September 2014 Biochemistry 3X03: Structure and Function of Macromolecules Contact Information Instructor Alba Guarné [email protected] Office: HSC-­‐4H32A Office Hours: by appointment only Teaching Assistant Ahmad Almawi [email protected] Course Website Course information will be posted on Avenue to Learn. If this course is not visible on your Avenue page, please contact Dr. Guarné Course Information Course Description We will discuss the potential and applicability of various structural biology techniques. From the structure of the DNA duplex in the early fifties to the design of sophisticated antibiotics, X-­‐ray crystallography has played an instrumental role in our current understanding of protein function at the molecular level. We will learn how crystal structures are solved and how the structural information is translated into functional information. Since proteins do not work on isolation, we will also learn how the structure and function of proteins can be studied within the context of macromolecular assemblies small angle X-­‐ray scattering (SAXS) techniques. Lectures will be combined with weekly journal club sessions and hands-­‐on projects on protein crystallization. Tuesday, Thursday and Friday 2:30-­‐3:20 pm BSB-­‐B154 Course Requirements Evaluation Test 1 (Oct 14) 35% Test 2 (December 2) 35% Journal Club (TBD) 20% Journal Club Evaluator (TDB) 5% Minute paper (Nov 7) 5% Lab project (optional) 10% (bonus) Grades will be posted on Avenue to Learn via the last five digits of your student number. By attending class the student is agreeing to this method of disclosure of grades. Course Schedule Sept 4 Introduction to the course, course organization and important dates Sept 5-­‐9-­‐11 X-­‐ray diffraction fundamentals 1 Sept 12 McPherson “Introduction to protein crystallization” Methods 2004, 34 Sept 16-­‐18 Crystallization techniques, crystal symmetry and data collection Sept 19 Garman “Cool crystals: macromolecular cryocryst. and radiation damage” Curr Opin Struct Biol 2003 Sept 23-­‐25 Data Collection and processing Sept 26 Dauter “Data collection Strategies” Acta Cryst 1999, D55 Sep30-­‐Oct2 Structure determination Oct 3 Liu et al “Multicrystal anomal diffraction for low-­‐resolution macromol. phasing” Acta Cryst 2011 D67 Oct 7-­‐9 Model Building, Refinement and structure validation Oct 10 Chen et al “MolProbity: all-­‐atom structure validation for macromol. crystallogr” Acta Cryst 2010 D66 Oct 14 TEST1 Oct 16 What to do without crystals? Oct 17 Lander et al “Go hybrid: EM, crystallography and beyond” Curr Opin Struct Biol 2012, 22 Oct 21-­‐23 Electron microscopy: a primer Oct 24 Jomaa et al “Understanding ribosome assembly: the structure of in vivo assembled inmature 30s subunits revealed by cryo-­‐electron microscopy” RNA 17 (4) Oct 28 Small angle X-­‐ray scattering: a primer Nov 4-­‐6 Sample preparation and data analysis Nov 7 BHT Meeting (minute paper) Nov 11-­‐13 Data Analysis: molecular weight determination Nov 14 Mylonas “Accuracy of MW determination of proteins in solution by SAXS” J Appl Cryst 2007 40 Nov 18-­‐20 Determination of oligomeric states and conformational changes Nov 21 Grant et al “SAXS as a complementary tool for high-­‐throughput struct studies” Biopolymers 2011, 95 Nov 25-­‐27 Combination of SAXS and X-­‐ray crystallography Nov 28 Q & A Dec 2 TEST 2 Work Submission Paper presentation should be submitted to the drop box on Avenue to Learn by 5 pm on the date the presentation. It is your responsibility to ensure that the final draft is submitted, as only one file can be uploaded. No additional time will be provided for technical difficulties. Individual questions from the evaluating team should be submitted to the TA by the end of the class. The minute paper from the BHT meeting should be handed in to the TA before leaving the meeting (and no later than 5 pm on November 7th). 2 Final Exam This course does NOT have a final exam. Late Work All work is due at 5 pm. Late penalties will be assessed at 10 % per day, including weekends. After 4 days, the assignment will not be accepted and a grade of 0 will be assigned. Missed Work If you are absent from the university for a minor medical reason, lasting fewer than 5 days, you may report your absence, one per term, without documentation, using the McMaster Student Absence Form (http://www.mcmaster.ca/msaf/). Absences for a long duration or for other reasons must be reported to the Associate Dean of Science office, with documentation, and relief may not necessarily be granted. After filling out the MSAF you must immediately contact your course instructor (normally within 2 working days) by email to learn what relief may be granted for the work you have missed and relevant details for submission or location of make-­‐up test. Please note that the MSAF may not be used for term work worth 30% or more, nor can it be used for the final exam. Remarking Work If you would like to have any work regraded, please adhere to the Department of Biochemistry and Biomedical Sciences Regrading Policy available here: http://fhs.mcmaster.ca/biochem/undergraduate/forms_and_procedures.html University Policies Academic Integrity You are expected to exhibit honesty and use ethical behaviour in all aspects of the learning process. Academic credentials you earn are rooted in principles of honesty and academic integrity. Academic dishonesty is to knowingly act or fail to act in a way that results or could result in unearned academic credit or advantage. This behaviour can result in serious consequences, e.g. the grade of zero on an assignment, loss of credit with a notation on the transcript (notation reads: “Grade of F assigned for academic dishonesty”), and/or suspension or expulsion from the university. It is your responsibility to understand what constitutes academic dishonesty. For information on the various types of academic dishonesty please refer to the Academic Integrity Policy, located at www.mcmaster.ca/academicintegrity. The following illustrates only three forms of academic dishonesty: 1. Plagiarism, e.g. the submission of work that is not one’s own or for which other credit had been obtained. 2. Improper collaboration in group work. 3. Copying or using unauthorized aids in tests and examinations. Course Online Content In this course we will be using (Avenue to Learn). Students should be aware that, when they access the electronic components of this course, private information such as first and last names, user 3 names for the McMaster email accounts, and program affiliation may become apparent to all other students in the same course. The available information is dependent on the technology used. Continuation in this course will be deemed consent to this disclosure. If you have questions or concerns about such disclosure, please discuss this with the course instructor. Student Accessibility Students who require academic accommodation must contact Student Accessibility Services (SAS) to make arrangements with a Program Coordinator. Academic accommodations must be arranged for each term of study. Student Accessibility Services can be contacted by phone 905-­‐525-­‐9140 ext. 28652 or e-­‐mail [email protected]. For further information, consult McMaster University’s Policy for Academic Accommodation of Students with Disabilities. Changes to the Course Outline The instructor and University reserve the right to modify elements of the course during the term. The University may change the dates and deadlines for any or all courses in extreme circumstances. If either type of modification becomes necessary, reasonable notice and communication with the students will be given with explanation and opportunity to comment on changes. It is the responsibility of students to check their McMaster email accounts and course websites weekly during the term and to note any changes. 4