Chapter 2   |   Metabolites go on specific journeys

Metabolic pathways are a multi-step series of biochemical reactions either breaking down a nutrient molecule or building up a biomolecule via metabolic intermediates. The pathways in mammalian cells atleast are quite complex with many intersections. They are essential for maintaining the homeostasis of an organism. In this chapter, we will visualize how carbon flows through a few of those key pathways.

 

1. This chapter can be viewed after students have completed chapter 1 and are introduced to biochemical pathways in Biochemistry and Metabolism. Students can view the animations in the 'PATHWAYS' section at their own pace. Alternatively, since the animations do not have audio the instructor can describe the pathway while the students watch the animations in class.

2. These animations focus only on metabolites and do not contain any enzyme information. They provide information on where high energy electrons are used or released. The instructor needs to provide more reaction details if desired.

3. Some sample discussion questions have been provided in the 'QUESTIONS' section of this page. Students are encouraged to engage with these questions either on their own or in a group after viewing the animations. This could be guided by the instructor.

4. The fluxes visualized in these animations are derived from data in research publications listed in the 'REFERENCES' section. The depicted fluxes are net fluxes in mammalian cells, so it is key to remember that forward and reverse fluxes for reversible reactions are not shown. The instructor may need to indicate that. The 'REFERENCES' section may also contain additional learning resources.

5. HOW TO READ THE ANIMATIONS? Each blue spherical particle in the animation represents a metabolite. This simplified representation has been used to clearly visualize the amount of flux. The unit of flux is nmoles/(h*µl of cells). In the animation, what occurs in 1 µl of cells in one hour has been shown in 1 cell in one second. It has been shown in one cell to show compartmentalization within a cell. In zoomed animations, the metabolite in focus has been representated by its carbon (C) chain structure.

PATHWAYS

  Glycolysis

This animation shows carbon flux from glucose (6-carbon (C) metabolite) through the catabolic pathway of glycolysis where glucose is broken down into pyruvate (3C metabolite) in the cytosol. Note the energy consumed and released during this process.Click here to download

 

 

  Glycolysis (zoomed)

This is a zoomed version of glycolysis with a metabolite represented in its carbon chain structure. The cyan flash represents occurence of a reaction or conversion of a metabolite.Click here to download

 

 

  Fermentation

This video shows the process of Fermentation - an anaerobic biochemical process in the cytosol. Imagine this mammalian cell to be a muscle cell while vigorously exercising. In that case, oxygen availability runs a bit low. Most of the pyruvate (3C metabolite) formed from glycolysis is reduced to lactate (3C metabolite). NADH is used up releasing NAD+ which is re-utilized during glycolysis to quickly produce more ATP for energy. In this case, carbon flux from glucose (6C metabolite) ends up in lactate (3C metabolite) that is mostly excreted from the cell.Click here to download

 

 

  TCA Cycle

This animation shows the Kreb's Cycle or Tricarboxylic Acid Cycle (TCA) or Citric Acid Cycle. In this catabolic pathway, acetyl CoA (2C metabolite) formed from pyruvate (3C metabolite) in the mitochondria, is oxidised releasing a lot of energy in the process. Here, the initial carbon flux from glucose (6C metabolite) eventually goes on to get oxidised into carbon dioxide (1C metabolite). The cofactors/coenzymes will proceed to the electron transport chain at the inner mitochondrial membrane, where oxygen is reduced to water and the protons pumped through the membrane power ATP synthase to make a lot of ATP. This process is called aerobic respiration or oxidative phosphorylation.Click here to download

 

 

  TCA Cycle (zoomed)

This is a zoomed version of the TCA cycle with a metabolite represented in its carbon chain structure. The cyan flash represents occurence of a reaction or conversion of a metabolite.Click here to download

 

 

  M-A Shuttle

The Malate-Aspartate or M-A Shuttle provides an important way to regulate glycolysis and lactate metabolism by transferring reducing equivalents (NADH) generated during these processes from the cytosol into the mitochondria for ATP production and utilization. Cytosolic NAD+ must then be regenerated to maintain glycolytic flux and lactate (3C metabolite) conversion to pyruvate (3C metabolite).Click here to download

 

 

  PPP

This animation shows carbon flux through the catabolic Pentose Phosphate Pathway or PPP in the cytosol. Glucose 6-phosphate (6C metabolite) is oxidised to ribose 5-phosphate (5C metabolite) and reduced coenzymes are produced. The products of PPP fuel anabolic pathways like nucleotide and fatty acid synthesis.Click here to download

 

 

  Citrate to Fatty Acid

In some cases, citrate (6C metabolite) produced during the TCA cycle can lead to the production of acetyl CoA (2C metabolite) in the cytosol, that goes into the synthesis of fatty acids (many carbon metabolite). Since this is an anabolic reaction it uses energy carriers like NADP+ and requires energy in the form of ATP. Here, carbon flux through citrate to fatty acids could be attributed to carbon from glucose (6C metabolite) or glutamine (5C metabolite) (See Chapter 3).Click here to download

QUESTIONS

1. In the TCA cycle animation if conversion of pyruvate to acetyl-CoA is blocked what would happen? Do you know which enzyme carries out this reaction? Do you also know how pyruvate enters the mitochondrial matrix?

2. When do you think you would see a reverse flux of production of pyruvate from lactate?

REFERENCES

1. Park et al., Metabolite concentrations, fluxes and free energies imply efficient enzyme usage. Nat Chem Biol. Vol2. 2016.

2. Jiang et al., Quantitative metabolic flux analysis reveals an unconventional pathway of fatty acid synthesis in cancer cells deficient for the mitochondrial citrate transport protein. Metab Eng. 43(Pt B). 2017.

3. Munger et al., Systems-level metabolic flux profiling identifies fatty acid synthesis as a target for antiviral therapy.Nat Biotechnol. 26(10) 2008.

4. Lu et al., Role of the Malate-Aspartate shuttle on the metabolic response to myocardial ischemia. J Theor Biol. 254(2) 2008.

 

OTHER VISUAL RESOURCES

1. Cellular respiration animations by Drew Berry and HHMI BioInteractive.

2. Animations on cell biology of the mitochondria by BioVisions and HarvardX.

TERMS OF USE

This work falls under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

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