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Related Concept Videos

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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Respiration Pathways01:26

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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...
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cAMP-dependent Protein Kinase Pathways01:25

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Cyclic Adenosine Monophosphate (cAMP) is an essential second messenger that activates protein kinase A (PKA) and regulates various biological processes. A single epinephrine molecule binds to GPCR and activates several heterotrimeric G proteins, each stimulating multiple adenylyl cyclase, amplifying the signal, and synthesizing large numbers of cAMP molecules. Small changes in cAMP concentration affect PKA activity. The binding of four cAMP molecules induces a conformational change in PKA,...
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Interactions Between Signaling Pathways01:19

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Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
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Enzyme-linked Receptors01:00

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Enzyme-linked receptors are proteins that act as both receptor and enzyme, activating multiple intracellular signals. This is a large group of receptors that include the receptor tyrosine kinase (RTK) family. Many growth factors and hormones bind to and activate the RTKs.
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Most plants use the C3 pathway for carbon fixation. However, some plants, such as sugar cane, corn, and cacti that grow in hot conditions, use alternative pathways to fix carbon and conserve energy loss due to photorespiration. Photorespiration is the process that occurs when the oxygen concentration is high. Under such conditions, the rubisco enzyme in the Calvin cycle binds O2 instead of CO2, which halts photosynthesis and consumes energy.
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A Web Tool for Generating High Quality Machine-readable Biological Pathways
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The Reactome Pathway Knowledgebase.

Antonio Fabregat1,2, Steven Jupe1, Lisa Matthews3

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.

Nucleic Acids Research
|November 18, 2017
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Summary
This summary is machine-generated.

Reactome is a biological pathway knowledgebase that archives cellular processes and aids in discovering functional relationships. Recent updates enhance its performance, accessibility, and data re-use for researchers.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Bioinformatics

Background:

  • The Reactome Knowledgebase offers detailed molecular pathways for cellular processes.
  • It serves as an archive and a tool for discovering functional relationships in biological data.
  • Growing complexity necessitates performance and accessibility improvements.

Purpose of the Study:

  • To enhance the Reactome Knowledgebase's performance, accessibility, and data re-use.
  • To support the continued growth in the size and complexity of Reactome.
  • To improve user experience for accessing and utilizing pathway information.

Main Methods:

  • Implemented a graph database for efficient data management.
  • Improved performance of data analysis and diagram viewer tools.
  • Developed new data structures and strategies for enhanced visualization.
  • Redesigned the website with adaptive design and interactive features.

Main Results:

  • Enhanced performance of data analysis and pathway visualization.
  • Improved website accessibility with interactive Enhanced High Level Diagrams (EHLDs).
  • Simplified navigation, subpathway highlighting, and zooming capabilities.
  • Enabled export of pathway diagrams for increased content re-use.

Conclusions:

  • Reactome provides a robust platform for understanding cellular processes and functional relationships.
  • Technical and design improvements enhance data accessibility and usability for researchers.
  • The updated knowledgebase facilitates deeper biological data exploration and re-use.