Biological chemistry ii

Lectures: 3 sessions / week, 1 hour / session

Recitations: 1 session / week, 1 hour / session

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.

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.

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.

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