Disclaimer
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
tRNA
Telomerase |
2.5 |
1-8: Exam 1 Review |
Exam 1 Review Problems
Energy in Translation
RNAWorld |
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
Glycolysis
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) |