biochemical cascade

 

  • In the first one, first messenger cross through the cell membrane, binding and activating intracellular receptors localized at nucleus or cytosol, which then act as transcriptional
    factors regulating directly gene expression.

  • A biochemical cascade, also known as a signaling cascade or signaling pathway, is a series of chemical reactions that occur within a biological cell when initiated by a stimulus.

  • This response is slower than the first because it involves more steps, like transcription of genes and then the effect of newly formed proteins in a specific target.

  • The pathways are a series of reactions, in which a zymogen (inactive enzyme precursor) of a serine protease and its glycoprotein co-factors are activated to become active
    components that then catalyze the next reaction in the cascade, ultimately resulting in cross-linked fibrin.

  • This stimulus, known as a first messenger, acts on a receptor that is transduced to the cell interior through second messengers which amplify the signal and transfer it to
    effector molecules, causing the cell to respond to the initial stimulus.

  • The complex formed produces or releases second messengers that integrate and adapt the signal, amplifying it, by activating molecular targets, which in turn trigger effectors
    that will lead to the desired cellular response.

  • This response is quick, as it involves regulation of molecules that are already present in the cell.

  • The secondary messengers like or could also induce or repress gene expression, via transcriptional factors.

  • The transcriptional factors are activated by the primary messengers, in most cases, due to their function as nuclear receptors for these messengers.

  • These receptors may have intrinsic catalytic activity or may be coupled to effector enzymes, or may also be associated to ionic channels.

  • [2] Different parts of the embryo have different concentrations of hedgehog signaling proteins, which give cells information to make the embryo develop properly and correctly
    into a head or a tail.

  • It is the case for the vast majority of responses as a consequence of the binding of the primary messengers to membrane receptors.

  • Another example, sonic hedgehog signaling pathway, is one of the key regulators of embryonic development and is present in all bilaterians.

  • [6] Another example, sonic hedgehog signaling pathway, is one of the key regulators of embryonic development and is present in all bilaterians.

  • [15] This specialized cell is capable of:[16] Regulate glucose metabolism[4][5][17] Via (transducers of regulated)/ Expression of enzymes for synthesis, storage and distribution
    of glucose Synthesis of acute phase proteins[18][19][20] Via (acute phase response element) Expression of reactive protein, globulin protease inhibitors, complement, coagulation and fibrinolytic systems and iron homeostasis Regulate iron homeostasis
    (acute phase independent)[4][20][21] Via Hepcidin expression Regulate lipid metabolism Via (response element) Expression of Exocrine production of bile salts and other compounds Degradate of toxic substances Via Expression of transporters
    Endocrine production Via (growth hormone response element) and expression Via (thyroid hormone response element) Angiotensinogen expression Regenerate itself by hepatocyte mitosis Cell growth, proliferation, survival, invasion and motility
    The hepatocyte also regulates other functions for constitutive synthesis of proteins (albumin) that influences the synthesis or activation of other molecules (synthesis of urea and essential amino acids), activate vitamin D, utilization of
    vitamin K, transporter expression of vitamin A and conversion of thyroxine.

  • The cadherin pathway also has an important function in survival and proliferation because it regulates the concentration of cytoplasmic.

  • When is free in the cytoplasm, normally it is degraded, however if the signalling is activated, degradation is inhibited and it is translocated to the nucleus where it forms
    a complex with transcription factors.

  • [8] Negative cascades include: Ischemic cascade Cell-specific biochemical cascades Epithelial cells[edit] Adhesion is an essential process to epithelial cells so that epithelium
    can be formed and cells can be in permanent contact with extracellular matrix and other cells.

  • In order to function, integrins have to form complexes with proteins.

  • Biochemical cascades include: The Complement system The Insulin Signaling Pathway The Sonic hedgehog Signaling Pathway The Adrenergic receptor Pathways The Acetylcholine receptor
    Pathways The Mitogen-activated protein kinase cascade Conversely, negative cascades include events that are in a circular fashion, or can cause or be caused by multiple events.

