# Biological Chemistry I

- Institution: Massachusetts Institute of Technology
- Department: Chemistry
- Taught by: Prof. John Essigmann, Prof. Joanne Stubbe, Dr. Bogdan Fedeles
- Term: Fall 2013
- Level: Undergraduate
- Language: English
- Subjects: Chemistry, Biology
- Source: [MIT OpenCourseWare](https://ocw.mit.edu/courses/5-07sc-biological-chemistry-i-fall-2013/)
- Licence: [CC BY-NC-SA 4.0](https://creativecommons.org/licenses/by-nc-sa/4.0/) (Non-commercial use only.)
- Syllabus: [at the source](https://ocw.mit.edu/courses/5-07sc-biological-chemistry-i-fall-2013/pages/syllabus/)
- Who can watch: Tweens profiles and older (sources give no ratings; placed by Invisible Network from the source's own words)

This course examines the chemical and physical properties of the cell and its building blocks, with special emphasis on the structures of proteins and principles of catalysis, as well as the chemistry of organic / inorganic cofactors required for chemical transformations within the cell. Topics encompass the basic principles of metabolism and regulation in pathways, including glycolysis, gluconeogenesis, fatty acid synthesis / degradation, pentose phosphate pathway, Krebs cycle and oxidative phosphorylation.

Course Format

This OCW Scholar course, designed for independent study, is closely modeled on the course taught on the MIT campus. The on-campus course has two types of class sessions: Lectures and recitations. The lectures meet three times each week and recitations meet once a week. In recitations, an instructor or Teaching Assistant elaborates on concepts presented in lecture, working through new examples with student participation, and answers questions.

MIT students who take the corresponding residential class typically report an average of 10–15 hours spent each week, including lectures, recitations, readings, homework, and exams. All students are encouraged to supplement the textbooks and readings with their own research.

The Scholar course has three major learning units, called Modules. Each module has been divided into a sequence of lecture sessions that include:

Textbook Readings

Lecture Notes or Storyboards

A video by Professor JoAnne Stubbe or Professor John Essigmann

Problem Sets and solutions

To help guide your learning, each of these problem sets are accompanied by Problem Solving Videos where Dr. Bogdan Fedeles solves one of the problems from the set.

