Our cells engage in protein production, and many of those proteins are enzymes responsible for the chemistry of life.
— Randy Schekman

  1. Structure Biology of the Citric Acid Cycle: The citric acid cycle is at the center of cellular metabolism. It plays a starring role in both the process of energy production and biosynthesis. [PDF]

  2. Regulation of Cholesterol Synthesis:

    • Part 1: Feedback Regulation of HMG CoA Reductase [iBiology Talk video]

    • Part 2: Schnyder Corneal Dystrophy: Importance of UBIAD1 in Regulation of Cholesterol [iBiology Talk video]

    • Goldstein, Joseph L., and Michael S. Brown. “A Century of Cholesterol and Coronaries: From Plaques to Genes and Statins.” Cell 161, no. 1 (2015): 161–72. [PDF | PMID: 25815993 | DOI Link]

  3. Regulation of Energy metabolism

  4. Lysosome role in metabolic signalling

    • Review in 2019: The lysosome as a cellular centre for signalling, metabolism and quality control (Rosalie and Roberto, 2019) [PDF | PMID: 30602725 | DOI Link]

  5. Nutrient sensing machinery

    • Cholesterol:
      — LYsosomal CHOlesterol Signaling protein (LYCHOS, previously annotated as G-protein coupled receptor 155), Reported at 25-Aug-2022 [PDF | PMID:36007018 | DOI Link]
      — PATCHED,
      — HMG-CoA reductase,
      — Niemann-Pick type C protein 1 (NPC1), Reported at 11-Jul-1997 [PDF | PMID:9211849 | DOI Link]
      — SREBP(Sterol regulatory element-binding protein),
      — SREBP cleavage-activating protein (SCAP),

    • Amino acids:
      Review: The Dawn of the Age of Amino Acid Sensors for the mTORC1 Pathway (Wolfson and Sabatini, 2017) [PDF | PMID:28768171 | DOI Link]
      — Leucine > Sestrin2
      — Arginine(Cytosolic) > CASTOR1 [(David M Sabatini’s lab, 24/03/2016) | PMID: 26972053]
      — Arginine(Cytosolic) > RBM39 [(Michael N Hall’s lab, 09/11/2023) | PMID: 37804830]
      — Arginine(lysosomal) > SLC38A9
      — S-adenosylmethionine > SAMTOR
      — S-adenosylmethionine > Unmet(Fly specific)
      GATOR2 > Nutrient sensing hub!? [CroyEM Structure of human GATOR2 complex]

    • Glucose:
      —AMPK

  6. Open questions

    • How cells sense, integrate and respond to nutrient availability and how lysosomes are involved in the process?
    • How amino acids were sensed? More amino acid sensors?
    • How different or similar the amino acid and nutrient inputs are that drive mTORC1/TORC1 signaling in diverse organisms?
    • Is GATOR2 the nutrient sensing hub complex ? How does it work to integrate multiple nutrient inputs?
    • How does brain sense the stress of energy supply and initiate its response program?

Textbooks

  1. Fundamentals of Biochemistry, Life at the Molecular Level, 5th edition [View PDF] textbookbioche001
  1. Lehninger Principles of Biochemistry, 4th edition [View PDF] textbookbioche002
  1. Molecular Biology of The Cell, 6th edition [View PDF] textbookbioche003

Online Courses

  1. BIOLOGICAL CHEMISTRY I, MIT OpenCourseWare [Source]

  2. BIOLOGICAL CHEMISTRY II, MIT OpenCourseWare [Source]

  3. BIOCHEMISTRY LABORATORY, MIT OpenCourseWare [Source]

    • Instructor: Dr. Elizabeth Vogel Taylor
    • LABORATORY MANUAL: Student manual on the laboratory activities of the course. [PDF]
    • EQUIPMENT AND SUPPLIES: A list of equipment and supplies used for the biochemistry laboratory activities of the course. [PDF]

  4. Principles of Biochemistry, HarvardX, EdX:
    This introduction to biochemistry explores the molecules of life, starting at simple building blocks and culminating in complex metabolism. [Source]

    • Instructors: Alain Viel, Rachelle Gaudet

  5. LIPID MAPS

  • Edward A. Dennis (2010) “LIPID MAPS Lipid Metabolomics Tutorial”:
    These tutorial videos were prepared for students in the UCSD School of Medicine and School of Pharmacy and Pharmaceutical Sciences by Professor Edward A. Dennis, Department of Chemistry and Biochemistry and Department of Pharmacology, School of Medicine, University of California, San Diego. [Tutorial outline PDF]
  1. LIPID MAPS Spring School, April 2021

Ref. Database