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CHEM 4630

Biochemistry of Proteins

CHEM 4630 Biochemistry of Proteins (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.

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Announcements

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

Note also that Tuesday January 17 is the last day for adding courses and VW day is Friday March 16.

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Course Outline - 2012

Lectures:

• TR 11:30 AM – 12:45 PM
• 111 Armes Building

Instructor:

Joe O'Neil

Office:

• Room: 390 Parker
• Phone: 474-6697
• E-mail: joneil@cc.umanitoba.ca

Textbook:

none required

References:

• File of papers that can be borrowed from me.

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

• Introduction to Protein Structure
  by C. Branden & J. Tooze
  1^st or 2^nd edition
  Garland Publishing, Inc. 1991
  QP551.B7635
  (available in bookstore).

• 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 (available in bookstore).
  

• Copies of midterm and final examinations from previous years are are available on-line at:
  Online Examinations, and are listed below.
  Working through them 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

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Evaluation:

Mid-Term Test 1 (in-class) Thursday February 9	20%
Essay due Tuesday February 28	20%
Mid-Term Test 2 (in-class) Tuesday March 20	20%
Final Exam set by Student Records (3 hr.)	40%

Note:

• VW day is Friday, March 16.

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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 go to the Department of Chemistry general office (360 Parker Building), fill in an application form, and pay the $5.00 fee. You can also fill in the form that can be found on the Department of Chemistry www site at Undergraduate Program under "Links & Forms".

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Academic Dishonesty: Please visit the Faculty of Science web site Cheating, Plagiarism etc.

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Topics:

• Protein Primary Structure
• HPLC Chromatography, Capillary Electrophoresis, Immobilized Metal Chelate Chromatography
• Amino Acid Analysis, Protein Sequencing
• Hydrodynamics
• Mass Spectrometry and Proteomics
• Peptide Synthesis
• Applications of Peptide Methods, Circular Dichroism, Fluorescence
• 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
• Protein dynamics
• Protein folding in cells
• The Protein Folding Problem
  

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Essay Guideline:

• Select a research paper dealing with protein structure or function from a journal published in 2011/12. Note: This paper must be approved by me before you begin writing your essay. 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. 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, preferably typed double spaced. Neat handwriting is acceptable. Note that grammar and spelling will be worth 15% of the essay mark. Use Figures to explain difficult or complicated concepts. Please provide 1 photocopy of the research paper with your essay. It is also a good idea to keep a copy of your essay for yourself.

• 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

• *** This is under construction ***Please fill out the essay submission form here: Testform
  

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Protein Dynamics Movies:

The following two movies were taken 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 from the WWW site ( Dr. Onufriev's WWW site ) of Dr. Alexey Onufriev of the Departments of Computer Science and P hysics 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 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

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Useful Web Sites for CHEM 4630:

PDB WWW Server

SCOP: Structural Classification of Proteins

Database of Macromolecular Movements

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Return to the Chemistry Department Course Descriptions

Return to Joe O'Neil's Home Page

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http://home.cc.umanitoba.ca/~joneil/CHEM4630.Course.outline.htm

Maintained by J. O'Neil

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