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A diagram of differently colored ribbons and helices shows the crystal structure of human PLP phosphatase, with pyridoxal 5'-phosphate (PLP), the active form of Vitamin B6, bound in the active site.

Course5.07SC75 lectures

Biological Chemistry I

Prof. John Essigmann, Prof. Joanne Stubbe and Dr. Bogdan Fedeles · Massachusetts Institute of Technology

Start with lecture 1 At MIT OpenCourseWare

About

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.

Lectures

Instructor Insights

  1. How Can You Not Think Enzymes Are Cool? 3 min · Video
  2. Research Focus: Ribonucleotide Reductases (RNRs) 5 min · Video
  3. Becoming a Toxicologist 5 min · Video
  4. Research Focus: Genetic Change 6 min · Video
  5. Focusing on the Morphological Unit of Life 2 min · Video
  6. Using a Vitamin Bottle as a Teaching Tool 3 min · Video
  7. Teaching Central Pathways to Help Students Understand Metabolism 2 min · Video
  8. Why Students Should Memorize Amino Acid Side Chains 6 min · Video
  9. Motivating Students to Study Metabolic Biochemistry with Oncology Applications 8 min · Video
  10. Advice for Next Teaching Generation: Focus Curricula on the Microbial World 6 min · Video

Lexicon

  1. Lexicon of Biochemical Reactions: Introduction 4 min · Video
  2. Lexicon of Biochemical Reactions: Redox Cofactors 30 min · Video
  3. Lexicon of Biochemical Reactions: Vitamin B6 / PLP 29 min · Video
  4. Lexicon of Biochemical Reactions: Cofactors Formed from Vitamin B12 25 min · Video

Session 1: What is Biochemistry?

  1. Session 1: Problem Set 1: Sizes and Equilibria 20 min · Video

Session 3: Enzymes and Catalysis

  1. Session 3: Enzymes and Catalysis 1 h 6 min · Video
  2. Session 3: Problem Set 2, Problem 1: Primary Structure 34 min · Video

Session 4: Enzyme Kinetics and Enzyme Inhibition

  1. Session 4: Problem Set 3, Question 2: Proteases: Mechanisms of Inhibition 29 min · Video

Session 5: Biochemical Transformations I

  1. Carbonyl Chemistry 37 min · Video
  2. Session 5: Problem Set 4, Problem 2: The Mechanism of HMG-CoA Synthase 27 min · Video

Session 7: Biochemical Transformations III

  1. Session 7: Problem Set 5, Problem 5: How Mannose, an Isomer of Glucose, Enters Glycolysis 16 min · Video

Session 8: Introduction to Sugar Chemistry and Carbohydrate Catabolism

  1. Session 8: Intro to Sugar Chemistry and Carbohydrate Catabolism 13 min · Video
  2. Session 8: Problem Set 6, Problem 2: Mechanism of Phosphoglycerate Mutase 14 min · Video

Session 9: Glycolysis and Early Stages of Respiration

  1. Session 9: Glycolysis and Early Stages of Respiration 24 min · Video

Session 10: Respiration: TCA Cycle

  1. Session 10: Respiration: TCA Cycle 19 min · Video
  2. Session 10: Problem Set 7, Problem 1: Tracing Labels through Pathways 22 min · Video

Session 11: Maintenance of Redox Neutrality

  1. Session 11: Maintenance of Redox Neutrality 12 min · Video

Session 12: Respiration: Electron Transport and Oxidative Phosphorylation

  1. Session 12: PLP (Pyridoxal Phosphate) Chemistry YouTube
  2. Session 12: Respiration: ETOP 21 min · Video
  3. Session 12: Problem Set 8, Question 2: Bioenergetics of the Electron Transport Chain 17 min · Video

Session 13: Respiration: Proton Pumps and ATP Synthesis

  1. Session 13: Respiration: Proton Pumps and ATP Synthesis 22 min · Video

Session 14: Lipid Catabolism: Fatty Acid Beta-Oxidation

  1. Session 14: Lipid Catabolism: Fatty Acid Beta-Oxidation 12 min · Video

Session 15: Special Cases in Fatty Acid Metabolism

  1. Session 15: Special Cases in Fatty Acid Metabolism 16 min · Video
  2. Session 15: Problem Set 9, Problem 1: Catabolism of Triacylglycerols 27 min · Video

Session 16: Ketogenesis, Diabetes and Starvation

  1. Session 16: Ketogenesis, Diabetes and Starvation 18 min · Video
  2. Session 16: The Science Behind Type II Diabetes 3 min · Video
  3. Session 16: Blood Sugar Fluctuations and Gluconeogenesis 4 min · Video
  4. Session 16: When Your Breath Smells Like Nail Polish Remover 3 min · Video

