Course Meeting Times

Lectures: 3 sessions / week, 1 hour / session

Recitations: 1 session / week, 1 hour / session


5.12 Organic Chemistry I and either 5.07 Biological Chemistry I or 7.05 General Biochemistry

Course Description

This course is an advanced treatment of biochemical mechanisms that underlie biological processes. Topics include macromolecular machines such as the ribosome, the proteasome, fatty acid synthases as a paradigm for polyketide synthases and non-ribosomal polypeptide synthases, and polymerases. Emphasis will be given to the experimental methods used to unravel how these processes fit into the cellular context as well as the coordinated regulation of these processes.


Eight modules will be covered during the semester. Each module consists of a series of topics covered in lecture.

  • General Background (Lecture 1)
  • Module 1: Translation (Lectures 2–7)
  • Module 2: Protein Folding (Lectures 8–11)
  • Module 3: Protein Degradation (Lectures 12–14)
  • Module 4: Polyketide and Nonribosomal Peptide Assembly Lines (Lectures 15–18)
  • Module 5: Cholesterol Biosynthesis and Cholesterol Homeostasis (Lectures 19–25)
  • Module 6: Metal Ion Homeostasis (Lectures 25–31)
  • Module 7: Reactive Oxygen Species (ROS) (Lectures 32–34)
  • Module 8: Nucleotide Metabolism (Lectures 34–36)

Required Reading

There is no required textbook for this course. However, a general biochemistry book is strongly recommended for background material, such as:

Voet, D., J. Voet, and C. Pratt. Fundamentals of Biochemistry: Life at the Molecular Level. 4th ed. Wiley, 2015. ISBN: 9780470547847.

Review articles pertaining to the lecture material are listed in the Readings section. These articles are intended to supplement lecture material. Some reviews will be significantly more comprehensive than what is covered in lecture.

The papers listed under "Readings" are related to lecture content. Students are expected to read these papers during the appropriate course modules. The papers listed under the "Related" tab in the Recitation videos are specific for recitation sections and will be critically evaluated during the weekly recitation sessions.


Each week in recitation, the Teaching Assistant, Prof. Nolan, Prof. Stubbe, or a guest will present case studies from the literature, and review experimental methods. Each week, there will be a recitation reading assignment from the primary literature. The assigned readings are listed in the Lecture & Recitation Videos section. There will also be a weekly recitation handout that provides information about techniques. Students should read the materials before recitation. Recitation material will be covered on the exams. Weekly attendance is mandatory.

Problem Sets

There will be 10 problem sets throughout the semester. The problem sets will be graded ✓-, ✓, ✓+. Students are welcome to work together on problem sets and study together. Nevertheless, it is important that students master the material on their own because exams are taken individually.

Mid-term Exams

There will be three mid-term exams (100 points / exam). The exams cover material from lecture, assigned readings, problem sets, and recitation materials. Students are permitted to bring one 8.5" x 11" sheet of paper, double sided, to each exam. Guidelines for what information is permitted to include on this exam sheet will be provided in advance of the first exam. Students must turn in this sheet with their exam.

Final Exam

This will be a 3-hour cumulative exam. Students are permitted to bring one 8.5" x 11" sheet of paper, double sided, to this exam, which must be turned in with their exams.


Exam I 100
Exam II 100
Exam III 100
Cumulative Final Exam 200
Total 500