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Related Concept Videos

Overview of Metabolism01:40

Overview of Metabolism

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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...
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Metabolism of Chemolithotrophs01:15

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Chemolithotrophs are microorganisms that obtain energy by oxidizing inorganic molecules such as hydrogen gas (H₂), ammonia (NH₃), reduced sulfur compounds (H₂S, S²⁻), and ferrous iron (Fe²⁺). Unlike heterotrophic organisms that rely on organic carbon, chemolithotrophs transfer electrons from these inorganic donors to the electron transport chain (ETC), generating a proton motive force (PMF) that drives ATP synthesis through oxidative phosphorylation.
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Other Glycolytic Pathways01:24

Other Glycolytic Pathways

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The pentose phosphate pathway (PPP) operates in parallel with glycolysis, facilitating the metabolism of both pentoses and glucose. This pathway consists of two distinct phases: the oxidative and non-oxidative phases. While it does not directly generate ATP, the intermediates formed during the process can integrate into glycolysis, contributing to cellular energy metabolism when required.Oxidative Phase: NADPH ProductionThe oxidative phase of the pentose phosphate pathway is primarily...
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Overview of Protein Metabolism01:21

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Proteins are broken down into amino acids during digestion. Unlike fats and carbohydrates, which are stored for later use, proteins are not. Instead, amino acids are either used to produce ATP through oxidation or contribute to the creation of new proteins for the growth and repair of the body. Any surplus amino acids from the diet are converted into glucose or triglycerides rather than excreted.
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Introduction to Metabolism01:30

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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...
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Amino Acid Biosynthetic Pathways01:29

Amino Acid Biosynthetic Pathways

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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...
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Related Experiment Video

Updated: Jul 31, 2025

A Web Tool for Generating High Quality Machine-readable Biological Pathways
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CAVE: a cloud-based platform for analysis and visualization of metabolic pathways.

Zhitao Mao1,2, Qianqian Yuan1,2, Haoran Li1,2

  • 1Biodesign Center, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.

Nucleic Acids Research
|May 9, 2023
PubMed
Summary
This summary is machine-generated.

Flux balance analysis (FBA) is crucial for metabolic engineering but requires coding skills. We developed CAVE, a cloud platform, to simplify FBA pathway calculation and visualization for biologists, aiding in metabolic engineering and target identification.

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Area of Science:

  • Metabolic Engineering
  • Computational Biology
  • Systems Biology

Background:

  • Flux balance analysis (FBA) is vital for optimizing chemical production in genome-scale metabolic models (GEMs).
  • Biologists face challenges with FBA due to coding skill requirements and time-consuming manual pathway visualization.
  • Existing tools lack integrated error correction and feature identification for metabolic pathways.

Purpose of the Study:

  • To develop an accessible cloud-based platform (CAVE) for FBA calculation, visualization, and model correction.
  • To enable biologists to easily analyze and engineer metabolic pathways without extensive coding knowledge.
  • To facilitate the identification of unique metabolic features and streamline error detection in GEMs.

Main Methods:

  • CAVE integrates FBA calculation with interactive pathway visualization.
  • The platform supports analysis of numerous published and user-uploaded GEMs.
  • CAVE includes model modification tools for gene/reaction addition or removal.

Main Results:

  • CAVE enables rapid analysis and visualization of metabolic pathways from over 100 GEMs.
  • The platform facilitates quicker identification of distinctive metabolic features within specific GEMs.
  • Users can easily correct pathway analysis errors and refine metabolic models using CAVE's modification functions.

Conclusions:

  • CAVE democratizes FBA for metabolic engineering by removing coding barriers.
  • The platform enhances the examination and correction of metabolic pathways, leading to more reliable results.
  • CAVE is a valuable tool for rational metabolic engineering across diverse organisms, complementing existing visualization methods.