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Bipartite Metabolic Graph Structure

Run the Bipartite Metabolic Graph Structure MicroSim Fullscreen

About This MicroSim

This MicroSim visualizes a bipartite metabolic network — a graph with two distinct node types: metabolites (circles, teal) and reactions (squares, orange). Directed edges show the flow of substrates into reactions and products out, capturing the structure of metabolic pathways as a graph.

Bipartite Graph Structure

In a bipartite metabolic graph:

  • Metabolite nodes represent chemical compounds (glucose, pyruvate, ATP, etc.)
  • Reaction nodes represent enzyme-catalyzed transformations
  • Substrate edges (metabolite → reaction) show which compounds are consumed
  • Product edges (reaction → metabolite) show which compounds are produced
  • Edges only connect metabolites to reactions (never metabolite-to-metabolite or reaction-to-reaction)

Why Bipartite?

The bipartite structure enforces the biological constraint that metabolites don't spontaneously convert into each other — they must pass through an enzyme-catalyzed reaction. This makes the graph more biologically accurate than a simple metabolite-metabolite network.

How to Use

  1. Click any node to highlight all its direct connections — substrates and products for reactions, or participating reactions for metabolites
  2. Hover for tooltips showing node details
  3. Drag nodes to rearrange the layout
  4. Trace pathways — Follow directed edges from substrates through reactions to products to trace metabolic flux

Suggested Exploration

  • Find glucose and trace all the reactions it participates in as a substrate
  • Identify metabolites that appear as products of one reaction and substrates of the next — these are the intermediates of a metabolic pathway
  • Look for hub metabolites (like ATP) that participate in many reactions — these are the currency metabolites of the cell

Iframe Embed Code

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Lesson Plan

Grade Level

College introductory bioinformatics

Duration

15-20 minutes

Prerequisites

  • Basic understanding of metabolic reactions (substrates, products, enzymes)
  • Knowledge of glycolysis or the citric acid cycle
  • Concept of bipartite graphs

Activities

  1. Exploration (5 min): Identify the two node types by shape and color. Click several reaction nodes and list their substrates and products. Verify that edges only connect metabolites to reactions.
  2. Pathway Tracing (5 min): Starting from glucose, follow the directed edges through sequential reactions. How many reaction steps can you trace? This reconstructs a metabolic pathway from graph structure alone.
  3. Hub Analysis (5 min): Which metabolites are connected to the most reactions? Why are molecules like ATP, NADH, and water considered "currency metabolites"? Should they be treated differently in network analysis?
  4. Assessment (3 min): Answer the reflection questions below.

Assessment

  1. What makes a metabolic graph "bipartite," and why is this structure biologically meaningful?
  2. Why can't you have a direct edge between two metabolite nodes in a bipartite metabolic graph?
  3. What is a "currency metabolite," and why might you want to remove these from network analysis?
  4. How would you use this graph to identify all the products that can be made from a given substrate?

References

  1. Bipartite graph — Wikipedia
  2. Metabolic network — Wikipedia
  3. Metabolic pathway — Wikipedia
  4. Glycolysis — Wikipedia