Session 17: Fatty Acid and Lipid Biosynthesis

  1. Session 17: Fatty Acid and Lipid Biosynthesis 22 min · Video

Session 18: Carbohydrate Biosynthesis I: Glycogen Synthesis

  1. Session 18: Carbohydrate Biosynthesis I: Glycogen Synthesis 8 min · Video

Session 19: Carbohydrate Biosynthesis II: Gluconeogenesis

  1. Session 19: Carbohydrate Biosynthesis II: Gluconeogenesis 20 min · Video
  2. Session 19: Problem Set 10, Problem 3: Gluconeogenesis 20 min · Video

Session 20: Carbohydrate Biosynthesis III: Pentose Phosphate Pathway

  1. Session 20: Carbohydrate Biosynthesis III: Pentose Phosphate Pathway 57 min · Video

Session 21: Regulation of Metabolism

  1. Session 21: Regulation of Metabolism 35 min · Video

Resource Index

  1. Lexicon of Biochemical Reactions: Introduction 4 min · Video
  2. Lexicon of Biochemical Reactions: Cofactors Formed from Vitamin B12 25 min · Video
  3. Lexicon of Biochemical Reactions: Vitamin B6 / PLP 29 min · Video
  4. Lexicon of Biochemical Reactions: Redox Cofactors 30 min · Video
  5. Problem Set 1, Problem 1: Sizes and Equilibria 20 min · Video
  6. Lecture 5: Enzymes and Catalysis 1 h 6 min · Video
  7. Problem Set 2, Problem 1: Primary Structure 34 min · Video
  8. Problem Set 3, Question 2: Proteases: Mechanisms of Inhibition 29 min · Video
  9. Session 5: Carbonyl Chemistry 37 min · Video
  10. Problem Set 4, Problem 2: The Mechanism of HMG-CoA Synthase 27 min · Video
  11. Problem Set 5, Problem 5: How Mannose, an Isomer of Glucose, Enters Glycolysis 16 min · Video
  12. ses 8: Intro to Sugar Chemistry and Carbohydrate Catabolism 13 min · Video
  13. Problem Set 6, Problem 2: Mechanism of Phosphoglycerate Mutase 14 min · Video
  14. ses 9: Glycolysis and Early Stages of Respiration 24 min · Video
  15. ses 10: Respiration: TCA Cycle 19 min · Video
  16. Problem Set 7, Problem 1: Tracing Labels through Pathways 22 min · Video
  17. Ses 11: Maintenance of Redox Neutrality 12 min · Video
  18. PLP (Pyridoxal Phosphate) Chemistry YouTube
  19. Ses 12: Respiration: ETOP 21 min · Video
  20. Problem Set 8, Question 2: Bioenergetics of the Electron Transport Chain 17 min · Video
  21. Ses 13: Respiration: Proton Pumps and ATP Synthesis 22 min · Video
  22. Ses 14: Lipid Catabolism: Fatty Acid Beta-Oxidation 12 min · Video
  23. Ses 15: Special Cases in Fatty Acid Metabolism 16 min · Video
  24. Problem Set 9, Problem 1: Catabolism of Triacylglycerols 27 min · Video
  25. Session 16: Ketogenesis, Diabetes and Starvation 18 min · Video
  26. Ses 17: Fatty Acid and Lipid Biosynthesis 22 min · Video
  27. Session 18: Carbohydrate Biosynthesis I: Glycogen Synthesis 8 min · Video
  28. ses19: Carbohydrate Biosynthesis II: Gluconeogenesis 20 min · Video
  29. Problem Set 10, Problem 3: Gluconeogenesis 20 min · Video
  30. ses20: Carbohydrate Biosynthesis III: Pentose Phosphate Pathway 57 min · Video
  31. ses21: Regulation of Metabolism 35 min · Video

Syllabus and materials

At MIT OpenCourseWare, as the course publishes them.

Credits and licence

Institution
Massachusetts Institute of Technology
Department
Chemistry
Taught by
Prof. John Essigmann, Prof. Joanne Stubbe, Dr. Bogdan Fedeles
Term
Fall 2013
Level
Undergraduate
Language
English
Subjects
Chemistry, Biology
Source
MIT OpenCourseWare
Licence
CC BY-NC-SA 4.0, as MIT OpenCourseWare states it. Non-commercial use only. MIT OpenCourseWare's terms
Attribution
Prof. John Essigmann, Prof. Joanne Stubbe, Dr. Bogdan Fedeles. Biological Chemistry I. Fall 2013. Massachusetts Institute of Technology: MIT OpenCourseWare, https://ocw.mit.edu/. License: Creative Commons BY-NC-SA.
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