introduction to the biological pathway
DESCRIPTION
Introduction to the biological pathway. 2003.02.07 POSTECH NLP lab 발표자 : 정설경. Contents. Introduction Cell Biological pathway Metabolic pathway Regulatory pathway Signal transduction pathway GPCR pathway Limitation & approach. Introduction – Cell (1). Cell 의 종류 Prokaryote - PowerPoint PPT PresentationTRANSCRIPT
Introduction to theIntroduction to the biological biological pathwaypathway
2003.02.072003.02.07POSTECH NLP labPOSTECH NLP lab
발표자발표자 : : 정설경정설경
2003.01.28 NLP lab Introduction to the biological pathway
ContentsContents
IntroductionIntroduction CellCell Biological pathwayBiological pathway
Metabolic pathwayMetabolic pathway Regulatory pathwayRegulatory pathway Signal transduction pathwaySignal transduction pathway GPCR pathwayGPCR pathway Limitation & approachLimitation & approach
2003.01.28 NLP lab Introduction to the biological pathway
• Cell 의 종류•Prokaryote
•Eukaryote
•Plant cell
•Animal cell
Introduction – Cell (1)Introduction – Cell (1)
2003.01.28 NLP lab Introduction to the biological pathway
Introduction – Cell (2)Introduction – Cell (2)
Cell structureCell structure Membrane structureMembrane structure
Plasma membranePlasma membrane Nuclear membraneNuclear membrane
Cell activityCell activity Physiological activityPhysiological activity Chemical activityChemical activity Main component: proteinMain component: protein
2003.01.28 NLP lab Introduction to the biological pathway
인지질의 구조
( phospholipid )
막 구조
( plasma membrane)
2003.01.28 NLP lab Introduction to the biological pathway
2003.01.28 NLP lab Introduction to the biological pathway
Introduction – Cell (2)Introduction – Cell (2)
Cell structureCell structure Membrane structureMembrane structure
Plasma membranePlasma membrane Nuclear membraneNuclear membrane
Cell activityCell activity Physiological activityPhysiological activity Chemical activityChemical activity Main component: Main component: proteinprotein
2003.01.28 NLP lab Introduction to the biological pathway
Protein structure (1)Protein structure (1)
2003.01.28 NLP lab Introduction to the biological pathway
Protein structure (2)Protein structure (2)
2003.01.28 NLP lab Introduction to the biological pathway
Ex> Membrane proteinEx> Membrane protein
2003.01.28 NLP lab Introduction to the biological pathway
Biological pathwayBiological pathway PathwayPathway
사전적사전적 : : 좁은 길좁은 길 , , 오솔길오솔길 , , 진로진로 (course)(course) 생화학생화학 : : 경로경로
Biological pathwayBiological pathway Molecular interaction network in biological Molecular interaction network in biological
processesprocesses Metabolic pathway, Regulatory pathwayMetabolic pathway, Regulatory pathway
Number of Pathway Number of Pathway 9644 pathways (PATHWAY database) 9644 pathways (PATHWAY database) 160 pathways involving 744 reactions and 791 160 pathways involving 744 reactions and 791
substrates (mouse)substrates (mouse)
2003.01.28 NLP lab Introduction to the biological pathway
Metabolic pathwayMetabolic pathway Carbohydrate MetabolismCarbohydrate Metabolism
Glycolysis/GluconeogenesisGlycolysis/Gluconeogenesis TCA cycle (Citrate cycle)TCA cycle (Citrate cycle)
Energy MetabolismEnergy Metabolism ATP synthesisATP synthesis
Lipid MetabolismLipid Metabolism Nucleotide MetabolismNucleotide Metabolism
purine, pyrimidine metabolismpurine, pyrimidine metabolism
Amino Acid MetabolismAmino Acid Metabolism Biodegradation of XenobioticsBiodegradation of Xenobiotics
2003.01.28 NLP lab Introduction to the biological pathway
2003.01.28 NLP lab Introduction to the biological pathway
Regulatory pathwayRegulatory pathway Genetic information processingGenetic information processing
Transcription, Translation, Sorting and Degradation. RTranscription, Translation, Sorting and Degradation. Replication and Repaireplication and Repair
Environmental information processingEnvironmental information processing Membrane transport, Signal transduction, Ligand receMembrane transport, Signal transduction, Ligand rece
ptor interactionptor interaction
Cellular processesCellular processes Cell motility, Cell growth and death, Cell communicatioCell motility, Cell growth and death, Cell communicatio
n, Development, Behaviorn, Development, Behavior
2003.01.28 NLP lab Introduction to the biological pathway
Signal transduction Signal transduction pathwaypathway
Category of signaling proteinCategory of signaling protein Signal moleculeSignal molecule ReceptorReceptor Intracellular signaling proteinIntracellular signaling protein Target proteinTarget protein
4 types of intercellular signaling4 types of intercellular signaling EndocrineEndocrine ParacrineParacrine Neuronal signalingNeuronal signaling Contact-dependent signalingContact-dependent signaling
2003.01.28 NLP lab Introduction to the biological pathway
Modulation by other molecule
Amplification
Divergence to multiple target
2003.01.28 NLP lab Introduction to the biological pathway
2003.01.28 NLP lab Introduction to the biological pathway
Signal transduction Signal transduction pathwaypathway
4 types of intercellular signaling4 types of intercellular signaling EndocrineEndocrine
Broad effect, specific receptorBroad effect, specific receptor hormoneshormones
Paracrine Paracrine Within local tissue, enzyme/extracellular matrixWithin local tissue, enzyme/extracellular matrix
Neuronal signalingNeuronal signaling Synapse of neuron, speedySynapse of neuron, speedy