  • [13][14] Hepatocytes[edit] The hepatocyte is a complex and multifunctional differentiated cell whose cell response will be influenced by the zone in hepatic lobule, because
    concentrations of oxygen and toxic substances present in the hepatic sinusoids change from periportal zone to centrilobular zone.

  • then is responsible for activation of several proteins, like (leads to activation of pathway, which consequently leads to activation of) and (can also activate).

  • then is responsible for activation of several proteins, like (leads to activation of pathway, which consequently leads to activation of) and (can also activate).

  • These receptors, that recognize the antigen soluble (cells) or linked to a molecule on Antigen Presenting Cells ( cells), do not have long cytoplasm tails, so they are anchored
    to signal proteins, which contain a long cytoplasmic tails with a motif that can be phosphorylated ( immunoreceptor tyrosine-based activation motif) and resulting in different signal pathways.

  • These receptors, that recognize the antigen soluble (cells) or linked to a molecule on Antigen Presenting Cells ( cells), do not have long cytoplasm tails, so they are anchored
    to signal proteins, which contain a long cytoplasmic tails with a motif that can be phosphorylated ( immunoreceptor tyrosine-based activation motif) and resulting in different signal pathways.

  • [43] The leukocyte adhesion cascade steps and the key molecules involved in each step After a vascular injury occurs, platelets are activated by locally exposed collagen (glycoprotein
    VI receptor), locally generated thrombin , platelet-derived (receptor) and that is either released from damaged cells or secreted from platelet dense granules.

  • [43] The leukocyte adhesion cascade steps and the key molecules involved in each step After a vascular injury occurs, platelets are activated by locally exposed collagen (glycoprotein
    VI receptor), locally generated thrombin , platelet-derived (receptor) and that is either released from damaged cells or secreted from platelet dense granules.

  • The differentiation of cells to plasma cells is also an example of a signal mechanism in lymphocytes, induced by a cytokine receptor.

  • The differentiation of cells to plasma cells is also an example of a signal mechanism in lymphocytes, induced by a cytokine receptor.

  • One example of a protein that binds to adaptor proteins and become activated is that is very important in the lymphocyte signal pathways.

  • One example of a protein that binds to adaptor proteins and become activated is that is very important in the lymphocyte signal pathways.

  • In this case, some interleukins bind to a specific receptor, which leads to activation of pathway.

  • In this case, some interleukins bind to a specific receptor, which leads to activation of pathway.

  • The canonical signaling involves binding of to and co-receptor, leading to phosphorylation and inhibition of β-catenin degradation, resulting in its accumulation and translocation
    to the nucleus, where it acts as a transcription factor.

  • The canonical signaling involves binding of to and co-receptor, leading to phosphorylation and inhibition of β-catenin degradation, resulting in its accumulation and translocation
    to the nucleus, where it acts as a transcription factor.

  • This pathway can be triggered via two mechanisms: physiological stimulus (like reduced O2 tension) and activation of the prostacyclin receptor.

  • This pathway can be triggered via two mechanisms: physiological stimulus (like reduced O2 tension) and activation of the prostacyclin receptor.

  • The antigen receptor and signal protein form a stable complex, named or , in or cells, respectively.

  • The antigen receptor and signal protein form a stable complex, named or , in or cells, respectively.

  • Consequently, the protein is translated and inhibits , allowing immunoglobulin genes transcription and activation of (important for the secretory apparatus formation and enhancing
    of protein synthesis).

  • Consequently, the protein is translated and inhibits , allowing immunoglobulin genes transcription and activation of (important for the secretory apparatus formation and enhancing
    of protein synthesis).

  • These proteins after phosphorylation become activated and allow binding of others enzymes that continue the biochemical cascade.

  • These proteins after phosphorylation become activated and allow binding of others enzymes that continue the biochemical cascade.

  • [50][51][52] Also, the coreceptors play an important role because they can improve the antigen/receptor binding and initiate parallel cascade events, like activation Kinase.

  • [50][51][52] Also, the coreceptors play an important role because they can improve the antigen/receptor binding and initiate parallel cascade events, like activation Kinase.

  • The activation leads to a higher expression of enzymes involved in glutathione syntheses and metabolism, that have a key role in antioxidant response.

