Biological Chemistry II

Course Info

Course Number/Code: 5.08J (Spring 2004)
Course Title: Biological Chemistry II
Course Level: Undergraduate
Offered By: Massachusetts Institute of Technology (MIT)
Department: Chemistry
Course Instructor(s): Prof. Joanne Stubbe
Prof. Alice Ting
Course Introduction:
Syllabus Help support MIT OpenCourseWare by shopping at! MIT OpenCourseWare offers direct links to to purchase the books cited in this course. Click on the Amazon logo to the left of any citation and purchase the book from, and MIT OpenCourseWare will receive up to 10% of all purchases you make. Your support will enable MIT to continue offering open access to MIT courses.Recommended Textbook

Voet, D., J. Voet. Biochemistry. New York: J. Wiley & Sons, 2003. ISBN: 9780471250906.

This course is divided into four subject area modules as described in the following table.


Size and Components of Cells and Implications with respect to RegulationSize of cells and components and implications with respect to regulatory mechanisms.Introduction to macromolecular machines.


Fatty Acid Synthases (FAS), Polyketide Synthases (PKS), and Non-ribosomal Polypeptide Synthases (NRPS)Initiation, elongation, termination and implications in human health. A paradigm for thinking about PKS and NRPS.Overview of the macromolecular machines with a common solution to the problems. Specific examples include erythromycin and enterobactin biosynthesis.Cholesterol biosythesis and homeostasis: implications in disease.


Translation: Loading, Initiation, Elongation, and Termination - A Machine in Action; Introduction to G-proteins: Switches or MotorsAn overview of translation: the players and the pacman view of the process.Methods to study macromolecular interactions: reconstitution experiments, crystallography, cryoelectron microscopy, footprinting and crosslinking, presteady state kinetics.Loading: tRNA synthases and their editing mechanisms.G proteins: switches or motors, EF-Tu and EF-G as examples in the elongation process. Molecular mimicry at work.The 50S ribosomal subunit: a view of peptide bond formation using RNA. Is chymotrypsin (a serine protease) a good model?The use of translation equipment to generate proteins containing unnatural amino acids in vitro and in vivo.


Crypts and Chambers: Macromolecular Machines involved in Protein Folding and DegradationProtein folding in vitro: Anfinsen's hypothesis.Protein folding in vivo: Hsp70/Hsp40: DNAJ and DNAK as a paradigm.Protein folding in vivo. Hsp6O Family (GroEL and GroES).26S Proteosome and the role of Ubiquitin in degradation.

Grading ACTIVITIESPOINTSProblem SetsWill not be graded, but will be dicussed in RecitationsExam I100Exam II100Exam III100Exam IV100Final Exam200 (Comprehensive)Total600

Recitations (Techniques and Discussion Sessions)

For one hour each week, Professor Ting will provide an in-depth view of technologies briefly outlined in class and used in the assigned journal papers. These classes will also be used to go over problem sets and to discuss lectures.


Assigned reading will include sections from your textbook to refresh your memory or to give you a good overview of a specific topic. It will also include a review article on each module to bring you up to date about recent advances in a specific area and an original paper that will highlight the use of a technique to solve a problem covered within the module. Additional background reading will be placed on reserve. Additional references will be given for those so inclined to read about one specific topic in more detail.

Molecular Graphics

In class, we will demonstrate three-dimensional structures using Rasmol, a molecular visualization program. We will provide the pdb files along with Rasmol scripts for the structures discussed per module, so that students can view them at their leisure.