Download doc BIOL210syllabus

Biology 201
Cell Biology and Metabolism
Profs. G. Brown, G.Brouhard and R. Levine
3 hours lecture per week
Conferences: run by the teaching assistant, Lydiane Gaborieux. These consist of a review
lecture material, and an opportunity to answer questions. They will be held on Mondays
and Tuesdays throughout the term, beginning in week 2 (January 11) from 3:30 to 5:00
pm in room W2/3B Stewart
G. Brown Info:
[email protected]
Phone 514 398 6426
Room N5/12, Stewart Building
Web page
Via WebCT
Course info: syllabus, mid-term and final exam dates, mid-term exam room assignments,
mid-term exam results
Readings for each lecture
Slides and voice recordings of each lecture
Grading Scheme
Mid-term examination: 25 multiple choice questions.
Counts for 25% of the final grade
Will be held on March 1, 6:30 to 8:00, room assignments to be announced
Absence because of illness: final counts for 100% of final grade
Final examination: 75 multiple choice questions; 25 on material from before the mid-term
and 50 from material given after the mid-term. Date, time to be announced.
Major topics, Jan. 4 – Feb. 15 (G. Brown)
 Energy and biological systems
 General aspects of metabolism
 Glycolysis and gluconeogenesis
 Citric acid cycle
 Membrane transport processes
 Oxidative phosphorylation
 Photosynthesis
 Protein translocation and targeting
 Vesicle mediated protein sorting
Readings:
Readings will be taken from Molecular Cell Biology, by Lodish et al., 6th edition and
from Biochemistry, by Berg et al., 5th edition. There is no need to purchase the Berg et
al. text. An activation code will be provided to students that will allow access to the
appropriate chapters on line. Further information will be provided in class and as
announcements on webCT.
The readings are intended to prepare you for lecture and to
clarify material covered in lecture. Examination questions for
Part I of this course will be based only on material covered in
lecture. You will not be tested on material in the readings that
was not covered in lecture.
Tentative lecture schedule and readings.
Lecture 1. Orientation. January 4
 An overview of metabolism from the standpoint of Escherichia coli.
 Enzymes and the specificity of metabolic reactions
 Chemical equilibrium
 Predicting the direction of a reaction
Readings: Lodish et al., pp. 49-51; Berg et al., pp. 373-375.
Lecture 2. Energy in Biological Systems I. January 6.
 Equilibrium, free energy and ΔG
 The standard free energy change, ΔG0’
 Relationship between ΔG0’ and Keq
 Additivity of standard free energy values
Readings: Lodish et al., pp.54-57.
Lecture 3. Energy in Biological Systems II. January 8.
 Enzymes, and activation energies and rates of reaction
 Hydrolysis of ATP to ADP and phosphate drives energy consuming processes
 Oxidation, reduction, respiration, oxidative phosphorylation
 Electron (and proton) carrier molecules
 Energy capture in proton gradients
Readings: Lodish et al., pp. 57 – 61; Berg et al. pp. 375-383.
Lecture 4. Glycolyis. January 11.
 Glycolysis in the grand scheme of metabolism
 Conversion of glucose to pyruvate takes place in several stages
Stage 1: Conversion of glucose to fructose 1,6 bisphosphate
Stage 2: Conversion of a 6C, 2P carbohydrate to two 3C, 1P carbohydrates
Stage 3: Conversion of GAL3P to pyruvate; formation of NADH and ATP.
 Regeneration of NAD+ from NADH
Readings: Berg et al., pp. 425-443.
Lecture 5. Regulation of glycolysis and gluconeogenesis. January 13.
 Allosteric regulation of glycolysis
 Pyruvate to glucose: bypassing the “irreversible” steps of glycolysis
 Reciprocal regulation of glycolysis and gluconeogenesis
Readings: Berg et al., pp. 443-464.
Lecture 6. Glycogen metabolism, pyruvate dehydrogenase. January 15.