  • The activation leads to a higher expression of enzymes involved in glutathione syntheses and metabolism, that have a key role in antioxidant response.

  • It is characterized by binding of to Frizzled and activation of G proteins and to an increase of intracellular levels of calcium through mechanisms involving.

  • It is characterized by binding of to Frizzled and activation of G proteins and to an increase of intracellular levels of calcium through mechanisms involving.

  • The family is essential for signal transduction in these cells, because it is responsible for phosphorylation of.

  • [62] Extrinsic regulation is made by signals from the niche, where stem cells are found, which is able to promote quiescent state and cell cycle activation in somatic stem
    cells.

  • In fetal stem cells, mitogens promote a relatively rapid transition through cooperative action of cyclin and cyclin to inactivate family proteins.

  • [58][59] Under certain circumstances adenosine stimulates bone destruction and in other situations it promotes bone formation, depending on the purinergic receptor that is
    being activated.

  • The signaling pathway leads to sperm cells capacitation; however, adenylyl cyclase in sperm cells is different from the somatic cells.

  • [61] At cell cycle level there is an increase of complexity of the mechanisms in somatic stem cells.

  • In the absence of mitogenic signals, and the transition are suppressed by cell cycle inhibitors including and family proteins.

  • This reduces the sensitivity of stem cells to mitogenic signals by inhibiting cyclin complexes.

  • There are some signaling pathways, such as (Leukemia inhibitory factor/Janus kinase/Signal transducer and activator of transcription 3) and (Bone morphogenetic proteins/ Mothers
    against decapentaplegic/ Inhibitor of differentiation), mediated by transcription factors, epigenetic regulators and others components, and they are responsible for self-renewal genes expression and inhibition of differentiation genes expression,
    respectively.

  • As a result, is hypophosphorylated and inhibits, promoting quiescence in -phase of the cell cycle.

  • [58] Adenosine may have opposite effects on bone metabolism, because while certain purinergic receptors stimulate adenylyl cyclase activity, others have the opposite effect.

  • In addition, calcium and together work to activate , which goes on to phosphorylate other molecules, leading to altered cellular activity.

  • Stem cells[edit] Self-renewal and differentiation abilities are exceptional properties of stem cells.

  • [68] Concomitantly, oocyte growth is initiated by binding of to its receptor in the oocyte, leading to the activation of , allowing oocyte survival and development.

  • [63] Asymmetric division is characteristic of somatic stem cells, maintaining the reservoir of stem cells in the tissue and production of specialized cells of the same.

  • The Rankl and Rank signaling pathway regulates osteoclastogenesis, as well as, the survival and activation of osteoclasts.

  • is activated and degrades, leading to cell cycle progression and oocyte maturation.

  • [110] The database is a collection of manually drawn pathway maps for metabolism, genetic information processing, environmental information processing such as signal transduction,
    ligand–receptor interaction and cell communication, various other cellular processes and human diseases, all based on extensive survey of published literature.

  • Pathway construction can have either a data-driven objective or a knowledge-driven objective Data-driven pathway construction is used to generate relationship information
    of genes or proteins identified in a specific experiment such as a microarray study.

  • [104] Knowledge-driven pathway construction entails development of a detailed pathway knowledge base for particular domains of interest, such as a cell type, disease, or system.

  • [107] Data repositories, which contain information regarding sequence data, metabolism, signaling, reactions, and interactions are a major source of information for pathway
    building.

  • [113] Pathway resources are expanded by utilizing homology information to translate pathway content between species and extending existing pathways with data derived from
    conserved protein interactions and coexpression.

  • [104] Pathway-related databases and tools Kegg [edit] The increasing amount of genomic and molecular information is the basis for understanding higher-order biological systems,
    such as the cell and the organism, and their interactions with the environment, as well as for medical, industrial and other practical applications.

  • The Kegg resource[109] provides a reference knowledge base for linking genomes to biological systems, categorized as building blocks in the genomic space, the chemical space,
    wiring diagrams of interaction networks and reaction networks, and ontologies for pathway reconstruction (database).

