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Related Concept Videos

Introduction to Metabolism01:30

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...
Respiration Pathways01:26

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...
Overview of Metabolism01:40

Overview of Metabolism

Living cells constantly carry out various chemical reactions which are necessary for their proper functioning. These reactions are interlinked to one another via multiple pathways. The collection of these chemical reactions is known as metabolism.
Plant Metabolism
Sunlight, the primary source of energy in plants, is first absorbed by the chlorophyll pigments present in their leaves. Plants then use this energy to carry out photosynthesis, where water is oxidized into oxygen and carbon dioxide...
Overview of Fatty Acid Metabolism01:28

Overview of Fatty Acid Metabolism

Lipids also are sources of energy that power cellular processes. Like carbohydrates, lipids are composed of carbon, hydrogen, and oxygen, but these atoms are arranged differently. Most lipids are nonpolar and hydrophobic. Major types include fats and oils, waxes, phospholipids, and steroids.
Fatty acids are catabolized in a process called beta-oxidation, which takes place in the matrix of the mitochondria and converts their fatty acid chains into two-carbon units of acetyl groups. The acetyl...
Amino Acid Biosynthetic Pathways01:29

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...
What is Metabolism?00:52

What is Metabolism?

Overview

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A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

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

Published on: February 8, 2017

Knowledge representation in metabolic pathway databases.

Miranda D Stobbe1, Gerbert A Jansen, Perry D Moerland

  • 1Bioinformatics Laboratory, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam, the Netherlands. Tel.: ++31 20 5667096; a.h.vankampen@amc.uva.nl.

Briefings in Bioinformatics
|December 4, 2012
PubMed
Summary
This summary is machine-generated.

Representing metabolic networks computationally is challenging. Analysis of five databases shows diverse approaches to handling missing or uncertain data, hindering integration.

Keywords:
evidence descriptionfatty acid beta oxidationknowledge representationmetabolic networkpathway databasesemantic standards

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Area of Science:

  • Systems Biology
  • Bioinformatics

Background:

  • Accurate, structured representation of metabolic networks is crucial for computational analysis.
  • Existing metabolic pathway databases employ diverse strategies for data representation, including handling uncertainty and missing information.

Purpose of the Study:

  • To analyze and compare the representation of key metabolic network concepts across major databases.
  • To identify limitations in current databases for detailed biological modeling and in silico predictions.

Main Methods:

  • Comparative analysis of five major metabolic pathway databases.
  • Evaluation of how concepts like compartments, enzymatic complexes, and reaction directionality are represented.
  • Detailed examination of three specific metabolic processes to illustrate database limitations.

Main Results:

  • Significant variations exist in how databases represent metabolic network components and handle data uncertainty.
  • Databases differ in their inclusion of crucial details like gene-protein-reaction relations and compartmentalization.
  • Current databases exhibit limitations in capturing the full biological complexity of metabolic networks.

Conclusions:

  • Conceptual differences among metabolic databases impede knowledge exchange and integration.
  • Standardized exchange formats have not yet resolved the challenges posed by these conceptual variations.