Contact-dependent signalingContact-dependent signaling Killer T cell (immune system)Killer T cell (immune system)
2003.01.28 NLP lab Introduction to the biological pathway
Signal receptorSignal receptor
Cell surface receptorsCell surface receptors On-Off signalingOn-Off signaling
Ion-channel linkedIon-channel linked G-protein linkedG-protein linked Enzyme linkedEnzyme linked
Intracellular receptorsIntracellular receptors Steroid, Thyroid hormoneSteroid, Thyroid hormone Retinol, Vitamin DRetinol, Vitamin D
2003.01.28 NLP lab Introduction to the biological pathway
2003.01.28 NLP lab Introduction to the biological pathway
G-protein linked G-protein linked receptorsreceptors
Structure of receptorsStructure of receptors N-terminal : extracellular regionN-terminal : extracellular region Seven-span transmembrane domainSeven-span transmembrane domain C-terminal : intracellular signal transduction regionC-terminal : intracellular signal transduction region
Desensitization of receptorsDesensitization of receptors PhospholylationPhospholylation
PKA, PKC or a member of G-protein-linked receptor kinases(GPKA, PKC or a member of G-protein-linked receptor kinases(GRKs) family RKs) family
Receptor inactivationReceptor inactivation Receptor sequestrationReceptor sequestration Receptor down-regulationReceptor down-regulation
2003.01.28 NLP lab Introduction to the biological pathway
G-protein (1)G-protein (1) αα ,,ββ ,,γγ subunit subunit
αα subunit: complex with GDP subunit: complex with GDP
Major familyMajor family
FamilFamilyy
Some Some membemembe
rr
Action Action mediatemediate
ddFunctionsFunctions
I Gs α Activate adenylyl cylclase, Ca2+ channels
II
Gi
α Inhibit adnylyl cyclase
βγ Activates K+ channel
Go
βγActivates K+ channel, inactivate Ca2+
channels
α and βγ Activates phospholipase C-β
Gt α Activates cyclic GMP phosphodiesterase
III Gq α Activates phospholipase C-β
2003.01.28 NLP lab Introduction to the biological pathway
G-protein (2)G-protein (2) Mechanism of G-proteinMechanism of G-protein
ActivationActivation Dissociation of Dissociation of αα-GDP, -GDP, βγβγ complex complex αα-GTP, -GTP, βγβγ complex complex target protein target protein
DeactivationDeactivation G-protein itself: GTPase G-protein itself: GTPase association of association of αα-GDP, -GDP, βγβγ complex complex
Target of activated G-proteinTarget of activated G-protein Direct – ion channel …Direct – ion channel … Indirect – second messengerIndirect – second messenger
Adenylate cylase Adenylate cylase cAMP cAMP Phospholipase C (PLC) Phospholipase C (PLC) diacylglycerol(DAG) & inositol 1,4,5- diacylglycerol(DAG) & inositol 1,4,5-
triphosphate(IPtriphosphate(IP33))
2003.01.28 NLP lab Introduction to the biological pathway
Pathway of indirect Pathway of indirect signalingsignaling
Pathway of cAMPPathway of cAMP cAMP cAMP protein kinas protein kinas
e A e A cell response cell response
Pathway of PLCPathway of PLC DAG DAG protein kinase protein kinase
CC IPIP33 Ca Ca2+2+ ↑ ↑
2003.01.28 NLP lab Introduction to the biological pathway
cAMP pathwaycAMP pathway
2003.01.28 NLP lab Introduction to the biological pathway
PLC pathway (1)PLC pathway (1)
2003.01.28 NLP lab Introduction to the biological pathway
PLC pathway (2)PLC pathway (2) CaCa2+2+ signaling signaling
Regulate 70% of protein kinaseRegulate 70% of protein kinase Regulated by Calcium binding protein, calmodulin(CARegulated by Calcium binding protein, calmodulin(CA
M)M) CaCa2+2+ Ca Ca2+2+-CaM complex -CaM complex CaM-kinase CaM-kinase
2003.01.28 NLP lab Introduction to the biological pathway
exampleexample
Smell receptorSmell receptor
Vision receptorVision receptor
2003.01.28 NLP lab Introduction to the biological pathway
LimitationLimitation
Cannot effectivelyCannot effectively Evaluate them for internal consistencyEvaluate them for internal consistency Evaluate them with consistency for new data : microarrEvaluate them with consistency for new data : microarr
aysays Refine them with respect to new dataRefine them with respect to new data Integrate them to produce system understandingIntegrate them to produce system understanding
They are too large and complexThey are too large and complex The printed word cannot be manipulated effectiveThe printed word cannot be manipulated effective
lyly
2003.01.28 NLP lab Introduction to the biological pathway
Solution: Solution: biological knowledge basesbiological knowledge bases Store biological knowledge and theories in Store biological knowledge and theories in
computers in a declarative formcomputers in a declarative form Amenable to computational analysis and generative Amenable to computational analysis and generative
user interfaces user interfaces
Accepted to store data in computers, but not Accepted to store data in computers, but not knowledgeknowledge Refined, interpreted, consensus viewsRefined, interpreted, consensus views
Establish ongoing efforts to curate (maintain, Establish ongoing efforts to curate (maintain, refine, embellish) these knowledge basesrefine, embellish) these knowledge bases
Such knowledge bases are an integral part of Such knowledge bases are an integral part of the scientific enterprisethe scientific enterprise
2003.01.28 NLP lab Introduction to the biological pathway
Pathway/Genome Pathway/Genome DatabaseDatabase
CELL
pathway
proteins
Genes
operons, promotors, DNA binding site
Chromosomes, plasmid
reactions
compounds