 Glucose metabolism during exercise
 Hormonal regulation of the metabolism of glycogen, a storage carbohydrate
 Metabolic fates of pyruvate
 The pyruvate dehydrogenase complex
Readings: Berg et al., pp. 465-472; Lodish et al., pp. 647-649.
Lecture 7. The tricarboxylic acid (TCA) cycle. January 18.
 TCA cycle reactions and energetics
Readings: Berg et al., pp. 473-478.
Lecture 8. Regulation of the TCA cycle. January 20.
 The central role of the TCA cycle in metabolism
 Allosteric regulation of the TCA cycle
Readings: Berg et al., pp. 478-482.
Lecture 9. Metabolism and physiology. January 22.
 The oxidation of fatty acids
 Metabolism and real life: athletics, marathons, diets
 General aspects of membrane transport
Readings: Lodish et al., pp. 489-493; Lodish et al., 438-440
Lecture 10. Membrane transport. January 25.
 Facilitated diffusion via carrier proteins
 Movement of ions across membranes
 Ion specific channels
 ATP powered pumps: the plasma membrane Na+/K+ ATPase
 ATP powered pumps: ABC transporters
Readings: Lodish et al., pp. 441-459.
Lecture 11. Biological redox reactions. January 27.
 The respiratory chain and the TCA cycle
 Redox couples: electron donor acceptor pairs
 An electron transfer chain: successive and oxidation of redox couples
 Standard redox potentials: ranking the reducing power of redox couples
Readings: Lodish et al., pp. 315-317. Berg et al., pp. 491-498.
Lecture 12.Oxidative phosphorylation I. January 29.
 Redox carriers, redox potential & ΔG in the respiratory (electron transfer) chain
 Electron transfer occurs through redox carriers in large membrane multi-protein
complexes
 Mobile electron carriers transfer electrons between complexes
 Proton pumping complexes
 Structure and reactions of complexes I, II, III and IV
Readings: Lodish et al. 493-502; Berg et al., pp. 498-507.
Lecture 13. Oxidative phosphorylation II. February 1.
 Peter Mitchell and the chemiosmotic theory
 Structure of the mitochondrial ATP synthase
 How proton translocation drives ATP synthesis
 The ATP/ADP translocase
Lodish et al., pp. 503-510; Berg et al., pp. 507-513; 515-523.
Lecture 14. Photosynthesis. February 3.
 Respiration vs photosynthesis
 How light can drive an energetically unfavourable reaction
 The two photosystems and photosynthetic electron transport
 CO2 fixation: the dark reactions of the Calvin cycle
Lodish et al., pp. 511-529.
Lecture 15. Protein targeting to the endoplasmic reticulum I. February 5.
 How proteins are targeted to specific locations in the cell
 An overview of the secretory pathway
 Protein translocation across the ER
Lodish et al., pp. 533-542.
Lecture 16. Protein targeting to the endoplasmic reticulum II. February 8.
 Insertion of proteins into the ER membrane
 Type II and III membrane proteins
 Postranslational protein modification in the ER
Lodish et al., pp. 542-552.
Lecture 17. Protein targeting: mitochondria, chloroplasts, nuclei. February 10.
 Protein import into the mitochondrial matrix
 Protein import into the inner membrane, outer membrane and intermembrane space
 Protein import into peroxisomes and nuclei
Lodish et al., pp. 557-575.
Lecture 18. Vesicular transport I. February 12.
 Vesicle-mediated transport of proteins from the ER
 Processes and factors in vesicle budding
 Vesicle fusion
 Protein trafficking between the ER and Golgi
Lodish et al., pp. 579-592.
Lecture 19. Vesicular transport II. February 15.
 Oligosaccharide processing, “quality control” mechanisms, and protein exit from the
ER
 Removal of mis-sorted ER proteins from the cis-Golgi
 Sorting of proteins to the lysosome
 Receptor-mediated endocytosis
Lodish et al., pp. 592-602, 606-617.