Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Introduction to Metabolism

Introduction to Metabolism

Metabolism encompasses all biochemical reactions in a living organism, facilitating both the breakdown and synthesis of biomolecules. These metabolic processes are categorized into catabolic and anabolic pathways, which operate in a coordinated manner to ensure energy balance and cellular function.Catabolic Pathways and Energy ReleaseCatabolic pathways involve the breakdown of complex macromolecules such as carbohydrates, lipids, and proteins into smaller structures like monosaccharides, fatty...

Amino Acid Biosynthetic Pathways

Amino Acid Biosynthetic Pathways

Amino acid biosynthesis is essential for cell growth, protein synthesis, and metabolic regulation. Cells generate essential and non-essential amino acids from metabolic intermediates to sustain vital biological functions. These intermediates originate from key metabolic pathways: glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Important precursors include α-ketoglutarate, pyruvate, oxaloacetate, phosphoenolpyruvate, and erythrose-4-phosphate, which provide...

Respiration Pathways

Respiration Pathways

Cellular respiration is a fundamental metabolic process that enables organisms to generate energy from organic molecules. One of its central pathways is the tricarboxylic acid (TCA) cycle, also known as the Krebs cycle, which plays a crucial role in energy production and biosynthetic processes.Conversion of Pyruvate to Acetyl-CoAThe pyruvate generated from glycolysis undergoes oxidative decarboxylation by the pyruvate dehydrogenase complex, producing acetyl-CoA, one molecule of NADH, and one...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Metabolic thermodynamics: pertinent reference state and energy potentials.

The FEBS journal·2026

Same author

Glycosyltransferases: glycoengineers in human milk oligosaccharide synthesis and manufacturing.

Frontiers in molecular biosciences·2025

Same author

Simulated digestions of free oligosaccharides and mucin-type O-glycans reveal a potential role for Clostridium perfringens.

Scientific reports·2024

Same author

In silico analysis of the human milk oligosaccharide glycome reveals key enzymes of their biosynthesis.

Scientific reports·2022

Same author

Parameter Reliability and Understanding Enzyme Function.

Molecules (Basel, Switzerland)·2022

Same author

Enzyme nomenclature and classification: the state of the art.

The FEBS journal·2021

Search research articles

Related Experiment Video

Updated: Jun 22, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Tracing metabolic pathways from enzyme data.

Andrew G McDonald¹, Keith F Tipton, Sinéad Boyce

¹Department of Biochemistry, Trinity College, Dublin 2, Ireland.

Biochimica Et Biophysica Acta

|July 1, 2009

Summary

This summary is machine-generated.

A new Reactions Database, derived from the IUBMB Enzyme List, facilitates metabolic pathway tracing in systems biology. This tool enables users to search reactions by substrate and visualize pathways using the Reaction Explorer application.

More Related Videos

CorrelationCalculator and Filigree: Tools for Data-Driven Network Analysis of Metabolomics Data

CorrelationCalculator and Filigree: Tools for Data-Driven Network Analysis of Metabolomics Data

Published on: November 10, 2023

Metabolic Pathway Confirmation and Discovery Through 13C-labeling of Proteinogenic Amino Acids

Metabolic Pathway Confirmation and Discovery Through ¹³C-labeling of Proteinogenic Amino Acids

Published on: January 26, 2012

Related Experiment Videos

Last Updated: Jun 22, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

CorrelationCalculator and Filigree: Tools for Data-Driven Network Analysis of Metabolomics Data

CorrelationCalculator and Filigree: Tools for Data-Driven Network Analysis of Metabolomics Data

Published on: November 10, 2023

Metabolic Pathway Confirmation and Discovery Through 13C-labeling of Proteinogenic Amino Acids

Metabolic Pathway Confirmation and Discovery Through ¹³C-labeling of Proteinogenic Amino Acids

Published on: January 26, 2012

Area of Science:

Systems Biology
Biochemistry
Bioinformatics

Background:

The IUBMB Enzyme List, while valuable for enzyme identification, lacks the detail required for metabolic pathway tracing in systems biology.
Existing databases often use generic reactions, necessitating supplementary searches in resources like BRENDA for comprehensive substrate information.
The increasing importance of pathway analysis in systems biology highlights the need for a dedicated resource.

Purpose of the Study:

To create a framework for tracing metabolic pathways involving specific enzymes or metabolites.
To develop a searchable Reactions Database from the IUBMB Enzyme List material.
To build the Reaction Explorer application for visualizing metabolic pathways.

Main Methods:

Compiled a Reactions Database from the IUBMB Enzyme List, enabling searches by substrate/product.
Integrated an extensive synonym glossary for chemical compound name variations.
Developed the Reaction Explorer application using REALbasic to query the Reactions Database and generate pathway diagrams.

Main Results:

The Reactions Database allows for pathway tracing starting from a selected substrate.
The Reaction Explorer application visually represents metabolic pathways based on user selections.
The system supports iterative pathway construction and offers options to modify or expand the pathway graph.

Conclusions:

The developed Reactions Database and Reaction Explorer application provide a crucial tool for metabolic pathway analysis in systems biology.
This resource overcomes the limitations of the IUBMB Enzyme List for pathway tracing.
The application facilitates a user-friendly approach to exploring complex metabolic networks.