastnosti kolagena. Trojna vijačnica. Gelacija kolagena v vodni raztopini. Strukturni principi globularnih proteinov in rentgensko sipanje na proteinih. Statistična mehanika elastičnih verig: Elastična energija in statistična vsota. Izračun statistične vsote in kvantno-mehanska analogija. Kratky- Porod model črvaste verige (wormlike chain model). Entropijska in entalpijska elastičnost. Sipalna funkcija črvaste verige in Peterlinov približek. Makroskopska elastičnost dolgih črvastih verig. Siggia-Marko interpolacijska formula za elastično enačbo stanja. Eksperimenti s spektroskopijo na atomsko silo in persistenčna dolžina DNK. Makromolekularne interakcije: Fenomenologija interakcij med makromolekulami. Privlačne in odbojne interakcije - DLVO terija. Teorija elektrostatskih interakcij v približku srednjega polja, Poisson- X-ray and light scattering: description of the basic experiments with light scattering. Scattered intensity in X-ray and optical light scattering. Equations of von Laue and Bragg. Cochran-Crick- Vand theory of scattering on helices and the Franklin-Gosling experiment. X-ray scattering on DNA and collagen. Light scattering on DNA solutions and the DNA persistence length. Structure of DNA: The basic properties of DNA molecular structure. Double helix: nitrogen bases and the phosphate backbone. Structural principles of the double helix of Watson-Crick. Deformations of DNA and macroscopic theory of elasticity. Limits of validity of the continuum description. Filamentous proteins: Structure of collagen. Description of the basic structural properties of filamentous proteins. Triple helix. Gelation of collagen in aqueous solutions. Globular proteins: Structural principles of globular proteins and X-ray scattering from globular proteins. Principles of protein structure determination. Statistical mechanics of polymer chains: Eastic energy and the statistical integral. Analogy with quantum mechanics. The Kratky-Porod worm-like chain. Entropy and enthalpy elasticity. The scattering function fo the wormlike chain and the Peterlin approximation. Macroscopic elasticity of polymeric chains. Siggia-Marko interpolation formula and the elastic equation of state. Experiments with atomic force spectroscopy and the persistence length of DNA. Macromolecular interactions: The phenomenology of interactions between macromolecules. The attraction and repulsion within the DLVO theory. Meanfield theory of electrostatic interactions. The Poisson-Boltzmann! 3
Temeljni literatura in viri / Readings: - M. Rubinstein & R.H. Colby, Polymer Physics (Oxford, 2003, 1-96, 137-196, 253-294) - C.R. Cantor in P.R. Schimmel: Biophysical Chemistry (Freeman and Comp. 1980, 687-842). - V. Bloomfield, D.M. Crothers, I. Tinoco: Nucleic acids (University Science Books, 2000, 1-31, 79-103) - M. D. Frank Kamenetskii : Unraveling DNA (1997) - H. Schiessel Biophysics for Beginners: A Journey through the Cell Nucleus (2013) - R. Podgornik, Physics of DNA (book manuscript, 2008) Cilji in kompetence: Uvod v osnovne lastnosti bioloških makromolekul, DNK in proteinov kot tudi osnovno razumevanje konceptov in metod raziskovanja biofizike. Objectives and competences: Introduction to the basic properties of biological macromolecules, DNA and proteins as well as to the general concepts and methods in biophysical research. Predvideni študijski rezultati: Znanje in razumevanje Razumevanje strukture osnovnih bioloških makromolekul. Razumevanje osnovnih principov eksperimentalnih tehnik raziskovanja makromolekul. Statistična mehanika makromolekularnih interakcij. Uporaba Pridobljeno znanje omogoči osnovno razumevanje lastnosti biomaterialov DNK in proteinov. Refleksija Primer uporabe statistične