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9/6/11 Planned schedule for Biomolecular Structure 2011 Updates including additional reading and assignments will be posted on course website: http://people.chem.umass.edu/thompson/Courses/BioStruct/Fall2011 Syllabus (last updated 9/5/11) CHEM 627 Fall 2011 BIOMOLECULAR STRUCTURE TTh 9:30-10:45, LGRT 1234 Schedule This course is aimed at first and second year graduate students and advanced undergraduates interested in understanding the structures and mechanisms of macromolecular structures in biology. You will learn about the physical basis for these structures, their folding, stability, and interactions with other molecules, as well as the structural basis of catalytic mechanisms. You will gain a working knowledge of computer programs for manipulating and understanding macromolecular structures and be introduced to X-ray crystallography and NMR techniques used for structure determination. This is an important foundation for students whose research focuses on understanding proteins and nucleic acids, or synthesizing molecules to mimic or interact with them. INSTRUCTOR: Lynmarie Thompson, LGRT 403E, 545-0827, office hours by appointment REQUIRED TEXT: Protein Structure & Function, by Gregory Petsko & Dagmar Ringe. PREREQUISITE: One year of organic chemistry. Introductory biochemistry or permission of instructor. GRADING: 25% 25% 25% 25% Exam I Due 9:30 am Oct 13 Exam II Due 9:30 am Nov 22 Presentation Nov 22 - Dec 8 Homework/quizzes 9:30 am on due date/Unannounced Grading cutoffs (minimal): A = 90-100, B = 80-89, C = 70-79, D = 60-69, F = below 60 Grading may also be curved upward later (eg a score of 89 may earn an A). Images: Molecular machines involved in harnessing energy (top, proteins bound to membrane) and self-replication (proteins bound to DNA, right side). Adapted from Protein Data Bank poster (pdf 5MB). Date Tu 9/6 Th 9/8 Tu 9/13 Th 9/15 Tu 9/20 Th 9/22 Tu Th Tu Th Tu Th Tu Th Tu Th Tu Th Tu Th Tu Th Tu Th Tu Th Tu Th 9/27 9/29 10/4 10/6 10/11 10/13 10/18 10/20 10/25 10/27 11/1 11/3 11/8 11/10 11/15 11/17 11/22 11/24 11/29 12/1 12/6 12/8 Topic Amino acids & Primary structure Secondary structure Pymol Workshop I in ISB 325 (CRC) Tertiary structure Protein folding & stability Universe of structures; Quaternary structure Protein binding and flexibility X-ray crystallography Pymol Workshop II in ISB 325 (CRC) X-ray crystallography NO CLASS (UMass Monday) NMR Catalysis Nucleic acid structure Nucleic acid structure Membrane protein structures Controlling proteins Controlling proteins The “omic” era Deducing structure from sequence Pymol Workshop III: movie making Deducing function Student Presentations NO CLASS Student Presentations Student Presentations Student Presentations Student Presentations Reading* 1-0 to 1-4 1-5 to 1-8 1-9 to 1-11 1-12 to 1-14 1-15 to 1-21 Homework 1 due 1-22, 2-0 to 2-5 5-1 to 5-3 Exam 1 distributed Exam 1 due 2-6 to 2-16 3-0 to 3-10 3-11 to 3-20 4-0, 4-4; Exam 2 distributed 4-6&7, 4-14&15 Exam 2 due Rest of chapter 4 Happy Thanksgiving! Quiz *A number of papers from the primary literature will also be assigned. Readings are in Protein Structure & Function by Petsko & Ringe, unless otherwise noted. back to top Proteins = polymers of 20 amino acids, connected by peptide bonds Covalent bonds determine only primary structure = defined sequence of amino acids Protein functions -- what is the structural basis? Binding Catalysis Switching Structural What protein are you interested in? Genes and disease Branden & Tooze, Intro to Protein Structure Secondary, tertiary & quaternary structure due to noncovalent interactions (+ S-S) unique 3-dimensional structure Proteopedia Protein Data Bank Pymol 1 9/6/11 Amino acid sidechains pKa s Environment shifts How do proteins fold into unique 3D structures? ≈5 12.5 6.0 How do proteins carry out such a huge array of functions? 8.3 10.8 ≈9 Predominant forms at pH 7. 2 9/6/11 RNA world hypothesis Why use proteins to carry out chemistry of life? X-Pro Torsion angles: Chi angles specify sidechain conformation. Focus on phi & psi which specify backbone conformation. Berg: Biochemistry 3 9/6/11 Peptide backbone conformation torsion or dihedral angles: -180˚ → +180˚ Fixed: CO-N = peptide bond (ω) = planar typically =180˚ (trans) deviations ∆ω = -20 to +10 OK some X-Pro = 0˚ (cis) Variable: N-Cα torsion = phi (ϑ) Cα-CO torsion = psi (ψ) Beta turn Reverse turn Hairpin turn β:-130,+125 α:-60,-50 Berg: Biochemistry 4 9/6/11 Alpha Helix 3.6 residues/turn; COi to NHi+4 H bonds 1.5Å/residue -- compact Helical wheels, sidechains out Helical wheels: 3.6 residues per turn Repeats after 5 turns = 18 residues (blue offset to see repeat) 5