• Biochemistry I (C340)
• Biochemistry II (C341)
• Molecular Chaperones (C640)
• Membrane Biochemistry (C843)

1. Introduction
   Thermodynamics
   Water
2. Biochemical molecules
   Amino acids, peptides
   Protein Structure: Primary, secondary, tertiary and quaternary levels
   Protein Function: Myoglobin, Hemoglobin and Allostery
   Enzymes: Mechanisms, Kinetics and Regulation
   Carbohydrates
3. Metabolism
   Bioenergetics
   Glycolysis and gluconeogenesis
   Pentose phosphate pathway
   Glycogen metabolism
   Fates of pyruvate
   Tricarboxylic acid cycle
   Electron transport chain
   Oxidative phosphorylation

         Learning biochemistry is like learning a new language, except that you learn the vocabulary, grammar, sentence structure and literature (the conceptual synthesis) all in the first semester!  Therefore it is important to come prepared, having completed all the prerequisites, and to keep up with the material.  You will be required to memorize the vocabulary—names and structures of amino acids, carbohydrates and some enzymes and coenzymes, and then put them together in “sentences” (pathways.)  In addition, you will do quantitative problems for thermodynamic and kinetic analyses of biochemical processes.  And you will be introduced to new and complex concepts, such as those involved in metabolism, allostery and other processes.  You will see that biochemistry is a universal language, one that will enable you to study any biological system at the molecular level.

• Pre-requisites: C113, C335 with a grade of C- or better

• The requirement for C113, General Chemistry II, insures completion of a full year of General Chemistry with a grade of C- or better in C111 as well as in C113.
• C335, Organic Chemistry II (which can only be taken after completing C333, Organic Chemistry I with a grade of C- or better) should be completed before taking Biochemistry. Students are unable to take C335 and C340 concurrently.
• C130, General Organic Chemistry, is not recommended as preparation for C340; students who have taken C130 should take C349, General Biochemistry, for the nonmajors level course.

• Structural organization of cells
• Basic thermodynamic concepts
• Nature of chemical bonds (H bonds, electrostatic, van der Waals and hydrophobic interactions)
• Definition of acids, bases
• pH, titration curves, Henderson-Hasselbach Equation
• Stereochemistry, chirality
• Chemical kinetics
• Organic mechanisms such as nucleophilic or electrophilic attack, elimination

• Part I
  • Integrating metabolism; N2 metabolism (Ch 25, 26)
  • Amino acid metabolism (Chapter 26, with 14)
  • Lipids and membranes (Chapter 9)
  • Cholesterol (part of Chapter 24)
• Part II
  • Lipid metabolism (Chapters 23 and 24)
  • Nucleotide structure (part of Chapter 6)
  • Nucleotide metabolism (Chapter 27)
  • Nucleic acids (rest of Chapter 6)
• Part III
  • Nucleic acid structure (Chapter 7)
  • Genetic information (Chapters 8 and 28)
  • DNA replication (Chapter 29)
• Part IV
  • Trascription (Chapter 30)
  • DNA/Protein Interactions
  • Translation: tRNA function (Chapter 31), ribosome structure (Chapter 32), mechanism of protein synthesis
  • Protein folding, targeting, degradation

• Pre-requisites: CHEM 340 with a grade of C- or better

• Molecular chaperones play a fundamental role in protein folding in cells, as well as stabilizing proteins under stress conditions and modulating the activity of certain proteins as a means of regulation. Until recently the wide variety of jobs performed in the cell by chaperones obscured their universal importance. Now chaperones are defined as "a family of unrelated classes of protein that mediate the correct assembly of other polypeptides but are not themselves components of the final functional structure."1
• This course will begin with a review of principles of protein structure and the nature of the unfolded state, and the thermodynamics and kinetics involved in protein folding. Then it will review the development of the chaperone concept, before turning to the studies of particular molecular chaperones such as heat shock proteins, components of protein translocation systems in bacteria and mitochondria, and inactivation of hormone receptors in eukaryotes. The structure and function of individual molecular chaperones from both prokaryotic and eukaryotic systems will be the topics of detailed student reports. The relevance of molecular chaperones to human disease will be highlighted.
• 1Hendrick and Hartl, Ann. Rev. Biochem. (1993) 62, 349.
  Prerequisites: C340. C300 or C351 and C341 recommended.

• To build on fundamental principles of protein biochemistry allowing a thorough study of the very active field of molecular chaperones, and to give advanced undergraduate and new graduate students opportunity to explore one area of biochemistry in depth and to move from the text to the review to the primary literature as they focus on specific topics.

• Principles of Protein Structure
• Protein unfolding: "denatured" and intermediate states
• Protein folding - thermodynamics and kinetics, techniques for studying folding
• Development of chaperone concept (When is a chaperone not a chaperone?)
• Structures and functions of well-characterized molecular chaperones

• Anfinsen's classic work
• Importance of Hydrogen bonds: Pace vs. Dill, Hecht
• The Molten Globule State
• Particular techniques, e.g. pulse nmr; mass spec
• Particular environments, e.g. mitochondria, E.R.
• NonProtein Chaperones: Welsh, Dowhan
• Chaperones for RNA: Herschlag
  etc.

• Prolyl isomerase
• Protein Disulfide isomerase
• The HSP70 chaperone system
• Chaperonins
• Chaperones involved in mitochondrial import
• Hsps and steroid receptor inactivation
• Refolding proteins from inclusion bodies
  and more!

• Structure in Protein Chemistry, C. Branden and J. Tooze, 1991, Garland Publishing Co.
• Structure in Protein Chemistry, J. Kyte, 1995, Garland Publ. Co.

• It is an exciting time to study biomembranes, with important developments in the structural biology of membrane components appearing regularly. We now have the structures of ~35 membrane proteins at the atomic level (not that many when you consider almost 7000 protein structures are in the database!) This year’s Nobel Prize in Chemistry was awarded to Rod MacKinnon and Peter Agre for the structures of the potassium channel and aquaporin. With the prediction that up to a third of the proteins encoded in the completed genomes are membrane proteins, the attempts to develop high throughput tools for the analysis of these membrane proteins, and wide interest in vital roles of the membrane in topics such as signaling, membrane proteins have moved back into the spotlight.
• In this course we will spend the first month studying the membrane properties that form the milieu for these proteins, then we will look at the structures and functions of membrane proteins whose structures are solved, and finally we will consider other, less understood but important and often intriguing functions of the membrane.

• Membrane models (review)
• Lipids: structure and diversity, phase properties
• Surfactants
• Membrane proteins: structural features
• Dynamics of lipid-protein interactions
• Membrane permeability and transport
  Membrane biogenesis
• Special topics

• Prerequisites:CHEM 341; CHEM 301 or 353 or consent of instructor