mehanike, elastomehanike in elektromagnetnega polja na strukturi in interakcijah biomolekul. Prenosljive spretnosti - niso vezane le na en predmet Prehod od osnovnih principov teoretične strukturne biofizike k razumevanju osnovnih lastnosti molekularnih gradnikov bioloških sistemov. Intended learning outcomes: Knowledge and understanding: Understadning of the structure of fundamental biological macromolecules. Understanding of the basic principles of experimental techniques of macromolecular research. Statistical mechanics of macromolecular interctions. Application: The acquired knowledge enables the basic understanding of biomaterial properties DNA and proteins Reflection: An example of the application of statmech, elastomechanics and electrodynamics to the structure and interactions of biomolecules. Transferable skills: A transition from the fundamental principles of theoretical structural biophysics to the understanding of the basic properties of molecular building blocks of biological systems.! 4
Metode poučevanja in učenja: Predavanja, seminarji, naloge in konzultacije. Learning and teaching methods: Lectures, seminars, homeworks and consultations Načini ocenjevanja: Vmesen in končni pisni izpit, opravljen seminar in oddana domača naloga ocene: 1-5 (negativno), 6-10 (pozitivno) (po Statutu UL) Delež (v %) / Weight (in %) 50% 50% Assessment: Midterm and final written exam, a delivered seminar and a handed in homework grading: 1-5 (fail), 6-10 (pass) (according to the Statute of UL) Reference nosilca / Lecturer's references:! 5
prof. dr. R. Podgornik: 1. Roger H. French, V. Adrian Parsegian, Rudolf Podgornik et al., Long Range Interactions in Nanoscale Science, REVIEWS OF MODERN PHYSICS, 82, 1887 2010. 2. Rudolf Podgornik, D. Harries, J. DeRouchey, H. H. Strey, and V. A. Parsegian, Interactions in Macromolecular Complexes Used as Nonviral Vectors for Gene Delivery, in Gene Therapy: Therapeutic Mechanisms and Strategies, N. Smyth Templeton, Marcel Dekker, New York (2008), Third Edition. 3. Antonio Siber, Anze Losdorfer Bozic and Rudolf Podgornik, Energies and pressures in viruses: contribution of nonspecific electrostatic interactions, Phys. Chem. Chem. Phys., 2012, 14, 3746 3765. 4. Ali Naji, Matej Kanduč, Roland R. Netz and Rudolf Podgornik: Exotic Electrostatics: Unusual Features of Electrostatic Interactions between Macroions, Understanding Soft Condensed Matter via Modeling and Computation Eds. W.-B. Hu & A.-C. Shi, Series in Soft Condensed Matter Edited by David Andelman and Günter Reiter, World Scientific, Singapore (2010). 5. Anže Lošdorfer Božic, Antonio Šiber and Rudolf Podgornik, Statistical analysis of sizes and shapes of virus capsids and their resulting elastic properties, Journal of Biological Physics March 2013, Volume 39, Issue 2, pp 215-228 (2013). prof. dr. M. Praprotnik: 1. Matej Praprotnik, Luigi Delle Site, Kurt Kremer. Multiscale simulation of soft matter: From scale bridging to adaptive resolution. Annu. Rev. Phys. Chem. 59, 545-571, 2008. 2. Staš Bevc, Christoph Junghans, Kurt Kremer, Matej Praprotnik. Adaptive resolution simulation of salt solutions. New J. Phys. 15, 105007, 2013. 3. Julija Zavadlav, Manuel N. Melo, Siewert J. Marrink, Matej Praprotnik. Adaptive resolution simulation of an atomistic protein in MARTINI water. J. Chem. Phys. 140, 054114, 2014. 4. Julija Zavadlav, Manuel N. Melo, Ana V. Cunha, Alex H. de Vries, Siewert J. Marrink, Matej Praprotnik. Adaptive resolution simulation of MARTINI solvents. J. Chem. Theory Comput. 10, 2591-2598, 2014. 5. Aleksandar Popadić, Jens H. Walther, Petros Koumoutsakos, Matej Praprotnik. Continuum simulations of water flow in carbon nanotube membranes. New J. Phys. 16, 082001, 2014.! 6