These are notes that were compiled for my stint as a MIT 7.05 Biochemistry TA. They are being posted online for the usage of later 7.05 classes. Special thanks to TA’01 Chris Allen & TA’02 Ken Olive. I have organized the notes according to the way they were used in recitation in S’03.

Software Required: Unless otherwise noted, all files are Adobe Acrobat Files and require version 6.0 or newer of the free Adobe Acrobat Reader.

Standard Disclaimer: I am human, hence I do make mistakes. It is quite possible that a worksheet with a mistake has been posted here. If you find something wrong here, please email me at alij at alum dot mit dot edu and let me know. I will be happy to fix it.

Recitation Files
Rec # Covering Lectures Files Available
1 1. Intro,
2. DNA & RNA,
3. Proteins,
4. DNA Replication,
5. Transcription & Splicing
Unit 1 & 2 Schedule
Recitation 01 Problems
Nucleic Acid Constituents
Key Features of DNA & RNA DNA & RNA Polymerases
RNA Sequence Overhead
Transcription in a Nutshell Amino Acids
Protein Purification
2 6. Genetic Code,
7. Translation and the Ribosome,
8. The Central Dogma
Recitation 02 Problems
Exam 1 Review Packet
Translation in a Nutshell
2.5 1-8: Exam 1 Review Exam 1 Review Problems
Energy in Translation
3 9. pH, Buffers & Titration Curves pH, pKa, Buffers & Titrations
4 10. Protein Structure
11. Protein Folding
12. Enzyme Chemistry
Recitation 04 Problems
Protein Structure and Determination Of
Protein Folding Problem
Serine Protease Action Template
5 13. Enzymes as Catalysts
14. Enzyme Kinetics
Recitation 05 Problems
Regulation of Enzymes
Inhibition of Enzymes
Thermodynamics for Biochemistry in a Nutshell
Enzyme Kinetics and Plots
6 15. Allostery
16. Hemoglobin and the Bohr Effect
17. Hormone Action
Recitation 06 Problems
Exam 2 Review Packet
Hemoglobin in a Nutshell
Hormone and Signal Transduction Supplement
6.5 9-17: Exam 2 Review Partial Solutions to Exam 2 Review Packet
7 18. Carbohydrates
19. Energy-rich compounds
20. Glycolysis
How to Ace Professor Brown’s Exams
Recitation 07 Problems
Big Chart
Making and Breaking Glycogen
Mechanisms of Isomerase & Mutase
Mechanism of Aldolase
Carbohydrates: Rings and Naming
The Common Carbohydrates
8 21. Glycolysis, regulation
22. Utilization of lactose and other sugars
23. TCA cycle
Recitation 08 Problems
Professor Brown Practice Set 1
Arsenate: The Glycolysis Poison
Those Pesky Co-Enzymes
The Many Enzymes of Pyruvate
The Many Fates of Pyruvate
Pyruvate Oxidase Particle
Sugars & Their Metabolism
Enzymes of the TCA Cycle
Krebs/TCA/Citric Acid Cycle
9 24. More TCA cycle Recitation 09 Problems
Professor Brown Practice Set 2
Regulation and Inhibition of Pathways
Coupling and Counting ATP
9.5 18-24: Exam 3 Review Exam 3 Review Session Problems
10 25. Membranes and Oxidative Phosphorylayion
26. Pentose Metabolism
Recitation 10 Problems (82 KB)
Even Bigger Pathways Chart (EXAMPLE ONLY) (55 KB)
Fatty Acid Biosynthesis (45 KB)
General Mechanisms of TA & TK (22 KB)
Mechanism of Transaldolase (29 KB)
Mechanism of Transketolase (19 KB)
Pentose Cycle (20 KB)
11 27. Photosynthesis
28. CO2 Assimilation
29. Lipids and fatty acid oxidation
30. Biosynthesis of lipids
Recitation 11 Problems (77 KB)
Professor Brown Practice Set 3 (32 KB)
Playing with Ammonia: Bleach Not Allowed (17 KB)
Uses of Acetyl CoA (15 KB)
Biosynthesis of Phospholipids (24 KB)
Pyridoxal-P (PLP) Mega Handout (56 KB)
The Screwed Up Nabisco Wannabe: Rubisco (15 KB)
The Fatty Acids (8 KB)
12 31. Nitrogen metabolism
32. Amino acid metabolism
33. One-carbon metabolism
Recitation 12 Problems (138 KB)
1 Carbon Metabolism (19 KB)
Amino Acid Entry into the TCA Cycle (25 KB)
Amino Acid Breakdown: General Scheme (30 KB)
Amino Acid Breakdown: Specific AAs (44 KB)
General Transformations by Enzyme (41 KB)
Oxygenases (22 KB)
Urea Cycle (21 KB)
13 34. Biosynthesis of pyrimidines
35. Biosynthesis of purines
Recitation 13 Problems (Almost all old exam questions) (93 KB)
Prymidine Biosynthesis (22 KB)
Purine Biosynthesis (27 KB)
2001 Exam 3 (64 KB)
2001 Exam 3 Solutions (169 KB)
Prof Brown Practice Set 3 Answers (745 KB)