1. Metabolism pathway

Provided by Gao Senquan, Chen Shurui, Diao Tongxin and Lu Minsi. We've also push it to Github repository (Available at https://github.com/maxwell-gao/CH_metabolism_path)

1.1. Preface

The majority of our figures are generated by Escher, COBRApy and models in Jupyter Lab. The BioRender is also used for figure creating.

We use COBRA as an analyzing tool based on omics data flux to reveal how the metabolism flux actually works in the living body.

This comprehensive homework is composed of three major parts: the source code we use, the figures we draw with various tools (we believe that you may find them so different from each other soon😂), and the document you are reading now (in the HTML form and the markdown form).

We aim to provide a creative form for biochemistry reviewing and understanding though we know that’s a hard work.

• 1. Metabolism pathway
  • 1.1. Preface
  • 1.2. Metabolism Overview
    • 1.2.1. The core metabolism
  • 1.3. Central carbon Metabolism
    • 1.3.1. Flux of central carbon
    • 1.3.2. EMP, TCA and PPP
    • 1.3.3. Glycolysis and Glycolytic Enzymes
    • 1.3.4. Glycogen Degradation
    • 1.3.5. Krebs Cycle
    • 1.3.6. Pentose Phosphate Pathway
    • 1.3.7. Oxidative Phosphorylation
    • 1.3.8. Warburg Effect
    • 1.3.9. The Cori Cyle: An Anaerobic Metabolic Method for Glucogenesis
  • 1.4. Fatty acid Metabolism
    • 1.4.1. Fatty Acid
  • 1.5. Amino acid Metabolism
    • 1.5.1. Amino Acid Catabolism and Urea Cycle
    • 1.5.2. Metabolism of Amino Acid Carbon Skeletons
  • 1.6. Nucleotide Metabolism
    • 1.6.1. Nucleotide Metabolism
  • 1.7. Reference

1.2. Metabolism Overview

1.2.1. The core metabolism

1.3. Central carbon Metabolism

1.3.1. Flux of central carbon

1.3.2. EMP, TCA and PPP

1.3.3. Glycolysis and Glycolytic Enzymes

1.3.4. Glycogen Degradation

1.3.5. Krebs Cycle

1.3.6. Pentose Phosphate Pathway

1.3.7. Oxidative Phosphorylation

1.3.8. Warburg Effect

1.3.9. The Cori Cyle: An Anaerobic Metabolic Method for Glucogenesis

1.4. Fatty acid Metabolism

1.4.1. Fatty Acid

1.5. Amino acid Metabolism

1.5.1. Amino Acid Catabolism and Urea Cycle

1.5.2. Metabolism of Amino Acid Carbon Skeletons

1.6. Nucleotide Metabolism

1.6.1. Nucleotide Metabolism

1.7. Reference

Heirendt L, Arreckx S, Pfau T, et al. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v. 3.0[J]. Nature protocols, 2019, 14(3): 639-702.
Rowe E, Palsson B O, King Z A. Escher-FBA: a web application for interactive flux balance analysis[J]. BMC systems biology, 2018, 12(1): 84.
Brunk E, Sahoo S, Zielinski D C, et al. Recon3D enables a three-dimensional view of gene variation in human metabolism[J]. Nature biotechnology, 2018, 36(3): 272.
Nelson D L, Lehninger A L, Cox M M. Lehninger principles of biochemistry[M]. Macmillan, 2008.
Nelson D L, Cox M M. Lehninger Principles of Biochemistry Lecture Notebook[M]. Macmillan, 2004.