COURSE OUTLINE Biochemistry I (CHEM 271) 2011F GENERAL INFORMATION

3 credits, Fall 2011 Tues / Thurs, 8:45 10:00, Loyola campus, HB-130. Prof. Stephen H. Kawai, Faculty of Arts & Science, Department of Chemistry & Biochemistry. Office: SP 201.08 / phone: 848 2424 ext. 3331 Email: chem271kawai@yahoo.ca Office hours: TBA Course web page available on Moodle (www.myconcordia.ca) Strategic Learning, collaborative study sessions, accompany this class -attendance is voluntary but strongly encouraged. Strategic Learning leader: Jack Cheong SL Sessions: TBA SL Website: http://learning.concordia.ca

TEXTBOOKS:
Biochemistry, 7th edition Berg, Tymoczko & Stryer Chemistry 271, Laboratory & Tutorial Manual Recommended: Students Companion to Biochemistry, 7th edition (on reserve in the library will be used for Chem375 & Chem477) Required:

GENERAL COMMENTS:
Biochemistry I (271) is a fascinating but intense covering a great deal of material. It is assumed that you have a sound knowledge of introductory organic chemistry (notably mechanisms), as well as topics covered in general chemistry (acid-base chemistry, thermodynamics, kinetics). Molecular models may also come in handy. The course has been organized into a series of PowerPoint lectures according to topic (see Schedule below). You will notice that there are two classes described as Catch-up & Review. These lecture times will be used to ensure that all of the required material be covered prior to the exams. The PowerPoint presentations do not replace the text and you will miss out on material if you do not attend all of the classes. Labs and tutorial sessions have been divided into two alternating groups (No changing sections once they are assigned). Please check the list outside the lab (SP310) to find your assigned group. If you have a valid problem, please contact Mr. Mihai Ciortea (SP238 / tel: 848 2424 3363) LABS WILL ONLY BEGIN DURING THE SECOND WEEK OF CLASSES

GRADING:
The final grade of the course is based on the marks obtained in the examinations, assignments and the laboratory marks. The composition of the final grade is as follows: Midterm Exam: Tutorials/Labs Final Exam: 25 % 25 % 50 % DATE: TBA DATE: TBA

There are no make-up midterm exams. If you miss a midterm you lose 25 % of your final mark. If you have to miss the midterm because you are very ill, or there is a sudden death in your immediate family, you must submit written proof (doctors letter, death certificate) to me within one week of the midterm. You must pass the tutorial/lab part of the course. Your grade will be based on quizzes, assignments and reports which will be scaled to a mark out of 25. You must obtain 12.5/25 or you will fail the course with an R grade on your transcript. You cannot write a tutorial quiz if you miss your tutorial section, and you cannot hand in a lab report if you miss your lab; you lose these marks if you are absent. Grading scale: F: 0 49.9, D-: 50-52.9, D: 53-56.9, D+: 57-59.9, C-: 60-62.9, C: 63-66.9, C+: 6769.9, B-: 70-72.9, B: 73-76.9, B+: 77-79.9, A-: 80-84.9, A: 85-89.9, A+: 90 and greater.
In the event of extraordinary circumstances beyond the University's control, the content and/or evaluation scheme in this course is subject to change.

ACADEMIC CONDUCT CODE:

MANDATORY QUIZ AND SEMINAR As part of this course, you are required to i) attend a Chemistry and Biochemistry Departmental Seminar on the academic conduct code and the appropriate use of information sources and ii) pass the online quiz associated with this seminar (note: passing grade for the quiz is 100%). The aim of this seminar is to clarify the academic conduct code in terms of what practices will be considered unacceptable with regards to work submitted for grading in Chemistry and Biochemistry courses. You are only exempt from repeating the seminar and the quiz if you have done both in Fall 2006 or more recently,* otherwise you are required to repeat both this term. This short seminar (1 hour) will be held at the following times (note that late-comers will not be admitted): Date Monday, Sep.12 Tuesday, Sep. 13 Tuesday, Sep. 13 Wednesday, Sep. 14 Wednesday, Sep. 14 Thursday, Sep. 15 Friday, Sep. 16 Time 16:45-17:45 16:45-17:45 20:30-21:30 16:45-17:45 20:30-21:30 16:45-17:45 16:45-17:45 Place CC-320 CC-308 CC-301 CC-308 SP-S110 CC-308 CC-308

As space for each of the seminars is limited by the room size, please sign up to your preferred time. Sign up sheets are available inside SP 201.01 (Departmental office). If you do not complete this course requirement, your final grade for the course may be lowered by one full letter grade with an incomplete notation until such time as this requirement is completed. Please refer to the undergraduate calendar (section 16.3.6) for details on removal of an incomplete notation. * You are exempt if you can locate your ID in the pdf file located on the CHEM 101 Moodle site (for guest login, go to: http://moodle.concordia.ca/moodle, Arts and Science, Chemistry and Biochemistry, Specialized Chemistry Sites, CHEM 101, look under FAQ). PLAGIARISM AND OTHER FORMS OF ACADEMIC DISHONESTY: The academic code of conduct can be found in section 17.10 of the academic calendar (http://registrar.concordia.ca/calendar/pdf/sec17.pdf). Any form of unauthorized collaboration,

cheating, copying or plagiarism found in this course will be reported and the appropriate sanctions applied. The mandatory seminar is a clear and fair opportunity to learn what our faculty regards as academic misconduct. Failure to take part in this learning opportunity and thus ignorance of these regulations is no excuse and will not result in a reduced sanction in any case where academic misconduct is observed.

