Biochemistry and Metabolism

  • Requirement for energy
    • Glycolysis
      • The fate of pyruvate
        • Aerobic
          • Mitochondria
          • Citric acid cycle
          • Oxidative: release electron
          • NAD+ and FAD
          • NADH and FADH2
        • Anaerobic
    • Citric acid cycle
      • Acetyl CoA + OAA --> Citrate
      • Alpha-ketoglutarate
      • Succinate
      • OAA
      • Energy release
        • Succinyl CoA --> Succinate (GDP to GTP)
        • NADH FADH2
      • Alternative fates of citric acid cycle intermediates
        • Carboxylation of pyruvate to OAA
        • Pyruvate carboxylase
    • Oxydative phosphorylation
      • Oxidative reactions
      • Electrons
      • NADH, FADH2
      • Electron transport chain
      • Inner mitochondrial membrane
      • Protons translocated out
      • Proton gradient
      • Enzyme complexes
        • Complex I (NADH-ubiquinone oxidoreductase)
        • Complex II (Succinate-ubiquinone oxireductase)
        • Complex III (Ubiquinol-cytochrome c oxireductase)
        • Complex IV (Cytochrome oxidative)
      • Oxygen
      • Fate of cytosolic NADH
        • Glycolysis
        • NADH
        • Mitochondrial electron transport chain
          • Indirect
          • via shuttles
            • Glycerol phosphate
            • Malate
        • Intramitochondial NAD+ or FAD
      • ATP synthesis
        • Complex I, III, and IV
          • Translocate protons out
          • Against electrochemical gradient
            • Proton-motive force
        • ATP synthase
          • Complex V
          • Inner mitochondrial membrane, membrane-spanning region (proton channel)
          • Rotation of shaft
          • ATP from ADP and Phosphate
        • ATP-ADP translocator
        • Stoichiometry of ATP synthesis
          • 1NADH --> 3ATP
          • FADH2 --> 2ATP
            • Bypass proton-pumping NADH-Q
          • Proton-motove force
            • ATP for ADP
            • Phosphate for hydroxide
          • Uncoupling proteins (mitochondria)
            • Dissipate H+ without forming ATP
          • Generate heat in brown fat
    • Pentose phosphate pathway
      • Glucose
      • Ribose, NADPH
      • Pentose phosphate pathway
      • Actively deciding cells
      • Ribose
        • Precursor for DNA and RNA
        • Sugar component CoA and NAD+
      • NADPH
        • Biosynthetic reactions
          • Fatty acid synthesis
          • Not interchangeable with NADH
      • Part 1
        • Glucose-6-phosphate
        • Ribose, NADPH
        • Liver, adipose tissue, lactating mammary gland, adrenal cortex, red blood cells
        • Reducing power of NADPH
        • Biosynthesis of cholesterol and fatty acids
        • Formation of glutathione in erythrocytes
        • Enzyme: Glucose-6-phosphate dehydrogenase  (G6PD)
          • Regulated by NADP+
        • Ribulose-5-phosphate
        • Ribose-5-phosphate
        • Results
          • Oxidation
          • 2NADPH, 1ribose-5-phosphatase
          • 1CO2 released
        • Irreversible
      • Part 2
        • Ribose
        • Reconverted
        • Glycolytic intermediates
        • Reversible and ubiquitous
        • Demands for NADPH and ribose not exactly matched
        • >NADPH needed
          • Excess ribose recycled
          • Non-oxydative reactions
          • 3pentoses to 2 hexoses and 1triose
          • Feedbacked into glycolysis
        • >Ribose
          • Ribose-5-phosphatase 
          • From glycolytic intermediates
  • Carbohydrates
    • Gluconeogenesis
      • Gluconeogenic substrates 
        • Amino acids
          • Diet
          • Proteolysis
        • Lactate
          • Exercising muscle
        • Glycerol
          • Triacylglycerols
      • Gluconeogenic pathway
        • Pyruvate to glucose
        • vs glycolysis
          • Pyruvate to phosphoenolpyruvate (PEP)
            • OAA intermediate
            • Enzymes
              • Pyruvate carboxylase
              • PEP carboxykinase
            • Hydrolysis
              • ATP
              • AGP
            • In glycolysis
              • Pyruvate kinase
              • Yielding ATP
          • Dephosphorylation
            • Fructose-1,6-biphosphanate to fructose-6-phosphate
            • Glucose-6-phosphate to glucose
            • No high-energy phosphate bonds
            • In glycolysis
              • Split high-energy phosphate bonds of ATP
    • Glycogen
      • Glycogen synthesis
      • Glycogenolysis
    • Glycosaminoglycans (mucopolysacharides)
    • Regulation of glucose metabolism
      • Response to hypoglycaemia
      • Response to exercise or stress
      • Response to rasied glucose levels
  • Fatty acids and lipids 
    • Fatty acids
      • Saturated vs unsaturated 
      • Nomenclature
      • Synthesis
        • Exit of acetyl CoA from the mitochondrion
        • Acetyl CoA carboxylation
          • Growth of the acyl chain
        • Elaongation and desaturation
        • Degradation
          • Oxidation of unsaturated fatty acids
        • Ketones bodies
          • Ketone body utilisation
    • Lipids
      • Triacylglycerols
        • Biosynthesis
        • Degradation
        • Hormonal regulation of fat metabolism
      • Phospholipids 
        • Phosphoglycerdes
        • Sphingolipids 
        • Glycolipids
  • Cholesterol and steroid hormones
    • Biosynthesis
    • Elimination
    • Steroid hormones
  • Amino acids and proteins
    • Amino acids 
      • Structure
      • Biosynthesis
      • Degradation
        • The urea cycle
      • Hormones derived from amino acids
        • Dopamine, adrenaline and noradrenaline
        • Thyroxine
        • Serotonin
        • GABA and glycine
        • Histamine
    • Proteins
      • Synthesis
      • Degradation
  • Haem
    • Biosynthesis
      • Regulation of harm synthesis
      • Degradation
  • Nucleotides
    • Purine synthesis
    • Pyrimidines synthesis
    • Salvage pathways
    • Purine degradation
    • Vitamins
      • Vitamin A
      • Vitamin B
      • Vitamin C
      • Vitamin D
      • Vitamin E
      • Vitamin K
    • Trace elements
      • Iron
      • Zinc
      • Copper
      • Selenium
      • Manganase and cobalt
      • Other (possible) trace elements



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