Pathways to model

[csmangum]

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

• Glycolysis: Converts glucose into pyruvate, generating ATP and NADH. #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.