## Lectures

1. [How Can You Not Think Enzymes Are Cool?](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/fcc74c28e854), 3 min (Video)
2. [Research Focus: Ribonucleotide Reductases (RNRs)](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/28bc3aa0739f), 5 min (Video)
3. [Becoming a Toxicologist](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/635b45b08203), 5 min (Video)
4. [Research Focus: Genetic Change](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/ed0a83d35922), 6 min (Video)
5. [Focusing on the Morphological Unit of Life](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/20bd5e978ae8), 2 min (Video)
6. [Using a Vitamin Bottle as a Teaching Tool](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/a9b8886b444c), 3 min (Video)
7. [Teaching Central Pathways to Help Students Understand Metabolism](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/255864706f0f), 2 min (Video)
8. [Why Students Should Memorize Amino Acid Side Chains](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/fc8c6dcef9a1), 6 min (Video)
9. [Motivating Students to Study Metabolic Biochemistry with Oncology Applications](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/a9f44f169e0d), 8 min (Video)
10. [Advice for Next Teaching Generation: Focus Curricula on the Microbial World](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/8f5e6b0bfcaf), 6 min (Video)
11. [Lexicon of Biochemical Reactions: Introduction](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/d0316a4baa44), 4 min (Video)
12. [Lexicon of Biochemical Reactions: Redox Cofactors](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/1c46adfc50b9), 30 min (Video)
13. [Lexicon of Biochemical Reactions: Vitamin B6 / PLP](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/c2d70a3e6ee9), 29 min (Video)
14. [Lexicon of Biochemical Reactions: Cofactors Formed from Vitamin B12](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/29be63c8dda8), 25 min (Video)
15. [Session 1: Problem Set 1: Sizes and Equilibria](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/071fd0cef04c), 20 min (Video)
16. [Session 3: Enzymes and Catalysis](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/b85ba4051efe), 1 h 6 min (Video)
17. [Session 3: Problem Set 2, Problem 1: Primary Structure](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/a07beb3bec20), 34 min (Video)
18. [Session 4: Problem Set 3, Question 2: Proteases: Mechanisms of Inhibition](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/5dd143a4effb), 29 min (Video)
19. [Carbonyl Chemistry](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/56a0093dec09), 37 min (Video)
20. [Session 5: Problem Set 4, Problem 2: The Mechanism of HMG-CoA Synthase](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/6ba070e83044), 27 min (Video)
21. [Session 7: Problem Set 5, Problem 5: How Mannose, an Isomer of Glucose, Enters Glycolysis](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/d5cd9d1abdf0), 16 min (Video)
22. [Session 8: Intro to Sugar Chemistry and Carbohydrate Catabolism](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/5addf0fc1ded), 13 min (Video)
23. [Session 8: Problem Set 6, Problem 2: Mechanism of Phosphoglycerate Mutase](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/355613617013), 14 min (Video)
24. [Session 9: Glycolysis and Early Stages of Respiration](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/236d0fcf5c7b), 24 min (Video)
25. [Session 10: Respiration: TCA Cycle](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/8005236b9c37), 19 min (Video)
26. [Session 10: Problem Set 7, Problem 1: Tracing Labels through Pathways](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/cb8d1ccde6bd), 22 min (Video)
27. [Session 11: Maintenance of Redox Neutrality](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/dee754cd46c2), 12 min (Video)
28. [Session 12: PLP (Pyridoxal Phosphate) Chemistry](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/829a7317f8a5) (YouTube)
29. [Session 12: Respiration: ETOP](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/77656f263bfd), 21 min (Video)
30. [Session 12: Problem Set 8, Question 2: Bioenergetics of the Electron Transport Chain](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/27d3621ee595), 17 min (Video)
31. [Session 13: Respiration: Proton Pumps and ATP Synthesis](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/b5ecb2c97f93), 22 min (Video)
32. [Session 14: Lipid Catabolism: Fatty Acid Beta-Oxidation](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/1fac33e3f334), 12 min (Video)
33. [Session 15: Special Cases in Fatty Acid Metabolism](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/75c8dd0d8e03), 16 min (Video)
34. [Session 15: Problem Set 9, Problem 1: Catabolism of Triacylglycerols](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/e9f0fa0edbb8), 27 min (Video)
35. [Session 16: Ketogenesis, Diabetes and Starvation](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/49a93bf643e2), 18 min (Video)
36. [Session 16: The Science Behind Type II Diabetes](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/b6b2c7963c4a), 3 min (Video)
37. [Session 16: Blood Sugar Fluctuations and Gluconeogenesis](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/c61a88985dd3), 4 min (Video)
