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Massachusetts Institute of Technology

Biological Chemistry I (Fall 2013)

Massachusetts Institute of Technology via MIT OpenCourseWare


Course Features
  • Video lectures
  • Captions/transcript
  • Special feature - video
  • Lecture notes
  • Assignments: problem sets with solutions
  • Resource Index
Educator Features
  • Instructor insights
Course Description

This course examines the chemical and physical properties of the cell and its building blocks, with special emphasis on the structures of proteins and principles of catalysis, as well as the chemistry of organic / inorganic cofactors required for chemical transformations within the cell. Topics encompass the basic principles of metabolism and regulation in pathways, including glycolysis, gluconeogenesis, fatty acid synthesis / degradation, pentose phosphate pathway, Krebs cycle and oxidative phosphorylation.

Course Format

This OCW Scholar course, designed for independent study, is closely modeled on the course taught on the MIT campus. The on-campus course has two types of class sessions: Lectures and recitations. The lectures meet three times each week and recitations meet once a week. In recitations, an instructor or Teaching Assistant elaborates on concepts presented in lecture, working through new examples with student participation, and answers questions.

MIT students who take the corresponding residential class typically report an average of 10–15 hours spent each week, including lectures, recitations, readings, homework, and exams. All students are encouraged to supplement the textbooks and readings with their own research.
The Scholar course has three major learning units, called Modules. Each module has been divided into a sequence of lecture sessions that include:

  • Textbook Readings
  • Lecture Notes or Storyboards
  • A video by Professor JoAnne Stubbe or Professor John Essigmann
  • Problem Sets and solutions

To help guide your learning, each of these problem sets are accompanied by Problem Solving Videos where Dr. Bogdan Fedeles solves one of the problems from the set.


Lexicon of Biochemical Reactions: Introduction.
Lexicon of Biochemical Reactions: Cofactors Formed from Vitamin B12.
Lexicon of Biochemical Reactions: Vitamin B6 / PLP.
Lexicon of Biochemical Reactions: Redox Cofactors.
Problem Set 1, Problem 1: Sizes and Equilibria.
5. Enzymes and Catalysis.
Problem Set 2, Problem 1: Primary Structure.
Problem Set 3, Problem 2: Proteases: Mechanisms of Inhibition.
Carbonyl Chemistry.
Problem Set 4, Problem 2: The Mechanism of HMG-CoA Synthase.
Problem Set 5, Problem 5: How Mannose, an Isomer of Glucose, Enters Glycolysis.
Introduction to Carbohydrate Catabolism.
Problem Set 6, Problem 2: Mechanism of Phosphoglycerate Mutase.
Glycolysis and Early Stages of Respiration.
Respiration: TCA Cycle.
Problem Set 7, Problem 1: Tracing Labels through Pathways.
Maintenance of Redox Neutrality.
Respiration: Electron Transport and Oxidative Phosphorylation.
Problem Set 8, Problem 2: Bioenergetics of the Electron Transport Chain.
Respiration: Proton Pumps and ATP Synthesis.
Lipod Catabolism: Fatty Acid Beta-Oxidation.
Special Cases in Fatty Acid Metabolism.
Problem Set 9, Problem 1: Catabolism of Triacylglycerols.
Ketogenesis, Diabetes, and Starvation.
The Science Behind Type II Diabetes.
Blood Sugar Fluctuations and Gluconeogenesis.
When Your Breath Smells Like Nail Polish Remover.
Fatty Acids and Lipid Biosynthesis.
Carbohydrate Biosynthesis I: Glycogen Synthesis.
Carbohydrate Biosynthesis II: Gluconeogenesis.
Problem Set 10, Problem 3: Gluconeogenesis.
Pentose Phosphate Pathway.
PLP (Pyridoxal Phosphate) Reactions.
Regulation of Metabolism.

Taught by

Prof. John Essigmann , Prof. JoAnne Stubbe and Dr. Bogdan Fedeles

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