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Amino Acid Biosynthetic Pathways01:29

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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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The gene encoding the main signaling molecules of the Wnt signaling pathways (the Wnt proteins) was discovered almost four decades ago by Nüsslein-Volhard and Wieschaus. They identified and originally named the gene "wingless" (wg) after a phenotype discovered during their landmark genetic screen in Drosophila for body pattern defects. At around the same time, another researcher named Harold Varmus found that a murine tumor virus activates the mammalian wg homolog, Int-1, which...
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Wnt is a zygotic effect gene that is expressed during very early embryonic development. It regulates various processes in animals starting from early development through the adult stage, such as organogenesis in the embryo and maintenance of neuronal and blood stem cells. Wnt proteins can induce a wide variety of intracellular pathways depending upon the specific abilities of different Wnt ligands to form a complex with shared and cognate receptors in the presence of different co-receptors. The...
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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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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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Several cytokine receptors have tightly bound Janus kinase or JAK proteins attached at their cytosolic tail. Small signaling molecules such as cytokines, growth hormones, or prolactins bind to the cytokine receptors and initiate their dimerization. The dimerization brings the cytosolic JAKs together that trans-phosphorylate and activates each other. The activated JAKs now phosphorylate cytosolic tails of the cytokine receptors, which serve as binding sites for adaptor proteins such as  SH2...
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Pathway Commons, a web resource for biological pathway data.

Ethan G Cerami1, Benjamin E Gross, Emek Demir

  • 1Computational Biology Center, Memorial Sloan-Kettering Cancer Center 1275 York Avenue, Box 460, New York, NY 10065, USA.

Nucleic Acids Research
|November 13, 2010
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Summary
This summary is machine-generated.

Pathway Commons is a central hub for biological pathway data, integrating information from multiple sources. It offers tools for biologists and developers to access and analyze pathway interactions across various organisms.

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Area of Science:

  • Systems Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • Biological pathways are crucial for understanding cellular functions.
  • Existing pathway data is often fragmented across various databases.
  • A unified resource is needed for comprehensive pathway analysis.

Purpose of the Study:

  • To create a centralized, integrated repository of biological pathway data.
  • To provide accessible tools for searching, browsing, and downloading pathway information.
  • To facilitate data sharing among pathway database providers.

Main Methods:

  • Integration of pathway data from multiple public databases.
  • Standardization of data representation using a common language.
  • Development of a web interface, download site, and web services.

Main Results:

  • Pathway Commons aggregates data from nine databases, containing over 1400 pathways and 687,000 interactions.
  • Provides a unified view of biochemical reactions, complex assemblies, and physical interactions.
  • Supports data access for biologists and software developers.

Conclusions:

  • Pathway Commons serves as a valuable, comprehensive resource for biological pathway exploration.
  • The platform facilitates research by integrating diverse pathway data.
  • Continuous expansion and updates ensure the resource remains current.