  • [114] In short, provides a means to rapidly interrogate complex experimental data for pathway-level changes in a diverse range of organisms.

  • [111] Genmapp [edit] Gene Map Annotator and Pathway Profiler [112] a free, open-source, stand-alone computer program is designed for organizing, analyzing, and sharing genome
    scale data in the context of biological pathways.

  • The pathway is further refined to include context-specific annotations such as species, cell/tissue type, or disease type.

  • Pathway building is the process of identifying and integrating the entities, interactions, and associated annotations, and populating the knowledge base.

  • The Reactome database containing a framework of possible reactions which, when combined with expression and enzyme kinetic data, provides the infrastructure for quantitative
    models, therefore, an integrated view of biological processes, which links such gene products and can be systematically mined by using bioinformatics applications.

  • [121][122] Pathway-oriented approaches for analyzing microarray data, by grouping long lists of individual genes, proteins, and/or other biological molecules according to
    the pathways they are involved in into smaller sets of related genes or proteins, which reduces the complexity, have proven useful for connecting genomic data to specific biological processes and systems.

  • The basic unit of the Reactome database is a reaction; reactions are then grouped into causal chains to form pathways[115] The Reactome data model allows us to represent many
    diverse processes in the human system, including the pathways of intermediary metabolism, regulatory pathways, and signal transduction, and high-level processes, such as the cell cycle.

  • Pathway-oriented approaches In the post-genomic age, high-throughput sequencing and gene/protein profiling techniques have transformed biological research by enabling comprehensive
    monitoring of a biological system, yielding a list of differentially expressed genes or proteins, which is useful in identifying genes that may have roles in a given phenomenon or phenotype.

  • [117] Although the primary curational domain is pathways from Homo sapiens, electronic projections of human pathways onto other organisms are regularly created via putative
    orthologs, thus making Reactome relevant to model organism research communities.

  • [119] In summary, Reactome provides high-quality curated summaries of fundamental biological processes in humans in a form of biologist-friendly visualization of pathways
    data, and is an open-source project.

  • In addition, a large number of pathway analytic methods exploit pathway knowledge in public repositories such as Gene Ontology or Kyoto Encyclopedia of Genes and Genomes,
    rather than inferring pathways from molecular measurements.

  • For instance, it can refer to the analysis physical interaction networks (e.g., protein–protein interactions), kinetic simulation of pathways, and steady-state pathway analysis
    (e.g., flux-balance analysis), as well as its usage in the inference of pathways from expression and sequence data.

  • Several functional enrichment analysis tools and algorithms[129] have been developed to enhance data interpretation.

  • [120] With DNA microarrays and genome-wide gene engineering, it is possible to screen global gene expression profiles to contribute a wealth of genomic data to the public
    domain.

  • In addition, tools can be used to analyze the roles of genes in metabolic pathways and show the biological relationships between genes or gene-products and may represent metabolic
    pathways.

  • By using a combined approach of Microarray-Bioinformatic technologies, a potential metabolic mechanism contributing to colorectal cancer has been demonstrated[131] Several
    environmental factors may be involved in a series of points along the genetic pathway to.

  • Applications of pathway analysis in medicine Colorectal cancer[edit] A program package MatchMiner was used to scan names for cloned genes of interest are scanned, then are
    input into GoMiner, which leveraged the to identify the biological processes, functions and components represented in the gene profile.

  • [131] Parkinson’s disease [edit] Cellular models are instrumental in dissecting a complex pathological process into simpler molecular events.

  • Emerging evidence that dietary restriction can forestall the development of is consistent with a major “metabolic” component to these disorders, and provides optimism that
    these devastating brain disorders of aging may be largely preventable.

  • Classical cellular models appear to be the correct choice for preliminary studies on the molecular action of new drugs or potential toxins and for understanding the role of
    single genetic factors.

  • Moreover, the availability of novel cellular systems, such as cybrids or induced pluripotent stem cells, offers the chance to exploit the advantages of an in vitro investigation,
    although mirroring more closely the cell population being affected.

  • In such a multifaceted picture, it is particularly important to identify experimental models that simplify the study of the different networks of proteins and genes involved.

 

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