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Natural Sciences > Earth, Atmospheric, and Planetary Sciences > Biological Chemistry II
 Biological Chemistry II  posted by  duggu   on 2/2/2008  Add Courseware to favorites Add To Favorites  
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Structural image of protein complex from PDB database.
The Structure Of Beta-Ketoacyl-[Acyl Carrier Protein] Synthase I In Complex With Thiolactomycin, Implications For Drug Design. PDB ID: 1FJ4.  Price, A. C., Choi, K., Heath, R. J., Li, Z., White, S. W., Rock, C. O.: Inhibition of Beta-Ketoacyl-[Acyl Carrier Protein] Synthases by Thiolactomycin and Cerulenin: Structure and Mechanism J.Biol.Chem. 276 pp. 6551 (2001). (Image courtesy of the Research Collaboratory for Structural Bioinformatics.  H.M.Berman, J.Westbrook, Z.Feng, G.Gilliland, T.N.Bhat, H.Weissig, I.N.Shindyalov, P.E.Bourne The Protein Data Bank. Nucleic Acids Research, 28 pp. 235-242 (2000).)

Course Highlights

The tools section includes information about various molecular graphics programs used to view three-dimensional structures in this course.

Course Description

This course deals with a more advanced treatment of the biochemical mechanisms that underlie biological processes. 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. Topics include macromolecular machines for energy and force transduction, regulation of biosynthetic and degradative pathways, and the structure and function of nucleic acids.

Technical Requirements

RasMol software is required to run the .spt and .pdb files found on this course site.

*Some translations represent previous versions of courses.



Amazon logo 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

Amazon logo 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 Regulation

Size 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 Motors

An 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 Degradation

Protein 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.


Problem Sets Will not be graded, but will be dicussed in Recitations
Exam I 100
Exam II 100
Exam III 100
Exam IV 100
Final Exam 200 (Comprehensive)
Total 600

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.


The calendar lists both lecture (L#) and recitation (TD#) sessions. Recitations are referred to as the Techniques and Discussion (TD) sessions. See syllabus for a description of the modules.

Module 1: Size and Components of Cells and Implications with respect to Regulation
L1 Introduction: cell constituents, prokaryotes vs. eukaryotes  
L2 Introduction (cont.)  
Module 2: Fatty Acid Synthases (FAS), Polyketide Synthases (PKS), and Non-ribosomal Polypeptide Synthases (NRPS)
L3 Fatty Acid Synthase: polymerization, biosynthesis, players, chemistry, structure, chemistry as a paradigm for PKS and NRPS, medical interlude  
L4 Experimental methods for elucidating FAS structure  
TD1 Beta-ketoacyl-ACP Synthase I (FabB)  
L5 Chemistry of FAS as paradigm for other molecular machines  
L6 Secondary metabolism: PKS, NRPS  
L7 Chemistry of PKS and NRPS: post-translational modification, initiation, elongation, decoration, termination, fidelity Problem set 1 due
TD2 Smith Paper  
L8 Chemistry of PKS and NRPS (cont.)  
L9 Chemistry of PKS and NRPS (cont. with specific examples) Problem set 2 due
L10 Biosynthesis of yersiniabactin and cholesterol Exam 1
TD3 Walsh Paper  
L11 Cholesterol biosynthesis  
L12 Cholesterol regulation and homeostasis  
L13 Sensing insoluble molecules  
TD4 Endocytosis of LDL and Radioactivity Techniques  
L14 Module 2: Regulation of the transcription level by insoluble metabolites and Module 3: Translation  
Module 3: Translation: Loading, Initiation, Elongation, and Termination - A Machine in Action; Introduction to G-proteins: Switches or Motors
L15 Translation (cont.) Problem set 3 due
L16 Elongation, termination, RNA polymerase  
TD5 Structure  
L17 Chemical methods for studying translation and the ribosome  
L18 Chemical methods for studying translation and the ribosome (cont.)  
L19 Chemical methods for studying translation and the ribosome (cont.) Problem set 4 due
TD6 Hydroxyl Radical Footprinting Exam 2
L20 Isoleucine tRNA synthetase  
TD7 Gel Electrophoresis; Photoaffinity Probes  
L21 tRNA synthase editing mechanisms; G proteins (EF-Tu/EF-G)  
L22 G proteins: motors  
TD8 Rodnina Paper  
L23 G proteins: switches  
L24 Peptide bond formation; new technologies using the ribosome Problem set 5 due
L25 Module 3: methods for the incorporation of unnatural amino acids and Module 4: what happens as a protein exits the ribosome? Exam 3
Module 4: Crypts and Chambers: Macromolecular Machines involved in Protein Folding and Degradation
TD9 FRET, Steady State  
L26 Protein folding in vitro  
TD10 Exam 3 Answers and Discussion  
L27 Protein folding: in vitro vs. in vivo; degradation  
L28 Protein folding in vivo  
L29 Chaperone proteins  
TD11 GroEl / GroES  
L30 GroEL/GroES  
L31 Proteases Problem set 6 due
L32 Proteosome Exam 4
TD12 DnaJ specificity  
L33 Proteosome (cont.)  
L34 Role of Ubiquitin in degradation  
L35 Degradation through polyubiquitination  
    Final Exam (3 hours. The first 30 minutes will cover the information since the last exam. The remaining two and a half hours will cover the entire semester.)   Tell A Friend