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Dooders / Pyology

A metaphorical model of a biological cell

MIT License

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Pathways to model #44

Open csmangum opened 1 month ago

csmangum commented 1 month ago

1. Central Metabolism (Energy production and basic cellular function)

[x] #45
[ ] Citric Acid Cycle (Krebs Cycle/TCA Cycle): Breaks down pyruvate into carbon dioxide, producing NADH, FADH2, and ATP.
[ ] Oxidative Phosphorylation/Electron Transport Chain: Uses NADH and FADH2 to produce ATP through redox reactions.
[ ] Pentose Phosphate Pathway (PPP): Provides NADPH and ribose-5-phosphate for nucleotide synthesis.

2. Macromolecule Synthesis Pathways (Building blocks for the cell)

[ ] Amino Acid Biosynthesis: Synthesis pathways for essential and non-essential amino acids.
[ ] Nucleotide Biosynthesis: Production of purines and pyrimidines for DNA and RNA.
[ ] Fatty Acid Synthesis: Pathways for creating lipids and membrane components.
[ ] Protein Synthesis (Translation): Process of translating mRNA into proteins using ribosomes.

3. Anabolic Pathways (Building up complex molecules)

[ ] Gluconeogenesis: Synthesis of glucose from non-carbohydrate sources.
[ ] Lipid Metabolism: Pathways for lipid synthesis and storage.
[ ] Photosynthesis: Includes light-dependent reactions and the Calvin cycle (for plant cells).

4. Catabolic Pathways (Breaking down complex molecules)

[ ] Beta-Oxidation: Breakdown of fatty acids into acetyl-CoA.
[ ] Amino Acid Degradation: Pathways to catabolize amino acids into intermediates for metabolism.

5. Regulatory Pathways

[ ] Cell Cycle Regulation: Mechanisms like cyclins and CDKs for controlling cell division.
[ ] Signal Transduction Pathways: Includes MAPK/ERK, cAMP, and receptor tyrosine kinase pathways.
[ ] Apoptosis Pathways: Mechanisms for programmed cell death.

6. Stress and Response Pathways

[ ] DNA Repair Mechanisms: Includes nucleotide excision repair and mismatch repair.
[ ] Antioxidant Pathways: Systems like the glutathione pathway.
[ ] Heat Shock Response: Involves heat shock proteins for stress management.

7. Transport Pathways

[ ] Membrane Transport Mechanisms: Channels, carriers, and pumps for molecule transport.
[ ] Endocytosis and Exocytosis: Mechanisms for intake and release of large molecules or particles.

8. Metabolic Regulation and Homeostasis

[ ] Hormonal Regulation: Pathways involving insulin, glucagon, and other energy-regulating hormones.
[ ] AMPK Pathway: Activates catabolic pathways when energy is low.

9. Cellular Growth and Repair

[ ] mTOR Pathway: Controls cell growth and protein synthesis in response to nutrients.
[ ] Autophagy Pathways: Processes for degrading and recycling cellular components.