COURSE TOPICS & LECTURE SCHEDULE:

Sept. 6 Sept. 8 Lecture 1 : Intro & Amino Acids: (STRYER: Chap. 2) Structures of the 20 amino acids grouped according to type Lecture 2 : Acids & Bases: Review of acid-base equilibria, Henderson-Hasselbach equation, pKa and pI, buffers

Sept.13 Lecture 3 : Primary Structure: (Chap. 2) Peptide bonds, amino acid sequence, Ramachandran plots, Non-Covalent Interactions: Properties of water, Van der Walls interactions, electrostatic interactions, H-bonding, hydrophobic interactions Sept. 15 Lecture 4 : Secondary Structure: (Chap. 2) a-helices, b-sheets, b-turns, coiled coils, collagen structure Sept. 20 Lecture 5 : Tertiary & Quaternary Structure: (Chap. 2) Supersecondary structures, protein folding, ribonuclease and disulfide bridges, structure of myoglobin (Mb), quaternary structure, Sept. 22 Lecture 6 : Hemoglobin: (Chap. 7) Mb-hemoglobin (Hb), oxygen- bindng to heme, structure of Hb, cooperativity, Bohr effect Sept. 27 Lecture 7 : Hemoglobinopathies: (Chap. 7) Sickle-Cell anemia, other Hb variants Exploring Proteins: (Chap. 3) Protein purification and analysis, (centrifugation, chromatographic techniques, electrophoresis) Sept. 29 Lecture 8 : Enzymes & Enzyme Mechanisms: (Chap. 9) Cofactors, carbonic anhydrase, phosphodiester cleavage, proteases (thermolysin, aspartyl proteases, intro to serine proteases) Oct 4 Oct 6 Oct 11 Lecture 9 : Serine Proteases: (Chap. 9) Detailed mechanism, origins of specificity Lecture 10 : Enzyme Kinetics: (Chap. 8) Thermodynamics of catalysis, review of kinetics, enzyme kinetics: Michaelis-Menton equation, Lineweaver-Burke plots. Lecture 11 : Enzyme Inhibitors: (Chap. 8) Reversible and reversible inhibition (competitive, uncompetitive and noncompetitive), Lineweaver-Burke plots, penicillin, transitionstate analogues Lecture 12 : REVIEW MIDTERM EXAM Lecture 14 : Regulatory Strategies: (Chap. 10) Allosteric regulation (ATCase), isozymes, covalent modification, zymogen activation Lecture 15 : Carbohydrates: (Chap. 11) Structure, conformational properties & chemistry of monosaccharides Lecture 16 : Nucleosides/-tides: (see Chap. 1) overview of structure, Carbohydrates 2: (Chap. 11) Disaccharides, starches, glycoproteins

Oct 13 Oct 18 Oct 20 Oct 25 Oct 27

OCTOBER 30: last day to withdraw from the course.

Nov 1 Nov 3 Nov 8

Lecture 17 : Overview of Metabolism: (Chap. 15) review of thermodynamics, ATP as energy currency, metabolic pathways (motifs, reaction types) Lecture 18 : Glycolysis: (Chap. 16) reactions (enzymes & mechanisms) Lecture 19 : Glycolysis 2: (Chap. 16) Fermentation, entry of other sugars, regulation of glycolysis (muscle & liver) Lecture 20 : Gluconeogenesis: (Chap. 16) Reactions (enzymes & mechanisms), reciprocal regulation, Cori cycle Lecture 21 : Glycogen Metabolism: Chap. 21) Glycogen breakdown, glycogen phosphorylase (structure & mechanism), regulation (muscle & liver) Lecture 22 : Glycogen Metabolism 2: (Chap. 21) Hormonal control, glycogen synthesis & regulation (Protein phosphatase 1) Lecture 23 : Citric Acid Cycle: (Chap. 17) Reactions (enzymes & mechanisms) Lecture 24 : Electron Transport Chain : (Chap. 18) Mitochondria, review of electrochemistry, reactions (enzyme complexes & mechanisms) Lecture 25 : ATP Synthesis: (Chap 18) Compartmentalization, chemiosmotic hypothesis, ATP synthase (structure & mechanism) Lecture 26 : REVIEW Lecture 27 : Special Topics

Nov 10 Nov 15 Nov 17 Nov 22 Nov 24 Nov 29 Dec 1 Dec 5

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