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Related Concept Videos

The Citric Acid Cycle: Overview01:37

The Citric Acid Cycle: Overview

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In aerobic organisms, the citric acid cycle is the second stage of cellular respiration wherein molecules derived from the breakdown of carbohydrates, proteins, and fats are oxidized into carbon dioxide and energy. This process is also known as the tricarboxylic acid (TCA) cycle as the first product of the cycle, citric acid, contains three carboxyl groups in its structure. Alternatively, this cycle is also referred to as the Krebs cycle, in honor of its discoverer Sir Hans Krebs.
The citric...
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Products of the Citric Acid Cycle00:53

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The cells of most organisms—including plants and animals—obtain usable energy through aerobic respiration, the oxygen-requiring version of cellular respiration. Aerobic respiration consists of four major stages: glycolysis, pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation. The third major stage, the citric acid cycle, is also known as the Krebs cycle or tricarboxylic acid (TCA) cycle.
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Overview of Carbohydrate Metabolism01:19

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Carbohydrate metabolism is a fundamental biochemical process that ensures a constant supply of energy to living cells. The most important carbohydrate is glucose, which can be broken down via glycolysis to enter into the Krebs cycle and eventually lead to the production of ATP through oxidative phosphorylation.
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The Citric Acid Cycle02:36

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The citric acid cycle, also known as the Krebs cycle or TCA cycle, consists of several energy-generating reactions that yield one ATP molecule, three NADH molecules, one FADH2 molecule, and two CO2 molecules.
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The Citric Acid Cycle: Output01:28

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The citric acid cycle is termed an amphibolic pathway as it operates both anabolically and catabolically. The cyclic reactions balance the flux of the substrates to provide an optimal concentration of NADH and ATP to the cell.
Regulation of Citric Acid Cycle
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Glucose is the source of nearly all energy used by organisms. The first step of converting glucose into usable energy is called glycolysis. Glycolysis occurs in the cytosol of the cell over two phases: an energy-requiring phase and an energy-releasing phase. Over the first three steps, glucose is converted into different forms and attached to two phosphate groups donated by two ATP molecules, resulting in an unstable sugar. In the next two stages, the unstable sugar splits into two sugar...
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A Web Tool for Generating High Quality Machine-readable Biological Pathways
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Circular van Krevelen diagram for visualizing metabolic pathways.

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  • 1The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA.

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|June 12, 2025
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Summary

This study introduces a novel circularized van Krevelen diagram for metabolic pathway visualization, addressing limitations of manual and existing automated methods. This chemically-based approach enhances consistency for scientific collaboration and data interpretation.

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Area of Science:

  • Biochemistry
  • Systems Biology
  • Bioinformatics

Background:

  • Traditional metabolic maps struggle to keep pace with emerging biochemical data due to manual layouts.
  • Existing automated metabolic pathway visualization methods lack consensus and broad adoption.
  • Effective visualization is crucial for interpreting complex biochemical datasets.

Purpose of the Study:

  • To develop a novel, automated approach for metabolic pathway visualization.
  • To establish a chemically-principled method for consistent and reliable pathway mapping.
  • To facilitate the interpretation of metabolomics data and the creation of updated metabolic maps.

Main Methods:

  • Development of a new visualization technique based on the circularized van Krevelen diagram.
  • Application of chemical principles to ensure consistency and accuracy in pathway representation.
  • Demonstration of utility through metabolomics data interpretation and map generation.

Main Results:

  • A novel, chemically-grounded method for metabolic pathway visualization was established.
  • The circularized van Krevelen diagram approach offers improved consistency over traditional methods.
  • The method provides a practical tool for metabolomics data interpretation.

Conclusions:

  • The circularized van Krevelen diagram offers a robust and consistent solution for metabolic pathway visualization.
  • This approach supports scientific collaboration by providing a standardized visualization method.
  • The technique has direct applications in analyzing metabolomics data and updating metabolic maps.