CHEM 4630

Biochemistry of Proteins

CHEM 4630 Biochemistry of Proteins Cr. Hrs. 3 (Formerly 002.463) The structure and function of proteins, their physical and chemical properties and methods for studying them. Not to be held with CHEM 4631. Prerequisite: a 'C' or better in one of CHEM 2370, CHEM 2371 (002.237), MBIO 2370, MBIO 2371 (060.237), the former 002.235, or the former 060.235.

Announcements

Please read this important notice from the Faculty of Science: Registration Advisory.

Note also that Monday, January 21 is the last day for adding courses and VW day is Wednesday, March 20.

Students with disabilities should contact Student Accessibility Services (Email; Phone: 204-474-7423; Web) to facilitate the implementation of accommodations.

Please contact me if you wish to discuss the accommodations recommended by Student Accessibility Services.

Course Outline - 2019

Lectures:

TR 11:30 AM – 12:45 PM
527 Buller Building

Instructor:

Dr. Joe O'Neil

Office:

Room: 390 Parker
Phone: 474-6697
E-mail: Joe.ONeil@umanitoba.ca

Textbook:

none required

References:

Introduction to Protein Structure
by C. Branden & J. Tooze
1^st or 2^nd edition
Garland Publishing, Inc. 1991, 1999
QP551.B7635

Proteins: Structures and Molecular Properties
by Thomas E. Creighton (1^st or 2^nd edition)
W.H. Freeman & Co. 1984, 1989, 1993
QP551.C737

How Proteins Work
by Mike Williamson
Garland Science, 2012
QD431.W536

Structure and Mechanism in Protein Science
by Alan Fersht
W. H. Freeman and Company, 1999
QD431.25.S85F47

Biophysical Chemistry Part 2
by C.R. Cantor and & P.R. Schimmel
Freeman & Co.
QH345.C36.

Structure in Protein Chemistry
by Jack Kyte
Garland Publishing, Inc. 1995
QP551.K98

Course notes will be distributed by email to your University of Manitoba email address.

Copies of midterm and final examinations from previous years are available below.
Working through the exams will help prepare you for the examinations.

1993 Mid-Term	1993 Final
1994 Mid-Term	1994 Final
1995 Mid-Term	1995 Final
1996 Mid-Term	1996 Final
1997 Mid-Term	1997 Final
1998 Mid-Term	1998 Final
1999 Mid-Term	1999 Final
2000 Mid-Term 1	2000 Mid-Term 2	2000 Final
2001 Mid-Term 1	2001 Mid-Term 2	2001 Final
2002 Mid-Term 1	2002 Mid-Term 2	2002 Final
2003 Mid-Term	2003 Final
2004 Mid-Term 1	2004 Mid-Term 2	2004 Final
2005 Mid-Term 1	2005 Mid-Term 2	2005 Final
2006 Mid-Term 1	2006 Mid- Term 2	2006 Final
2007 Mid-Term 1	2007 Mid- Term 2	2007 Final
2008Sp Mid-Term 1	2008Sp Mid- Term 2	2008Sp Final
2008Fa Mid-Term 1	2008Fa Mid- Term 2	2008Fa Final
2010 Mid-Term 1	2010 Mid-Term 2	2010 Final
2012 Mid-Term 1	2012 Mid- Term 2	2012 Final
2013 Mid-Term 1	2013 Mid- Term 2	2013 Final
2014 Mid-Term 1	2014 Mid- Term 2	2014 Final
2015 Mid-Term 1	2015 Mid- Term 2	2015 Final
2016 Mid-Term 1	2016 Mid- Term 2	2016 Final
2017 Mid-Term 1	2017 Mid- Term 2	2017 Final
2018 Mid-Term 1	2018 Mid- Term 2	2018 Final
2019 Mid-Term 1	2019 Mid- Term 2	2019 Final

Evaluation:

Mid-Term Test 1 (in-class) Tuesday February 12	20%
Essay due Tuesday February 26	20%
Mid-Term Test 2 (in-class) Tuesday March 19	20%
Final Exam set by Student Records (3 hr.)	40%

LetterGrades.pdf

Note:

VW day is Wednesday, March 20.

Final Exam Review

Students in the Faculty of Science are permitted to review their final exams before the deadline for appealing final grades (Final Grade Appeal). If you wish to view your final exam please fill in and submit an electronic application form: Final Exam Viewing Form.

