Course Outline: CHEM 3FF3 BIO-ORGANIC CHEMISTRY

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Topics in bio-organic chemistry focusing on catalysis in chemistry and nature.

Three lectures, one lab (three hours); Term 2

Prerequisite:  One of CHEM 2BB3 or 2OB3.

Antirequisite: CHEM 3F03

 

Brief description (from Chemistry department web site):

Bio-Organic Chemistry:  Chemistry 3FF3 is a study of the organic chemistry of biological molecules, with a special emphasis on chemical principles. In this course, we will consider the structure, properties and reactivity of biological molecules. We will also study their synthesis and their roles in biological processes. We will cover NMR as a means of understanding and characterizing molecules.

Course Outline:

Title:                 Bio-organic Chemistry

Instructor:         Dr. A. Pedrech, ABB-417 email:adriennepedrech@hotmail.com

Content:           An extension of basic organic chemistry as applied to the mechanisms by which biologically relevant molecules react and exert their effects.

Detailed            CHEM 3FF3 is a study of chemical biology.  The course starts with a

Description:      study of the structures of small bio-molecules, e.g. carbohydrates, nucleotides, and amino acids.  The origins of these structures in the pre-biotic world are discussed.  Next, the formation of large bio-molecules (oligosaccharides, nucleic acids and amino acids) from these building blocks is described in terms of the RNA world hypothesis.  The chemistry behind both the formation and degradation of these compounds both in vitro and in vivo in the modern world will be covered through study of the properties of acetals, phosphate esters and amides. Principles of, and mechanisms for catalysis of biological reactions by chemical catalysts and enzymes will be compared and contrasted, with emphasis on learning about complex biological systems from simpler chemical ones. Chemists also learn from biology, and this will be illustrated by the design of simple chemical systems that mimic some of the features of the biological process, i.e. biomimetic chemistry.  Enzyme inhibition and its significance to the pharmaceutical industry will be discussed, as will applications of enzymes in organic synthesis. Other topics will include catalytic antibodies, co-factor chemistry and biochemistry, ribozymes, peptide nucleic acids and supramolecular chemistry, as time permits. Use of advanced methods for structure determination (NMR, X-ray crystallography) will be described, and illustrated in the lab.

 

Textbook:         Dobson, C.M., Gerrard, J.A. and Pratt, A.J.  “Foundations of Chemical Biology,” OUP, 2001. (Optional, available in bookstore)

Other               An organic chemistry textbook (e.g. Solomons)

Sources:           A biochemistry textbook (e.g. Garrett)

Buckberry, L. & Teesdale, P. “Essentials of Biological Chemistry” Wiley, Chichester. 2001: some examples are taken from this book.

Dugas, H. "Bio-organic Chemistry" Springer-Verlag, New York 3rd. Ed. 1996 (2nd. Ed, 1989 is OK): some examples are taken from this book.

Waldman, H. & Janning, P.  “Chemical Biology” Wiley, 2004: some examples taken from this book.

These will be available as needed on reserve in Thode library.

# of Lectures: 3 Lectures/week

# of Labs:         8 + 1 bonus

# of Exams:      1 midterm + 1 final  

Evaluation:        Assignments (2):           10%

Midterm Exam:             20%

Final Exam:                   50% (3 h, scheduled by registrar)

Laboratory:                  20% (15% write-ups, 5% performance mark)

Times:              Lectures:                      CNH/B107, MW 8:30 F 10:30

Office Hours:                T 10:00-12:30 & F 1:00-2:30 or by appointment

Laboratory:                  start week of Mon. Jan. 7, 2008

                                    ABB  302, 306 2:30-5:30 Mon

                                    ABB 306 2:30-5:30 Fri


Midterm test:                Fri. Feb. 29, 2008 at 7:00 pm

Assignments:                 (1) Out Feb. 6, due Feb. 13, 2008.

(2) Out Mar. 7, due Mar. 14, 2008.

NOTE:             LATE ASSIGNMENTS WILL NOT BE ACCEPTED! MEDICALS: for assignments, labs and midterm: must be filed at Associate Deans’ offices

Calculators:      The McMaster standard calculator (Casio fx991) will be allowed in examinations.

Web site:          http://www.chemistry.mcmaster.ca/courses/3f03/index.html

And then select 3FF3 (Course description, assignments, etc.)

Reserve:           Course notes will be available on reserve in Thode library, and will be updated approximately weekly (Friday), after the lectures.

Laboratory:      Labs begin on Monday, January 7th. Lockers will be assigned, general rules on safety will be discussed and the first lab will be completed. Eye protection in accordance with the McMaster eyewear policy is MANDATORY. This means goggles must be worn at all times in the lab.  Lab coats are recommended.  Open shoes are not permitted.  You must obey all safety instructions; failure to do so may result in loss of marks (a negative safety mark) and exclusion from the lab with a grade of zero.  The lab mark is composed of written reports (15%) and a technique mark (5%) assigned by the Teaching Assistants. Follow your TA’s instructions for submission of reports.  Late reports will be penalized at the rate of 20% for day one, and 50% for day 2, unless a medical is filed.

Academic         Academic dishonesty is not qualitatively different from other types of

Dishonesty:       dishonesty. It consists of misrepresentation by deception or by other fraudulent means. In an academic setting this may include any number of forms such as: copying or the use of unauthorized aids in tests, examinations and laboratory reports; plagiarism, i.e., the submission of work that is not one's own or for which previous credit has been obtained, unless the previously submitted work was presented as such to the instructor of the second course and has been acceptable for credit by the instructor of that course; aiding and abetting another student's dishonesty giving false information for the purposes of gaining admission or credit; giving false information for the purposes of obtaining deferred examinations or extension of deadlines; and/or forging or falsifying McMaster University documents.

Academic dishonesty can result in serious consequences, e.g. a grade of zero, loss of credit with a notation on the transcript, and/or suspension or expulsion from the University. It is YOUR responsibility to understand what constitutes academic dishonesty. For more information, see: http://www.mcmaster.ca/senate/academic/ac_integrity.htm

In CHEM 3FF3, ALL cases of academic dishonesty will be prosecuted to the maximum penalty allowed.

 

Detailed outline of lectures (subject to change):

 

Available on the website