1

5.07 Syllabus: Fall 2007

Course Syllabus: Lecture topics and exam dates are noted below on the course syllabus. The lecture schedule is subject to slight changes. Chapters/pages refer to Voet and Voet, Biochemistry, 3rd edition.

Date

Lecture Topic

Reading Assignment
Chapter 1 pp. 317; Chapter 2 pp. 39-49; Workbook I & Problem Set I

Lecturer

September
Wed. 5 1. Composite biomolecules and their linking functional groups; molecules that are hydrophobic, hydrophilic, or amphiphilic; effect of charge and pKa on the hydrophilicity of biomolecules 2. Amino acids, primary structures and backbone conformations of peptides and proteins; Ramachandran diagrams 3. Peptide and protein secondary structuressheets and helices; structures of globular proteins; dimeric helical coiled coils; helical wheels as packing predictors 4. (Problem set I is due) Protein tertiary structure; energetics of protein folding; structural and energetic features of folded globular proteins; introduction to myoglobin, an oxygencarrying protein. DSK

Fri. 7

Chapter 4 pp. 6574; Workbook II

DSK

Mon. 10

Copy of last years Quiz I

DSK

Wed. 12

Answers to PS I V & V Chapter 8 pp. 219-255; Problem set II

DSK

Fri. 14

Mon. 17

5. Introduction to Chapter 10 pp. hemoglobin; quantitative 320-338 oxygen binding; Hill equation; R & T states. 6. Hemoglobin; quantitative See Lecture 5 cooperative oxygen binding; structures of R & T states. modulation of oxygen binding by hemoglobin, Bohr effect, BPG binding. transport of oxygen from lung to tissue. 20-Minute Quiz on Workbook & PS1 7. (PS II is due) Summary of hemoglobin biochemistry and biophysics; Introduction to lipids and membranes; quantitative oxygen binding Chapter 12 pp. 382-402; 407414; review questions on Chapter 10; PS III; Answers to PS II (see Lecture 7); 2002 HE II w/answers; summary of contents of HE I

DSK

DSK

Wed. 19

DSK

Fri. 21

8. Triacylglycerols, glycerophospholipids, lipid aggregatesmicelles and bilayers, Plasma membranes as lipid bilayersstructure and physical properties, cholesterol, structures and functions of membrane proteins HOUR EXAM I 9. Summary of membranes and lipids; Introduction to sugars -- structures, stereochemistry, acetal and hemiacetal linkages.

DSK

Wed. 26 Fri. 28

Workbook III; Chapter 11

DSK

October
Mon. 1 10. Monosaccharides and oligosaccharides; stereochemistry of the acetal linkage; glycogen and cellulose; glycoproteins; Introduction to kinetics of enzyme-catalyzed reactions 11. Enzyme kinetics; irreversible, competitive, noncompetitive inhibition 12. (PS III is due ) Summary of enzyme kinetics; acid and base-catalyzed mechanisms; base catalyzed ester and amide hydrolysis; enolization, the aldol condensation 13. Nitrogen chemistry imines and enamines; cofactor catalysis; PLP and TPP; analogies from simple bioorganic examples 14. (PS IV is due) Review of PLP and TPP catalysis; introduction to biochemical oxidation and reduction 15. Oxidation-reduction continued; biochemical hydride transfer; experimental distinctions between hydride and proton transfer; chemistry of NADH/NAD+ and their simpler bioorganic analogs Chapter 14 pp. 472-487 DSK

Wed. 3

(see Lecture 10)

DSK

Fri. 5

Answers to PS III; Workbook IV; Problem Set IV

DSK

Wed. 10

(see Lecture 12)

DSK

Fri. 12

(see Lecture 12)

DSK

Mon. 15

Answers to PS IV; Workbook V; Problem Set V

DSK

4 Wed. 17 16. (PS V is due) OxidationReduction continued; one and two-electron transfer chemistry of quinones and flavins and their simple bioorganic analogs; review of cofactor chemistry. 17. Bioenergetics HOUR EXAM II 18. Introduction to metabolism: High-energy compounds; glycolysis 19. Polysaccharide catabolism; optional endings for glycolysis 20. Pathways that intersect with glycolysis 21. (PS VI is due) Citric acid cycle 22. Citric acid cycle, continued; electron transport, oxidative phosphorylation (Q cycle, [Fe-S] proteins) HOUR EXAM III 23. ATP synthesis driven by proton gradients; lipid catabolism 24. ATP synthesis driven by proton gradients 25. (PS VII is due) Lipid catabolism 26. Lipid catabolism, ketone bodies 27. Anaplerotic reactions; Gluconeogenesis 28. (PS VIII is due) Anaplerosis and gluconeogenesis, continued; glyoxylate cycle Answers to PS V; DSK 2002 HE II with answers; summary of contents of HE II

Fri. 19 Mon. 22 Wed. 24

Chapter 3 pp. 51-60 DSK Skim pp. 549-565; read pp. 566-577 (Chapter 16), pp. 581-607 (Chapter 17) Read pp. 607-613 (Chapter 17), 626647 (Chapter 18); skim remainder of chapter Read pp. 765-794 (Chapter 21) Read pp. 797-839 (Chapter 22) Chapter 22 SL

Fri. 26

SL

Mon. 29 Wed. 31

SL SL

November
Fri. 2 SL

Mon. 5 Wed. 7 Fri. 9 Wed. 14 Fri. 16 Mon. 19 Wed. 21

Chapter 22 Read pp. 909-930 (Chapter 25) __ Read pp. 843-851 (Chapter 23) __ Read pp. 862-868 (Chapter 23)

SL SL SL SL SL SL

5 Mon. 26 29. Pentose phosphate pathway HOUR EXAM IV 30. Light and dark reactions of photosynthesis (overview). Lipid biosynthesis 31. (PS IX due) Lipid biosynthesis; integration of metabolic processes 32. Integration, continued; Nucleic acid structure; replication 33. (PS X due) Replication, continued. RNA synthesis and post-translational processing 34. Regulation of gene expression 35. Protein synthesis Read pp. 11071113 (Vol. 2, Chapter 29); pp. 1135-1152 Skim 1152-1162; read 1216-1237 (Chapter 31); skim 1254-1264 Chapter 24 (skim); Read pp. 930-942 (Chapter 25); Chapter 27 SL

Wed. 28 Fri. 30

SL

December
Mon. 3 SL

Wed. 5

SL

Fri. 7

SL

Mon. 10 Wed. 12

Skim 1295-1306; Read 1306-1337

SL SL