CHEM/MBIO 2370 Biochemistry 2: Catabolism, Synthesis and Information Pathways--Syllabus

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1 An introductory course dealing with the basic metabolic processes that occur in living cells including the production and use of metabolic energy, the breakdown and synthesis of biomolecules, the synthesis of DNA, RNA and proteins; and the regulation of these processes. In order to register in this course, a grade of C or better is required for both Biochemistry 1 (2360) and Organic Chemistry 1 (2210). Instructors: Dr. P. Pelka <pelkap@cc.umanitoba.ca>, 427 Buller Bldg. Dr. P. C. Loewen <ploewen@ms.umanitoba.ca>, 410 Buller Bldg. Dr. E. Nichols <umnichoe@cc.umanitoba.ca>, 413 Parker Bldg. Marking: Mid-term exam: 25% Lab-Write ups: 15% Lab exam: 10% Final Exam: 50%

2 Exam Format: 1. The midterm exam will include short and long answer questions with no laboratory questions included. It is scheduled for the evening of TBA (a 2 hour exam). The exam will be written in rooms 100 and 200 Fletcher Argue and 231 and 235 Isbister. Specific room assignments will be announced in class and in an update to this page. 2. The lab exam worth 10% of the final grade is scheduled for Monday April from 7 to 8 PM. 3. The final exam will include short and long answer questions and will be scheduled by Student Records in mid-april as a three hour exam. 4. Copies of course notes and previous midterm and final examinations can be found on a web page at peter.loewenlabs.ca and click on the CHEM/MBIO button.

3 Texts: 1. Lehninger Principles of Biochemistry by Nelson and Cox, 5 th Edition. 2. Laboratory Manual, 2013 Labs: Students wanting an exemption must enquire at the Chemistry General Office, Room 350 Parker, and must register in B99. Laboratories start the week of Monday, January 14, The biochemistry laboratories are located on the 4th floor of the Parker Building. You must attend the laboratory for which you are registered.

4 Course Outline: GLYCOLYSIS and PENTOSE-PHOSPHATE PATHWAY (~3 Lectures) - details glucose degradation including structures and enzymes - alcoholic fermentation - PPP as an alternate path for glucose oxidation TCA CYCLE (~ 1 lecture) - detailed description of pyruvate dehydrogenase and the production of acetyl-s-coa - details of cycle including structures and enzymes ETC AND OXIDATIVE PHOSPHORYLATION (~2 Lectures) - description of the intermediates and structure - emphasis on electron flow and energy release - ATP synthesis - chemiosmotic mechanism BALANCING REACTIONS & REGULATION (~1 Lecture) - anaplerotic or balancing reactions - regulation of glycolysis and TCA cycle

5 FATTY ACID OXIDATION (~2 Lectures) - role of lipases and phospholipases - transport and the carnitine cycle - β-oxidation of saturated, straight-chain, even #C atoms - fate of propionyl-s-coa derived from odd #C atoms AMINO ACID OXIDATION & UREA PRODUCTION (~3 Lectures) - transamination, significance and mechanism - oxidative deamination - production of gln and its use N transporter in mammalian blood - urea cycle - amino acid degradation including asp, ala, glu and gln - three examples of degradation pathways: thr/gly/ser, tyr/phe and val

6 CARBOHYDRATE SYNTHESIS (~4 Lectures) - the overall reactions of photosynthesis - the light reactions and generation of ATP and NADPH - the dark reactions in both C-3 and C-4 plants - gluconeogenesis - life on acetate (glyoxylate cycle) - glycogen synthesis and regulation LIPID SYNTHESIS (~2 Lectures) - fatty acid synthesis of palmitic acid - introduction of unsaturations - triacylglycerol and membrane phospholipid synthesis - cholesterol metabolism N-FIXATION, AMINO ACID NUCLEOTIDE SYNTHESIS (~3 Lectures) - N-cycle and N-fixation - N assimilation involving glu and gln

7 N-FIXATION, AMINO ACID NUCLEOTIDE SYNTHESIS (cont d) - three examples of amino acid synthesis: ser/gly, val, asp/thr/ile - purine nucleotide synthesis by the de novo and salvage pathways - pyrimidine nucleotide synthesis - nucleotide kinases, pyrophosphorylases, CTP synthesis - deoxynucleotide synthesis including dtmp NUCLEIC ACID METABOLISM (~2 Lecture) - DNA replication including the semi-conservative model and enzymology - transcription and RNA polymerase c. PROTEIN SYNTHESIS (~1 Lecture) - mechanism of translation including initiation, elongation, termination - genetic code and the Wobble Hypothesis REGULATION (~1 Lecture) - control of enzyme activity including branched pathways - control in catabolic and anabolic operons using the lac and trp operons as examples