Academic Integrity: All faculty and students at the University of Manitoba are expected to act with academic integrity. For information on this topic please visit the Faculty of Science web site Cheating, Plagiarism etc. and read the appropriate sections of the Academic Calendar.

Topics:

Protein and Peptide Purification: HPLC Chromatography, Immobilized Metal Chelate Chromatography, Affinity Chromatography
Protein Primary Structure
Amino Acid Analysis, Protein Sequencing
Peptide Synthesis
Applications of Peptide Methods, Circular Dichroism, Fluorescence
Protein Structure Determination
Protein Secondary and Tertiary Structure
α-helix, β-sheet, turns, and others
Motifs and Domains
All α Proteins, All β Proteins, Green Fluorescent Protein, α+β Proteins
Membrane Proteins
Conformational changes: GPCR's, glycogen phosphorylase, hemoglobin, GTPases & myosin
Protein dynamics, protein design
Protein folding in cells
The Protein Folding Problem

Essay Guideline:

Select a research paper dealing with protein structure or function from a journal published in 2018/19. Note: This paper must be approved by me before you begin writing your essay. See the on-line research paper approval form below. Review articles are not acceptable. Suggested journals include Biochemistry, Journal of Biological Chemistry, Nature, Science, PNAS, Proteins: Structure, Function and Genetics, Protein Science but not Scientific American. In your essay describe and explain the research presented in the paper. Begin with a background section (Introduction) in which you familiarize your readers (e.g. 4^th year students) with the scientific problem tackled by the authors. Use references as appropriate but note that the purpose of the paper is not to do an exhaustive literature search. Explain the methods used by the authors to solve the problem and explain the interpretations of the data presented. Are other interpretations possible? Finally, describe questions that are still unanswered when the results of the paper are considered. Suggest experiments that might answer those questions but note that the paper is not to be a research proposal. Make sure you give credit to all sources of information in the text of your essay not just at the end. If you include a figure from a source you must write your own figure legend. In this exercise, direct quotes from other authors are generally inappropriate as your task is to explain the concepts in your own words.
The essay should be approximately 2,500 words in length. Please double-space your type. Note that grammar and spelling will be worth 15% of the essay mark. Use Figures to explain difficult or complicated concepts. Please submit a PDF electronic document (or MS Word) using the essay submission form below.
The penalty for late essays is 5%/week; the first penalty is applied 7 days after the deadline. Essays cannot be accepted after the end of classes.
Essay Marking Guideline
Please fill out the research paper approval form here: Research Paper Approval Form
The approval table can be viewed here: Research Paper Approval Table
Please submit your essay at the following link. Please use a simple name for your essay such as "YourName.pdf". Essay Submission Form

Protein Dynamics Movies:

The following two movies were taken with permission from the WWW site (Dr. Kneller's WWW Site) of Prof. Dr. G. Kneller, Centre de Biophysique Moleculaire, F-45071 Orleans. The first movie shows the motions of the 8 alpha-helices of Myoglobin during a 24 picosecond dynamics simulation:
Myoglobin Helices

The next movie shows the liquid-like dynamics of some of the side-chains in the protein over the same period of time. These are the motions that permit oxygen to diffuse from the external environment into the protein interior where it binds to the heme iron.
Myoglobin Side-Chains

The next movie was taken with permission from the WWW site ( Dr. Onufriev's WWW site ) of Dr. Alexey Onufriev of the Departments of Computer Science and Physics at Virginia Tech. It shows Myoglobin in a space-filling representation. In the interior are cavities big enough to hold an oxygen molecule. Over 15 ps, movements of side-chains changes the positions of the cavities permitting oxygen to diffuse through the protein to the heme. According to Dr. Onufriev, there is only one pathway that will permit oxygen to diffuse from outside the protein to the heme.
Myoglobin Cavity Dynamics

The next movies were taken with permission from the WWW site (Dr. Gerstein's WWW Site ) of Dr. Mark Gerstein of Yale University Departments of Molecular Biophysics and Biochemistry and Computer Science. They illustrates several views of the large conformational change that the Chaperonin large sub-unit GroEL underogoes between the open and closed states of the Anfinsen cage.

GroEL Spacefilling Representation
GroEL Ribbon Representation
GroEL Rotated