38. [Session 16: When Your Breath Smells Like Nail Polish Remover](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/ffb0fca334d0), 3 min (Video)
39. [Session 17: Fatty Acid and Lipid Biosynthesis](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/32683613bb1f), 22 min (Video)
40. [Session 18: Carbohydrate Biosynthesis I: Glycogen Synthesis](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/5e236f2c6d43), 8 min (Video)
41. [Session 19: Carbohydrate Biosynthesis II: Gluconeogenesis](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/fd10c5b8be7e), 20 min (Video)
42. [Session 19: Problem Set 10, Problem 3: Gluconeogenesis](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/385b430205a5), 20 min (Video)
43. [Session 20: Carbohydrate Biosynthesis III: Pentose Phosphate Pathway](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/5ce323e09f3a), 57 min (Video)
44. [Session 21: Regulation of Metabolism](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/5e8708df1bc6), 35 min (Video)
45. [Lexicon of Biochemical Reactions: Introduction](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/6c2ad4bc1178), 4 min (Video)
46. [Lexicon of Biochemical Reactions: Cofactors Formed from Vitamin B12](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/b6c0423e18b7), 25 min (Video)
47. [Lexicon of Biochemical Reactions: Vitamin B6 / PLP](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/b2a93defa6a1), 29 min (Video)
48. [Lexicon of Biochemical Reactions: Redox Cofactors](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/7d639e71f816), 30 min (Video)
49. [Problem Set 1, Problem 1: Sizes and Equilibria](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/a76a24477fe8), 20 min (Video)
50. [Lecture 5: Enzymes and Catalysis](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/501663bf84bb), 1 h 6 min (Video)
51. [Problem Set 2, Problem 1: Primary Structure](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/d7cc613c8751), 34 min (Video)
52. [Problem Set 3, Question 2: Proteases: Mechanisms of Inhibition](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/43ed8352c83b), 29 min (Video)
53. [Session 5: Carbonyl Chemistry](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/35c5686f95cc), 37 min (Video)
54. [Problem Set 4, Problem 2: The Mechanism of HMG-CoA Synthase](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/6d034b3f1c1e), 27 min (Video)
55. [Problem Set 5, Problem 5: How Mannose, an Isomer of Glucose, Enters Glycolysis](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/0670ef080aa3), 16 min (Video)
56. [ses 8: Intro to Sugar Chemistry and Carbohydrate Catabolism](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/3ef11c5d5423), 13 min (Video)
57. [Problem Set 6, Problem 2: Mechanism of Phosphoglycerate Mutase](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/3245c8670b8a), 14 min (Video)
58. [ses 9: Glycolysis and Early Stages of Respiration](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/b40288d6c101), 24 min (Video)
59. [ses 10: Respiration: TCA Cycle](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/424cbe381a4c), 19 min (Video)
60. [Problem Set 7, Problem 1: Tracing Labels through Pathways](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/7dc1329a625c), 22 min (Video)
61. [Ses 11: Maintenance of Redox Neutrality](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/fc1d7b4c147b), 12 min (Video)
62. [PLP (Pyridoxal Phosphate) Chemistry](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/6e3524cb8da3) (YouTube)
63. [Ses 12: Respiration: ETOP](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/44f0a8c4f6df), 21 min (Video)
64. [Problem Set 8, Question 2: Bioenergetics of the Electron Transport Chain](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/5040953c6d08), 17 min (Video)
65. [Ses 13: Respiration: Proton Pumps and ATP Synthesis](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/d5df6a35bf4e), 22 min (Video)
66. [Ses 14: Lipid Catabolism: Fatty Acid Beta-Oxidation](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/c69d9c55e5de), 12 min (Video)
67. [Ses 15: Special Cases in Fatty Acid Metabolism](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/36cbdee933c6), 16 min (Video)
68. [Problem Set 9, Problem 1: Catabolism of Triacylglycerols](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/d0c935021eff), 27 min (Video)
69. [Session 16: Ketogenesis, Diabetes and Starvation](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/fe9accff08d6), 18 min (Video)
70. [Ses 17: Fatty Acid and Lipid Biosynthesis](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/1b30018874cb), 22 min (Video)
71. [Session 18: Carbohydrate Biosynthesis I: Glycogen Synthesis](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/964aff2a42ee), 8 min (Video)
72. [ses19: Carbohydrate Biosynthesis II: Gluconeogenesis](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/191ab384e879), 20 min (Video)
73. [Problem Set 10, Problem 3: Gluconeogenesis](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/feb48b1f8f75), 20 min (Video)
74. [ses20: Carbohydrate Biosynthesis III: Pentose Phosphate Pathway](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/ffc94b205c2e), 57 min (Video)
75. [ses21: Regulation of Metabolism](https://invisiblenetwork.ai/learn/mit/5-07sc-biological-chemistry-i-fall-2013/d759cecc8351), 35 min (Video)